1
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Tian S, Li G, Turnell-Ritson RC, Fei Z, Bornet A, Nazeeruddin MK, Dyson PJ. Controlling Tin Halide Perovskite Oxidation Dynamics in Solution for Perovskite Optoelectronic Devices. Angew Chem Int Ed Engl 2024; 63:e202407193. [PMID: 38744679 DOI: 10.1002/anie.202407193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
As a leading contender to replace lead halide perovskites, tin-based perovskites have demonstrated ever increasing performance in solar cells and light-emitting diodes (LEDs). They tend to be processed with dimethyl sulfoxide (DMSO) solvent, which has been identified as a major contributor to the Sn(II) oxidation during film fabrication, posing a challenge to the further improvement of Sn-based perovskites. Herein, we use NMR spectroscopy to investigate the kinetics of the oxidation of SnI2, revealing that autoamplification takes place, accelerating the oxidation as the reaction progresses. We propose a mechanism consistent with these observations involving water participation and HI generation. Building upon these insights, we have developed low-temperature Sn-based perovskite LEDs (PeLEDs) processed at 60 °C, achieving enhanced external quantum efficiencies (EQEs). Our research underscores the substantial potential of low-temperature DMSO solvent processes and DMSO-free solvent systems for fabricating oxidation-free Sn-based perovskites, shaping the future direction in processing Sn-containing perovskite materials and optoelectronic devices.
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Affiliation(s)
- Shun Tian
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Guixiang Li
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Roland C Turnell-Ritson
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Zhaofu Fei
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Aurélien Bornet
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Mohammad Khaja Nazeeruddin
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
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2
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Sherwin WB. Pan-Evo: The Evolution of Information and Biology's Part in This. BIOLOGY 2024; 13:507. [PMID: 39056700 PMCID: PMC11273748 DOI: 10.3390/biology13070507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Many people wonder whether biology, including humans, will benefit or experience harm from new developments in information such as artificial intelligence (AI). Here, it is proposed that biological and non-biological information might be components of a unified process, 'Panevolution' or 'Pan-Evo', based on four basic operations-innovation, transmission, adaptation, and movement. Pan-Evo contains many types of variable objects, from molecules to ecosystems. Biological innovation includes mutations and behavioural changes; non-biological innovation includes naturally occurring physical innovations and innovation in software. Replication is commonplace in and outside biology, including autocatalytic chemicals and autonomous software replication. Adaptation includes biological selection, autocatalytic chemicals, and 'evolutionary programming', which is used in AI. The extension of biological speciation to non-biological information creates a concept called 'Panspeciation'. Panevolution might benefit or harm biology, but the harm might be minimal if AI and humans behave intelligently because humans and the machines in which an AI resides might split into vastly different environments that suit them. That is a possible example of Panspeciation and would be the first speciation event involving humans for thousands of years. This event will not be particularly hostile to humans if humans learn to evaluate information and cooperate better to minimise both human stupidity and artificial simulated stupidity (ASS-a failure of AI).
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Affiliation(s)
- William B Sherwin
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Science, UNSW-Sydney, Sydney, NSW 2052, Australia
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3
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Wu H, Chen QX, Su Y, Chen Z. The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis. Angew Chem Int Ed Engl 2024; 63:e202404838. [PMID: 38654551 DOI: 10.1002/anie.202404838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.
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Affiliation(s)
- Huimin Wu
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Qing-Xuan Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yang Su
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
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4
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Borsley S, Leigh DA, Roberts BMW. Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction. Angew Chem Int Ed Engl 2024; 63:e202400495. [PMID: 38568047 DOI: 10.1002/anie.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Indexed: 05/03/2024]
Abstract
Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.
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Affiliation(s)
- Stefan Borsley
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - David A Leigh
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - Benjamin M W Roberts
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
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5
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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6
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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7
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Bayram I, Parra-Escudero C, Decker EA, Lu J. Mathematical Modeling of Alpha-Tocopherol Early Degradation Kinetics to Predict the Shelf-Life of Bulk Oils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4939-4946. [PMID: 38401060 DOI: 10.1021/acs.jafc.3c08272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
The kinetics of lipid oxidation includes a lag phase followed by an exponential increase in oxidation products, which cause rancidity. Current models focus on the slope of this exponential curve for shelf-life estimation, which still requires the measurement of full oxidation kinetics. In this paper, we analyzed the formation of lipid oxidation products in stripped soybean oil containing different levels of α-tocopherol. The lag phases of lipid hydroperoxides and headspace hexanal formation were found to have a strong positive correlation with the α-tocopherol depletion time. We propose that the kinetics of antioxidant (α-tocopherol) depletion occur during the lag phase and could serve as an early shelf-life indicator. Our results showed that α-tocopherol degradation can be described by Weibull kinetics over a wide range of initial concentrations. Furthermore, we conducted in silico investigations using Monte Carlo simulations to critically evaluate the feasibility and sensitivity of the shelf-life prediction using early antioxidant degradation kinetics. Our results revealed that the shelf life of soybean oil may be accurately predicted as early as 20% of the overall shelf life. This innovative approach provides a more efficient and faster assessment of shelf life, ultimately reducing waste and enhancing product quality.
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Affiliation(s)
- Ipek Bayram
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Carlos Parra-Escudero
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Eric A Decker
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
| | - Jiakai Lu
- Department of Food Science, University of Massachusetts, Chenoweth Laboratory, Amherst, 01003 Massachusetts, United States
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8
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Sakref Y, Rivoire O. On the exclusion of exponential autocatalysts by sub-exponential autocatalysts. J Theor Biol 2024; 579:111714. [PMID: 38128753 DOI: 10.1016/j.jtbi.2023.111714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Selection among autocatalytic species fundamentally depends on their growth law: exponential species, whose number of copies grows exponentially, are mutually exclusive, while sub-exponential ones, whose number of copies grows polynomially, can coexist. Here we consider competitions between autocatalytic species with different growth laws and make the simple yet counterintuitive observation that sub-exponential species can exclude exponential ones while the reverse is, in principle, impossible. This observation has implications for scenarios pertaining to the emergence of natural selection.
