Literature DB >> 21754498

4-(2-{[4-Amino-6-(4-nitro-benz-yl)-5-oxo-4,5-dihydro-1,2,4-triazin-3-yl]sulfan-yl}acet-yl)-3-phenyl-sydnone.

Hoong-Kun Fun, Mohd Mustaqim Rosli, Balakrishna Kalluraya.   

Abstract

In the crystal, C(20)H(15)N(7)O(6)S, the dihedral angle between the oxadiazole and triazine rings is 86.94 (7)°. The oxadiazole ring makes a dihedral angle of 52.96 (8)° with the phenyl ring, while the triazine ring makes a dihedral angle of 82.08 (7)° with the benzene ring. In the structure, mol-ecules are linked by a pair of N-H⋯O hydrogen bonds, forming an inversion dimer. The dimers are further stacked along the a axis via N-H⋯N hydrogen bonds. Weak inter-molecular C-H⋯O inter-actions are also observed.

Entities:  

Year:  2011        PMID: 21754498      PMCID: PMC3089265          DOI: 10.1107/S1600536811014504

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


Related literature

For the biological activity of sydnone derivatives, see: Rai et al. (2008 ▶); Jyothi et al. (2008 ▶); Kalluraya et al. (2008a ▶,b ▶). For a related structure, see: Fun et al. (2011 ▶).

Experimental

Crystal data

C20H15N7O6S M = 481.45 Triclinic, a = 6.4071 (1) Å b = 10.1629 (2) Å c = 17.1521 (3) Å α = 106.372 (1)° β = 92.400 (1)° γ = 97.551 (1)° V = 1058.61 (3) Å3 Z = 2 Mo Kα radiation μ = 0.21 mm−1 T = 297 K 0.51 × 0.34 × 0.17 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.900, T max = 0.965 21821 measured reflections 7793 independent reflections 5330 reflections with I > 2σ(I) R int = 0.030

