




Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536814020169/hb7279sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S1600536814020169/hb7279Isup2.hkl |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S1600536814020169/hb7279IIsup3.hkl |
![]() | Chemical Markup Language (CML) file https://doi.org/10.1107/S1600536814020169/hb7279Isup4.cml |
![]() | Chemical Markup Language (CML) file https://doi.org/10.1107/S1600536814020169/hb7279IIsup5.cml |
CCDC references: 1023201; 1023202
Key indicators
Structure: I- Single-crystal X-ray study
- T = 173 K
- Mean
(C-C) = 0.004 Å
- R factor = 0.035
- wR factor = 0.091
- Data-to-parameter ratio = 15.5
- Single-crystal X-ray study
- T = 173 K
- Mean
(C-C) = 0.004 Å
- R factor = 0.058
- wR factor = 0.163
- Data-to-parameter ratio = 13.4
checkCIF/PLATON results
No syntax errors found Datablock: I
Alert level C PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds ............... 0.0043 Ang.
Alert level G PLAT005_ALERT_5_G No _iucr_refine_instructions_details in the CIF Please Do ! PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms .............. 2 Report PLAT033_ALERT_4_G Flack x Value Deviates > 2*sigma from Zero ..... 0.056 PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L= 0.600 5 Note
0 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 1 ALERT level C = Check. Ensure it is not caused by an omission or oversight 4 ALERT level G = General information/check it is not something unexpected 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 2 ALERT type 5 Informative message, check
Datablock: II
Alert level C PLAT242_ALERT_2_C Low Ueq as Compared to Neighbors for ..... N5 Check PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 3.702 Check PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 16 Report
Alert level G PLAT005_ALERT_5_G No _iucr_refine_instructions_details in the CIF Please Do ! PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms .............. 2 Report PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L= 0.600 14 Note
0 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 3 ALERT level C = Check. Ensure it is not caused by an omission or oversight 3 ALERT level G = General information/check it is not something unexpected 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 2 ALERT type 5 Informative message, check
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).
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.
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].
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).
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).
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).
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).
C8H13N4+·Cl− | Dx = 1.395 Mg m−3 |
Mr = 200.67 | Cu Kα radiation, λ = 1.54184 Å |
Orthorhombic, P212121 | Cell parameters from 2676 reflections |
