Water-mediated inter­molecular inter­actions in 1,2-O-cyclo­hexyl­idene-myo-inositol: a qu­anti­tative analysis

The syntheses of new myo-inositol derivatives have received much attention due to their important biological activities. 1,2-O-Cyclo­hexyl­idene-myo-inositol is an important inter­mediate formed during the syntheses of certain myo-inositol derivatives. We report herein the crystal structure of 1,2-O-cyclo­hexyl­idene-myo-inositol dihydrate, C₁₂H₂₀O₆·2H₂O, which is an inter­mediate formed during the syntheses of myo-inositol phosphate derivatives, to demonstrate the participation of water mol­ecules and hy­droxy groups in the formation of several inter­molecular O—H...O inter­actions, and to determine a low-energy conformation. The title myo-inositol derivative crystallizes with two water mol­ecules in the asymmetric unit in the space group C2/c, with Z = 8. The water mol­ecules facilitate the formation of an extensive O—H...O hydrogen-bonding network that assists in the formation of a dense crystal packing. Furthermore, geometrical optimization and frequency analysis was carried out using density functional theory (DFT) calculations with B3LYP hybrid functionals and 6-31G(d), 6-31G(d,p) and 6-311G(d,p) basis sets. The theoretical and experimental structures were found to be very similar, with only slight deviations. The inter­molecular inter­actions were qu­anti­tatively analysed using Hirshfeld surface analysis and 2D (two-dimensional) fingerplot plots, and the total lattice energy was calculated.

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: APEX2 (Bruker, 2009); data reduction: SAINT-Plus (Bruker, 2012); program(s) used to solve structure: SHELXL97 (Sheldrick, 2008) in WinGX (Farrugia, 2012); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) in WinGX (Farrugia, 2012); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), CAMERON (Watkin & Prout, 1993) and Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009).

1,2-O-Cyclohexylidene-myo-inositol dihydrate

Crystal data

C12H20O6·2H2O	F(000) = 1272
Mr = 296.31	Dx = 1.447 Mg m^−3
Monoclinic, C2/c	Melting point: 454 K
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 38.459 (3) Å	Cell parameters from 8730 reflections
b = 8.6208 (7) Å	θ = 2.4–26.1°
c = 8.2420 (7) Å	µ = 0.12 mm^−1
β = 95.371 (2)°	T = 298 K
V = 2720.6 (4) Å^3	Block, white
Z = 8	0.45 × 0.35 × 0.35 mm

Data collection

Bruker APEXII CCD diffractometer	2347 reflections with I > 2σ(I)
Radiation source: fine-focus sealed X-ray tube	Rint = 0.129
φ and ω scans	θmax = 28.3°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −51→51
Tmin = 0.935, Tmax = 0.972	k = −11→11
38263 measured reflections	l = −11→10
3391 independent reflections

Refinement

Refinement on F^2	1 restraint
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.055	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.140	w = 1/[σ^2(Fo^2) + (0.0598P)^2 + 0.8204P] where P = (Fo^2 + 2Fc^2)/3
S = 1.24	(Δ/σ)max < 0.001
3391 reflections	Δρmax = 0.20 e Å^−3
261 parameters	Δρmin = −0.21 e Å^−3

Special details

Experimental. The data was collected with the Bruker cryosystem a low-temperature attachment.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles

Refinement. Reflections were merged by SHELXL according to the crystal class for the calculation of statistics and refinement.

_reflns_Friedel_fraction is defined as the number of unique Friedel pairs measured divided by the number that would be possible theoretically, ignoring centric projections and systematic absences.

