research communications
2-[Carbamothioyl(2-hydroxyethyl)amino]ethyl benzoate:
Hirshfeld surface analysis and computational studyaResearch Centre for Crystalline Materials, School of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
*Correspondence e-mail: edwardt@sunway.edu.my
The title di-substituted thiourea, C12H16N2O3S, has the hydroxylethyl and ethyl benzoate substituents bound to the same amine-N atom, and is twisted, having a (+)syn-clinal conformation with the Namine—C—C—O(hydroxyl, carbonyl) torsion angles of 49.39 (13) and 59.09 (12)°, respectively; the dihedral angle between the almost planar CN2S core and the pendent benzene ring is 69.26 (4)°. In the crystal, supramolecular layers propagating in the ac plane are formed via a combination of hydroxyl-O—H⋯S(thione), amine-N—H⋯O(hydroxyl, carbonyl) hydrogen-bonds. The layers stack along the b axis with inter-digitation of the benzene rings allowing the formation of π–π stacking [inter-centroid separation = 3.8722 (7) Å] and parallel C=O⋯π interactions. A computational chemistry study shows the conventional hydrogen bonding in the crystal leads to significant electrostatic stabilization but dispersion terms are also apparent, notably through the interactions involving the benzene residue.
Keywords: crystal structure; thiourea; hydrogen bonding; Hirshfeld surface analysis; computational chemistry.
CCDC reference: 2004940
1. Chemical context
The title compound, (I), was characterized crystallographically in a continuation of recent structural studies of tri-substituted thiourea derivatives formulated as (HOCH2CH2)2NC(=S)N(H)C(=O)C6H4-R-4 for R = Me (Tan, Azizan et al., 2019) and R = NO2 (Tan et al., 2020): these molecules are known for their various applications including biological activity (Saeed et al., 2014). A convenient synthesis for these molecules is via the reaction of NH4(NCS), R2NH and ArC(=O)Cl to yield R2NC(=S)N(H)C(=O)Ar. In an experiment with R = CH2CH2OH and Ar = C6H5, the solution was also heated resulting in an apparent rearrangement with deprotonation of one hydroxyethyl group followed by nucleophilic attachment at the carbonyl-C atom along with protonation of the primary amine and cleavage of the original N—C(=O) bond to yield (I), formulated as H2NC(=S)N(CH2CH2OH)CH2CH2OC(=O)C6H5. The molecular structure of (I) was determined by X-ray crystallography and the supramolecular association investigated by Hirshfeld surface analysis and computational chemistry.
2. Structural commentary
The molecule of (I) is shown in Fig. 1 and comprises a di-substituted thiourea molecule with both substitutions occurring at the same amine atom. The CN2S atoms of the thiourea core are almost planar, exhibiting a r.m.s. deviation = 0.0054 Å, with the appended C2 and C4 atoms lying 0.0236 (18) and 0.0216 (16) Å to either side of the plane. The conformation of the C2-hydroxylethyl residue is (+)syn-clinal as indicated by the N2—C2—C3—O1 torsion angle of 49.39 (13)°. The CO2 residue is close to co-planar with the (C7–C12)-benzene ring to which it is connected, forming a dihedral angle of 4.83 (9)°. The dihedral angle between the least-squares planes through the CN2S core and the benzene ring is 69.26 (4)°, indicating the molecule is highly twisted. Finally, the N2—C4—C5—O2 torsion angle of 59.09 (12)° is indicative of a (+)syn-clinal configuration about the C—C bond, thereby confirming the twisted nature of the molecule.
