Isopropyl 3-deoxy-α-D-ribo-hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside), C9H18O5, (I), crystallizes from a methanol–ethyl acetate solvent mixture at room temperature in a 4C1 chair conformation that is slightly distorted towards the C5SC1 twist-boat form. A comparison of the structural parameters in (I), methyl α-D-glucopyranoside, (II), α-D-glucopyranosyl-(1→4)-D-glucitol (maltitol), (III), and 3-deoxy-α-D-ribo-hexopyranose (3-deoxy-α-D-glucopyranose), (IV), shows that most endocyclic and exocyclic bond lengths, valence bond angles and torsion angles in the aldohexopyranosyl rings are more affected by anomeric configuration, aglycone structure and/or the conformation of exocyclic substituents, such as hydroxymethyl groups, than by monodeoxygenation at C3. The structural effects observed in the crystal structures of (I)–(IV) were confirmed though density functional theory (DFT) calculations in computed structures (I)c–(IV)c. Exocyclic hydroxymethyl groups adopt the gauche–gauche (gg) conformation (H5 anti to O6) in (I) and (III), and the gauche–trans (gt) conformation (C4 anti to O6) in (II) and (IV). The O-glycoside linkage conformations in (I) and (III) resemble those observed in disaccharides containing β-(1→4) linkages.
Supporting information
CCDC reference: 2098123
Data collection: APEX3 (Bruker, 2018); cell refinement: SAINT (Bruker, 2018); data reduction: SAINT (Bruker, 2018); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020) and XP (Bruker, 2018); software used to prepare material for publication: CIFTAB (Sheldrick, 2008).
Isopropyl 3-deoxy-
α-<it>D</it>-
ribo-hexopyranoside
top
Crystal data top
| C9H18O5 | F(000) = 448 |
| Mr = 206.23 | Dx = 1.297 Mg m−3 |
| Monoclinic, I2 | Cu Kα radiation, λ = 1.54184 Å |
| a = 13.7349 (11) Å | Cell parameters from 9799 reflections |
| b = 5.0575 (4) Å | θ = 3.7–70.5° |
| c = 16.0800 (12) Å | µ = 0.89 mm−1 |
| β = 109.020 (7)° | T = 120 K |
| V = 1056.00 (15) Å3 | Tablet, colorless |
| Z = 4 | 0.34 × 0.12 × 0.07 mm |
Data collection top
Bruker PHOTON-II
diffractometer | 1976 independent reflections |
| Radiation source: Incoatec micro-focus | 1889 reflections with I > 2σ(I) |
| Detector resolution: 7.41 pixels mm-1 | Rint = 0.062 |
| combination of ω and φ–scans | θmax = 70.8°, θmin = 3.7° |
Absorption correction: numerical
