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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 70| Part 10| October 2014| Pages 203-206

Crystal structures of 4-(pyrimidin-2-yl)piperazin-1-ium chloride and 4-(pyrimidin-2-yl)piperazin-1-ium nitrate

aDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India, and bDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA
*Correspondence e-mail: jjasinski@keene.edu

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 30 August 2014; accepted 7 September 2014; online 13 September 2014)

The title salts, C8H13N4+·Cl, (I), and C8H13N4+·NO3, (II), contain linked pyridinium–piperazine heterocycles. In both salts, the piperazine ring adopts a chair conformation with protonation at the N atom not linked to the other ring. In the crystal of (I), weak N—H⋯Cl inter­actions are observed, leading to zigzag chains along [100]. In the crystal of (II), both H atoms on the NH2+ group form bifurcated N—H⋯(O,O) hydrogen bonds. Weak C—H⋯O inter­actions are also observed. These bonds collectively link the components into infinite chains along [100].

1. Chemical context

Pyrimidine-containing compounds exhibit various biological activities (Goldmann & Stoltefuss, 1991[Goldmann, S. & Stoltefuss, J. (1991). Angew. Chem. Int. Ed. Engl. 30, 1559-1578.]) and related fused heterocycles are unique classes of heterocyclic compounds that exhibit a broad spectrum of biological activities such as anti­cancer (Amin et al., 2009[Amin, K. M., Hanna, M. M., Abo-Youssef, H. E., Riham, F. & George, R. F. (2009). Eur. J. Med. Chem. 44, 4572-4584.]; Pandey et al., 2004[Pandey, S., Suryawanshi, S. N., Gupta, S. & Srivastava, V. M. L. (2004). Eur. J. Med. Chem. 39, 969-973.]), anti­viral (Ibrahim & El-Metwally, 2010[Ibrahim, D. A. & El-Metwally, A. M. (2010). Eur. J. Med. Chem. 45, 1158-1166.]), anti­bacterial (Kuyper et al., 1996[Kuyper, L. F., Garvey, J. M., Baccanari, D. P., Champness, J. N., Stammers, D. K. & Beddell, C. R. (1996). Bioorg. Med. Chem. Lett. 4, 593-602.]) and anti-oxidant (Padmaja et al., 2009[Padmaja, A., Payani, T., Reddy, G. D., Dinneswara Reddy, G. & Padmavathi, V. (2009). Eur. J. Med. Chem. 44, 4557-4566.]), anti­depressant (Kim et al., 2010[Kim, J. Y., Kim, D. & Kang, S. Y. (2010). Bioorg. Med. Chem. Lett. 20, 6439-6442.]) and possess anti-inflammatory effects (Clark et al., 2007[Clark, M. P., George, K. M. & Bookland, R. G. (2007). Bioorg. Med. Chem. Lett. 17, 1250-1253.]). In addition, several piperazine derivatives have reached the stage of clinical application; among the known drugs that are used to treat anxiety is a pyrimidinylpiperazinyl compound, bu­spirone (trade name BuSpar®) (Tollefson et al., 1991[Tollefson, G. D., Lancaster, S. P. & Montague-Clouse, J. (1991). Psychopharmacol. Bull. 27, 163-170.]). Our research group has published a number of papers on incorporated heterocyclic ring structures, viz. imatinibium dipicrate (Jasinski et al., 2010[Jasinski, J. P., Butcher, R. J., Hakim Al-Arique, Q. N. M., Yathirajan, H. S. & Narayana, B. (2010). Acta Cryst. E66, o411-o412.]), 1-(2-hy­droxy­eth­yl)-4-[3-(2-tri­fluoro­methyl-9H-thioxanthen-9-yl­idene)prop­yl]piperazine-1,4-diium dichloride, which is the di­hydro­chloride salt of flupentixol (Siddegowda et al., 2011a[Siddegowda, M. S., Butcher, R. J., Akkurt, M., Yathirajan, H. S. & Narayana, B. (2011a). Acta Cryst. E67, o2079-o2080.]) and opipramolium fumarate (Siddegowda et al., 2011b[Siddegowda, M. S., Jasinski, J. P., Golen, J. A., Yathirajan, H. S. & Swamy, M. T. (2011b). Acta Cryst. E67, o2296.]). Other related crystal structures are 4-(pyrimidin-2-yl)piperazin-1-ium (E)-3-carb­oxy­prop-2-enoate (Yamuna et al., 2014a[Yamuna, T. S., Kaur, M., Jasinski, J. P. & Yathirajan, H. S. (2014a). Acta Cryst. E70, o702-o703.]), flupentixol tartarate and enrofloxacinium oxalate (Yamuna et al., 2014b[Yamuna, T. S., Kaur, M., Anderson, B. J., Jasinski, J. P. & Yathirajan, H. S. (2014b). Acta Cryst. E70, o206-o207.],c[Yamuna, T. S., Kaur, M., Anderson, B. J., Jasinski, J. P. & Yathirajan, H. S. (2014c). Acta Cryst. E70, o200-o201.]). As part of our ongoing studies in this area, we report herein the crystal structures of the title salts, (I)[link] and (II)[link].