Various restraints, for example riding model, were used on the hydrogen atoms. All hydrogen atom evident from the difference maps. There appears to be disorder among the hydrogen atoms on atoms O5, O6, and the two water molecules O7 and O8. Successive trials with placement and refinement of hydrogen atoms resulted in the model deposited, with only one short H···H contact distance.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.13181 (3)	0.11890 (16)	0.82458 (16)	0.0139 (4)
O2	0.14165 (3)	0.32282 (16)	0.65515 (16)	0.0138 (4)
O3	0.08365 (4)	0.55158 (15)	0.70889 (16)	0.0160 (4)
O4	0.03829 (4)	0.43349 (16)	0.93025 (16)	0.0144 (4)
O5	0.02128 (3)	0.11220 (16)	0.89709 (17)	0.0170 (4)
O6	0.07640 (4)	−0.08649 (15)	0.81162 (17)	0.0157 (4)
C1	0.10407 (5)	0.1245 (2)	0.6947 (2)	0.0120 (6)
C2	0.10464 (5)	0.2942 (2)	0.6505 (2)	0.0121 (6)
C3	0.08820 (5)	0.3984 (2)	0.7725 (2)	0.0117 (6)
C4	0.05265 (5)	0.3387 (2)	0.8116 (2)	0.0116 (6)
C5	0.05495 (5)	0.1712 (2)	0.8713 (2)	0.0117 (6)
C6	0.07008 (5)	0.0650 (2)	0.7490 (2)	0.0117 (6)
C7	0.15910 (5)	0.2109 (2)	0.7687 (2)	0.0146 (6)
O7	0.02069 (4)	0.25520 (17)	0.39098 (17)	0.0170 (5)
C8	0.17810 (6)	0.2966 (3)	0.9113 (3)	0.0191 (7)
C9	0.20799 (6)	0.3936 (3)	0.8548 (3)	0.0254 (7)
C10	0.23303 (6)	0.2941 (3)	0.7669 (3)	0.0292 (8)
C11	0.21388 (6)	0.2082 (3)	0.6237 (3)	0.0233 (7)
C12	0.18374 (6)	0.1127 (3)	0.6789 (3)	0.0185 (6)
O8	0.14014 (5)	0.2676 (2)	0.3013 (2)	0.0245 (6)
H1	0.1103 (6)	0.058 (2)	0.609 (3)	0.015 (6)*
H2	0.0948 (6)	0.321 (3)	0.541 (3)	0.019 (6)*
H3	0.1049 (6)	0.400 (3)	0.878 (3)	0.022 (6)*
H3A	0.10229	0.60178	0.72855	0.0240*
H4	0.0361 (6)	0.343 (3)	0.711 (3)	0.015 (5)*
H4A	0.05188	0.43435	1.01620	0.0216*
H5	0.01059	0.17741	0.94958	0.0254*
H5A	0.0696 (5)	0.172 (2)	0.976 (3)	0.014 (5)*
H6	0.0517 (5)	0.058 (2)	0.648 (2)	0.007 (5)*
H6A	0.08822	−0.13656	0.74875	0.0235*
H8A	0.1883 (6)	0.210 (3)	0.989 (3)	0.021 (6)*
H8B	0.1612 (6)	0.365 (3)	0.963 (3)	0.016 (6)*
H9A	0.2201 (7)	0.445 (3)	0.951 (3)	0.030 (7)*
H9B	0.1967 (6)	0.477 (3)	0.790 (3)	0.027 (7)*
H10A	0.2438 (7)	0.212 (3)	0.846 (3)	0.034 (7)*
H10B	0.2503 (7)	0.351 (3)	0.732 (3)	0.032 (7)*
H11A	0.2294 (7)	0.141 (3)	0.569 (3)	0.033 (7)*
H11B	0.2042 (7)	0.284 (3)	0.538 (3)	0.042 (8)*
H12A	0.1929 (5)	0.025 (3)	0.754 (2)	0.011 (5)*
H12B	0.1706 (6)	0.064 (3)	0.596 (3)	0.026 (7)*
H7A	0.0239 (7)	0.351 (2)	0.406 (3)	0.033 (7)*
H8C	0.1319 (8)	0.188 (4)	0.306 (4)	0.056 (12)*
H8D	0.1447 (8)	0.300 (4)	0.406 (4)	0.061 (10)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0107 (7)	0.0172 (8)	0.0137 (7)	−0.0012 (6)	−0.0001 (5)	0.0041 (6)
O2	0.0114 (7)	0.0164 (7)	0.0138 (7)	−0.0001 (6)	0.0023 (5)	0.0032 (6)
O3	0.0185 (8)	0.0104 (7)	0.0186 (7)	−0.0026 (6)	−0.0007 (6)	0.0038 (6)
O4	0.0183 (8)	0.0138 (7)	0.0115 (7)	0.0020 (6)	0.0031 (6)	−0.0028 (5)
O5	0.0145 (8)	0.0138 (7)	0.0242 (8)	0.0004 (6)	0.0104 (6)	−0.0027 (6)
O6	0.0175 (8)	0.0093 (7)	0.0208 (8)	0.0036 (6)	0.0048 (6)	−0.0004 (6)
C1	0.0113 (10)	0.0143 (10)	0.0102 (9)	0.0022 (8)	0.0006 (8)	−0.0001 (8)
C2	0.0112 (10)	0.0143 (10)	0.0111 (10)	−0.0012 (8)	0.0021 (8)	0.0005 (8)
C3	0.0145 (10)	0.0089 (10)	0.0116 (9)	0.0006 (8)	0.0001 (8)	0.0019 (8)
C4	0.0137 (10)	0.0120 (10)	0.0091 (9)	0.0007 (8)	0.0019 (8)	−0.0020 (8)
C5	0.0112 (10)	0.0132 (10)	0.0106 (9)	−0.0024 (8)	0.0013 (8)	0.0000 (8)
C6	0.0136 (10)	0.0091 (10)	0.0123 (9)	0.0000 (8)	0.0006 (8)	0.0012 (8)
C7	0.0123 (10)	0.0169 (11)	0.0146 (10)	−0.0006 (8)	0.0009 (8)	0.0044 (8)
O7	0.0210 (8)	0.0113 (8)	0.0189 (8)	−0.0008 (6)	0.0028 (6)	−0.0007 (6)
C8	0.0157 (11)	0.0223 (12)	0.0192 (11)	−0.0014 (9)	0.0008 (9)	−0.0008 (9)
C9	0.0203 (12)	0.0272 (13)	0.0278 (12)	−0.0076 (11)	−0.0020 (10)	−0.0001 (11)
C10	0.0148 (12)	0.0387 (16)	0.0343 (14)	−0.0084 (11)	0.0028 (10)	0.0033 (12)
C11	0.0168 (12)	0.0270 (13)	0.0271 (12)	0.0012 (10)	0.0073 (10)	0.0016 (10)
C12	0.0162 (11)	0.0177 (11)	0.0217 (11)	0.0002 (9)	0.0029 (9)	−0.0010 (9)
O8	0.0274 (10)	0.0224 (10)	0.0242 (9)	0.0018 (8)	0.0056 (7)	0.0020 (8)