(SADABS; Krause et al., 2015) | h = −16→16 |
| Tmin = 0.787, Tmax = 0.994 | k = −6→6 |
| 11702 measured reflections | l = −19→19 |
Refinement top
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: mixed |
| R[F2 > 2σ(F2)] = 0.041 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.105 | w = 1/[σ2(Fo2) + (0.0607P)2 + 0.4315P]
where P = (Fo2 + 2Fc2)/3 |
| S = 1.08 | (Δ/σ)max < 0.001 |
| 1976 reflections | Δρmax = 0.19 e Å−3 |
| 141 parameters | Δρmin = −0.24 e Å−3 |
| 1 restraint | Absolute structure: Flack x determined using 774 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013) |
| Primary atom site location: dual | Absolute structure parameter: 0.11 (12) |
Special details top
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top| | x | y | z | Uiso*/Ueq | |
| O1 | 0.68915 (12) | 0.5805 (4) | 0.37509 (11) | 0.0263 (4) | |
| O2 | 0.69471 (13) | 0.4545 (4) | 0.20866 (12) | 0.0296 (4) | |
| H2O | 0.728 (3) | 0.315 (9) | 0.214 (3) | 0.055 (11)* | |
| O4 | 0.37421 (15) | 0.7884 (5) | 0.22265 (14) | 0.0391 (5) | |
| H4O | 0.315 (3) | 0.727 (9) | 0.210 (3) | 0.054 (11)* | |
| O5 | 0.55131 (11) | 0.2881 (4) | 0.35832 (11) | 0.0275 (4) | |
| O6 | 0.33085 (14) | 0.1938 (5) | 0.32116 (15) | 0.0403 (5) | |
| H6O | 0.363 (2) | 0.088 (7) | 0.3067 (19) | 0.019 (7)* | |
| C1 | 0.64012 (16) | 0.3488 (5) | 0.33426 (16) | 0.0256 (5) | |
| H1 | 0.689748 | 0.197906 | 0.351073 | 0.031* | |
| C2 | 0.60806 (17) | 0.3912 (5) | 0.23532 (16) | 0.0257 (5) | |
| H2 | 0.575131 | 0.225994 | 0.204708 | 0.031* | |
| C3 | 0.53099 (18) | 0.6171 (5) | 0.20867 (16) | 0.0280 (6) | |
| H3A | 0.506808 | 0.637171 | 0.143889 | 0.034* | |
| H3B | 0.564478 | 0.784371 | 0.235026 | 0.034* | |
| C4 | 0.43968 (17) | 0.5601 (6) | 0.24003 (17) | 0.0292 (6) | |
| H4 | 0.400362 | 0.405639 | 0.206740 | 0.035* | |
| C5 | 0.47615 (17) | 0.4976 (6) | 0.33787 (17) | 0.0299 (6) | |
| H5 | 0.508077 | 0.659714 | 0.371288 | 0.036* | |
| C6 | 0.39025 (19) | 0.4035 (7) | 0.37074 (18) | 0.0365 (7) | |
| H6A | 0.420739 | 0.345331 | 0.432608 | 0.044* | |
| H6B | 0.344038 | 0.554464 | 0.369861 | 0.044* | |
| C7 | 0.75087 (17) | 0.5488 (6) | 0.46627 (16) | 0.0285 (6) | |
| H7 | 0.721028 | 0.404685 | 0.493057 | 0.034* | |
| C8 | 0.86015 (19) | 0.4748 (7) | 0.47172 (19) | 0.0403 (7) | |
| H8A | 0.858502 | 0.317248 | 0.435790 | 0.060* | |