[Scheme 1]

2. Structural commentary

The structure of (I)[link] and its atom numbering are shown in Fig. 1[link]. It consists of a pyrimidylpiperazine cation joined by the C1/N3 atoms of each unit and a chloride anion. The C1—N3 bond is 1.373 (3) Å long, which compares favorably with similar ionic structures containing this cation [1.369 (3) (Yamuna et al., 2014a[Yamuna, T. S., Kaur, M., Jasinski, J. P. & Yathirajan, H. S. (2014a). Acta Cryst. E70, o702-o703.]), and 1.36 (6) and 1.37 (1) Å (Ding et al., 2014[Ding, X.-H., Li, Y.-H., Wang, S. & Huang, W. (2014). J. Mol. Struct. 1062, 61-67.])]. The N3/C5/C6/N4/C7/C8 piperazine unit adopts a slightly distorted chair conformation with protonation at the N4 nitro­gen atom. The structure of (II)[link] and its atom numbering are shown in Fig. 2[link]. Similarly, it consists of a pyrimidylpiperazine cation joined by the C1/N3 atoms of each unit and a nitrate anion. The C1—N3 bond is 1.369 (3) Å, also in the range of the related structures described above. The N3/C5/C6/N4/C7/C8 piperazine unit also adopts a slightly distorted chair conformation with protonation at the N4 atom.

[Figure 1]
Figure 1
ORTEP drawing of C8H13N4+·Cl, (I)[link], showing 30% probability displacement ellipsoids.
[Figure 2]
Figure 2
ORTEP drawing of C8H13N4+·NO3, (II)[link], showing 30% probability displacement ellipsoids.

3. Supra­molecular features

In the crystal of (I)[link], N4—H4A⋯Cl1 and N4—H4B⋯Cl1 inter­actions are observed between pyrimidylpiperazine cations and chloride anions, forming zigzag chains along [100] (Fig. 3[link] and Table 1[link]). In the crystal of (II)[link], both of the H atoms on the N4 atom of the pyrimidylpiperazine cation are bifurcated, forming N—H⋯(O,O) hydrogen bonds (Fig. 4[link] and Table 2[link]). Additional C—H⋯O inter­actions between the pyrimidyl unit and the nitrate anion are present which, in concert with the N—H⋯O hydrogen bonds between the piperazine group and nitrate anions, form infinite chains along [100].

Table 1
Hydrogen-bond geometry (Å, °) for (I)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N4—H4A⋯Cl1 0.91 2.21 3.102 (2) 167
N4—H4B⋯Cl1i 0.91 2.21 3.114 (2) 175
Symmetry code: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1].

Table 2
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N4—H4A⋯O2i 0.91 1.92 2.829 (3) 177
N4—H4A⋯O3i 0.91 2.52 3.138 (3) 126
N4—H4B⋯O1 0.91 2.35 3.197 (3) 155
N4—H4B⋯O2 0.91 2.10 2.900 (3) 146
C3—H3⋯O1ii 0.95 2.46 3.240 (3) 140
C4—H4⋯O2iii 0.95 2.51 3.291 (3) 139
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) -x, -y+1, -z+1; (iii) x-1, y, z.
[Figure 3]
Figure 3
Mol­ecular packing for C8H13N4+·Cl, (I)[link], viewed along the b axis. Dashed lines indicate N—H⋯Cl inter­actions forming zigzag chains along the a axis (see Table 1[link] for details). H atoms not involved in hydrogen bonding have been omitted for clarity.
[Figure 4]
Figure 4
Mol­ecular packing for C8H13N4+·NO3, (II)[link], viewed along the c axis. Dashed lines indicate N—H⋯O hydrogen bonds and additional C—H⋯O inter­actions forming infinite chains along [100] (see Table 2[link] for details). H atoms not involved in hydrogen bonding have been omitted for clarity.

4. Database survey

A search of the Cambridge Structural Database (Version 5.35, last update May 2014: Allen 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]) revealed only three structures containing the 4-(pyrimidin-2-yl)piperazin-1-ium cation similar to the structures reported here. These include the salts of 4-(pyrimidin-2-yl)piperazin-1-ium 3-carb­oxy­prop-2-enoate (Yamuna et al. 2014a[Yamuna, T. S., Kaur, M., Jasinski, J. P. & Yathirajan, H. S. (2014a). Acta Cryst. E70, o702-o703.]), 4-(pyrimidin-2-yl)piperazin-1-ium hydrogen D-tartrate monohydrate (Ding et al., 2014[Ding, X.-H., Li, Y.-H., Wang, S. & Huang, W. (2014). J. Mol. Struct. 1062, 61-67.]) and 4-(pyrimidin-2-yl)piperazin-1-ium hydrogen L-tartrate monohydrate (Ding et al. 2014[Ding, X.-H., Li, Y.-H., Wang, S. & Huang, W. (2014). J. Mol. Struct. 1062, 61-67.]). The 3-carb­oxy­prop-2-enoate complex crystallizes in space group P21/c while the two hydrogen (D and L)-tartrate monohydrate salts both crystallize in P212121. In comparison, title salt (I)[link] crystallizes in P212121 while (II)[link] crystallizes in space group P21/c. In addition, as a related observation, 109 structures containing the pyrimidine–piperazine unit were also identified in this search. Some of these include, uniquely, the 4-(pyrimidin-2-yl)piperazin-1-yl unit itself. These include 1-[4-(pyrimidin-2-yl)piperazin-1-yl]ethanone, (1-methyl-1H-pyrrol-2-yl)[4-(pyrimidin-2-yl)piperazin-1-yl]methanone, [4-(pyrimidin-2-yl)piperazin-1-yl](2-thien­yl)methanone, (4-fluoro­phen­yl)[4-(pyrimidin-2-yl)piperazin-1-yl]methanone (Spencer et al., 2011[Spencer, J., Patel, H., Callear, S. K., Coles, S. J. & Deadman, J. J. (2011). Tetrahedron Lett., 52, 5905-5909.]), (E)-1-phenyl-3-[4-(pyrimidin-2-yl)piperazin-1-yl]propan-1-one oxime (Kolasa et al., 2006[Kolasa, T., et al. (2006). J. Med. Chem. 49, 5093-5109.]), N-(4-chloro­phen­yl)-4-(pyrimidin-2-yl)piperazine-1-carboxamide (Li, 2011[Li, Y.-F. (2011). Acta Cryst. E67, o2575.]) and 6-{3-[4-(pyrimidin-2-yl)piperazin-1-yl]prop­yl}-2,3-di­hydro-5H-[1,4]dithiino[2,3-c]pyrrole-5,7(6H)-dione (Bielenica et al., 2011[Bielenica, A., Kossakowski, J., Struga, M., Dybala, I., La Colla, P., Tamburini, E. & Loddo, R. (2011). Med. Chem. Res. 20, 1411-1420.]).