3. Supramolecular features
As anticipated, hydrogen bonding plays a key role in the supramolecular assembly of (I); see Table 1 for geometrical data. The combination of hydroxyl-O—H⋯S(thione) and amine-N—H⋯O(hydroxyl) hydrogen bonds connect molecules into a supramolecular tape propagating along the a-axis direction, Fig. 2(a). These hydrogen bonds also lead to the formation of 12-membered {⋯HO⋯HNCS}2 and 14-membered {⋯OC2NCNH}2 synthons, each disposed about a centre of inversion, and linked via the edges defined by the amine-N—H⋯O(hydroxyl) hydrogen bonds. The tape has a step-ladder topology and projecting laterally to either side of the tape are the remaining amine-H and carbonyl-O atoms, which form the donors and acceptors of amine-N—H⋯O(carbonyl) hydrogen bonds to link the tapes into a layer in the ac plane, Fig. 2(b). The directional links between layers are twofold, namely π–π stacking between the centrosymmetrically related benzene rings [inter-centroid separation = 3.8722 (7)° for 2 − x, 1 − y, 1 − z] and parallel C=O⋯π interactions, Table 1 and Fig. 2(c). These interactions are possible owing to the inter-digitation of the benzene rings along the b-axis direction, as highlighted in Fig. 2(d).
4. Hirshfeld surface analysis
Structure (I) was subjected to a Hirshfeld surface analysis in order to gain further understanding into the molecular interactions existing within the crystal. This was achieved through Crystal Explorer 17 (Turner et al., 2017) using established methods (Tan, Jotani et al., 2019). A list of dnorm contact distances for all identified interactions is given in Table 2. As noted from Fig. 3, several red spots of variable intensity were identified on the Hirshfeld surface of (I), being indicative of close interactions with contact distances shorter than the sum of the respective van der Waals (vdW) radii (Spackman & Jayatilaka, 2009). In particular, the most intense red spot is observed for the amine-N1—H2N⋯O1(hydroxyl) hydrogen bond with a dnorm distance of 1.92 Å, which is significantly shorter, by 0.69 Å [= Δ|(dnorm – ΣvdW)H⋯O| in Table 2], than the vdW value of 2.61 Å (adjusted to neutron values). Other prominent features are due to the hydroxyl-O1—H1O⋯S1(thione) and amine-N1—H1N⋯O3(carbonyl) hydrogen bonds. Less intense features on the dnorm maps of Fig. 3 are due to benzene-C9—H9⋯C1(thione) and methylene-C3—H3B⋯H8(benzene) interactions, and the diminutive spots arise from weaker methylene-C5⋯O3(carbonyl), methylene-C2—H2A⋯S1(thione) and benzene-C9—H9⋯S1(thione) contacts at distances just shorter or approximately equivalent to the values of the respective ΣvdW radii. Apart from the conventional hydrogen bonds and other interactions involving hydrogen, several interactions involving the aromatic ring are apparent.
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Thus, π(benzene)–π(benzene) interactions, with an inter-centroid separation = 3.8722 (7) Å, as well as parallel C6=O3⋯Cg(C7–C11) interactions, occurring on either side of a reference benzene ring, are validated through further Hirshfeld surface analysis. The presence of π–π interactions are supported by the shape complementarity between the aromatic rings as evidenced from the planar stacking arrangement illustrated through the Hirshfeld surface mapped with curvedness in Fig. 4(a). As for the C=O⋯π interaction, the shape-index on the Hirshfeld surface reveals that there are complementary concave and convex shapes indicated by the red and blue regions around the centre of aromatic ring and ester-C6 atom, respectively, in Fig. 4(b). This suggests the interaction could involve a significant contribution from the C6 atom; the C6⋯Cg(benzene) separation is 3.5026 (11) Å as opposed to the O3⋯Cg(benzene) separation of 3.6604 (10) Å, Table 1.
