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Crystal structure, Hirshfeld surface analysis and inter­action energy and DFT studies of (S)-10-propargyl­pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dione

aLaboratory of Applied Organic Chemistry, Sidi Mohamed Ben Abdellah University, Faculty of Sciences and Techniques, Road Immouzer, BP 2202 Fez, Morocco, bUSR 3290 Miniaturisation pour l'analyse, la synthèse et la protéomique, 59655, Villeneuve d'Ascq Cedex, Université Lille1, France, cDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Turkey, dUnité de Catalyse et de Chimie du Solide (UCCS), UMR 8181, Ecole Nationale Supérieure de Chimie de Lille, Université Lille 1, 59650 Villeneuve d'Ascq Cedex, France, and eLaboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
*Correspondence e-mail: DouniaJeroundi2019@gmail.com

Edited by A. J. Lough, University of Toronto, Canada (Received 27 January 2020; accepted 26 February 2020; online 3 March 2020)

The title compound, C15H14N2O2, consists of pyrrole and benzodiazepine units linked to a propargyl moiety, where the pyrrole and diazepine rings adopt half-chair and boat conformations, respectively. The absolute configuration was assigned on the the basis of L-proline, which was used in the synthesis of benzodiazepine. In the crystal, weak C—HBnz⋯ODiazp and C—HProprg⋯ODiazp (Bnz = benzene, Diazp = diazepine and Proprg = proparg­yl) hydrogen bonds link the mol­ecules into two-dimensional networks parallel to the bc plane, enclosing R44(28) ring motifs, with the networks forming oblique stacks along the a-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.8%), H⋯C/C⋯H (25.7%) and H⋯O/O⋯H (20.1%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. Computational chemistry indicates that in the crystal, C—H⋯O hydrogen-bond energies are 38.8 (for C—HBnz⋯ODiazp) and 27.1 (for C—HProprg⋯ODiazp) kJ mol−1. Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined mol­ecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.

1. Chemical context

Over the past few decades, compounds bearing heterocyclic nuclei have received much attention of chemists and biologists because of their importance in the development of chemotherapeutic agents and a wide variety of drugs (Cargill et al., 1974[Cargill, C., Bachmann, E. & Zbinden, G. (1974). J. Natl Cancer Inst. 53, 481-486.]; Micale et al., 2004[Micale, N., Vairagoundar, R., Yakovlev, A. G. & Kozikowski, A. P. (2004). J. Med. Chem. 47, 6455-6458.]; Hadac et al., 2006[Hadac, E. M., Dawson, E. S., Darrow, J. W., Sugg, E. E., Lybrand, T. P. & Miller, L. J. (2006). J. Med. Chem. 49, 850-863.]; Ourahou et al., 2011[Ourahou, S., Zouihri, H., Massoui, M., Essassi, E. M. & Ng, S. W. (2011). Acta Cryst. E67, o1906.]). 1,4-Benzodiazepines and their derivatives have attracted the attention of chemists since the early 1960s, mainly because of the broad spectrum of biological properties exhibited by this class of compounds, in particular their psychopharmacological properties (Thurston & Langley, 1986[Thurston, D. E. & Langley, D. R. (1986). J. Org. Chem. 51, 705-712.]; Kamal et al., 2007[Kamal, A., Reddy, K. L., Devaiah, V., Shankaraiah, N., Reddy, G. S. K. & Raghavan, S. (2007). J. Comb. Chem. 9, 29-42.]; Antonow et al., 2007[Antonow, D., Jenkins, T. C., Howard, P. W. & Thurston, D. E. (2007). Bioorg. Med. Chem. 15, 3041-3053.]; Archer & Sternbach, 1968[Archer, G. A. & Sternbach, L. H. (1968). Chem. Rev. 68, 747-784.]; Mohiuddin et al., 1986[Mohiuddin, C., Reddy, P. S., Ahmed, K. & Ratnam, C. V. (1986). Heterocycles, 24, 3489-3530.], Bose et al., 1992[Bose, D. S., Thompson, A. S., Ching, J. A., Hartley, J. A., Berardini, M. D., Jenkins, T. C., Neidle, S., Hurley, L. H. & Thurston, D. E. (1992). J. Am. Chem. Soc. 114, 4939-4941.]; Gregson et al., 2004[Gregson, S. T., Howard, P. W., Gullick, D. R., Hamaguchi, A., Corcoran, K. E., Brooks, N. A., Hartley, J. A., Jenkins, T. C., Patel, S., Guille, M. J. & Thurston, D. E. (2004). J. Med. Chem. 47, 1161-1174.]). The vast commercial success of these medicinal agents has resulted in their chemistry being a major focus of research in the field of medicinal chemistry and many such ring systems having been described (Benzeid et al., 2009a[Benzeid, H., Essassi, E. M., Saffon, N., Garrigues, B. & Ng, S. W. (2009a). Acta Cryst. E65, o2322.],b[Benzeid, H., Saffon, N., Garrigues, B., Essassi, E. M. & Ng, S. W. (2009b). Acta Cryst. E65, o2684.]; Randles & Storr, 1984[Randles, K. R. & Storr, R. C. (1984). J. Chem. Soc. 22, 1485-1486.]; Sugasawa et al., 1985[Sugasawa, T., Adachi, M., Sasakura, K., Matsushita, A., Eigyo, M., Shiomi, T., Shintaku, H., Takahara, Y. & Murata, S. (1985). J. Med. Chem. 28, 699-707.]; Cipolla et al., 2009[Cipolla, L., Araújo, A. C., Airoldi, C. & Bini, D. (2009). Anticancer Agents Med. Chem. 9, 1-31.]). Pyrrolo­[2,1-c][1,4]benzodiazepines are a group of potent chemicals produced by Streptomyces species. For their anti­cancer activity, see: Bose et al. (1992[Bose, D. S., Thompson, A. S., Ching, J. A., Hartley, J. A., Berardini, M. D., Jenkins, T. C., Neidle, S., Hurley, L. H. & Thurston, D. E. (1992). J. Am. Chem. Soc. 114, 4939-4941.]); Cargill et al. (1974[Cargill, C., Bachmann, E. & Zbinden, G. (1974). J. Natl Cancer Inst. 53, 481-486.]); Gregson et al. (2004[Gregson, S. T., Howard, P. W., Gullick, D. R., Hamaguchi, A., Corcoran, K. E., Brooks, N. A., Hartley, J. A., Jenkins, T. C., Patel, S., Guille, M. J. & Thurston, D. E. (2004). J. Med. Chem. 47, 1161-1174.]).

