2-[Carbamo­thio­yl(2-hy­droxy­eth­yl)amino]­ethyl benzoate: crystal structure, Hirshfeld surface analysis and computational study

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

doi:10.1107/S2056989020006829

2-[Carbamothioyl(2-hydroxyethyl)amino]ethyl benzoate: crystal structure, Hirshfeld surface analysis and computational study

The title di-substituted thiourea has hydroxylethyl and ethyl benzoate substituents bound to the same amine-N atom; overall the molecule is twisted. Supramolecular layers are formed in the crystal, with the molecules connected by O—H

S and N—H

O(carbonyl, hydroxyl) hydrogen bonds.

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

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989020006829/hb7918sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989020006829/hb7918Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989020006829/hb7918Isup3.cml Supplementary material

CCDC reference: 2004940

checkCIF report

Key indicators

Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.002 Å
R factor = 0.027
wR factor = 0.072
Data-to-parameter ratio = 15.2

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    S1       --C1       .        7.8 s.u.

Author Response: This is a quite a sensitive alert. In this case, there is no question as to the chemical composition of the molecule.


Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          5 Note
PLAT154_ALERT_1_G The s.u.'s on the Cell Angles are Equal ..(Note)      0.002 Degree
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          2 Report
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          3 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         24 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          7 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   0 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
   3 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: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXS (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

2-[Carbamothioyl(2-hydroxyethyl)amino]ethyl benzoate top

Crystal data top

C₁₂H₁₆N₂O₃S	Z = 2
M_r = 268.33	F(000) = 284
Triclinic, P1	D_x = 1.420 Mg m⁻³
a = 7.1608 (2) Å	Cu Kα radiation, λ = 1.54184 Å
b = 8.8771 (2) Å	Cell parameters from 11731 reflections
c = 10.0728 (2) Å	θ = 5.0–76.3°
α = 96.815 (2)°	µ = 2.33 mm⁻¹
β = 96.057 (2)°	T = 100 K
γ = 95.990 (2)°	Block, colourless
V = 627.78 (3) Å³	0.14 × 0.10 × 0.09 mm

Data collection top

XtaLAB Synergy, Dualflex, AtlasS2 diffractometer	2608 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source	2530 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.028
Detector resolution: 5.2558 pixels mm^-1	θ_max = 76.6°, θ_min = 4.5°
ω scans	h = −8→9
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2018)	k = −11→11
T_min = 0.656, T_max = 1.000	l = −12→11
15863 measured reflections

