Crystal structure of 2,6-bis­(3-hy­droxy-3-methyl­but-1-yn-1-yl)pyridine monohydrate

Koizumi, T.; Takata, T.

doi:10.1107/S2056989020013304

Crystal structure of 2,6-bis(3-hydroxy-3-methylbut-1-yn-1-yl)pyridine monohydrate

T. Koizumi and T. Takata

In the crystal, the hydrogen bonds between the pyridine molecule and the water molecule, viz. O_hydroxy—H

O_water, O_hydroxy—H

O_hydroxy, O_water—H

O_hydroxy, and O_water—H

N_pyridine, result in the formation of a ribbon structure running along [01 $\overline{1}$ ].

Keywords: crystal structure; pyridine; hydrogen bonding; π–π stacking.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989020013304/is5553sup1.cif Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989020013304/is5553Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989020013304/is5553Isup3.cml Supplementary material

CCDC reference: 2035321

checkCIF report

Key indicators

Single-crystal X-ray study
T = 113 K
Mean (C-C) = 0.002 Å
R factor = 0.029
wR factor = 0.082
Data-to-parameter ratio = 10.8

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT915_ALERT_3_B No Flack x Check Done: Low Friedel Pair Coverage         36 %

Alert level C
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         25 Report

Alert level G
PLAT371_ALERT_2_G Long   C(sp2)-C(sp1) Bond  C1       - C6       .       1.44 Ang.
PLAT371_ALERT_2_G Long   C(sp2)-C(sp1) Bond  C5       - C11      .       1.44 Ang.
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         71 Note
PLAT913_ALERT_3_G Missing # of Very Strong Reflections in FCF ....          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          6 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   1 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   5 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2019); cell refinement: CrysAlis PRO (Rigaku OD, 2019); data reduction: CrysAlis PRO (Rigaku OD, 2019); program(s) used to solve structure: Olex2.solve (Bourhis et al., 2015); program(s) used to refine structure: Olex2.refine (Bourhis et al., 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

4-[6-(3-Hydroxy-3-methylbut-1-yn-1-yl)pyridin-2-yl]-2-methylbut-3-yn-2-ol monohydrate top

Crystal data top

C₁₅H₁₇NO₂·H₂O	D_x = 1.175 Mg m⁻³
M_r = 261.31	Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, Fdd2	Cell parameters from 4276 reflections
a = 31.9834 (14) Å	θ = 4.2–74.9°
b = 27.7358 (13) Å	µ = 0.66 mm⁻¹
c = 6.6610 (4) Å	T = 113 K
V = 5908.9 (5) Å³	Plate, white
Z = 16	0.34 × 0.1 × 0.1 mm
F(000) = 2240

Data collection top

Rigaku XtaLAB Synergy R, DW system, HyPix diffractometer	2071 independent reflections
Radiation source: Rotating-anode X-ray tube, Rigaku (Cu) X-ray Source	2045 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.015
Detector resolution: 10.0000 pixels mm^-1	θ_max = 75.0°, θ_min = 4.2°
ω scans	h = −40→25
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2019)	k = −22→34
T_min = 0.817, T_max = 1.000	l = −8→5
4676 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.029	w = 1/[σ²(F_o²) + (0.0555P)² + 3.7832P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.082	(Δ/σ)_max < 0.001
S = 1.04	Δρ_max = 0.18 e Å⁻³
2071 reflections	Δρ_min = −0.19 e Å⁻³
192 parameters	Absolute structure: Flack x determined using 495 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute structure parameter: 0.02 (11)
Primary atom site location: iterative

