Furanosic forms of sugars: Conformational equilibrium of methyl β-d-ribofuranoside

Article abstract of DOI:10.1039/c6cc01180b

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 β-d-ribofuranoside in a supersonic jet expansion. Both conformers adopt a near twisted (³T₂) ring conformation with the methoxy and hydroxymethyl substituents involved in various intramolecular hydrogen bonds.

Full text of DOI:10.1039/c6cc01180b

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Furanosic forms of sugars: Conformational
equilibrium of methyl βꢀDꢀribofuranoside
Cite this: DOI: 10.1039/x0xx00000x
a
a
a,b
c
Patricia Écija, Iciar Uriarte, Lorenzo Spada, Benjamin G. Davis, Walther
b
a
d
a
Caminati, Francisco J. Basterretxea, Alberto Lesarri,* Emilio J. Cocinero*
Received 00th January 2015,
Accepted 00th January 2015
DOI: 10.1039/x0xx00000x
www.rsc.org/
This is the first investigation of an isolated ribofuranose unit
in the gas phase, revealing the intrinsic conformational
landscape of the biologically active sugar form. We report the
rotational spectra of two conformers of methyl βꢀDꢀ
Ribofuranoside rings play different biochemical functions. In
most species they appear as informational molecules and catalysts
(
RNA), as substrates (ATP or sugarꢀdiphosphoꢀnucleosides), or as
7
cofactors (NAD(P) or NAD(P)H). Remarkably, their roles are often
critical: DNA analogues in which the furanose rings are exchanged
ribofuranoside in
a supersonic jet expansion. Both
by pyranoses produce double helices with much stronger base
3
8
conformers adopt a near twisted ( T ) ring conformation pairing, but unsuitable to replace DNA. Biochemical functionality
2
with the methoxy and hydroxymethyl substituents involved in riboseꢀbased biomolecules probably relies on multiply related
factors and functional optimization does not necessarily correlate
with simple properties in the ground state. Changes in furanose
in various intramolecular hydrogen bonds.
conformation can also critically modulate the ability of nucleosides
Sugars are flexible polymorphic species, exhibiting complex
constitutional, configurational and conformational isomerism. The
to act as substrates with enzymes associated to disease processes,
9
e.g. HIVꢀ1 reverse transcriptase. Furanosides also appear as part of
intramolecular reaction between carbonyl (typically reducing
oligosaccharides in plants and microbial organisms like bacteria,
terminus) and hydroxyl groups gives rise to cyclic hemiacetal/ketals,
1
0
fungi and parasites, although not in humans or in mammals.
particularly stable for fiveꢀ or sixꢀmembered ring forms (furanose or
pyranose, respectively, Scheme 1). Large amplitude motions, like
ring puckering, inversion or pseudorotation, combine with the
internal rotation of the hydroxyl groups to produce a rich conforꢀ
mational landscape, even in the most elementary monosaccharide
units. A recent microwave spectroscopy study on ribose proved that
this aldopentose is a pyranose (1) in the gasꢀphase, with six
Ultimately, the evolutionary preference for furanoses in RNA
and other biomolecules may have a chemical origin, associated
perhaps with the greater or differing flexibility of the fiveꢀmembered
ring. Saturated fiveꢀmembered rings are structurally unique, as the
small differences in energy between twisted and envelope forms give
rise to pseudorotation, a quasiꢀmonodimensional largeꢀamplitudeꢀ
11
ꢀ
1
motion in which puckering rotates around the ring. Furanose ringꢀ
puckered species thus interconvert without passing through planar
species, making it difficult to specify conformational properties and
coexisting lowꢀenergy (ꢀE < 6 kJ mol ) conformers differing in ring
1
4
1
2
conformation ( C or C ) and epimerization (α/β). Other rotational
4
1
3
and vibrational studies of fiveꢀ or sixꢀcarbon monosaccharides also
confirmed the pyranose preference of free molecules, which had also
pseudorotation pathways.
A first pseudorotation model for
12
4
,5
6
nucleosides was developed by Altona and Sundaralingam (AS).
Cremer and Pople (CP) later solved the puckering problem using
vibrational analysis and developed systematic curvilinear CP
been previously observed in the crystal
and liquid phases.
However, the preferred ribopyranose form starkly contrasts with the
biological use of fiveꢀmembered βꢀribofuranose rings (2).