| H8B | 0.900822 | 0.437631 | 0.533031 | 0.060* | |
| H8C | 0.891504 | 0.621728 | 0.449842 | 0.060* | |
| C9 | 0.7460 (2) | 0.8055 (7) | 0.51170 (19) | 0.0410 (7) | |
| H9A | 0.673854 | 0.852857 | 0.501534 | 0.062* | |
| H9B | 0.779289 | 0.944714 | 0.488209 | 0.062* | |
| H9C | 0.781656 | 0.786285 | 0.574997 | 0.062* | |
Atomic displacement parameters (Å2) top| | U11 | U22 | U33 | U12 | U13 | U23 |
| O1 | 0.0155 (7) | 0.0324 (9) | 0.0283 (8) | −0.0017 (7) | 0.0035 (6) | 0.0009 (7) |
| O2 | 0.0203 (8) | 0.0336 (10) | 0.0393 (9) | 0.0035 (8) | 0.0157 (7) | 0.0028 (8) |
| O4 | 0.0177 (9) | 0.0480 (12) | 0.0507 (11) | 0.0075 (9) | 0.0100 (8) | 0.0059 (10) |
| O5 | 0.0147 (8) | 0.0357 (10) | 0.0322 (8) | −0.0022 (7) | 0.0080 (6) | 0.0025 (8) |
| O6 | 0.0195 (9) | 0.0493 (13) | 0.0553 (13) | −0.0061 (9) | 0.0166 (9) | −0.0035 (11) |
| C1 | 0.0135 (9) | 0.0303 (14) | 0.0337 (12) | −0.0008 (9) | 0.0087 (8) | −0.0001 (10) |
| C2 | 0.0161 (9) | 0.0291 (13) | 0.0328 (11) | −0.0024 (9) | 0.0092 (8) | −0.0011 (10) |
| C3 | 0.0168 (10) | 0.0342 (14) | 0.0324 (12) | 0.0015 (10) | 0.0072 (9) | 0.0036 (11) |
| C4 | 0.0140 (10) | 0.0350 (14) | 0.0370 (13) | 0.0001 (10) | 0.0060 (9) | −0.0005 (11) |
| C5 | 0.0131 (11) | 0.0399 (16) | 0.0368 (13) | 0.0011 (10) | 0.0085 (9) | −0.0036 (11) |
| C6 | 0.0184 (11) | 0.0542 (18) | 0.0386 (13) | −0.0029 (12) | 0.0116 (10) | −0.0011 (13) |
| C7 | 0.0192 (11) | 0.0372 (14) | 0.0268 (11) | −0.0034 (10) | 0.0045 (9) | 0.0037 (10) |
| C8 | 0.0177 (11) | 0.0564 (18) | 0.0419 (14) | 0.0002 (12) | 0.0030 (10) | 0.0128 (14) |
| C9 | 0.0430 (15) | 0.0434 (16) | 0.0328 (13) | −0.0072 (14) | 0.0071 (11) | −0.0003 (13) |
Geometric parameters (Å, º) top
| O1—C1 | 1.403 (3) | C3—H3B | 0.9900 |
| O1—C7 | 1.443 (3) | C4—C5 | 1.521 (3) |
| O2—C2 | 1.427 (3) | C4—H4 | 1.0000 |
| O2—H2O | 0.83 (5) | C5—C6 | 1.518 (3) |
| O4—C4 | 1.434 (3) | C5—H5 | 1.0000 |
| O4—H4O | 0.83 (5) | C6—H6A | 0.9900 |
| O5—C1 | 1.428 (3) | C6—H6B | 0.9900 |
| O5—C5 | 1.440 (3) | C7—C9 | 1.502 (4) |
| O6—C6 | 1.415 (4) | C7—C8 | 1.521 (3) |
| O6—H6O | 0.78 (3) | C7—H7 | 1.0000 |
| C1—C2 | 1.521 (3) | C8—H8A | 0.9800 |
| C1—H1 | 1.0000 | C8—H8B | 0.9800 |
| C2—C3 | 1.521 (3) | C8—H8C | 0.9800 |
| C2—H2 | 1.0000 | C9—H9A | 0.9800 |
| C3—C4 | 1.524 (3) | C9—H9B | 0.9800 |
| C3—H3A | 0.9900 | C9—H9C | 0.9800 |
| | | |
