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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 77| Part 6| June 2021| Pages 638-642
https://doi.org/10.1107/S205698902100503X

Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-amino-5-methyl­phen­yl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide

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Gamal Al Ati,a Karim Chkirate,a Joel T. Mague,b Nadeem Abad,c* Redouane Achoura and El Mokhtar Essassia

aLaboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco, bDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, and cDepartment of Biochemistry, Faculty of Education & Science, Al-Baydha University, Yemen
*Correspondence e-mail: abadnadeem3@gmail.com

Edited by G. Diaz de Delgado, Universidad de Los Andes, Venezuela (Received 30 March 2021; accepted 11 May 2021; online 14 May 2021)

The title mol­ecule, C13H16N4O, adopts an angular conformation. In the crystal a layer structure is generated by N—H⋯O and N—H⋯N hydrogen bonds together with C—H⋯π(ring) inter­actions. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (53.8%), H⋯C/C⋯H (21.7%), H⋯N/N⋯H (13.6%), and H⋯O/O⋯H (10.8%) inter­actions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/ 6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO–LUMO energy gap is 5.0452 eV.

CCDC reference: 2083102

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1. Chemical context

Nitro­gen-based structures have attracted more attention in recent years because of their inter­esting properties in structural and inorganic chemistry (Lahmidi et al., 2018[Lahmidi, S., Sebbar, N. K., Hökelek, T., Chkirate, K., Mague, J. T. & Essassi, E. M. (2018). Acta Cryst. E74, 1833-1837.]; Chkirate et al., 2020a[Chkirate, K., Fettach, S., El Hafi, M., Karrouchi, K., Elotmani, B., Mague, J. T., Radi, S., Faouzi, M. E. A., Adarsh, N. N., Essassi, E. M. & Garcia, Y. (2020a). J. Inorg. Biochem. 208, 21-28.]; Taia et al., 2020[Taia, A., Essaber, M., Aatif, A., Chkirate, K., Hökelek, T., Mague, J. T. & Sebbar, N. K. (2020). Acta Cryst. E76, 962-966.]; Al Ati et al., 2021[Al Ati, G., Chkirate, K., Mashrai, A., Mague, J. T., Ramli, Y., Achour, R. & Essassi, E. M. (2021). Acta Cryst. E77, 18-22.]). The pyrazolyl-acetamide family is important in medicinal chemistry because of the wide range of pharmacological applications (Deprez-Poulain et al., 2011[Deprez-Poulain, R., Cousaert, N., Toto, P., Willand, N. & Deprez, B. (2011). Eur. J. Med. Chem. 46, 3867-3876.]) such as anti-inflammatory (Sunder et al., 2013[Sunder, K. S. & Maleraju, J. (2013). Drug Invent. Today, 5, 288-295.]), anti­microbial and anti­cancer (Jitender Dev et al., 2017[Jitender Dev, G., Poornachandra, Y., Ratnakar Reddy, K., Naresh Kumar, R., Ravikumar, N., Krishna Swaroop, D., Ranjithreddy, P., Shravan Kumar, G., Nanubolu, J. B., Ganesh Kumar, C. & Narsaiah, B. (2017). Eur. J. Med. Chem. 130, 223-239.]) and as an anti-amoebic agent (Shukla et al., 2020[Shukla, B. K. & Yadava, U. (2020). Heliyon, 6, e04176.]). They also have anti­oxidant activity (Chkirate et al., 2019a[Chkirate, K., Fettach, S., Karrouchi, K., Sebbar, N. K., Essassi, E. M., Mague, J. T., Radi, S., Faouzi, M. E. A., Adarsh, N. N. & Garcia, Y. (2019a). J. Inorg. Biochem. 191, 21-28.]) and have been biologically evaluated (Yan et al., 2021[Yan, W., Zhang, L., Lv, F., Moccia, M., Carlomagno, F., Landry, C., Santoro, M., Gosselet, F., Frett, B. & Li, H. (2021). Eur. J. Med. Chem. 216, 113265.]). Given the wide range of therapeutic applications for such compounds, and in a continuation of the work already carried out for the synthesis of compounds resulting from 1,5-benzodiazepine (Chkirate et al., 2001[Chkirate, K., Regragui, R., Essassi, E. M. & Pierrot, M. (2001). Z. Kristallogr. New Cryst. Struct. 216, 635-636.], 2018[Chkirate, K., Sebbar, N. K., Hökelek, T., Krishnan, D., Mague, J. T. & Essassi, E. M. (2018). Acta Cryst. E74, 1669-1673.], 2019b[Chkirate, K., Kansiz, S., Karrouchi, K., Mague, J. T., Dege, N. & Essassi, E. M. (2019b). Acta Cryst. E75, 33-37.], 2020b[Chkirate, K., Karrouchi, K., Dege, N., Sebbar, N. K., Ejjoummany, A., Radi, S., Adarsh, N. N., Talbaoui, A., Ferbinteanu, M., Essassi, E. M. & Garcia, Y. (2020b). New J. Chem. 44, 2210-2221.], 2021[Chkirate, K., Azgaou, K., Elmsellem, H., El Ibrahimi, B., Sebbar, N. K., Anouar, E. H., Benmessaoud, M., El Hajjaji, S. & Essassi, E. M. (2021). J. Mol. Liq. 321, 114750.]; Idrissi et al., 2021[Idrissi, A., Chkirate, K., Abad, N., Djerrari, B., Achour, R., Essassi, E. M. & Van Meervelt, L. (2021). Acta Cryst. E77, 396-401.]) a similar approach gave the title compound, N-(2-amino-5-methyl­phen­yl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide, (I)[link]. Besides the synthesis, we also report the mol­ecular and crystal structures along with a Hirshfeld surface analysis and a density functional theory computational calculation carried out at the B3LYP/6–311 G(d,p) level.

