title: Theoretical study on the factors controlling the stability of the borate complexes of ribose, arabinose, lyxose, and xylose.
abstract: Recent experimental studies suggest that complexation with borate minerals stabilizes ribose, and that the borate complex of ribose is more stable than those of related aldopentoses, that is, arabinose, lyxose, and xylose. These findings have revived the debate on the plausibility of the RNA-world theory, because they provide an explanation for the stabilization and selection of ribose in prebiotic conditions. In this paper we unravel the factors that make the ribose-borate complex the most stable one. For this purpose, we have investigated the structure and stability of the ribose-, arabinose-, lyxose-, and xylose-borate complexes using density functional theory and a continuum solvent approach. The computed results reveal that in the aldopentose-borate complexes, the electrostatic field of the borate is strong enough to change the orientation of the nearby hydroxyl groups compared to noncomplexed aldopentoses. In addition, we show that the distinct stability of the ribose-borate 2:1 complex can be attributed to 1) a strong hydrogen bond between the ribose 3-OH and one of the negatively charged borate oxygen atoms, and 2) a favorable contact between the aqueous medium and the 5-CH(2)OH group due to the space separation between the 5-CH(2)OH group and the borate anion.
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. judit@ncbr.chemi.muni.cz
authors.forename: Judit E
authors.initials: JE
authors.lastname: Sponer
authors.forename: Bobby G
authors.initials: BG
authors.lastname: Sumpter
authors.forename: Jerzy
authors.initials: J
authors.lastname: Leszczynski
authors.forename: Jirí
authors.initials: J
authors.lastname: Sponer
authors.forename: Miguel
authors.initials: M
authors.lastname: Fuentes-Cabrera
mesh_terms: D001089:Arabinose / Q000737:chemistry; D001881:Borates / Q000737:chemistry*; D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry; D015394:Molecular Structure; D010429:Pentoses / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry; D014994:Xylose / Q000737:chemistry
chemical_list: D001881:Borates; D046911:Macromolecular Substances; D010429:Pentoses; C043333:lyxose; D012266:Ribose; D014994:Xylose; D001089:Arabinose