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.131 S = 1.04 7793 reflections 315 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.25 e Å−3 Δρmin = −0.23 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811014504/is2702sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811014504/is2702Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H15N7O6SZ = 2
Mr = 481.45F(000) = 496
Triclinic, P1Dx = 1.510 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.4071 (1) ÅCell parameters from 5430 reflections
b = 10.1629 (2) Åθ = 3.7–30.1°
c = 17.1521 (3) ŵ = 0.21 mm1
α = 106.372 (1)°T = 297 K
β = 92.400 (1)°Block, yellow
γ = 97.551 (1)°0.51 × 0.34 × 0.17 mm
V = 1058.61 (3) Å3
Bruker SMART APEXII CCD area-detector diffractometer7793 independent reflections
Radiation source: fine-focus sealed tube5330 reflections with I > 2σ(I)
graphiteRint = 0.030
φ and ω scansθmax = 32.8°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −9→9
Tmin = 0.900, Tmax = 0.965k = −15→15
21821 measured reflectionsl = −26→26
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.131H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0615P)2 + 0.084P] where P = (Fo2 + 2Fc2)/3
7793 reflections(Δ/σ)max < 0.001
315 parametersΔρmax = 0.25 e Å3
0 restraintsΔρmin = −0.23 e Å3
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 of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/Ueq
S10.76158 (5)0.56912 (4)0.39458 (2)0.04815 (10)
N11.40303 (17)0.45428 (11)0.21692 (6)0.0388 (2)
N21.5454 (2)0.37194 (13)0.20533 (8)0.0525 (3)
N30.73930 (15)0.81262 (11)0.49757 (6)0.0362 (2)
N41.14452 (17)0.85392 (13)0.56156 (7)0.0460 (3)
N51.06998 (16)0.73678 (12)0.49822 (7)0.0430 (2)
N60.8522 (4)0.87248 (18)0.93514 (10)0.0851 (6)
N70.52842 (19)0.77429 (15)0.46377 (9)0.0531 (3)
O11.51411 (17)0.29797 (10)0.26042 (7)0.0531 (3)
O21.29331 (18)0.28459 (11)0.35900 (7)0.0565 (3)
O31.07909 (19)0.62369 (11)0.28170 (7)0.0604 (3)
O40.68160 (17)1.01247 (11)0.58890 (6)0.0536 (3)
O50.6980 (4)0.9118 (2)0.96790 (12)0.1335 (8)
O60.9522 (4)0.7945 (2)0.95653 (11)0.1279 (8)
C11.2266 (3)0.54038 (16)0.11647 (9)0.0520 (3)
H1A1.10030.48750.12100.062*
C21.2384 (3)0.61847 (18)0.06204 (10)0.0643 (4)
H2A1.11810.61980.03020.077*
C31.4275 (3)0.69420 (17)0.05489 (10)0.0653 (5)
H3A1.43470.74440.01710.078*
C41.6052 (3)0.69646 (18)0.10286 (11)0.0660 (4)
H4A1.73150.74910.09800.079*
C51.5974 (3)0.62030 (16)0.15882 (10)0.0541 (3)
H5A1.71660.62130.19190.065*
C61.4068 (2)0.54316 (13)0.16354 (7)0.0412 (3)
C71.3425 (2)0.33732 (13)0.30715 (8)0.0411 (3)
C81.27298 (19)0.44150 (12)0.27599 (7)0.0352 (2)
C91.1124 (2)0.52770 (12)0.30653 (7)0.0382 (2)
C100.9904 (2)0.48508 (14)0.37157 (8)0.0438 (3)
H10A1.08340.50660.42100.053*
H10B0.94640.38550.35350.053*
C110.87411 (17)0.71923 (13)0.47012 (7)0.0347 (2)
C120.8018 (2)0.93081 (13)0.56189 (7)0.0380 (2)
C131.0230 (2)0.94417 (13)0.59158 (7)0.0392 (3)
C141.1084 (2)1.06316 (14)0.66524 (8)0.0484 (3)
H14A1.04971.14560.66350.058*
H14B1.26091.08310.66620.058*
C151.0474 (2)1.02257 (13)0.74039 (8)0.0418 (3)
C160.8680 (3)1.05963 (15)0.77747 (9)0.0516 (3)
H16A0.78981.11760.75920.062*
C170.8036 (3)1.01111 (17)0.84163 (10)0.0592 (4)
H17A0.68211.03500.86630.071*
C180.9234 (3)0.92666 (15)0.86812 (9)0.0575 (4)
C191.1038 (3)0.89030 (17)0.83385 (10)0.0652 (5)
H19A1.18340.83420.85330.078*
C201.1651 (3)0.93889 (16)0.76961 (9)0.0559 (4)
H20A1.28750.91510.74550.067*
H2N70.492 (3)0.848 (2)0.4511 (12)0.084 (6)*
H1N70.456 (3)0.764 (2)0.5051 (13)0.077 (6)*
U11U22U33U12U13U23
S10.03577 (16)0.0519 (2)0.0551 (2)0.01356 (13)0.00911 (13)0.00898 (15)
N10.0436 (5)0.0376 (5)0.0387 (5)0.0140 (4)0.0093 (4)0.0123 (4)