In order to confirm the above findings, particularly the short contacts as well as the interactions involving the aromatic ring, electrostatic potential (ESP) mapping was also performed on the Hirshfeld surface using the DFT-B3LYP quantum level of theory and 6-31G(d,p) basis set as available in Crystal Explorer 17 (Turner et al., 2017). The ESP charge for each H-atom donor and acceptor of the relevant close contacts are tabulated in Table 3. As expected for the conventional hydrogen bonds detected through PLATON (Spek, 2020), significant differences are observed in the electrostatic potentials of the hydrogen-bond donor and acceptor atoms, indicating a strong attraction. Similar observations are noted for the other identified contacts but with smaller differences with the notable exception of the methylene-C3—H3B⋯H8(benzene) contact, for which both interacting hydrogen atoms exhibit a positive electrostatic potential signifying that the interaction is dispersive in nature. As for the π–π interaction, it has already been established that the contacts arise to charge complementarity between the rings. Concerning the C=O3⋯π contact, occurring between benzene rings separated by an inter-centroid separation of 4.5890 (7) Å, the ester-C6 atom exhibits positive ESP of +0.0127 a.u. on one side to complement the negative ESP of −0.0114 a.u. at the centre of the aromatic ring it interacts with, Fig. 5(a). At the same time it has an ESP charge of +0.0223 a.u. on the reverse side that complements the other side of a symmetry related aromatic ring, involved in the π–π contact with an inter-centroid distance of 3.8722 (7) Å, with the ESP charge of −0.0091 a.u., Fig. 5(b).
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The close contacts were also investigated through fingerprint plot analysis, shown in the upper views of Fig. 6. The dnorm-mapped Hirshfeld surfaces for the most prominent point-to-point interactions, giving rise to the most discernible peaks in the fingerprint plots, are shown in the lower views of Fig. 6. In general, (I) exhibits a paw-like, overall fingerprint profile, Fig. 6(a), which can be mainly delineated into H⋯H (51.1%), H⋯O/ O⋯H (14.6%), H⋯S/ S⋯H (14.5%), H⋯C/ C⋯H (7.2%), C⋯C (6.0%) contacts, Fig. 6(b)–(e), as well as other minor contacts which constitute about 6.0% of the remaining contacts. A further analysis on the respective fingerprint plots shows that the distribution for the (internal)-O⋯H-(external), (internal)-S⋯H-(external) and (internal)-C⋯H-(external) are slightly more dominant than the (internal)-H⋯X-(external) counterparts (X = O, S, and C), with the distribution being 8.0, 9.3 and 4.0% as against 6.6, 5.2 and 3.2%, respectively. These results tally with the fact that (I) has more hydrogen-bond acceptors than hydrogen-bond donor atoms. Nonetheless, both (internal)-X⋯H-(external) and (internal)-H⋯X-(external) exhibit equivalent contact distances that are tipped at the minimum di + de values, which correspond to the specified contacts in Table 2.
5. Computational chemistry
The calculation of the interaction energy for all pairwise molecules in (I) was performed through Crystal Explorer 17 (Turner et al., 2017) with the purpose of studying the strength of each interaction/set of interactions identified from the Hirshfeld surface analysis. Hence, the electrostatic (Eele), polarization (Epol), dispersion (Edis) and exchange-repulsion (Erep) terms were calculated with the results tabulated in Table 4.
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Among all the interactions, it is the amine-N1—H2N⋯O1(hydroxyl) hydrogen bond, that closes the connected 12-membered {⋯HO⋯HNCS}2 and 14-membered {⋯OC2NCNH}2 synthons, that has the greatest interaction energy, Eint = −85.6 kJ mol−1. Next most stabilizing are the amine-N1—H1N⋯O3(carbonyl) and methylene-C5⋯O3(carbonyl) contacts between centrosymmetrically related molecules [−66.1 kJ mol−1], the ester-C6⋯π(benzene), benzene-C9—H9⋯S1(thione) and benzene-C9–H9⋯C1(thione) contacts with a combined Eint of −48.3 kJ mol−1 and hydroxyl-O1–H1O⋯S1(thione) [−28.8 kJ mol−1]. Close in energy to latter is that due to π–π [Cg1⋯Cg1 = 3.8722 (7) Å] with Eint = −28.3 kJ mol−1. Next most significant are the pairwise ethylene-C2—H2A⋯S1(thione) interactions (Eint = −23.1 kJ mol−1) then methylene-C3—H3B⋯H8(benzene) (Eint = −4.3 kJ mol−1).