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	0.35948 (3)	0.32551 (4)	0.6275 (2)	0.0246 (3)
O2	0.34219 (3)	0.65799 (4)	0.3581 (2)	0.0216 (3)
O3	0.38487 (4)	0.74210 (5)	0.3415 (3)	0.0329 (4)
N1	0.27513 (4)	0.49371 (5)	0.5965 (3)	0.0166 (3)
H1	0.3733 (8)	0.3523 (9)	0.623 (5)	0.041 (7)*
H2	0.3550 (7)	0.6863 (9)	0.339 (5)	0.037 (6)*
H2A	0.195964	0.419764	0.615414	0.022*
H3	0.158347	0.492523	0.628127	0.023*
H3A	0.4117 (8)	0.7423 (8)	0.345 (5)	0.033 (6)*
H3B	0.3782 (8)	0.7679 (10)	0.288 (5)	0.042 (7)*
H4	0.194772	0.565882	0.611513	0.022*
H9A	0.313194	0.255773	0.504956	0.037*
H9B	0.271146	0.285849	0.469227	0.037*
H9C	0.290932	0.282373	0.689425	0.037*
H10A	0.353762	0.360767	0.264577	0.041*
H10B	0.310243	0.336577	0.202018	0.041*
H10C	0.350205	0.303410	0.244822	0.041*
H14A	0.303649	0.733924	0.513951	0.036*
H14B	0.271251	0.704803	0.651137	0.036*
H14C	0.269906	0.699027	0.412177	0.036*
H15A	0.369017	0.641198	0.719381	0.043*
H15B	0.333112	0.668096	0.843702	0.043*
H15C	0.364036	0.698483	0.703467	0.043*
C1	0.25351 (4)	0.45203 (5)	0.6000 (3)	0.0160 (3)
C2	0.21008 (5)	0.44989 (5)	0.6118 (3)	0.0182 (3)
C3	0.18798 (5)	0.49280 (6)	0.6182 (3)	0.0193 (4)
C4	0.20942 (4)	0.53608 (5)	0.6100 (3)	0.0183 (3)
C5	0.25298 (4)	0.53508 (5)	0.5995 (3)	0.0159 (3)
C6	0.27810 (5)	0.40863 (6)	0.5837 (3)	0.0186 (4)
C7	0.29850 (5)	0.37292 (5)	0.5576 (3)	0.0190 (4)
C8	0.32310 (5)	0.32951 (6)	0.5046 (3)	0.0179 (4)
C9	0.29729 (5)	0.28434 (6)	0.5457 (3)	0.0244 (4)
C10	0.33542 (6)	0.33286 (6)	0.2844 (3)	0.0275 (4)
C11	0.27666 (4)	0.57928 (5)	0.5862 (3)	0.0170 (3)
C12	0.29570 (4)	0.61579 (6)	0.5643 (3)	0.0178 (3)
C13	0.31907 (5)	0.66164 (5)	0.5422 (3)	0.0181 (4)
C14	0.28820 (5)	0.70362 (6)	0.5287 (3)	0.0238 (4)
C15	0.34897 (6)	0.66791 (7)	0.7178 (4)	0.0290 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0193 (5)	0.0161 (5)	0.0383 (9)	−0.0015 (4)	−0.0082 (6)	0.0042 (6)
O2	0.0195 (5)	0.0166 (5)	0.0287 (7)	−0.0014 (4)	0.0053 (6)	0.0013 (6)
O3	0.0154 (5)	0.0246 (6)	0.0586 (11)	−0.0014 (4)	0.0000 (7)	0.0166 (7)
N1	0.0161 (5)	0.0165 (6)	0.0173 (8)	0.0000 (4)	−0.0002 (6)	0.0005 (6)
C1	0.0187 (7)	0.0157 (7)	0.0138 (8)	0.0000 (5)	−0.0010 (7)	0.0008 (7)
C2	0.0186 (6)	0.0176 (7)	0.0182 (9)	−0.0035 (5)	−0.0006 (7)	0.0009 (7)
C3	0.0144 (6)	0.0230 (8)	0.0205 (9)	−0.0004 (6)	−0.0009 (7)	0.0010 (8)
C4	0.0175 (7)	0.0180 (7)	0.0195 (9)	0.0022 (5)	0.0000 (7)	0.0000 (7)
C5	0.0183 (7)	0.0157 (7)	0.0136 (9)	−0.0003 (5)	0.0001 (7)	0.0007 (7)
C6	0.0185 (7)	0.0174 (7)	0.0200 (9)	−0.0027 (5)	−0.0010 (7)	0.0019 (7)
C7	0.0178 (6)	0.0168 (7)	0.0225 (9)	−0.0029 (5)	0.0009 (7)	0.0029 (8)
C8	0.0163 (6)	0.0143 (7)	0.0232 (10)	0.0003 (5)	−0.0017 (7)	0.0024 (7)
C9	0.0228 (7)	0.0164 (7)	0.0339 (11)	−0.0046 (6)	−0.0014 (8)	0.0015 (8)
C10	0.0299 (8)	0.0245 (8)	0.0280 (11)	0.0067 (7)	0.0065 (8)	0.0042 (8)
C11	0.0174 (7)	0.0175 (7)	0.0161 (8)	0.0017 (5)	−0.0005 (7)	−0.0004 (7)
C12	0.0173 (6)	0.0172 (7)	0.0190 (9)	0.0025 (6)	−0.0001 (6)	−0.0009 (7)
C13	0.0179 (7)	0.0135 (7)	0.0229 (10)	0.0004 (5)	0.0002 (7)	0.0001 (7)
C14	0.0230 (7)	0.0161 (7)	0.0322 (11)	0.0031 (6)	0.0025 (8)	0.0023 (8)
C15	0.0340 (9)	0.0203 (8)	0.0327 (11)	−0.0043 (7)	−0.0129 (8)	0.0014 (8)