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Affiliation(s)
- Yann Sakref
- Gulliver, CNRS, ESPCI Paris, Université PSL, 75005 Paris, France.
| | - Olivier Rivoire
- Gulliver, CNRS, ESPCI Paris, Université PSL, 75005 Paris, France.
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9
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Sakref Y, Muñoz-Basagoiti M, Zeravcic Z, Rivoire O. On Kinetic Constraints That Catalysis Imposes on Elementary Processes. J Phys Chem B 2023; 127:10950-10959. [PMID: 38091487 DOI: 10.1021/acs.jpcb.3c04627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis.
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Affiliation(s)
- Yann Sakref
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Maitane Muñoz-Basagoiti
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Zorana Zeravcic
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Olivier Rivoire
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
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10
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Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
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Affiliation(s)
- Dharm Dev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bhawna Sharma
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Centre for Nano and Material Sciences, Jain Global Campus, Bangalore, Karnataka 560070, India
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Enrique Peacock-Lopez
- Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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11
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Baum DA, Peng Z, Dolson E, Smith E, Plum AM, Gagrani P. The ecology-evolution continuum and the origin of life. J R Soc Interface 2023; 20:20230346. [PMID: 37907091 PMCID: PMC10618062 DOI: 10.1098/rsif.2023.0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Prior research on evolutionary mechanisms during the origin of life has mainly assumed the existence of populations of discrete entities with information encoded in genetic polymers. Recent theoretical advances in autocatalytic chemical ecology establish a broader evolutionary framework that allows for adaptive complexification prior to the emergence of bounded individuals or genetic encoding. This framework establishes the formal equivalence of cells, ecosystems and certain localized chemical reaction systems as autocatalytic chemical ecosystems (ACEs): food-driven (open) systems that can grow due to the action of autocatalytic cycles (ACs). When ACEs are organized in meta-ecosystems, whether they be populations of cells or sets of chemically similar environmental patches, evolution, defined as change in AC frequency over time, can occur. In cases where ACs are enriched because they enhance ACE persistence or dispersal ability, evolution is adaptive and can build complexity. In particular, adaptive evolution can explain the emergence of self-bounded units (e.g. protocells) and genetic inheritance mechanisms. Recognizing the continuity between ecological and evolutionary change through the lens of autocatalytic chemical ecology suggests that the origin of life should be seen as a general and predictable outcome of driven chemical ecosystems rather than a phenomenon requiring specific, rare conditions.
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Affiliation(s)
- David A. Baum
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53705, USA
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Zhen Peng
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
- Department of Geoscience, University of Wisconsin, Madison, WI 53706, USA
| | - Emily Dolson
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Smith
- Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Alex M. Plum
- Department of Physics, University of California, San Diego, CA 92093, USA
| | - Praful Gagrani
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53705, USA
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12
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Wang H, Cheng Z, Yuan L, Ren L, Pan C, Epstein IR, Gao Q. Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design. J Am Chem Soc 2023; 145:23152-23159. [PMID: 37844139 DOI: 10.1021/jacs.3c07076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In biological or abiotic systems, rhythms occur, owing to the coupling between positive and negative feedback loops in a reaction network. Using the Semenov-Whitesides oscillatory network for thioester hydrolysis as a prototype, we experimentally and theoretically analyzed the role of fast and slow inhibitors in oscillatory reaction networks. In the presence of positive feedback, a single fast inhibitor generates a time delay, resulting in two saddle-node bifurcations and bistability in a continuously stirred tank reactor. A slow inhibitor produces a node-focus bifurcation, resulting in damped oscillations. With both fast and slow inhibitors present, the node-focus bifurcation repeatedly modulates the saddle-node bifurcations, producing stable periodic oscillations. These fast and slow inhibitions result in a pair of time delays between steeply ascending and descending dynamics, which originate from the positive and negative feedbacks, respectively. This pattern can be identified in many chemical relaxation oscillators and oscillatory models, e.g., the bromate-sulfite pH oscillatory system, the Belousov-Zhabotinsky reaction, the trypsin oscillatory system, and the Boissonade-De Kepper model. This study provides a novel understanding of chemical and biochemical rhythms and suggests an approach to designing such behavior.
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Affiliation(s)
- Hongzhang Wang
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Zhenfang Cheng
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Ling Yuan
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Lin Ren
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, Zhejiang, P. R. China
| | - Changwei Pan
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Irving R Epstein
- Department of Chemistry and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Qingyu Gao
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
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13
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Peng Z, Adam ZR, Fahrenbach AC, Kaçar B. Assessment of Stoichiometric Autocatalysis across Element Groups. J Am Chem Soc 2023; 145:22483-22493. [PMID: 37722081 PMCID: PMC10591316 DOI: 10.1021/jacs.3c07041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Indexed: 09/20/2023]
Abstract
Autocatalysis has been proposed to play critical roles during abiogenesis. These proposals are at odds with a limited number of known examples of abiotic (and, in particular, inorganic) autocatalytic systems that might reasonably function in a prebiotic environment. In this study, we broadly assess the occurrence of stoichiometries that can support autocatalytic chemical systems through comproportionation. If the product of a comproportionation reaction can be coupled with an auxiliary oxidation or reduction pathway that furnishes a reactant, then a Comproportionation-based Autocatalytic Cycle (CompAC) can exist. Using this strategy, we surveyed the literature published in the past two centuries for reactions that can be organized into CompACs that consume some chemical species as food to synthesize more autocatalysts. 226 CompACs and 44 Broad-sense CompACs were documented, and we found that each of the 18 groups, lanthanoid series, and actinoid series in the periodic table has at least two CompACs. Our findings demonstrate that stoichiometric relationships underpinning abiotic autocatalysis could broadly exist across a range of geochemical and cosmochemical conditions, some of which are substantially different from the modern Earth. Meanwhile, the observation of some autocatalytic systems requires effective spatial or temporal separation between the food chemicals while allowing comproportionation and auxiliary reactions to proceed, which may explain why naturally occurring autocatalytic systems are not frequently observed. The collated CompACs and the conditions in which they might plausibly support complex, "life-like" chemical dynamics can directly aid an expansive assessment of life's origins and provide a compendium of alternative hypotheses concerning false-positive biosignatures.
