3,3-Bis(2-hy­droxy­eth­yl)-1-(4-nitro­benzo­yl)thio­urea: crystal structure, Hirshfeld surface analysis and computational study

Tan, S.L.; Jotani, M.M.; Tiekink, E.R.T.

doi:10.1107/S2056989019017328

3,3-Bis(2-hydroxyethyl)-1-(4-nitrobenzoyl)thiourea: crystal structure, Hirshfeld surface analysis and computational study

S. L. Tan, M. M. Jotani and E. R. T. Tiekink

In the title tri-substituted thiourea molecule, a substantial twist is evident as seen in the dihedral angle of 65.92 (12)° between the planes through the CN₂S residue and the 4-nitroaryl ring; an intramolecular N—H

O hydrogen bond leading to an S(7) loop is noted. In the molecular packing, O—H

O and O—H

S hydrogen bonds lead to supramolecular layers propagating in the ab plane.

Keywords: crystal structure; thiourea; nitro group; hydrogen bonding; Hirshfeld surface analysis; computational chemistry.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989019017328/hb7880sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989019017328/hb7880Isup2.hkl Contains datablock I

CCDC reference: 1919879

checkCIF report

Key indicators

Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.002 Å
R factor = 0.037
wR factor = 0.093
Data-to-parameter ratio = 16.2

checkCIF/PLATON results

No syntax errors found



Datablock: I


Alert level C
PLAT230_ALERT_2_C Hirshfeld Test Diff for    S1       --C1       .        5.4 s.u.
PLAT230_ALERT_2_C Hirshfeld Test Diff for    O4       --N3       .        5.5 s.u.

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          6 Note
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical          ? Check
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          2 Report
PLAT802_ALERT_4_G CIF Input Record(s) with more than 80 Characters          1 Info
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          3 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
   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
   6 ALERT level G = General information/check it is not something unexpected

   1 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
   1 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: SMART (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

(I) top

Crystal data top

C₁₂H₁₅N₃O₅S	F(000) = 656
M_r = 313.33	D_x = 1.482 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 7.4203 (2) Å	Cell parameters from 2434 reflections
b = 10.3241 (3) Å	θ = 2.3–25.8°
c = 18.4191 (6) Å	µ = 0.26 mm⁻¹
β = 95.471 (2)°	T = 100 K
V = 1404.62 (7) Å³	Block, pale yellow
Z = 4	0.12 × 0.11 × 0.09 mm

Data collection top

Bruker SMART APEX diffractometer	3233 independent reflections
Radiation source: fine-focus sealed tube	2621 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.041
φ and ω scans	θ_max = 27.5°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −9→9
T_min = 0.970, T_max = 0.977	k = −13→13
13082 measured reflections	l = −23→23