5. Synthesis and crystallization

For the preparation of title salt (I)[link], a mixture of 1-(pyrimidin-2-yl)piperazine (0.2 g) and concentrated hydro­chloric acid (5 ml) was stirred well over a magnetic stirrer at room temperature for 10 min and then warmed at 313 K for another 10 min. A white precipitate was obtained, which was dried in the open air overnight and then dissolved in hot dimethyl sulfoxide solvent. After few days, colourless blocks were obtained on slow evaporation (m.p. above 563 K).

For the preparation of title salt (II)[link], a mixture of 1-(pyrim­idin-2-yl)piperazine, from Sigma–Aldrich (0.2 g), and concentrated nitric acid (5 ml) was stirred well over a magnetic stirrer at room temperature for 10 min. A white precipitate was obtained immediately, which was dried in the open air overnight and then dissolved in water. After a few days, colourless blocks were obtained on slow evaporation (m.p. 463–470 K).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. In both (I)[link] and (II)[link], all of the H atoms were placed in their calculated positions and then refined using a riding model with C—H bond lengths of 0.93 (CH) or 0.97 Å (CH2) and N—H bond lengths of 0.97 Å. Isotropic displacement parameters for these atoms were set at 1.2Ueq(CH,CH2,NH).

Table 3
Experimental details

  (I) (II)
Crystal data
Chemical formula C8H13N4+·Cl C8H13N4+·NO3
Mr 200.67 227.23
Crystal system, space group Orthorhombic, P212121 Monoclinic, P21/c
Temperature (K) 173 173
a, b, c (Å) 6.84764 (17), 7.27667 (18), 19.1751 (5) 10.5272 (6), 7.2230 (3), 14.1575 (7)
α, β, γ (°) 90, 90, 90 90, 107.341 (6), 90
V3) 955.46 (4) 1027.58 (9)
Z 4 4
Radiation type Cu Kα Cu Kα
μ (mm−1) 3.21 0.98
Crystal size (mm) 0.26 × 0.14 × 0.08 0.22 × 0.16 × 0.06
 
Data collection
Diffractometer Agilent Agilent Eos Gemini Agilent Agilent Eos Gemini
Absorption correction Multi-scan (CrysAlis RED; Agilent, 2012[Agilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.]) Multi-scan (CrysAlis RED; Agilent, 2012[Agilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.])
Tmin, Tmax 0.417, 1.000 0.727, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 5514, 1841, 1761 6218, 1960, 1752
Rint 0.045 0.040
(sin θ/λ)max−1) 0.615 0.613
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.091, 1.08 0.058, 0.163, 1.10
No. of reflections 1841 1960
No. of parameters 119 146
H-atom treatment H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.23, −0.20 0.42, −0.25
Absolute structure Flack x determined using 687 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 0.056 (15)
Computer programs: CrysAlis PRO and CrysAlis RED (Agilent, 2012[Agilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.]), SUPERFLIP (Palatinus & Chapuis, 2007[Palatinus, L. & Chapuis, G. (2007). J. Appl. Cryst. 40, 786-790.]), SHELXL2012 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) 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


Chemical context top

Pyrimidine-containing compounds exhibit various biological activities (Goldmann & Stoltefuss, 1991) and related fused heterocycles are unique classes of heterocyclic compounds that exhibit a broad spectrum of biological activities such as anti­cancer (Amin et al., 2009; Pandey et al., 2004), anti­viral (Ibrahim & El-Metwally, 2010), anti­bacterial (Kuyper et al., 1996) and anti-oxidant (Padmaja et al., 2009), anti­depressant (Kim et al., 2010) and possess anti-inflammatory effects (Clark et al., 2007). In addition, several piperazine derivatives have reached the stage of clinical application; among the known drugs that are used to treat anxiety is a pyrimidinylpiperazinyl compound, bu­spirone and BuSpar® (Tollefson et al., 1991). Our research group has published a number of papers on incorporated heterocyclic ring structures, viz. imatinibium dipicrate (Jasinski et al., 2010), 1-(2-hy­droxy­ethyl)-4-[3-(2-tri­fluoro­methyl-9H-thioxanthen-9-yl­idene)propyl]­piperazine-1,4-diium dichloride, which is the di­hydro­chloride salt of flupentixol (Siddegowda et al., 2011a) and opipramolium fumarate (Siddegowda et al., 2011b). Other related crystal structures are 4-(pyrimidin-2-yl)piperazin-1-ium (E)-3-carb­oxy­prop-2-enoate (Yamuna et al., 2014a), flupentixol tartarate and enrofloxacinium oxalate (Yamuna et al., 2014b,c). As part of our ongoing studies in this area, we report herein the crystal structures of the title salts, (I) and (II).

