Literature DB >> 24940275

4-(Pyrimidin-2-yl)piperazin-1-ium (E)-3-carb-oxy-prop-2-enoate.

Thammarse S Yamuna¹, Manpreet Kaur¹, Jerry P Jasinski², H S Yathirajan¹.

Abstract

In the cation of the title salt, C8H13N4 (+)·C4H3O4 (-), the piperazinium ring adopts a slightly distorteded chair conformation. In the crystal, a single strong O-H⋯O inter-molecular hydrogen bond links the anions, forming chains along the c-axis direction. The chains of anions are linked by the cations, via N-H⋯O hydrogen bonds, forming sheets parallel to (100). These layers are linked by weak C-H⋯O hydrogen bonds, forming a three-dimensional structure. In addition, there are weak π-π inter-actions [centroid-centroid distance = 3.820 (9) Å] present involving inversion-related pyrimidine rings.

Entities: Chemical Disease Species

Year: 2014 PMID： 24940275 PMCID： PMC4051061 DOI： 10.1107/S1600536814011489

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For heterocyclic compounds that exhibit a broad spectrum of biological activities see: Amin et al. (2009 ▶); Clark et al. (2007 ▶); Ibrahim & El-Metwally (2010 ▶); Kim et al. (2010 ▶); Kuyper et al. (1996 ▶); Padmaja et al. (2009 ▶); Pandey et al. (2004 ▶). For piperazine-based compounds of biological and chemotherapeutic importance, see: Abdel-Jalil et al. (2010 ▶). For piperazine derivatives that have reached the stage of clinical application among the known drugs to treat anxiety, see: Tollefson et al. (1991 ▶). For related structures, see: Betz et al. (2011 ▶); Fun et al. (2012 ▶); Jasinski et al. (2010 ▶, 2011 ▶); Kavitha et al. (2013 ▶); Ravikumar & Sridhar (2005 ▶); Siddegowda et al. (2011 ▶). For puckering parameters, see Cremer & Pople (1975 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C8H13N4 +·C4H3O4 − M = 280.29 Monoclinic, a = 12.3425 (5) Å b = 7.0365 (3) Å c = 14.7178 (6) Å β = 94.213 (3)° V = 1274.77 (9) Å3 Z = 4 Cu Kα radiation μ = 0.94 mm−1 T = 173 K 0.22 × 0.16 × 0.06 mm

Data collection

Agilent Xcalibur Eos Gemini diffractometer Absorption correction: multi-scan (CrysAlis PRO and CrysAlis RED; Agilent, 2012 ▶). T min = 0.840, T max = 1.000 8262 measured reflections 2455 independent reflections 2090 reflections with I > 2σ(I) R int = 0.039

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.111 S = 1.06 2455 reflections 186 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.23 e Å−3 Δρmin = −0.27 e Å−3 Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; 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. Crystal structure: contains datablock(s) I. DOI: 10.1107/S1600536814011489/su2736sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814011489/su2736Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814011489/su2736Isup3.cml CCDC reference: 1003662 Additional supporting information: crystallographic information; 3D view; checkCIF report

C₈H₁₃N₄⁺·C₄H₃O₄⁻	F(000) = 592
M_r = 280.29	D_x = 1.460 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
a = 12.3425 (5) Å	Cell parameters from 3297 reflections
b = 7.0365 (3) Å	θ = 3.6–71.5°
c = 14.7178 (6) Å	µ = 0.94 mm⁻¹
β = 94.213 (3)°	T = 173 K
V = 1274.77 (9) Å³	Block, colourless
Z = 4	0.22 × 0.16 × 0.06 mm

Agilent Xcalibur Eos Gemini diffractometer	2455 independent reflections
Radiation source: Enhance (Cu) X-ray Source	2090 reflections with I > 2σ(I)
Detector resolution: 16.0416 pixels mm^-1	R_int = 0.039
ω scans	θ_max = 71.1°, θ_min = 3.6°
Absorption correction: multi-scan (CrysAlis PRO and CrysAlis RED; Agilent, 2012).	h = −14→15
T_min = 0.840, T_max = 1.000	k = −8→6
8262 measured reflections	l = −17→17

