Intra­molecular 1,5-S...N σ-hole inter­action in (E)-N′-(pyridin-4-yl­methyl­idene)thio­phene-2-carbohydrazide

The hydrazide-hydrazone forms inverse dimers via hydrogen bonding, but its conformation is defined by the presence of an intra­molecular chalcogen bond. Electrostatic forces dominate in the crystal packing and give rise to a layered supra­molecular structure.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.040
• wR factor = 0.101
• Data-to-parameter ratio = 21.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.035 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          2 Report

Alert level G
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          2 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.         10 Info

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 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
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: SAINT (Bruker, 2016); cell refinement: APEX3 (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: OLEX2(Dolomanov et al., 2009), Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).

(E)-N'-(Pyridin-4-ylmethylidene)thiophene-2-carbohydrazide

Crystal data

C11H9N3OS	F(000) = 480
Mr = 231.27	Dx = 1.467 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 12.0600 (8) Å	Cell parameters from 8101 reflections
b = 4.4531 (3) Å	θ = 2.2–32.3°
c = 19.9528 (13) Å	µ = 0.29 mm^−1
β = 102.228 (2)°	T = 100 K
V = 1047.24 (12) Å^3	Needle, clear colourless
Z = 4	0.49 × 0.04 × 0.01 mm

Data collection

Bruker APEXII CCD diffractometer	3767 independent reflections
Radiation source: Sealed Source Mo with TRIUMPH optics	2821 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.059
ω and phi scans	θmax = 32.4°, θmin = 2.2°
Absorption correction: multi-scan (AXScale; Bruker, 2016)	h = −18→18
Tmin = 0.694, Tmax = 0.746	k = −6→6
25531 measured reflections	l = −30→30

Refinement

Refinement on F^2	0 restraints
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.040	Only H-atom coordinates refined
wR(F^2) = 0.101	w = 1/[σ^2(Fo^2) + (0.0482P)^2 + 0.4155P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max < 0.001
3767 reflections	Δρmax = 0.44 e Å^−3
172 parameters	Δρmin = −0.28 e Å^−3

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
S1	0.86385 (3)	0.41227 (8)	0.09663 (2)	0.01759 (9)
O1	0.57985 (7)	−0.0566 (2)	0.08737 (5)	0.01585 (19)
N1	0.67837 (8)	0.4814 (2)	−0.01319 (5)	0.0121 (2)
C3	0.86828 (11)	1.1139 (3)	−0.10148 (7)	0.0177 (3)
C6	0.63662 (10)	0.6002 (3)	−0.07173 (6)	0.0123 (2)
N2	0.61184 (9)	0.2710 (2)	0.00868 (5)	0.0125 (2)
C8	0.75495 (10)	0.1986 (3)	0.11541 (6)	0.0128 (2)
C7	0.64471 (10)	0.1304 (3)	0.06997 (6)	0.0119 (2)
N3	0.82339 (9)	1.2476 (3)	−0.16131 (6)	0.0170 (2)
C1	0.70133 (10)	0.8252 (3)	−0.10079 (6)	0.0117 (2)
C10	0.89639 (12)	0.1627 (4)	0.21440 (7)	0.0214 (3)
C2	0.81256 (10)	0.9054 (3)	−0.06925 (7)	0.0158 (2)
C9	0.78539 (11)	0.0796 (3)	0.18034 (7)	0.0191 (3)
C5	0.65308 (11)	0.9644 (3)	−0.16254 (6)	0.0146 (2)
C4	0.71673 (11)	1.1716 (3)	−0.19047 (7)	0.0162 (2)
C11	0.94837 (11)	0.3405 (3)	0.17495 (7)	0.0190 (3)
H2	0.5467 (15)	0.214 (4)	−0.0197 (9)	0.023*
H6	0.5592 (15)	0.543 (4)	−0.0981 (9)	0.023*
H5	0.5756 (15)	0.918 (4)	−0.1848 (9)	0.023*
H2A	0.8487 (14)	0.813 (4)	−0.0278 (9)	0.023*
H4	0.6850 (14)	1.273 (4)	−0.2329 (9)	0.023*
H9	0.7381 (14)	−0.038 (4)	0.1991 (9)	0.023*
H3	0.9464 (15)	1.168 (4)	−0.0810 (9)	0.023*
H11	1.0212 (15)	0.424 (4)	0.1851 (9)	0.023*
H10	0.9262 (15)	0.103 (4)	0.2563 (9)	0.023*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.01205 (14)	0.02312 (18)	0.01612 (15)	−0.00603 (12)	−0.00037 (11)	0.00258 (13)
O1	0.0135 (4)	0.0181 (5)	0.0154 (4)	−0.0049 (3)	0.0018 (3)	0.0027 (4)
N1	0.0121 (4)	0.0104 (5)	0.0142 (5)	−0.0024 (4)	0.0038 (4)	−0.0003 (4)
C3	0.0130 (5)	0.0181 (6)	0.0217 (6)	−0.0037 (5)	0.0030 (5)	0.0006 (5)
C6	0.0109 (5)	0.0115 (5)	0.0141 (5)	−0.0010 (4)	0.0022 (4)	−0.0012 (5)
N2	0.0106 (4)	0.0129 (5)	0.0131 (5)	−0.0036 (4)	0.0008 (4)	0.0012 (4)
C8	0.0108 (5)	0.0133 (5)	0.0140 (5)	−0.0018 (4)	0.0021 (4)	−0.0006 (5)
C7	0.0112 (5)	0.0114 (6)	0.0130 (5)	0.0001 (4)	0.0025 (4)	−0.0007 (4)
N3	0.0178 (5)	0.0156 (5)	0.0189 (5)	−0.0027 (4)	0.0069 (4)	−0.0006 (4)
C1	0.0131 (5)	0.0100 (5)	0.0127 (5)	−0.0002 (4)	0.0040 (4)	−0.0014 (4)
C10	0.0176 (6)	0.0279 (7)	0.0158 (6)	−0.0019 (5)	−0.0034 (5)	0.0021 (5)
C2	0.0136 (5)	0.0160 (6)	0.0170 (6)	−0.0008 (5)	0.0011 (4)	0.0019 (5)
C9	0.0162 (6)	0.0244 (7)	0.0156 (6)	−0.0033 (5)	0.0010 (5)	0.0023 (5)
C5	0.0150 (5)	0.0146 (6)	0.0139 (5)	−0.0018 (4)	0.0022 (4)	−0.0013 (5)
C4	0.0205 (6)	0.0152 (6)	0.0134 (5)	−0.0017 (5)	0.0043 (5)	0.0005 (5)
C11	0.0118 (5)	0.0246 (7)	0.0183 (6)	−0.0021 (5)	−0.0018 (5)	−0.0017 (5)