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Affiliation(s)
- Zhen Peng
- Department
of Bacteriology, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Zachary R. Adam
- Department
of Bacteriology, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Geoscience, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Albert C. Fahrenbach
- School
of Chemistry, Australian Centre for Astrobiology and the UNSW RNA
Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Betül Kaçar
- Department
of Bacteriology, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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14
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Sloboda D, Weber CC, Bakis E. A kinetics study of copper-catalysed click reactions in ionic liquids. Org Biomol Chem 2023; 21:7984-7993. [PMID: 37755136 DOI: 10.1039/d3ob00237c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions are of extensive interest in chemical synthesis. While the use of ionic liquids (ILs) as solvents for synthesis has been widely explored in recent years, the understanding of their influence on the mechanism and reactivity of CuAAC reactions remains poorly understood. Here, we investigate the kinetics of a phenylacetylene-benzylazide and acetylene-benzylazide CuAAC reaction to probe the influence of IL structure, including the role of the base used to promote the reaction and the importance of water content. The use of 'wet' ILs led to remarkable changes in the kinetic profile of the reaction by eliminating the initial induction period. The reaction rate was found to be dependent on the copper(I) source. The effect of an added base was also studied, with the use of a tertiary amine-bearing IL leading to high conversions in under 5 min at ambient temperature. The results of this study highlight the nature and complexity of CuAAC reactions in ILs. As more ILs are getting involved in industrial processes, the data obtained from this study are valuable for better understanding processes that affect the CuAAC reaction in IL media and for creating customized systems for organic synthesis, thus improving the efficiency and sustainability of such processes.
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Affiliation(s)
- Diana Sloboda
- Faculty of Chemistry, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia.
| | - Cameron C Weber
- School of Chemical Sciences, University of Auckland, 23 Symonds St, Auckland, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Eduards Bakis
- Faculty of Chemistry, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia.
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15
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Lantos E, Tóth Á, Horváth D. Oscillatory dynamics in a reaction network based on imine hydrolysis. CHAOS (WOODBURY, N.Y.) 2023; 33:103104. [PMID: 37782830 DOI: 10.1063/5.0169860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
We have built an autocatalytic reaction network, based on the hydrolysis of certain imines, which exhibits bistability in an open system. The positive feedback originates from the interplay of fast acid-base equilibria, leading to hydroxide ion production, and pH-dependent hydrolysis rates. The addition of a first-order removal of the autocatalyst can result in sustained pH oscillations close to physiological conditions. The unit-amplitude pH oscillations are accompanied by the stoichiometric conversion of imine into amine back and forth. A systematic parameter search is carried out to characterize the rich observable dynamics and identify the evolving bifurcations.
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Affiliation(s)
- Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
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16
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Ter Harmsel M, Maguire OR, Runikhina SA, Wong ASY, Huck WTS, Harutyunyan SR. A catalytically active oscillator made from small organic molecules. Nature 2023; 621:87-93. [PMID: 37673989 PMCID: PMC10482680 DOI: 10.1038/s41586-023-06310-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 06/12/2023] [Indexed: 09/08/2023]
Abstract
Oscillatory systems regulate many biological processes, including key cellular functions such as metabolism and cell division, as well as larger-scale processes such as circadian rhythm and heartbeat1-4. Abiotic chemical oscillations, discovered originally in inorganic systems5,6, inspired the development of various synthetic oscillators for application as autonomous time-keeping systems in analytical chemistry, materials chemistry and the biomedical field7-17. Expanding their role beyond that of a pacemaker by having synthetic chemical oscillators periodically drive a secondary function would turn them into significantly more powerful tools. However, this is not trivial because the participation of components of the oscillator in the secondary function might jeopardize its time-keeping ability. We now report a small molecule oscillator that can catalyse an independent chemical reaction in situ without impairing its oscillating properties. In a flow system, the concentration of the catalytically active product of the oscillator shows sustained oscillations and the catalysed reaction is accelerated only during concentration peaks. Augmentation of synthetic oscillators with periodic catalytic action allows the construction of complex systems that, in the future, may benefit applications in automated synthesis, systems and polymerization chemistry and periodic drug delivery.
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Affiliation(s)
- Matthijs Ter Harmsel
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Oliver R Maguire
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Sofiya A Runikhina
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, University of Twente, Enschede, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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17
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Lantos E, Mótyán G, Frank É, Eelkema R, van Esch J, Horváth D, Tóth Á. Dynamics of hydroxide-ion-driven reversible autocatalytic networks. RSC Adv 2023; 13:20243-20247. [PMID: 37416909 PMCID: PMC10321365 DOI: 10.1039/d3ra04215d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
In living systems adaptive regulation requires the presence of nonlinear responses in the underlying chemical networks. Positive feedbacks, for example, can lead to autocatalytic bursts that provide switches between two stable states or to oscillatory dynamics. The stereostructure stabilized by hydrogen bonds provides an enzyme its selectivity, rendering pH regulation essential for its functioning. For effective control, triggers by small concentration changes play roles where the strength of feedback is important. Here we show that the interaction of acid-base equilibria with simple reactions with pH-dependent rate can lead to the emergence of a positive feedback in hydroxide ion concentration during the hydrolysis of some Schiff bases in the physiological pH range. The underlying reaction network can also support bistability in an open system.
