research communications
4-Nitrobenzyl 3,4-bis(acetyloxy)-2-(4-methoxyphenyl)pyrrolidine-1-carboxylate:
Hirshfeld surface analysis and computational chemistryaLaboratório de Cristalografia, Esterodinâmica e Modelagem Molecular, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil, bDepartmento de Física, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil, cInstituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil, dInstituto de Química, Universidade Estadual de Campinas, UNICAMP, C.P. 6154, CEP 13084-917 Campinas, Brazil, and eResearch Centre for Crystalline Materials, School of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
*Correspondence e-mail: ignez@df.ufscar.br
The title compound, C23H24N2O9, is a tetra-substituted pyrrolidine derivative with a twisted conformation, with the twist evident in the C—C bond bearing the adjacent acetyloxy substituents. These are flanked on one side by a C-bound 4-methoxyphenyl group and on the other by a methylene group. The almost sp2-N atom [sum of angles = 357°] bears a 4-nitrobenzyloxycarbonyl substituent. In the crystal, ring-methylene-C—H⋯O(acetyloxy-carbonyl) and methylene-C—H⋯O(carbonyl) interactions lead to supramolecular layers lying parallel to (01); the layers stack without directional interactions between them. The analysis of the calculated Hirshfeld surfaces indicates the combined importance of H⋯H (42.3%), H⋯O/O⋯H (37.3%) and H⋯C/C⋯H (14.9%) surface contacts. Further, the interaction energies, largely dominated by the dispersive term, point to the stabilizing influence of H⋯H and O⋯O contacts in the inter-layer region.
Keywords: crystal structure; pyrrolidine; Hirshfeld surface analysis; NCI plots; computational chemistry.
CCDC reference: 2009242
1. Chemical context
The structure of the title tetra-substituted pyrrolidine derivative, (I), was determined in connection with our on-going structural studies characterizing key synthetic intermediates in the synthesis of various α-glucosidase inhibitors (Zukerman-Schpector et al., 2017; Dallasta Pedroso et al., 2020). α-Glucosidase inhibitors are an important class of drugs employed in the treatment of a variety of diseases such as cancer, cystic fibrosis, diabetes and influenza (Kiappes et al., 2018; Dhameja & Gupta, 2019).
More specifically, (I) was generated during a study designed to synthesize the hydroxylated proline derivative, (2R,3S,4R)-3,4-dihydroxypyrrolidine-2-carboxylic acid, (II) (Garcia, 2008). In addition to being an α-glucosidase inhibitor, (II) is also found as a sub-structure of natural bioactive compounds such as, for example, a component of the repeated deca-peptide sequence of the adhesive protein Mytilus edulis foot protein 1 (Mefp1), which is produced by the marine mussel Mytilus edulis and is responsible for the fixation capacity of the mussel to rock (Taylor & Weir, 2000). The synthetic study determined that in the final stages of the reaction sequence towards (II), it was not possible to smoothly remove the N-bound 4-nitrobenzyloxycarbonyl (PNZ) protecting group via catalytic hydrogenation as the ensuing mixture was difficult to purify. Therefore, it proved necessary to remove the PNZ protecting group through acid hydrolysis at reflux temperature, resulting in a low overall yield (34%) suggesting that there was no advantage in using PNZ.
The crystal and molecular structures of (I) are described herein with this experimental study complemented by a detailed analysis of the molecular packing by a combination of Hirshfeld surface analysis, non-covalent interaction plots and computational chemistry.
2. Structural commentary
The molecular structure of (I), Fig. 1, is constructed about a tetra-substituted pyrrolidine ring with a N1-bound (4-nitrophenyl)ethylcarboxylate group and, respectively, C1–C3-bound 4-methoxyphenyl, acetyloxy and acetyloxy substituents. For the illustrated molecule, Fig. 1, the of the C1–C3 atoms follows the sequence R, R and S, but it is noted that due crystal symmetry, the centrosymmetric contains equal numbers of the enantiomers. The conformation of the five-membered ring is twisted about the C2—C3 bond with the C1—C2—C3—C4 torsion angle being 39.70 (16)°, consistent with a (+)syn-clinal configuration. The sum of the angles about the N1 atom is 356.7°, indicating an approximate sp2 centre. The N1-bound group occupies an equatorial position with those at the C1–C3 centres being bisectional, equatorial and axial, respectively (Spek, 2020). When viewed towards the approximate plane through the pyrrolidine ring, the N-bound carboxylate group is approximately co-planar, i.e. excluding the nitrobenzene residue. The C1-substituent lies to the opposite side of the plane than the C2 and C3-acetyloxy groups; the dihedral angle between the acetyloxy CO2 planes is 57.7 (2)°.
With respect to the least-squares plane through the pyrrolidine ring, the nitrobenzene and methoxybenzene rings are splayed, as seen in the dihedral angles of 58.58 (8) and 77.65 (6)°, respectively; the dihedral angle between the benzene rings is 50.56 (5)°. There is a twist in the nitrobenzene ring as seen in the value of the C11—C10—N2—O4 torsion angle of 17.7 (3)°. By contrast, the methoxy group is co-planar with the ring to which it is connected, as shown by the C15—C16—O5—C19 torsion angle of 176.2 (2)°.
