Crystal structure and Hirshfeld surface analysis of 1,3-diethynyladamantane

Domasevitch, K.V.; Degtyarenko, A.S.

doi:10.1107/S2056989020005964

Crystal structure and Hirshfeld surface analysis of 1,3-diethynyladamantane

K. V. Domasevitch and A. S. Degtyarenko

The title compound exhibits exceptionally weak intermolecular C—H

π hydrogen bonding of the ethynyl groups, with the corresponding H

π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding compliments distal contacts of the CH (aliphatic)

π type [H

π = 3.12 (2)–3.14 (2) Å] to sustain supramolecular layers.

Keywords: crystal structure; C—H

π hydrogen bond; Hirschfeld surface analysis; adamantane; terminal alkyne.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989020005964/lh5958sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989020005964/lh5958Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989020005964/lh5958Isup3.cml Supplementary material

CCDC reference: 2000259

checkCIF report

Key indicators

Single-crystal X-ray study
T = 213 K
Mean (C-C) = 0.002 Å
R factor = 0.044
wR factor = 0.124
Data-to-parameter ratio = 13.6

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.437 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         16 Report
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....         10 Note

Alert level G
PLAT230_ALERT_2_G Hirshfeld Test Diff for    C1       --C5       .       10.6 s.u.
PLAT230_ALERT_2_G Hirshfeld Test Diff for    C3       --C7       .        8.9 s.u.
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          3 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         18 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.         14 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 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
   4 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: IPDS Software (Stoe & Cie, 2000); cell refinement: IPDS Software (Stoe & Cie, 2000); data reduction: IPDS Software (Stoe & Cie, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018/1 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: WinGX (Farrugia, 2012).

(I) top

Crystal data top

C₁₄H₁₆	F(000) = 400
M_r = 184.27	D_x = 1.123 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 11.3214 (9) Å	Cell parameters from 8000 reflections
b = 6.7426 (6) Å	θ = 3.3–28.0°
c = 14.9478 (12) Å	µ = 0.06 mm⁻¹
β = 107.234 (9)°	T = 213 K
V = 1089.82 (16) Å³	Prism, colorless
Z = 4	0.26 × 0.23 × 0.20 mm

Data collection top

Stoe IPDS diffractometer	R_int = 0.039
Radiation source: fine-focus sealed tube	θ_max = 28.0°, θ_min = 3.3°
φ oscillation scans	h = −14→14
9458 measured reflections	k = −8→8
2593 independent reflections	l = −19→19
1885 reflections with I > 2σ(I)

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.044	Hydrogen site location: difference Fourier map
wR(F²) = 0.124	All H-atom parameters refined
S = 0.99	w = 1/[σ²(F_o²) + (0.086P)²] where P = (F_o² + 2F_c²)/3
2593 reflections	(Δ/σ)_max < 0.001
191 parameters	Δρ_max = 0.29 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