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)] = 0.037	Hydrogen site location: mixed
wR(F²) = 0.093	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.042P)² + 0.3083P] where P = (F_o² + 2F_c²)/3
3233 reflections	(Δ/σ)_max = 0.001
200 parameters	Δρ_max = 0.33 e Å⁻³
3 restraints	Δρ_min = −0.25 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
S1	0.74915 (5)	0.45567 (4)	0.59498 (2)	0.02217 (12)
O1	0.72148 (15)	0.75229 (11)	0.77993 (8)	0.0313 (3)
H1O	0.760 (3)	0.8221 (13)	0.7992 (11)	0.047*
O2	0.16441 (15)	0.47542 (11)	0.65347 (6)	0.0219 (3)
H2O	0.0554 (16)	0.466 (2)	0.6367 (12)	0.051 (7)*
O3	0.88241 (15)	0.29890 (10)	0.73714 (6)	0.0221 (3)
O4	1.35804 (19)	0.56698 (14)	1.06330 (7)	0.0407 (4)
O5	1.3728 (2)	0.35951 (15)	1.07036 (8)	0.0538 (4)
N1	0.52846 (17)	0.57554 (12)	0.67890 (7)	0.0168 (3)
N2	0.80071 (17)	0.51231 (12)	0.73839 (7)	0.0174 (3)
H2N	0.801 (2)	0.5824 (12)	0.7648 (8)	0.021*
N3	1.3235 (2)	0.45902 (16)	1.03874 (8)	0.0300 (4)
C1	0.6860 (2)	0.51602 (14)	0.67325 (8)	0.0167 (3)
C2	0.4669 (2)	0.61682 (14)	0.74939 (8)	0.0181 (3)
H2A	0.5141	0.5555	0.7879	0.022*
H2B	0.3330	0.6135	0.7461	0.022*
C3	0.5291 (2)	0.75230 (15)	0.77061 (10)	0.0232 (4)
H3A	0.4853	0.8146	0.7320	0.028*
H3B	0.4800	0.7783	0.8166	0.028*
C4	0.4055 (2)	0.60787 (16)	0.61391 (8)	0.0211 (3)
H4A	0.4779	0.6236	0.5723	0.025*
H4B	0.3402	0.6889	0.6232	0.025*
C5	0.2690 (2)	0.50167 (17)	0.59362 (9)	0.0224 (3)
H5A	0.1876	0.5288	0.5506	0.027*
H5B	0.3329	0.4220	0.5807	0.027*
C6	0.89516 (19)	0.40521 (14)	0.76552 (8)	0.0163 (3)
C7	1.0107 (2)	0.42635 (14)	0.83615 (8)	0.0172 (3)
C8	1.0674 (2)	0.54755 (15)	0.86196 (9)	0.0205 (3)
H8	1.0348	0.6228	0.8340	0.025*
C9	1.1712 (2)	0.55922 (16)	0.92821 (9)	0.0229 (4)
H9	1.2105	0.6417	0.9463	0.027*
C10	1.2160 (2)	0.44763 (17)	0.96720 (9)	0.0225 (4)
C11	1.1652 (2)	0.32570 (16)	0.94236 (9)	0.0249 (4)
H11	1.2000	0.2507	0.9702	0.030*
C12	1.0628 (2)	0.31546 (15)	0.87614 (9)	0.0222 (3)
H12	1.0275	0.2325	0.8576	0.027*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0180 (2)	0.0320 (2)	0.0167 (2)	0.00001 (16)	0.00252 (15)	−0.00347 (16)
O1	0.0161 (6)	0.0216 (6)	0.0562 (9)	−0.0018 (5)	0.0031 (6)	−0.0148 (6)
O2	0.0150 (6)	0.0302 (6)	0.0202 (6)	−0.0025 (5)	0.0007 (5)	0.0039 (5)
O3	0.0206 (6)	0.0177 (6)	0.0274 (6)	0.0012 (4)	−0.0010 (5)	−0.0045 (5)
O4	0.0425 (8)	0.0469 (8)	0.0303 (7)	−0.0041 (7)	−0.0090 (6)	−0.0105 (6)
O5	0.0680 (11)	0.0522 (9)	0.0356 (8)	−0.0006 (8)	−0.0231 (8)	0.0156 (7)
N1	0.0158 (6)	0.0181 (6)	0.0166 (6)	0.0005 (5)	0.0015 (5)	0.0018 (5)
N2	0.0171 (7)	0.0172 (6)	0.0177 (6)	0.0020 (5)	0.0000 (5)	−0.0032 (5)
N3	0.0241 (8)	0.0442 (10)	0.0212 (7)	−0.0019 (7)	−0.0010 (6)	0.0024 (7)
C1	0.0150 (7)	0.0157 (7)	0.0190 (8)	−0.0025 (6)	0.0003 (6)	0.0011 (6)
C2	0.0167 (8)	0.0183 (7)	0.0198 (7)	0.0008 (6)	0.0035 (6)	−0.0007 (6)
C3	0.0162 (8)	0.0208 (8)	0.0324 (9)	0.0023 (6)	0.0009 (7)	−0.0043 (7)
C4	0.0178 (8)	0.0258 (8)	0.0191 (8)	0.0014 (6)	−0.0007 (6)	0.0069 (7)
C5	0.0169 (8)	0.0334 (9)	0.0167 (8)	−0.0003 (7)	0.0010 (6)	0.0013 (7)
C6	0.0125 (7)	0.0175 (7)	0.0193 (7)	−0.0003 (6)	0.0041 (6)	−0.0001 (6)
C7	0.0136 (7)	0.0198 (8)	0.0187 (8)	0.0012 (6)	0.0038 (6)	0.0008 (6)
C8	0.0188 (8)	0.0194 (8)	0.0228 (8)	−0.0006 (6)	0.0003 (6)	0.0034 (6)
C9	0.0215 (8)	0.0223 (8)	0.0243 (8)	−0.0039 (6)	−0.0001 (7)	−0.0029 (7)
C10	0.0174 (8)	0.0329 (9)	0.0169 (8)	0.0008 (7)	−0.0005 (6)	0.0005 (7)
C11	0.0257 (9)	0.0238 (8)	0.0248 (8)	0.0049 (7)	0.0004 (7)	0.0077 (7)
C12	0.0224 (8)	0.0185 (8)	0.0254 (8)	0.0027 (6)	0.0008 (7)	−0.0001 (6)

