51
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Danger G, Plasson R, Pascal R. Pathways for the formation and evolution of peptides in prebiotic environments. Chem Soc Rev 2012; 41:5416-29. [PMID: 22688720 DOI: 10.1039/c2cs35064e] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.
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Affiliation(s)
- Grégoire Danger
- Spectrométries et Dynamique Moléculaire, Physique des Interactions Ioniques et Moléculaires (UMR CNRS 7345, Université de Provence) - Centre de St Jérôme - case 252, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France.
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52
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Coveney PV, Swadling JB, Wattis JAD, Greenwell HC. Theory, modelling and simulation in origins of life studies. Chem Soc Rev 2012; 41:5430-46. [PMID: 22677708 DOI: 10.1039/c2cs35018a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the "systems chemistry" level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life.
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Affiliation(s)
- Peter V Coveney
- Centre for Computational Science, Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK.
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53
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Plasson R, Tsuji M, Kamata M, Asakura K. Reactivity of alanylalanine diastereoisomers in neutral and acid aqueous solutions: a versatile stereoselectivity. ORIGINS LIFE EVOL B 2011; 41:413-35. [PMID: 21562847 DOI: 10.1007/s11084-011-9240-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 04/08/2011] [Indexed: 10/18/2022]
Abstract
A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the stereoselectivity of the involved reactions, there is a huge interest in amino acid derivatives for explaining the spontaneous emergence of homochirality on primitive Earth. The corresponding kinetic and thermodynamic parameters are however still poorly known in the literature. We studied the reactivity of alanylalanine in acidic to neutral conditions as a model system. The hydrolysis into amino acids, the epimerization of the N-terminal residue, and the cyclization into diketopiperazine could be successfully identified and studied. This kinetic investigation highlighted interesting behaviors. Complex mechanisms were observed in very acidic conditions. The relative kinetic stability of the diastereoisomers of the dipeptide is highly dependent of the pH, with the possibility to dynamically destabilize the thermodynamically more stable diastereoisomers. The existence of the cyclization of dipeptides adds complexity to the system. On one hand it brings additional stereoselectivities; on the other hand fast racemization of heterochiral dipeptides is obtained.
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Affiliation(s)
- Raphaël Plasson
- Department of Applied Chemistry, Keio University, Hiyoshi, Kohoku-ku, Yokohamashi, Japan.
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54
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Meinert C, de Marcellus P, d'Hendecourt LLS, Nahon L, Jones NC, Hoffmann SV, Bredehöft JH, Meierhenrich UJ. Photochirogenesis: photochemical models on the absolute asymmetric formation of amino acids in interstellar space. Phys Life Rev 2011; 8:307-30. [PMID: 21924690 DOI: 10.1016/j.plrev.2011.08.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 08/26/2011] [Indexed: 11/25/2022]
Abstract
Proteins of all living organisms including plants, animals, and humans are made up of amino acid monomers that show identical stereochemical L-configuration. Hypotheses for the origin of this symmetry breaking in biomolecules include the absolute asymmetric photochemistry model by which interstellar ultraviolet (UV) circularly polarized light (CPL) induces an enantiomeric excess in chiral organic molecules in the interstellar/circumstellar media. This scenario is supported by a) the detection of amino acids in the organic residues of UV-photo-processed interstellar ice analogues, b) the occurrence of L-enantiomer-enriched amino acids in carbonaceous meteorites, and c) the observation of CPL of the same helicity over large distance scales in the massive star-forming region of Orion. These topics are of high importance in topical biophysical research and will be discussed in this review. Further evidence that amino acids and other molecules of prebiotic interest are asymmetrically formed in space comes from studies on the enantioselective photolysis of amino acids by UV-CPL. Also, experiments have been performed on the absolute asymmetric photochemical synthesis of enantiomer-enriched amino acids from mixtures of astrophysically relevant achiral precursor molecules using UV-circularly polarized photons. Both approaches are based on circular dichroic transitions of amino acids that will be highlighted here as well. These results have strong implications on our current understanding of how life's precursor molecules were possibly built and how life selected the left-handed form of proteinogenic amino acids.
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Affiliation(s)
- Cornelia Meinert
- Faculté des Sciences, UMR 6001 CNRS, LCMBA, University of Nice-Sophia Antipolis, 28 Avenue Valrose, 06108 Nice, France.