2. Structural commentary

The N2/C8/C9/O1 portion of the title mol­ecule is planar (r.m.s. deviation = 0.0013 Å) with the mean planes of the C1–C6 and N3/N4/C10–C12 rings inclined to the above plane by 86.56 (6) and 72.84 (7)°, respectively, giving the mol­ecule an angular shape (Fig. 1[link]). Bond distances and angles are as expected for the given formulation.

[Scheme 1]
[Figure 1]
Figure 1
Mol­ecular structure of the title compound with the labelling scheme. The ellipsoids are drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, inversion-related pairs of N1—H1B⋯O1, and N2—H2A⋯N1 hydrogen bonds, together with C11—H11⋯Cg2 inter­actions (Table 1[link]) form chains of mol­ecules extending along the a-axis direction (Fig. 2[link]). The chains are connected into layers parallel to (100) by N4—H4⋯O1 hydrogen bonds (Table 1[link] and Fig. 3[link]). Inter­molecular inter­actions viewed down the c axis are shown in Fig. 3[link].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1B⋯O1i 0.91 2.13 3.0284 (19) 171
N2—H2A⋯N1ii 0.91 2.14 3.0354 (17) 170
C2—H2⋯O1i 0.95 2.62 3.334 (2) 132
N4—H4⋯O1iii 0.91 (1) 1.99 (1) 2.8625 (17) 163 (2)
Symmetry codes: (i) [-x+1, -y+1, -z+1]; (ii) [-x+2, -y+1, -z+1]; (iii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A portion of one chain projected onto (011) with N—H⋯O and N—H⋯N hydrogen bonds depicted, respectively, by light-purple and light-blue dashed lines. The C—H⋯π(ring) inter­actions are depicted by green dashed lines. Hydrogen atoms not involved in inter­actions have been omitted for clarity.
[Figure 3]
Figure 3
Packing arrangement viewed along the c-axis direction of the main isomer with inter­molecular inter­actions shown as in Fig. 2[link].

4. Hirshfeld surface analysis

The CrystalExplorer program (Turner et al., 2017[Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. The University of Western Australia.]) was used to investigate and visualize further the inter­molecular inter­actions of (I)[link]. The Hirshfeld surface plotted over dnorm in the range −0.6149 to 1.3177 a.u. is shown in Fig. 4[link]a. The electrostatic potential calculated using the STO-3G basis set at the Hartree–Fock level of theory and mapped on the Hirshfeld surface over the range ±0.05 a.u. clearly shows the positions of close inter­molecular contacts in the compound (Fig. 4[link]b). The positive electrostatic potential (blue region) over the surface indicates hydrogen-donor potential, whereas the hydrogen-bond acceptors are represented by negative electrostatic potential (red region). The shape-index (Fig. 5[link]) generated in the range −1 to 1 Å reveals that there are no significant π–π inter­actions, normally indicated by adjacent red and blue triangles.

[Figure 4]
Figure 4
(a) View of the three-dimensional Hirshfeld surface of the title compound, plotted over dnorm in the range of −0.6149 to 1.3177 a.u. (b) View of the three-dimensional Hirshfeld surface of the title compound plotted over the electrostatic potential energy in the range −0.0500 to 0.0500 a.u. using the STO-3 G basis set at the Hartree–Fock level of theory.
[Figure 5]
Figure 5
Hirshfeld surface of the title compound plotted over shape-index.

The overall two-dimensional fingerprint plot (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. 3814-3816.]) is shown in Fig. 6[link]a, while those delineated into H⋯H, H⋯C/C⋯H, H⋯N/N⋯H and H⋯O/O⋯H contacts are illustrated in Fig. 6[link]b–e, respectively, together with their relative contributions to the Hirshfeld surface (HS). The most important inter­action is H⋯H, contributing 53.8% to the overall crystal packing, which is reflected in Fig. 6[link]b as widely scattered points of high density due to the large hydrogen content of the mol­ecule, with the tip at de = di = 1.18 Å. In the presence of C—H inter­actions, the pair of characteristic wings in the fingerprint plot delineated into H⋯C/C⋯H contacts (21.7% contribution to the HS), Fig. 6[link]c, has the tips at de + di = 2.76 Å. The pair of scattered points of spikes in the fingerprint plot delineated into H⋯N/N⋯H, Fig. 6[link]d (13.6%), have the tips at de + di = 2.01 Å. Finally, the H⋯O/O⋯H contacts, Fig. 6[link]e, make only a 10.8% contribution to the HS and have a low-density distribution of points.

[Figure 6]
Figure 6
The full two-dimensional fingerprint plots for the title compound, showing (a) all inter­actions, and those delineated into (b) H⋯H, (c) H⋯C/C⋯H, (d) H⋯N/N⋯H and (e) H⋯O/O⋯H inter­actions. The di and de values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface.

