Isomorphous crystal structures of chlorodi­acetyl­ene and iododi­acetyl­ene derivatives: simultaneous hydrogen and halogen bonds on carbon­yl

tert-Butyl (5-chloro­penta-2,4-diyn-1-yl)carbamate and tert-butyl (5-iodo­penta-2,4-diyn-1-yl)carbamate are new members of the isostructural family of compounds with the general formula BocNHCH₂CCCCX (X = H, Cl, Br, I). In the crystals of all these di­acetyl­enes, mol­ecules are linked via a bifurcated N—H...O hydrogen bond and C—X...O halogen bond involving the same carbonyl group.

Key indicators

Structure: II

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.036
• wR factor = 0.089
• Data-to-parameter ratio = 17.3

Structure: IV

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.022
• wR factor = 0.054
• Data-to-parameter ratio = 19.5

checkCIF/PLATON results

No syntax errors found



Datablock: II


Alert level C
PLAT373_ALERT_2_C Long    C(sp)-C(sp)   Bond  C2     -   C3     ..       1.38 Ang.
PLAT761_ALERT_1_C CIF Contains no X-H Bonds ......................     Please Check
PLAT762_ALERT_1_C CIF Contains no X-Y-H or H-Y-H Angles ..........     Please Check
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          9 Report
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density.          0 Note

Alert level G
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          1 Report
PLAT230_ALERT_2_G Hirshfeld Test Diff for    Cl1    --  C1      ..       10.3 s.u.
PLAT431_ALERT_2_G Short Inter HL..A  Contact Cl1    ..  O1      ..       3.13 Ang.
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          5 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          8 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   5 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

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




Datablock: IV


Alert level C
PLAT373_ALERT_2_C Long    C(sp)-C(sp)   Bond  C2     -   C3     ..       1.38 Ang.

Alert level G
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          1 Report
PLAT431_ALERT_2_G Short Inter HL..A  Contact I1     ..  O2      ..       2.94 Ang.
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          3 Note

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

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

---

Computing details

For both structures, data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).

tert-Butyl (5-chloropenta-2,4-diyn-1-yl)carbamate (II)

Crystal data

C10H12ClNO2	F(000) = 448
Mr = 213.66	Dx = 1.283 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 8841 reflections
a = 10.336 (3) Å	θ = 2.8–26.4°
b = 9.171 (3) Å	µ = 0.32 mm^−1
c = 11.870 (3) Å	T = 173 K
β = 100.656 (5)°	Plate, orange
V = 1105.8 (5) Å^3	0.34 × 0.22 × 0.02 mm
Z = 4

Data collection

Bruker APEXII diffractometer	2249 independent reflections
Radiation source: sealed x-ray tube	1755 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.045
φ or ω oscillation scans	θmax = 26.4°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→12
Tmin = 0.66, Tmax = 0.745	k = −11→11
16132 measured reflections	l = −9→14

Refinement

Refinement on F^2	0 constraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.036	H-atom parameters constrained
wR(F^2) = 0.089	w = 1/[σ^2(Fo^2) + (0.0397P)^2 + 0.2863P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max < 0.001
2249 reflections	Δρmax = 0.22 e Å^−3
130 parameters	Δρmin = −0.21 e Å^−3
0 restraints