Structural commentary top

The structure of (I) and its atom numbering are shown in Fig. 1. It consists of a pyrimidylpiperazine cation joined by the C1/N3 atoms of each unit and a chloride anion. The C1—N3 bond is 1.373 (3) Å long, which compares favorably with similar ionic structures containing this cation [1.369 (3) (Yamuna et al., 2014a), and 1.36 (6) and 1.37 (1) Å (Ding et al., 2014)]. The N3/C5/C6/N4/C7/C8 piperazine unit adopts a slightly distorted chair conformation with protonation at the N4 nitro­gen atom. The structure of (II) and its atom numbering are shown in Fig. 2. Similarly, it consists of a pyrimidylpiperazine cation joined by the C1/N3 atoms of each unit and a nitrate anion. The C1—N3 bond is 1.369 (3) Å, also in the range of the related structures described above. The N3/C5/C6/N4/C7/C8 piperazine unit also adopts a slightly distorted chair conformation with protonation at the N4 atom.

Supra­molecular features top

In the crystal of (I), N4—H4A···Cl1 and N4—H4B···Cl1 inter­actions are observed between chloride anions and pyrimidylpiperazine cations, forming zigzag chains along [100] (Fig. 3 and Table 1). In the crystal of (II), both of the H atoms on the N4 atom of the pyrimidylpiperazine cation are bifurcated, forming N—H···(O,O) hydrogen bonds (Fig. 4 and Table 2). Additional C—H···O inter­actions between the pyrimidyl unit and the nitrate anion are present which, in concert with the N—H···O hydrogen bonds between the piperazine group and nitrate anions, form infinite chains along [100].

Database survey top

A search of the Cambridge Structural Database (Version 5.35, last update May 2014: Allen 2002) revealed only three structures containing the 4-(pyrimidin-2-yl)piperazin-1-ium cation similar to the structures reported here. These include the salts of 4-(pyrimidin-2-yl)piperazin-1-ium 3-carb­oxy­prop-2-enoate (Yamuna et al. 2014a), 4-(pyrimidin-2-yl)piperazin-1-ium hydrogen D-tartrate monohydrate (Ding et al., 2014) and 4-(pyrimidin-2-yl)piperazin-1-ium hydrogen L-tartrate monohydrate (Ding et al. 2014). The 3-carb­oxy­prop-2-enoate complex crystallizes in space group P21/c while the two hydrogen (D and L)-tartrate monohydrate salts both crystallize in the P212121. In comparison, title salt (I) crystallizes in P212121 while (II) crystallizes in space group P21/c. In addition, as a related observation, 109 structures containing the pyrimidine–piperazine unit were also identified in this search. Some of these include, uniquely, the 4-(pyrimidin-2-yl)piperazin-1-yl unit itself. These include 1-[4-(pyrimidin-2-yl)piperazin-1-yl]ethanone, (1-methyl-1H-pyrrol-2-yl)[4-(pyrimidin-2-yl)piperazin-1-yl]methanone, [4-(pyrimidin-2-yl)piperazin-1-yl](2-thienyl)methanone, (4-fluoro­phenyl)[4-(pyrimidin-2-yl)piperazin-1-yl]methanone (Spencer et al., 2011), (E)-1-phenyl-3-[4-(pyrimidin-2-yl)piperazin-1-yl]propan-1-one oxime (Kolasa et al., 2006), N-(4-chloro­phenyl)-4-(pyrimidin-2-yl)piperazine-1-carboxamide (Li, 2011) and 6-{3-[4-(pyrimidin-2-yl)piperazin-1-yl]propyl}-2,3-di­hydro-5H-[1,4]dithiino[2,3-c]pyrrole-5,7(6H)-dione (Bielenica et al., 2011).

Synthesis and crystallization top

For the preparation of title salt (I), a mixture of 1-(pyrimidin-2-yl)piperazine (0.2 g) and concentrated hydro­chloric acid (5 ml) was stirred well over a magnetic stirrer at room temperature for 10 min and then warmed at 313 K for another 10 min. A white precipitate was obtained, which was dried in the open air overnight and then dissolved in hot di­methyl sulfoxide solvent. After few days, colourless blocks were obtained on slow evaporation (m.p. above 563 K).

For the preparation of title salt (II), a mixture of 1-(pyrimidin-2-yl)piperazine, from Sigma–Aldrich (0.2 g), and concentrated nitric acid (5 ml) was stirred well over a magnetic stirrer at room temperature for 10 min. A white precipitate was obtained immediately, which was dried in the open air overnight and then dissolved in water. After a few days, colourless blocks were obtained on slow evaporation (m.p. 463–470 K).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 3. In both (I) and (II), all of the H atoms were placed in their calculated positions and then refined using a riding model with C—H bond lengths of 0.93 (CH) or 0.97 Å (CH2) and N—H bond lengths of 0.97 Å. Isotropic displacement parameters for these atoms were set at 1.2Ueq(CH,CH2,NH).

Related literature top

For related literature, see: Allen (2002); Amin et al. (2009); Bielenica et al. (2011); Clark et al. (2007); Ding et al. (2014); Goldmann & Stoltefuss (1991); Ibrahim & El-Metwally (2010); Jasinski et al. (2010); Kim et al. (2010); Kolasa et al. (2006); Kuyper et al. (1996); Li (2011); Padmaja et al. (2009); Pandey et al. (2004); Siddegowda et al. (2011a, 2011b); Spencer et al. (2011); Tollefson et al. (1991); Yamuna et al. (2014a, 2014b, 2014c).