13
coordinates, generally applicable to any cycloalkane. Both models
define furanoside puckering in terms of amplitude (q) and phase
coordinates (φAS and φCP phase conventions are shifted by a constant
angle). Noticeably, a first survey of crystal structures revealed that
furanoside conformations in nucleosides display
a
bimodal
14
distribution, with two preferred puckering regions around φ =288º
CP
3
15
(
φAS=18º, envelope E ≡ C ´ꢀendo) or φ =72º (φAS=162º, envelope
3 CP
2
E ≡ C ´ꢀendo). This twoꢀstate model has been instrumental for
puckering determination in solution using NMR vicinal spinꢀspin
coupling parameters. More recent structural investigations on
furanose glycosides showed similar clustering in conformational
2
16
Scheme 1. The pyranose (1) and furanose (2) constitutional isomers of ribose,
together with methylꢀβꢀDꢀribofuranoside (3), in Haworth representations.
1
0
space, but heavily dependent on the pentose configuration. In
particular, βꢀribofuranosides locate around puckering phases of
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φ =252º (envelope E ) in the solid state. Recurrently, the question
CP
2
thus arises: does the furanose conformation in the crystal or solution
reflect intrinsic ring puckering properties, or is it imposed by the
environment?
We answer this question by exploring the molecular structure of
the fiveꢀmembered ring unit of an isolated monosaccharide in the
gasꢀphase. We analyzed methyl βꢀDꢀribofuranoside (3) using a
combination of chemical synthesis, microwave spectroscopy,
supersonic jet expansion techniques, ultrafast laser vaporization and
computational methods. The target pentose was specifically
synthesized (see ESI) to lock the molecule as a fiveꢀmembered ring,
preventing the formation of the pyranose form dominant in gas
phase. Our main objectives include the first observation of
conformational preferences of furanose forms in C5 and C6 sugars,
the determination of the number of coexisting species for the free
molecule, and the comparison with the structural data in condensed Fig. 1 A section of the experimental spectrum of methyl βꢀDꢀribofuranoside in
the region 7ꢀ10 GHz, with two typical rotational transitions split by internal
rotation of the methyl group (each transition additionally split by Doppler effect).
phases. The conformational landscape was explored at different
levels, including ringꢀpuckering preferences, dynamics of the
hydroxyl and hydroxymethyl groups, intramolecular hydrogen
The hyperfine effects were attributed to the internal rotation of
bonding and internal rotation of the methyl group. Our results give a
the Oꢀ1 methyl group in the ribofuranoside, detectable in rotational
valuable perspective on the intrinsic structural preferences of this
2
1
spectra for small or moderate potential energy barriers. The
experimental observations were reproduced to experimental
biologically important aldopentofuranose, clarifying previous Xꢀray
1
7
18
19
and neutron diffraction, NMR and ab initio data.
The computational study included
2
2
accuracy with a semirigidꢀrotor Watson Hamiltonian (Sꢀreduction).
The internal rotation effects were analyzed with the Wood’s internalꢀ
a
comprehensive
conformational search combining molecular mechanics (MMFFs)
and special search algorithms based on stochastic and vibrational
23
axisꢀmethod (IAM) method. Table 2 presents the results of leastꢀ
squares fits of the experimental transitions of both conformers,
which yielded accurate values of the rotational constants, the quartic
centrifugal distortion constants and the internal rotation barrier
height (theoretical predictions in Table S2, ESI). The full set of
transitions is collected in Tables S3 and S4 (ESI). No lines
attributable to other conformers were observed in the spectrum.
20
mode analysis, together with ab initio (MP2) and densityꢀ
functionalꢀtheory (M06ꢀ2X, B3LYP) molecular orbital
reoptimizations, which refined the initial estimations. The final
conformational energies and rotational constants are in Tables S1
and S2 (ESI), while Table 1 gives the puckering properties, dipole
moments and Gibbs energies for the six conformers with energies
ꢀ
1
within 5 kJ mol .
Table 2: Experimental parameters for the two detected conformations of
methyl βꢀDꢀribofuranoside, and comparison with the MP2 predictions.
Table 1: Prediction of conformational energies for methyl βꢀDꢀribofuranose.
