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Furanosic Forms of Sugars: Conformational Equilibrium of Methyl B-D-Ribofuranoside† Cite This: Chem

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Furanosic Forms of Sugars: Conformational Equilibrium of Methyl B-D-Ribofuranoside† Cite This: Chem ChemComm View Article Online COMMUNICATION View Journal | View Issue Furanosic forms of sugars: conformational equilibrium of methyl b-D-ribofuranoside† Cite this: Chem. Commun., 2016, 52,6241 Patricia E´cija,a Iciar Uriarte,a Lorenzo Spada,ab Benjamin G. Davis,c Received 5th February 2016, Walther Caminati,b Francisco J. Basterretxea,a Alberto Lesarri*d and Accepted 1st April 2016 Emilio J. Cocinero*a DOI: 10.1039/c6cc01180b www.rsc.org/chemcomm The investigation of an isolated ribofuranose unit in the gas phase reveals the intrinsic conformational landscape of the biologically active sugar form. We report the rotational spectra of two conformers of methyl b-D-ribofuranoside in a supersonic jet expansion. Both 3 conformers adopt a near twisted ( T2) ring conformation with the methoxy and hydroxymethyl substituents involved in various intra- molecular hydrogen bonds. Scheme 1 The pyranose (1) and furanose (2) constitutional isomers of ribose, together with methyl-b-D-ribofuranoside (3), in Haworth projection. Sugars are flexible polymorphic species, exhibiting complex con- stitutional, configurational and conformational isomerism. The intramolecular reaction between carbonyl (typically reducing (RNA), as substrates (ATP or sugar-diphospho-nucleosides), or as terminus) and hydroxyl groups gives rise to cyclic hemiacetal/ cofactors (NAD(P) or NAD(P)H).7 Remarkably, their roles are often ketals, particularly stable for five- or six-membered ring forms critical: DNA analogues in which thefuranoseringsareexchanged (furanose or pyranose, respectively, Scheme 1). Large amplitude by pyranoses produce double helices with much stronger base motions, like ring puckering, inversion or pseudorotation, com- pairing, but are unsuitable to replace DNA.8 The biochemical bine with the internal rotation of the hydroxyl groups to produce a functionality in ribose-based biomolecules probably relies on Published on 01 April 2016. Downloaded by University of Oxford 04/05/2016 20:35:27. rich conformational landscape, even in the most elementary mono- multiple related factors and functional optimization does not saccharide units. A recent microwave spectroscopy study on ribose necessarily correlate with simple properties in the ground state. proved that this aldopentose is a pyranose (1) in the gas-phase, with Changes in the furanose conformation can also critically modulate six coexisting low-energy (DE o 6kJmolÀ1) conformers differing in the ability of nucleosides to act as substrates with enzymes 1 4 1 9 ring conformation ( C4 or C1) and epimerization (a/b). Other associated with disease processes, e.g. HIV-1 reverse transcriptase. rotational2 and vibrational3 studies of five- or six-carbon monosac- Furanosides also appear as part of oligosaccharides in plants and charides also confirmed the pyranose preference of free molecules, microbial organisms like bacteria, fungi and parasites, although which had also been previously observed in the crystal4,5 and liquid not in humans or in mammals.10 phases.6 However, the preferred ribopyranose form starkly contrasts Ultimately, the evolutionary preference for furanoses in RNA and with the biological use of five-membered b-ribofuranose rings (2). other biomolecules may have a chemical origin, associated perhaps Ribofuranoside rings play different biochemical functions. In with the greater or differing flexibility of the five-membered ring. most species they appear as informational molecules and catalysts Saturated five-membered rings are structurally unique, as the small differences in energy between twisted and envelope forms give a rise to pseudorotation, a quasi-monodimensional large-amplitude- Departamento de Quı´mica Fı´sica, Facultad de Ciencia y Tecnologı´a, 11 Universidad del Paı´s Vasco (UPV/EHU), Apartado 644, 48080 Bilbao, Spain. motion in which the puckering rotates around the ring. The E-mail: [email protected] furanose ring-puckered species thus may interconvert without b Dipartimento di Chimica ‘‘G. Ciamician’’, Universita` di Bologna, Via Selmi 2, passing through the planar species, making it difficult to specify 1-40126 Bologna, Italy conformational properties and pseudorotation pathways. The first c Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK d pseudorotation model for nucleosides was developed by Altona Departamento de Quı´mica Fı´sica y Quı´mica Inorga´nica, Universidad de 12 Valladolid, 47011 Valladolid, Spain. E-mail: [email protected] and Sundaralingam (AS). Cremer and Pople (CP) later solved the † Electronic supplementary information (ESI) available: Rotational transitions puckering problem using vibrational analysis and developed 13 and theoretical predictions. See DOI: 10.1039/c6cc01180b systematic curvilinear CP coordinates, generally applicable to This journal is © The Royal Society of Chemistry 2016 Chem. Commun., 2016, 52, 6241--6244 | 6241 View Article Online Communication ChemComm any cycloalkane. Both models define furanoside