3. Supramolecular features
The only directional non-covalent interactions of note in the crystal of (I) are two weak C—H⋯O contacts as listed in Table 1. The presence of ring-methylene-C4—H⋯O7(acetyloxy-carbonyl) interactions lead to helical chains along the b-axis direction, being propagated by 21 symmetry. The other interactions falling within the distance criteria of PLATON (Spek, 2020) are methylene-C6—H⋯O1(carbonyl) interactions, formed between centrosymmetrically related (4-nitrophenyl)ethylcarboxylate groups, which lead to the formation of ten-membered {⋯OCOCH}2 synthons. These serve to connect the helical chains into a layer lying parallel to (01), Fig. 2(a). A view of the unit-cell contents is shown in Fig. 2(b), highlighting the stacking of layers, without directional interactions between them.
4. Non-covalent interaction plots
The aforementioned weak C—H⋯O contacts identified in Supramolecular features were also evaluated by calculating non-covalent interaction plots (Johnson et al., 2010; Contreras-García et al., 2011). In short, these calculations indicate whether non-bonding contacts are attractive, weakly attractive or repulsive. The methylene-C6—H⋯O1(carbonyl) interactions giving rise to the ten-membered {⋯OCOCH}2 synthons are highlighted in the upper view of Fig. 3(a) with the green isosurface between the interacting atoms and the distinctive blue feature in the reduced density gradient (RDG) versus sign(λ2)ρ(r) plot in the lower view, i.e. indicating the density value is less than 0.0 a.u., suggest these interactions are weakly attractive. The same is true for the ring-methylene-C4—H⋯O7(acetyloxy-carbonyl) interactions that lead to the helical chain, Fig. 3(b).
5. Hirshfeld surface analysis
The Hirshfeld surface analysis of (I) involved the calculation of the dnorm-surface plots, electrostatic potential (calculated using the STO-3G basis set at the Hartree–Fock level of theory) and two-dimensional fingerprint plots following literature procedures (Tan et al., 2019) using Crystal Explorer 17 (Turner et al., 2017). The weak methylene-C6—H⋯O1(carbonyl) interactions are reflected as bright-red spots near the methylene-H6A and carbonyl-O1 atoms on the dnorm-surface plot of (I) shown in Fig. 4. Additional diffuse red spots are also noted near the methoxy-O5 and carbonyl-O7 atoms in Fig. 4, which reflect their participation in short C5⋯O5 and C4⋯O7 contacts with separations ∼0.1 Å shorter than the sum of their van der Waals radii, Table 2. Further, faint spots near atom H4B as well as the O5 and O7 atoms (each difficult to discern in Fig. 4) are attributed to methylene-C4—H4B⋯O7(carbonyl) and O2⋯O5 short contacts, being ∼0.02 Å shorter than their respective sums of the van der Waals radii, Table 2.
In the views of Fig. 5, the faint red spots that appear near the methylene (H6B), benzyl (C15 and H9), methyl (C21) and nitro (O4) atoms correspond to long-range intra-layer methylene-C6—H6B⋯C15(benzyl), benzyl-C9—H9⋯C21(methyl) interactions and inter-layer O4⋯O4 short contacts, Table 2. The Hirshfeld surface mapped over the electrostatic potential in Fig. 6 highlights the donors and acceptors of the indicated interactions through blue (positive electrostatic potential) and red (negative electrostatic potential), respectively.
As illustrated in Fig. 7(a), the two-dimensional fingerprint plot for the Hirshfeld surface of (I) is shown in the upper left and lower right sides of the de and di diagonal axes, and those delineated into H⋯H, H⋯O/O⋯H, H⋯C/C⋯H, O⋯O and O⋯C/C⋯O contacts are illustrated in Fig. 7(b)–(f), respectively. The percentage contributions from different interatomic contacts are summarized in Table 3. The H⋯H contacts contribute 42.3% to the overall Hirshfeld surface with the shortest contact, manifested in the round-shape peak tipped at de = di ∼2.4 Å, Fig. 7(b), corresponding to the H17⋯H23B inter-layer contact listed in Table 2. The H⋯O/O⋯H contacts contribute 37.3% to the overall Hirshfeld surface, reflecting the significant C—H⋯O contacts evident in the packing, Tables 1 and 2. The shortest contacts are reflected as two sharp spikes at de + di ∼2.5 Å in Fig. 7(c). The H⋯C/C⋯H contacts that match the long-range C—H⋯C interactions discussed above are shown as a pairs of forceps-like tips at de + di ∼2.7 Å in the fingerprint plot delineated into H⋯C/C⋯H contacts, Fig. 7(d). Although both O⋯O and O⋯C/C⋯O contacts appear at de + di ∼3.0 Å in the respective fingerprint plots, Fig. 7(e) and (f), their contributions to the overall Hirshfeld surface are only 2.1 and 1.2%, respectively. The other interatomic contacts have a negligible effect on the molecular packing as their accumulated contribution is about 2.2%.
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6. Energy frameworks
The pairwise interaction energies between the molecules in the crystal of (I) were calculated by summing up four energy components, comprising the electrostatic (Eele), polarization (Epol), dispersion (Edis) and exchange-repulsion (Erep) energies as per the literature (Turner et al., 2017). In the present study, the energy framework of (I) was generated by employing the 6-31G(d,p) basis set with the B3LYP function. The individual energy components as well as the total interaction energies are collated in Table 4. As anticipated, the dispersive component makes the major contribution to the interaction energies owing to the absence of conventional hydrogen bonding in the crystal. The most significant stabilization energies are found in the intra-layer region and arise from the directional contacts outlined in Hirshfeld surface analysis as well as two additional C—H⋯O interactions, i.e. methylene-C4—H4A⋯O4(nitro) and methyl-C21—H21C⋯O4(nitro) with H⋯O separations of 2.63 and 2.77 Å, respectively.