a = 6.84764 (17) Å | θ = 4.6–71.5° |
b = 7.27667 (18) Å | µ = 3.21 mm−1 |
c = 19.1751 (5) Å | T = 173 K |
V = 955.46 (4) Å3 | Irregular, colourless |
Z = 4 | 0.26 × 0.14 × 0.08 mm |
F(000) = 424 |
Agilent Agilent Eos Gemini diffractometer | 1841 independent reflections |
Radiation source: Enhance (Cu) X-ray Source | 1761 reflections with I > 2σ(I) |
Detector resolution: 16.0416 pixels mm-1 | Rint = 0.045 |
ω scans | θmax = 71.4°, θmin = 4.6° |
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012) | h = −8→8 |
Tmin = 0.417, Tmax = 1.000 | k = −8→4 |
5514 measured reflections | l = −23→23 |
Refinement on F2 | H-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) = 0.091 | Δρmax = 0.23 e Å−3 |
S = 1.08 | Δρmin = −0.20 e Å−3 |
1841 reflections | Extinction correction: SHELXL2012 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
119 parameters | Extinction coefficient: 0.0073 (13) |
0 restraints | Absolute structure: Flack x determined using 687 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al. (2013) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.056 (15) |
Hydrogen site location: inferred from neighbouring sites |
C8H13N4+·Cl− | V = 955.46 (4) Å3 |
Mr = 200.67 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 6.84764 (17) Å | µ = 3.21 mm−1 |
b = 7.27667 (18) Å | T = 173 K |
c = 19.1751 (5) Å | 0.26 × 0.14 × 0.08 mm |
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 = 1.000 | Rint = 0.045 |
5514 measured reflections |
R[F2 > 2σ(F2)] = 0.035 | H-atom parameters constrained |
wR(F2) = 0.091 | Δρmax = 0.23 e Å−3 |
S = 1.08 | Δρmin = −0.20 e Å−3 |
1841 reflections | Absolute structure: Flack x determined using 687 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al. (2013) |
119 parameters | Absolute structure parameter: 0.056 (15) |
0 restraints |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.08383 (9) | 0.49612 (9) | 0.48653 (3) | 0.0262 (2) | |
N1 | 0.6948 (4) | 0.6820 (3) | 0.81551 (12) | 0.0251 (5) | |
N2 | 0.9664 (4) | 0.5690 (3) | 0.74930 (13) | 0.0286 (6) | |
N3 | 0.6688 (3) | 0.6293 (3) | 0.69659 (12) | 0.0224 (5) | |
N4 | 0.4359 (4) | 0.6322 (3) | 0.57422 (12) | 0.0258 (5) | |
H4A | 0.3467 | 0.5800 | 0.5451 | 0.031* | |
H4B | 0.4718 | 0.7422 | 0.5556 | 0.031* | |
C1 | 0.7813 (4) | 0.6281 (4) | 0.75588 (14) | 0.0208 (5) | |
C2 | 0.8040 (4) | 0.6746 (4) | 0.87274 (15) | 0.0269 (6) | |
H2 | 0.7471 | 0.7097 | 0.9159 | 0.032* | |
C3 | 0.9968 (5) | 0.6181 (4) | 0.87217 (16) | 0.0318 (7) | |
H3 | 1.0742 | 0.6147 | 0.9133 | 0.038* | |
C4 | 1.0692 (5) | 0.5668 (4) | 0.80773 (17) | 0.0330 (7) | |
H4 | 1.2013 | 0.5274 | 0.8052 | 0.040* | |
C5 | 0.7582 (4) | 0.5944 (4) | 0.62855 (14) | 0.0245 (6) | |
H5A | 0.8701 | 0.5096 | 0.6341 | 0.029* | |
H5B | 0.8076 | 0.7111 | 0.6088 | 0.029* | |
C6 | 0.6103 (4) | 0.5108 (4) | 0.57949 (14) | 0.0278 (6) | |