5. Density functional theory calculations

The structure in the gas phase of the title compound was optimized by means of density functional theory. The density functional theory calculation was performed by the hybrid B3LYP method and the 6–311 G(d,p) basis-set, which is based on Becke's model (Becke, 1993[Becke, A. D. (1993). J. Chem. Phys. 98, 5648-5652.]) and considers a mixture of the exact (Hartree–Fock) and density functional theory exchange utilizing the B3 functional, together with the LYP correlation functional (Lee et al., 1988[Lee, C., Yang, W. & Parr, R. G. (1988). Phys. Rev. B, 37, 785-789.]). After obtaining the converged geometry, the harmonic vibrational frequencies were calculated at the same theoretical level to confirm that the number of imaginary frequencies is zero for the stationary point. Both the geometry optimization and harmonic vibrational frequency analysis of the title compound were done with the Gaussian 09 program (Frisch et al., 2009[Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A. Jr, Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, O., Foresman, J. B., Ortiz, J. V., Cioslowski, J. & Fox, D. J. (2009). Gaussian 09. Revision A.02. Gaussian Inc, Wallingford, CT, USA.]). Theoretical and experimental results related to bond lengths and angles are in good agreement and are summarized in Table 2[link]. Calculated numerical values for the title compound including electronegativity (χ), hardness (η), ionization potential (I), dipole moment (μ), electron affinity (A), electrophilicity (ω) and softness (σ) are collated in Table 3[link]. The electron transition from the highest occupied mol­ecular orbital (HOMO) to the lowest unoccupied mol­ecular orbital (LUMO) energy level is shown in Fig. 7[link]. The HOMO and LUMO are localized in the plane extending over the whole N-(2-amino-5-methyl­phen­yl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide system. The energy band gap [ΔE = ELUMO − EHOMO] of the mol­ecule is 5.0452 eV, and the frontier mol­ecular orbital energies, EHOMO and ELUMO, are −5.3130 and −0.2678 eV, respectively.

Table 2
Comparison of selected (X-ray and density functional theory) bond lengths and angles (Å, °)

  X-ray B3LYP/6–311G(d,p)
N1—C1 1.4112 (17) 1.4114
N2—C6 1.4347 (17) 1.4139
N2—C8 1.3471 (17) 1.3692
O1—C8 1.2376 (16) 1.2179
N3—C10 1.3425 (18) 1.3316
N3—N4 1.3635 (19) 1.3524
N4—C12 1.3534 (19) 1.3598
C8—C9 1.5119 (18) 1.5409
C9—C10 1.496 (2) 1.5007
     
C2—C1—N1 121.12 (12) 122.0542
C6—C1—N1 120.68 (12) 119.3119
C1—C6—N2 119.89 (11) 116.726
C5—C6—N2 119.46 (12) 123.4969
O1—C8—N2 122.20 (12) 125.0222
N2—C8—C9 116.22 (11) 114.6561
O1—C8—C9 121.58 (12) 120.2798
N3—C10—C9 119.95 (13) 120.7841
N3—C10—C11 111.17 (12) 110.8968
C10—N3—N4 104.22 (12) 104.754
C12—N4—N3 112.76 (12) 113.2928
N4—C12—C11 106.48 (13) 105.3557
N4—C12—C13 122.33 (14) 122.8603

Table 3
Calculated energies

Mol­ecular Energy Compound (I)
Total Energy TE (eV) −21754.8403
EHOMO (eV) −5.3130
ELUMO (eV) −0.2678
Gap, ΔE (eV) 5.0452
Dipole moment, μ (Debye) 6.7706
Ionization potential, I (eV) 5.3130
Electron affinity, A 0.2678
Electronegativity, χ 2.7904
Hardness, η 2.5226
Electrophilicity, index ω 1.5433
Softness, σ 0.3964
Fraction of electron transferred, ΔN 0.8344
[Figure 7]
Figure 7
The energy band gap of N-(2-amino-5-methyl­phen­yl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide.

6. Database survey

A search of the Cambridge Structural Database (CSD version 5.40, updated March 2020; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) with the 2-(5-methyl-1H-pyrazol-3-yl)acetamide fragment yielded multiple matches. Of these, two had an N-(2-amino­phen­yl) substituent comparable to (I)[link] and they are shown in Fig. 8[link]. The first compound (II) (refcode XITFUE; Chkirate et al., 2019c[Chkirate, K., Kansiz, S., Karrouchi, K., Mague, J. T., Dege, N. & Essassi, E. M. (2019c). Acta Cryst. E75, 154-158.]) carries N-(2-{[(4-methyl­phen­yl)methyl­idene]amino}­phen­yl) on nitro­gen 2. The second one (III) (refcode YODZEZ; Chkirate et al., 2019a[Chkirate, K., Fettach, S., Karrouchi, K., Sebbar, N. K., Essassi, E. M., Mague, J. T., Radi, S., Faouzi, M. E. A., Adarsh, N. N. & Garcia, Y. (2019a). J. Inorg. Biochem. 191, 21-28.]) carries N-(2-amino­phen­yl) on nitro­gen 2. The pyrazole ring (N3/N4/C10–C12) in XITFUE is inclined to the C1–C6 benzene ring by 70.83 (8)°. In YODZEZ, the dihedral angle between the mean planes of the 2-amino­phenyl and pyrazolyl rings is 65.63 (8)°. In (I)[link], the N2/C8/C9/O1 fragment is planar (r.m.s. deviation = 0.0013 Å) with the mean planes of the C1–C6 and N3/N4/C10–C12 rings inclined to the above plane by 86.56 (6) and 72.84 (7)°, respectively, which is approximately the same as in XITFUE, but less tilted than in YODZEZ.