puckering in terms Table 1 Prediction of conformational energies for methyl b-D-ribofuranoside of amplitude (q) and phase coordinates (jAS and jCP phase conven- a b À1 c d Species DG /kJ mol q /Å j/deg ma /D mb/D mc/D tions are shifted by a constant angle). Noticeably, a first survey of 3 1(T2) 0.0/0.0/0.0 0.385 264.7 0.0 À0.3 À1.2 crystal structures revealed that furanoside conformations in nucleo- 3 2(T2) 0.8/1.2/0.9 0.397 260.7 À0.9 À3.5 À0.9 14 3 sides display a bimodal distribution, with two preferred puckering 3(T2) 2.9/0.4/2.2 0.397 266.4 À1.6 À3.5 1.7 3 0 15 regions around jCP =2881 (jAS =181, envelope E C3 -endo) 4(E2) 3.5/4.6/2.9 0.400 252.3 1.3 À4.1 0.7 2 2 0 5(E) 3.7/2.0/1.5 0.382 62.7 À2.1 À0.3 À0.5 jCP =721 (jAS =1621,envelope E C2 -endo). This two-state 6(E2) 4.9/5.0/3.6 0.391 247.8 À0.9 À1.4 2.9 model has been instrumental for puckering determination in a b solution using NMR vicinal spin–spin coupling parameters.16 Conformational notation in ref. 15. MP2/M06-2X/B3LYP calculations with a 6-311++G(d,p) basis set; relative Gibbs free energies at 298 K. More recent structural investigations on furanose glycosides c Cremer–Pople puckering parameters defined in ref. 13. d Electric dipole showed a similar clustering in the conformational space, but moment components (ma, mb, mc). they were heavily dependent on the pentose configuration.10 In particular, b-ribofuranosides are located around the puckering phases of jCP =2521 (envelope E2) in the solid state. Recurrently, the question thus arises: does the furanose conformation in the crystal or solution reflect the intrinsic ring puckering properties, or is it imposed by the environment? We answer this question by exploring the molecular structure of the five-membered ring unit of an isolated monosaccharide in the gas-phase. We analyzed methyl b-D-ribofuranoside (3)usinga combination of chemical synthesis, microwave spectroscopy, supersonic jet expansion techniques, ultrafast laser vaporization and computational methods. The target pentose was specifically synthesized (see the ESI†) to lock the molecule as a five-membered ring, preventing the formation of the pyranose form dominant in the gas phase. Our main objectives include the observation of conformational preferences of furanose forms in C5 and C6 Fig. 1 A section of the experimental spectrum of methyl b-D- ribofuranoside in the region 7–10 GHz, with two typical rotational transi- sugars, the determination of the number of coexisting species of tions split by internal rotation of the methyl group (each transition the free molecule, and the comparison with the structural data in additionally split by Doppler effect). condensed phases. The conformational landscape was explored at different levels, including ring-puckering preferences, dynamics of the hydroxyl and hydroxymethyl groups, intramolecular hydrogen Both datasets were mutually exclusive and they clearly corresponded bonding and internal rotation of the methyl group. Our results give to two different carrier species. Their similarity in rotational con- a valuable perspective on the intrinsic structural preferences of this stants suggested that they are indeed isomers of the same molecule. Published on 01 April 2016. Downloaded by University of Oxford 04/05/2016 20:35:27. biologically important aldopentofuranose, clarifying previous X-ray Some of the observed lines showed small hyperfine effects for the and neutron diffraction,17 NMR18 and ab initio data.19 two species, splitting some individual transitions into two close The computational study included a comprehensive confor- components separated by less than 20 kHz. mational search combining molecular mechanics (MMFFs) and The hyperfine effects were attributed to the internal rotation of special search algorithms based on stochastic and vibrational the O-1 methyl group in the ribofuranoside, detectable in the mode analysis,20 together with ab initio (MP2) and density- rotational spectra for small or moderate potential energy barriers.21 functional-theory (M06-2X, B3LYP) molecular orbital reoptimiza- The experimental observations were reproduced to experi- tions, which refined the initial estimations. The final conformational mental accuracy using a semirigid-rotor Watson Hamiltonian energies and rotational constants are in Tables S1 and S2 (S-reduction).22 The internal rotation effects were analyzed using (ESI†), while Table 1 gives the puckering properties, dipole Wood’s internal-axis-method (IAM).23 Table 2 presents the results moments and Gibbs energies for the six conformers with of least-squares fits of the experimental transitions of both energies within 5 kJ molÀ1. conformers, which yielded accurate values of the rotational The calculated conformational stabilities were checked against constants, the quartic centrifugal distortion constants and the the experimental microwave spectrum in the 6–14 GHz frequency internal rotation barrier height. The full set of transitions is region. The molecular jet was probed using a Fourier-transform collected in Tables S3 and S4 (ESI†). No lines attributable to other microwave (FT-MW) spectrometer equipped with an UV ultrafast conformers were observed in the spectrum.
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