Isopropyl 3-de­oxy-α-d-ribo-hexo­pyran­oside (isopropyl 3-de­oxy-α-d-gluco­pyran­oside): evaluating trends in structural parameters

Lin, J.; Oliver, A.G.; Meredith, R.J.; Carmichael, I.; Serianni, A.S.

doi:10.1107/S205322962100749X

Isopropyl 3-deoxy-α-D-ribo-hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside): evaluating trends in structural parameters

J. Lin, A. G. Oliver, R. J. Meredith, I. Carmichael and A. S. Serianni

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 ^C5S_C1 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.

Keywords: crystal structure; isopropyl 3-deoxy-α-D-ribo-hexopyranoside; isopropyl 3-deoxy-α-D-glucopyranoside; DFT; chemical synthesis.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S205322962100749X/qf3048sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S205322962100749X/qf3048Isup2.hkl Contains datablock I

CCDC reference: 2098123

Computing details top

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
M_r = 206.23	D_x = 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	R_int = 0.062
combination of ω and φ–scans	θ_max = 70.8°, θ_min = 3.7°
Absorption correction: numerical (SADABS; Krause et al., 2015)	h = −16→16
T_min = 0.787, T_max = 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(F_o²) + (0.0607P)² + 0.4315P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
1976 reflections	Δρ_max = 0.19 e Å⁻³
141 parameters	Δρ_min = −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	U_iso*/U_eq
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	gg^a	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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Isopropyl 3-de­oxy-α-D-ribo-hexo­pyran­oside (isopropyl 3-de­oxy-α-D-gluco­pyran­oside): evaluating trends in structural parameters

Supporting information

Isopropyl 3-deoxy-α-D-ribo-hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside): evaluating trends in structural parameters