| C1—O1—C7 | 114.6 (2) | O5—C5—C4 | 111.04 (19) |
| C2—O2—H2O | 105 (3) | C6—C5—C4 | 113.21 (19) |
| C4—O4—H4O | 104 (3) | O5—C5—H5 | 108.9 |
| C1—O5—C5 | 113.08 (19) | C6—C5—H5 | 108.9 |
| C6—O6—H6O | 114 (2) | C4—C5—H5 | 108.9 |
| O1—C1—O5 | 112.01 (19) | O6—C6—C5 | 114.2 (2) |
| O1—C1—C2 | 107.6 (2) | O6—C6—H6A | 108.7 |
| O5—C1—C2 | 109.38 (17) | C5—C6—H6A | 108.7 |
| O1—C1—H1 | 109.3 | O6—C6—H6B | 108.7 |
| O5—C1—H1 | 109.3 | C5—C6—H6B | 108.7 |
| C2—C1—H1 | 109.3 | H6A—C6—H6B | 107.6 |
| O2—C2—C3 | 108.6 (2) | O1—C7—C9 | 107.1 (2) |
| O2—C2—C1 | 111.12 (18) | O1—C7—C8 | 109.1 (2) |
| C3—C2—C1 | 109.8 (2) | C9—C7—C8 | 112.6 (2) |
| O2—C2—H2 | 109.1 | O1—C7—H7 | 109.3 |
| C3—C2—H2 | 109.1 | C9—C7—H7 | 109.3 |
| C1—C2—H2 | 109.1 | C8—C7—H7 | 109.3 |
| C2—C3—C4 | 109.7 (2) | C7—C8—H8A | 109.5 |
| C2—C3—H3A | 109.7 | C7—C8—H8B | 109.5 |
| C4—C3—H3A | 109.7 | H8A—C8—H8B | 109.5 |
| C2—C3—H3B | 109.7 | C7—C8—H8C | 109.5 |
| C4—C3—H3B | 109.7 | H8A—C8—H8C | 109.5 |
| H3A—C3—H3B | 108.2 | H8B—C8—H8C | 109.5 |
| O4—C4—C5 | 110.1 (2) | C7—C9—H9A | 109.5 |
| O4—C4—C3 | 108.3 (2) | C7—C9—H9B | 109.5 |
| C5—C4—C3 | 110.65 (18) | H9A—C9—H9B | 109.5 |
| O4—C4—H4 | 109.3 | C7—C9—H9C | 109.5 |
| C5—C4—H4 | 109.3 | H9A—C9—H9C | 109.5 |
| C3—C4—H4 | 109.3 | H9B—C9—H9C | 109.5 |
| O5—C5—C6 | 105.7 (2) | | |
| | | |
| C7—O1—C1—O5 | 77.4 (2) | C2—C3—C4—C5 | 52.9 (3) |
| C7—O1—C1—C2 | −162.35 (18) | C1—O5—C5—C6 | −177.9 (2) |
| C5—O5—C1—O1 | 57.7 (2) | C1—O5—C5—C4 | 58.9 (3) |
| C5—O5—C1—C2 | −61.5 (3) | O4—C4—C5—O5 | −173.36 (19) |
| O1—C1—C2—O2 | 57.6 (2) | C3—C4—C5—O5 | −53.6 (3) |
| O5—C1—C2—O2 | 179.5 (2) | O4—C4—C5—C6 | 67.9 (3) |
| O1—C1—C2—C3 | −62.5 (2) | C3—C4—C5—C6 | −172.3 (2) |
| O5—C1—C2—C3 | 59.4 (3) | O5—C5—C6—O6 | −70.4 (3) |
| O2—C2—C3—C4 | −177.49 (19) | C4—C5—C6—O6 | 51.4 (3) |
| C1—C2—C3—C4 | −55.8 (3) | C1—O1—C7—C9 | −147.9 (2) |
| C2—C3—C4—O4 | 173.7 (2) | C1—O1—C7—C8 | 89.9 (2) |
Hydrogen-bond geometry (Å, º) top
| D—H···A | D—H | H···A | D···A | D—H···A |
| O2—H2O···O1i | 0.83 (5) | 2.41 (4) | 3.055 (2) | 135 (4) |
| O2—H2O···O2i | 0.83 (5) | 2.27 (5) | 3.025 (2) | 152 (4) |
| O4—H4O···O6ii | 0.83 (5) | 1.91 (5) | 2.714 (3) | 163 (5) |
| O6—H6O···O4iii | 0.78 (3) | 2.07 (3) | 2.772 (3) | 150 (3) |
| Symmetry codes: (i) −x+3/2, y−1/2, −z+1/2; (ii) −x+1/2, y+1/2, −z+1/2; (iii) x, y−1, z. |