H6A | 0.6694 | 0.4948 | 0.5328 | 0.033* | |
H6B | 0.5705 | 0.3883 | 0.5969 | 0.033* | |
C7 | 0.3448 (4) | 0.6631 (4) | 0.64394 (14) | 0.0246 (6) | |
H7A | 0.2964 | 0.5449 | 0.6628 | 0.030* | |
H7B | 0.2323 | 0.7475 | 0.6392 | 0.030* | |
C8 | 0.4936 (4) | 0.7449 (4) | 0.69357 (14) | 0.0233 (6) | |
H8A | 0.5297 | 0.8698 | 0.6777 | 0.028* | |
H8B | 0.4359 | 0.7553 | 0.7407 | 0.028* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0230 (3) | 0.0300 (4) | 0.0255 (3) | −0.0007 (3) | −0.0033 (2) | 0.0015 (3) |
N1 | 0.0252 (12) | 0.0254 (11) | 0.0246 (11) | −0.0008 (10) | −0.0007 (10) | −0.0015 (9) |
N2 | 0.0240 (14) | 0.0310 (12) | 0.0309 (12) | 0.0064 (10) | 0.0001 (10) | 0.0014 (10) |
N3 | 0.0184 (11) | 0.0255 (11) | 0.0233 (11) | 0.0044 (9) | 0.0015 (9) | −0.0022 (10) |
N4 | 0.0228 (12) | 0.0290 (11) | 0.0256 (11) | −0.0051 (10) | −0.0032 (10) | 0.0005 (10) |
C1 | 0.0217 (13) | 0.0157 (11) | 0.0251 (13) | 0.0000 (10) | 0.0013 (11) | 0.0022 (10) |
C2 | 0.0342 (16) | 0.0238 (13) | 0.0229 (13) | −0.0013 (12) | 0.0000 (12) | −0.0001 (11) |
C3 | 0.0353 (16) | 0.0287 (14) | 0.0314 (14) | −0.0017 (14) | −0.0114 (14) | 0.0056 (12) |
C4 | 0.0238 (14) | 0.0339 (14) | 0.0413 (17) | 0.0072 (13) | −0.0056 (14) | 0.0062 (13) |
C5 | 0.0208 (13) | 0.0292 (14) | 0.0233 (13) | 0.0030 (11) | 0.0031 (11) | −0.0032 (11) |
C6 | 0.0256 (14) | 0.0316 (14) | 0.0261 (13) | 0.0000 (14) | 0.0035 (10) | −0.0058 (12) |
C7 | 0.0200 (13) | 0.0272 (13) | 0.0267 (14) | −0.0009 (11) | −0.0007 (11) | 0.0007 (11) |
C8 | 0.0186 (13) | 0.0244 (12) | 0.0268 (13) | 0.0046 (12) | −0.0004 (12) | −0.0027 (11) |
N1—C1 | 1.346 (4) | C3—H3 | 0.9500 |
N1—C2 | 1.329 (4) | C3—C4 | 1.383 (4) |
N2—C1 | 1.344 (4) | C4—H4 | 0.9500 |
N2—C4 | 1.323 (4) | C5—H5A | 0.9900 |
N3—C1 | 1.373 (3) | C5—H5B | 0.9900 |
N3—C5 | 1.463 (3) | C5—C6 | 1.510 (4) |
N3—C8 | 1.466 (3) | C6—H6A | 0.9900 |
N4—H4A | 0.9100 | C6—H6B | 0.9900 |
N4—H4B | 0.9100 | C7—H7A | 0.9900 |
N4—C6 | 1.489 (4) | C7—H7B | 0.9900 |
N4—C7 | 1.492 (3) | C7—C8 | 1.516 (4) |
C2—H2 | 0.9500 | C8—H8A | 0.9900 |
C2—C3 | 1.383 (4) | C8—H8B | 0.9900 |
C2—N1—C1 | 116.2 (2) | N3—C5—H5B | 109.6 |
C4—N2—C1 | 115.2 (3) | N3—C5—C6 | 110.2 (2) |
C1—N3—C5 | 120.2 (2) | H5A—C5—H5B | 108.1 |
C1—N3—C8 | 119.7 (2) | C6—C5—H5A | 109.6 |
C5—N3—C8 | 114.0 (2) | C6—C5—H5B | 109.6 |
H4A—N4—H4B | 108.0 | N4—C6—C5 | 110.0 (2) |
C6—N4—H4A | 109.4 | N4—C6—H6A | 109.7 |
C6—N4—H4B | 109.4 | N4—C6—H6B | 109.7 |
C6—N4—C7 | 111.3 (2) | C5—C6—H6A | 109.7 |
C7—N4—H4A | 109.4 | C5—C6—H6B | 109.7 |
C7—N4—H4B | 109.4 | H6A—C6—H6B | 108.2 |
N1—C1—N3 | 117.0 (2) | N4—C7—H7A | 109.7 |
N2—C1—N1 | 126.0 (2) | N4—C7—H7B | 109.7 |
N2—C1—N3 | 116.9 (2) | N4—C7—C8 | 109.9 (2) |
N1—C2—H2 | 118.6 | H7A—C7—H7B | 108.2 |
N1—C2—C3 | 122.9 (3) | C8—C7—H7A | 109.7 |
C3—C2—H2 | 118.6 | C8—C7—H7B | 109.7 |
C2—C3—H3 | 122.3 | N3—C8—C7 | 110.4 (2) |
C2—C3—C4 | 115.5 (3) | N3—C8—H8A | 109.6 |