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55
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Wagner N, Rubinov B, Ashkenasy G. β-Sheet-induced chirogenesis in polymerization of oligopeptides. Chemphyschem 2011; 12:2771-80. [PMID: 21898751 DOI: 10.1002/cphc.201100292] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 07/17/2011] [Indexed: 11/07/2022]
Abstract
The origin of long homochiral biopolymers in living systems has recently been the focus of intense research. In one particular research line, scientists studied, experimentally and theoretically, chiral amplification obtained during peptide formation by polymerization of amino acid building blocks. It was suggested that processes leading to temporal or spatial separation, and thus, to the growth of homochiral polymers at the expense of their heterochiral counterparts, can explain the chirality observed in larger molecules. We introduce a simple model and stochastic simulation for the polymerization of amino acids and β-sheet formation, showing the crucial effects of the β sheets on the distributions of peptide lengths. When chiral affinities are included, racemic β sheets of alternating homochiral strands lead to the formation of chiral peptides, the isotacticity of which increases with length, consistent with previous experimental results in aqueous solutions. The tendency to form isotactic peptides is shown for both initially racemic and initially nonracemic systems, as well as for closed and open systems. We suggest that these or similar mechanisms may explain the origin of chiroselectivity in prebiotic environments.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
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56
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Activation of carboxyl group with cyanate: peptide bond formation from dicarboxylic acids. Amino Acids 2011; 42:2331-41. [PMID: 21769498 DOI: 10.1007/s00726-011-0975-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/29/2011] [Indexed: 10/18/2022]
Abstract
The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth. The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the 1H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution (pH 2.2-5.5). The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution. The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.
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57
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Chiral recognition and complexation behaviour of β-CyD vs. l- and dl-serine by FTIR-ATR spectroscopy. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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58
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Weissbuch I, Lahav M. Crystalline Architectures as Templates of Relevance to the Origins of Homochirality. Chem Rev 2011; 111:3236-67. [DOI: 10.1021/cr1002479] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Isabelle Weissbuch
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot, Israel, 76100
| | - Meir Lahav
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot, Israel, 76100
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59
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60
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Blanco C, Hochberg D. Chiral polymerization: symmetry breaking and entropy production in closed systems. Phys Chem Chem Phys 2011; 13:839-49. [DOI: 10.1039/c0cp00992j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Sajewicz M, Matlengiewicz M, Leda M, Gontarska M, Kronenbach D, Kowalska T, Epstein IR. Spontaneous oscillatory in vitro chiral conversion of simple carboxylic acids and its possible mechanism. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1739] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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62
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Fransson L, Moberg C. Gaining Selectivity by Combining Catalysts: Sequential versus Recycling Processes. ChemCatChem 2010. [DOI: 10.1002/cctc.201000267] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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63
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Dzwolak W. Vortex-induced chiral bifurcation in aggregating insulin. Chirality 2010; 22 Suppl 1:E154-60. [DOI: 10.1002/chir.20896] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 05/03/2010] [Indexed: 11/06/2022]
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64
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Sajewicz M, Gontarska M, Kronenbach D, Leda M, Kowalska T, Epstein IR. Condensation oscillations in the peptidization of phenylglycine. ACTA ACUST UNITED AC 2010. [DOI: 10.1186/1759-2208-1-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
In earlier studies, we showed that certain low-molecular-weight carboxylic acids (profens, amino acids, hydroxy acids) can undergo spontaneous in vitro chiral conversion accompanied by condensation to from oligomers, and we proposed two simple models to describe these processes. Here, we present the results of investigations using non-chiral high-performance liquid chromatography with diode array detector (HPLC-DAD) and mass spectrometry (MS) on the dynamics of peptidization of S-, R-, and rac-phenylglycine dissolved in 70% aqueous ethanol and stored for times up to one year. The experimental results demonstrate that peptidization of phenylglycine can occur in an oscillatory fashion. We also describe, and carry out simulations with, three models that capture key aspects of the oscillatory condensation and chiral conversion processes.