Geometric parameters (Å, º)

O1—C1	1.440 (2)	C10—C11	1.524 (3)
O1—C7	1.426 (2)	C11—C12	1.526 (3)
O2—C2	1.442 (2)	C1—H1	0.96 (2)
O2—C7	1.463 (2)	C2—H2	0.97 (2)
O3—C3	1.426 (2)	C3—H3	1.03 (2)
O4—C4	1.425 (2)	C4—H4	1.00 (2)
O5—C5	1.426 (2)	C5—H5A	0.99 (2)
O6—C6	1.417 (2)	C6—H6	1.042 (17)
O3—H3A	0.8400	O7—H7A	0.843 (18)
O4—H4A	0.8400	C8—H8B	1.00 (2)
O5—H5	0.8400	C8—H8A	1.04 (3)
O6—H6A	0.8400	C9—H9A	0.99 (3)
C1—C6	1.511 (3)	C9—H9B	0.97 (3)
C1—C2	1.508 (2)	C10—H10B	0.90 (3)
C2—C3	1.529 (2)	C10—H10A	1.02 (3)
C3—C4	1.523 (3)	C11—H11A	0.97 (3)
C4—C5	1.525 (2)	C11—H11B	1.01 (3)
C5—C6	1.517 (2)	C12—H12A	1.02 (2)
C7—C8	1.517 (3)	C12—H12B	0.91 (2)
C7—C12	1.515 (3)	O8—H8C	0.76 (3)
C8—C9	1.529 (3)	O8—H8D	0.91 (3)
C9—C10	1.523 (3)
C1—O1—C7	104.94 (13)	C3—C2—H2	108.8 (15)
C2—O2—C7	107.27 (13)	O3—C3—H3	110.1 (14)
C3—O3—H3A	109.00	C2—C3—H3	107.4 (14)
C4—O4—H4A	109.00	C4—C3—H3	109.1 (13)
C5—O5—H5	109.00	O4—C4—H4	106.9 (14)
C6—O6—H6A	109.00	C3—C4—H4	109.1 (14)
O1—C1—C6	111.71 (13)	C5—C4—H4	108.5 (15)
C2—C1—C6	115.69 (15)	O5—C5—H5A	109.0 (12)
O1—C1—C2	100.70 (14)	C4—C5—H5A	106.7 (10)
O2—C2—C3	110.49 (14)	C6—C5—H5A	111.3 (11)
C1—C2—C3	113.26 (14)	O6—C6—H6	108.5 (10)
O2—C2—C1	101.32 (14)	C1—C6—H6	108.9 (10)
O3—C3—C2	110.28 (14)	C5—C6—H6	107.0 (10)
O3—C3—C4	108.00 (15)	C7—C8—H8A	104.8 (14)
C2—C3—C4	112.04 (14)	C7—C8—H8B	109.4 (14)
O4—C4—C3	111.39 (14)	C9—C8—H8A	109.3 (13)
C3—C4—C5	111.22 (15)	C9—C8—H8B	110.1 (14)
O4—C4—C5	109.63 (14)	H8A—C8—H8B	113 (2)
O5—C5—C4	111.09 (15)	C8—C9—H9A	108.2 (15)
O5—C5—C6	107.09 (14)	C8—C9—H9B	105.2 (14)
C4—C5—C6	111.79 (14)	C10—C9—H9A	111.3 (15)
C1—C6—C5	112.84 (15)	C10—C9—H9B	115.1 (15)
O6—C6—C1	107.29 (15)	H9A—C9—H9B	105 (2)
O6—C6—C5	112.18 (14)	C9—C10—H10A	108.8 (14)
O1—C7—C8	109.66 (15)	C9—C10—H10B	111.5 (17)
O1—C7—C12	111.11 (16)	C11—C10—H10A	107.2 (14)
O2—C7—C8	109.48 (15)	C11—C10—H10B	109.7 (16)
O1—C7—O2	105.43 (14)	H10A—C10—H10B	108 (2)
O2—C7—C12	109.06 (15)	C10—C11—H11A	112.1 (15)
C8—C7—C12	111.89 (18)	C10—C11—H11B	110.4 (15)