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)] = 0.027	Hydrogen site location: mixed
wR(F²) = 0.072	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.0387P)² + 0.2837P] where P = (F_o² + 2F_c²)/3
2608 reflections	(Δ/σ)_max = 0.001
172 parameters	Δρ_max = 0.28 e Å⁻³
3 restraints	Δρ_min = −0.29 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	0.37572 (4)	0.27008 (3)	1.03290 (3)	0.01701 (9)
O1	0.95223 (11)	0.15258 (9)	1.06895 (9)	0.02017 (19)
H1O	1.0641 (15)	0.1717 (19)	1.0521 (17)	0.030*
O2	0.70466 (11)	0.26850 (9)	0.61989 (8)	0.01658 (17)
O3	0.60618 (13)	0.20970 (10)	0.39867 (8)	0.02231 (19)
N1	0.35269 (14)	0.03143 (11)	0.84534 (10)	0.0167 (2)
H1N	0.396 (2)	−0.0360 (14)	0.7896 (13)	0.020*
H2N	0.2480 (16)	0.0025 (16)	0.8779 (14)	0.020*
N2	0.63866 (13)	0.18528 (10)	0.87909 (9)	0.01420 (19)
C1	0.46322 (16)	0.15473 (12)	0.91223 (11)	0.0146 (2)
C2	0.76658 (16)	0.31983 (13)	0.94513 (12)	0.0169 (2)
H2A	0.692935	0.407323	0.960760	0.020*
H2B	0.861614	0.347207	0.884739	0.020*
C3	0.86760 (16)	0.29131 (13)	1.07870 (12)	0.0183 (2)
H3A	0.966872	0.377706	1.111775	0.022*
H3B	0.775824	0.287765	1.145528	0.022*
C4	0.71451 (16)	0.08514 (13)	0.77635 (11)	0.0158 (2)
H4A	0.676376	−0.022672	0.787412	0.019*
H4B	0.854379	0.103147	0.790497	0.019*
C5	0.64657 (16)	0.11088 (13)	0.63421 (11)	0.0170 (2)
H5A	0.702102	0.042030	0.568493	0.020*
H5B	0.507114	0.088915	0.617061	0.020*
C6	0.67210 (15)	0.30367 (13)	0.49377 (11)	0.0162 (2)
C7	0.72974 (15)	0.46730 (13)	0.48446 (11)	0.0158 (2)
C8	0.70318 (16)	0.51705 (14)	0.35804 (12)	0.0180 (2)
H8	0.641338	0.448875	0.282694	0.022*
C9	0.76728 (17)	0.66610 (14)	0.34284 (12)	0.0214 (2)
H9	0.752018	0.699503	0.256588	0.026*
C10	0.85375 (17)	0.76653 (14)	0.45357 (13)	0.0218 (3)
H10	0.899045	0.868220	0.442592	0.026*
C11	0.87453 (17)	0.71919 (14)	0.58064 (13)	0.0212 (2)
H11	0.930722	0.789112	0.656580	0.025*
C12	0.81286 (16)	0.56950 (13)	0.59597 (12)	0.0182 (2)
H12	0.827287	0.536650	0.682476	0.022*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01619 (15)	0.01550 (15)	0.01948 (15)	0.00207 (10)	0.00422 (10)	0.00084 (10)
O1	0.0143 (4)	0.0183 (4)	0.0283 (5)	0.0016 (3)	0.0032 (3)	0.0041 (3)
O2	0.0206 (4)	0.0148 (4)	0.0137 (4)	−0.0014 (3)	0.0016 (3)	0.0025 (3)
O3	0.0282 (5)	0.0199 (4)	0.0162 (4)	−0.0027 (3)	−0.0008 (3)	−0.0003 (3)
N1	0.0162 (5)	0.0147 (5)	0.0184 (5)	−0.0008 (4)	0.0025 (4)	0.0015 (4)
N2	0.0149 (4)	0.0131 (4)	0.0141 (4)	0.0001 (3)	0.0018 (3)	0.0012 (3)
C1	0.0162 (5)	0.0140 (5)	0.0144 (5)	0.0020 (4)	0.0001 (4)	0.0057 (4)
C2	0.0170 (5)	0.0127 (5)	0.0203 (5)	−0.0024 (4)	0.0030 (4)	0.0017 (4)
C3	0.0170 (5)	0.0157 (5)	0.0203 (6)	−0.0002 (4)	0.0005 (4)	−0.0021 (4)
C4	0.0172 (5)	0.0146 (5)	0.0160 (5)	0.0027 (4)	0.0033 (4)	0.0019 (4)
C5	0.0203 (5)	0.0136 (5)	0.0163 (5)	−0.0011 (4)	0.0030 (4)	0.0007 (4)
C6	0.0139 (5)	0.0201 (6)	0.0147 (5)	0.0019 (4)	0.0024 (4)	0.0019 (4)
C7	0.0134 (5)	0.0176 (6)	0.0169 (5)	0.0030 (4)	0.0029 (4)	0.0028 (4)
C8	0.0178 (5)	0.0207 (6)	0.0160 (5)	0.0057 (4)	0.0015 (4)	0.0017 (4)
C9	0.0234 (6)	0.0233 (6)	0.0206 (6)	0.0095 (5)	0.0048 (5)	0.0085 (5)
C10	0.0209 (6)	0.0164 (5)	0.0301 (6)	0.0050 (4)	0.0058 (5)	0.0061 (5)
C11	0.0202 (6)	0.0190 (6)	0.0231 (6)	0.0024 (4)	0.0001 (5)	−0.0007 (5)
C12	0.0180 (5)	0.0204 (6)	0.0162 (5)	0.0027 (4)	0.0009 (4)	0.0028 (4)