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Affiliation(s)
- Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
| | - Gergő Mótyán
- Department of Organic Chemistry, University of Szeged Dóm tér 8. Szeged H-6720 Hungary
| | - Éva Frank
- Department of Organic Chemistry, University of Szeged Dóm tér 8. Szeged H-6720 Hungary
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft Netherlands
| | - Jan van Esch
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft Netherlands
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
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18
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Wolfram M, Tiwari MK, Hassenkam T, Li M, Bjerrum MJ, Meldal M. Cascade autohydrolysis of Alzheimer's Aβ peptides. Chem Sci 2023; 14:4986-4996. [PMID: 37206405 PMCID: PMC10189894 DOI: 10.1039/d2sc06668h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Protein/peptide self-assembly into amyloid structures associates with major neurodegenerative disorders such as Alzheimer's disease (AD). Soluble assemblies (oligomers) of the Aβ peptide and their aggregates are perceived as neurotoxic species in AD. While screening for synthetic cleavage agents that could break down such aberrant assemblies through hydrolysis, we observed that the assemblies of Aβ oligopeptides, containing the nucleation sequence Aβ14-24 (H14QKLVFFAEDV24), could act as cleavage agents by themselves. Autohydrolysis showed a common fragment fingerprint among various mutated Aβ14-24 oligopeptides, Aβ12-25-Gly and Aβ1-28, and full-length Aβ1-40/42, under physiologically relevant conditions. Primary endoproteolytic autocleavage at the Gln15-Lys16, Lys16-Leu17 and Phe19-Phe20 positions was followed by subsequent exopeptidase self-processing of the fragments. Control experiments with homologous d-amino acid enantiomers Aβ12-25-Gly and Aβ16-25-Gly showed the same autocleavage pattern under similar reaction conditions. The autohydrolytic cascade reaction (ACR) was resilient to a broad range of conditions (20-37 °C, 10-150 μM peptide concentration at pH 7.0-7.8). Evidently, assemblies of the primary autocleavage fragments acted as structural/compositional templates (autocatalysts) for self-propagating autohydrolytic processing at the Aβ16-21 nucleation site, showing the potential for cross-catalytic seeding of the ACR in larger Aβ isoforms (Aβ1-28 and Aβ1-40/42). This result may shed new light on Aβ behaviour in solution and might be useful in the development of intervention strategies to decompose or inhibit neurotoxic Aβ assemblies in AD.
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Affiliation(s)
- Martin Wolfram
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Tue Hassenkam
- Globe Institute, Section for Geobiology, Copenhagen University Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Ming Li
- Technical University of Denmark, The Danish Hydrocarbon Research and Technology Centre Elektrovej, 2800 Kongens Lyngby Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Morten Meldal
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
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19
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Kim HE, Choi JH, Chung WJ. Fluorine-Assisted Rearrangement of Geminal Azidofluorides to Imidoyl Fluorides. J Org Chem 2023. [PMID: 37130141 DOI: 10.1021/acs.joc.3c00183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Organoazide rearrangement constitutes versatile synthetic strategies but typically requires an extremely strong acid and/or a high reaction temperature. Our group recently discovered the remarkable accelerating effect of the geminal fluorine substituent that enables the facile rearrangement of azides into imidoyl fluorides without the aid of acid under much milder reaction conditions. The role of geminal fluorine was elucidated by both experimental and computational investigations. This new reactivity led to the development of a practical one-step tandem preparative method for potentially useful and bench-stable imidoyl fluorides from a wide range of structurally diverse geminal chlorofluorides. Our additional efforts to expand the reaction scope regarding the migrating group, halogen, and carbonyl function are described, and the synthetic utility of the imidoyl fluoride products was demonstrated in hopes of promoting the use of this under-appreciated functional group in the synthetic organic community.
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Affiliation(s)
- Ha Eun Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Won-Jin Chung
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
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20
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Boon WQ, Dijkstra M, van Roij R. Coulombic Surface-Ion Interactions Induce Nonlinear and Chemistry-Specific Charging Kinetics. PHYSICAL REVIEW LETTERS 2023; 130:058001. [PMID: 36800467 DOI: 10.1103/physrevlett.130.058001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
While important for many industrial applications, chemical reactions responsible for the charging of solids in water are often poorly understood. We theoretically investigate the charging kinetics of solid-liquid interfaces and find that the time-dependent equilibration of surface charge contains key information not only on the reaction mechanism, but also on the valency of the reacting ions. We construct a nonlinear differential equation describing surface charging by combining chemical Langmuir kinetics and electrostatic Poisson-Boltzmann theory. Our results reveal a clear distinction between late-time (near-equilibrium) and short-time (far-from-equilibrium) relaxation rates, the ratio of which contains information on the charge valency and ad- or desorption mechanism of the charging process. Similarly, we find that single-ion reactions can be distinguished from two-ion reactions, as the latter show an inflection point during equilibration. Interestingly, such inflection points are characteristic of autocatalytic reactions, and we conclude that the Coulombic ion-surface interaction is an autocatalytic feedback mechanism.
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Affiliation(s)
- W Q Boon
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
| | - M Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - R van Roij
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
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21
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Pavlinova P, Lambert CN, Malaterre C, Nghe P. Abiogenesis through gradual evolution of autocatalysis into template-based replication. FEBS Lett 2023; 597:344-379. [PMID: 36203246 DOI: 10.1002/1873-3468.14507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022]
Abstract
How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.
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Affiliation(s)
- Polina Pavlinova
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Camille N Lambert
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Christophe Malaterre
- Laboratory of Philosophy of Science (LAPS) and Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), Canada
| | - Philippe Nghe
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
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22
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Kordes BR, Ascherl L, Rüdinger C, Melchin T, Agarwal S. Competition between Hydrolysis and Radical Ring-Opening Polymerization of MDO in Water. Who Makes the Race? Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Laura Ascherl
- Wacker Chemie AG, Hanns-Seidel-Platz 4, 81737 München, Germany
| | | | - Timo Melchin
- Wacker Chemie AG, Hanns-Seidel-Platz 4, 81737 München, Germany
| | - Seema Agarwal
- Macromolecular Chemistry II, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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23
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Vibhute MA, Mutschler H. A Primer on Building Life‐Like Systems. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mahesh A. Vibhute
- TU Dortmund University Department of Chemistry and Chemical Biology Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Hannes Mutschler
- TU Dortmund University Department of Chemistry and Chemical Biology Otto-Hahn-Str. 4a 44227 Dortmund Germany
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24
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Unterberger J, Nghe P. Stoechiometric and dynamical autocatalysis for diluted chemical reaction networks. J Math Biol 2022; 85:26. [PMID: 36071258 DOI: 10.1007/s00285-022-01798-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/25/2022]
Abstract
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. (PNAS 117(41):25230-25236, 2020) gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions such that the balance for all autocatalytic species is strictly positive, and investigated minimal autocatalytic networks, called autocatalytic cores. By contrast, spontaneous autocatalysis-namely, exponential amplification of all species internal to a reaction network, starting from a diluted regime, i.e. low concentrations-is a dynamical property. We introduce here a topological condition (Top) for autocatalysis, namely: restricting the reaction network description to highly diluted species, we assume existence of a strongly connected component possessing at least one reaction with multiple products (including multiple copies of a single species). We find this condition to be necessary and sufficient for stoechiometric autocatalysis. When degradation reactions have small enough rates, the topological condition further ensures dynamical autocatalysis, characterized by a strictly positive Lyapunov exponent giving the instantaneous exponential growth rate of the system. The proof is generally based on the study of auxiliary Markov chains. We provide as examples general autocatalytic cores of Type I and Type III in the typology of Blokhuis et al. (PNAS 117(41):25230-25236, 2020) . In a companion article (Unterberger in Dynamical autocatalysis for autocatalytic cores, 2021), Lyapunov exponents and the behavior in the growth regime are studied quantitatively beyond the present diluted regime .