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65
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Danger G, Plasson R, Pascal R. An experimental investigation of the evolution of chirality in a potential dynamic peptide system: N-terminal epimerization and degradation into diketopiperazine. ASTROBIOLOGY 2010; 10:651-662. [PMID: 20735255 DOI: 10.1089/ast.2009.0450] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The APED model (activation-polymerization-epimerization-depolymerization) is a unique example of a chemical system that allows symmetry breaking through a dynamic process involving indirect network autocatalysis. In its simplest version, the autocatalytic behavior of this model partly relies on the reproduction of local chiral centers in dipeptides through an epimerization process, with a thermodynamic preference for homochiral chains. We studied the reactivity of di- and tripeptides, containing a N-terminal phenylglycine (Phg) residue, as model compounds for the experimental determination of the kinetic and thermodynamic parameters related to the N-terminal epimerization process. Although the N-terminal residue is prone to spontaneous epimerization, catalysis was required for the epimerization to reach the equilibrium state in reasonable time. Unexpectedly, the observed equilibrium diastereoisomeric excesses have shown a general tendency for more stable heterochiral peptides, especially strong in the case of dipeptides. In parallel to this process, a stereoselective peptide cleavage through diketopiperazine formation was observed. Contrary to the N-terminal epimerization of peptides, the diketopiperazine formation did not need any catalyst, and heterochiral peptides were shown to be dynamically unstabilized, as they were cleaved faster than homochiral peptides. The validity of the extrapolation of these results to other residues and longer peptide chains is discussed, and some directions for future developments of the theoretical model are given.
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Affiliation(s)
- Grégoire Danger
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 1, Université de Montpellier 2, Montpellier, France.
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66
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67
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Lente G. Open system approaches in deterministic models of the emergence of homochirality. Chirality 2010; 22:907-13. [DOI: 10.1002/chir.20853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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68
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Plasson R, Brandenburg A. Homochirality and the need for energy. ORIGINS LIFE EVOL B 2010; 40:93-110. [PMID: 19911301 DOI: 10.1007/s11084-009-9181-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 09/16/2009] [Indexed: 11/30/2022]
Abstract
The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations, have been developed during the last decades, focusing on the non-linear kinetic aspects. Besides the absolute necessity of self-amplification processes, the importance of energetic aspects is often underestimated. Going down to the most fundamental aspects, the distinction between a single object-that can be intrinsically asymmetric-and a collection of objects-whose racemic state is the more stable one-must be emphasized. A system of strongly interacting objects can be described as one single object retaining its individuality and a single asymmetry; weakly or non-interacting objects keep their own individuality, and are prone to racemize towards the equilibrium state. In the presence of energy fluxes, systems can be maintained in an asymmetric non-equilibrium steady-state. Such dynamical systems can retain their asymmetry for times longer than their racemization time.
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69
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Hochberg D. Effective potential and chiral symmetry breaking. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:016106. [PMID: 20365431 DOI: 10.1103/physreve.81.016106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Indexed: 05/29/2023]
Abstract
The nonequilibrium effective potential is calculated for the Frank model of spontaneous mirror-symmetry breaking in chemistry in which external noise is introduced to account for random environmental effects. The well-mixed limit, corresponding to negligible diffusion, and the case of diffusion in two space dimensions are studied in detail. White noise has a disordering effect in the former case, whereas in the latter case a phase transition occurs for external noise exceeding a critical intensity which racemizes the system.
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70
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Gleiser M, Walker SI. Toward homochiral protocells in noncatalytic peptide systems. ORIGINS LIFE EVOL B 2009; 39:479-93. [PMID: 19370399 DOI: 10.1007/s11084-009-9166-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 03/20/2009] [Indexed: 10/20/2022]
Abstract
The activation-polymerization-epimerization-depolymerization (APED) model of Plasson et al. has recently been proposed as a mechanism for the evolution of homochirality on prebiotic Earth. The dynamics of the APED model in two-dimensional spatially-extended systems is investigated for various realistic reaction parameters. It is found that the APED system allows for the formation of isolated homochiral proto-domains surrounded by a racemate. A diffusive slowdown of the APED network induced, for example, through tidal motion or evaporating pools and lagoons leads to the stabilization of homochiral bounded structures as expected in the first self-assembled protocells.
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Affiliation(s)
- Marcelo Gleiser
- Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755, USA.
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71
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Crusats J, Hochberg D, Moyano A, Ribó JM. Frank Model and Spontaneous Emergence of Chirality in Closed Systems. Chemphyschem 2009; 10:2123-31. [DOI: 10.1002/cphc.200900181] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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72
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On-line sample stacking of peptides in capillary electrophoresis for the study of prebiotic reactions between alpha,alpha-dialkylated amino acids and amino acid N-carboxyanhydrides. J Chromatogr A 2009; 1216:5748-54. [PMID: 19539298 DOI: 10.1016/j.chroma.2009.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/20/2009] [Accepted: 06/03/2009] [Indexed: 11/23/2022]
Abstract
The reaction between alpha,alpha-dialkylated amino acids and amino acid N-carboxyanhydrides is slow leading to low concentrations of products (peptides). The detection by capillary electrophoresis of the analytes contained in such samples is therefore a challenging issue. In this work, on-line sample pre-concentration methods based on field-amplified sample stacking have been implemented and compared. Because of the high ionic strength present in the sample matrix, samples were diluted with an organic solvent prior to analysis to decrease the sample conductivity. Different modes of sample injection (field amplified sample injection (FASI), hydrodynamic normal sample stacking (NSS) or large volume sample stacking (LVSS)) were compared. Pre-concentration factors of 20 for FASI, about 30-40 for NSS and 60 for LVSS were obtained for the analysis of (l,l) dipeptide of valine in a large excess of isovaline and 0.2M of ionic strength. For LVSS application and resolution optimisation, a new non-covalent coating based on the partial modification of the capillary surface was used to tune the electroosmotic flow magnitude and to pump the sample matrix out of the capillary. This on-line sample pre-concentration step allowed confirming that oligopeptides including alpha,alpha-dialkylated amino acids are formed during the reaction between alpha,alpha-dialkylated amino acids and N-carboxyanhydride amino acids.