Computing details top

For both compounds, data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis RED (Agilent, 2012); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007); program(s) used to refine structure: SHELXL2012 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. ORTEP drawing of C8H13N4+.Cl-, (I), showing 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. ORTEP drawing of C8H13N4+.NO3-, (II), showing 30% probability displacement ellipsoids.
[Figure 3] Fig. 3. Molecular packing for C8H13N4+.Cl-, (I), viewed along the b axis. Dashed lines indicate N—H···Cl interactions forming zigzag chains along the a axis (see Table 1 for details). H atoms not involved in hydrogen bonding have been omitted for clarity.
[Figure 4] Fig. 4. Molecular packing for C8H13N4+.NO3-, (II), viewed along the c axis. Dashed lines indicate N—H···O hydrogen bonds and additional C—H···O interactions forming infinite chains along [100] (see Table 2 for details). H atoms not involved in hydrogen bonding have been omitted for clarity.
(I) 4-(Pyrimidin-2-yl)piperazin-1-ium chloride top
Crystal data top
C8H13N4+·ClDx = 1.395 Mg m3
Mr = 200.67Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, P212121Cell parameters from 2676 reflections
a = 6.84764 (17) Åθ = 4.6–71.5°
b = 7.27667 (18) ŵ = 3.21 mm1
c = 19.1751 (5) ÅT = 173 K
V = 955.46 (4) Å3Irregular, colourless
Z = 40.26 × 0.14 × 0.08 mm
F(000) = 424
Data collection top
Agilent Agilent Eos Gemini
diffractometer
1841 independent reflections
Radiation source: Enhance (Cu) X-ray Source1761 reflections with I > 2σ(I)
Detector resolution: 16.0416 pixels mm-1Rint = 0.045
ω scansθmax = 71.4°, θmin = 4.6°
Absorption correction: multi-scan
(CrysAlis RED; Agilent, 2012)
h = 88
Tmin = 0.417, Tmax = 1.000k = 84
5514 measured reflectionsl = 2323
Refinement top
Refinement on F2H-atom parameters constrained
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0504P)2 + 0.1163P]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.035(Δ/σ)max < 0.001
wR(F2) = 0.091Δρmax = 0.23 e Å3
S = 1.08Δρmin = 0.20 e Å3
1841 reflectionsExtinction correction: SHELXL2012 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
119 parametersExtinction coefficient: 0.0073 (13)
0 restraintsAbsolute structure: Flack x determined using 687 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al. (2013)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.056 (15)
Hydrogen site location: inferred from neighbouring sites
Crystal data top
C8H13N4+·ClV = 955.46 (4) Å3
Mr = 200.67Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 6.84764 (17) ŵ = 3.21 mm1
b = 7.27667 (18) ÅT = 173 K
c = 19.1751 (5) Å0.26 × 0.14 × 0.08 mm
Data collection top
Agilent Agilent Eos Gemini
diffractometer
1841 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Agilent, 2012)
1761 reflections with I > 2σ(I)
Tmin = 0.417, Tmax = 1.000Rint = 0.045
5514 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.091Δρmax = 0.23 e Å3
S = 1.08Δρmin = 0.20 e Å3
1841 reflectionsAbsolute structure: Flack x determined using 687 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al. (2013)
119 parametersAbsolute structure parameter: 0.056 (15)
0 restraints
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
Cl10.08383 (9)0.49612 (9)0.48653 (3)0.0262 (2)
N10.6948 (4)0.6820 (3)0.81551 (12)0.0251 (5)
N20.9664 (4)0.5690 (3)0.74930 (13)0.0286 (6)
N30.6688 (3)0.6293 (3)0.69659 (12)0.0224 (5)
N40.4359 (4)0.6322 (3)0.57422 (12)0.0258 (5)
H4A0.34670.58000.54510.031*
H4B0.47180.74220.55560.031*
C10.7813 (4)0.6281 (4)0.75588 (14)0.0208 (5)
C20.8040 (4)0.6746 (4)0.87274 (15)0.0269 (6)
H20.74710.70970.91590.032*
C30.9968 (5)0.6181 (4)0.87217 (16)0.0318 (7)
H31.07420.61470.91330.038*
C41.0692 (5)0.5668 (4)0.80773 (17)0.0330 (7)
H41.20130.52740.80520.040*
C50.7582 (4)0.5944 (4)0.62855 (14)0.0245 (6)
H5A0.87010.50960.63410.029*
H5B0.80760.71110.60880.029*
C60.6103 (4)0.5108 (4)0.57949 (14)0.0278 (6)
H6A0.66940.49480.53280.033*
H6B0.57050.38830.59690.033*
C70.3448 (4)0.6631 (4)0.64394 (14)0.0246 (6)
H7A0.29640.54490.66280.030*
H7B0.23230.74750.63920.030*
C80.4936 (4)0.7449 (4)0.69357 (14)0.0233 (6)
H8A0.52970.86980.67770.028*
H8B0.43590.75530.74070.028*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0230 (3)0.0300 (4)0.0255 (3)0.0007 (3)0.0033 (2)0.0015 (3)
N10.0252 (12)0.0254 (11)0.0246 (11)0.0008 (10)0.0007 (10)0.0015 (9)
N20.0240 (14)0.0310 (12)0.0309 (12)0.0064 (10)0.0001 (10)0.0014 (10)