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The stabilization energies in the inter-layer region are also dominated by the Edis terms associated with the H⋯H contacts as well as the long-range C—H⋯O interactions (−14.4 kJ mol−1). For the former, the maximum energy is not found for the shortest H17⋯H23B contact (−7.1 kJ mol−1), Table 2 and Fig. 8(b), but rather for a pair of benzene-H⋯H(methyl) interactions occurring in close proximity in a hydrogen-rich region but at longer separations (−34.2 kJ mol−1). For the inter-layer O4⋯O4 contact mentioned above, there are almost equal contributions from Eele and Edis, Table 4, giving rise to a total interaction energy of −27.7 kJ mol−1. The magnitudes of intermolecular energies are represented graphically in Fig. 8, and clearly demonstrate the dominance of the Edis in the molecular packing.
7. Database survey
There are relatively few related structures having a similar substitution pattern to the tetra-substituted pyrrolidine ring of (I). The chemical diagrams for the two most closely related structures, (III), which has two hydroxyl substituents rather than acetyloxy (ALAVOA; Qian et al., 2016), and (IV), which has more complex substituents (RAJDUC; Coleman et al., 2004), are shown in Fig. 9.
8. Synthesis and crystallization
To a solution of 4-nitrobenzyl (2S,3S,4R)-3,4-dihydroxy-2-(4-methoxyphenyl)pyrrolidine-1-carboxylate (602 mg, 1.55 mmol) in CH2Cl2 (15 ml) were added pyridine (0.80 ml, 18.584 mmol), acetic anhydride (3.00 ml, 31.8 mmol) and N,N-dimethyl-4-aminopyridine (2.00 mg, 0.0164 mmol). The solution was stirred for 2 h at room temperature, concentrated in a rota-evaporator and the residue dissolved in EtOAc (10 ml). The resulting solution was washed with a HCl 5% solution (3 × 5 ml) and with saturated solutions of NaHCO3 (2 × 5 ml) and of NaCl (5 ml). The phases were separated and the organic phase was dried with anhydrous Na2SO4, filtered and concentrated in vacuo.
The residue was purified by flash n-hexane elution gradient (1:3 and 1:2). Yield: 716 mg (98%). Colourless irregular crystals for the X-ray analysis were obtained by the slow evaporation of its n-hexane solution. M.p. 409.5–410.5 K. The 1H and 13C{1H} NMR reflect the presence of two conformational rotamers in solution. 1H NMR (500 MHz, C6D6): δ = 7.75 (d, J = 7.3 Hz, 0.4H); 7.65 (d, J = 7.9 Hz, 1.2H); 7.18 (m, 1.9H); 6.99 (d, J = 7.9 Hz, 1.1H); 6.76 (d, J = 7.0 Hz, 0.5H); 6.72 (d, J = 7.3 Hz, 0.6H); 6.65 (d, J = 7.9 Hz, 1.3H); 6.37 (d, J = 9.3 Hz, 1H); 5.42 (s, 0.2H); 5.33 (m, 1.9H); 5.00 (s, 0.5H); 4.92 (d, J = 13.7 Hz, 0.6H); 4.74 (s, 0.6H); 4.44 (d, J = 13.7 Hz, 0.6H); 3.89 (m, 1.8H); 3.72 (s, 0.3H); 3.29 (s, 3H); 3.35–3.23 (m, 0.3H); 1.61–1.60 (2s, 6H). 1H NMR (500 MHz, CDCl3, TMS r.t.): δ = 8.23 (d, J = 8.2 Hz, 0.6H); 8.00 (d, J = 8.2 Hz, 1.2H); 7.53 (d, J = 7.9 Hz, 0.7H); 7.16 (m, 2H); 6.96 (d, J = 8.5 Hz, 1.2H); 6.88 (d, J = 8.5 Hz, 2.0H); 5.45–5.32 (m, 1H); 5.31–5.18 (m, 2.3H); 5.01–4.87 (m, 1.6H); 4.13 (m, 0.3H); 4.06 (dd, J = 11.6 Hz and 6.4 Hz, 0.7H); 3.85–3.67 (s + m, 4.1H); 2.12-2.07 (4s, 6H). 13C{1H} NMR (125 MHz, CDCl3, r.t.): δ = 169.9; 169.8; 159.4; 159.2; 154.2; 154.1; 147.6; 147.2; 143.6; 143.4; 130.6; 129.4; 128.1; 127.5; 126.8; 126.7; 123.7; 123.4; 114.2; 78.2; 69.2; 68.7; 65.7; 65.5; 64.7; 64.1; 55.3; 55.2; 49.0; 48.4; 20.8; 20.7; 20.6.
in silica gel, using an EtOAc/9. details
Crystal data, data collection and structure . The carbon-bound H atoms were placed in calculated positions (C—H = 0.93–0.98 Å) and were included in the in the riding model approximation, with Uiso(H) set to 1.2–1.5Ueq(C).