[Scheme 1]

In a continuation of our research work on the advancement of benzodiazepine derivatives, we have developed a new synthethis for 10-propargyl­pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dione (Fig. 1[link]) in good yield from pyrrolo­[2,1-c][1,4]benzodiazepine with propargylbromide in the presence of tetra-n-butyl­ammonium bromide (TBAB) as catalyst and potassium carbonate as base (Makosza & Jonczyk, 1976[Makosza, M. & Jonczyk, A. (1976). Org. Synth. 55, 91.]). The synthesized compound was characterized by single-crystal X-ray diffraction as well as Hirshfeld surface analysis. The results of the calculations by density functional theory (DFT), carried out at the B3LYP/6-311G (d,p) level, are compared with the experimentally determined mol­ecular structure in the solid state.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

2. Structural commentary

The title compound, (I)[link], consists of pyrrole and benzodiazepine units linked to a propargyl moiety (Fig. 1[link]). The five-membered pyrrole ring (N1/C8/C10–C12) adopts a half-chair conformation [puckering parameters q2 = 0.376 (3) Å and θ = 94.4 (4)°] while the seven-membered diazepine ring (N1/N2/C1/C6–C9) adopts a boat conformation [QT = 0.9262 (13), q2 = 0.9070 (14), q3 = 0.1875 (16) Å, φ2 = 105.6 (4) and φ = 161.4 (5)°]. In the propargyl moiety, the N2—C13—C14 and C13—C14—C15 bond angles are 112.66 (17)° and 177.4 (3)°, respectively.

3. Supra­molecular features

In the crystal, weak C—HBnz⋯ODiazp and C—HProprg⋯ODiazp (Bnz = benzene, Diazp = diazepine and Proprg = proparg­yl) hydrogen bonds (Table 1[link]) link the mol­ecules into two-dimensional networks parallel to the bc plane, enclosing [R_{4}^{4}](28) ring motifs (Fig. 2[link]), with the networks forming oblique stacks along the a-axis direction.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯O2vii 0.93 2.53 3.252 (2) 135
C13—H13A⋯O1viii 0.97 2.54 3.395 (3) 147
Symmetry codes: (vii) x, y, z+1; (viii) [-x+1, y-{\script{1\over 2}}, -z+1].
[Figure 2]
Figure 2
A partial packing diagram viewed along the a-axis direction with weak inter­molecular C—HBnz⋯ODiazp and C—HProprg⋯ODiazp (Bnz = benzene, Diazp = diazepine and Proprg = proparg­yl) hydrogen bonds (dashed lines). H atoms not included in hydrogen bonding have been omitted for clarity.