Geometric parameters (Å, º) top

S1—C1	1.6777 (16)	C3—H3A	0.9900
O1—C3	1.4218 (19)	C3—H3B	0.9900
O1—H1O	0.843 (10)	C4—C5	1.515 (2)
O2—C5	1.4331 (19)	C4—H4A	0.9900
O2—H2O	0.844 (10)	C4—H4B	0.9900
O3—C6	1.2156 (18)	C5—H5A	0.9900
O4—N3	1.221 (2)	C5—H5B	0.9900
O5—N3	1.220 (2)	C6—C7	1.504 (2)
N1—C1	1.334 (2)	C7—C8	1.389 (2)
N1—C4	1.4723 (19)	C7—C12	1.396 (2)
N1—C2	1.4796 (19)	C8—C9	1.385 (2)
N2—C6	1.3771 (19)	C8—H8	0.9500
N2—C1	1.4038 (19)	C9—C10	1.381 (2)
N2—H2N	0.871 (9)	C9—H9	0.9500
N3—C10	1.479 (2)	C10—C11	1.379 (2)
C2—C3	1.512 (2)	C11—C12	1.378 (2)
C2—H2A	0.9900	C11—H11	0.9500
C2—H2B	0.9900	C12—H12	0.9500

C3—O1—H1O	110.5 (15)	C5—C4—H4B	109.1
C5—O2—H2O	108.2 (16)	H4A—C4—H4B	107.8
C1—N1—C4	121.38 (13)	O2—C5—C4	110.21 (13)
C1—N1—C2	123.19 (13)	O2—C5—H5A	109.6
C4—N1—C2	115.41 (12)	C4—C5—H5A	109.6
C6—N2—C1	125.31 (13)	O2—C5—H5B	109.6
C6—N2—H2N	119.3 (11)	C4—C5—H5B	109.6
C1—N2—H2N	115.1 (11)	H5A—C5—H5B	108.1
O5—N3—O4	123.33 (16)	O3—C6—N2	123.57 (14)
O5—N3—C10	118.05 (15)	O3—C6—C7	121.17 (13)
O4—N3—C10	118.63 (15)	N2—C6—C7	115.20 (13)
N1—C1—N2	114.23 (13)	C8—C7—C12	119.91 (14)
N1—C1—S1	123.83 (12)	C8—C7—C6	123.75 (14)
N2—C1—S1	121.89 (11)	C12—C7—C6	116.34 (14)
N1—C2—C3	112.40 (13)	C9—C8—C7	120.31 (15)
N1—C2—H2A	109.1	C9—C8—H8	119.8
C3—C2—H2A	109.1	C7—C8—H8	119.8
N1—C2—H2B	109.1	C10—C9—C8	118.14 (15)
C3—C2—H2B	109.1	C10—C9—H9	120.9
H2A—C2—H2B	107.9	C8—C9—H9	120.9
O1—C3—C2	108.01 (12)	C11—C10—C9	122.97 (15)
O1—C3—H3A	110.1	C11—C10—N3	118.37 (15)
C2—C3—H3A	110.1	C9—C10—N3	118.66 (15)
O1—C3—H3B	110.1	C12—C11—C10	118.26 (15)
C2—C3—H3B	110.1	C12—C11—H11	120.9
H3A—C3—H3B	108.4	C10—C11—H11	120.9
N1—C4—C5	112.61 (13)	C11—C12—C7	120.37 (15)
N1—C4—H4A	109.1	C11—C12—H12	119.8
C5—C4—H4A	109.1	C7—C12—H12	119.8
N1—C4—H4B	109.1