C4—C3—H3 | 122.3 | N3—C8—H8B | 109.6 |
N2—C4—C3 | 124.2 (3) | C7—C8—H8A | 109.6 |
N2—C4—H4 | 117.9 | C7—C8—H8B | 109.6 |
C3—C4—H4 | 117.9 | H8A—C8—H8B | 108.1 |
N3—C5—H5A | 109.6 | ||
N1—C2—C3—C4 | −0.8 (4) | C4—N2—C1—N1 | −0.6 (4) |
N3—C5—C6—N4 | 55.8 (3) | C4—N2—C1—N3 | −178.9 (3) |
N4—C7—C8—N3 | −54.5 (3) | C5—N3—C1—N1 | 172.5 (2) |
C1—N1—C2—C3 | 1.0 (4) | C5—N3—C1—N2 | −9.0 (4) |
C1—N2—C4—C3 | 0.8 (4) | C5—N3—C8—C7 | 55.2 (3) |
C1—N3—C5—C6 | 151.9 (2) | C6—N4—C7—C8 | 57.4 (3) |
C1—N3—C8—C7 | −152.4 (2) | C7—N4—C6—C5 | −58.1 (3) |
C2—N1—C1—N2 | −0.3 (4) | C8—N3—C1—N1 | 21.8 (4) |
C2—N1—C1—N3 | 178.0 (2) | C8—N3—C1—N2 | −159.8 (2) |
C2—C3—C4—N2 | −0.2 (5) | C8—N3—C5—C6 | −55.8 (3) |
D—H···A | D—H | H···A | D···A | 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+1/2, −y+3/2, −z+1. |
C8H13N4+·NO3− | F(000) = 480 |
Mr = 227.23 | Dx = 1.469 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 10.5272 (6) Å | Cell parameters from 2763 reflections |
b = 7.2230 (3) Å | θ = 6.2–71.4° |
c = 14.1575 (7) Å | µ = 0.98 mm−1 |
β = 107.341 (6)° | T = 173 K |
V = 1027.58 (9) Å3 | Irregular, colourless |
Z = 4 | 0.22 × 0.16 × 0.06 mm |
Agilent Agilent Eos Gemini diffractometer | 1960 independent reflections |
Radiation source: Cu Kα | 1752 reflections with I > 2σ(I) |
Detector resolution: 16.0416 pixels mm-1 | Rint = 0.040 |
ω scans | θmax = 71.0°, θmin = 4.4° |
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012) | h = −9→12 |
Tmin = 0.727, Tmax = 1.000 | k = −8→8 |
6218 measured reflections | l = −17→16 |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-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 = 1.10 | Δρmax = 0.42 e Å−3 |
1960 reflections | Δρmin = −0.25 e Å−3 |
146 parameters | Extinction correction: SHELXL2012 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0099 (14) |
Primary atom site location: structure-invariant direct methods |
C8H13N4+·NO3− | V = 1027.58 (9) Å3 |
Mr = 227.23 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 10.5272 (6) Å | µ = 0.98 mm−1 |
b = 7.2230 (3) Å | T = 173 K |
c = 14.1575 (7) Å | 0.22 × 0.16 × 0.06 mm |
β = 107.341 (6)° |
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 = 1.000 | Rint = 0.040 |
6218 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.163 | H-atom parameters constrained |
S = 1.10 | Δρmax = 0.42 e Å−3 |
1960 reflections | Δρmin = −0.25 e Å−3 |
146 parameters |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.4119 (2) | 0.6964 (4) | 0.41222 (17) | 0.0615 (7) | |
O2 | 0.50951 (18) | 0.6257 (2) | 0.30424 (14) | 0.0381 (5) | |
O3 | 0.55020 (17) | 0.8884 (2) | 0.37996 (13) | 0.0323 (5) | |
N5 | 0.49103 (17) | 0.7390 (3) | 0.36677 (13) | 0.0238 (4) | |
N1 | 0.00592 (19) | 0.2396 (3) | 0.48106 (14) | 0.0291 (5) | |
N2 | −0.11846 (18) | 0.3821 (3) | 0.32856 (15) | 0.0273 (5) | |
N3 | 0.10930 (18) | 0.3372 (3) | 0.36702 (14) | 0.0268 (5) | |