Geometric parameters (Å, º) top

S1—C1	1.7082 (11)	C4—C5	1.5141 (15)
O1—C3	1.4259 (14)	C4—H4A	0.9900
O1—H1O	0.840 (9)	C4—H4B	0.9900
O2—C6	1.3462 (14)	C5—H5A	0.9900
O2—C5	1.4460 (13)	C5—H5B	0.9900
O3—C6	1.2121 (14)	C6—C7	1.4847 (16)
N1—C1	1.3454 (15)	C7—C12	1.3941 (16)
N1—H1N	0.874 (9)	C7—C8	1.3974 (16)
N1—H2N	0.876 (9)	C8—C9	1.3859 (17)
N2—C1	1.3424 (15)	C8—H8	0.9500
N2—C2	1.4706 (14)	C9—C10	1.3876 (18)
N2—C4	1.4688 (14)	C9—H9	0.9500
C2—C3	1.5203 (16)	C10—C11	1.3919 (18)
C2—H2A	0.9900	C10—H10	0.9500
C2—H2B	0.9900	C11—C12	1.3876 (17)
C3—H3A	0.9900	C11—H11	0.9500
C3—H3B	0.9900	C12—H12	0.9500

C3—O1—H1O	108.6 (12)	H4A—C4—H4B	107.8
C6—O2—C5	114.66 (8)	O2—C5—C4	108.15 (9)
C1—N1—H1N	122.3 (10)	O2—C5—H5A	110.1
C1—N1—H2N	117.4 (10)	C4—C5—H5A	110.1
H1N—N1—H2N	117.2 (14)	O2—C5—H5B	110.1
C1—N2—C2	121.80 (9)	C4—C5—H5B	110.1
C1—N2—C4	121.91 (9)	H5A—C5—H5B	108.4
C2—N2—C4	116.29 (9)	O3—C6—O2	122.83 (10)
N2—C1—N1	118.46 (10)	O3—C6—C7	124.38 (10)
N2—C1—S1	121.95 (8)	O2—C6—C7	112.78 (9)
N1—C1—S1	119.57 (9)	C12—C7—C8	119.92 (11)
N2—C2—C3	112.00 (9)	C12—C7—C6	122.18 (10)
N2—C2—H2A	109.2	C8—C7—C6	117.88 (10)
C3—C2—H2A	109.2	C9—C8—C7	119.84 (11)
N2—C2—H2B	109.2	C9—C8—H8	120.1
C3—C2—H2B	109.2	C7—C8—H8	120.1
H2A—C2—H2B	107.9	C8—C9—C10	120.01 (11)
O1—C3—C2	112.86 (9)	C8—C9—H9	120.0
O1—C3—H3A	109.0	C10—C9—H9	120.0
C2—C3—H3A	109.0	C11—C10—C9	120.41 (11)
O1—C3—H3B	109.0	C11—C10—H10	119.8
C2—C3—H3B	109.0	C9—C10—H10	119.8
H3A—C3—H3B	107.8	C12—C11—C10	119.75 (11)
N2—C4—C5	112.81 (9)	C12—C11—H11	120.1
N2—C4—H4A	109.0	C10—C11—H11	120.1
C5—C4—H4A	109.0	C11—C12—C7	120.01 (11)
N2—C4—H4B	109.0	C11—C12—H12	120.0
C5—C4—H4B	109.0	C7—C12—H12	120.0

C2—N2—C1—N1	178.51 (9)	O3—C6—C7—C12	−177.03 (11)
C4—N2—C1—N1	−2.38 (15)	O2—C6—C7—C12	1.55 (15)
C2—N2—C1—S1	0.22 (15)	O3—C6—C7—C8	1.20 (17)
C4—N2—C1—S1	179.33 (8)	O2—C6—C7—C8	179.78 (9)
C1—N2—C2—C3	82.67 (13)	C12—C7—C8—C9	2.89 (17)
C4—N2—C2—C3	−96.49 (11)	C6—C7—C8—C9	−175.38 (10)
N2—C2—C3—O1	49.39 (13)	C7—C8—C9—C10	−1.46 (17)
C1—N2—C4—C5	80.00 (13)	C8—C9—C10—C11	−0.84 (18)
C2—N2—C4—C5	−100.85 (11)	C9—C10—C11—C12	1.71 (18)
C6—O2—C5—C4	172.96 (9)	C10—C11—C12—C7	−0.26 (18)
N2—C4—C5—O2	59.09 (12)	C8—C7—C12—C11	−2.03 (17)
C5—O2—C6—O3	−2.74 (15)	C6—C7—C12—C11	176.17 (10)
C5—O2—C6—C7	178.64 (9)