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73
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74
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Lente G, Ditrói T. Stochastic Kinetic Analysis of the Frank Model. Stochastic Approach to Flow-Through Reactors. J Phys Chem B 2009; 113:7237-42. [DOI: 10.1021/jp900276h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gábor Lente
- Department of Inorganic and Analytical Chemistry, University of Debrecen, POB 21, Debrecen, H-4010 Hungary
| | - Tamás Ditrói
- Department of Inorganic and Analytical Chemistry, University of Debrecen, POB 21, Debrecen, H-4010 Hungary
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75
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Blackmond DG. Challenging the concept of “recycling” as a mechanism for the evolution of homochirality in chemical reactions. Chirality 2009; 21:359-62. [DOI: 10.1002/chir.20592] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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76
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Plasson R, Bersini H. Energetic and Entropic Analysis of Mirror Symmetry Breaking Processes in a Recycled Microreversible Chemical System. J Phys Chem B 2009; 113:3477-90. [DOI: 10.1021/jp803807p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Hugues Bersini
- Nordita, Stockholm, Sweden, IRIDIA, ULB, Brussels, Belgium
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77
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Abstract
A coevolutionary model is discussed that incorporates the logical structure of constitutional chemistry and its kinetics on the one hand and the topological evolution of the chemical reaction network on the other hand. The motivation for designing this model is twofold. First, experiments that are to provide insight into chemical problems should be expressed in a syntax that remains as close as possible to real chemistry. Second, the study of physical properties of the complex chemical reaction networks requires growing models that incorporate features realistic from a biochemical perspective. In this article the theory and algorithms underlying the coevolutionary model are explained, and two illustrative examples are provided. These examples show that one needs to be careful in making general claims concerning the structure of chemical reaction networks.
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Affiliation(s)
- Tom Lenaerts
- SWITCH Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.
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78
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Mauksch M, Tsogoeva SB. Spontaneous emergence of homochirality via coherently coupled antagonistic and reversible reaction cycles. Chemphyschem 2008; 9:2359-71. [PMID: 18942050 DOI: 10.1002/cphc.200800226] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Asymmetric synthesis aims at obtaining enantio-enriched products in stereoselective reactions under a chiral influence. We demonstrate both mathematically and numerically that, even under nominally achiral conditions, fully homochiral steady states can be obtained in open reactive systems by spontaneous mirror-symmetry breaking in the homogenous solution phase when the autocatalytic reaction network is closed in the form of coherently coupled antagonistic reversible reaction cycles which, paradoxically, allow for complete recycling of the reactant. We show that the fully reversible Frank mechanism for spontaneous mirror-symmetry breaking is closely related to the Lotka-Volterra system, which models predator-prey relations in ecosystems. Amplification of total enantiomeric excess and the principle of microscopic reversibility are not in conflict for all conceivable reactions. A viable and widely applicable reaction protocol is introduced and discussed, and it permits the theoretical implications to be applied to practical laboratory examples. Implications for the possible origin of biological homochirality on early earth are discussed.