4. Hirshfeld surface analysis

In order to visualize the inter­molecular inter­actions in the crystal of the title compound, a Hirshfeld surface (HS) analysis (Hirshfeld, 1977[Hirshfeld, H. L. (1977). Theor. Chim. Acta, 44, 129-138.]; Spackman & Jayatilaka, 2009[Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19-32.]) was carried out using Crystal Explorer 17.5 (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.]). In the HS plotted over dnorm (Fig. 3[link]), the white surface indicates contacts with distances equal to the sum of van der Waals radii, and the red and blue colours indicate distances shorter (in close contact) or longer (distinct contact) than the van der Waals radii, respectively (Venkatesan et al., 2016[Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H. & Sundius, T. (2016). Spectrochim. Acta Part A, 153, 625-636.]). The bright-red spots appearing near O1, O2 and hydrogen atom H13A indicate their roles as the respective donors and acceptors; they also appear as blue and red regions corresponding to positive and negative potentials on the HS mapped over electrostatic potential (Spackman et al., 2008[Spackman, M. A., McKinnon, J. J. & Jayatilaka, D. (2008). CrystEngComm, 10, 377-388.]; Jayatilaka et al., 2005[Jayatilaka, D., Grimwood, D. J., Lee, A., Lemay, A., Russel, A. J., Taylor, C., Wolff, S. K., Cassam-Chenai, P. & Whitton, A. (2005). TONTO - A System for Computational Chemistry. Available at: http://hirshfeldsurface.net/]) shown in Fig. 4[link]. Here the blue regions indicate positive electrostatic potential (hydrogen-bond donors), while the red regions indicate negative electrostatic potential (hydrogen-bond acceptors). The shape-index of the HS is a tool to visualize the ππ stacking by the presence of adjacent red and blue triangles; if there are no adjacent red and/or blue triangles, then there are no ππ inter­actions. Fig. 5[link] clearly suggests that there are no ππ inter­actions in (I)[link].

[Figure 3]
Figure 3
View of the three-dimensional Hirshfeld surface of the title compound plotted over dnorm in the range −0.1285 to 1.4451 a.u.
[Figure 4]
Figure 4
View of the three-dimensional Hirshfeld surface of the title compound plotted over 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. Hydrogen-bond donors and acceptors are shown as blue and red regions around the atoms, corresponding to positive and negative potentials, respectively.
[Figure 5]
Figure 5
Hirshfeld surface of the title compound plotted over shape-index.

The overall two-dimensional fingerprint plot, Fig. 6[link]a, and those delineated into H⋯H, H⋯C/C⋯H, H⋯O/O⋯H, C⋯C and H⋯N/N⋯H contacts (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) are illustrated in Fig. 6[link] bf, respectively, together with their relative contributions to the Hirshfeld surface. The most important inter­action is H⋯H contributing 49.8% 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 = 1.13 Å. In the absence of C—H ⋯ π inter­actions, the pairs of characteristic wings in Fig. 6[link]c arises from H⋯C/C⋯H contacts (25.7% contribution to the HS); the pair of spikes have tips at de + di = 2.80 Å. The thin and thick pairs of scattered points of wings in the fingerprint plot delineated into H⋯O/O⋯H contacts (Fig. 6[link]d, 20.1%) have a symmetrical distribution of points with the edges at de + di = 2.42 and 2.44 Å, respectively. The C⋯C contacts (Fig. 6[link]e, 1.8%) have a pliers-shaped distribution of points with the tips at de + di = 3.47 Å. Finally, the H ⋯ N/N⋯H inter­actions (1.8%) are reflected in Fig. 6[link]f as thick wings with the tips at de + di = 3.04 Å. Selected contacts are listed in Table 2[link].