details are summarized in Table 5
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Supporting information
CCDC reference: 2009242
https://doi.org/10.1107/S2056989020007914/hb7923sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020007914/hb7923Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989020007914/hb7923Isup3.cml
Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1989); cell
CAD-4 EXPRESS (Enraf–Nonius, 1989); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SIR2014 (Burla et al., 2015); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), MarvinSketch (ChemAxon, 2010) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).C23H24N2O9 | F(000) = 1984 |
Mr = 472.44 | Dx = 1.376 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
a = 23.6396 (5) Å | Cell parameters from 9984 reflections |
b = 8.2906 (2) Å | θ = 2.6–25.4° |
c = 24.7683 (5) Å | µ = 0.11 mm−1 |
β = 110.013 (1)° | T = 293 K |
V = 4561.13 (18) Å3 | Irregular, colourless |
Z = 8 | 0.40 × 0.36 × 0.18 mm |
Enraf–Nonius TurboCAD-4 diffractometer | Rint = 0.020 |
Radiation source: Enraf–Nonius FR590 | θmax = 25.4°, θmin = 1.8° |
non–profiled ω/2θ scans | h = −28→28 |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | k = −7→10 |
Tmin = 0.686, Tmax = 0.745 | l = −29→29 |
22357 measured reflections | 3 standard reflections every 120 min |
4172 independent reflections | intensity decay: 2% |
3646 reflections with I > 2σ(I) |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.112 | H-atom parameters constrained |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0475P)2 + 5.1476P] where P = (Fo2 + 2Fc2)/3 |
4172 reflections | (Δ/σ)max = 0.001 |
310 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.22 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 | ||
C1 | 0.41109 (7) | 0.33440 (18) | 0.82213 (6) | 0.0313 (3) | |
H1 | 0.439778 | 0.265045 | 0.812398 | 0.038* | |
C2 | 0.35064 (7) | 0.33405 (19) | 0.77230 (7) | 0.0336 (4) | |
H2 | 0.327740 | 0.430457 | 0.774943 | 0.040* | |
C3 | 0.31777 (7) | 0.1856 (2) | 0.78170 (7) | 0.0378 (4) | |
H3 | 0.274273 | 0.192051 | 0.761254 | 0.045* | |
C4 | 0.33330 (7) | 0.1864 (2) | 0.84615 (7) | 0.0403 (4) | |
H4A | 0.304809 | 0.251133 | 0.857137 | 0.048* | |
H4B | 0.333567 | 0.077780 | 0.860767 | 0.048* | |
C5 | 0.43296 (7) | 0.20974 (18) | 0.91863 (7) | 0.0345 (4) | |
C6 | 0.53264 (8) | 0.2143 (2) | 0.98048 (8) | 0.0528 (5) | |
H6A | 0.542252 | 0.103154 | 0.974917 | 0.063* | |
H6B | 0.516931 | 0.217441 | 1.011878 | 0.063* | |
C7 | 0.58827 (8) | 0.3154 (2) | 0.99508 (7) | 0.0417 (4) | |
C8 | 0.64314 (9) | 0.2417 (3) | 1.02204 (9) | 0.0565 (5) | |
H8 | 0.644787 | 0.130582 | 1.027501 | 0.068* | |
C9 | 0.69526 (9) | 0.3306 (3) | 1.04088 (10) | 0.0645 (6) | |
H9 | 0.732107 | 0.280446 | 1.058971 | 0.077* | |
C10 | 0.69219 (8) | 0.4939 (3) | 1.03263 (8) | 0.0528 (5) | |
C11 | 0.63872 (9) | 0.5713 (3) | 1.00515 (9) | 0.0544 (5) | |
H11 | 0.637581 | 0.682263 | 0.999450 | 0.065* | |
C12 | 0.58661 (8) | 0.4804 (2) | 0.98615 (8) | 0.0494 (5) | |
H12 | 0.550017 | 0.530722 | 0.967144 | 0.059* | |
C13 | 0.43684 (7) | 0.50197 (18) | 0.83547 (6) | 0.0316 (3) | |
C14 | 0.40971 (7) | 0.6175 (2) | 0.85901 (7) | 0.0372 (4) | |