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Affiliation(s)
- Michael Mauksch
- Department of Chemistry and Pharmacy, Chair of Organic Chemistry I, University of Erlangen-Nuremberg, Henkestrasse 42, 91054 Erlangen, Germany
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79
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Blackmond D. “If Pigs Could Fly” Chemistry: A Tutorial on the Principle of Microscopic Reversibility. Angew Chem Int Ed Engl 2008; 48:2648-54. [DOI: 10.1002/anie.200804566] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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80
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Blackmond D. “Wenn Schweine fliegen könnten”: Zum Prinzip der mikroskopischen Reversibilität. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804566] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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81
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Lente G. Thermodynamic unfeasibilty of recycling in chiral autocatalytic kinetic models. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11144-008-5366-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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82
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Blackmond DG. Response to “Comment on ‘A Re-Examination of Reversibility in Reaction Models for the Spontaneous Emergence of Homochirality’”. J Phys Chem B 2008. [DOI: 10.1021/jp8040378] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Donna G. Blackmond
- Department of Chemistry and Department of Chemical Engineering and Chemical Technology, Imperial College, London SW7 2AZ, United Kingdom
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83
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Plasson R. Comment on “Re-Examination of Reversibility in Reaction Models for the Spontaneous Emergence of Homochirality”. J Phys Chem B 2008; 112:9550-2; discussion 9553-5. [DOI: 10.1021/jp803588z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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84
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Chiral bifurcation in aggregating insulin: an induced circular dichroism study. J Mol Biol 2008; 379:9-16. [PMID: 18439622 DOI: 10.1016/j.jmb.2008.03.057] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 01/14/2008] [Accepted: 03/23/2008] [Indexed: 11/22/2022]
Abstract
The structural unambiguity of folding is lost when disordered protein molecules convert into beta-sheet-rich fibrils. The resulting polymorphism of protein aggregates has been studied in the context of its biomedical consequences. Events underlying the conformational variance of amyloid fibrils, as well as physicochemical boundaries between folding and misfolding pathways, remain obscure. Bifurcation and chiral mesoscopic-scale organization of amyloid fibrils are new aspects of protein misfolding. Here we characterize bifurcation events accompanying insulin fibrillation upon intensive vortexing. Upon agitation, two types of insulin fibrils with opposite chiral senses are formed; however, predominance of either species is only stochastically determined. The uncertainty of fibrils' chiral sense holds only for fibrils grown within the physiological temperature range, while above 50 degrees C, the bifurcation is no longer observed--fibrils' chiral moieties become uniformly biased towards ligand probes, as revealed by the extrinsic Cotton effect of thioflavin T, Congo red, and molecular iodine. According to transmission electron microscopy and scanning electron microscopy data, chiral variants of insulin fibrils consist of fibrous superstructures, distinct from spherulites, formed by the protein in nonagitated solutions. Gradual dissociation of the fibrils in the presence of dimethyl sulfoxide is noncooperative and can be resolved into three distinct phases: decay of the higher-order chiral structures, breakdown of fibrils, and unfolding of intermolecular beta-sheet. The chiral aggregates are also destabilized by elution of NaCl implying that Debye screening of charged beta-sheets provided by chloride counterions is needed for sustaining their kinetic stability. At elevated temperatures, cross-seeding of agitated insulin samples with preformed fibrils revealed a chiral conflict that prevented the passing of structural features of mother seeds to daughter fibrils in a manner typical of amyloid "strains."
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85
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Mauksch M, Tsogoeva SB, Wei S, Martynova IM. Demonstration of spontaneous chiral symmetry breaking in asymmetric Mannich and Aldol reactions. Chirality 2007; 19:816-25. [PMID: 17786910 DOI: 10.1002/chir.20474] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spontaneous symmetry breaking in reactive systems, known as a rare physical phenomenon and for the Soai autocatalytic irreversible reaction, might in principle also occur in other, more common asymmetric reactions when the chiral product is capable to promote its formation and an element of "nonlinearity" is involved in the reaction scheme. Such phenomena are long sought after in chemistry as a possible explanation for the biological homochirality of biomolecules. We have investigated homogeneous organic stereoselective Mannich and Aldol reactions, in which the product is capable to form H-bridged complexes with the prochiral educt, and found by applying NMR spectroscopy, HPLC analysis, and optical rotation measurements 0.3-50.8% of random product enantiomeric excess under essentially achiral reaction conditions. These findings imply a hitherto overlooked mechanism for spontaneous symmetry breaking and, hence, a novel approach to the problem of absolute asymmetric synthesis and could have also potential significance for the conundrum of homochirality.
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Affiliation(s)
- Michael Mauksch
- Institute of Organic Chemistry I, University of Erlangen-Nuremberg, Henkestrasse 42, 91052 Erlangen, Germany
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86
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Abstract
A recently proposed model of non-autocatalytic reactions in dipeptide formation that leads to spontaneous symmetry breaking and homochirality was examined. The model is governed by activation, polymerization, epimerization, and depolymerization of amino acids. Symmetry breaking was determined to result primarily from the different rates of reactions that involve homodimers and heterodimers, i.e., stereoselective reactions, and the fact that epimerization can only occur on the N-terminal residue and not on the C-terminal residue. This corresponds to an auto-inductive cyclic process that works only in one direction. It is argued that epimerization mimics autocatalytic behavior as well as mutual antagonism, both of which are known to be crucial for the production of full homochirality.