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.040	w = 1/[σ²(F_o²) + (0.0626P)² + 0.2118P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.111	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.23 e Å⁻³
2455 reflections	Δρ_min = −0.27 e Å⁻³
186 parameters	Extinction correction: SHELXL2012 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0012 (3)
Primary atom site location: structure-invariant direct methods

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	U_iso*/U_eq
N1A	0.73318 (9)	0.69373 (17)	0.20819 (8)	0.0218 (3)
H1AA	0.6882	0.7451	0.1554	0.026*
H1AB	0.6968	0.5788	0.2299	0.026*
N2A	0.91562 (9)	0.69808 (17)	0.33676 (8)	0.0212 (3)
N3A	0.98791 (10)	0.77052 (18)	0.48251 (9)	0.0244 (3)
N4A	1.09665 (9)	0.62261 (18)	0.37363 (9)	0.0248 (3)
C1A	0.74267 (11)	0.8382 (2)	0.28219 (10)	0.0223 (3)
H1AC	0.6694	0.8739	0.2997	0.027*
H1AD	0.7785	0.9539	0.2605	0.027*
C2A	0.80895 (11)	0.7569 (2)	0.36402 (10)	0.0214 (3)
H2AA	0.8179	0.8540	0.4127	0.026*
H2AB	0.7707	0.6463	0.3882	0.026*
C3A	0.91155 (11)	0.5639 (2)	0.26058 (9)	0.0230 (3)
H3AA	0.8806	0.4418	0.2798	0.028*
H3AB	0.9861	0.5395	0.2429	0.028*
C4A	0.84275 (11)	0.6420 (2)	0.17953 (10)	0.0232 (3)
H4AA	0.8782	0.7557	0.1554	0.028*
H4AB	0.8355	0.5453	0.1306	0.028*
C5A	1.00316 (11)	0.69522 (19)	0.40052 (10)	0.0186 (3)
C6A	1.07633 (13)	0.7795 (2)	0.54032 (11)	0.0281 (4)
H6A	1.0695	0.8347	0.5985	0.034*
C7A	1.17713 (12)	0.7133 (2)	0.52036 (12)	0.0287 (4)
H7A	1.2390	0.7224	0.5625	0.034*
C8A	1.18203 (12)	0.6329 (2)	0.43523 (12)	0.0285 (4)
H8A	1.2495	0.5823	0.4194	0.034*
O1B	0.45437 (8)	0.79460 (16)	0.54884 (7)	0.0247 (3)
O2B	0.62685 (8)	0.69817 (16)	0.54483 (7)	0.0274 (3)
O3B	0.48860 (8)	0.68609 (15)	0.21591 (6)	0.0227 (3)
O4B	0.33707 (8)	0.85812 (15)	0.22066 (6)	0.0228 (3)
C1B	0.53605 (11)	0.73177 (19)	0.50805 (9)	0.0170 (3)
C2B	0.51599 (11)	0.70263 (19)	0.40767 (9)	0.0173 (3)
H2B	0.5605	0.6157	0.3779	0.021*
C3B	0.43843 (11)	0.79386 (19)	0.35918 (9)	0.0174 (3)
H3B	0.3918	0.8740	0.3906	0.021*
C4B	0.41910 (10)	0.77939 (19)	0.25776 (9)	0.0159 (3)
H1B	0.473 (2)	0.801 (4)	0.624 (2)	0.091 (10)*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1A	0.0163 (6)	0.0294 (7)	0.0188 (6)	−0.0046 (5)	−0.0057 (5)	0.0051 (5)
N2A	0.0132 (6)	0.0313 (7)	0.0186 (6)	0.0027 (4)	−0.0023 (4)	−0.0025 (5)
N3A	0.0187 (6)	0.0321 (7)	0.0216 (7)	0.0000 (5)	−0.0037 (5)	−0.0027 (5)
N4A	0.0156 (6)	0.0291 (7)	0.0294 (7)	0.0033 (5)	−0.0019 (5)	−0.0006 (5)
C1A	0.0141 (6)	0.0272 (7)	0.0249 (7)	0.0001 (5)	−0.0025 (5)	0.0018 (6)
C2A	0.0128 (6)	0.0314 (7)	0.0194 (7)	0.0014 (5)	−0.0014 (5)	−0.0016 (6)
C3A	0.0208 (7)	0.0297 (8)	0.0180 (7)	0.0028 (5)	−0.0019 (5)	−0.0023 (6)
C4A	0.0214 (7)	0.0312 (8)	0.0165 (7)	−0.0020 (6)	−0.0009 (5)	0.0003 (6)
C5A	0.0145 (6)	0.0202 (7)	0.0204 (7)	−0.0013 (5)	−0.0031 (5)	0.0030 (5)
C6A	0.0260 (8)	0.0332 (8)	0.0236 (8)	−0.0031 (6)	−0.0082 (6)	−0.0005 (6)
C7A	0.0209 (7)	0.0297 (8)	0.0333 (9)	−0.0019 (6)	−0.0125 (6)	0.0050 (6)
C8A	0.0149 (7)	0.0286 (8)	0.0409 (9)	0.0023 (5)	−0.0054 (6)	0.0016 (7)
O1B	0.0196 (5)	0.0454 (7)	0.0092 (5)	0.0021 (4)	0.0008 (4)	−0.0006 (4)
O2B	0.0216 (5)	0.0433 (7)	0.0163 (5)	0.0075 (4)	−0.0064 (4)	−0.0044 (4)
O3B	0.0221 (5)	0.0362 (6)	0.0094 (5)	0.0091 (4)	−0.0006 (4)	−0.0012 (4)
O4B	0.0183 (5)	0.0329 (6)	0.0164 (5)	0.0056 (4)	−0.0043 (4)	−0.0029 (4)
C1B	0.0173 (6)	0.0209 (7)	0.0126 (7)	−0.0017 (5)	−0.0007 (5)	0.0011 (5)
C2B	0.0166 (6)	0.0241 (7)	0.0111 (6)	−0.0008 (5)	0.0009 (5)	−0.0004 (5)
C3B	0.0170 (6)	0.0244 (7)	0.0109 (6)	0.0008 (5)	0.0020 (5)	−0.0020 (5)
C4B	0.0153 (6)	0.0206 (7)	0.0115 (6)	−0.0012 (5)	−0.0001 (5)	0.0001 (5)

