Piperazines are important pharmacophores that are found in many biologically active compounds across a number of different therapeutic areas (Berkheij et al., 2005 ▸; Brockunier et al., 2004 ▸; Bogatcheva et al., 2006 ▸) such as antifungal (Upadhayaya et al., 2004 ▸), anti-bacterial, anti-malarial and anti-psychotic agents (Chaudhary et al., 2006 ▸). The pharmacological properties of phenylpiperazines and their derivatives have been described by Cohen et al. (1982 ▸), Conrado et al. (2008 ▸), Neves et al. (2003 ▸), and by Hanano et al. (2000 ▸). The design and synthesis of phenylpiperazine derivatives as potent anticancer agents for prostate cancer have been described by Demirci et al. (2019 ▸). Many pharmaceutical compounds are derived from 1-phenylpiperazine, viz., oxypertine, trazodone, nefazodone, etc. Valuable insights into recent advances in antimicrobial activity of piperazine derivatives have been provided by Kharb et al. (2012 ▸). A review of current pharmacological and toxicological information for piperazine derivatives was conducted by Elliott (2011 ▸).4-Nitrophenylpiperazinium chloride monohydrate has been used as an intermediate in the synthesis of anticancer drugs, transcriptase inhibitors and antifungal reagents, and is also an important reagent for potassium channel openers, which show considerable biomolecular current-voltage rectification characteristics (Lu, 2007 ▸). The inclusion behaviours of 4-sulfonatocalix[n]arenes (SCXn) (n = 4, 6, 8) with 1-(4-nitrophenyl)piperazine (NPP) were investigated by UV and fluorescence spectroscopies at different pH values (Zhang et al., 2014 ▸). The design, synthesis and biological profiling of aryl piperazine-based scaffolds for the management of androgen-sensitive prostatic disorders has also been reported by Gupta et al. (2016 ▸). 4-Nitrophenylpiperazine was the starting material in the synthesis and biological evaluation of novel piperazine containing hydrazone derivatives (Kaya et al., 2016 ▸).In view of the importance of piperazines in general and the use of 4-nitrophenylpiperazine and 1-phenylpiperazine in particular, this paper reports the synthesis and crystal structures of 1-benzoyl-4-(4-nitrophenyl)piperazine, C17H17N3O3, (I) and 1-(4-bromobenzoyl)phenylpiperazine, C17H17BrN2O, (II).
Structural commentary
There are no unusual bond distances or angles in either I or II. The asymmetric unit of I (see scheme) contains two molecules, suffixed ‘A’ and ‘B’ in Fig. 1 ▸. Each consists of a central piperazine ring in a chair conformation, with a benzoyl and nitrophenyl group attached to different nitrogen atoms. The nitro groups are almost coplanar with their attached benzene rings, forming dihedral angles of 4.4 (2) and 3.0 (2)° for molecules A and B, respectively. The phenyl rings are twisted out of planarity with the carbonyl group and its linkage to the piperazine rings, giving N1—C11—C12—C13 torsion angles of −46.8 (3) and 45.4 (3)° for A and B, respectively. The dihedral angles between the phenyl and nitrobenzene rings are 51.52 (6)° in A and 57.23 (7)° in B. Compound II on the other hand has just one molecule in its asymmetric unit (Fig. 2 ▸). The piperazine ring is also in a chair conformation and the brominated ring is torsioned [N1—C11—C12—C13 = 46.4 (4)°] to a similar degree to that in I, but the dihedral angle between the phenyl and brominated benzene rings is larger, at 86.6 (1)°.
Figure 1
An ellipsoid plot (50% probability) of I showing the two molecules in the asymmetric unit.
Figure 2
An ellipsoid plot (50% probability) of II.