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87
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Plasson R, Kondepudi DK, Bersini H, Commeyras A, Asakura K. Emergence of homochirality in far-from-equilibrium systems: mechanisms and role in prebiotic chemistry. Chirality 2007; 19:589-600. [PMID: 17559107 DOI: 10.1002/chir.20440] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Since the model proposed by Frank (Frank FC, Biochem Biophys Acta 1953;11:459-463), several alternative models have been developed to explain how an asymmetric non-racemic steady state can be reached by a chirally symmetric chemical reactive system. This paper explains how a stable non-racemic regime can be obtained as a symmetry breaking occurring in a far-from-equilibrium reactive system initiated with an initial imbalance. Departing from the variations around the original Frank's model that are commonly described in the literature, i.e. open-flow systems of direct autocatalytic reactions, we discuss recent developments emphasizing both an active recycling of components and an autocatalytic network of simple reactions. We will present our APED model as the most natural realization of such thermodynamic openness and non-equilibrium, of recycling and of network autocatalysis, each of these in prebiotic conditions. The different experimental and theoretical models in the literature will be classified according to mechanism. The place and role of such self-structured networks responsible for the presence of homochirality in the primitive Earth will be detailed.
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Affiliation(s)
- Raphaël Plasson
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohamashi, Japan.
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88
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Gleiser M. Asymmetric spatiotemporal evolution of prebiotic homochirality. ORIGINS LIFE EVOL B 2007; 37:235-51. [PMID: 17131085 DOI: 10.1007/s11084-006-9058-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 11/02/2006] [Indexed: 10/23/2022]
Abstract
The role of asymmetry on the evolution of prebiotic homochirality is investigated in the context of autocatalytic polymerization reaction networks. A model featuring enantiometric cross-inhibition and chiral bias is used to study the diffusion equations controlling the spatiotemporal development of left and right-handed domains. Bounds on the chiral bias are obtained based on present-day constraints on the emergence of life on early Earth. The viability of biasing mechanisms such as weak neutral currents and circularly polarized UV light is discussed. The results can be applied to any hypothetical planetary platform.
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Affiliation(s)
- Marcelo Gleiser
- Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755, USA.
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89
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Abstract
The formation of a single homochiral solid phase from crystallization of achiral compounds has recently been under discussion. We show that the state of single solid-phase homochirality does not represent a more stable thermodynamic state than that of a racemate consisting of two separate homochiral solids. We introduce the term "chiral amnesia" as a more appropriate molecular-level description than "chiral recognition" to describe the driving force for establishing solid-phase homochirality in the case of achiral molecules that form chiral solids as well as in the case of rapidly racemizing enantiomers.
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Affiliation(s)
- Donna G Blackmond
- Department of Chemistry and Department of Chemical Engineering and Chemical Technology, Imperial College, London SW7 2AZ, UK.
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90
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Sun Q, Bai Y, He G, Duan C, Lin Z, Meng Q. Spontaneous resolution of silver double helicates consisting of achiral ligands with several aromatic rings. Chem Commun (Camb) 2007:2777-9. [PMID: 17009460 DOI: 10.1039/b604066g] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Symmetric breaking of silver double helicates through spontaneous crystallization was achieved via incorporation of C-H...pi and pi-pi stacking interactions of achiral ligands consisting of several aromatic rings.
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Affiliation(s)
- Qiaozhen Sun
- Coordination Chemistry Institute, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, 210093, PR China
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91
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Bielski R, Tencer M. A possible path to the RNA world: enantioselective and diastereoselective purification of ribose. ORIGINS LIFE EVOL B 2007; 37:167-75. [PMID: 17136434 DOI: 10.1007/s11084-006-9022-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 08/01/2006] [Indexed: 11/26/2022]
Abstract
A theoretical mechanism resulting in the prebiotic appearance of enantiopure ribose, which would be needed for the origin of RNA and the "RNA world" is proposed. The mechanism simultaneously explains the emergence of biological homochirality and could answer the question of why nucleic acids are based on ribose rather than another sugar. Cleavage of certain non-chiral mineral crystals is known to lead to formation of chiral surfaces. In a chromatography-like process a mixture of racemic carbohydrates originating from the formose reaction is proposed to have been separated on such a chiral surface. Monosaccharides interact with surfaces through their hydroxyl groups, either by hydrogen bond formation or complex formation with metal ions. alpha-Ribopyranose, which has all hydroxyl groups on one side of the ring, is known to interact more strongly than other sugars with surfaces, as corroborated by certain chromatographic and electrophoresis data. A similar scenario leading to enantiopure ribose is separation on a flat, but not necessarily chiral surface in the presence of a strong electric field capable of orienting highly polar derivatives of sugars.