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Affiliation(s)
- Jérémie Unterberger
- Institut Elie Cartan, Laboratoire Associé au CNRS UMR 7502, Université de Lorraine, B.P. 239, 54506, Vandœuvre-lès-Nancy Cedex, France.
| | - Philippe Nghe
- UMR CNRS-ESPCI Chimie Biologie Innovation 8231, ESPCI Paris, Université Paris Sciences Lettres, 10 rue Vauquelin, 75005, Paris, France
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25
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Urgoitia G, Herrero MT, SanMartin R. Metal-Catalyzed, Photo-Assisted Selective Transformation of Tertiary Alkylbenzenes and Polystyrenes into Carbonyl Compounds. CHEMSUSCHEM 2022; 15:e202200940. [PMID: 35713591 PMCID: PMC9544855 DOI: 10.1002/cssc.202200940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Every year, thousands of tons of polystyrene are produced and discarded, filling landfills and polluting the marine environment. Although several degradation alternatives have been proposed, the need for an effective procedure for the chemical recycling of polystyrene still remains. Here, a vanadium-catalyzed reaction, assisted by visible light, promoted the direct, selective conversion of tertiary alkylbenzenes into acetophenone and other ketone derivatives. Likewise, standard polystyrene samples as well as polystyrenes from insulation and packaging waste could be chemically recycled into acetophenone in a scalable way regardless of their molecular weight, polydispersity, or form. Preliminary mechanistic investigations revealed the participation of singlet oxygen, superoxide, and hydroxyl radical species in this homogenously catalyzed process. Acetophenone could be used as an additive to accelerate the reaction and to increase the yields in some cases.
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Affiliation(s)
- Garazi Urgoitia
- Department of Organic and Inorganic ChemistryFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Sarriena auzoa, z/g.48940LeioaSpain
| | - María Teresa Herrero
- Department of Organic and Inorganic ChemistryFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Sarriena auzoa, z/g.48940LeioaSpain
| | - Raul SanMartin
- Department of Organic and Inorganic ChemistryFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Sarriena auzoa, z/g.48940LeioaSpain
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26
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Park S, Lee H, Yang H. Sensitive Affinity-Based Biosensor Using the Autocatalytic Activation of Trypsinogen Mutant by Trypsin with Low Self-activation. ACS APPLIED BIO MATERIALS 2022; 5:4516-4522. [PMID: 35972302 DOI: 10.1021/acsabm.2c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-propagating autocatalytic reactions of proteases that can provide high signal amplification have not been applied to affinity-based biosensors owing to the limited number of fast autocatalytic proteolytic reactions available and the self-activation of protease proenzymes. Here, we report that a self-propagating autocatalytic reaction based on the autocatalytic activation of the trypsinogen mutant by trypsin facilitates high signal amplification and a low background level, resulting in a low detection limit for prostate-specific antigen (PSA). A commercially available trypsinogen mutant minimizes the self-activation of trypsinogen by trypsinogen. Trypsin, which is used as a catalytic label in a sandwich-type immunosensor, converts the trypsinogen mutant into trypsin; the generated trypsin then further converts the trypsinogen mutant into trypsin. The autocatalytically produced trypsin proteolytically cleaves the peptide bond of a trypsin substrate, resulting in the liberation of electrochemically active 4-aminophenol (AP). The electrochemical oxidation of AP at a modified indium tin oxide (ITO) electrode induces electrochemical-chemical redox cycling involving the ITO electrode, AP, and a reductant. The triple combination of autocatalytic activation, proteolytic cleavage, and redox cycling results in a high electrochemical signal level. The detection limit for PSA obtained using a trypsin label and trypsinogen (∼7 pg/mL) is lower than that obtained using a trypsin label alone (∼100 pg/mL). This study demonstrated that autocatalytically activating a proenzyme is a very useful method for highly amplifying signals.
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Affiliation(s)
- Seonhwa Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Hyoeun Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
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27
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Wessels A, Klussmann M, Breugst M, Schlörer NE, Berkessel A. Formation of Breslow Intermediates from N‐Heterocyclic Carbenes and Aldehydes Involves Autocatalysis by the Breslow Intermediate, and a Hemiacetal. Angew Chem Int Ed Engl 2022; 61:e202117682. [PMID: 35238462 PMCID: PMC9325009 DOI: 10.1002/anie.202117682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Under aprotic conditions, the stoichiometric reaction of N‐heterocyclic carbenes (NHCs) such as imidazolidin‐2‐ylidenes with aldehydes affords Breslow Intermediates (BIs), involving a formal 1,2‐C‐to‐O proton shift. We herein report kinetic studies (NMR), complemented by DFT calculations, on the mechanism of this kinetically disfavored H‐translocation. Variable time normalization analysis (VTNA) revealed that the kinetic orders of the reactants vary for different NHC‐to‐aldehyde ratios, indicating different and ratio‐dependent mechanistic regimes. We propose that for high NHC‐to‐aldehyde ratios, the H‐shift takes place in the primary, zwitterionic NHC‐aldehyde adduct. With excess aldehyde, the zwitterion is in equilibrium with a hemiacetal, in which the H‐shift occurs. In both regimes, the critical H‐shift is auto‐catalyzed by the BI. Kinetic isotope effects observed for R‐CDO are in line with our proposal. Furthermore, we detected an H‐bonded complex of the BI with excess NHC (NMR).