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
C1	0.28206 (10)	−0.04337 (17)	0.21845 (8)	0.0389 (3)
C2	0.27667 (12)	−0.1572 (2)	0.27676 (9)	0.0504 (3)
C3	0.11946 (10)	0.07256 (18)	−0.11933 (8)	0.0398 (3)
C4	0.05502 (13)	0.0009 (2)	−0.18880 (10)	0.0543 (4)
C5	0.28328 (9)	0.09619 (15)	0.14311 (7)	0.0322 (2)
C6	0.20113 (9)	0.01414 (14)	0.04951 (7)	0.0303 (2)
C7	0.19844 (9)	0.15694 (15)	−0.03144 (7)	0.0314 (2)
C8	0.33158 (10)	0.18505 (18)	−0.03602 (9)	0.0396 (3)
C9	0.41216 (11)	0.2689 (2)	0.05677 (9)	0.0456 (3)
C10	0.41510 (10)	0.1250 (2)	0.13649 (9)	0.0435 (3)
C11	0.23145 (13)	0.29881 (17)	0.16114 (9)	0.0421 (3)
C12	0.22953 (13)	0.44094 (16)	0.08120 (9)	0.0457 (3)
C13	0.14768 (11)	0.35843 (16)	−0.01119 (9)	0.0406 (3)
C14	0.36049 (14)	0.46899 (19)	0.07563 (11)	0.0548 (4)
H2	0.2661 (16)	−0.248 (3)	0.3202 (13)	0.077 (5)*
H4	0.0043 (17)	−0.063 (3)	−0.2445 (14)	0.072 (5)*
H6A	0.2336 (11)	−0.1137 (19)	0.0358 (9)	0.036 (3)*
H6B	0.1179 (12)	−0.0042 (17)	0.0536 (9)	0.036 (3)*
H8A	0.3640 (14)	0.055 (2)	−0.0489 (10)	0.049 (4)*
H8B	0.3328 (12)	0.269 (2)	−0.0870 (10)	0.042 (3)*
H9	0.4956 (14)	0.283 (2)	0.0525 (11)	0.057 (4)*
H10A	0.4668 (14)	0.175 (2)	0.1950 (11)	0.053 (4)*
H10B	0.4484 (14)	−0.008 (2)	0.1243 (11)	0.052 (4)*
H11A	0.1490 (15)	0.280 (2)	0.1688 (11)	0.058 (4)*
H11B	0.2825 (14)	0.356 (2)	0.2211 (11)	0.052 (4)*
H12	0.1974 (14)	0.567 (2)	0.0945 (11)	0.056 (4)*
H13A	0.1440 (14)	0.445 (2)	−0.0645 (11)	0.055 (4)*
H13B	0.0615 (15)	0.340 (2)	−0.0080 (11)	0.055 (4)*
H14A	0.3613 (15)	0.561 (2)	0.0255 (12)	0.061 (4)*
H14B	0.4157 (17)	0.527 (3)	0.1360 (14)	0.074 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0379 (5)	0.0402 (6)	0.0369 (6)	−0.0020 (4)	0.0086 (5)	0.0026 (5)
C2	0.0523 (7)	0.0520 (7)	0.0450 (7)	−0.0029 (6)	0.0112 (6)	0.0153 (6)
C3	0.0396 (6)	0.0448 (6)	0.0369 (6)	0.0016 (5)	0.0142 (5)	0.0037 (5)
C4	0.0516 (7)	0.0702 (9)	0.0391 (7)	−0.0116 (6)	0.0102 (6)	−0.0021 (6)
C5	0.0346 (5)	0.0304 (5)	0.0328 (6)	−0.0021 (4)	0.0120 (4)	0.0029 (4)
C6	0.0315 (5)	0.0256 (5)	0.0353 (6)	0.0008 (4)	0.0122 (4)	0.0014 (4)
C7	0.0329 (5)	0.0306 (5)	0.0327 (5)	0.0022 (4)	0.0127 (4)	0.0018 (4)
C8	0.0381 (6)	0.0458 (6)	0.0404 (7)	−0.0007 (5)	0.0202 (5)	0.0029 (5)
C9	0.0362 (6)	0.0577 (7)	0.0459 (7)	−0.0133 (5)	0.0166 (5)	0.0038 (6)
C10	0.0323 (5)	0.0549 (7)	0.0413 (7)	−0.0056 (5)	0.0079 (5)	0.0046 (5)
C11	0.0579 (7)	0.0335 (6)	0.0404 (7)	−0.0029 (5)	0.0232 (6)	−0.0043 (5)
C12	0.0689 (8)	0.0238 (5)	0.0505 (7)	0.0003 (5)	0.0271 (6)	−0.0015 (5)
C13	0.0486 (6)	0.0308 (5)	0.0461 (7)	0.0097 (5)	0.0197 (5)	0.0088 (5)
C14	0.0748 (9)	0.0412 (7)	0.0505 (8)	−0.0249 (6)	0.0218 (7)	−0.0010 (6)

Geometric parameters (Å, º) top

C1—C2	1.1763 (17)	C8—H8B	0.952 (14)
C1—C5	1.4708 (15)	C9—C10	1.5293 (18)
C2—H2	0.927 (19)	C9—C14	1.530 (2)
C3—C4	1.1812 (19)	C9—H9	0.971 (16)
C3—C7	1.4673 (16)	C10—H10A	0.957 (16)
C4—H4	0.96 (2)	C10—H10B	1.012 (15)
C5—C6	1.5354 (15)	C11—C12	1.5269 (16)
C5—C10	1.5370 (14)	C11—H11A	0.982 (15)
C5—C11	1.5418 (15)	C11—H11B	0.988 (16)
C6—C7	1.5396 (14)	C12—C14	1.5213 (19)
C6—H6A	0.982 (13)	C12—C13	1.5222 (19)
C6—H6B	0.970 (13)	C12—H12	0.967 (16)
C7—C13	1.5396 (14)	C13—H13A	0.980 (16)
C7—C8	1.5408 (13)	C13—H13B	0.999 (16)
C8—C9	1.5250 (18)	C14—H14A	0.976 (17)
C8—H8A	0.993 (14)	C14—H14B	1.013 (19)