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Affiliation(s)
- Roman Bielski
- Value Recovery Inc., 510 Heron Drive, Bridgeport, NJ 08014, USA.
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92
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93
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Lente G. The effect of parity violation on kinetic models of enantioselective autocatalysis. Phys Chem Chem Phys 2007; 9:6134-41. [DOI: 10.1039/b711546f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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94
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Crusats J, Veintemillas-Verdaguer S, Ribó JM. Homochirality as a Consequence of Thermodynamic Equilibrium? Chemistry 2006; 12:7776-81. [PMID: 16933347 DOI: 10.1002/chem.200600580] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent results on the crystallisation/dissolution equilibrium of enantiomorphic crystals of NaClO3 lead to the conclusion that liquid-phase systems composed of achiral or fast racemising compounds yielding enantiomorphic solid phases (racemic conglomerates) can derive spontaneously to a single homochiral solid phase. This is a thermodynamically driven total resolution, which can only occur when the system is so perturbed that chiral recognition between the species of the system becomes feasible.
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Affiliation(s)
- Joaquim Crusats
- Departament de Química Orgànica Universitat de Barcelona, c. Martí i Franquès 1.08028 Barcelona, Catalonia, Spain.
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95
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Asakura K, Plasson R, Kondepudi DK. Experimental evidence and theoretical analysis for the chiral symmetry breaking in the growth front of conglomerate crystal phase of 1,1'-binaphthyl. CHAOS (WOODBURY, N.Y.) 2006; 16:037116. [PMID: 17014250 DOI: 10.1063/1.2352852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chirally asymmetric states, chemical oscillations, propagating chemical waves, and spatial patterns, are examples of far-from-equilibrium self-organization. We have found that the crystal growth front of 1,1(')-binaphthyl shows many of the characteristics of an open system in which chiral symmetry breaking has occurred. From its supercooled molten phase, 1,1(')-binaphthyl crystallizes as a conglomerate of R and S crystals when the temperature is above 145 degrees C. In addition, 1,1(')-binaphthyl in its molten phase is always racemic due to its high racemization rate. Under appropriate conditions, bimodal probability distribution of enantiomeric excess (ee) with maxima around 60% was observed. The ee was mass independent, indicating that the growth front maintains a constant ee. A kinetic model that theoretically analyzes the chiral symmetry breaking transition in the growth front of a conglomerate crystal phase was formulated. Computer simulation of the model reproduced not only the average but also the large variation of the ee observed in crystallization experiments.
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Affiliation(s)
- Kouichi Asakura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku, Yokohama 223-8522, Japan.
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96
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Schmidt P. Evolution of homochirality by epimerization of random peptide chains. A stochastic model. ORIGINS LIFE EVOL B 2006; 36:391-411. [PMID: 16791733 DOI: 10.1007/s11084-005-9007-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 11/20/2005] [Accepted: 11/20/2005] [Indexed: 10/24/2022]
Abstract
A cyclic process is described which is constituted of polymerization, epimerization, and hydrolysis steps. During the first cycle peptides with random sequences are formed from racemic amino acids. A small portion of these peptides have substructures with a terminal residue linked to a homochiral sequence of optical antipodes. In such a substructure the terminal residue is assumed to invert into its mirror image so that a thermodynamically favourable epimeric stucture with continuous homochirality is formed. In the hydrolysis step the peptides are split back to monomeric units with retention of configuration. Due to stochastic differences between L- and D-substructures a net excess of one of the enantiomers results. This excess enhances the probability of the formation of substructures having the dominant configuration in the next cycle. It is shown by probabilistic considerations and computer simulations that this mechanism generates an autocatalytic growth of one of the enantiomers which finally results in homochiral populations of amino acids. The number of cycles necessary to attain homochirality depends on the number of residues of the substructure, on the chain length distribution of the polymers and on the total number of amino acid units.
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Affiliation(s)
- Peter Schmidt
- Suedtiroler Ring 28, D 67273, Weisenheim/Berg, Germany.
