Six Pyranoside Forms of Free 2‐Deoxy‐<scp>D</scp>‐ribose

Peña, Isabel; Cocinero, Emilio J.; Cabezas, Carlos; Lesarri, Alberto; Mata, Santiago; Écija, Patricia; Daly, Adam M.; Cimas, Álvaro; Bermúdez, Celina; Basterretxea, Francisco J.; Blanco, Susana; Fernández, José A.; López, Juan C.; Castaño, Fernando; Alonso, José L.

doi:10.1002/anie.201305589

Cited by 51 publications

(32 citation statements)

References 57 publications

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“…In addition, spectral measurements have been extended to all five monosubstituted 13 C species and the endocyclic 18 O species in their natural abundance (~1.1% and~0.2%) for the most abundant c-β-pyr-1 C 4 -1 conformer using laser ablation combined with MB-FTMW. The isotopic information was used to derive its structure [224]. The population ratios for α and β conformers estimated from transition intensities indicate that 2DR exists in the gas phase as a mixture of approximately 10% of α-and 90% of β-pyranose forms, thus displaying the dominant β-1 C 4 pyranose form, as found in the previous X-ray crystalline study [236].…”

Section: -Deoxy-d-ribose and Ribosementioning

confidence: 80%

“…The low-temperature environment of a supersonic expansion provides the ideal medium for preparing individual conformers of sugars in virtual isolation conditions, ready to be interrogated by a short burst of microwave radiation. To date, rotational investigations of monosaccharides have been carried out for C 4 sugars [222], C 5 sugars [62,223,224], and C 6 sugars [225][226][227]. All factors contributing to stabilization of the observed species are given in the next sections.…”

Section: Cytosinementioning

confidence: 99%

“…¼ 89-90 C) has been recently unveiled [224] using CP-FTMW spectroscopy in conjunction with a picosecond laser ablation LA source. The broadband spectra of Fig.…”

Section: -Deoxy-d-ribose and Ribosementioning

confidence: 99%

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Microwave Spectroscopy of Biomolecular Building Blocks

Alonso

López

2014

Topics in Current Chemistry

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Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment.

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Section: -Deoxy-d-ribose and Ribosementioning

confidence: 80%

Section: Cytosinementioning

confidence: 99%

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Microwave Spectroscopy of Biomolecular Building Blocks

Alonso

López

2014

Topics in Current Chemistry

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“…Experimental information on low energy conformers can be obtained by spectroscopic methods (see, e.g., Refs. [3][4][5][6][7][8][9][10]. The most powerful technique for conformational identification in the gas phase is rotational spectroscopy, which has been successfully applied in combination with laser ablation 11,12 to determine the conformations of many natural amino acids.…”

Section: Introductionmentioning

confidence: 99%

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

Comitani

Rossi

Ceriotti

et al. 2017

The Journal of Chemical Physics

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Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketchmap analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

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“…The conformational panorama of isolated 2-deoxy-D-ribose (m.p. ¼ 89-90 C) has been recently unveiled [224] using CP-FTMW spectroscopy in conjunction with a picosecond laser ablation LA source. The broadband spectra of Fig.…”

Section: -Deoxy-d-ribose and Ribosementioning

confidence: 99%