Conf. 1
Experiment
Conf. 2
Experiment
1295.21 1443.5094(14)
ꢁ
D
a
/
ꢁ
D
b
/
c
ꢁ /
a
b
ꢀ1
q /
Å
φ /
deg
Species ꢀG /kJ mol
c
d
D
ꢀ1.2
ꢀ0.9
1.7
0.7
ꢀ0.5
2.9
Theory
Theory
3
1
2
3
( T
2
2
2
)
)
)
0.0/0.0/0.0
0.8/1.2/0.9
2.9/0.4/2.2
3.5/4.6/2.9
3.7/2.0/1.5
4.9/5.0/3.6
0.385
0.397
0.397
0.400
0.382
264.7
260.7
266.4
252.3
62.7
0.0
ꢀ0.9
ꢀ1.6
1.3
ꢀ2.1
ꢀ0.9
ꢀ0.3
ꢀ3.5
ꢀ3.5
ꢀ4.1
ꢀ0.3
ꢀ1.4
a
A/MHz
B/MHz
C/MHz
1307.1463(55)
1095.47128(50) 1101.10
1438.72
943.70
674.86
3
( T
3
924.98477(53)
661.97710(32)
0.2752(48)
( T
717.8046(49)
0.953(81)
718.90
4
5
6
(E
( E)
(E
2
)
2
D
D
D
J
/kHz
JK/kHz
/kHz
ꢀ0.339(88)
ꢀ1.264(27)
2
)
0.391
247.8
a
b
Conformational notation in 15. MP2/M06ꢀ2X/B3LYP calculations with a 6ꢀ
11++G(d,p) basis set; Relative Gibbs free energies at 298 K. CremerꢀPople
puckering parameters in 13. Electric dipole moment components (ꢁ , ꢁ , ꢁ ).
a b c
K
1.702(97)
c
3
d
d
1
/Hz
0.723(66)
ꢀ0.277(24)
7.304(13)
4.7
ꢀ0.1004(31)
d
2
/Hz
b
ꢀ1
V
3
/kJ mol
7.90
7.503(64)
8.23
The calculated conformational stabilities were checked against
the experimental microwave spectrum in the 6ꢀ14 GHz frequency
region. The molecular jet was probed with a Fourierꢀtransform
microwave (FTꢀMW) spectrometer equipped with an UV ultrafast
c
σ
N
/kHz
d
3.0
32
46
a
b
Uncertainties in units of the last digit. Internal rotation barrier. The geometrical
2
1
parameters I
α
(=3.195 uÅ ) and <(i,a), <(i,b), <(i,c) (=23.1º, 81.3º, 68.8º, 51.4º,
laser vaporization system (experimental details in ESI). Two
4
3.9º and 72.3°, respectively, for conformers 1 and 2) have been fixed to the ab
different sets of rotational transitions were independently assigned initio values. Standard deviation of the fit. Number of transitions.
c
d
(
(
Figure 1). The first set was composed exclusively of Rꢀbranch
The conformational assignment of the two isomers relied on
multiple arguments. An initial comparison of the rotational constants
in Table 2 showed good agreement for the two lowestꢀlying
conformations (relative errors below 1% for the global minimum, <
J+1←J) µ ꢀtype transitions, with angular momentum quantum
c
numbers spanning values J=2ꢀ6. The second set included only Rꢀ
branch µ ꢀtype rotational transitions (J=2ꢀ7). Both datasets were
b
mutually exclusive and they clearly corresponded to two different
carrier species. The similarity in rotational constants suggested that
they are indeed isomers of the same molecule. Some of the observed
lines showed small hyperfine effects for the two species, splitting
some individual transitions into two close components separated by
less than 20 kHz.
2
% for the second conformer). The prediction of (harmonic)
centrifugal distortion constants was also consistent in magnitude and
sign with the proposed assignment. Finally, the methyl group V
3
ꢀ1
barrier increase for conformer 2 (V = 7.3 vs. 7.5 kJ mol ) is in
3
ꢀ
1
agreement with the ab initio predictions (7.9 vs. 8.2 kJ mol ). This
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Fig. 3 Comparison of the conformational landscape of the βꢀribofuranoside ring
in the gas phase and crystal structures. a) Upper panel: Results of the ab initio
conformational search for methyl βꢀDꢀribofuranoside (twelve most stable
structures; experimental conformers with green solid circles). b) Lower panel: A
survey of 30 fragment structures of furanose glycosides in the Cambridge
Structural Database (CSD, data from ref. 10, blue crosses), together with the 2
crystal structures of methyl βꢀDꢀribofuranoside observed by neutron diffraction in
Fig. 2 Intramolecular hydrogen bonding distances (Å) and relative Gibbs
energy (MP2) for the two observed conformers of methyl βꢀDꢀribofuranose.
evidence fully confirms the conformational assignments in Table 2
and Figure 2 (interactive 3D model in Figures S1, S2, ESI).