[Figure 8]
Figure 8
Structures similar to (I)[link]: (II) (CSD refcode XITFUE) and (III) (CSD refcode YODZEZ) obtained in the database search. The search fragment is indicated in blue.

7. Synthesis and crystallization

2 g (9.3 mmol) of (Z)-4-(2-oxo­propyl­idene)-1,5-benzodiazepin-2-one and a stoichiometric amount of hydrazine were refluxed in ethanol (40 mL) for 2 h. After concentration of the solvent volume to 20 mL, the solution was allowed to stand; the precipitate formed was filtered off and then recrystallized in ethanol. Single crystals were obtained after recrystallization from methanol in the presence of MnCl2·4H2O, which was left at room temperature for 72 h. Yield: 70%.

8. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 4[link]. H atoms were included as riding contributions in idealized positions (N—H = 0.88–0.91 Å, C—H = 0.95–0.99 Å) with isotropic displacement parameters 1.2–1.5 times those of the attached atoms. Residual density observed after the initial refinement converged was identified as an isomer of the primary mol­ecule having the C7 methyl group attached to C3 instead of to C4 and with a refined occupancy of 5%. The final model was generated with a combination of rigid group and restrained refinement to make the minor component have a comparable geometry to that of the major component.

Table 4
Experimental details

Crystal data
Chemical formula C13H16N4O
Mr 244.30
Crystal system, space group Monoclinic, P21/c
Temperature (K) 150
a, b, c (Å) 7.1271 (3), 8.9295 (3), 19.2508 (7)
β (°) 94.683 (1)
V (Å3) 1221.06 (8)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.37 × 0.26 × 0.16
 
Data collection
Diffractometer Bruker D8 QUEST PHOTON 3 diffractometer
Absorption correction Numerical (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.93, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections 66426, 5120, 4794
Rint 0.028
(sin θ/λ)max (Å−1) 0.794
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.067, 0.164, 1.23
No. of reflections 5120
No. of parameters 212
No. of restraints 32
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.44, −0.33
Computer programs: APEX3 and SAINT (Bruker, 2020[Bruker (2020). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2018/1 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information

CCDC reference: 2083102

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S205698902100503X/dj2025sup1.cif

Supporting information file. DOI: https://doi.org/10.1107/S205698902100503X/dj2025Isup3.cml

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698902100503X/dj2025Isup5.hkl

checkCIF report


Computing details top

Data collection: APEX3 (Bruker, 2020); cell refinement: SAINT (Bruker, 2020); data reduction: SAINT (Bruker, 2020); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/1 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

N-(2-Amino-5-methylphenyl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide top
Crystal data top
C13H16N4OF(000) = 520
Mr = 244.30Dx = 1.329 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 7.1271 (3) ÅCell parameters from 9878 reflections
b = 8.9295 (3) Åθ = 2.5–34.4°
c = 19.2508 (7) ŵ = 0.09 mm−1
β = 94.683 (1)°T = 150 K
V = 1221.06 (8) Å3Parallelepiped, colourless
Z = 40.37 × 0.26 × 0.16 mm
Data collection top
Bruker D8 QUEST PHOTON 3
diffractometer		5120 independent reflections
Radiation source: fine-focus sealed tube4794 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.028
Detector resolution: 7.3910 pixels mm-1θmax = 34.4°, θmin = 2.5°
φ and ω scansh = −11→11
Absorption correction: numerical
(SADABS; Krause et al., 2015)		k = −14→14
Tmin = 0.93, Tmax = 0.99l = −30→30
66426 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.067Hydrogen site location: mixed
wR(F2) = 0.164H atoms treated by a mixture of independent and constrained refinement
S = 1.23 w = 1/[σ2(Fo2) + (0.0465P)2 + 0.8885P]
where P = (Fo2 + 2Fc2)/3
5120 reflections(Δ/σ)max = 0.007
212 parametersΔρmax = 0.44 e Å−3
32 restraintsΔρmin = −0.33 e Å−3
Special details top

Experimental. The diffraction data were obtained from 9 sets of frames, each of width 0.5° in ω or φ, collected with scan parameters determined by the "strategy" routine in APEX3. The scan time was 15 sec/frame.