Supramolecular features
There are no conventional hydrogen bonds in either I or II, but there are weaker C—H⋯O contacts (Table 1 ▸). For I, SHELXL identifies a number of ‘potential’ hydrogen-bonding interactions, but most of these have poor geometry for hydrogen bonds. The shortest donor–acceptor distances occur for the bifurcated pair C6B—H6B⋯O1A and C7B—H7B⋯O1A within the chosen asymmetric unit. A similar bifurcated pair of contacts C6A—H6A⋯O1B
i and C7A—H7A⋯O1B
i [symmetry code: (i) x, y, z + 1] occur between the A and B molecules in adjacent (along c) asymmetric units. In combination, these interactions lead to double chains that extend parallel to [001] (Fig. 3 ▸). In contrast to I, SHELXL identifies no ‘potential’ hydrogen bonds for II. Mercury (Macrae et al., 2020 ▸) on the other hand, which has different default parameters for flagging hydrogen bonds, identifies a bifurcated pair, C13—H13⋯O1ii and C14—H14⋯O1ii [symmetry code: (ii) x, y + 1, z] (Table 1 ▸). A clearer picture of this interaction is provided by a view of the Hirshfeld surface plotted over d
norm, as calculated by CrystalExplorer (Spackman et al., 2021 ▸), which highlights contacts shorter than the van der Waals radius sum as red blobs (Fig. 4 ▸). This bifurcated pair of interactions link molecules of II into chains that extend along [010]. The various atom–atom contacts as quantified in Hirshfeld surface analysis fingerprint plots are given in Figs. 5 ▸ and 6 ▸.
Table 1
Short intermolecular C—H⋯O contacts (Å, °) in I and II
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
I
C6B—H6B⋯O1A
0.95
2.50
3.140 (2)
124.5
C7B—H7B⋯O1A
0.95
2.58
3.171 (2)
120.3
C6A—H6A⋯O1Bi
0.95
2.47
3.173 (2)
131.0
C7A—H7A⋯O1Bi
0.95
2.78
3.317 (2)
116.8
II
C13—H13⋯O1ii
0.95
2.60
3.018 (4)
107.3
C14—H14⋯O1ii
0.95
2.68
3.052 (4)
104.0
Symmetry codes: (i) x, y, z + 1; (ii) x, y − 1, z
Figure 3
A partial packing plot of I, showing close contacts (dashed lines) that connect the molecules into chains parallel to the c-axis.
Figure 4
A partial packing plot of II, showing the Hirshfeld surface of the central molecule, highlighting (red blobs) the bifurcated close contacts (dashed lines) that join the molecules into chains parallel to the b-axis.
Figure 5
Hirshfeld surface analysis fingerprint plots showing the relative coverage of different atom-atom contacts in I: (a) H⋯H = 38.3%, (b) O⋯H/H⋯O = 28.8%, (c) C⋯H/H⋯C = 24.1%, (d) N⋯H/H⋯N = 4.1%, (e) C⋯O/O.·C = 2.4%, (f) C⋯C = 1.8%. All other contacts are negligible.
Figure 6
Hirshfeld surface analysis fingerprint plots showing the relative coverage of different atom-atom contacts in II: (a) H⋯H = 45.5%, (b) C⋯H/H⋯C = 26.8, (c) Br⋯H/H⋯Br = 12.6%, (d) O⋯H/H⋯O = 7.1%, (e) N⋯H/H.·N = 3.1%, (f) O⋯Br/Br⋯O = 1.7%, (g) Br⋯Br = 1.1%, (h) C⋯Br/Br⋯C = 1.0%, (i) C⋯O/O⋯C = 0.8%. All other contacts are negligible.
Database survey
There are numerous crystal structures related to I and II in the Cambridge Structure Database (CSD v5.42 with updates through June 2022; Groom et al., 2016 ▸). A search on the central core, piperazine-1-carbaldehyde gave 834 hits whereas search fragments 4-benzoylpiperazine and 4-phenylpiperazine-1-carbaldehyde gave 132 and 110 hits, respectively. A search on 1-benzoyl-4-phenylpiperazine gave 20 hits, two of which have little in common with I or II. An NMR-based investigation of conformational behaviour in solution by Wodtke et al. (2018 ▸) of acyl-functionalized piperazines includes the crystal structures of 1-(4-fluorobenzoyl)-4-(4-nitrophenyl)piperazine (BIQYIM), 1-(4-bromobenzoyl)-4-(4-nitrophenyl)piperazine (BIRHES), and 1-(3-bromobenzoyl)-4-(4-nitrophenyl)piperazine (BIRHIW). Six new 1-aroyl-4-(4-methoxyphenyl)piperazines (VONFOW, VONGAJ, VONGEN, VONGIR, VONGOX, VONGUD) were prepared using coupling reactions between benzoic acids and N-(4-methoxyphenyl)piperazine (Kiran Kumar et al., 2019 ▸). Six 1-halobenzoyl-4-(2-methoxyphenyl)piperazines (FALHEJ, FALHIN, FALHOT, FALHUZ, FALJAH, FALJEL) with a variety of disorder, pseudosymmetry and twinning were described by Harish Chinthal et al. (2021 ▸). 1-(3,5-Dinitrobenzoyl)-4-(2-methoxyphenyl)piperazine (LAHBIJ) was published by Harish Chinthal et al. (2020 ▸). The remaining two hits are piperazine derivatives with (2-methoxyphenylsulfanyl)benzoyl groups plus 2,3-dichlorophenyl (DEGHAZ: Chu et al., 2006 ▸) and 2-methoxyphenyl (SAYYEX: Li et al., 2006 ▸).