C2—C1—C5	177.47 (13)	C10—C9—H9	108.6 (9)
C1—C2—H2	175.6 (11)	C14—C9—H9	110.9 (9)
C4—C3—C7	178.31 (12)	C9—C10—C5	109.45 (10)
C3—C4—H4	177.5 (11)	C9—C10—H10A	110.9 (9)
C1—C5—C6	109.07 (8)	C5—C10—H10A	109.2 (8)
C1—C5—C10	111.08 (9)	C9—C10—H10B	110.3 (9)
C6—C5—C10	108.93 (9)	C5—C10—H10B	108.7 (8)
C1—C5—C11	110.04 (9)	H10A—C10—H10B	108.3 (12)
C6—C5—C11	108.63 (9)	C12—C11—C5	109.71 (9)
C10—C5—C11	109.04 (9)	C12—C11—H11A	112.4 (9)
C5—C6—C7	110.88 (8)	C5—C11—H11A	109.1 (9)
C5—C6—H6A	110.0 (7)	C12—C11—H11B	109.6 (8)
C7—C6—H6A	107.8 (7)	C5—C11—H11B	110.6 (9)
C5—C6—H6B	109.0 (7)	H11A—C11—H11B	105.4 (12)
C7—C6—H6B	109.6 (7)	C14—C12—C13	109.69 (10)
H6A—C6—H6B	109.4 (10)	C14—C12—C11	109.43 (11)
C3—C7—C6	109.04 (9)	C13—C12—C11	110.14 (10)
C3—C7—C13	110.74 (9)	C14—C12—H12	109.6 (9)
C6—C7—C13	108.60 (8)	C13—C12—H12	110.0 (10)
C3—C7—C8	110.64 (8)	C11—C12—H12	108.0 (9)
C6—C7—C8	108.67 (9)	C12—C13—C7	109.79 (10)
C13—C7—C8	109.10 (9)	C12—C13—H13A	112.7 (9)
C9—C8—C7	109.55 (9)	C7—C13—H13A	107.3 (9)
C9—C8—H8A	110.4 (9)	C12—C13—H13B	110.1 (9)
C7—C8—H8A	108.9 (8)	C7—C13—H13B	108.9 (9)
C9—C8—H8B	111.2 (8)	H13A—C13—H13B	107.9 (13)
C7—C8—H8B	110.8 (8)	C12—C14—C9	109.43 (9)
H8A—C8—H8B	106.0 (11)	C12—C14—H14A	110.6 (10)
C8—C9—C10	110.04 (10)	C9—C14—H14A	109.3 (9)
C8—C9—C14	109.64 (11)	C12—C14—H14B	110.7 (10)
C10—C9—C14	109.70 (10)	C9—C14—H14B	109.7 (10)
C8—C9—H9	108.0 (9)	H14A—C14—H14B	107.1 (13)

C1—C5—C6—C7	179.35 (8)	C11—C5—C10—C9	−59.23 (13)
C10—C5—C6—C7	−59.25 (11)	C1—C5—C11—C12	−178.36 (10)
C11—C5—C6—C7	59.41 (10)	C6—C5—C11—C12	−59.03 (12)
C5—C6—C7—C3	179.79 (8)	C10—C5—C11—C12	59.57 (13)
C5—C6—C7—C13	−59.44 (11)	C5—C11—C12—C14	−60.35 (13)
C5—C6—C7—C8	59.12 (10)	C5—C11—C12—C13	60.31 (13)
C3—C7—C8—C9	−178.86 (10)	C14—C12—C13—C7	60.10 (12)
C6—C7—C8—C9	−59.18 (12)	C11—C12—C13—C7	−60.41 (12)
C13—C7—C8—C9	59.07 (12)	C3—C7—C13—C12	178.84 (9)
C7—C8—C9—C10	60.81 (13)	C6—C7—C13—C12	59.14 (11)
C7—C8—C9—C14	−59.92 (12)	C8—C7—C13—C12	−59.15 (11)
C8—C9—C10—C5	−60.73 (13)	C13—C12—C14—C9	−60.41 (14)
C14—C9—C10—C5	59.97 (14)	C11—C12—C14—C9	60.52 (14)
C1—C5—C10—C9	179.33 (10)	C8—C9—C14—C12	60.44 (13)
C6—C5—C10—C9	59.17 (13)	C10—C9—C14—C12	−60.51 (14)

Geometry of the shortest C—H···π contacts (Å, °) top

Cg is a group centroid.

D—H···π	D—H	H···π	D···A	D—H···π
Contacts with ethyne CH donors
C2—H2···Cg(C3C4)ⁱ	0.927 (19)	2.91 (2)	3.679 (2)	140.7 (14)
C4—H4···Cg(C3C4)ⁱⁱ	0.96 (2)	3.12 (2)	3.958 (2)	146.5 (14)

Contacts with aliphatic CH donors
C6—H6B···Cg(C3C4)ⁱⁱⁱ	0.970 (13)	3.12 (2)	4.030 (2)	155.9 (10)
C10—H10A···Cg(C1C2)^iv	0.957 (16)	3.14 (2)	3.853 (2)	133.0 (10)
C12—H12···Cg(C1C2)^v	0.967 (16)	3.14 (2)	3.904 (2)	136.7 (12)

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

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