Cremer–Pople structural parameters for compounds (I)–(IV) top| Compound | ϕ (°) | θ (°) | Q (Å) | q2 | q3 |
| (I) | 81 (4) | 4.1 (3) | 0.573 (3) | 0.037 (3) | 0.572 (3) |
| (II) | 117 (6) | 1.7 (2) | 0.569 (2) | 0.022 (2) | 0.569 (2) |
| (III) | 313.7 (8) | 11.05 (15) | 0.5674 (15) | 0.1087 (15) | 0.5569 (15) |
| (IV) | 59.0 (16) | 4.80 (14) | 0.5734 (14) | 0.0484 (14) | 0.5714 (14) |
Selected structural parameters (Å, °) in compounds (I)–(IV) top| Structure parameter | Compound | | | |
| (I) | (II)d | (III)a | (IV) |
| Bond lengths | | | | |
| C1—C2 | 1.521 (3) | 1.529 | 1.537 (2) | 1.525 (2) |
| C2—C3 | 1.521 (3) | 1.521 | 1.527 (2) | 1.522 (2) |
| C3—C4 | 1.524 (3) | 1.531 | 1.529 (2) | 1.530 (2) |
| C4—C5 | 1.521 (3) | 1.529 | 1.525 (2) | 1.533 (2) |
| C5—C6 | 1.518 (3) | 1.516 | 1.516 (2) | 1.509 (2) |
| C1—O1 | 1.403 (3) | 1.401 | 1.405 (2) | 1.400 (2) |
| C1—O5 | 1.428 (3) | 1.414 | 1.427 (2) | 1.415 (2) |
| C2—O2 | 1.427 (3) | 1.410 | 1.428 (2) | 1.423 (2) |
| C3—O3 | | 1.420 | 1.429 (2) | |
| C4—O4 | 1.434 (3) | 1.414 | 1.426 (2) | 1.432 (2) |
| C5—O5 | 1.440 (3) | 1.428 | 1.453 (2) | 1.438 (2) |
| C6—O6 | 1.415 (4) | 1.421 | 1.419 (2) | 1.429 (2) |
| O1—C7 | 1.444 (3) | 1.422 | | |
| O1—C4' | | | 1.448 (2) | |
| | | | |
| Angles | | | | |
| C5—O5—C1 | 113.08 (19) | 113.49 | 112.6 (1) | 112.78 (10) |
| O5—C1—O1 | 112.01 (19) | 113.03 | 111.4 (1) | 105.67 (10) |
| C2—C1—O1 | 107.6 (2) | 106.99 | 107.5 (1) | 110.32 (10) |
| C2—C3—C4 | 109.7 (2) | 109.24 | 111.8 (1) | 110.76 (11) |
| C1—O1—C7 | 114.6 (2) | 113.82 | | |
| C1—O1—C4' | | | 116.2 (1) | |
| | | | |
| Torsion angles | | | | |
| C1—C2—C3—C4 | -55.8 (3) | -55.32 | -45.6 (2) | -54.39 (14) |
| C1—O5—C5—C4 | 58.9 (3) | 58.43 | 66.7 (1) | 60.09 (13) |
| C4—C5—C6—O6 | 51.4 (3) (gg) | –164.33 (gt) | 54.3 (2) (gg) | -165.04 (10) (gt) |
| O5—C5—C6—O6 | -70.4 (3) | 73.94 | -64.8 (1) | 74.22 (13) |
| C2—C1—O1—C7/C4' (ϕ)b | -162.34 (18) | -175.22 | -165.3 (1) | |
| O5—C1—O1—C7/C4' (ϕ') | 77.4 (2) | 62.67 | 73.2 (1) | |
| C1—O1—C7—C8 (ψ)c | 89.9 (2) | | | |
| C1—O1—C7—C9 (ψ') | –147.9 (2) | | | |
| C1—O1—C4'—C3' (ψ) | | | 94.0 (1) | |
| C1—O1—C4'—C5' (ψ') | | | –139.1 (1) | |
| Notes: (a) In compound (III), the atoms in the aldohexopyranosyl ring
are unprimed and those in the acyclic alditol aglycone are primed (see
Scheme 1) to simplify structural comparisons between (I)–(IV). (b)