N1A—H1AA	0.9900	C3A—C4A	1.5157 (19)
N1A—H1AB	0.9900	C4A—H4AA	0.9900
N1A—C1A	1.4883 (19)	C4A—H4AB	0.9900
N1A—C4A	1.4909 (18)	C6A—H6A	0.9500
N2A—C2A	1.4640 (17)	C6A—C7A	1.380 (2)
N2A—C3A	1.4637 (18)	C7A—H7A	0.9500
N2A—C5A	1.3782 (17)	C7A—C8A	1.380 (2)
N3A—C5A	1.3438 (19)	C8A—H8A	0.9500
N3A—C6A	1.3351 (19)	O1B—C1B	1.2890 (17)
N4A—C5A	1.3477 (18)	O1B—H1B	1.12 (3)
N4A—C8A	1.3407 (19)	O2B—C1B	1.2311 (17)
C1A—H1AC	0.9900	O3B—C4B	1.2742 (16)
C1A—H1AD	0.9900	O4B—C4B	1.2445 (16)
C1A—C2A	1.5173 (19)	C1B—C2B	1.4941 (17)
C2A—H2AA	0.9900	C2B—H2B	0.9500
C2A—H2AB	0.9900	C2B—C3B	1.3181 (19)
C3A—H3AA	0.9900	C3B—H3B	0.9500
C3A—H3AB	0.9900	C3B—C4B	1.4977 (17)

