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Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution.

ABSTRACT: We investigate the molecular geometry of the carboxyl group of formic acid in acetonitrile and aqueous solutions at room temperature with two-dimensional infrared spectroscopy (2D-IR). We found that the carboxyl group adopts two distinct configurations: a configuration in which the carbonyl group is oriented antiparallel to the hydroxyl (anti-conformer), and a configuration in which the carbonyl group is oriented at an angle of ?60° with respect to the hydroxyl (syn-conformer). These results constitute the first experimental evidence that carboxyl groups exist as two distinct and long-living conformational isomers in aqueous solution at room temperature.

SUBMITTER: Giubertoni G

PROVIDER: S-EPMC6589744 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution.

Giubertoni Giulia G Sofronov Oleksandr O OO Bakker Huib J HJ

The journal of physical chemistry letters 20190531 12

We investigate the molecular geometry of the carboxyl group of formic acid in acetonitrile and aqueous solutions at room temperature with two-dimensional infrared spectroscopy (2D-IR). We found that the carboxyl group adopts two distinct configurations: a configuration in which the carbonyl group is oriented antiparallel to the hydroxyl (anti-conformer), and a configuration in which the carbonyl group is oriented at an angle of ∼60° with respect to the hydroxyl (syn-conformer). These results con ...[more]

PMID: 31125521

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Project description:The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.

Dataset Information

Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution.

Publications

Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution.

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