H14 | 0.376437 | 0.589579 | 0.868927 | 0.045* | |
C15 | 0.43136 (8) | 0.7731 (2) | 0.86789 (8) | 0.0412 (4) | |
H15 | 0.412718 | 0.849067 | 0.883778 | 0.049* | |
C16 | 0.48067 (8) | 0.8167 (2) | 0.85329 (8) | 0.0438 (4) | |
C17 | 0.50828 (8) | 0.7033 (2) | 0.83008 (9) | 0.0513 (5) | |
H17 | 0.541530 | 0.731489 | 0.820158 | 0.062* | |
C18 | 0.48621 (8) | 0.5466 (2) | 0.82156 (8) | 0.0430 (4) | |
H18 | 0.505194 | 0.470334 | 0.806132 | 0.052* | |
C19 | 0.54992 (12) | 1.0247 (3) | 0.85250 (17) | 0.1022 (11) | |
H19A | 0.583775 | 0.962689 | 0.875791 | 0.153* | |
H19B | 0.557073 | 1.137012 | 0.861793 | 0.153* | |
H19C | 0.544479 | 1.008448 | 0.812661 | 0.153* | |
C20 | 0.31789 (8) | 0.3956 (2) | 0.67329 (7) | 0.0412 (4) | |
C21 | 0.33733 (10) | 0.4076 (3) | 0.62226 (9) | 0.0641 (6) | |
H21A | 0.341021 | 0.301250 | 0.608472 | 0.096* | |
H21B | 0.375514 | 0.461491 | 0.632865 | 0.096* | |
H21C | 0.307975 | 0.467627 | 0.592548 | 0.096* | |
C22 | 0.31168 (8) | −0.0347 (2) | 0.71859 (8) | 0.0416 (4) | |
C23 | 0.34279 (10) | −0.1848 (2) | 0.71099 (9) | 0.0565 (5) | |
H23A | 0.329284 | −0.273887 | 0.728173 | 0.085* | |
H23B | 0.385482 | −0.171936 | 0.729165 | 0.085* | |
H23C | 0.333649 | −0.205264 | 0.670751 | 0.085* | |
N1 | 0.39393 (6) | 0.25809 (16) | 0.86773 (6) | 0.0352 (3) | |
N2 | 0.74834 (9) | 0.5888 (3) | 1.05360 (8) | 0.0727 (6) | |
O1 | 0.41991 (6) | 0.12222 (15) | 0.95189 (5) | 0.0462 (3) | |
O2 | 0.48803 (5) | 0.27396 (14) | 0.92893 (5) | 0.0394 (3) | |
O3 | 0.79605 (8) | 0.5171 (3) | 1.06567 (10) | 0.1097 (8) | |
O4 | 0.74408 (9) | 0.7331 (3) | 1.05857 (8) | 0.0893 (6) | |
O5 | 0.49776 (7) | 0.97485 (16) | 0.86316 (8) | 0.0654 (4) | |
O6 | 0.36272 (5) | 0.33834 (15) | 0.71959 (5) | 0.0410 (3) | |
O7 | 0.26983 (6) | 0.4321 (2) | 0.67504 (6) | 0.0632 (4) | |
O8 | 0.34399 (5) | 0.04280 (14) | 0.76655 (5) | 0.0441 (3) | |
O9 | 0.26372 (7) | 0.0104 (2) | 0.68714 (6) | 0.0684 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0301 (8) | 0.0308 (8) | 0.0299 (8) | 0.0021 (6) | 0.0061 (6) | 0.0014 (6) |
C2 | 0.0311 (8) | 0.0356 (8) | 0.0303 (8) | 0.0036 (6) | 0.0057 (6) | −0.0026 (6) |
C3 | 0.0270 (8) | 0.0371 (9) | 0.0431 (9) | 0.0004 (6) | 0.0039 (7) | −0.0050 (7) |
C4 | 0.0319 (8) | 0.0426 (9) | 0.0435 (9) | −0.0059 (7) | 0.0091 (7) | 0.0002 (7) |
C5 | 0.0390 (9) | 0.0266 (7) | 0.0342 (8) | 0.0002 (6) | 0.0075 (7) | 0.0010 (7) |
C6 | 0.0460 (10) | 0.0521 (11) | 0.0440 (10) | −0.0034 (9) | −0.0057 (8) | 0.0169 (9) |
C7 | 0.0402 (9) | 0.0491 (10) | 0.0295 (8) | −0.0012 (8) | 0.0037 (7) | 0.0018 (7) |
C8 | 0.0469 (11) | 0.0589 (12) | 0.0545 (12) | 0.0051 (9) | 0.0055 (9) | 0.0106 (10) |
C9 | 0.0381 (10) | 0.0846 (17) | 0.0617 (13) | 0.0065 (10) | 0.0053 (9) | 0.0104 (12) |
C10 | 0.0394 (10) | 0.0797 (15) | 0.0384 (10) | −0.0140 (10) | 0.0121 (8) | −0.0139 (10) |
C11 | 0.0595 (12) | 0.0502 (11) | 0.0546 (12) | −0.0096 (9) | 0.0207 (10) | −0.0123 (9) |
C12 | 0.0407 (10) | 0.0497 (11) | 0.0518 (11) | 0.0012 (8) | 0.0082 (8) | −0.0019 (9) |
C13 | 0.0315 (8) | 0.0317 (8) | 0.0264 (7) | −0.0002 (6) | 0.0032 (6) | 0.0023 (6) |
C14 | 0.0380 (9) | 0.0376 (9) | 0.0369 (9) | −0.0017 (7) | 0.0140 (7) | 0.0002 (7) |
C15 | 0.0452 (10) | 0.0365 (9) | 0.0411 (9) | 0.0006 (7) | 0.0139 (8) | −0.0052 (7) |