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.40035 (19)	0.0211 (2)	0.15762 (16)	0.0343 (4)
C2	0.50716 (18)	−0.0266 (2)	0.15615 (16)	0.0336 (4)
C3	0.63096 (19)	−0.0798 (2)	0.15309 (16)	0.0336 (4)
C4	0.73990 (19)	−0.1223 (2)	0.15037 (16)	0.0334 (4)
C5	0.87519 (17)	−0.1687 (2)	0.14761 (17)	0.0339 (4)
H5A	0.882935	−0.274828	0.16243	0.041*
H5B	0.894345	−0.150569	0.070125	0.041*
C6	1.04144 (17)	−0.15939 (19)	0.32333 (15)	0.0271 (4)
C7	1.22986 (18)	−0.11065 (19)	0.47967 (15)	0.0304 (4)
C8	1.1748 (2)	−0.1841 (2)	0.57483 (17)	0.0439 (5)
H8A	1.106364	−0.122368	0.597047	0.066*
H8B	1.245644	−0.198955	0.641132	0.066*
H8C	1.136913	−0.278618	0.547923	0.066*
C9	1.32333 (19)	−0.2075 (2)	0.42986 (18)	0.0408 (5)
H9A	1.278745	−0.298815	0.40299	0.061*
H9B	1.400577	−0.228971	0.488902	0.061*
H9C	1.351283	−0.15766	0.365371	0.061*
C10	1.2953 (2)	0.0332 (2)	0.52078 (19)	0.0449 (5)
H10A	1.324136	0.082715	0.456527	0.067*
H10B	1.371735	0.014414	0.581378	0.067*
H10C	1.232365	0.095115	0.550916	0.067*
Cl1	0.24981 (4)	0.08590 (5)	0.15756 (4)	0.03061 (14)
N1	0.97160 (14)	−0.09282 (16)	0.23144 (13)	0.0314 (4)
H1	0.984766	0.000739	0.221551	0.038*
O1	1.03225 (13)	−0.28874 (13)	0.34594 (11)	0.0361 (3)
O2	1.12149 (12)	−0.06256 (12)	0.38708 (11)	0.0311 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0342 (11)	0.0349 (11)	0.0334 (11)	−0.0009 (9)	0.0055 (8)	0.0009 (8)
C2	0.0337 (11)	0.0333 (10)	0.0323 (11)	−0.0036 (8)	0.0019 (8)	0.0007 (8)
C3	0.0333 (11)	0.0300 (10)	0.0346 (11)	−0.0005 (8)	−0.0011 (8)	0.0016 (8)
C4	0.0339 (11)	0.0279 (10)	0.0350 (11)	−0.0023 (8)	−0.0028 (8)	−0.0006 (8)
C5	0.0309 (10)	0.0311 (10)	0.0368 (11)	0.0013 (8)	−0.0014 (8)	−0.0030 (8)
C6	0.0264 (9)	0.0222 (9)	0.0323 (10)	−0.0014 (7)	0.0045 (7)	−0.0023 (7)
C7	0.0311 (10)	0.0269 (10)	0.0299 (10)	0.0017 (8)	−0.0026 (8)	0.0021 (8)
C8	0.0524 (13)	0.0429 (12)	0.0369 (12)	0.0014 (10)	0.0091 (10)	0.0049 (9)
C9	0.0344 (11)	0.0415 (12)	0.0451 (13)	0.0056 (9)	0.0037 (9)	0.0019 (9)
C10	0.0468 (13)	0.0339 (11)	0.0462 (13)	−0.0041 (10)	−0.0121 (10)	−0.0007 (9)
Cl1	0.0268 (2)	0.0320 (3)	0.0337 (3)	0.00451 (19)	0.00733 (18)	0.00090 (19)
N1	0.0303 (8)	0.0220 (8)	0.0381 (9)	−0.0024 (7)	−0.0036 (7)	0.0013 (7)
O1	0.0409 (8)	0.0217 (7)	0.0427 (8)	−0.0034 (6)	0.0003 (6)	0.0014 (6)
O2	0.0314 (7)	0.0220 (7)	0.0358 (8)	−0.0009 (5)	−0.0049 (6)	−0.0006 (5)

Geometric parameters (Å, º)

C1—C2	1.191 (3)	C6—N1	1.339 (2)
C1—Cl1	1.666 (2)	C6—O2	1.347 (2)
C2—C3	1.376 (3)	C7—O2	1.484 (2)
C3—C4	1.198 (3)	C7—C9	1.511 (3)
C4—C5	1.468 (3)	C7—C8	1.513 (3)
C5—N1	1.449 (2)	C7—C10	1.521 (3)
C6—O1	1.224 (2)
C2—C1—Cl1	178.9 (2)	O2—C7—C9	109.55 (15)
C1—C2—C3	179.0 (2)	O2—C7—C8	110.41 (15)
C4—C3—C2	178.2 (2)	C9—C7—C8	112.70 (16)
C3—C4—C5	177.8 (2)	O2—C7—C10	102.12 (14)
N1—C5—C4	112.49 (16)	C9—C7—C10	110.89 (17)
O1—C6—N1	124.66 (17)	C8—C7—C10	110.67 (17)
O1—C6—O2	125.48 (17)	C6—N1—C5	122.64 (16)
N1—C6—O2	109.86 (15)	C6—O2—C7	121.42 (13)
O1—C6—N1—C5	0.3 (3)	N1—C6—O2—C7	−166.78 (14)
O2—C6—N1—C5	−178.98 (15)	C9—C7—O2—C6	59.3 (2)
C4—C5—N1—C6	111.1 (2)	C8—C7—O2—C6	−65.4 (2)
O1—C6—O2—C7	13.9 (3)	C10—C7—O2—C6	176.85 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.88	2.09	2.935	162
C1—Cl1···O1^ii	1.67	3.13	4.793	179