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
O1—H1O···S1ⁱ	0.84 (1)	2.35 (1)	3.1746 (9)	169 (2)
N1—H2N···O1ⁱⁱ	0.88 (1)	2.04 (1)	2.8582 (13)	155 (1)
N1—H1N···O3ⁱⁱⁱ	0.88 (1)	2.30 (1)	3.1218 (13)	158 (1)
C6—O3···Cg1^iv	1.21 (1)	3.66 (1)	3.5026 (12)	73 (1)

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

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

Contact	Distance	ΣvdW	Δ\|(d_norm - ΣvdW)\|	Symmetry operation
H2N···O1^b	1.92	2.61	0.69	1 - x, - y, 2 - z
H1O···S1^b	2.21	2.89	0.68	1 + x, y, z
H1N···O3^b	2.17	2.61	0.44	1 - x, - y, 1 - z
H3B···H8	2.08	2.18	0.10	x, y, 1 + z
H9···C1	2.60	2.79	0.19	1 - x, 1 - y, 1 - z
C5···O3	3.17	3.22	0.05	1 - x, - y, 1 - z
H2A···S1	2.87	2.89	0.02	1 - x, 1 - y, 2 - z
H9···S1	2.89	2.89	0.00	1 - x, 1 - y, 1 - z

Notes: (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; (b) these interactions correspond to conventional hydrogen bonds.

Electrostatic potential charge (V_ESP) for each hydrogen atom donor and acceptor in (I) participating in a close contact identified through Hirshfeld surface analysis top

Contact	Electrostatic potential, V_ESP (a.u.)		Δ\|V_ESP\|
	H-donor	H-acceptor
H2N···O1	0.1446	-0.0654	0.2100
H1O···S1	0.1488	-0.0607	0.2095
H1N···O3	0.1248	-0.0601	0.1849
H9···C1	0.0441	-0.0119	0.0560
H3B···H8	0.0066	0.0229	0.0163
C5···O3	0.0581	-0.0562	0.1143
H2A···S1	0.0239	-0.0589	0.0828
H9···S1	0.0219	-0.0458	0.0677

A summary of interaction energies (kJ mol^-1) calculated for (I) top

Contact	E_ele	E_pol	E_dis	E_rep	E_tot	symmetry operation
{N1—H2N···O1}₂	-91.6	-13.5	-39.5	59.1	-85.6	1 - x, - y, 2 - z
{N1—H1N···O3}₂ + {C5···O3}₂	-56.9	-10.1	-26.5	27.4	-66.1	1 - x, - y, 1 - z
C6···π(benzene) +
{C9—H9···S1}₂ +
{C9—H9···C1}₂	-21.6	-3.0	-57.1	33.2	-48.3	1 - x, 1 - y, 1 - z
O1—H1O···S1	-47.2	-7.5	-10.6	36.5	-28.8	1 + x, y, z
π(benzene)–π(benzene)	-0.4	-1.6	-43.2	17.0	-28.3	2 - x, 1 - y, 1 - z
{C2—H2A···S1}₂	-14.6	-5.1	-14.7	11.3	-23.1	1 - x, 1 - y, 2 - z
C3—H3B···H8	1.1	-1.8	-12.7	9.1	-4.3	x, y, 1 + z

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2-[Carbamo­thio­yl(2-hy­droxy­eth­yl)amino]­ethyl benzoate: crystal structure, Hirshfeld surface analysis and computational study

Supporting information

Key indicators

checkCIF/PLATON results

2-[Carbamothioyl(2-hydroxyethyl)amino]ethyl benzoate: crystal structure, Hirshfeld surface analysis and computational study