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Affiliation(s)
- Alina Wessels
- Department of Chemistry Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
| | - Martin Klussmann
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Borchers GmbH Berghausener Straße 100 40764 Langenfeld Germany
| | - Martin Breugst
- Department of Chemistry Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
| | - Nils E. Schlörer
- Department of Chemistry Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
| | - Albrecht Berkessel
- Department of Chemistry Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
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28
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Arya A, Ray J, Sharma S, Cruz Simbron R, Lozano A, Smith HB, Andersen JL, Chen H, Meringer M, Cleaves HJ. An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions. Chem Sci 2022; 13:4838-4853. [PMID: 35655880 PMCID: PMC9067619 DOI: 10.1039/d2sc00256f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022] Open
Abstract
A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes over others. Some degree of molecular complexity likely had to be supplied by environmental processes to produce entailed self-replicating processes. The origin of entailment, therefore, must connect to fundamental chemistry that builds molecular complexity. We present here an open-source chemoinformatic workflow to model abiological chemistry to discover such entailment. This pipeline automates generation of chemical reaction networks and their analysis to discover novel compounds and autocatalytic processes. We demonstrate this pipeline's capabilities against a well-studied model system by vetting it against experimental data. This workflow can enable rapid identification of products of complex chemistries and their underlying synthetic relationships to help identify autocatalysis, and potentially self-organization, in such systems. The algorithms used in this study are open-source and reconfigurable by other user-developed workflows.
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Affiliation(s)
- Aayush Arya
- Department of Physics, Lovely Professional University Jalandhar Delhi-GT Road Phagwara Punjab 144411 India
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
| | - Jessica Ray
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Department of Biochemistry, Deshbandhu College, University of Delhi New Delhi 110019 India
| | - Romulo Cruz Simbron
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Laboratorio de Investigación Fisicoquímica (LABINFIS), Universidad Nacional de Ingeniería Av. Túpac Amaru 210 Lima Peru
- Centro de Tecnologías de la Información y Comunicaciones (CTIC UNI), Universidad Nacional de Ingenieria Av. Túpac Amaru 210 Lima Peru
| | - Alejandro Lozano
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Unidad Profesional Interdisciplinaria de Biotecnología - Instituto Politécnico Nacional 550 Av. Acueducto 07340 Mexico City Mexico
| | - Harrison B Smith
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo Japan
| | - Jakob Lykke Andersen
- Department of Mathematics and Computer Science, University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Huan Chen
- National High Magnetic Field Laboratory Tallahassee Florida 32310 USA
| | - Markus Meringer
- German Aerospace Center (DLR) 82234 Oberpfaffenhofen Wessling Germany
| | - Henderson James Cleaves
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo Japan
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29
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Wessels A, Klussmann M, Breugst M, Schlörer NE, Berkessel A. Die Bildung von Breslow‐Intermediaten aus N‐heterocyclischen Carbenen und Aldehyden verläuft autokatalytisch und mit einem Halbacetal als Intermediat. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alina Wessels
- Department für Chemie Organische Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Martin Klussmann
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
- Borchers GmbH Berghausener Straße 100 40764 Langenfeld Deutschland
| | - Martin Breugst
- Department für Chemie Organische Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Nils E. Schlörer
- Department für Chemie Organische Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Albrecht Berkessel
- Department für Chemie Organische Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
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30
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out-of-Equilibrium Self-Replication Allows Selection for Dynamic Kinetic Stability in a System of Competing Replicators. Angew Chem Int Ed Engl 2022; 61:e202117605. [PMID: 35179808 PMCID: PMC9314957 DOI: 10.1002/anie.202117605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 12/16/2022]
Abstract
Among the key characteristics of living systems are their ability to self‐replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self‐replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out‐of‐equilibrium replication–destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication‐destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass‐action‐kinetics model. These results represent one of the few experimental manifestations of selection among competing self‐replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marc Geerts
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.,Origins Center, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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31
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Kondoros BA, Jójárt-Laczkovich O, Berkesi O, Szabó-Révész P, Csóka I, Ambrus R, Aigner Z. Development of Solvent-Free Co-Ground Method to Produce Terbinafine Hydrochloride Cyclodextrin Binary Systems; Structural and In Vitro Characterizations. Pharmaceutics 2022; 14:pharmaceutics14040744. [PMID: 35456578 PMCID: PMC9025016 DOI: 10.3390/pharmaceutics14040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Molecular complexation with cyclodextrins (CDs) has long been a known process for modifying the physicochemical properties of problematic active pharmaceutical ingredients with poor water solubility. In current times, the focus has been on the solvent-free co-grinding process, which is an industrially feasible process qualifying as a green technology. In this study, terbinafine hydrochloride (TER), a low solubility antifungal drug was used as a model drug. This study aimed to prepare co-ground products and follow through the preparation process of the co-grinding method in the case of TER and two amorphous CD derivatives: (2-hydroxypropyl)-β-cyclodextrin (HPBCD); heptakis-(2,6-di-O-methyl)-β-cyclodextrin (DIMEB). For this evaluation, the following analytical tools and methods were used: phase solubility studies, differential scanning calorimetry (DSC), X-ray powder diffractometry (XRPD), hot-stage X-ray powder diffractometry (HOT-XRPD), Fourier-transform infrared (FT-IR), Raman spectroscopy, and Scanning Electron Microscopy (SEM). Furthermore, in vitro characterization (dissolution and diffusion studies) was performed in two kinds of dissolution medium without enzymes. In the XRPD and SEM studies, it was found that the co-grinding of the components resulted in amorphous products. FT-IR and Raman spectroscopies confirmed the formation of an inclusion complex through the unsaturated aliphatic chain of TER and CDs. In vitro characterization suggested better dissolution properties for both CDs and decreased diffusion at higher pH levels in the case of HPBCD.