H1AA—N1A—H1AB	108.1	N1A—C4A—H4AA	109.8
C1A—N1A—H1AA	109.6	N1A—C4A—H4AB	109.8
C1A—N1A—H1AB	109.6	C3A—C4A—H4AA	109.8
C1A—N1A—C4A	110.45 (10)	C3A—C4A—H4AB	109.8
C4A—N1A—H1AA	109.6	H4AA—C4A—H4AB	108.2
C4A—N1A—H1AB	109.6	N3A—C5A—N2A	116.82 (12)
C3A—N2A—C2A	114.29 (11)	N3A—C5A—N4A	126.34 (13)
C5A—N2A—C2A	119.56 (12)	N4A—C5A—N2A	116.80 (13)
C5A—N2A—C3A	119.55 (11)	N3A—C6A—H6A	118.1
C6A—N3A—C5A	115.41 (13)	N3A—C6A—C7A	123.76 (15)
C8A—N4A—C5A	115.36 (13)	C7A—C6A—H6A	118.1
N1A—C1A—H1AC	109.8	C6A—C7A—H7A	122.2
N1A—C1A—H1AD	109.8	C8A—C7A—C6A	115.59 (14)
N1A—C1A—C2A	109.39 (11)	C8A—C7A—H7A	122.2
H1AC—C1A—H1AD	108.2	N4A—C8A—C7A	123.47 (14)
C2A—C1A—H1AC	109.8	N4A—C8A—H8A	118.3
C2A—C1A—H1AD	109.8	C7A—C8A—H8A	118.3
N2A—C2A—C1A	109.41 (12)	C1B—O1B—H1B	111.6 (15)
N2A—C2A—H2AA	109.8	O1B—C1B—C2B	115.42 (12)
N2A—C2A—H2AB	109.8	O2B—C1B—O1B	125.37 (12)
C1A—C2A—H2AA	109.8	O2B—C1B—C2B	119.20 (12)
C1A—C2A—H2AB	109.8	C1B—C2B—H2B	119.0
H2AA—C2A—H2AB	108.2	C3B—C2B—C1B	121.98 (13)
N2A—C3A—H3AA	109.5	C3B—C2B—H2B	119.0
N2A—C3A—H3AB	109.5	C2B—C3B—H3B	117.9
N2A—C3A—C4A	110.78 (12)	C2B—C3B—C4B	124.24 (12)
H3AA—C3A—H3AB	108.1	C4B—C3B—H3B	117.9
C4A—C3A—H3AA	109.5	O3B—C4B—C3B	116.94 (11)
C4A—C3A—H3AB	109.5	O4B—C4B—O3B	124.90 (12)
N1A—C4A—C3A	109.46 (11)	O4B—C4B—C3B	118.15 (12)

N1A—C1A—C2A—N2A	57.34 (15)	C5A—N3A—C6A—C7A	−1.5 (2)
N2A—C3A—C4A—N1A	−54.53 (16)	C5A—N4A—C8A—C7A	−0.6 (2)
N3A—C6A—C7A—C8A	−0.6 (2)	C6A—N3A—C5A—N2A	−174.86 (13)
C1A—N1A—C4A—C3A	59.07 (15)	C6A—N3A—C5A—N4A	2.9 (2)
C2A—N2A—C3A—C4A	54.41 (16)	C6A—C7A—C8A—N4A	1.8 (2)
C2A—N2A—C5A—N3A	−8.22 (19)	C8A—N4A—C5A—N2A	175.90 (13)
C2A—N2A—C5A—N4A	173.80 (12)	C8A—N4A—C5A—N3A	−1.9 (2)
C3A—N2A—C2A—C1A	−55.43 (16)	O1B—C1B—C2B—C3B	23.25 (19)
C3A—N2A—C5A—N3A	−158.13 (13)	O2B—C1B—C2B—C3B	−155.66 (14)
C3A—N2A—C5A—N4A	23.89 (19)	C1B—C2B—C3B—C4B	176.05 (12)
C4A—N1A—C1A—C2A	−60.83 (14)	C2B—C3B—C4B—O3B	−6.6 (2)
C5A—N2A—C2A—C1A	153.15 (13)	C2B—C3B—C4B—O4B	173.29 (13)
C5A—N2A—C3A—C4A	−154.17 (13)