The crystal of (I) is mainly sustained by electrostatic forces owing to the presence of the relatively strong hydrogen-bonding interactions, viz. amine-N1—H1N⋯O3(carbonyl) that propagates along the c axis together with amine-N1—H2N⋯O1(hydroxyl) and hydroxyl-O1—H1O⋯S1(thione), which extend along the a axis, thereby forming a step-ladder framework as shown in Fig. 7(a). On the other hand, significant dispersion force is also present as evidenced from the wire mesh-like dispersion energy framework predominantly governed by the π–π interactions, with contributions from the interactions involving the benzene-C9 atom, Fig. 7(b). Overall, the combination of electrostatic and dispersion forces leads to a cuboid-like framework shown in Fig. 7(c).
6. Database survey
Crystal-structure determinations of organic molecules of the general formula R(R′)NC(=S)NH2 are comparatively rare with the simplest derivative being the R = R′ = Me species, the almost planar molecule being first reported in 1994 (WIFKOL; Pathirana et al., 1994). Similarly, derivatives bearing hydroxyl groups are uncommon and include the relatively simple derivatives shown in Fig. 8, i.e. acyclic (II) (IYAYAJ; Griffiths et al., 2010) and cyclic imidazolidine-2-thione (III) (DOJSUT; Lee et al., 2018).
7. Synthesis and crystallization
Compound (I) was synthesized by gently heating an acetone mixture (30 ml) containing ammonium thiocyanate (Fisher, 1 mmol), benzoyl chloride (Acros, 1 mmol) and bis(hydroxyethyl)amine (Acros, 1 mmol). The solution was concentrated to half of the initial volume under heating and a white precipitate was obtained upon cooling the solution to room temperature. Colourless blocks were formed through recrystallization of the crude product from acetone solution. M.p. 388.6–390.1 K. IR (cm−1): 3419 ν(OH), 3323 ν(NH2)asym, 3222 ν(NH2)sym, 3058 ν(CH)arom, 3002–2881 ν(CH), 1706 ν(COO), 1647 ν(C=O), 1600 δ(NH), 1523 ν(C=C), 1270 ν(CN), 1053 ν(C=S), 711 δ(CH).
8. Refinement
Crystal data, data collection and structure . The carbon-bound H atoms were placed in calculated positions (C—H = 0.95–0.98 Å) and were included in the in the riding-model approximation, with Uiso(H) set to 1.2Ueq(C). The oxygen- and nitrogen-bound H atoms were located from a difference-Fourier map and refined with O—H = 0.84±0.01 Å and N—H = 0.88±0.01 Å, and with Uiso(H) set to 1.5Ueq(O) or 1.2Ueq(N).
details are summarized in Table 5
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Supporting information
CCDC reference: 2004940
https://doi.org/10.1107/S2056989020006829/hb7918sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020006829/hb7918Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989020006829/hb7918Isup3.cml
Data collection: CrysAlis PRO (Rigaku OD, 2018); cell
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).C12H16N2O3S | Z = 2 |
Mr = 268.33 | F(000) = 284 |
Triclinic, P1 | Dx = 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 |
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 | Rint = 0.028 |
Detector resolution: 5.2558 pixels mm-1 | θmax = 76.6°, θmin = 4.5° |
ω scans | h = −8→9 |
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2018) | k = −11→11 |
Tmin = 0.656, Tmax = 1.000 | l = −12→11 |
15863 measured reflections |
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(Fo2) + (0.0387P)2 + 0.2837P] where P = (Fo2 + 2Fc2)/3 |
2608 reflections | (Δ/σ)max = 0.001 |
172 parameters | Δρmax = 0.28 e Å−3 |
3 restraints | Δρmin = −0.29 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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) |
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···Cg1iv | 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. |
Contact | Distance | ΣvdW | Δ|(dnorm - ΣvdW)| | Symmetry operation |
H2N···O1b | 1.92 | 2.61 | 0.69 | 1 - x, - y, 2 - z |
H1O···S1b | 2.21 | 2.89 | 0.68 | 1 + x, y, z |
H1N···O3b | 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. |
Contact | Electrostatic potential, VESP (a.u.) | Δ|VESP| | |
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 |
Contact | Eele | Epol | Edis | Erep | Etot | 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 |
Funding information
Crystallographic research at Sunway University is supported by Sunway University Sdn Bhd (grant No. STR-RCTR-RCCM-001-2019).
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