N4 | 0.33344 (18) | 0.3134 (3) | 0.29632 (15) | 0.0278 (5) | |
H4A | 0.3814 | 0.2536 | 0.2617 | 0.033* | |
H4B | 0.3777 | 0.4191 | 0.3216 | 0.033* | |
C1 | −0.0049 (2) | 0.3204 (3) | 0.39365 (16) | 0.0220 (5) | |
C2 | −0.1085 (3) | 0.2126 (3) | 0.50188 (19) | 0.0346 (6) | |
H2 | −0.1054 | 0.1544 | 0.5627 | 0.042* | |
C3 | −0.2307 (2) | 0.2647 (4) | 0.4398 (2) | 0.0362 (6) | |
H3 | −0.3111 | 0.2420 | 0.4553 | 0.043* | |
C4 | −0.2290 (2) | 0.3519 (3) | 0.3537 (2) | 0.0329 (6) | |
H4 | −0.3113 | 0.3927 | 0.3097 | 0.039* | |
C5 | 0.2387 (2) | 0.2876 (4) | 0.43489 (16) | 0.0282 (5) | |
H5A | 0.2266 | 0.2035 | 0.4867 | 0.034* | |
H5B | 0.2848 | 0.4005 | 0.4676 | 0.034* | |
C6 | 0.3222 (2) | 0.1932 (3) | 0.37877 (17) | 0.0270 (5) | |
H6A | 0.4121 | 0.1674 | 0.4242 | 0.032* | |
H6B | 0.2808 | 0.0738 | 0.3519 | 0.032* | |
C7 | 0.1993 (2) | 0.3620 (3) | 0.22801 (17) | 0.0277 (5) | |
H7A | 0.1537 | 0.2483 | 0.1960 | 0.033* | |
H7B | 0.2095 | 0.4461 | 0.1755 | 0.033* | |
C8 | 0.1166 (2) | 0.4552 (3) | 0.28517 (17) | 0.0276 (5) | |
H8A | 0.1571 | 0.5756 | 0.3112 | 0.033* | |
H8B | 0.0258 | 0.4789 | 0.2407 | 0.033* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0614 (14) | 0.0836 (17) | 0.0562 (13) | −0.0362 (13) | 0.0431 (11) | −0.0184 (12) |
O2 | 0.0436 (10) | 0.0314 (10) | 0.0460 (11) | −0.0072 (8) | 0.0238 (8) | −0.0153 (8) |
O3 | 0.0379 (9) | 0.0249 (9) | 0.0353 (9) | −0.0045 (7) | 0.0129 (7) | −0.0021 (7) |
N5 | 0.0175 (9) | 0.0301 (10) | 0.0240 (9) | −0.0015 (7) | 0.0064 (7) | 0.0012 (8) |
N1 | 0.0292 (10) | 0.0327 (11) | 0.0282 (10) | 0.0020 (8) | 0.0126 (8) | 0.0038 (8) |
N2 | 0.0210 (9) | 0.0270 (10) | 0.0331 (11) | 0.0037 (7) | 0.0071 (8) | 0.0001 (8) |
N3 | 0.0189 (9) | 0.0380 (11) | 0.0243 (9) | 0.0068 (8) | 0.0075 (7) | 0.0087 (8) |
N4 | 0.0231 (9) | 0.0278 (10) | 0.0368 (11) | −0.0042 (8) | 0.0153 (8) | −0.0045 (8) |
C1 | 0.0207 (10) | 0.0220 (10) | 0.0246 (11) | 0.0023 (8) | 0.0087 (8) | −0.0035 (8) |
C2 | 0.0416 (14) | 0.0328 (13) | 0.0372 (13) | −0.0021 (11) | 0.0235 (11) | −0.0014 (10) |
C3 | 0.0300 (13) | 0.0340 (13) | 0.0525 (15) | −0.0049 (10) | 0.0247 (11) | −0.0130 (12) |
C4 | 0.0224 (11) | 0.0304 (12) | 0.0456 (15) | 0.0020 (9) | 0.0098 (10) | −0.0063 (11) |
C5 | 0.0208 (11) | 0.0395 (13) | 0.0234 (11) | 0.0087 (9) | 0.0054 (9) | 0.0023 (9) |
C6 | 0.0219 (10) | 0.0296 (12) | 0.0293 (11) | 0.0038 (9) | 0.0074 (9) | 0.0014 (9) |
C7 | 0.0291 (11) | 0.0305 (12) | 0.0255 (11) | −0.0013 (9) | 0.0111 (9) | 0.0039 (9) |
C8 | 0.0267 (11) | 0.0290 (12) | 0.0283 (11) | 0.0033 (9) | 0.0098 (9) | 0.0080 (9) |
O1—N5 | 1.233 (3) | C2—C3 | 1.376 (4) |
O2—N5 | 1.263 (2) | C3—H3 | 0.9500 |
O3—N5 | 1.232 (2) | C3—C4 | 1.377 (4) |
N1—C1 | 1.342 (3) | C4—H4 | 0.9500 |
N1—C2 | 1.337 (3) | C5—H5A | 0.9900 |
N2—C1 | 1.349 (3) | C5—H5B | 0.9900 |
N2—C4 | 1.333 (3) | C5—C6 | 1.512 (3) |