C4—N1—C1—N2	169.47 (13)	O3—C6—C7—C12	−16.0 (2)
C2—N1—C1—N2	−8.8 (2)	N2—C6—C7—C12	161.02 (14)
C4—N1—C1—S1	−8.0 (2)	C12—C7—C8—C9	−1.8 (2)
C2—N1—C1—S1	173.80 (11)	C6—C7—C8—C9	178.89 (14)
C6—N2—C1—N1	134.76 (15)	C7—C8—C9—C10	0.1 (2)
C6—N2—C1—S1	−47.8 (2)	C8—C9—C10—C11	1.4 (3)
C1—N1—C2—C3	89.24 (17)	C8—C9—C10—N3	−178.75 (15)
C4—N1—C2—C3	−89.11 (16)	O5—N3—C10—C11	4.8 (2)
N1—C2—C3—O1	−62.76 (17)	O4—N3—C10—C11	−174.96 (16)
C1—N1—C4—C5	91.30 (17)	O5—N3—C10—C9	−175.05 (17)
C2—N1—C4—C5	−90.33 (16)	O4—N3—C10—C9	5.2 (2)
N1—C4—C5—O2	57.76 (17)	C9—C10—C11—C12	−1.1 (3)
C1—N2—C6—O3	−3.6 (2)	N3—C10—C11—C12	179.10 (15)
C1—N2—C6—C7	179.39 (13)	C10—C11—C12—C7	−0.8 (2)
O3—C6—C7—C8	163.29 (15)	C8—C7—C12—C11	2.2 (2)
N2—C6—C7—C8	−19.7 (2)	C6—C7—C12—C11	−178.47 (14)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the (C7–C12) ring.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O1	0.87 (1)	1.88 (1)	2.6749 (17)	151 (1)
O1—H1O···O2ⁱ	0.84 (2)	1.87 (2)	2.7075 (17)	176 (2)
O2—H2O···S1ⁱⁱ	0.84 (1)	2.33 (1)	3.1724 (12)	175 (2)
C2—H2B···O3ⁱ	0.99	2.53	3.2305 (18)	127
C5—H5A···S1ⁱⁱⁱ	0.99	2.77	3.4915 (17)	130
C8—H8···O3^iv	0.95	2.36	3.2147 (19)	150
N3—O4···Cg1^v	1.22 (1)	3.63 (1)	3.6927 (16)	83 (1)

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

Selected geometric parameters (Å, °) for (I) determined experimentally (X-ray) and from theory (DFT) top

Parameter	X-ray	Theory
C1═S1	1.6777 (16)	1.668
C1—N1	1.334 (2)	1.366
C1—N2	1.4038 (19)	1.410
C6—O3	1.2156 (18)	1.219
C6—N2	1.3771 (19)	1.388

S1—C1—N1	123.83 (12)	124.7
S1—C1—N2	121.89 (11)	121.8
N1—C1—N2	114.23 (13)	113.4
O3—C6—N2	123.57 (14)	124.3
O3—C6—C7	121.17 (13)	121.1
N2—C6—C7	115.20 (13)	114.5

S1—C1—N2—C6	-47.8 (2)	-44.6
S1—C1—N1—C2	173.80 (11)	167.8
S1—C1—N1—C4	-8.0 (2)	-7.2
O3—C6—N2—C1	-3.6 (2)	-16.5
O3—C6—C7—C8	163.29 (15)	152.7
N1—C2—C3—O1	-62.76 (17)	-69.3
N1—C4—C5—O2	57.76 (17)	68.4

A summary of short interatomic contacts (Å) in (I)^a top

Contact	Distance	Symmetry operation
H1O···H2O	2.23	1 - x, 1/2 + y, 3/2 - z
C1···C3	3.368 (2)	1 - x, -1/2 + y, 3/2 - z
C1···H3B	2.71	1 - x, -1/2 + y, 3/2 - z
C3···O3	3.0819 (19)	1 - x, 1/2 + y, 3/2 - z
C3···O5	3.168 (2)	2 - x, 1 - y, 1 - z
H3B···O5	2.65	2 - x, 1 - y, 1 - z
C5···H1O	2.61	1 - x, -1/2 + y, 3/2 - z
C6···O2	3.0924 (18)	1 + x, y, z
C6···H2O	2.81	1 + x, y, z

Note: (a) The interatomic distances are calculated in Crystal Explorer 17 (Turner et al., 2017) whereby the X—H bond lengths are adjusted to their neutron values.

Enrichment ratios for (I) top

Parameter	Ratio
H···H	0.88
C···H	0.85
O···H	1.26
S···H	1.66
C···O	1.34

Percentage contributions of interatomic contacts to the Hirshfeld surface for (I) top

Contact	Percentage contribution
H···H	31.8
O···H/H···O	30.7
C···H/H···C	10.3
S···H/H···S	13.9
C···O/O···C	5.8
N···H/H···N	1.9
O···O	1.6
C···N/N···C	1.5
C···C	1.3
N···O/O···N	0.9
N···N	0.3

Summary of interaction energies (kcal mol^-1) calculated for several directional contacts in (I) top

Contact	E_tot
O1—H1O···O2	-14.04
O2—H2O···S1	-5.60
C8—H8···O3	-10.05

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3,3-Bis(2-hy­droxy­eth­yl)-1-(4-nitro­benzo­yl)thio­urea: crystal structure, Hirshfeld surface analysis and computational study

Supporting information

Key indicators

checkCIF/PLATON results

3,3-Bis(2-hydroxyethyl)-1-(4-nitrobenzoyl)thiourea: crystal structure, Hirshfeld surface analysis and computational study