Geometric parameters (Å, º)

S1—C11	1.7055 (14)	C8—C7	1.4736 (16)
S1—C8	1.7259 (12)	N3—C4	1.3381 (17)
O1—C7	1.2410 (15)	C1—C5	1.3918 (17)
N1—C6	1.2839 (16)	C1—C2	1.4019 (17)
N1—N2	1.3643 (14)	C10—C11	1.360 (2)
C3—N3	1.3413 (18)	C10—C9	1.4161 (19)
C3—C2	1.3821 (18)	C10—H10	0.879 (17)
C3—H3	0.974 (17)	C2—H2A	0.944 (17)
C6—C1	1.4631 (17)	C9—H9	0.912 (18)
C6—H6	1.002 (17)	C5—C4	1.3900 (18)
N2—C7	1.3561 (15)	C5—H5	0.968 (17)
N2—H2	0.901 (18)	C4—H4	0.963 (17)
C8—C9	1.3756 (18)	C11—H11	0.936 (18)
C11—S1—C8	91.85 (6)	C2—C1—C6	122.44 (11)
C6—N1—N2	115.48 (10)	C11—C10—C9	112.28 (12)
N3—C3—C2	124.61 (12)	C11—C10—H10	125.6 (12)
N3—C3—H3	115.8 (10)	C9—C10—H10	122.2 (12)
C2—C3—H3	119.5 (10)	C3—C2—C1	118.39 (12)
N1—C6—C1	120.21 (11)	C3—C2—H2A	121.5 (10)
N1—C6—H6	121.1 (10)	C1—C2—H2A	120.1 (10)
C1—C6—H6	118.7 (10)	C8—C9—C10	112.84 (12)
C7—N2—N1	121.75 (10)	C8—C9—H9	122.8 (11)
C7—N2—H2	119.0 (11)	C10—C9—H9	124.3 (11)
N1—N2—H2	119.0 (11)	C4—C5—C1	119.19 (12)
C9—C8—C7	121.75 (11)	C4—C5—H5	121.3 (10)
C9—C8—S1	110.68 (9)	C1—C5—H5	119.5 (10)
C7—C8—S1	127.51 (9)	N3—C4—C5	123.72 (12)
O1—C7—N2	118.73 (11)	N3—C4—H4	115.5 (10)
O1—C7—C8	120.41 (11)	C5—C4—H4	120.8 (10)
N2—C7—C8	120.86 (11)	C10—C11—S1	112.35 (10)
C4—N3—C3	116.38 (11)	C10—C11—H11	129.3 (11)
C5—C1—C2	117.70 (11)	S1—C11—H11	118.3 (11)
C5—C1—C6	119.85 (11)

Hydrogen-bond geometry (Å, °)

D-H···A	D-H	H···A	D···A	D-H···A
N2-H2···O1^i	0.902 (18)	1.942 (18)	2.8376 (14)	171.8 (18)
C11-H11···N3^ii	0.936 (19)	2.501 (18)	3.3664 (18)	153.9 (14)

Symmetry codes: (i) 1-x,-y,-z; (ii) 2-x,2-y,-z