N3—C1 | 1.369 (3) | C6—H6A | 0.9900 |
N3—C5 | 1.459 (3) | C6—H6B | 0.9900 |
N3—C8 | 1.459 (3) | C7—H7A | 0.9900 |
N4—H4A | 0.9100 | C7—H7B | 0.9900 |
N4—H4B | 0.9100 | C7—C8 | 1.512 (3) |
N4—C6 | 1.487 (3) | C8—H8A | 0.9900 |
N4—C7 | 1.496 (3) | C8—H8B | 0.9900 |
C2—H2 | 0.9500 | ||
O1—N5—O2 | 118.2 (2) | C3—C4—H4 | 118.2 |
O3—N5—O1 | 121.9 (2) | N3—C5—H5A | 109.7 |
O3—N5—O2 | 119.82 (18) | N3—C5—H5B | 109.7 |
C2—N1—C1 | 115.6 (2) | N3—C5—C6 | 109.86 (18) |
C4—N2—C1 | 115.5 (2) | H5A—C5—H5B | 108.2 |
C1—N3—C5 | 121.45 (19) | C6—C5—H5A | 109.7 |
C1—N3—C8 | 121.92 (18) | C6—C5—H5B | 109.7 |
C5—N3—C8 | 114.01 (18) | N4—C6—C5 | 110.12 (18) |
H4A—N4—H4B | 108.0 | N4—C6—H6A | 109.6 |
C6—N4—H4A | 109.4 | N4—C6—H6B | 109.6 |
C6—N4—H4B | 109.4 | C5—C6—H6A | 109.6 |
C6—N4—C7 | 111.33 (17) | C5—C6—H6B | 109.6 |
C7—N4—H4A | 109.4 | H6A—C6—H6B | 108.2 |
C7—N4—H4B | 109.4 | N4—C7—H7A | 109.7 |
N1—C1—N2 | 126.0 (2) | N4—C7—H7B | 109.7 |
N1—C1—N3 | 116.88 (19) | N4—C7—C8 | 109.99 (18) |
N2—C1—N3 | 117.06 (19) | H7A—C7—H7B | 108.2 |
N1—C2—H2 | 118.3 | C8—C7—H7A | 109.7 |
N1—C2—C3 | 123.4 (2) | C8—C7—H7B | 109.7 |
C3—C2—H2 | 118.3 | N3—C8—C7 | 109.85 (18) |
C2—C3—H3 | 122.1 | N3—C8—H8A | 109.7 |
C2—C3—C4 | 115.8 (2) | N3—C8—H8B | 109.7 |
C4—C3—H3 | 122.1 | C7—C8—H8A | 109.7 |
N2—C4—C3 | 123.6 (2) | C7—C8—H8B | 109.7 |
N2—C4—H4 | 118.2 | H8A—C8—H8B | 108.2 |
N1—C2—C3—C4 | −1.3 (4) | C4—N2—C1—N1 | −2.7 (3) |
N3—C5—C6—N4 | 55.5 (3) | C4—N2—C1—N3 | 175.4 (2) |
N4—C7—C8—N3 | −55.3 (2) | C5—N3—C1—N1 | −6.3 (3) |
C1—N1—C2—C3 | −0.7 (4) | C5—N3—C1—N2 | 175.4 (2) |
C1—N2—C4—C3 | 0.2 (3) | C5—N3—C8—C7 | 56.9 (3) |
C1—N3—C5—C6 | 141.1 (2) | C6—N4—C7—C8 | 56.9 (2) |
C1—N3—C8—C7 | −141.2 (2) | C7—N4—C6—C5 | −57.0 (2) |
C2—N1—C1—N2 | 2.9 (3) | C8—N3—C1—N1 | −166.9 (2) |
C2—N1—C1—N3 | −175.2 (2) | C8—N3—C1—N2 | 14.8 (3) |
C2—C3—C4—N2 | 1.6 (4) | C8—N3—C5—C6 | −57.0 (3) |
D—H···A | D—H | H···A | D···A | 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−1/2, −z+1/2; (ii) −x, −y+1, −z+1; (iii) x−1, y, z. |
D—H···A | D—H | H···A | D···A | 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+1/2, −y+3/2, −z+1. |
D—H···A | D—H | H···A | D···A | 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−1/2, −z+1/2; (ii) −x, −y+1, −z+1; (iii) x−1, y, z. |
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 |
V (Å3) | 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 diffractometer | Agilent Agilent Eos Gemini diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Agilent, 2012) | Multi-scan (CrysAlis RED; Agilent, 2012) |
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 (Å−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) | ? |
Absolute structure parameter | 0.056 (15) | ? |
Computer programs: CrysAlis PRO (Agilent, 2012), CrysAlis RED (Agilent, 2012), SUPERFLIP (Palatinus & Chapuis, 2007), SHELXL2012 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).