C7—C8—C9	110.60 (19)	C12—C11—H11A	109.5 (16)
C8—C9—C10	111.3 (2)	C12—C11—H11B	108.5 (15)
C9—C10—C11	111.16 (19)	H11A—C11—H11B	105 (2)
C10—C11—C12	110.9 (2)	C7—C12—H12A	108.3 (11)
C7—C12—C11	111.8 (2)	C7—C12—H12B	107.2 (15)
O1—C1—H1	108.0 (14)	C11—C12—H12A	110.6 (11)
C2—C1—H1	113.1 (12)	C11—C12—H12B	114.1 (16)
C6—C1—H1	107.4 (13)	H12A—C12—H12B	104 (2)
O2—C2—H2	106.3 (14)	H8C—O8—H8D	106 (3)
C1—C2—H2	116.2 (15)
C7—O1—C1—C2	−43.11 (16)	C2—C3—C4—C5	55.05 (18)
C7—O1—C1—C6	−166.48 (14)	C2—C3—C4—O4	177.68 (14)
C1—O1—C7—C12	−91.05 (17)	O3—C3—C4—O4	−60.68 (17)
C1—O1—C7—O2	26.96 (16)	O3—C3—C4—C5	176.70 (13)
C1—O1—C7—C8	144.73 (16)	O4—C4—C5—O5	60.37 (18)
C2—O2—C7—C12	120.33 (16)	C3—C4—C5—C6	−56.44 (19)
C7—O2—C2—C1	−26.72 (16)	O4—C4—C5—C6	179.93 (15)
C7—O2—C2—C3	93.59 (15)	C3—C4—C5—O5	−176.00 (13)
C2—O2—C7—O1	0.95 (17)	C4—C5—C6—C1	51.3 (2)
C2—O2—C7—C8	−116.94 (16)	O5—C5—C6—O6	−65.51 (18)
C6—C1—C2—C3	44.6 (2)	O5—C5—C6—C1	173.16 (14)
C6—C1—C2—O2	162.97 (14)	C4—C5—C6—O6	172.60 (15)
C2—C1—C6—O6	−169.97 (14)	O1—C7—C8—C9	178.85 (17)
O1—C1—C6—O6	−55.56 (18)	O2—C7—C8—C9	−65.9 (2)
O1—C1—C6—C5	68.50 (18)	C12—C7—C8—C9	55.1 (2)
O1—C1—C2—O2	42.40 (15)	O1—C7—C12—C11	−177.88 (17)
C2—C1—C6—C5	−45.9 (2)	O2—C7—C12—C11	66.3 (2)
O1—C1—C2—C3	−75.94 (18)	C8—C7—C12—C11	−54.9 (2)
O2—C2—C3—O3	77.97 (18)	C7—C8—C9—C10	−55.7 (3)
C1—C2—C3—O3	−169.16 (15)	C8—C9—C10—C11	56.1 (3)
C1—C2—C3—C4	−48.8 (2)	C9—C10—C11—C12	−55.1 (3)
O2—C2—C3—C4	−161.70 (14)	C10—C11—C12—C7	54.5 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3A···O8^i	0.84	1.89	2.724 (2)	170
O4—H4A···O3^i	0.84	1.91	2.754 (2)	177
O5—H5···O4	0.84	2.46	2.853 (2)	109
O5—H5···O7^ii	0.84	1.98	2.776 (2)	158
O6—H6A···O8^iii	0.84	2.30	2.914 (2)	130
O7—H7A···O4^iv	0.843 (18)	1.944 (18)	2.779 (2)	171 (3)
O8—H8C···O6^v	0.76 (3)	2.31 (3)	2.914 (2)	137 (3)
O8—H8D···O2	0.91 (3)	2.08 (3)	2.950 (3)	161 (3)

Symmetry codes: (i) x, −y+1, z+1/2; (ii) −x, y, −z+3/2; (iii) x, −y, z+1/2; (iv) x, −y+1, z−1/2; (v) x, −y, z−1/2.