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Tavani F, Frateloreto F, Del Giudice D, Capocasa G, Di Berto Mancini M, Busato M, Lanzalunga O, Di Stefano S, D'Angelo P. Coupled X-ray Absorption/UV-vis Monitoring of a Prototypical Oscillating Reaction. J Phys Chem Lett 2024; 15:7312-7319. [PMID: 38984831 DOI: 10.1021/acs.jpclett.4c01569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Oscillating reactions are among the most intriguing phenomena in chemistry, but many questions on their mechanisms still remain unanswered, due to their intrinsic complexity and to the low sensitivity of the most common spectroscopic techniques toward the reaction brominated species. In this work, we investigate the cerium ion-catalyzed Belousov-Zhabotinsky (BZ) oscillating reaction by means of time-resolved X-ray absorption spectroscopy (XAS), in combination with UV-vis spectroscopy and unsupervised machine learning, multivariate curve resolution, and kinetic analyses. Altogether, we provide new insights into the collective oscillatory behavior of the key brominated species involved in the classical BZ reaction and measure previously unreported oscillations in their concentrations through Br K-edge XAS, while simultaneously tracking the oscillatory Ce4+-to-Ce3+ transformation by coupling XAS with UV-vis spectroscopy. Our work evidences the potential of the XAS technique to investigate the mechanisms of oscillatory chemical systems whose species are often not detectable with conventional experimental methods.
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Affiliation(s)
- Francesco Tavani
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Federico Frateloreto
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Daniele Del Giudice
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Giorgio Capocasa
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Marika Di Berto Mancini
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Matteo Busato
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | - Paola D'Angelo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
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Müller S, Flamm C, Stadler PF. What makes a reaction network "chemical"? J Cheminform 2022; 14:63. [PMID: 36123755 PMCID: PMC9484159 DOI: 10.1186/s13321-022-00621-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reaction networks (RNs) comprise a set X of species and a set [Formula: see text] of reactions [Formula: see text], each converting a multiset of educts [Formula: see text] into a multiset [Formula: see text] of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix [Formula: see text] have been discussed extensively in the chemical literature. Here, we provide sufficient conditions for [Formula: see text] that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively. RESULTS Chemically plausible RNs allow neither a perpetuum mobile, i.e., a "futile cycle" of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of the stoichiometric matrix [Formula: see text]. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and-in a stricter sense-futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. It is also sufficient for the existence of a realization in terms of sum formulas, obeying conservation of "atoms". In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless [Formula: see text] implies that they are "obligatory isomers". In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved. In particular, for every conservative RN, there exists a Lewis realization, in which any two compounds are realized by pairwisely distinct multigraphs. Finally, we show that, in general, there are infinitely many realizations for a given conservative RN. CONCLUSIONS "Chemical" RNs are directed hypergraphs with a stoichiometric matrix [Formula: see text] whose left kernel contains a strictly positive vector and whose right kernel does not contain a futile cycle involving an irreversible reaction. This simple characterization also provides a concise specification of random models for chemical RNs that additionally constrain [Formula: see text] by rank, sparsity, or distribution of the non-zero entries. Furthermore, it suggests several interesting avenues for future research, in particular, concerning alternative representations of reaction networks and infinite chemical universes.
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Affiliation(s)
- Stefan Müller
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria
| | - Christoph Flamm
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Peter F. Stadler
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, 04107 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases University Leipzig, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
- Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, 111321 Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
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Liu Y, Pérez-Mercader J, Kiss IZ. Synchronization of Belousov-Zhabotinsky oscillators with electrochemical coupling in a spontaneous process. CHAOS (WOODBURY, N.Y.) 2022; 32:093128. [PMID: 36182363 DOI: 10.1063/5.0096689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
A passive electrochemical coupling approach is proposed to induce spontaneous synchronization between chemical oscillators. The coupling exploits the potential difference between a catalyst redox couple in the Belousov-Zhabotinsky (BZ) reaction, without external feedback, to induce surface reactions that impact the kinetics of the bulk system. The effect of coupling in BZ oscillators under batch condition is characterized using phase synchronization measures. Although the frequency of the oscillators decreases nonlinearly over time, by a factor of 2 or more within 100 cycles, the coupling is strong enough to maintain synchronization. In such a highly drifting system, the Gibbs-Shannon entropy of the cyclic phase difference distribution can be used to quantify the coupling effect. We extend the Oregonator BZ model to account for the drifting natural frequencies in batch condition and for electrochemical coupling, and numerical simulations of the effect of acid concentration on synchronization patterns are in agreement with the experiments. Because of the passive nature of coupling, the proposed coupling scheme can open avenues for designing pattern recognition and neuromorphic computation systems using chemical reactions in a spontaneous process.