C16 | 0.0407 (9) | 0.0327 (9) | 0.0521 (11) | −0.0051 (7) | 0.0085 (8) | −0.0015 (8) |
C17 | 0.0409 (10) | 0.0440 (10) | 0.0746 (14) | −0.0085 (8) | 0.0269 (10) | −0.0028 (9) |
C18 | 0.0395 (9) | 0.0381 (9) | 0.0541 (11) | 0.0003 (7) | 0.0195 (8) | −0.0042 (8) |
C19 | 0.0737 (17) | 0.0508 (14) | 0.194 (4) | −0.0262 (13) | 0.061 (2) | −0.0194 (18) |
C20 | 0.0432 (10) | 0.0369 (9) | 0.0345 (9) | 0.0017 (7) | 0.0017 (7) | −0.0005 (7) |
C21 | 0.0683 (14) | 0.0829 (16) | 0.0367 (10) | −0.0014 (12) | 0.0123 (10) | 0.0033 (10) |
C22 | 0.0423 (10) | 0.0399 (9) | 0.0401 (9) | −0.0079 (7) | 0.0110 (8) | −0.0029 (7) |
C23 | 0.0630 (13) | 0.0459 (11) | 0.0595 (13) | −0.0002 (9) | 0.0196 (10) | −0.0112 (9) |
N1 | 0.0330 (7) | 0.0341 (7) | 0.0328 (7) | −0.0050 (6) | 0.0042 (6) | 0.0035 (6) |
N2 | 0.0582 (12) | 0.1074 (18) | 0.0531 (11) | −0.0282 (12) | 0.0200 (9) | −0.0212 (11) |
O1 | 0.0504 (7) | 0.0427 (7) | 0.0422 (7) | −0.0020 (6) | 0.0116 (6) | 0.0132 (6) |
O2 | 0.0364 (6) | 0.0372 (6) | 0.0338 (6) | −0.0042 (5) | −0.0019 (5) | 0.0075 (5) |
O3 | 0.0421 (10) | 0.154 (2) | 0.1255 (18) | −0.0190 (12) | 0.0188 (10) | −0.0200 (15) |
O4 | 0.0919 (13) | 0.1010 (15) | 0.0811 (13) | −0.0485 (12) | 0.0372 (11) | −0.0322 (11) |
O5 | 0.0564 (8) | 0.0360 (7) | 0.1062 (13) | −0.0139 (6) | 0.0308 (8) | −0.0144 (7) |
O6 | 0.0363 (6) | 0.0518 (7) | 0.0304 (6) | 0.0068 (5) | 0.0058 (5) | −0.0001 (5) |
O7 | 0.0482 (8) | 0.0815 (11) | 0.0506 (8) | 0.0230 (7) | 0.0050 (6) | 0.0112 (7) |
O8 | 0.0352 (6) | 0.0376 (6) | 0.0502 (7) | 0.0009 (5) | 0.0024 (5) | −0.0093 (5) |
O9 | 0.0561 (9) | 0.0722 (10) | 0.0559 (9) | 0.0083 (8) | −0.0077 (7) | −0.0200 (8) |
C1—N1 | 1.468 (2) | C12—H12 | 0.9300 |
C1—C13 | 1.507 (2) | C13—C18 | 1.376 (2) |
C1—C2 | 1.536 (2) | C13—C14 | 1.388 (2) |
C1—H1 | 0.9800 | C14—C15 | 1.377 (2) |
C2—O6 | 1.4293 (19) | C14—H14 | 0.9300 |
C2—C3 | 1.516 (2) | C15—C16 | 1.381 (3) |
C2—H2 | 0.9800 | C15—H15 | 0.9300 |
C3—O8 | 1.444 (2) | C16—O5 | 1.369 (2) |
C3—C4 | 1.511 (2) | C16—C17 | 1.378 (3) |
C3—H3 | 0.9800 | C17—C18 | 1.388 (3) |
C4—N1 | 1.472 (2) | C17—H17 | 0.9300 |
C4—H4A | 0.9700 | C18—H18 | 0.9300 |
C4—H4B | 0.9700 | C19—O5 | 1.409 (3) |
C5—O1 | 1.214 (2) | C19—H19A | 0.9600 |
C5—N1 | 1.344 (2) | C19—H19B | 0.9600 |
C5—O2 | 1.3476 (19) | C19—H19C | 0.9600 |
C6—O2 | 1.4371 (19) | C20—O7 | 1.191 (2) |
C6—C7 | 1.496 (3) | C20—O6 | 1.354 (2) |
C6—H6A | 0.9700 | C20—C21 | 1.488 (3) |
C6—H6B | 0.9700 | C21—H21A | 0.9600 |
C7—C8 | 1.382 (3) | C21—H21B | 0.9600 |
C7—C12 | 1.385 (3) | C21—H21C | 0.9600 |
C8—C9 | 1.373 (3) | C22—O9 | 1.195 (2) |
C8—H8 | 0.9300 | C22—O8 | 1.337 (2) |
C9—C10 | 1.368 (3) | C22—C23 | 1.490 (3) |
C9—H9 | 0.9300 | C23—H23A | 0.9600 |
C10—C11 | 1.372 (3) | C23—H23B | 0.9600 |
C10—N2 | 1.476 (3) | C23—H23C | 0.9600 |
C11—C12 | 1.382 (3) | N2—O3 | 1.218 (3) |
C11—H11 | 0.9300 | N2—O4 | 1.210 (3) |
N1—C1—C13 | 115.20 (13) | C18—C13—C1 | 120.44 (15) |
N1—C1—C2 | 101.03 (12) | C14—C13—C1 | 121.24 (14) |
C13—C1—C2 | 111.89 (12) | C15—C14—C13 | 120.91 (16) |
N1—C1—H1 | 109.5 | C15—C14—H14 | 119.5 |
C13—C1—H1 | 109.5 | C13—C14—H14 | 119.5 |
C2—C1—H1 | 109.5 | C14—C15—C16 | 120.28 (16) |
O6—C2—C3 | 115.70 (13) | C14—C15—H15 | 119.9 |
