The Limited Roles of Autocatalysis and Enantiomeric Cross-Inhibition in Achieving Homochirality in Dilute Systems

Brandenburg, Axel

doi:10.1007/s11084-019-09579-4

Cited by 13 publications

(10 citation statements)

References 39 publications

(49 reference statements)

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“…• Modeling homochirality at the origin of life (Brandenburg and Multamäki 2004;Brandenburg 2019), • Modeling of patterned photochemical systems (Emond et al 2012),…”

Section: Discussionmentioning

confidence: 99%

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained

Brandenburg,

Johansen,

Bourdin

et al. 2020

Preprint

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code can also evolve Lagrangian (inertial and noninertial) particles, their coagulation and condensation, as well as their interaction with the fluid. A related module has also been adapted to perform ray tracing and to solve the eikonal equation.The code is being used for Cartesian, cylindrical, and spherical geometries, but further extensions are possible. One can choose between different time stepping schemes and different spatial derivative operators. High-order first and second derivatives are used to deal with weakly compressible turbulent flows. There are also different diffusion operators to allow for both direct numerical simulations (DNS) and various types of large-eddy simulations (LES). High-level functionalityAn idea about the range of available modules can be obtained by inspecting the examples under pencil-code/samples/. Those are low resolution versions related to applications published in the literature. Some of the run directories of actual production runs are published through Zenodo. Below a list of method papers that describe the various applications and tests:

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“…• Modeling homochirality at the origin of life (Brandenburg and Multamäki 2004;Brandenburg 2019), • Modeling of patterned photochemical systems (Emond et al 2012),…”

Section: Discussionmentioning

confidence: 99%

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained

Brandenburg,

Johansen,

Bourdin

et al. 2020

Preprint

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“…A chemical process must have favored one stereochemical configuration over the other, and functional selection may then have led to homochirality [4] . What that process was, however, remains open to debate [5,6] …”

Section: Introductionmentioning

confidence: 99%

Determining the Diastereoselectivity of the Formation of Dipeptidonucleotides by NMR Spectroscopy

Doppleb

Bremer

Bechthold

et al. 2021

Chemistry A European J

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Proteins are composed of l‐amino acids, but nucleic acids and most oligosaccharides contain d‐sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate‐linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Here we report how the diastereoselectivity of the first peptide coupling of the peptido RNA pathway can be determined in situ by NMR spectroscopy. When a racemic mixture of an amino acid ester was allowed to react with an 5′‐aminoacidyl nucleotide, diastereomeric ratios of up to 72 : 28 of the resulting dipeptido nucleotides were found by integration of 31P‐ or 1H‐NMR peaks. The highest diastereomeric excess was found for the homochiral coupling product d‐Ser‐d‐Trp, phosphoramidate‐linked to adenosine 5′‐monophosphate with its d‐ribose ring. When control reactions with an N‐acetyl amino acid and valine methyl ester were run in organic solvent, the diastereoselectivity was found to be lower, with diastereomeric ratios≤62 : 38. The results from the exploratory study thus indicate that the ribonucleotide residue not only facilitates the coupling of lipophilic amino acids in aqueous medium but also the formation of a homochiral dipeptide. The methodology described here may be used to search for other stereoselective reactions that shed light on the origin of homochirality.

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“…During the early period of peptide synthesis, the appearance of aminoacylation and the set of nucleotide RNA aptamers was probably followed by establishment of homochirality of sugars and proteinogenic amino acids, which is a prerequisite for stepwise transition from the RNA world of primordial life forms to DNA-and protein-based organisms (Tamura 2008;Yarus et al 2009;Polyansky and Zagrovic 2013;Sczepanski and Joyce 2014;Brandenburg 2019). This research contributes to the development of different theories on the origin and evolution of the genetic code, the translation system, and the manifold factors affecting the process of protein biosynthesis on ribosomes (Woese et al 2000;Orgel 2004;Copley et al 2005;Rogalski et al 2008;Francis 2013;Higgs and Lehman 2015;Wong et al 2016;Koonin and Novozhilov 2017;Doig 2017;Yarus 2017;Kun and Radványi 2018;Tupper et al 2020;Bartoš 2020, 2021).…”

Section: Introductionmentioning

confidence: 99%

Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code

Saralov

2021

Acta Biotheor

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Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature T m , the T m :M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis-and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of -C=O and/or -NH 2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M-T m diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, T m , photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.

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The Limited Roles of Autocatalysis and Enantiomeric Cross-Inhibition in Achieving Homochirality in Dilute Systems

Cited by 13 publications

References 39 publications

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained

Determining the Diastereoselectivity of the Formation of Dipeptidonucleotides by NMR Spectroscopy

Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code

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