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An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S205252061303388X/gw5022sup1.cif
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S205252061303388X/gw5022Isup2.hkl
Contains datablock I

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S205252061303388X/gw5022sup3.pdf
Residual density map and geometrical parameters

CCDC reference: 921916

Computing details top

Data collection: KAPPA APEX BRUKER-AXS; cell refinement: SAINTPLUS (BRUKER-AXS); data reduction: SAINTPLUS (BRUKER-AXS); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELX97 (Sheldrick, 2007) XD2006 (Koritsanszky et al., 2006); molecular graphics: ORTEP (Farrugia, 1997) PLATON (Spek, 2003) XD2006 (Koritsanszky et al., 2006); software used to prepare material for publication: XD2006 (Koritsanszky et al., 2006).

(I) top
Crystal data top
C5H5N3OZ = 4
Mr = 119.09Dx = 1.45 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4578 reflections
a = 3.6173 (3) Åθ = 2.0–50.1°
b = 6.7413 (5) ŵ = 0.11 mm1
c = 22.4625 (16) ÅT = 100 K
β = 92.395 (4)°Needle, colourless
V = 547.28 (1) Å30.3 × 0.2 × 0.15 mm
Data collection top
Bruker Kappa APEX II CCD detector
diffractometer
4991 reflections with > 2.0σ(I)
φ and ω scansRint = 0.039
Absorption correction: analyticalθmax = 51.1°, θmin = 1.8°
Tmin = 0.913, Tmax = 0.943h = 67
60977 measured reflectionsk = 1414
5880 independent reflectionsl = 4848
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.080H atoms treated by a mixture of independent and constrained refinement
S = 2.00Weighting scheme based on measured s.u.'s w2 = 1/[s2(Fo2)]
4486 reflections(Δ/σ)max = 0.0001
221 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.31 e Å3
Special details top

Refinement. Reflections were merged with SORTAV (Blessing, 1995)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O(1)0.04793 (15)0.53200 (7)0.08373 (2)0.017
N(1)0.46128 (12)1.01005 (6)0.089959 (18)0.012
N(3)0.23007 (16)0.73021 (7)0.00873 (2)0.018
N(2)0.43667 (14)0.93030 (7)0.212208 (19)0.016
C(2)0.33506 (11)0.83736 (5)0.110271 (17)0.010
C(5)0.19390 (12)0.68607 (6)0.065867 (18)0.012
C(3)0.32544 (12)0.79671 (6)0.171033 (18)0.013
C(4)0.55574 (13)1.10413 (6)0.191690 (19)0.015
C(1)0.57000 (12)1.14395 (6)0.130926 (19)0.014
H(3A)0.3581460.8575140.0020220.028
H(3)0.2225360.6550940.1860970.024
H(1)0.6735241.2854280.1161190.021
H(4)0.6386111.2155930.2242920.026
H(3B)0.1445080.6305280.0223760.034
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O(1)0.02489 (19)0.01328 (14)0.01325 (14)0.01034 (14)0.00178 (14)0.00013 (12)
N(1)0.01611 (15)0.01028 (12)0.01089 (13)0.00431 (11)0.00107 (11)0.00003 (10)
N(3)0.0284 (2)0.01550 (15)0.01040 (14)0.01173 (15)0.00102 (14)0.00024 (12)
N(2)0.02147 (18)0.01514 (15)0.01045 (14)0.00331 (14)0.00012 (13)0.00021 (12)
C(2)0.01223 (14)0.00943 (11)0.00984 (12)0.00265 (10)0.00083 (10)0.00013 (10)
C(5)0.01543 (15)0.01026 (12)0.01062 (13)0.00478 (11)0.00102 (11)0.00005 (10)
C(3)0.01691 (16)0.01156 (12)0.01079 (13)0.00282 (11)0.00071 (11)0.00097 (10)
C(4)0.01758 (17)0.01359 (14)0.01233 (14)0.00327 (12)0.00016 (12)0.00243 (11)
C(1)0.01715 (16)0.01057 (12)0.01303 (14)0.00431 (11)0.00102 (12)0.00100 (11)
Geometric parameters (Å, º) top
O(1)—C(5)1.2395 (5)N(2)—C(4)1.3370 (6)
N(1)—C(2)1.3377 (5)C(2)—C(5)1.5011 (5)
N(1)—C(1)1.3364 (5)C(2)—C(3)1.3940 (5)
N(3)—C(5)1.3293 (6)C(3)—H(3)1.0840 (4)
N(3)—H(3A)1.0094 (4)C(4)—C(1)1.3941 (6)
N(3)—H(3B)1.0087 (4)C(4)—H(4)1.0828 (4)
N(2)—C(3)1.3406 (6)C(1)—H(1)1.0821 (4)
C(2)—N(1)—C(1)116.60 (4)N(3)—C(5)—C(2)116.42 (4)
C(5)—N(3)—H(3A)119.08 (4)N(2)—C(3)—C(2)121.63 (4)
C(5)—N(3)—H(3B)118.68 (4)N(2)—C(3)—H(3)118.25 (4)
H(3A)—N(3)—H(3B)122.10 (4)C(2)—C(3)—H(3)120.11 (4)
C(3)—N(2)—C(4)116.27 (4)N(2)—C(4)—C(1)122.13 (4)
N(1)—C(2)—C(5)118.44 (3)N(2)—C(4)—H(4)117.33 (4)
N(1)—C(2)—C(3)121.86 (4)C(1)—C(4)—H(4)120.53 (4)
C(5)—C(2)—C(3)119.69 (3)N(1)—C(1)—C(4)121.48 (4)
O(1)—C(5)—N(3)124.10 (4)N(1)—C(1)—H(1)118.64 (4)
O(1)—C(5)—C(2)119.47 (4)C(4)—C(1)—H(1)119.87 (4)
C(1)—N(1)—C(2)—C(5)177.28 (6)N(1)—C(2)—C(5)—O(1)174.12 (6)
C(1)—N(1)—C(2)—C(3)1.52 (4)N(1)—C(2)—C(5)—N(3)4.72 (4)
C(2)—N(1)—C(1)—C(4)0.67 (4)N(1)—C(2)—C(3)—N(2)1.14 (4)
C(2)—N(1)—C(1)—H(1)179.95 (6)N(1)—C(2)—C(3)—H(3)179.76 (6)
H(3A)—N(3)—C(5)—O(1)178.53 (8)C(3)—C(2)—C(5)—O(1)4.71 (4)
H(3A)—N(3)—C(5)—C(2)2.69 (4)C(3)—C(2)—C(5)—N(3)176.45 (6)
H(3B)—N(3)—C(5)—O(1)2.81 (5)C(5)—C(2)—C(3)—N(2)177.64 (6)
H(3B)—N(3)—C(5)—C(2)178.41 (7)C(5)—C(2)—C(3)—H(3)1.45 (4)
C(4)—N(2)—C(3)—C(2)0.19 (4)N(2)—C(4)—C(1)—N(1)0.65 (4)
C(3)—N(2)—C(4)—C(1)1.05 (4)N(2)—C(4)—C(1)—H(1)178.72 (7)
C(4)—N(2)—C(3)—H(3)178.92 (6)H(4)—C(4)—C(1)—N(1)178.50 (7)
C(3)—N(2)—C(4)—H(4)178.13 (7)H(4)—C(4)—C(1)—H(1)2.13 (4)
 

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