O6—C2—C1 | 108.19 (12) | C16—C15—H15 | 119.9 |
C3—C2—C1 | 105.25 (13) | O5—C16—C17 | 125.10 (17) |
O6—C2—H2 | 109.2 | O5—C16—C15 | 115.33 (17) |
C3—C2—H2 | 109.2 | C17—C16—C15 | 119.56 (16) |
C1—C2—H2 | 109.2 | C16—C17—C18 | 119.65 (17) |
O8—C3—C4 | 107.94 (14) | C16—C17—H17 | 120.2 |
O8—C3—C2 | 109.73 (13) | C18—C17—H17 | 120.2 |
C4—C3—C2 | 101.92 (13) | C13—C18—C17 | 121.37 (17) |
O8—C3—H3 | 112.2 | C13—C18—H18 | 119.3 |
C4—C3—H3 | 112.2 | C17—C18—H18 | 119.3 |
C2—C3—H3 | 112.2 | O5—C19—H19A | 109.5 |
N1—C4—C3 | 103.88 (13) | O5—C19—H19B | 109.5 |
N1—C4—H4A | 111.0 | H19A—C19—H19B | 109.5 |
C3—C4—H4A | 111.0 | O5—C19—H19C | 109.5 |
N1—C4—H4B | 111.0 | H19A—C19—H19C | 109.5 |
C3—C4—H4B | 111.0 | H19B—C19—H19C | 109.5 |
H4A—C4—H4B | 109.0 | O7—C20—O6 | 122.57 (17) |
O1—C5—N1 | 124.23 (15) | O7—C20—C21 | 126.14 (17) |
O1—C5—O2 | 124.12 (15) | O6—C20—C21 | 111.29 (16) |
N1—C5—O2 | 111.62 (14) | C20—C21—H21A | 109.5 |
O2—C6—C7 | 109.81 (15) | C20—C21—H21B | 109.5 |
O2—C6—H6A | 109.7 | H21A—C21—H21B | 109.5 |
C7—C6—H6A | 109.7 | C20—C21—H21C | 109.5 |
O2—C6—H6B | 109.7 | H21A—C21—H21C | 109.5 |
C7—C6—H6B | 109.7 | H21B—C21—H21C | 109.5 |
H6A—C6—H6B | 108.2 | O9—C22—O8 | 123.71 (17) |
C8—C7—C12 | 119.00 (18) | O9—C22—C23 | 125.35 (17) |
C8—C7—C6 | 118.12 (17) | O8—C22—C23 | 110.92 (15) |
C12—C7—C6 | 122.73 (17) | C22—C23—H23A | 109.5 |
C9—C8—C7 | 120.8 (2) | C22—C23—H23B | 109.5 |
C9—C8—H8 | 119.6 | H23A—C23—H23B | 109.5 |
C7—C8—H8 | 119.6 | C22—C23—H23C | 109.5 |
C10—C9—C8 | 119.0 (2) | H23A—C23—H23C | 109.5 |
C10—C9—H9 | 120.5 | H23B—C23—H23C | 109.5 |
C8—C9—H9 | 120.5 | C5—N1—C1 | 124.66 (13) |
C9—C10—C11 | 121.97 (19) | C5—N1—C4 | 119.39 (14) |
C9—C10—N2 | 118.7 (2) | C1—N1—C4 | 112.69 (12) |
C11—C10—N2 | 119.3 (2) | O3—N2—O4 | 124.1 (2) |
C10—C11—C12 | 118.5 (2) | O3—N2—C10 | 118.1 (2) |
C10—C11—H11 | 120.8 | O4—N2—C10 | 117.8 (2) |
C12—C11—H11 | 120.8 | C5—O2—C6 | 113.56 (13) |
C11—C12—C7 | 120.73 (18) | C16—O5—C19 | 118.13 (17) |
C11—C12—H12 | 119.6 | C20—O6—C2 | 116.07 (13) |
C7—C12—H12 | 119.6 | C22—O8—C3 | 117.36 (13) |
C18—C13—C14 | 118.23 (15) | ||
N1—C1—C2—O6 | −155.47 (12) | C15—C16—C17—C18 | 0.1 (3) |
C13—C1—C2—O6 | 81.46 (16) | C14—C13—C18—C17 | −0.7 (3) |
N1—C1—C2—C3 | −31.22 (15) | C1—C13—C18—C17 | 175.80 (16) |
C13—C1—C2—C3 | −154.29 (13) | C16—C17—C18—C13 | 0.5 (3) |
O6—C2—C3—O8 | 44.85 (17) | O1—C5—N1—C1 | −166.43 (16) |
C1—C2—C3—O8 | −74.51 (15) | O2—C5—N1—C1 | 15.2 (2) |
O6—C2—C3—C4 | 159.06 (13) | O1—C5—N1—C4 | −8.4 (3) |
C1—C2—C3—C4 | 39.70 (16) | O2—C5—N1—C4 | 173.30 (14) |
O8—C3—C4—N1 | 83.80 (15) | C13—C1—N1—C5 | −68.82 (19) |
C2—C3—C4—N1 | −31.73 (16) | C2—C1—N1—C5 | 170.43 (14) |
O2—C6—C7—C8 | −148.04 (18) | C13—C1—N1—C4 | 131.85 (14) |
O2—C6—C7—C12 | 36.3 (3) | C2—C1—N1—C4 | 11.10 (16) |
C12—C7—C8—C9 | 1.3 (3) | C3—C4—N1—C5 | −147.44 (15) |
C6—C7—C8—C9 | −174.4 (2) | C3—C4—N1—C1 | 13.09 (18) |
C7—C8—C9—C10 | 0.1 (3) | C9—C10—N2—O3 | 16.0 (3) |
C8—C9—C10—C11 | −1.2 (3) | C11—C10—N2—O3 | −163.5 (2) |
C8—C9—C10—N2 | 179.30 (19) | C9—C10—N2—O4 | −162.9 (2) |
C9—C10—C11—C12 | 0.9 (3) | C11—C10—N2—O4 | 17.7 (3) |
N2—C10—C11—C12 | −179.61 (18) | O1—C5—O2—C6 | 7.0 (2) |
C10—C11—C12—C7 | 0.6 (3) | N1—C5—O2—C6 | −174.71 (15) |