(ref. 17, red circles). CremerꢀPople (CP) puckering amplitudes (q) represented
The ringꢀpuckering properties were analyzed quantitatively, as radial values. Pseudorotation angles given in the CP (φCP) and Altonaꢀ
1
3
Sundaralingan (AS) conventions (φAS). Conformer notation in ref. 15.
using the CP coordinates in Figure 3. The two detected isomers
have similar puckering phases (φ =264.7º and 260.7º, respectively),
CP
3
2
4
3
tional space, represented by the T ꢀE , E and E structures in
2 2
intermediate between a twistedꢀ T and an envelopeꢀE2 ring
2
Figure 3 (ab initio structures in Tables S5ꢀS7, ESI).
The three most stable structures (<3 kJ mol ) share a twisted T
and envelope E character, but most of the following conformations
up to ca. 8 kJ mol move toward the neighboring envelope E . The
higherꢀenergy forms of the isolated molecule comprise also
envelopes E and E, which appear at relative energies above 3.7 and
.3 kJ mol (MP2), respectively, and become the most abundant in
the upper range of the analyzed energy window. The two observed
conformations for the isolated molecule simply represent alternative
configurations of the sugar hydroxymethyl sideꢀchain (the third
conformer being equivalent to the global minimum with reversed
O ꢀH···O hydrogen bond orientation). In previous rotational
conformation. Puckering amplitudes are also very similar (q=0.385
ꢀ
1
3
and 0.397 Å, respectively). The hydroxymethyl side chain adopts the
2
+
gauche staggered orientation of Scheme 2, either G (τ (O ꢀC ꢀC ꢀ
2
1
5´ 5´
4´
ꢀ
1
–
C )= +56.2º) for the global minimum or G (τ = ꢀ58.1º) for the
2
3
´
1
second conformer. Conversely, the methyl group is always trans
2
4
with respect to C2´ (T: τ2 (C ꢀO ꢀC ꢀC ) = 174.4º and 178.9º,
M
1´ 1´ 2´
ꢀ
1
3
+
7
respectively), so the observed conformations are denoted T G T
global minimum) and T G T.
2
3
–
(
2
3
´
2´
studies it was argued that intramolecular hydrogen bonding is the
1
,2
primarily stabilizing effect in isolated monosaccharides. In methyl
βꢀDꢀribofuranoside the hydrogen bond pattern seems to favor
ꢀ
1
ꢀ1
conformer 2, predicted only 0.8 kJ mol (MP2) to 1.2 kJ mol
M06ꢀ2X) above the global minimum. However, the predicted
stability could also reflect other contributions, like hyperconjugative
Scheme 2 Notation for staggered orientations around the C4’ꢀC5’ bond.
(
24
effects, previously suggested in tetrahydrofuran
and other
The two ring hydroxyl groups, on opposite sides of the methoxy
and hydroxymethyl substituents, finally arrange to reach the highest
possible number of internal hydrogen bonds. The global minimum
monosaccharides. Unfortunately, the small energy difference
between both conformations cannot be verified experimentally, as
the lack of common selection rules precludes estimating intensity
ratios. Noticeably, the neutron diffraction experiments of methyl βꢀ
exhibits two unconnected hydrogen bonds: a weak contact O ꢀ
5
´
H···O with the hydroxymethyl group (MP2: r(H··· O )=2.4 Å) and
4
´
4´
Dꢀribofuranoside also identified two conformations with E ringꢀ
2
3
a O ꢀH···O link (MP2: r(H···O )=2.17 Å). The second conformer
2
´
3´
3´
puckering (φ =258.6º, 249.6º), relatively close to the T2ꢀE2
CP
17
displays a network of two successive O ꢀH···O ꢀH··· O hydrogen
2
´
3´
5´
structures observed here. The two observed crystal structures
mostly differ in the orientation of the ring substituents, which are
both oriented trans to favor intermolecular hydrogen bonding,
concomitant with this condensed phase. No intramolecular hydrogen
bond is apparent in the crystal structures.
bonds involving three hydroxyl groups (MP2: r(H···O )=2.17 Å,
3´
r(H···O )=2.29 Å).
5
´
In conclusion, the combination of rotational data and ab initio
calculations provides a direct comparison between βꢀribofuranoside
ring conformations in the gas phase and crystal structures. The
isolated molecule preferably occupies three regions of the conformaꢀ
The comparison between the conformational behavior of an
isolated unit of methyl βꢀDꢀribofuranoside and that of the molecule
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embedded in a crystal matrix reveals features of the factors affecting
molecular structure. The ring puckering characteristics of the
ribofuranose unit are very similar in the gas and crystal phases, and
clearly suggest that the puckering forces associated with the
minimization of ring strain originate from the ring configuration and
number and position of substitutents, not from crystal forces. This
argument is reinforced by comparison with the puckering
characteristics of a set of 30 structural fragments in the Cambridge
Structural Database (CSD), shown in the lower panel of Figure 3,
Sci., 2014
,
5
, 515; I. Peña, C. Cabezas, J. L. Alonso, Angew. Chem.