Either torsion angle ϕ or ϕ' can be used to define rotation
about the C1—O1 bonds in (I)–(III). (c) Either ψ or ψ' can be used
to define rotation about the O1—C7 or O1—C4' bonds in (I) and (III),
respectively. (d) S.u. values were not reported in the original article. |
DFT-calculated bond lengths (°), angles (°) and torsion angles (°)
in (I)c–(IV)c top| Structure | gga | gt | tg | gg | gt | tg |
| O1—O7 bond length | | | O1—C4' bond length | | |
| (I)c | 1.452 | 1.452 | 1.453 | | | |
| (II)c | 1.431 | 1.431 | 1.431 | | | |
| (III)c | | | | 1.445 | 1.435 | 1.446 |
| C1—O5 bond length | | | C5—O5 bond length | | |
| (I)c | 1.420 | 1.419 | 1.422 | 1.439 | 1.441 | 1.437 |
| (II)c | 1.422 | 1.423 | 1.425 | 1.439 | 1.441 | 1.437 |
| (III)c | 1.414 | 1.412 | 1.417 | 1.440 | 1.442 | 1.438 |
| (IV)c | 1.427 | 1.427 | 1.430 | 1.432 | 1.434 | 1.431 |
| C5—O5—C1 angle | | | | | |
| (I)c | 115.2 | 115.7 | 115.6 | | | |
| (II)c | 114.5 | 114.9 | 114.8 | | | |
| (III)c | 116.0 | 115.8 | 116.0 | | | |
| (IV)c | 113.8 | 114.1 | 114.3 | | | |
| O5—C1—O1 angle | | | | | |
| (I)c | 113.7 | 113.5 | 113.7 | | | |
| (II)c | 112.5 | 112.7 | 112.5 | | | |
| (III)c | 112.6 | 112.9 | 112.5 | | | |
| (IV)c | 107.6 | 107.6 | 107.5 | | | |
| C2—C1—O1 angle | | | | | |
| (I)c | 107.1 | 107.5 | 107.3 | | | |
| (II)c | 109.4 | 109.4 | 109.4 | | | |
| (III)c | 109.7 | 107.7 | 109.9 | | | |
| (IV)c | 109.4 | 109.5 | 109.5 | | | |
| C2–C3–C4 bond angle | | | | | |
| (I)c | 110.9 | 111.2 | 111.1 | | | |
| (II)c | 110.4 | 110.6 | 110.5 | | | |
| (III)c | 109.7 | 110.4 | 109.9 | | | |
| C1—O1—C7 angle | | | C1–O1–C4' angle | | |
| (I)c | 117.4 | 117.2 | 117.4 | | | |
| (II)c | 114.1 | 114.1 | 114.2 | | | |
| (III)c | | | | 118.2 | 117.6 | 118.8 |
| O5—C1—O1—C7 torsion angle | | | O5—C1—O1—C4' torsion angle | | |
| (I)c | 83.0 | 92.7 | 82.2 | | | |
| (II)c | 70.6 | 70.9 | 70.9 | | | |
| (III)c | | | | 101.1 | 86.7 | 103.2 |
| C2—C1—O1—C7 torsion angle | | | C2—C1—O1—C4' torsion angle | | |
| (I)c | 205.5 | 215.0 | 204.5 | | | |
| (II)c | 192.3 | 192.6 | 192.4 | | | |
| (III)c | | | | 223.1 | 208.3 | 224.9 |
| Note: (a gg, gt and tg refer to the conformation of
the exocyclic hydroxymethyl group in the geometry-optimized structures
(I)c–(IV)c (see text). |
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