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97
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Shibata R, Saito Y, Hyuga H. Diffusion accelerates and enhances chirality selection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:026117. [PMID: 17025513 DOI: 10.1103/physreve.74.026117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 05/30/2006] [Indexed: 05/12/2023]
Abstract
The diffusion effect on chirality selection in a two-dimensional reaction-diffusion model is studied by Monte Carlo simulations. The model consists of achiral reactants A which turn into either of the chiral products R or S in a solvent of chemically inactive vacancies V . The reaction contains a nonlinear autocatalysis as well as a recycling process, and the chiral symmetry breaking is monitored by an enantiomeric excess (ee) phi. Without dilution a strong nonlinear autocatalysis ensures chiral symmetry breaking. By diluting a diffusionless system, the ee phi decreases and a racemic state is recovered below a critical concentration c(c) . When the diffusion is allowed, the steady value of phi increases and c(c) decreases. As for the relation between the ee phi and the concentration c , a formula interpolating between the diffusionless (D=0) and the homogeneous (D=infinity) limits is proposed by incorporating the diffusional enhancement of the concentrations of chiral species. Diffusion also accelerates the development of the chiral order, and the time required to establish the order in a system of a size L(2) is inversely proportional to the diffusion constant D as L(2)/D .
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Affiliation(s)
- Ryo Shibata
- Department of Physics, Keio University, Yokohama 223-8522, Japan
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98
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Plasson R, Kondepudi DK, Asakura K. Three-Dimensional Description of the Spontaneous Onset of Homochirality on the Surface of a Conglomerate Crystal Phase. J Phys Chem B 2006; 110:8481-7. [PMID: 16623535 DOI: 10.1021/jp057511y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The spontaneous emergence of homochirality in an initially racemic system can be obtained in far-from-equilibrium states. Traditional models do not take into account the influence of inhomogeneities, while they may be of great importance. What would happen when one configuration emerges at one position, and the opposite one at another position? We present a discrete three-dimensional model of conglomerate crystallization, based on 1,1'-binaphthyl crystallization experiments, that takes into account the position and environment of every single elementary growth subunit. Stochastic simulations were performed to predict the evolution of the crystallization process. It is shown that the traditional view of the symmetry breaking can then be extended. Fluctuations of the fixed points related to inhomogeneities are observed, and complex behavior, such as local instabilities, transient structures, and chaotic behavior, can emerge. Our modeling indicates that such complex phenomena could cause large fluctuation of the final enantiomeric excess that is observed experimentally in binaphthyl crystallization. The results presented in this article show the importance of inhomogeneities in understanding enantiomeric excess generated in crystallization and the inadequacy of the models based on the assumption of homogeneity.
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Affiliation(s)
- Raphaël Plasson
- Department of Applied Chemistry, Faculty of Sciences and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
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99
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Lente G. Stochastic Kinetic Models of Chiral Autocatalysis: A General Tool for the Quantitative Interpretation of Total Asymmetric Synthesis. J Phys Chem A 2005; 109:11058-63. [PMID: 16331951 DOI: 10.1021/jp054613f] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A continuous time discrete state stochastic kinetic approach is used to study various chiral autocatalytic models in which the possibility of total asymmetric synthesis arises. It is shown that this approach is superior to the deterministic approaches used earlier and is able to interpret many aspects of chiral autocatalysis. First-order autocatalysis, independently of further kinetic details of the system, leads to a unique final statistical distribution of enantiomers. Higher order autocatalysis, on the other hand, leads to a final state where one of the enantiomers is in overwhelming excess over the other. Criteria are postulated to differentiate between inherently stochastic phenomena in chiral autocatalytic reactions and irreproducibility because of insufficient control of external factors.
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Affiliation(s)
- Gábor Lente
- University of Debrecen, Department of Inorganic and Analytical Chemistry, Debrecen 10, P.O.B. 21, Hungary H-4010.
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100
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Abstract
The paper describes methodology of using three independent macroscopic factors affecting molecular orientation to accomplish separation of a racemic mixture without the presence of any other chiral compounds, i. e., absolute enantioselective separation (AES) which is an extension of a concept of applying these factors to absolute asymmetric synthesis. The three factors may be applied simultaneously or, if their effects can be retained, consecutively. The resulting three mutually orthogonal or near orthogonal directors constitute a true chiral influence and their scalar triple product is the measure of the chirality of the system. AES can be executed in a chromatography-like microfluidic process in the presence of an electric field. It may be carried out on a chemically modified flat surface, a monolithic polymer column made of a mesoporous material, each having imparted directional properties. Separation parameters were estimated for these media and possible implications for the natural homochirality are discussed.
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