Synthesis and crystallization
Synthetic routes for compounds similar to I and II have already been reported by two separate research groups (Kumari et al., 2015 ▸; Wodtke et al., 2018 ▸). The present syntheses are totally different from those earlier reports. 1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (109 mg, 0.7 mmol), 1-hydroxybenzotriazole (68 mg, 0.5 mmol) and triethylamine (0.5 ml, 1.5 mmol) were added to a solution of benzoic acid (0.5 mmol) or 4-bromobenzoic acid (0.5 mmol) in N,N-dimethylformamide (5 ml) and the resulting mixture was stirred for 20 min at 273 K. A solution of 1-(4-nitrophenyl)piperazine (104 mg, 0.5 mmol) or 1-phenylpiperazine (81 mg, 0.5 mmol) in N,N-dimethylformamide (5 ml) was then added and stirring was continued overnight at ambient temperature. Reaction schemes are summarized in Fig. 7 ▸. When the reactions were confirmed to be complete using thin-layer chromatography, each mixture was quenched with water (10 ml) and extracted with ethyl acetate (20 ml). Each organic fraction was separated and washed successively with an aqueous hydrochloric acid solution (1 mol dm−3), a saturated solution of sodium hydrogencarbonate, and lastly with brine. The organic phases were dried over anhydrous sodium sulfate and the solvent was removed under reduced pressure. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation, at ambient temperature and in the presence of air, of solutions in ethyl acetate (I: yield 81%, m.p. 428–430 K; II: yield 75%, m.p. 394–396 K).
Figure 7
Reaction schemes for the synthesis of I and II. EDC·HCl = 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride, HOBt = 1-hydroxybenzotriazole, TEA = triethylamine, DMF = dimethylformamide.
Data collection and structure refinement
For I, an orange, irregular block-shaped crystal was mounted using polyisobutene oil on the tip of a fine glass fibre in a copper mounting pin. Cu Kα radiation was chosen to facilitate setting the correct absolute structure, which was definitively established by variants of Flack’s parameter (Flack & Bernardinelli, 1999 ▸; Hooft et al., 2008 ▸; Parsons et al., 2013 ▸). For II, the available sample consisted of colourless plates, none of which were single crystals. A suitable specimen was mounted in the same way as for I. Diffraction data collected at 90 K showed two slightly mis-aligned, but sharp and distinct reciprocal lattices. These were not related by any rational twin operation, but by a seemingly arbitrary ∼4° rotation, presumably due to mis-stacking of aggregated plates. Nevertheless, for data acquisition and processing, facilities for handling twinning by non-merohedry were used. For a brief discussion of true twins vs aggregates, see Parkin (2021 ▸). The absolute structure was again determined unambiguously via the Flack parameter and related methods. Crystal data, data collection and refinement statistics are summarized in Table 2 ▸. For both structures, hydrogen atoms were included using riding models, with constrained distances set to 0.95 Å (Csp
2H) and 0.99 Å (R
2CH2). U
iso(H) parameters were set to 1.2U
eq of the attached atom.