Table 2
Selected interatomic distances (Å)

O1⋯C15i 3.273 (4) O2⋯H4ii 2.69
O1⋯C13ii 3.395 (3) N1⋯N2 2.898 (2)
O2⋯C2iii 3.252 (2) C2⋯C10v 3.558 (3)
O2⋯C11 3.303 (3) C4⋯C12vi 3.552 (4)
O2⋯C4ii 3.397 (3) C5⋯C14 3.090 (4)
O1⋯H8iv 2.82 C7⋯C15i 3.512 (4)
O1⋯H12Aiv 2.76 C1⋯H8 2.69
O1⋯H2 2.63 C3⋯H12Avi 2.90
O1⋯H10A 2.73 C3⋯H11Bv 2.87
O1⋯H15i 2.81 C5⋯H13A 2.86
O1⋯H13Aii 2.54 C6⋯H8 2.69
O2⋯H2iii 2.53 C7⋯H13Aii 2.93
O2⋯H12B 2.45 C13⋯H5 2.66
O2⋯H13B 2.32 C14⋯H5 2.92
O2⋯H11A 2.89 H5⋯H13A 2.32
Symmetry codes: (i) x-1, y, z; (ii) [-x+1, y+{\script{1\over 2}}, -z+1]; (iii) x, y, z-1; (iv) [-x, y+{\script{1\over 2}}, -z+1]; (v) [-x, y-{\script{1\over 2}}, -z+1]; (vi) x+1, y, z+1.
[Figure 6]
Figure 6
The full two-dimensional fingerprint plots for the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) H⋯C/C⋯H, (d) H⋯O/O⋯H, (e) C⋯C and (f) H⋯N/N⋯H inter­actions. The di and de values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface contacts.

The Hirshfeld surface representations with the function dnorm plotted onto the surface are shown for the H⋯H, H⋯C/C⋯H and H⋯O/O⋯H inter­actions in Fig. 7[link]ac, respectively.

[Figure 7]
Figure 7
Hirshfeld surface representations with the function dnorm plotted onto the surface for (a) H⋯H, (b) H⋯C/C⋯H and (c) H⋯O/O⋯H inter­actions.

The Hirshfeld surface analysis confirms the importance of H-atom contacts in establishing the packing. The large number of H⋯H, H⋯C/C⋯H and H⋯O/O⋯H inter­actions suggest that van der Waals inter­actions and hydrogen bonding play the major roles in the crystal packing (Hathwar et al., 2015[Hathwar, V. R., Sist, M., Jørgensen, M. R. V., Mamakhel, A. H., Wang, X., Hoffmann, C. M., Sugimoto, K., Overgaard, J. & Iversen, B. B. (2015). IUCrJ, 2, 563-574.]).

5. Inter­action energy calculations

The inter­molecular inter­action energies were calculated using the CE–B3LYP/6–31G(d,p) energy model in Crystal Explorer 17.5 (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.]), where a cluster of mol­ecules is generated by applying crystallographic symmetry operations with respect to a selected central mol­ecule within a default radius of 3.8 Å (Turner et al., 2014[Turner, M. J., Grabowsky, S., Jayatilaka, D. & Spackman, M. A. (2014). J. Phys. Chem. Lett. 5, 4249-4255.]). The total inter­molecular energy (Etot) is the sum of electrostatic (Eele), polarization (Epol), dispersion (Edis) and exchange-repulsion (Erep) energies (Turner et al., 2015[Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D. & Spackman, M. A. (2015). Chem. Commun. 51, 3735-3738.]) with scale factors of 1.057, 0.740, 0.871 and 0.618, respectively (Mackenzie et al., 2017[Mackenzie, C. F., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). IUCrJ, 4, 575-587.]). Hydrogen-bonding inter­action energies (in kJ mol−1) were calculated as −13.2 (Eele), −3.8 (Epol), −45.1 (Edis), 27.8 (Erep) and −38.8 (Etot) for C2—H2⋯O2 and −10.7 (Eele), −4.0 (Epol), −25.8 (Edis), 15.7 (Erep) and −27.1 (Etot) for C13—H13A⋯O1.