N30.0184 (11)0.0255 (11)0.0233 (11)0.0044 (9)0.0015 (9)0.0022 (10)
N40.0228 (12)0.0290 (11)0.0256 (11)0.0051 (10)0.0032 (10)0.0005 (10)
C10.0217 (13)0.0157 (11)0.0251 (13)0.0000 (10)0.0013 (11)0.0022 (10)
C20.0342 (16)0.0238 (13)0.0229 (13)0.0013 (12)0.0000 (12)0.0001 (11)
C30.0353 (16)0.0287 (14)0.0314 (14)0.0017 (14)0.0114 (14)0.0056 (12)
C40.0238 (14)0.0339 (14)0.0413 (17)0.0072 (13)0.0056 (14)0.0062 (13)
C50.0208 (13)0.0292 (14)0.0233 (13)0.0030 (11)0.0031 (11)0.0032 (11)
C60.0256 (14)0.0316 (14)0.0261 (13)0.0000 (14)0.0035 (10)0.0058 (12)
C70.0200 (13)0.0272 (13)0.0267 (14)0.0009 (11)0.0007 (11)0.0007 (11)
C80.0186 (13)0.0244 (12)0.0268 (13)0.0046 (12)0.0004 (12)0.0027 (11)
Geometric parameters (Å, º) top
N1—C11.346 (4)C3—H30.9500
N1—C21.329 (4)C3—C41.383 (4)
N2—C11.344 (4)C4—H40.9500
N2—C41.323 (4)C5—H5A0.9900
N3—C11.373 (3)C5—H5B0.9900
N3—C51.463 (3)C5—C61.510 (4)
N3—C81.466 (3)C6—H6A0.9900
N4—H4A0.9100C6—H6B0.9900
N4—H4B0.9100C7—H7A0.9900
N4—C61.489 (4)C7—H7B0.9900
N4—C71.492 (3)C7—C81.516 (4)
C2—H20.9500C8—H8A0.9900
C2—C31.383 (4)C8—H8B0.9900
C2—N1—C1116.2 (2)N3—C5—H5B109.6
C4—N2—C1115.2 (3)N3—C5—C6110.2 (2)
C1—N3—C5120.2 (2)H5A—C5—H5B108.1
C1—N3—C8119.7 (2)C6—C5—H5A109.6
C5—N3—C8114.0 (2)C6—C5—H5B109.6
H4A—N4—H4B108.0N4—C6—C5110.0 (2)
C6—N4—H4A109.4N4—C6—H6A109.7
C6—N4—H4B109.4N4—C6—H6B109.7
C6—N4—C7111.3 (2)C5—C6—H6A109.7
C7—N4—H4A109.4C5—C6—H6B109.7
C7—N4—H4B109.4H6A—C6—H6B108.2
N1—C1—N3117.0 (2)N4—C7—H7A109.7
N2—C1—N1126.0 (2)N4—C7—H7B109.7
N2—C1—N3116.9 (2)N4—C7—C8109.9 (2)
N1—C2—H2118.6H7A—C7—H7B108.2
N1—C2—C3122.9 (3)C8—C7—H7A109.7
C3—C2—H2118.6C8—C7—H7B109.7
C2—C3—H3122.3N3—C8—C7110.4 (2)
C2—C3—C4115.5 (3)N3—C8—H8A109.6
C4—C3—H3122.3N3—C8—H8B109.6
N2—C4—C3124.2 (3)C7—C8—H8A109.6
N2—C4—H4117.9C7—C8—H8B109.6
C3—C4—H4117.9H8A—C8—H8B108.1
N3—C5—H5A109.6
N1—C2—C3—C40.8 (4)C4—N2—C1—N10.6 (4)
N3—C5—C6—N455.8 (3)C4—N2—C1—N3178.9 (3)
N4—C7—C8—N354.5 (3)C5—N3—C1—N1172.5 (2)
C1—N1—C2—C31.0 (4)C5—N3—C1—N29.0 (4)
C1—N2—C4—C30.8 (4)C5—N3—C8—C755.2 (3)
C1—N3—C5—C6151.9 (2)C6—N4—C7—C857.4 (3)
C1—N3—C8—C7152.4 (2)C7—N4—C6—C558.1 (3)
C2—N1—C1—N20.3 (4)C8—N3—C1—N121.8 (4)
C2—N1—C1—N3178.0 (2)C8—N3—C1—N2159.8 (2)
C2—C3—C4—N20.2 (5)C8—N3—C5—C655.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···Cl10.912.213.102 (2)167
N4—H4B···Cl1i0.912.213.114 (2)175
Symmetry code: (i) x+1/2, y+3/2, z+1.
(II) 4-(Pyrimidin-2-yl)piperazin-1-ium nitrate top
Crystal data top
C8H13N4+·NO3F(000) = 480
Mr = 227.23Dx = 1.469 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54184 Å
a = 10.5272 (6) ÅCell parameters from 2763 reflections
b = 7.2230 (3) Åθ = 6.2–71.4°
c = 14.1575 (7) ŵ = 0.98 mm1
β = 107.341 (6)°T = 173 K
V = 1027.58 (9) Å3Irregular, colourless
Z = 40.22 × 0.16 × 0.06 mm
Data collection top
Agilent Agilent Eos Gemini
diffractometer
1960 independent reflections
Radiation source: Cu Kα1752 reflections with I > 2σ(I)
Detector resolution: 16.0416 pixels mm-1Rint = 0.040
ω scansθmax = 71.0°, θmin = 4.4°
Absorption correction: multi-scan
(CrysAlis RED; Agilent, 2012)
h = 912
Tmin = 0.727, Tmax = 1.000k = 88
6218 measured reflectionsl = 1716
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.058 w = 1/[σ2(Fo2) + (0.0789P)2 + 0.9595P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.163(Δ/σ)max < 0.001
S = 1.10Δρmax = 0.42 e Å3
1960 reflectionsΔρmin = 0.25 e Å3
146 parametersExtinction correction: SHELXL2012 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0099 (14)
Primary atom site location: structure-invariant direct methods
Crystal data top
C8H13N4+·NO3V = 1027.58 (9) Å3
Mr = 227.23Z = 4
Monoclinic, P21/cCu Kα radiation
a = 10.5272 (6) ŵ = 0.98 mm1
b = 7.2230 (3) ÅT = 173 K
c = 14.1575 (7) Å0.22 × 0.16 × 0.06 mm
β = 107.341 (6)°
Data collection top
Agilent Agilent Eos Gemini
diffractometer
1960 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Agilent, 2012)
1752 reflections with I > 2σ(I)
Tmin = 0.727, Tmax = 1.000Rint = 0.040
6218 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0580 restraints
wR(F2) = 0.163H-atom parameters constrained
S = 1.10Δρmax = 0.42 e Å3
1960 reflectionsΔρmin = 0.25 e Å3
146 parameters
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
O10.4119 (2)0.6964 (4)0.41222 (17)0.0615 (7)
O20.50951 (18)0.6257 (2)0.30424 (14)0.0381 (5)
O30.55020 (17)0.8884 (2)0.37996 (13)0.0323 (5)
N50.49103 (17)0.7390 (3)0.36677 (13)0.0238 (4)
N10.00592 (19)0.2396 (3)0.48106 (14)0.0291 (5)