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.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. H-atoms were included as riding contributions in idealized positions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. Residual density observed after the initial refinement converged was identified as an isomer of the primary molecule having the C7 methyl group attached to C3 instead of to C4 and with a refined occupancy of 5%. The final model was generated with a combination of rigid group and restrained refinement to make the minor component have a comparable geometry to that of the major component.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
O10.59624 (16)0.37274 (17)0.37033 (6)0.0232 (2)0.9480 (17)
N10.71759 (18)0.54183 (13)0.54033 (7)0.0217 (2)0.9480 (17)
H1A0.7056850.5758000.4956190.032*0.9480 (17)
H1B0.6253760.5781030.5657050.032*0.9480 (17)
N20.87261 (16)0.36438 (14)0.43708 (6)0.0194 (2)0.9480 (17)
H2A0.9976750.3860100.4388290.029*0.9480 (17)
O1A0.611 (2)0.392 (4)0.3551 (15)0.0232 (2)0.0520 (17)
N1A0.726 (2)0.5270 (12)0.5246 (10)0.0217 (2)0.0520 (17)
H1C0.7144070.5609920.4799010.032*0.0520 (17)
H1D0.6340980.5632940.5499910.032*0.0520 (17)
N2A0.892 (3)0.379 (3)0.4164 (9)0.0194 (2)0.0520 (17)
H2C1.0106320.4085610.4196180.023*0.0520 (17)
C10.71306 (17)0.38417 (14)0.54490 (7)0.0183 (2)0.9480 (17)
C20.63639 (19)0.31229 (16)0.60084 (8)0.0211 (2)0.9480 (17)
H20.5814420.3703260.6352310.025*0.9480 (17)
C30.63985 (19)0.15736 (16)0.60656 (8)0.0217 (2)0.9480 (17)
H30.5880380.1110150.6450850.026*0.9480 (17)
C40.71811 (19)0.06826 (15)0.55670 (7)0.0201 (2)0.9480 (17)
C50.79467 (18)0.13954 (15)0.50122 (7)0.0190 (2)0.9480 (17)
H50.8487610.0810790.4667730.023*0.9480 (17)
C60.79337 (17)0.29531 (14)0.49529 (7)0.0173 (2)0.9480 (17)
C70.7163 (2)−0.10021 (16)0.56184 (9)0.0267 (3)0.9480 (17)
H7A0.762818−0.1434280.5197180.040*0.9480 (17)
H7B0.587355−0.1347750.5664030.040*0.9480 (17)
H7C0.797458−0.1319270.6027340.040*0.9480 (17)
C80.76818 (18)0.39484 (15)0.37725 (7)0.0181 (2)0.9480 (17)
C90.87268 (19)0.45874 (17)0.31874 (7)0.0233 (3)0.9480 (17)
H9A1.0094310.4584030.3327920.028*0.9480 (17)
H9B0.8506120.3942390.2770430.028*0.9480 (17)
C1A0.7392 (15)0.3693 (12)0.5253 (6)0.0183 (2)0.0520 (17)
C2A0.664 (2)0.2879 (16)0.5780 (7)0.0211 (2)0.0520 (17)
H2B0.6042710.3383980.6135390.025*0.0520 (17)
C3A0.677 (2)0.1325 (16)0.5786 (8)0.0217 (2)0.0520 (17)
C4A0.764 (2)0.0586 (12)0.5266 (9)0.0201 (2)0.0520 (17)
H4A0.773122−0.0475550.5270240.024*0.0520 (17)
C5A0.839 (2)0.1400 (14)0.4739 (8)0.0190 (2)0.0520 (17)
H5A0.8993730.0894940.4383000.023*0.0520 (17)
C6A0.827 (2)0.2954 (14)0.4732 (7)0.0173 (2)0.0520 (17)
C7A0.603 (4)0.043 (3)0.6369 (11)0.0267 (3)0.0520 (17)
H7D0.5455420.1108600.6691770.040*0.0520 (17)
H7E0.508277−0.0284210.6175750.040*0.0520 (17)
H7F0.706943−0.0114420.6619870.040*0.0520 (17)
C8A0.783 (2)0.415 (3)0.3584 (9)0.0181 (2)0.0520 (17)
C9A0.890 (3)0.487 (2)0.3025 (7)0.0233 (3)0.0520 (17)
H9C1.0251010.4950790.3180910.028*0.0520 (17)
H9D0.8761720.4270220.2591730.028*0.0520 (17)
N30.67894 (16)0.63909 (15)0.24804 (6)0.0255 (3)0.9480 (17)
N40.65868 (16)0.79091 (15)0.24611 (6)0.0252 (3)0.9480 (17)
H40.574 (3)0.834 (3)0.2145 (10)0.036 (6)*0.9480 (17)
C100.81137 (15)0.61509 (16)0.30054 (6)0.0208 (2)0.9480 (17)