6. DFT calculations

The optimized structure of the title compound in the gas phase was generated theoretically via density functional theory (DFT) using standard B3LYP functional and 6–311 G(d,p) basis-set calculations (Becke, 1993[Becke, A. D. (1993). J. Chem. Phys. 98, 5648-5652.]) as implemented in GAUSSIAN 09 (Frisch et al., 2009[Frisch, M. J., et al. (2009). GAUSSIAN09. Gaussian Inc., Wallingford, CT, USA.]). The theoretical and experimental results were in good agreement (Table 3[link]). The highest-occupied mol­ecular orbital (HOMO), acting as an electron donor, and the lowest-unoccupied mol­ecular orbital (LUMO), acting as an electron acceptor, are very important parameters for quantum chemistry. When the energy gap is small, the mol­ecule is highly polarizable and has high chemical reactivity. The DFT calculations provide some important information on the reactivity and site selectivity of the mol­ecular framework. EHOMO and ELUMO clarify the inevitable charge-exchange collaboration inside the studied material, and are given in Table 4[link] along with the electronegativity (χ), hardness (η), potential (μ), electrophilicity (ω) and softness (σ). The significance of η and σ is to evaluate both the reactivity and stability. The electron transition from the HOMO to the LUMO energy level is shown in Fig. 8[link]. The HOMO and LUMO are localized in the plane extending from the whole 10-propargyl­pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dione ring. The energy band gap [ΔE = ELUMO − EHOMO] of the mol­ecule is 3.4829 eV, and the frontier mol­ecular orbital energies, EHOMO and ELUMO are −4.0030 and −0.5203 eV, respectively.

Table 3
Comparison of the selected (X-ray and DFT) geometric data (Å, °)

Bonds/angles X-ray B3LYP/6–311G(d,p)
O1—C7 1.231 (2) 1.30064
O2—C9 1.222 (2) 1.30459
N1—C7 1.337 (2) 1.44900
N1—C8 1.474 (2) 1.42892
N1—C10 1.476 (2) 1.41852
N2—C6 1.429 (2) 1.45461
N2—C9 1.362 (2) 1.45679
N2—C13 1.478 (2) 1.48990
     
C7—N1—C8 124.64 (14) 125.54242
C7—N1—C10 122.81 (16) 120.48706
C8—N1—C10 112.28 (14) 111.27162
C6—N2—C13 118.67 (14) 116.39016
C9—N2—C6 123.48 (14) 122.08303
C9—N2—C13 116.98 (15) 113.69042
C1—C6—N2 122.46 (14) 120.60573
C5—C6—N2 118.13 (15) 117.33963

Table 4
Calculated energies

Mol­ecular Energy (a.u.) (eV) Compound (I)
Total Energy, TE (eV) −22499
EHOMO (eV) −4.0030
ELUMO (eV) −0.5203
Gap ΔE (eV) 3.4829
Dipole moment, μ (Debye) 2.2189
Ionization potential, I (eV) 4.0030
Electron affinity, A 0.5203
Electronegativity, χ 2.2617
Hardness, η 1.7414
Electrophilicity index, ω 1.4687
Softness, σ 0.5742
Fraction of electron transferred, ΔN 1.3605
[Figure 8]
Figure 8
The energy band gap of the title compound.

7. Database survey

A alkyl­ated analogue has been reported, viz. 10-allyl-2,3-di­hydro-1H-pyrrolo­[2,1-c][1,4]benzodiazepine-5,11(10H,11aH)-dione (Benzeid et al., 2009a[Benzeid, H., Saffon, N., Garrigues, B., Essassi, E. M. & Ng, S. W. (2009b). Acta Cryst. E65, o2684.]), as well as three similar structures, 2-hy­droxy-10-propargyl­pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dione monohydrate (Ourahou et al. 2010[Ourahou, S., Chammache, M., Zouihri, H., Essassi, E. M. & Ng, S. W. (2010). Acta Cryst. E66, o731.]), rac-9,10-dimeth­oxy-3-methyl-6-phenyl-7,7adi­hydro­benzo[b]benzo[4,5]iso­thia­zolo[2,3-d][1,4]diazepine 12,12-dioxide (Bassin et al., 2011[Bassin, J. P., Shah, V. P., Martin, L. & Horton, P. N. (2011). Acta Cryst. E67, o684-o685.]) and (S)-2,3,5,10,11,11a-hexa­hydro-1H-pyrrolo­[2,1-c][1,4]benzodiazepine-3,11-dione (Cheng et al. 2007[Cheng, M.-S., Ma, C., Liu, J.-H., Sha, Y. & Wang, Q.-H. (2007). Acta Cryst. E63, o4605.]).

8. Synthesis and crystallization

The synthesis of pyrrolo­benzodiazepine is a simple condensation of isatoic anhydride on L-proline. Pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dione (2.15 mmol), propargyl bromide (2.15 mmol) and potassium carbonate (4.3 mmol) along with a catalytic amount of tetra-n-butyl ammonium bromide were stirred in N,N-di­methyl­formamide (20 ml) for 72 h. The solid material was removed by filtration and the solvent evaporated under vacuum. The residue was separated by chromatography on silica gel with an n-hexa­ne–ethyl acetate (1:9) solvent system. The title compound was obtained as colourless crystals in 70% yield upon evaporation of the solvent.

9. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 5[link]. The C-bound H atoms were positioned geometrically, with C—H = 0.93 Å (for aromatic and propagyl moiety's H atoms), 0.98 Å (for methine H atom) and 0.97 Å (for methyl­ene H atoms), and constrained to ride on their parent atoms, with Uiso(H) = 1.Ueq(C).

Table 5
Experimental details

Crystal data
Chemical formula C15H14N2O2
Mr 254.28
Crystal system, space group Monoclinic, P21
Temperature (K) 299
a, b, c (Å) 8.4959 (2), 9.6479 (2), 8.7619 (2)
β (°) 116.921 (1)
V3) 640.36 (3)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.39 × 0.37 × 0.16
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2013[Bruker (2013). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.684, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 12206, 3821, 3349
Rint 0.024
(sin θ/λ)max−1) 0.714
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.103, 1.06
No. of reflections 3821
No. of parameters 172
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.20, −0.15
Absolute structure Flack x determined using 1347 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter −0.4 (3)
Computer programs: APEX3 and SAINT (Bruker, 2013[Bruker (2013). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Computing details top

Data collection: APEX3 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

(S)-10-(Prop-2-yn-1-yl)pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dione top
Crystal data top
C15H14N2O2F(000) = 268
Mr = 254.28Dx = 1.319 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 8.4959 (2) ÅCell parameters from 6478 reflections
b = 9.6479 (2) Åθ = 2.6–28.5°
c = 8.7619 (2) ŵ = 0.09 mm1
β = 116.921 (1)°T = 299 K
V = 640.36 (3) Å3Plate, clear light colourless
Z = 20.39 × 0.37 × 0.16 mm
Data collection top
Bruker APEXII CCD
diffractometer
3349 reflections with I > 2σ(I)
φ and ω scansRint = 0.024
Absorption correction: multi-scan
(SADABS; Bruker, 2013)
θmax = 30.5°, θmin = 2.6°
Tmin = 0.684, Tmax = 0.746h = 1212
12206 measured reflectionsk = 1313
3821 independent reflectionsl = 1212
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.039 w = 1/[σ2(Fo2) + (0.0554P)2 + 0.0351P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.103(Δ/σ)max < 0.001
S = 1.06Δρmax = 0.20 e Å3
3821 reflectionsΔρmin = 0.15 e Å3
172 parametersAbsolute structure: Flack x determined using 1347 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute structure parameter: 0.4 (3)
Primary atom site location: dual
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
xyzUiso*/Ueq
O10.1993 (2)0.71379 (15)0.67243 (19)0.0515 (4)
O20.2576 (2)0.4767 (2)0.15885 (17)0.0621 (4)
N10.10489 (19)0.59648 (15)0.42473 (19)0.0384 (3)
N20.41816 (19)0.46005 (16)0.44625 (18)0.0389 (3)
C10.3344 (2)0.49614 (17)0.68011 (19)0.0342 (3)
C20.3604 (2)0.4606 (2)0.8441 (2)0.0441 (4)
H20.2979760.5075840.8920400.053*
C30.4764 (3)0.3576 (2)0.9365 (2)0.0518 (5)