Geometric parameters (Å, º) top

O2—C13	1.436 (2)	C4—C3	1.384 (2)
O2—H2	0.89 (3)	C13—C14	1.529 (2)
O1—C8	1.427 (2)	C13—C15	1.521 (3)
O1—H1	0.86 (3)	C2—H2A	0.9500
O3—H3A	0.86 (3)	C2—C3	1.385 (2)
O3—H3B	0.83 (3)	C3—H3	0.9500
N1—C1	1.3473 (19)	C9—H9A	0.9800
N1—C5	1.3488 (19)	C9—H9B	0.9800
C1—C6	1.442 (2)	C9—H9C	0.9800
C1—C2	1.393 (2)	C10—H10A	0.9800
C8—C7	1.481 (2)	C10—H10B	0.9800
C8—C9	1.525 (2)	C10—H10C	0.9800
C8—C10	1.522 (3)	C14—H14A	0.9800
C5—C4	1.3952 (19)	C14—H14B	0.9800
C5—C11	1.444 (2)	C14—H14C	0.9800
C12—C11	1.191 (2)	C15—H15A	0.9800
C12—C13	1.482 (2)	C15—H15B	0.9800
C7—C6	1.199 (2)	C15—H15C	0.9800
C4—H4	0.9500

C13—O2—H2	107 (2)	C3—C2—C1	118.31 (13)
C8—O1—H1	109.4 (19)	C3—C2—H2A	120.8
H3A—O3—H3B	105 (2)	C4—C3—C2	119.44 (13)
C1—N1—C5	117.40 (12)	C4—C3—H3	120.3
N1—C1—C6	115.80 (12)	C2—C3—H3	120.3
N1—C1—C2	123.32 (13)	C8—C9—H9A	109.5
C2—C1—C6	120.85 (13)	C8—C9—H9B	109.5
O1—C8—C7	111.09 (14)	C8—C9—H9C	109.5
O1—C8—C9	105.94 (14)	H9A—C9—H9B	109.5
O1—C8—C10	110.27 (13)	H9A—C9—H9C	109.5
C7—C8—C9	109.73 (13)	H9B—C9—H9C	109.5
C7—C8—C10	108.51 (15)	C8—C10—H10A	109.5
C10—C8—C9	111.32 (16)	C8—C10—H10B	109.5
N1—C5—C4	122.83 (14)	C8—C10—H10C	109.5
N1—C5—C11	116.47 (12)	H10A—C10—H10B	109.5
C4—C5—C11	120.68 (14)	H10A—C10—H10C	109.5
C11—C12—C13	178.5 (2)	H10B—C10—H10C	109.5
C6—C7—C8	174.6 (2)	C13—C14—H14A	109.5
C5—C4—H4	120.7	C13—C14—H14B	109.5
C3—C4—C5	118.66 (14)	C13—C14—H14C	109.5
C3—C4—H4	120.7	H14A—C14—H14B	109.5
C12—C11—C5	176.4 (2)	H14A—C14—H14C	109.5
C7—C6—C1	176.0 (2)	H14B—C14—H14C	109.5
O2—C13—C12	106.48 (13)	C13—C15—H15A	109.5
O2—C13—C14	109.61 (14)	C13—C15—H15B	109.5
O2—C13—C15	109.95 (14)	C13—C15—H15C	109.5
C12—C13—C14	109.48 (12)	H15A—C15—H15B	109.5
C12—C13—C15	109.82 (15)	H15A—C15—H15C	109.5
C15—C13—C14	111.38 (14)	H15B—C15—H15C	109.5
C1—C2—H2A	120.8

N1—C1—C2—C3	0.7 (3)	C5—N1—C1—C6	176.16 (16)
N1—C5—C4—C3	0.1 (3)	C5—N1—C1—C2	−1.8 (3)
C1—N1—C5—C4	1.3 (3)	C5—C4—C3—C2	−1.3 (3)
C1—N1—C5—C11	−177.20 (15)	C11—C5—C4—C3	178.62 (17)
C1—C2—C3—C4	0.9 (3)	C6—C1—C2—C3	−177.14 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.86 (3)	1.90 (3)	2.7640 (15)	175 (3)
O2—H2···O3	0.89 (3)	1.82 (2)	2.7052 (17)	170 (3)
O3—H3A···N1ⁱⁱ	0.86 (3)	2.02 (3)	2.8790 (18)	179 (3)
O3—H3B···O1ⁱⁱⁱ	0.83 (3)	2.01 (3)	2.8361 (19)	173 (3)

Symmetry codes: (i) −x+3/4, y−1/4, z+1/4; (ii) −x+3/4, y+1/4, z−1/4; (iii) x, y+1/2, z−1/2.

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Crystal structure of 2,6-bis­(3-hy­droxy-3-methyl­but-1-yn-1-yl)pyridine monohydrate

Supporting information

Key indicators

checkCIF/PLATON results

Crystal structure of 2,6-bis(3-hydroxy-3-methylbut-1-yn-1-yl)pyridine monohydrate