C110.87425 (16)0.75120 (17)0.33163 (7)0.0218 (2)0.9480 (17)
H110.9667360.7640310.3695720.026*0.9480 (17)
C120.77310 (17)0.86140 (17)0.29529 (6)0.0219 (3)0.9480 (17)
C130.7758 (2)1.0282 (2)0.30308 (9)0.0301 (3)0.9480 (17)
H13A0.8981831.0597450.3251500.045*0.9480 (17)
H13B0.6759801.0590710.3321520.045*0.9480 (17)
H13C0.7549721.0749050.2570330.045*0.9480 (17)
N3A0.6378 (14)0.668 (2)0.2606 (3)0.0255 (3)0.0520 (17)
N4A0.6309 (16)0.819 (2)0.2618 (3)0.0252 (3)0.0520 (17)
H4B0.5305260.8686040.2446960.036 (6)*0.0520 (17)
C10A0.8062 (14)0.639 (2)0.2901 (3)0.0208 (2)0.0520 (17)
C11A0.900 (2)0.773 (2)0.3088 (5)0.0218 (2)0.0520 (17)
H11B1.0237310.7804100.3309020.026*0.0520 (17)
C12A0.783 (3)0.891 (2)0.2898 (6)0.0219 (3)0.0520 (17)
C13A0.809 (4)1.053 (3)0.2971 (9)0.0301 (3)0.0520 (17)
H13D0.9349501.0735350.3197070.045*0.0520 (17)
H13E0.7972471.0997500.2508830.045*0.0520 (17)
H13F0.7137331.0941590.3255230.045*0.0520 (17)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0175 (4)0.0273 (6)0.0240 (6)−0.0023 (4)−0.0030 (4)0.0038 (5)
N10.0196 (5)0.0157 (5)0.0292 (6)0.0003 (4)−0.0008 (4)0.0004 (4)
N20.0152 (4)0.0210 (5)0.0216 (5)−0.0027 (4)−0.0012 (4)0.0056 (4)
O1A0.0175 (4)0.0273 (6)0.0240 (6)−0.0023 (4)−0.0030 (4)0.0038 (5)
N1A0.0196 (5)0.0157 (5)0.0292 (6)0.0003 (4)−0.0008 (4)0.0004 (4)
N2A0.0152 (4)0.0210 (5)0.0216 (5)−0.0027 (4)−0.0012 (4)0.0056 (4)
C10.0140 (5)0.0165 (5)0.0237 (6)−0.0001 (4)−0.0026 (4)0.0018 (4)
C20.0183 (5)0.0204 (6)0.0245 (6)0.0016 (4)0.0020 (4)0.0013 (5)
C30.0192 (5)0.0217 (6)0.0244 (6)−0.0005 (4)0.0029 (4)0.0049 (5)
C40.0185 (5)0.0165 (5)0.0250 (6)−0.0017 (4)−0.0003 (4)0.0042 (4)
C50.0184 (5)0.0170 (5)0.0211 (5)−0.0004 (4)−0.0003 (4)0.0012 (4)
C60.0153 (5)0.0163 (5)0.0200 (5)−0.0016 (4)−0.0012 (4)0.0032 (4)
C70.0276 (6)0.0175 (6)0.0350 (7)−0.0023 (5)0.0027 (5)0.0061 (5)
C80.0183 (5)0.0153 (5)0.0204 (6)0.0008 (4)0.0000 (4)0.0021 (4)
C90.0233 (6)0.0237 (6)0.0233 (6)0.0026 (5)0.0052 (5)0.0059 (5)
C1A0.0140 (5)0.0165 (5)0.0237 (6)−0.0001 (4)−0.0026 (4)0.0018 (4)
C2A0.0183 (5)0.0204 (6)0.0245 (6)0.0016 (4)0.0020 (4)0.0013 (5)
C3A0.0192 (5)0.0217 (6)0.0244 (6)−0.0005 (4)0.0029 (4)0.0049 (5)
C4A0.0185 (5)0.0165 (5)0.0250 (6)−0.0017 (4)−0.0003 (4)0.0042 (4)
C5A0.0184 (5)0.0170 (5)0.0211 (5)−0.0004 (4)−0.0003 (4)0.0012 (4)
C6A0.0153 (5)0.0163 (5)0.0200 (5)−0.0016 (4)−0.0012 (4)0.0032 (4)
C7A0.0276 (6)0.0175 (6)0.0350 (7)−0.0023 (5)0.0027 (5)0.0061 (5)
C8A0.0183 (5)0.0153 (5)0.0204 (6)0.0008 (4)0.0000 (4)0.0021 (4)
C9A0.0233 (6)0.0237 (6)0.0233 (6)0.0026 (5)0.0052 (5)0.0059 (5)
N30.0249 (6)0.0251 (6)0.0254 (5)0.0008 (4)−0.0042 (4)0.0001 (4)
N40.0234 (5)0.0266 (6)0.0244 (6)0.0024 (4)−0.0054 (4)0.0024 (5)
C100.0180 (5)0.0231 (6)0.0210 (5)0.0005 (4)0.0003 (4)0.0049 (4)
C110.0175 (5)0.0257 (6)0.0213 (6)0.0004 (4)−0.0027 (4)0.0026 (5)
C120.0179 (5)0.0232 (7)0.0243 (6)0.0012 (5)0.0005 (4)0.0033 (5)
C130.0283 (8)0.0251 (7)0.0368 (8)0.0005 (6)0.0012 (6)0.0012 (6)
N3A0.0249 (6)0.0251 (6)0.0254 (5)0.0008 (4)−0.0042 (4)0.0001 (4)
N4A0.0234 (5)0.0266 (6)0.0244 (6)0.0024 (4)−0.0054 (4)0.0024 (5)
C10A0.0180 (5)0.0231 (6)0.0210 (5)0.0005 (4)0.0003 (4)0.0049 (4)
C11A0.0175 (5)0.0257 (6)0.0213 (6)0.0004 (4)−0.0027 (4)0.0026 (5)
C12A0.0179 (5)0.0232 (7)0.0243 (6)0.0012 (5)0.0005 (4)0.0033 (5)
C13A0.0283 (8)0.0251 (7)0.0368 (8)0.0005 (6)0.0012 (6)0.0012 (6)