H30.4910320.3345621.0451790.062*
C40.5709 (3)0.2888 (2)0.8670 (3)0.0525 (5)
H40.6505550.2198230.9295880.063*
C50.5477 (3)0.3218 (2)0.7046 (3)0.0466 (4)
H50.6113990.2743960.6584010.056*
C60.4297 (2)0.42536 (17)0.6096 (2)0.0347 (3)
C70.2084 (2)0.61152 (17)0.5927 (2)0.0360 (3)
C80.0974 (2)0.47097 (19)0.3258 (2)0.0383 (3)
H80.0888770.3874990.3853190.046*
C90.2629 (2)0.4673 (2)0.3002 (2)0.0396 (4)
C100.0288 (3)0.7001 (2)0.3214 (3)0.0540 (5)
H10A0.0219930.7921980.3377580.065*
H10B0.1268790.7011510.3494690.065*
C110.0863 (3)0.6494 (3)0.1404 (3)0.0668 (7)
H11A0.0098040.6853710.0946190.080*
H11B0.2069840.6768030.0659100.080*
C120.0705 (3)0.4919 (3)0.1595 (3)0.0561 (5)
H12A0.1718130.4526600.1671030.067*
H12B0.0601510.4499160.0639010.067*
C130.5822 (3)0.4646 (3)0.4271 (3)0.0522 (5)
H13A0.6184670.3706910.4191180.063*
H13B0.5587980.5120360.3213050.063*
C140.7252 (3)0.5347 (3)0.5684 (3)0.0559 (5)
C150.8456 (4)0.5887 (4)0.6817 (4)0.0771 (8)
H150.9408200.6313900.7712340.092*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0594 (8)0.0445 (7)0.0560 (9)0.0014 (7)0.0310 (7)0.0151 (6)
O20.0678 (9)0.0904 (12)0.0351 (7)0.0028 (9)0.0293 (6)0.0011 (8)
N10.0379 (7)0.0392 (8)0.0384 (8)0.0031 (6)0.0175 (6)0.0009 (6)
N20.0431 (7)0.0439 (8)0.0358 (7)0.0055 (7)0.0233 (6)0.0027 (6)
C10.0366 (8)0.0360 (8)0.0303 (7)0.0079 (6)0.0155 (6)0.0054 (6)
C20.0487 (9)0.0538 (11)0.0312 (8)0.0131 (9)0.0191 (7)0.0088 (8)
C30.0566 (11)0.0604 (12)0.0291 (8)0.0183 (10)0.0112 (8)0.0028 (8)
C40.0526 (11)0.0467 (11)0.0432 (10)0.0022 (9)0.0085 (9)0.0108 (8)
C50.0476 (10)0.0408 (10)0.0479 (10)0.0048 (8)0.0186 (8)0.0039 (8)
C60.0380 (8)0.0349 (8)0.0314 (8)0.0015 (6)0.0160 (7)0.0001 (6)
C70.0379 (8)0.0362 (8)0.0400 (9)0.0062 (6)0.0230 (7)0.0055 (6)
C80.0425 (8)0.0395 (8)0.0326 (7)0.0066 (7)0.0166 (6)0.0036 (7)
C90.0507 (9)0.0383 (8)0.0340 (8)0.0012 (8)0.0228 (7)0.0013 (7)
C100.0473 (10)0.0560 (12)0.0551 (12)0.0131 (9)0.0201 (9)0.0082 (9)
C110.0597 (13)0.0829 (17)0.0490 (12)0.0237 (13)0.0169 (10)0.0158 (12)
C120.0469 (10)0.0737 (15)0.0373 (9)0.0080 (10)0.0099 (8)0.0042 (9)
C130.0510 (10)0.0661 (13)0.0520 (11)0.0141 (10)0.0343 (9)0.0040 (10)
C140.0480 (11)0.0657 (13)0.0659 (14)0.0053 (10)0.0364 (11)0.0103 (11)
C150.0588 (14)0.093 (2)0.0800 (19)0.0120 (14)0.0319 (13)0.0044 (15)
Geometric parameters (Å, º) top
O1—C71.231 (2)C5—C61.393 (2)
O2—C91.222 (2)C8—H80.9800
N1—C71.337 (2)C8—C91.521 (3)
N1—C81.474 (2)C8—C121.522 (3)
N1—C101.476 (2)C10—H10A0.9700
N2—C61.429 (2)C10—H10B0.9700
N2—C91.362 (2)C10—C111.513 (3)
N2—C131.478 (2)C11—H11A0.9700
C1—C21.394 (2)C11—H11B0.9700
C1—C61.399 (2)C11—C121.527 (4)
C1—C71.493 (2)C12—H12A0.9700
C2—H20.9300C12—H12B0.9700
C2—C31.376 (3)C13—H13A0.9700
C3—H30.9300C13—H13B0.9700
C3—C41.378 (3)C13—C141.450 (3)
C4—H40.9300C14—C151.176 (4)
C4—C51.382 (3)C15—H150.9300
C5—H50.9300
O1···C15i3.273 (4)O2···H4ii2.69
O1···C13ii3.395 (3)N1···N22.898 (2)