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Affiliation(s)
- Yifan Liu
- Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - István Z Kiss
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, Missouri 63103, USA
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Wodlei F, Hristea MR, Alberti G. Periodic Motion in the Chaotic Phase of an Unstirred Ferroin-Catalyzed Belousov Zhabotinsky Reaction. Front Chem 2022; 10:881691. [PMID: 35873054 PMCID: PMC9304747 DOI: 10.3389/fchem.2022.881691] [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: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
The Belousov Zhabotinsky reaction, a self-organized oscillatory color-changing reaction, can show complex behavior when left unstirred in a cuvette environment. The most intriguing behavior is the transition from periodicity to chaos and back to periodicity as the system evolves in time. It was shown that this happens thanks due to the decoupling of reaction, diffusion and convection. We have recently discovered that, as the so-called chaotic transient takes place, periodic bulk motions in form of convective cells are created in the reaction solution. In this work we investigated this phenomenon experimentally by changing cuvette size and reaction volume, in order to allow different types of convection patterns to appear. So far, we have observed single and double convection cells in the system. There are indications that the convection patterns are connected to the duration of the chaotic phase. A simplified mathematical model confirms the form and dynamics of the observed convection cells and explains the connection between chemical chaos and hydrodynamical order.
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Abstract
Unconventional and, specifically, wave computing has been repeatedly studied in laboratory based experiments by utilizing chemical systems like a thin film of Belousov–Zhabotinsky (BZ) reactions. Nonetheless, the principles demonstrated by this chemical computer were mimicked by mathematical models to enhance the understanding of these systems and enable a more detailed investigation of their capacity. As expected, the computerized counterparts of the laboratory based experiments are faster and less expensive. A further step of acceleration in wave-based computing is the development of electrical circuits that imitate the dynamics of chemical computers. A key component of the electrical circuits is the memristor which facilitates the non-linear behavior of the chemical systems. As part of this concept, the road-map of the inspiration from wave-based computing on chemical media towards the implementation of equivalent systems on oscillating memristive circuits was studied here. For illustration reasons, the most straightforward example was demonstrated, namely the approximation of Boolean gates.
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Unified representation of Life's basic properties by a 3-species Stochastic Cubic Autocatalytic Reaction-Diffusion system of equations. Phys Life Rev 2022; 41:64-83. [DOI: 10.1016/j.plrev.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 01/01/2023]
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Draper T, Poros-Tarcali E, Pérez-Mercader J. pH Oscillating System for Molecular Computation as a Chemical Turing Machine. ACS OMEGA 2022; 7:6099-6103. [PMID: 35224372 PMCID: PMC8867811 DOI: 10.1021/acsomega.1c06505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
It has previously been demonstrated that native chemical Turing machines can be constructed by exploiting the nonlinear dynamics of the homogeneous oscillating Belousov-Zhabotinsky reaction. These Turing machines can perform word recognition of a Chomsky type 1 context sensitive language (CSL), demonstrating their high computing power. Here, we report on a chemical Turing machine that has been developed using the H2O2-H2SO4-SO3 2--CO3 2- pH oscillating system. pH oscillators are different to bromate oscillators in two key ways: the proton is the autocatalytic agent, and at least one of the reductants is always fully consumed in each turnover-meaning the system has to be operated as a flow reactor. Through careful design, we establish a system that can also perform Chomsky type 1 CSL word recognition and demonstrate its power through the testing of a series of in-language and out-of-language words.
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Affiliation(s)
- Thomas
C. Draper
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
| | - Eszter Poros-Tarcali
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
| | - Juan Pérez-Mercader
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
- Santa
Fe Institute, Santa Fe, New Mexico 87501, United States
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Draper TC, Dueñas-Díez M, Pérez-Mercader J. Exploring the symbol processing 'time interval' parametric constraint in a Belousov-Zhabotinsky operated chemical Turing machine. RSC Adv 2021; 11:23151-23160. [PMID: 35480432 PMCID: PMC9036302 DOI: 10.1039/d1ra03856g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Chemical reactions are powerful molecular recognition machines. This power has been recently harnessed to build actual instances of each class of experimentally realizable computing automata, using exclusively small-molecule chemistry (i.e. without requiring biomolecules). The most powerful of them, a programmable Turing machine, uses the Belousov–Zhabotinsky oscillatory chemistry, and accepts/rejects input sequences through a dual oscillatory and thermodynamic output signature. The time interval between the aliquots representing each letter of the input is the parameter that determines the time it takes to run the computation. Here, we investigate this critical performance parameter, and its effect not only on the computation speed, but also on the robustness of the accept/reject oscillatory and thermodynamic criteria. Our work demonstrates that the time interval is a non-trivial design parameter, whose choice should be made with great care. The guidelines we provide can be used in the optimization of the speed, robustness, and energy efficiency of chemical automata computations. Chemical reactions are powerful molecular recognition machines.![]()
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Affiliation(s)
- Thomas C Draper
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA
| | - Marta Dueñas-Díez
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA.,Repsol Technology Lab c/Agustín de Betancourt, s/n., 28935, Móstoles Madrid Spain
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA.,Santa Fe Institute Santa Fe New Mexico 87501 USA
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