Geometric parameters (Å, º) top
O1—C81.2376 (16)C3A—C4A1.3900
N1—C11.4112 (17)C3A—C7A1.508 (3)
N1—H1A0.9099C4A—C5A1.3900
N1—H1B0.9099C4A—H4A0.9500
N2—C81.3471 (17)C5A—C6A1.3900
N2—C61.4347 (17)C5A—H5A0.9500
N2—H2A0.9100C7A—H7D0.9800
O1A—C8A1.238 (3)C7A—H7E0.9800
N1A—C1A1.412 (3)C7A—H7F0.9800
N1A—H1C0.9099C8A—C9A1.511 (3)
N1A—H1D0.9100C9A—C10A1.496 (3)
N2A—C8A1.347 (3)C9A—H9C0.9900
N2A—C6A1.434 (3)C9A—H9D0.9900
N2A—H2C0.8800N3—C101.3425 (18)
C1—C61.3995 (19)N3—N41.3635 (19)
C1—C21.4022 (19)N4—C121.3534 (19)
C2—C31.388 (2)N4—H40.907 (9)
C2—H20.9500C10—C111.412 (2)
C3—C41.397 (2)C11—C121.3766 (19)
C3—H30.9500C11—H110.9500
C4—C51.3925 (18)C12—C131.497 (2)
C4—C71.5077 (19)C13—H13A0.9800
C5—C61.3956 (18)C13—H13B0.9800
C5—H50.9500C13—H13C0.9800
C7—H7A0.9800N3A—C10A1.311 (12)
C7—H7B0.9800N3A—N4A1.351 (17)
C7—H7C0.9800N4A—C12A1.331 (16)
C8—C91.5119 (18)N4A—H4B0.8800
C9—C101.496 (2)C10A—C11A1.397 (16)
C9—H9A0.9900C11A—C12A1.375 (17)
C9—H9B0.9900C11A—H11B0.9500
C1A—C2A1.3900C12A—C13A1.468 (17)
C1A—C6A1.3900C13A—H13D0.9800
C2A—C3A1.3900C13A—H13E0.9800
C2A—H2B0.9500C13A—H13F0.9800
C1—N1—H1A113.0C6A—C5A—H5A120.0
C1—N1—H1B107.5C4A—C5A—H5A120.0
H1A—N1—H1B111.9C5A—C6A—C1A120.0
C8—N2—C6121.97 (11)C5A—C6A—N2A120.1 (13)
C8—N2—H2A117.4C1A—C6A—N2A119.7 (13)
C6—N2—H2A120.6C3A—C7A—H7D109.5
C1A—N1A—H1C110.0C3A—C7A—H7E109.5
C1A—N1A—H1D113.5H7D—C7A—H7E109.5
H1C—N1A—H1D111.9C3A—C7A—H7F109.5
C8A—N2A—C6A123.6 (15)H7D—C7A—H7F109.5
C8A—N2A—H2C118.2H7E—C7A—H7F109.5
C6A—N2A—H2C118.2O1A—C8A—N2A120.4 (18)
C6—C1—C2118.12 (12)O1A—C8A—C9A126 (2)
C6—C1—N1120.68 (12)N2A—C8A—C9A113.7 (11)
C2—C1—N1121.12 (12)C10A—C9A—C8A106.6 (14)
C3—C2—C1120.77 (13)C10A—C9A—H9C110.4
C3—C2—H2119.6C8A—C9A—H9C110.4
C1—C2—H2119.6C10A—C9A—H9D110.4
C2—C3—C4121.24 (13)C8A—C9A—H9D110.4
C2—C3—H3119.4H9C—C9A—H9D108.6
C4—C3—H3119.4C10—N3—N4104.22 (12)
C5—C4—C3118.03 (12)C12—N4—N3112.76 (12)
C5—C4—C7120.82 (13)C12—N4—H4126.7 (16)
C3—C4—C7121.13 (13)N3—N4—H4120.5 (16)
C4—C5—C6121.19 (12)N3—C10—C11111.17 (12)
C4—C5—H5119.4N3—C10—C9119.95 (13)
C6—C5—H5119.4C11—C10—C9128.88 (12)
C5—C6—C1120.64 (12)C12—C11—C10105.37 (12)
C5—C6—N2119.46 (12)C12—C11—H11127.3
C1—C6—N2119.89 (11)C10—C11—H11127.3
C4—C7—H7A109.5N4—C12—C11106.48 (13)
C4—C7—H7B109.5N4—C12—C13122.33 (14)
H7A—C7—H7B109.5C11—C12—C13131.18 (14)
C4—C7—H7C109.5C12—C13—H13A109.5
H7A—C7—H7C109.5C12—C13—H13B109.5
H7B—C7—H7C109.5H13A—C13—H13B109.5
O1—C8—N2122.20 (12)C12—C13—H13C109.5
O1—C8—C9121.58 (12)H13A—C13—H13C109.5
N2—C8—C9116.22 (11)H13B—C13—H13C109.5
C10—C9—C8111.99 (9)C10A—N3A—N4A102.8 (12)
C10—C9—H9A109.2C12A—N4A—N3A117.0 (13)
C8—C9—H9A109.2C12A—N4A—H4B121.5
C10—C9—H9B109.2N3A—N4A—H4B121.5
C8—C9—H9B109.2N3A—C10A—C11A110.3 (14)
H9A—C9—H9B107.9N3A—C10A—C9A125.8 (16)
C2A—C1A—C6A120.0C11A—C10A—C9A123.9 (14)
C2A—C1A—N1A119.99 (8)C12A—C11A—C10A108.4 (13)
C6A—C1A—N1A120.01 (8)C12A—C11A—H11B125.8
C1A—C2A—C3A120.0C10A—C11A—H11B125.8
C1A—C2A—H2B120.0N4A—C12A—C11A101.4 (13)
C3A—C2A—H2B120.0N4A—C12A—C13A127.2 (19)
C4A—C3A—C2A120.0C11A—C12A—C13A131.3 (18)
C4A—C3A—C7A119.3 (14)C12A—C13A—H13D109.5
C2A—C3A—C7A120.6 (14)C12A—C13A—H13E109.5
C3A—C4A—C5A120.0H13D—C13A—H13E109.5
C3A—C4A—H4A120.0C12A—C13A—H13F109.5
C5A—C4A—H4A120.0H13D—C13A—H13F109.5
C6A—C5A—C4A120.0H13E—C13A—H13F109.5
C6—C1—C2—C3−0.18 (19)C2A—C1A—C6A—N2A175.7 (15)
N1—C1—C2—C3−177.18 (12)N1A—C1A—C6A—N2A−4.3 (15)