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

tert-Butyl (5-iodopenta-2,4-diyn-1-yl)carbamate (IV)

Crystal data

C10H12INO2	F(000) = 592
Mr = 305.11	Dx = 1.635 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 9940 reflections
a = 11.1587 (16) Å	θ = 2.3–26.4°
b = 9.0288 (13) Å	µ = 2.56 mm^−1
c = 12.9899 (18) Å	T = 173 K
β = 108.731 (2)°	Prism, yellow
V = 1239.4 (3) Å^3	0.36 × 0.3 × 0.28 mm
Z = 4

Data collection

Bruker APEXII diffractometer	2532 independent reflections
Radiation source: sealed x-ray tube	2342 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.02
φ or ω oscillation scans	θmax = 26.4°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→13
Tmin = 0.675, Tmax = 0.745	k = −11→11
17970 measured reflections	l = −15→16

Refinement

Refinement on F^2	0 constraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.022	H-atom parameters constrained
wR(F^2) = 0.054	w = 1/[σ^2(Fo^2) + (0.0203P)^2 + 1.7447P] where P = (Fo^2 + 2Fc^2)/3
S = 1.08	(Δ/σ)max = 0.001
2532 reflections	Δρmax = 1.32 e Å^−3
130 parameters	Δρmin = −0.69 e Å^−3
0 restraints

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.2157 (2)	1.0340 (3)	0.3437 (2)	0.0328 (6)
C2	0.3210 (2)	1.0012 (3)	0.34873 (19)	0.0304 (5)
C3	0.4425 (2)	0.9623 (3)	0.35280 (19)	0.0279 (5)
C4	0.5465 (2)	0.9286 (3)	0.35525 (19)	0.0275 (5)
C5	0.6760 (2)	0.8938 (3)	0.35692 (19)	0.0282 (5)
H5A	0.736704	0.927089	0.42691	0.034*
H5B	0.684833	0.785076	0.352172	0.034*
C6	0.7111 (2)	0.8882 (2)	0.18051 (19)	0.0219 (4)
C7	0.7579 (3)	0.9226 (3)	0.0094 (2)	0.0344 (6)
C8	0.7976 (4)	1.0622 (3)	−0.0367 (3)	0.0511 (8)
H8A	0.730469	1.136625	−0.049832	0.077*
H8B	0.812386	1.038609	−0.105307	0.077*
H8C	0.875616	1.101212	0.015278	0.077*
C9	0.6338 (4)	0.8624 (4)	−0.0654 (3)	0.0559 (9)
H9A	0.611252	0.772368	−0.033698	0.084*
H9B	0.642508	0.839113	−0.136337	0.084*
H9C	0.567195	0.936832	−0.074587	0.084*
C10	0.8637 (3)	0.8100 (4)	0.0377 (3)	0.0506 (8)
H10A	0.936443	0.849222	0.095807	0.076*
H10B	0.888703	0.789497	−0.02666	0.076*
H10C	0.834626	0.718248	0.062297	0.076*
N1	0.7077 (2)	0.9636 (2)	0.26832 (16)	0.0263 (4)
H1	0.725256	1.058913	0.272455	0.032*
O1	0.73962 (17)	0.97953 (18)	0.11063 (13)	0.0272 (4)
O2	0.69111 (17)	0.75519 (18)	0.16743 (14)	0.0289 (4)
I1	0.04221 (2)	1.09875 (2)	0.33737 (2)	0.03907 (7)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0294 (14)	0.0398 (14)	0.0301 (13)	0.0020 (11)	0.0106 (10)	0.0027 (11)
C2	0.0333 (14)	0.0328 (13)	0.0263 (12)	−0.0012 (11)	0.0110 (10)	0.0031 (10)
C3	0.0312 (14)	0.0309 (13)	0.0250 (11)	−0.0015 (10)	0.0139 (10)	0.0011 (10)
C4	0.0337 (14)	0.0284 (12)	0.0236 (11)	−0.0036 (10)	0.0135 (10)	0.0005 (9)
C5	0.0298 (13)	0.0321 (13)	0.0259 (12)	0.0007 (10)	0.0132 (10)	0.0032 (10)
C6	0.0180 (11)	0.0216 (11)	0.0271 (11)	0.0013 (8)	0.0087 (9)	0.0020 (9)
C7	0.0490 (17)	0.0323 (13)	0.0293 (13)	−0.0017 (12)	0.0229 (12)	−0.0034 (10)
C8	0.085 (3)	0.0407 (17)	0.0437 (17)	−0.0055 (16)	0.0430 (18)	0.0016 (13)
C9	0.067 (2)	0.065 (2)	0.0325 (15)	−0.0141 (18)	0.0106 (15)	−0.0046 (15)
C10	0.065 (2)	0.0415 (17)	0.063 (2)	0.0074 (15)	0.0446 (18)	−0.0051 (15)
N1	0.0334 (11)	0.0215 (10)	0.0304 (10)	−0.0039 (8)	0.0191 (9)	−0.0015 (8)
O1	0.0396 (10)	0.0196 (8)	0.0293 (9)	0.0004 (7)	0.0209 (7)	0.0004 (7)
O2	0.0348 (10)	0.0197 (8)	0.0352 (9)	−0.0030 (7)	0.0157 (8)	−0.0001 (7)
I1	0.02499 (10)	0.04928 (12)	0.04157 (11)	0.00657 (8)	0.00878 (7)	0.00614 (8)