O2···C2iii3.252 (2)C2···C10v3.558 (3)
O2···C113.303 (3)C4···C12vi3.552 (4)
O2···C4ii3.397 (3)C5···C143.090 (4)
O1···H8iv2.82C7···C15i3.512 (4)
O1···H12Aiv2.76C1···H82.69
O1···H22.63C3···H12Avi2.90
O1···H10A2.73C3···H11Bv2.87
O1···H15i2.81C5···H13A2.86
O1···H13Aii2.54C6···H82.69
O2···H2iii2.53C7···H13Aii2.93
O2···H12B2.45C13···H52.66
O2···H13B2.32C14···H52.92
O2···H11A2.89H5···H13A2.32
C7—N1—C8124.64 (14)C9—C8—C12112.98 (15)
C7—N1—C10122.81 (16)C12—C8—H8110.8
C8—N1—C10112.28 (14)O2—C9—N2122.16 (17)
C6—N2—C13118.67 (14)O2—C9—C8122.34 (16)
C9—N2—C6123.48 (14)N2—C9—C8115.42 (14)
C9—N2—C13116.98 (15)N1—C10—H10A111.2
C2—C1—C6118.81 (16)N1—C10—H10B111.2
C2—C1—C7117.02 (15)N1—C10—C11102.59 (18)
C6—C1—C7124.15 (14)H10A—C10—H10B109.2
C1—C2—H2119.3C11—C10—H10A111.2
C3—C2—C1121.41 (18)C11—C10—H10B111.2
C3—C2—H2119.3C10—C11—H11A111.0
C2—C3—H3120.2C10—C11—H11B111.0
C2—C3—C4119.60 (18)C10—C11—C12103.65 (19)
C4—C3—H3120.2H11A—C11—H11B109.0
C3—C4—H4119.9C12—C11—H11A111.0
C3—C4—C5120.23 (19)C12—C11—H11B111.0
C5—C4—H4119.9C8—C12—C11103.60 (18)
C4—C5—H5119.7C8—C12—H12A111.0
C4—C5—C6120.63 (19)C8—C12—H12B111.0
C6—C5—H5119.7C11—C12—H12A111.0
C1—C6—N2122.46 (14)C11—C12—H12B111.0
C5—C6—N2118.13 (15)H12A—C12—H12B109.0
C5—C6—C1119.32 (15)N2—C13—H13A109.1
O1—C7—N1122.16 (17)N2—C13—H13B109.1
O1—C7—C1121.40 (16)H13A—C13—H13B107.8
N1—C7—C1116.43 (14)C14—C13—N2112.66 (17)
N1—C8—H8110.8C14—C13—H13A109.1
N1—C8—C9108.01 (14)C14—C13—H13B109.1
N1—C8—C12103.06 (16)C15—C14—C13177.4 (3)
C9—C8—H8110.8C14—C15—H15180.0
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1/2, z+1; (iii) x, y, z1; (iv) x, y+1/2, z+1; (v) x, y1/2, z+1; (vi) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O2vii0.932.533.252 (2)135
C13—H13A···O1viii0.972.543.395 (3)147
Symmetry codes: (vii) x, y, z+1; (viii) x+1, y1/2, z+1.
Comparison of the selected (X-ray and DFT) geometric data (Å, °) top
Bonds/anglesX-rayB3LYP/6-311G(d,p)
O1—C71.231 (2)1.30064
O2—C91.222 (2)1.30459
N1—C71.337 (2)1.44900
N1—C81.474 (2)1.42892
N1—C101.476 (2)1.41852
N2—C61.429 (2)1.45461
N2—C91.362 (2)1.45679
N2—C131.478 (2)1.48990
C7—N1—C8124.64 (14)125.54242
C7—N1—C10122.81 (16)120.48706
C8—N1—C10112.28 (14)111.27162
C6—N2—C13118.67 (14)116.39016
C9—N2—C6123.48 (14)122.08303
C9—N2—C13116.98 (15)113.69042
C1—C6—N2122.46 (14)120.60573
C5—C6—N2118.13 (15)117.33963
Calculated energies top
Molecular Energy (a.u.) (eV)Compound (I)
Total Energy, TE (eV)-22498.546
EHOMO (eV)-4.0030
ELUMO (eV)-0.5203
Gap ΔE (eV)3.4829
Dipole moment, µ (Debye)2.2189
Ionisation potential, I (eV)4.0030
Electron affinity, A0.5203
Electronegativity, χ2.2617
Hardness, η1.7414
Electrophilicity index, ω1.4687
Softness, σ0.5742
Fraction of electron transferred, ΔN1.3605
 

Funding information

TH is grateful to Hacettepe University Scientific Research Project Unit (grant No. 013 D04 602 004).

References

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