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Affiliation(s)
- Balázs Attila Kondoros
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
| | - Orsolya Jójárt-Laczkovich
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
| | - Ottó Berkesi
- Department of Physical Chemistry and Materials Science, Faculty of Science and Informatics, University of Szeged, H-6720 Szeged, Hungary;
| | - Piroska Szabó-Révész
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
| | - Ildikó Csóka
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
| | - Rita Ambrus
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
- Correspondence: ; Tel.: +36-62-545-575
| | - Zoltán Aigner
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, H-6720 Szeged, Hungary; (B.A.K.); (O.J.-L.); (P.S.-R.); (I.C.); (Z.A.)
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32
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out‐of‐equilibrium self‐replication allows selection for dynamic kinetic stability in a system of competing replicators. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Juntian Wu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Marc Geerts
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Omer Markovitch
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Charalampos G. Pappas
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Kai Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sijbren Otto
- Stratingh Institute University of Groningen Centre for Systems Chemistry Nijenborgh 4 9747AG Groningen NETHERLANDS
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33
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Polterauer D, Roberge DM, Hanselmann P, Littich R, Hone CA, Kappe CO. A continuous flow investigation of sulfonyl chloride synthesis using N-chloroamides: optimization, kinetics and mechanism. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00280a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a continuous flow protocol for the synthesis of sulfonyl chlorides from disulfides and thiols, using 1,3-dichloro-5,5-dimethylhydantoin (DCH) as a dual-function reagent for oxidative chlorination.
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Affiliation(s)
- Dominik Polterauer
- Center for Continuous Synthesis and Processing (CCFLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, A-8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | | | - Paul Hanselmann
- Chemical Manufacturing Technologies, Lonza AG, CH-3930 Visp, Switzerland
| | - Ryan Littich
- Chemical Manufacturing Technologies, Lonza AG, CH-3930 Visp, Switzerland
| | - Christopher A. Hone
- Center for Continuous Synthesis and Processing (CCFLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, A-8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - C. Oliver Kappe
- Center for Continuous Synthesis and Processing (CCFLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, A-8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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34
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Sevim İ. Design of Subreplicating Systems from an Existing Self-Replicating Diels-Alder Reaction System by Isosteric Replacement. J Org Chem 2021; 86:14964-14973. [PMID: 34633828 DOI: 10.1021/acs.joc.1c01695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The key feature of non-enzymatic self-replicating systems is the formation of catalytically active ternary complexes in which product templates direct precursors into spatial proximity to allow the formation of new covalent bonds. It is possible to create new replicating species by simply evaluating the ternary active complex of an existing replicating system and applying proper isosteric replacements. In this study, we have evaluated the formerly reported self-replicating Diels-Alder reaction having 61 and 33% selectivity for two diastereomeric replicators. An isosteric replacement on the spacer part connecting recognition and reactive sites of the maleimide component was applied by considering the symmetry of catalytically active ternary complexes, and it was shown that self-replication was conserved. Analysis of the new system showed 77 and 21% diastereoselectivity for the two new replicating species. Seeding experiments indicated autocatalytic activity of both replicators. In other words, both replicators compete with each other by catalyzing their own formation from the same reagent source. Another modification was applied by aiming selective blocking of the autocatalytic cycle of the competing diastereomer. The new system showed a diastereoselectivity of about 94% for the favored replicator. The kinetic data of both systems were analyzed by modeling with SimFit simulations.
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Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
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35
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Hui P, Branca M, Limoges B, Mavré F. An autocatalytic organic reaction network based on cross-catalysis. Chem Commun (Camb) 2021; 57:11374-11377. [PMID: 34647564 DOI: 10.1039/d1cc05121k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here we report a simple autocatalytic organic reaction network based on the redox chemistry of quinones and reactive oxygen species. Autocatalysis arises from the cross-activation between the H2O2-catalyzed deprotection of a pro-benzoquinone arylboronic ester probe and the benzoquinone-catalyzed H2O2 production through redox cyling with ascorbate in an aerated buffered solution.
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Affiliation(s)
- Pan Hui
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, F-75013 Paris, France.
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36
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Secular changes in human reproduction and assisted reproductive technologies. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Since the middle to late 20th century the majority of children born in the developing world have been likely to enter into post-reproductive age. Currently, child mortality is at its lowest level in human history. While more children are living to post reproductive age, approximately 15% of couples are experiencing infecundity. This is either a result of one or both members of the couple being infecund, or, despite both being fecund, the interaction between them prevents fertility for some reason. Assisted reproductive technologies have provided many infertile couples an opportunity to have children. Assisted reproductive technologies operate by intervening and manipulating gametic and intrauterine natural selection. This paper discusses the possible influence of assisted reproductive technologies on child development. This paper outlines some of the reported changes in children resulting from assisted reproductive technologies. Although, few people are either aware or care about possible long term consequences of relaxed natural selection contributed by medical intervention (i.e. assisted reproductive technologies) we have little understanding to what extent such medical interference may affect long term fitness in humans.
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37
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Miao X, Paikar A, Lerner B, Diskin‐Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yael Diskin‐Posner
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Guy Shmul
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
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38
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Tan J, Deng Z, Song C, Xu J, Zhang Y, Yu Y, Hu J, Liu S. Coordinating External and Built-In Triggers for Tunable Degradation of Polymeric Nanoparticles via Cycle Amplification. J Am Chem Soc 2021; 143:13738-13748. [PMID: 34411484 DOI: 10.1021/jacs.1c05617] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The selective activation of nanovectors in pathological tissues is of crucial importance to achieve optimized therapeutic outcomes. However, conventional stimuli-responsive nanovectors lack sufficient sensitivity because of the slight difference between pathological and normal tissues. To this end, the development of nanovectors capable of responding to weak pathological stimuli is of increasing interest. Herein, we report the fabrication of amphiphilic polyurethane nanoparticles containing both external and built-in triggers. The activation of external triggers leads to the liberation of highly reactive primary amines, which subsequently activates the built-in triggers with the release of more primary amines in a positive feedback manner, thereby triggering the degradation of micellar nanoparticles in a cycle amplification model. The generality and versatility of the cycle amplification concept have been successfully verified using three different triggers including reductive milieu, light irradiation, and esterase. We demonstrate that these stimuli-responsive nanoparticles show self-propagating degradation performance even in the presence of trace amounts of external stimuli. Moreover, we confirm that the esterase-responsive nanoparticles can discriminate cancer cells from normal ones by amplifying the esterase stimulus that is overexpressed in cancer cells, thereby enabling the selective release of encapsulated payloads and killing cancer cells. This work presents a robust strategy to fabricate stimuli-responsive nanocarriers with highly sensitive property toward external stimuli, showing promising applications in cancer therapy with minimized side effects.