D—H···A	D—H	H···A	D···A	D—H···A
N1A—H1AA···O2Bⁱ	0.99	1.79	2.7601 (15)	166
N1A—H1AB···O4Bⁱⁱ	0.99	1.78	2.7493 (16)	167
C8A—H8A···O2Bⁱⁱⁱ	0.95	2.53	3.3133 (18)	140
O1B—H1B···O3B^iv	1.12 (3)	1.35 (3)	2.4679 (13)	176 (3)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1A—H1AA⋯O2B ⁱ	0.99	1.79	2.7601 (15)	166
N1A—H1AB⋯O4B ⁱⁱ	0.99	1.78	2.7493 (16)	167
C8A—H8A⋯O2B ⁱⁱⁱ	0.95	2.53	3.3133 (18)	140
O1B—H1B⋯O3B ^iv	1.12 (3)	1.35 (3)	2.4679 (13)	176 (3)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

14 in total

1. Paliperidone: 3-{2-[4-(6-fluoro-1,2-benzoxazol-3-yl)piperidin-1-yl]eth-yl}-9-hy-droxy-2-methyl-1,6,7,8,9,9a-hexa-hydro-pyrido[1,2-a]pyrimidin-4-one.

Authors: Richard Betz; Thomas Gerber; Eric Hosten; Alaloor S Dayananda; Hemmige S Yathirajan; Saji Thomas
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2011-10-12

2. Development of new pyrrolopyrimidine-based inhibitors of Janus kinase 3 (JAK3).

Authors: Michael P Clark; Kelly M George; Roger G Bookland; Jack Chen; Steven K Laughlin; Kumar D Thakur; Wenlin Lee; Jan R Davis; Ed J Cabrera; Todd A Brugel; John C VanRens; Matthew J Laufersweiler; Jennifer A Maier; Mark P Sabat; Adam Golebiowski; Vijay Easwaran; Mark E Webster; Biswanath De; George Zhang
Journal: Bioorg Med Chem Lett Date: 2006-12-09 Impact factor: 2.823

3. The association of buspirone and its metabolite 1-pyrimidinylpiperazine in the remission of comorbid anxiety with depressive features and alcohol dependency.

Authors: G D Tollefson; S P Lancaster; J Montague-Clouse
Journal: Psychopharmacol Bull Date: 1991

4. Synthesis, analgesic and anti-inflammatory activities evaluation of some bi-, tri- and tetracyclic condensed pyrimidines.

Authors: Kamilia M Amin; Mona M Hanna; Hanan E Abo-Youssef; Riham F George
Journal: Eur J Med Chem Date: 2009-07-01 Impact factor: 6.514

5. Synthesis, antimicrobial and antioxidant activities of substituted pyrazoles, isoxazoles, pyrimidine and thioxopyrimidine derivatives.

Authors: A Padmaja; T Payani; G Dinneswara Reddy; V Padmavathi
Journal: Eur J Med Chem Date: 2009-06-28 Impact factor: 6.514

6. Pyrrolo[2,3-d]pyrimidines and pyrido[2,3-d]pyrimidines as conformationally restricted analogues of the antibacterial agent trimethoprim.

Authors: L F Kuyper; J M Garvey; D P Baccanari; J N Champness; D K Stammers; C R Beddell
Journal: Bioorg Med Chem Date: 1996-04 Impact factor: 3.641

7. Lomefloxacinium picrate.

Authors: Jerry P Jasinski; Ray J Butcher; M S Siddegowda; H S Yathirajan; Q N M Hakim Al-Arique
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2011-01-26

8. 1-(2-Hy-droxy-eth-yl)-4-{3-[(E)-2-(trifluoro-meth-yl)-9H-thioxanthen-9-yl-idene]prop-yl}piperazine-1,4-diium bis-(3-carb-oxy-prop-2-enoate).

Authors: M S Siddegowda; Ray J Butcher; Mehmet Akkurt; H S Yathirajan; A R Ramesh
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2011-07-13