C8—C7—C12—C11 | −1.7 (3) | C7—C6—O2—C5 | −168.20 (15) |
C6—C7—C12—C11 | 173.92 (19) | C17—C16—O5—C19 | −4.5 (3) |
N1—C1—C13—C18 | 137.44 (16) | C15—C16—O5—C19 | 176.2 (2) |
C2—C1—C13—C18 | −107.93 (17) | O7—C20—O6—C2 | −4.1 (2) |
N1—C1—C13—C14 | −46.17 (19) | C21—C20—O6—C2 | 175.16 (15) |
C2—C1—C13—C14 | 68.47 (19) | C3—C2—O6—C20 | 85.09 (17) |
C18—C13—C14—C15 | 0.4 (2) | C1—C2—O6—C20 | −157.16 (13) |
C1—C13—C14—C15 | −176.07 (15) | O9—C22—O8—C3 | 2.4 (3) |
C13—C14—C15—C16 | 0.1 (3) | C23—C22—O8—C3 | −176.13 (15) |
C14—C15—C16—O5 | 179.04 (16) | C4—C3—O8—C22 | 141.18 (15) |
C14—C15—C16—C17 | −0.4 (3) | C2—C3—O8—C22 | −108.54 (16) |
O5—C16—C17—C18 | −179.27 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4B···O7i | 0.97 | 2.60 | 3.129 (2) | 115 |
C6—H6A···O1ii | 0.97 | 2.54 | 3.250 (2) | 130 |
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) −x+1, −y, −z+2. |
Contact | Distance | Symmetry operation |
C6—H6A···O1b | 2.47 | -x + 1, -y, -z + 2 |
C4—H4B···O7b | 2.55 | -x + 1/2, y - 1/2, -z + 3/2 |
C4···O7 | 3.13 | -x + 1/2, y + 1/2, -z + 3/2 |
C5···O5 | 3.08 | x, y - 1, z |
O2···O5 | 3.02 | x, y - 1, z |
C6—H6B···C15 | 2.73 | -x + 1, -y + 1, -z + 2 |
C9—H9···C21 | 2.75 | x + 1/2, -y + 1/2, z + 1/2 |
O4···O4 | 2.75 | -x + 3/2, -y + 3/2, -z + 2 |
H17···H23B | 2.35 | -x + 1, y + 1, -z + 3/2 |
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 the interactions listed in Table 1. |
Contact | Percentage contribution |
H···H | 42.3 |
H···O/O···H | 37.3 |
H···C/C···H | 14.9 |
O···O | 2.1 |
O···C/C···O | 1.2 |
Others | 2.2 |
Contact | R (Å) | Eele | Epol | Edis | Erep | Etot |
Intra-layer region | ||||||
C4—H4B···O7i + | ||||||
C4···O7i | 10.99 | -17.8 | -6.1 | -29.1 | 18.3 | -37.3 |
C6—H6A···O1ii | 9.21 | -23.8 | -6.9 | -23.2 | 21.7 | -37.0 |
C5···O5iii + | ||||||
O2···O5iii | 8.29 | -8.4 | -2.7 | -56.3 | 29.1 | -41.8 |
C9—H9···C21iv | 14.12 | -12.7 | -3.4 | -20.5 | 12.0 | -26.4 |
C6—H6B···C15v + | ||||||
C4—H4A···O4v | 6.55 | -18.1 | -4.5 | -87.1 | 52.8 | -65.8 |
C21—H21C···O4vi | 15.04 | -2.1 | -1.0 | -3.7 | 1.5 | -5.2 |
Inter-layer region | ||||||
H17···H23Bvii | 10.38 | 2.9 | -1.2 | -16.5 | 8.2 | -7.1 |
H17···H21Bvii + | ||||||
H18···H21Bviii | 6.24 | -1.1 | -1.6 | -52.9 | 23.0 | -34.2 |
O4···O4ix | 13.71 | -16.1 | -4.4 | -16.2 | 10.8 | -27.7 |
C8—H8···O3x | 12.70 | -5.4 | -1.3 | -10.2 | 1.9 | -14.4 |
Symmetry codes: (i) -x + 1/2, y - 1/2, -z + 3/2; (ii) -x + 1, -y, -z + 2; (iii) x, y - 1, z; (iv) x + 1/2, -y + 1/2, z + 1/2; (v) -x + 1, -y + 1, -z + 2; (vi) x - 1/2, -y + 3/2, z - 1/2; (vii) -x + 1, y + 1, - z + 3/2; (viii) -x + 1, y, -z + 3/2; (ix) -x + 3/2, -y + 3/2, -z + 2; (x) -x + 3/2, -y + 1/2, -z + 2. |
Footnotes
‡Additional correspondence author, e-mail: edwardt@sunway.edu.my.
Funding information
The Brazilian agencies Coordination for the Improvement of Higher Education Personnel, CAPES, Finance Code 001 and the National Council for Scientific and Technological Development (CNPq) are acknowledged for grant Nos. 312210/2019–1, 433957/2018–2 and 406273/2015–4 to IC, for a fellowship 303207/2017–5 to JZS and a scholarship to SDP. Sunway University Sdn Bhd is also thanked for funding (grant No. STR-RCTR-RCCM-001–2019).
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