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Int. Ed. 2015
,
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3
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E. J. Cocinero, P. Çarçabal, Spectroscopy and Structure of Biological
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M. Sundaralingam, Biopol
E. Breitmaier, U. Hollstein, Org. Magn. Reson
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49, 4503.
5
6
.
1969, 7, 821.
similarly centered around E . Furthermore, crystal data show that a
2
.
1976, 8, 573; S. J.
change in the substituents’ stereochemistry radically alters the ring
1
0
, 8
puckering. This view is confirmed by previous NMR studies,
emphasizing the dominant influence of the anomeric substituent on
.
,
2
5
7
W. Saenger, Principles of Nucleic Acid Structure; SpringerꢀVerlag:
the ring conformation in liquid phase. Natural Bond Orbital
calculations in Table S8 (ESI) are consistent with electronic
hyperconjugation originated by the methoxy and ring oxygen atoms
New York, 1984.
8
9
A. Eschenmoser, Science, 1999
H. Ford, Jr., F. Dai, L. Mu, M. A. Siddiqui, M. C. Nicklaus, L.
Anderson, V. E. Marquez, J. J. Barchi, Biochem., 2000 39, 2581; V.
, 284, 2118.
(endo/exo anomeric effects), but its contribution is relatively similar
for the four lowest lying conformers. The molecular stability would
thus primarily result from a combination of orbital effects reducing
ring strain, complemented with the effects of intramolecular
,
E. Marquez, P. Wang, M. C. Nicklaus, M. Maiera, M. Manoharana,
J. K. Christmanb, N. K. Banavalic, A. D. Mackerell, Jr. Nucleos.
hydrogen bonding. As
a consequence, the presence of the
Nucleot. Nucl., 2001
0 H. A. Taha, M. R. Richards, T. L. Lowary, Chem. Rev., 2013
851.
, 20, 451 and references therein.
heterocyclic bases found in nucleosides surely influences the
conformational properties of the flexible ring, thereby determining
its final biological properties.
1
1
, 113,
1
1 J. Laane, Vibrational Spectra and Structure; J. R. Durig, Ed.; Marcel
The results for methyl βꢀDꢀribofuranoside highlight the value of
current crystal structures but also call for additional gasꢀphase
experiments on related furanosides, nucleosides and nucleotides,
both to assess the theoretical models and to compare with
conventional data from condensed media. Considering the vital role
of ribofuranosides in all life forms, it is remarkable that their
structural properties free of any environmental effects have been
unknown until now. These new results provide empirical data that
may help to inform structural, predictive and enzymological RNA
Dekker, Inc.: New York, 1972; pp. 26ꢀ50.
1
1
1
2 C. Altona, M. Sundaralingam, J. Am. Chem. Soc., 1972
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4 H. P. M. de Leeuw, C. A. G. Haasnoot, C. Altona, Isr. J. Chem.,
980 20, 108.
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primed atom notation used in nucleosides is adopted for simplicity.
, 428; Z. Dzakula,
M. DeRider, J. L. Markley, J. Am. Chem. Soc., 1996 118, 12796.
, 94, 8205.
,
1
,
1
,
,
(and DNA) biology. In this sense, the emergence of new techniques 16 F. de Leeuw, C. Altona, J. Comp. Chem., 1983
, 4
in rotational spectroscopy is helping to provide a global view of the
inherent structural properties of these biomolecular building blocks.
,
17 A. G. Evdokimov, A. J. K. Gilboa, T. F. Koetzle, W. T. Klooster, A.
J. Schultz, S. A. Mason, A. Albinati, F. Frolow, Acta Crystallogr. B,
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001
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Universidad del País Vasco (UPV/EHU), Apartado 644, 48080 Bilbao
(
Spain), emiliojose.cocinero@ehu.eus
b
,
Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via
1
2
Selmi 2, 1ꢀ40126 Bologna (Italy)
2
,
c
Chemistry Department, Oxford University, Chemistry Research
Laboratory, 12 Mansfield Road, OX1 3TA Oxford (United Kingdom)
,
d
Departamento de Química Física y Química Inorgánica, Universidad de
,
Valladolid, 47011 Valladolid (Spain), lesarri@qf.uva.es
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