C1—C2—C3—C4−0.5 (2)C8A—N2A—C6A—C5A90 (3)
C2—C3—C4—C50.6 (2)C8A—N2A—C6A—C1A−86 (3)
C2—C3—C4—C7−178.08 (13)C6A—N2A—C8A—O1A9 (5)
C3—C4—C5—C6−0.09 (19)C6A—N2A—C8A—C9A−173 (2)
C7—C4—C5—C6178.64 (13)O1A—C8A—C9A—C10A59 (4)
C4—C5—C6—C1−0.60 (19)N2A—C8A—C9A—C10A−119 (2)
C4—C5—C6—N2−179.60 (11)C10—N3—N4—C12−0.05 (3)
C2—C1—C6—C50.73 (18)N4—N3—C10—C110.05 (2)
N1—C1—C6—C5177.74 (12)N4—N3—C10—C9−179.92 (3)
C2—C1—C6—N2179.72 (11)C8—C9—C10—N3−95.38 (12)
N1—C1—C6—N2−3.27 (18)C8—C9—C10—C1184.65 (12)
C8—N2—C6—C590.79 (16)N3—C10—C11—C12−0.04 (4)
C8—N2—C6—C1−88.21 (16)C9—C10—C11—C12179.93 (5)
C6—N2—C8—O14.1 (2)N3—N4—C12—C110.02 (5)
C6—N2—C8—C9−176.27 (12)N3—N4—C12—C13179.89 (4)
O1—C8—C9—C1064.49 (19)C10—C11—C12—N40.01 (5)
N2—C8—C9—C10−115.16 (14)C10—C11—C12—C13−179.84 (5)
C6A—C1A—C2A—C3A0.0C10A—N3A—N4A—C12A0.00 (3)
N1A—C1A—C2A—C3A180.0N4A—N3A—C10A—C11A0.00 (3)
C1A—C2A—C3A—C4A0.0N4A—N3A—C10A—C9A180.00 (4)
C1A—C2A—C3A—C7A177.6 (19)C8A—C9A—C10A—N3A−69.6 (15)
C2A—C3A—C4A—C5A0.0C8A—C9A—C10A—C11A110.4 (15)
C7A—C3A—C4A—C5A−177.6 (18)N3A—C10A—C11A—C12A0.00 (5)
C3A—C4A—C5A—C6A0.0C9A—C10A—C11A—C12A179.99 (6)
C4A—C5A—C6A—C1A0.0N3A—N4A—C12A—C11A0.00 (5)
C4A—C5A—C6A—N2A−175.7 (15)N3A—N4A—C12A—C13A180.00 (5)
C2A—C1A—C6A—C5A0.0C10A—C11A—C12A—N4A0.00 (6)
N1A—C1A—C6A—C5A180.0C10A—C11A—C12A—C13A180.00 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1B···O1i0.912.133.0284 (19)171
N2—H2A···N1ii0.912.143.0354 (17)170
C2—H2···O1i0.952.623.334 (2)132
N4—H4···O1iii0.91 (1)1.99 (1)2.8625 (17)163 (2)
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+2, −y+1, −z+1; (iii) −x+1, y+1/2, −z+1/2.
Comparison of selected (X-ray and density functional theory) bond lengths and angles (Å, °) top
X-rayB3LYP/6–311G(d,p)
N1—C11.4112 (17)1.4114
N2—C61.4347 (17)1.4139
N2—C81.3471 (17)1.3692
O1—C81.2376 (16)1.2179
N3—C101.3425 (18)1.3316
N3—N41.3635 (19)1.3524
N4—C121.3534 (19)1.3598
C8—C91.5119 (18)1.5409
C9—C101.496 (2)1.5007
C2—C1—N1121.12 (12)122.0542
C6—C1—N1120.68 (12)119.3119
C1—C6—N2119.89 (11)116.726
C5—C6—N2119.46 (12)123.4969
O1—C8—N2122.20 (12)125.0222
N2—C8—C9116.22 (11)114.6561
O1—C8—C9121.58 (12)120.2798
N3—C10—C9119.95 (13)120.7841
N3—C10—C11111.17 (12)110.8968
C10—N3—N4104.22 (12)104.754
C12—N4—N3112.76 (12)113.2928
N4—C12—C11106.48 (13)105.3557
N4—C12—C13122.33 (14)122.8603
Calculated energies top
Molecular EnergyCompound (I)
Total Energy TE (eV)-21754.8403
EHOMO (eV)-5.3130
ELUMO (eV)-0.2678
Gap, ΔE (eV)5.0452
Dipole moment, µ (Debye)6.7706
Ionization potential, I (eV)5.3130
Electron affinity, A0.2678
Electronegativity, χ2.7904
Hardness, η2.5226
Electrophilicity, index ω1.5433
Softness, σ0.3964
Fraction of electron transferred, ΔN0.8344
 

Acknowledgements

JTM thanks Tulane University for support of the Tulane Crystallography Laboratory. Author contribution are as follows. Conceptualization, GAA and KC; methodology, GAA; investigation, KC and NA; theoretical calculations, KC; writing (original draft) KC; writing (review and editing of the manuscript) NA; supervision, KC, EME and RA; crystal-structure determination and validation, JTM.

References

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ISSN: 2056-9890
Volume 77| Part 6| June 2021| Pages 638-642
https://doi.org/10.1107/S205698902100503X
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