Geometric parameters (Å, º)

C1—C2	1.193 (4)	C7—C9	1.514 (4)
C1—I1	1.999 (3)	C7—C8	1.521 (4)
C2—C3	1.385 (4)	C8—H8A	0.98
C3—C4	1.191 (4)	C8—H8B	0.98
C4—C5	1.472 (3)	C8—H8C	0.98
C5—N1	1.452 (3)	C9—H9A	0.98
C5—H5A	0.99	C9—H9B	0.98
C5—H5B	0.99	C9—H9C	0.98
C6—O2	1.223 (3)	C10—H10A	0.98
C6—O1	1.338 (3)	C10—H10B	0.98
C6—N1	1.340 (3)	C10—H10C	0.98
C7—O1	1.486 (3)	N1—H1	0.88
C7—C10	1.512 (4)
C2—C1—I1	177.3 (3)	H8A—C8—H8B	109.5
C1—C2—C3	179.1 (3)	C7—C8—H8C	109.5
C4—C3—C2	179.4 (3)	H8A—C8—H8C	109.5
C3—C4—C5	177.4 (3)	H8B—C8—H8C	109.5
N1—C5—C4	112.5 (2)	C7—C9—H9A	109.5
N1—C5—H5A	109.1	C7—C9—H9B	109.5
C4—C5—H5A	109.1	H9A—C9—H9B	109.5
N1—C5—H5B	109.1	C7—C9—H9C	109.5
C4—C5—H5B	109.1	H9A—C9—H9C	109.5
H5A—C5—H5B	107.8	H9B—C9—H9C	109.5
O2—C6—O1	125.7 (2)	C7—C10—H10A	109.5
O2—C6—N1	124.3 (2)	C7—C10—H10B	109.5
O1—C6—N1	110.00 (19)	H10A—C10—H10B	109.5
O1—C7—C10	109.6 (2)	C7—C10—H10C	109.5
O1—C7—C9	109.6 (2)	H10A—C10—H10C	109.5
C10—C7—C9	113.4 (3)	H10B—C10—H10C	109.5
O1—C7—C8	101.7 (2)	C6—N1—C5	122.3 (2)
C10—C7—C8	110.5 (3)	C6—N1—H1	118.8
C9—C7—C8	111.5 (3)	C5—N1—H1	118.8
C7—C8—H8A	109.5	C6—O1—C7	121.17 (18)
C7—C8—H8B	109.5
O2—C6—N1—C5	−1.7 (4)	N1—C6—O1—C7	175.9 (2)
O1—C6—N1—C5	178.5 (2)	C10—C7—O1—C6	−58.9 (3)
C4—C5—N1—C6	−103.9 (3)	C9—C7—O1—C6	66.1 (3)
O2—C6—O1—C7	−3.9 (4)	C8—C7—O1—C6	−175.8 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^i	0.88	2.04	2.881	160
C1—I1···O2^ii	2.00	2.95	4.919	168

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