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Affiliation(s)
- Jiajia Tan
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Zhengyu Deng
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Chengzhou Song
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jie Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yuben Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jinming Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Shiyong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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39
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Branca M, Calvet C, Limoges B, Mavré F. Specific Versus Non-specific Response in Exponential Molecular Amplification from Cross-Catalysis: Modeling the Influence of Background Amplifications on the Analytical Performances. Chemphyschem 2021; 22:1611-1621. [PMID: 34038617 DOI: 10.1002/cphc.202100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Indexed: 11/05/2022]
Abstract
Molecule based signal amplifications relying on an autocatalytic process may represent an ideal strategy for the development of ultrasensitive analytical or bioanalytical assays, the main reason being the exponential nature of the amplification. However, to take full advantage of such amplification rates, high stability of the starting co-reactants is required in order to avoid any undesirable background amplification. Here, on the basis of a simple kinetic model of cross-catalysis including a certain degree of intrinsic instability of co-reactants, we highlight the key parameters governing the analytical response of the system and discuss the analytical performances that are expected from a given kinetic set. In particular, we show how the detection limit is directly related to the relative instability of reactants within each catalytic loop. The model is validated with an experimental dataset and is intended to serve as a guide in the design and optimization of autocatalytic molecular-based amplification systems with improved analytical performances.
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Affiliation(s)
- Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
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40
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Miao X, Paikar A, Lerner B, Diskin-Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out-of-Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021; 60:20366-20375. [PMID: 34144635 DOI: 10.1002/anie.202105790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Indexed: 02/05/2023]
Abstract
Autocatalytic reaction networks are instrumental for validating scenarios for the emergence of life on Earth and for synthesizing life de novo. Here, we demonstrate that dimeric thioesters of tripeptides with the general structure (Cys-Xxx-Gly-SEt)2 form strongly interconnected autocatalytic reaction networks that predominantly generate macrocyclic peptides up to 69 amino acids long. Some macrocycles of 6-12 amino acids were isolated from the product pool and were characterized by NMR spectroscopy and single-crystal X-ray analysis. We studied the autocatalytic formation of macrocycles in a flow reactor in the presence of acrylamide, whose conjugate addition to thiols served as a model "removal" reaction. These results indicate that even not template-assisted autocatalytic production combined with competing removal of molecular species in an open compartment could be a feasible route for selecting functional molecules during the pre-Darwinian stages of molecular evolution.
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Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Shmul
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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41
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van der Helm MP, de Beun T, Eelkema R. On the use of catalysis to bias reaction pathways in out-of-equilibrium systems. Chem Sci 2021; 12:4484-4493. [PMID: 34163713 PMCID: PMC8179475 DOI: 10.1039/d0sc06406h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Catalysis is an essential function in living systems and provides a way to control complex reaction networks. In natural out-of-equilibrium chemical reaction networks (CRNs) driven by the consumption of chemical fuels, enzymes provide catalytic control over pathway kinetics, giving rise to complex functions. Catalytic regulation of man-made fuel-driven systems is far less common and mostly deals with enzyme catalysis instead of synthetic catalysts. Here, we show via simulations, illustrated by literature examples, how any catalyst can be incorporated in a non-equilibrium CRN and what their effect is on the behavior of the system. Alteration of the catalysts' concentrations in batch and flow gives rise to responses in maximum conversion, lifetime (i.e. product half-lives and t90 - time to recover 90% of the reactant) and steady states. In situ up or downregulation of catalysts' levels temporarily changes the product steady state, whereas feedback elements can give unusual concentration profiles as a function of time and self-regulation in a CRN. We show that simulations can be highly effective in predicting CRN behavior. In the future, shifting the focus from enzyme catalysis towards small molecule and metal catalysis in out-of-equilibrium systems can provide us with new reaction networks and enhance their application potential in synthetic materials, overall advancing the design of man-made responsive and interactive systems.
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Affiliation(s)
- Michelle P van der Helm
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands +31 15 27 81035
| | - Tuanke de Beun
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands +31 15 27 81035
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands +31 15 27 81035
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42
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Robust Dynamics of Synthetic Molecular Systems as a Consequence of Broken Symmetry. Symmetry (Basel) 2020. [DOI: 10.3390/sym12101688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The construction of molecular robot-like objects that imitate living things is an important challenge for current chemists. Such molecular devices are expected to perform their duties robustly to carry out mechanical motion, process information, and make independent decisions. Dissipative self-organization plays an essential role in meeting these purposes. To produce a micro-robot that can perform the above tasks autonomously as a single entity, a function generator is required. Although many elegant review articles featuring chemical devices that mimic biological mechanical functions have been published recently, the dissipative structure, which is the minimum requirement for mimicking these functions, has not been sufficiently discussed. This article aims to show clearly that dissipative self-organization is a phenomenon involving autonomy, robustness, mechanical functions, and energy transformation. Moreover, it reports the results of recent experiments with an autonomous light-driven molecular device that achieves all of these features. In addition, a chemical model of cell-amplification is also discussed to focus on the generation of hierarchical movement by dissipative self-organization. By reviewing this research, it may be perceived that mainstream approaches to synthetic chemistry have not always been appropriate. In summary, the author proposes that the integration of catalytic functions is a key issue for the creation of autonomous microarchitecture.
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