N20.11846 (18)0.3821 (3)0.32856 (15)0.0273 (5)
N30.10930 (18)0.3372 (3)0.36702 (14)0.0268 (5)
N40.33344 (18)0.3134 (3)0.29632 (15)0.0278 (5)
H4A0.38140.25360.26170.033*
H4B0.37770.41910.32160.033*
C10.0049 (2)0.3204 (3)0.39365 (16)0.0220 (5)
C20.1085 (3)0.2126 (3)0.50188 (19)0.0346 (6)
H20.10540.15440.56270.042*
C30.2307 (2)0.2647 (4)0.4398 (2)0.0362 (6)
H30.31110.24200.45530.043*
C40.2290 (2)0.3519 (3)0.3537 (2)0.0329 (6)
H40.31130.39270.30970.039*
C50.2387 (2)0.2876 (4)0.43489 (16)0.0282 (5)
H5A0.22660.20350.48670.034*
H5B0.28480.40050.46760.034*
C60.3222 (2)0.1932 (3)0.37877 (17)0.0270 (5)
H6A0.41210.16740.42420.032*
H6B0.28080.07380.35190.032*
C70.1993 (2)0.3620 (3)0.22801 (17)0.0277 (5)
H7A0.15370.24830.19600.033*
H7B0.20950.44610.17550.033*
C80.1166 (2)0.4552 (3)0.28517 (17)0.0276 (5)
H8A0.15710.57560.31120.033*
H8B0.02580.47890.24070.033*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0614 (14)0.0836 (17)0.0562 (13)0.0362 (13)0.0431 (11)0.0184 (12)
O20.0436 (10)0.0314 (10)0.0460 (11)0.0072 (8)0.0238 (8)0.0153 (8)
O30.0379 (9)0.0249 (9)0.0353 (9)0.0045 (7)0.0129 (7)0.0021 (7)
N50.0175 (9)0.0301 (10)0.0240 (9)0.0015 (7)0.0064 (7)0.0012 (8)
N10.0292 (10)0.0327 (11)0.0282 (10)0.0020 (8)0.0126 (8)0.0038 (8)
N20.0210 (9)0.0270 (10)0.0331 (11)0.0037 (7)0.0071 (8)0.0001 (8)
N30.0189 (9)0.0380 (11)0.0243 (9)0.0068 (8)0.0075 (7)0.0087 (8)
N40.0231 (9)0.0278 (10)0.0368 (11)0.0042 (8)0.0153 (8)0.0045 (8)
C10.0207 (10)0.0220 (10)0.0246 (11)0.0023 (8)0.0087 (8)0.0035 (8)
C20.0416 (14)0.0328 (13)0.0372 (13)0.0021 (11)0.0235 (11)0.0014 (10)
C30.0300 (13)0.0340 (13)0.0525 (15)0.0049 (10)0.0247 (11)0.0130 (12)
C40.0224 (11)0.0304 (12)0.0456 (15)0.0020 (9)0.0098 (10)0.0063 (11)
C50.0208 (11)0.0395 (13)0.0234 (11)0.0087 (9)0.0054 (9)0.0023 (9)
C60.0219 (10)0.0296 (12)0.0293 (11)0.0038 (9)0.0074 (9)0.0014 (9)
C70.0291 (11)0.0305 (12)0.0255 (11)0.0013 (9)0.0111 (9)0.0039 (9)
C80.0267 (11)0.0290 (12)0.0283 (11)0.0033 (9)0.0098 (9)0.0080 (9)
Geometric parameters (Å, º) top
O1—N51.233 (3)C2—C31.376 (4)
O2—N51.263 (2)C3—H30.9500
O3—N51.232 (2)C3—C41.377 (4)
N1—C11.342 (3)C4—H40.9500
N1—C21.337 (3)C5—H5A0.9900
N2—C11.349 (3)C5—H5B0.9900
N2—C41.333 (3)C5—C61.512 (3)
N3—C11.369 (3)C6—H6A0.9900
N3—C51.459 (3)C6—H6B0.9900
N3—C81.459 (3)C7—H7A0.9900
N4—H4A0.9100C7—H7B0.9900
N4—H4B0.9100C7—C81.512 (3)
N4—C61.487 (3)C8—H8A0.9900
N4—C71.496 (3)C8—H8B0.9900
C2—H20.9500
O1—N5—O2118.2 (2)C3—C4—H4118.2
O3—N5—O1121.9 (2)N3—C5—H5A109.7
O3—N5—O2119.82 (18)N3—C5—H5B109.7
C2—N1—C1115.6 (2)N3—C5—C6109.86 (18)
C4—N2—C1115.5 (2)H5A—C5—H5B108.2
C1—N3—C5121.45 (19)C6—C5—H5A109.7
C1—N3—C8121.92 (18)C6—C5—H5B109.7
C5—N3—C8114.01 (18)N4—C6—C5110.12 (18)
H4A—N4—H4B108.0N4—C6—H6A109.6
C6—N4—H4A109.4N4—C6—H6B109.6
C6—N4—H4B109.4C5—C6—H6A109.6
C6—N4—C7111.33 (17)C5—C6—H6B109.6
C7—N4—H4A109.4H6A—C6—H6B108.2
C7—N4—H4B109.4N4—C7—H7A109.7
N1—C1—N2126.0 (2)N4—C7—H7B109.7
N1—C1—N3116.88 (19)N4—C7—C8109.99 (18)
N2—C1—N3117.06 (19)H7A—C7—H7B108.2
N1—C2—H2118.3C8—C7—H7A109.7
N1—C2—C3123.4 (2)C8—C7—H7B109.7
C3—C2—H2118.3N3—C8—C7109.85 (18)
C2—C3—H3122.1N3—C8—H8A109.7
C2—C3—C4115.8 (2)N3—C8—H8B109.7
C4—C3—H3122.1C7—C8—H8A109.7
N2—C4—C3123.6 (2)C7—C8—H8B109.7
N2—C4—H4118.2H8A—C8—H8B108.2
N1—C2—C3—C41.3 (4)C4—N2—C1—N12.7 (3)
N3—C5—C6—N455.5 (3)C4—N2—C1—N3175.4 (2)
N4—C7—C8—N355.3 (2)C5—N3—C1—N16.3 (3)
C1—N1—C2—C30.7 (4)C5—N3—C1—N2175.4 (2)
C1—N2—C4—C30.2 (3)C5—N3—C8—C756.9 (3)
C1—N3—C5—C6141.1 (2)C6—N4—C7—C856.9 (2)
C1—N3—C8—C7141.2 (2)C7—N4—C6—C557.0 (2)
C2—N1—C1—N22.9 (3)C8—N3—C1—N1166.9 (2)
C2—N1—C1—N3175.2 (2)C8—N3—C1—N214.8 (3)
C2—C3—C4—N21.6 (4)C8—N3—C5—C657.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···O2i0.911.922.829 (3)177
N4—H4A···O3i0.912.523.138 (3)126
N4—H4B···O10.912.353.197 (3)155
N4—H4B···O20.912.102.900 (3)146
C3—H3···O1ii0.952.463.240 (3)140
C4—H4···O2iii0.952.513.291 (3)139
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x, y+1, z+1; (iii) x1, y, z.
Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···Cl10.912.213.102 (2)167
N4—H4B···Cl1i0.912.213.114 (2)175
Symmetry code: (i) x+1/2, y+3/2, z+1.
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···O2i0.911.922.829 (3)177
N4—H4A···O3i0.912.523.138 (3)126
N4—H4B···O10.912.353.197 (3)155
N4—H4B···O20.912.102.900 (3)146
C3—H3···O1ii0.952.463.240 (3)140
C4—H4···O2iii0.952.513.291 (3)139
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x, y+1, z+1; (iii) x1, y, z.

