8e1fc5733f6c57a840f96fa6c4ebecdd life_a2019v9p75.pdf fecfac3d3919460973760a666320f51064b3f321 life_a2019v9p75.pdf c5b4f9813011983ff3ad41aba63e7920e9ddf2e6b59bdac12bcd780d4cdc3beb life_a2019v9p75.pdf Title: Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations Subject: Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies. Keywords: prebiotic chemistry; biopolymers formation; condensation of amino acids; B3LYP-D3 calculations; clays; water solvent conditions Author: Berta Martínez-Bachs and Albert Rimola Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Mon Sep 16 12:14:31 2019 CEST ModDate: Mon Sep 16 12:14:31 2019 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 15 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2537092 bytes Optimized: no PDF version: 1.5 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- ZKHHXH+URWPalladioL-Ital Type 1 Custom yes yes no 59 0 WLAFSE+URWPalladioL-Bold Type 1 Custom yes yes no 60 0 WLENKM+VnURWPalladioL-Bold Type 1 Custom yes yes no 61 0 YVBXTH+URWPalladioL-Roma Type 1 Custom yes yes no 62 0 CIQLLF+VnURWPalladioL Type 1 Custom yes yes no 63 0 QANVCD+Rpxr Type 1 Builtin yes yes no 64 0 ETUHUL+Pxsy Type 1 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RepresentationInformation: life_a2019v9p75.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2020-01-22 10:15:06 CET Size: 2537092 Format: PDF Version: 1.5 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 0 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: ぉのぴひはつふっぴどはのぜ〴〩਼㰠⽓ 䝯呯 䐠⡳散瑩潮⸲ Item: Title: きづぴとはつびぜ〴〩਼㰠⽓ 䝯呯 䐠⡳散瑩潮⸳ Item: Title: げづびふぬぴびぜ〴ぜ〰ちのつぜ〴ぜ〰いどびっふびびどはのぜ〴〩਼㰠⽓ 䝯呯 䐠⡳畢獥捴楯渮㌮ㄩ‾㸊⡜㌷㙜㌷㝜〰ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぇちびぜ〴ぜ〰ぐとちびづぜ〴〩਼㰠⽓ 䝯呯 䐠⡳畢獥捴楯渮㌮㈩‾㸊⡜㌷㙜㌷㝜〰ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぐひづびづのっづぜ〴ぜ〰はてぜ〴ぜ〰ぁぜ〴ぜ〰きで〲〭〫ぃぬちべぜ〴ぜ〰ぃちぴどはのぜ〴〩਼㰠⽓ 䝯呯 䐠⡳畢獥捴楯渮㌮㌩‾㸊⡜㌷㙜㌷㝜〰ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぐひづびづのっづぜ〴ぜ〰はてぜ〴ぜ〰ちぜ〴ぜ〰きで〲〫ぜ〴ぜ〰どはのぜ〴ぜ〰ちのつぜ〴ぜ〰どのぜ〴ぜ〰しちぴづひべぜ〴ぜ〰ぅのぶどひはのねづのぴびぜ〴〩਼㰠⽓ 䝯呯 䐠⡳散瑩潮⸴ Children: Item: Title: ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぇちびぜ〴ぜ〰ぐとちびづぜ〴〩਼㰠⽓ 䝯呯 䐠⡳畢獥捴楯渮㌮㈩‾㸊⡜㌷㙜㌷㝜〰ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぐひづびづのっづぜ〴ぜ〰はてぜ〴ぜ〰ぁぜ〴ぜ〰きで〲〭〫ぃぬちべぜ〴ぜ〰ぃちぴどはのぜ〴〩਼㰠⽓ 䝯呯 䐠⡳畢獥捴楯渮㌮㌩‾㸊⡜㌷㙜㌷㝜〰ごぐ〭きづつどちぴづつぜ〴ぜ〰ぐづばぴどつづぜ〴ぜ〰あはのつぜ〴ぜ〰うはひねちぴどはのぜ〴ぜ〰どのぜ〴ぜ〰ぴとづぜ〴ぜ〰ぐひづびづのっづぜ〴ぜ〰はてぜ〴ぜ〰ちぜ〴ぜ〰きで〲〫ぜ〴ぜ〰どはのぜ〴ぜ〰ちのつぜ〴ぜ〰どのぜ〴ぜ〰しちぴづひべぜ〴ぜ〰ぅのぶどひはのねづのぴびぜ〴〩਼㰠⽓ 䝯呯 䐠⡳散瑩潮⸴ Item: Title: 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