Table 2
Experimental details
I
II
Crystal data
Chemical formula
C17H17N3O3
C17H17BrN2O
Mr
311.33
345.23
Crystal system, space group
Orthorhombic, Pna21
Monoclinic, P21
Temperature (K)
90
90
a, b, c (Å)
18.7779 (4), 10.0699 (2), 15.7288 (3)
7.5162 (3), 6.1125 (2), 15.7249 (5)
α, β, γ (°)
90, 90, 90
90, 98.625 (1), 90
V (Å3)
2974.18 (10)
714.28 (4)
Z
8
2
Radiation type
Cu Kα
Mo Kα
μ (mm−1)
0.80
2.88
Crystal size (mm)
0.24 × 0.18 × 0.12
0.35 × 0.20 × 0.06
Data collection
Diffractometer
Bruker D8 Venture dual source
Bruker D8 Venture dual source
Absorption correction
Multi-scan (SADABS; Krause et al., 2015 ▸)
Multi-scan (TWINABS; Sheldrick, 2012 ▸)
Tmin, Tmax
0.854, 0.942
0.568, 0.806
No. of measured, independent and observed [I > 2σ(I)] reflections
24139, 5684, 5575
6918, 6918, 6410
Rint
0.027
0.065
(sin θ/λ)max (Å−1)
0.625
0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.028, 0.075, 1.04
0.023, 0.049, 1.04
No. of reflections
5684
6918
No. of parameters
416
191
No. of restraints
1
1
H-atom treatment
H-atom parameters constrained
H-atom parameters constrained
Δρmax, Δρmin (e Å−3)
0.18, −0.16
0.29, −0.22
Absolute structure
Flack x determined using 2442 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013 ▸)
Flack x determined using 1306 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013 ▸)
Absolute structure parameter
0.01 (5)
0.012 (4)
Computer programs: APEX3 (Bruker, 2016 ▸), SHELXT (Sheldrick, 2015a
▸), SHELXL2019/2 (Sheldrick, 2015b
▸), SHELXTL and XP in SHELXTL (Sheldrick, 2008 ▸) and publCIF (Westrip, 2010 ▸).
Crystal structure: contains datablock(s) I, II, global. DOI: 10.1107/S2056989022009008/tx2058sup1.cifStructure factors: contains datablock(s) I. DOI: 10.1107/S2056989022009008/tx2058Isup2.hklStructure factors: contains datablock(s) II. DOI: 10.1107/S2056989022009008/tx2058IIsup3.hklCCDC references: 2205954, 2205953Additional supporting information: crystallographic information; 3D view; checkCIF report
C17H17N3O3
Dx = 1.391 Mg m−3
Mr = 311.33
Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, Pna21
Cell parameters from 9920 reflections
a = 18.7779 (4) Å
θ = 4.4–74.3°
b = 10.0699 (2) Å
µ = 0.80 mm−1
c = 15.7288 (3) Å
T = 90 K
V = 2974.18 (10) Å3
Cut block, orange
Z = 8
0.24 × 0.18 × 0.12 mm
F(000) = 1312
Bruker D8 Venture dual source diffractometer
5684 independent reflections
Radiation source: microsource
5575 reflections with I > 2σ(I)
Detector resolution: 7.41 pixels mm-1
Rint = 0.027
φ and ω scans
θmax = 74.5°, θmin = 4.7°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)
h = −23→23
Tmin = 0.854, Tmax = 0.942
k = −12→11
24139 measured reflections
l = −17→19
Refinement on F2
Hydrogen site location: difference Fourier map
Least-squares matrix: full
H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.028
w = 1/[σ2(Fo2) + (0.0371P)2 + 0.6857P] where P = (Fo2 + 2Fc2)/3
Primary atom site location: structure-invariant direct methods
Absolute structure: Flack x determined using 2442 quotients
[(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
Secondary atom site location: difference Fourier map
Absolute structure parameter: 0.01 (5)
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 progress was checked using Platon (Spek, 2020) and by
an R-tensor (Parkin, 2000). The final model was further checked
with the IUCr utility checkCIF.
Secondary atom site location: difference Fourier map
Least-squares matrix: full
Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.023
H-atom parameters constrained
wR(F2) = 0.049
w = 1/[σ2(Fo2) + (0.0158P)2 + 0.0999P] where P = (Fo2 + 2Fc2)/3
S = 1.04
(Δ/σ)max = 0.001
6918 reflections
Δρmax = 0.29 e Å−3
191 parameters
Δρmin = −0.22 e Å−3
1 restraint
Absolute structure: Flack x determined using 1306 quotients
[(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods
Absolute structure parameter: 0.012 (4)
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 progress was checked using Platon (Spek, 2020) and by
an R-tensor (Parkin, 2000). The final model was further checked
with the IUCr utility checkCIF. Refined as a 2-component aggregate.
Authors: Linda L Brockunier; Jiafang He; Lawrence F Colwell; Bahanu Habulihaz; Huaibing He; Barbara Leiting; Kathryn A Lyons; Frank Marsilio; Reshma A Patel; Yohannes Teffera; Joseph K Wu; Nancy A Thornberry; Ann E Weber; Emma R Parmee Journal: Bioorg Med Chem Lett Date: 2004-09-20 Impact factor: 2.823