Experimental details

(I)(II)
Crystal data
Chemical formulaC8H13N4+·ClC8H13N4+·NO3
Mr200.67227.23
Crystal system, space groupOrthorhombic, P212121Monoclinic, P21/c
Temperature (K)173173
a, b, c (Å)6.84764 (17), 7.27667 (18), 19.1751 (5)10.5272 (6), 7.2230 (3), 14.1575 (7)
α, β, γ (°)90, 90, 9090, 107.341 (6), 90
V3)955.46 (4)1027.58 (9)
Z44
Radiation typeCu KαCu Kα
µ (mm1)3.210.98
Crystal size (mm)0.26 × 0.14 × 0.080.22 × 0.16 × 0.06
Data collection
DiffractometerAgilent Agilent Eos Gemini
diffractometer
Agilent Agilent Eos Gemini
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Agilent, 2012)
Multi-scan
(CrysAlis RED; Agilent, 2012)
Tmin, Tmax0.417, 1.0000.727, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
5514, 1841, 1761 6218, 1960, 1752
Rint0.0450.040
(sin θ/λ)max1)0.6150.613
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.091, 1.08 0.058, 0.163, 1.10
No. of reflections18411960
No. of parameters119146
H-atom treatmentH-atom parameters constrainedH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.23, 0.200.42, 0.25
Absolute structureFlack x determined using 687 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al. (2013)?
Absolute structure parameter0.056 (15)?

Computer programs: CrysAlis PRO (Agilent, 2012), CrysAlis RED (Agilent, 2012), SUPERFLIP (Palatinus & Chapuis, 2007), SHELXL2012 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

 

Acknowledgements

TSY thanks the University of Mysore for research facilities and is also grateful to the Principal, Maharani's Science College for Women, Mysore, for giving permission to undertake research. JPJ acknowledges the NSF–MRI program (grant No. CHE-1039027) for funds to purchase the X-ray diffractometer.

References

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Volume 70| Part 10| October 2014| Pages 203-206
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