N20.0569 (7)0.0522 (7)0.0586 (7)0.0271 (5)0.0224 (6)0.0211 (6)
N30.0302 (4)0.0467 (5)0.0407 (5)0.0173 (4)0.0105 (4)0.0210 (4)
N40.0339 (5)0.0572 (7)0.0483 (6)0.0106 (5)0.0098 (4)0.0150 (5)
N50.0310 (5)0.0536 (6)0.0477 (6)0.0155 (4)0.0102 (4)0.0147 (5)
N60.1383 (18)0.0596 (9)0.0504 (8)−0.0176 (10)0.0025 (10)0.0201 (7)
N70.0326 (5)0.0653 (8)0.0628 (8)0.0238 (5)0.0036 (5)0.0135 (6)
O10.0586 (6)0.0485 (5)0.0657 (6)0.0301 (5)0.0198 (5)0.0259 (5)
O20.0658 (7)0.0529 (6)0.0680 (6)0.0225 (5)0.0167 (5)0.0374 (5)
O30.0766 (7)0.0571 (6)0.0694 (7)0.0392 (6)0.0293 (6)0.0371 (5)
O40.0598 (6)0.0541 (6)0.0554 (6)0.0336 (5)0.0097 (5)0.0177 (5)
O50.181 (2)0.1328 (17)0.1005 (13)0.0027 (15)0.0624 (14)0.0588 (12)
O60.212 (2)0.1014 (12)0.0919 (11)0.0126 (13)0.0041 (13)0.0687 (11)
C10.0579 (8)0.0514 (8)0.0478 (7)0.0030 (6)−0.0001 (6)0.0193 (6)
C20.0845 (12)0.0638 (10)0.0494 (8)0.0089 (9)−0.0052 (8)0.0264 (7)
C30.0971 (14)0.0556 (9)0.0515 (8)0.0105 (9)0.0159 (9)0.0280 (7)
C40.0753 (11)0.0606 (10)0.0676 (10)0.0017 (8)0.0239 (9)0.0287 (8)
C50.0531 (8)0.0571 (8)0.0553 (8)0.0070 (7)0.0109 (6)0.0209 (7)
C60.0510 (7)0.0393 (6)0.0364 (6)0.0113 (5)0.0102 (5)0.0131 (5)
C70.0440 (6)0.0350 (6)0.0491 (7)0.0139 (5)0.0080 (5)0.0157 (5)
C80.0373 (6)0.0334 (5)0.0390 (6)0.0113 (4)0.0073 (4)0.0139 (4)
C90.0417 (6)0.0365 (6)0.0401 (6)0.0141 (5)0.0074 (5)0.0126 (5)
C100.0462 (7)0.0436 (7)0.0486 (7)0.0187 (5)0.0152 (5)0.0178 (5)
C110.0305 (5)0.0442 (6)0.0386 (5)0.0149 (4)0.0137 (4)0.0211 (5)
C120.0436 (6)0.0423 (6)0.0388 (6)0.0177 (5)0.0119 (5)0.0230 (5)
C130.0400 (6)0.0438 (6)0.0413 (6)0.0083 (5)0.0116 (5)0.0221 (5)
C140.0534 (8)0.0445 (7)0.0499 (7)0.0040 (6)0.0077 (6)0.0190 (6)
C150.0499 (7)0.0350 (6)0.0403 (6)0.0085 (5)0.0014 (5)0.0102 (5)
C160.0597 (9)0.0499 (8)0.0527 (8)0.0211 (6)0.0097 (6)0.0205 (6)
C170.0697 (10)0.0567 (9)0.0513 (8)0.0109 (7)0.0181 (7)0.0132 (7)
C180.0912 (12)0.0417 (7)0.0373 (6)−0.0004 (7)0.0020 (7)0.0130 (5)
C190.0953 (13)0.0524 (8)0.0544 (9)0.0241 (9)−0.0070 (9)0.0219 (7)
C200.0632 (9)0.0554 (8)0.0547 (8)0.0252 (7)0.0043 (7)0.0177 (7)
S1—C111.7448 (13)C3—C41.370 (3)
S1—C101.7951 (13)C3—H3A0.9300
N1—N21.3013 (15)C4—C51.391 (2)
N1—C81.3616 (15)C4—H4A0.9300
N1—C61.4550 (16)C5—C61.380 (2)
N2—O11.3693 (15)C5—H5A0.9300
N3—C111.3660 (14)C7—C81.4242 (16)
N3—C121.3820 (17)C8—C91.4572 (16)
N3—N71.4079 (15)C9—C101.5165 (17)
N4—C131.2914 (17)C10—H10A0.9700
N4—N51.3797 (16)C10—H10B0.9700
N5—C111.2966 (15)C12—C131.4615 (18)
N6—O61.205 (3)C13—C141.5049 (19)
N6—O51.214 (3)C14—C151.5112 (18)
N6—C181.472 (2)C14—H14A0.9700
N7—H2N70.90 (2)C14—H14B0.9700
N7—H1N70.89 (2)C15—C161.381 (2)
O1—C71.4212 (16)C15—C201.3856 (19)
O2—C71.1937 (16)C16—C171.384 (2)
O3—C91.2083 (15)C16—H16A0.9300
O4—C121.2156 (15)C17—C181.377 (2)
C1—C61.373 (2)C17—H17A0.9300
C1—C21.384 (2)C18—C191.366 (3)
C1—H1A0.9300C19—C201.380 (2)
C2—C31.377 (3)C19—H19A0.9300
C2—H2A0.9300C20—H20A0.9300
C11—S1—C10100.23 (6)O3—C9—C10123.28 (11)
N2—N1—C8114.78 (10)C8—C9—C10113.88 (10)
N2—N1—C6114.59 (10)C9—C10—S1113.41 (9)
C8—N1—C6130.62 (10)C9—C10—H10A108.9
N1—N2—O1105.29 (10)S1—C10—H10A108.9
C11—N3—C12121.18 (10)C9—C10—H10B108.9
C11—N3—N7116.60 (11)S1—C10—H10B108.9
C12—N3—N7121.80 (10)H10A—C10—H10B107.7
C13—N4—N5120.91 (11)N5—C11—N3123.75 (12)
C11—N5—N4118.18 (11)N5—C11—S1121.37 (9)
O6—N6—O5122.9 (2)N3—C11—S1114.86 (9)
O6—N6—C18118.8 (2)O4—C12—N3122.00 (12)
O5—N6—C18118.2 (2)O4—C12—C13125.50 (12)
N3—N7—H2N7106.2 (14)N3—C12—C13112.50 (10)
N3—N7—H1N7104.2 (14)N4—C13—C12123.40 (12)
H2N7—N7—H1N7107.5 (19)N4—C13—C14118.21 (12)
N2—O1—C7110.84 (9)C12—C13—C14118.20 (11)
C6—C1—C2118.12 (15)C13—C14—C15108.09 (10)
C6—C1—H1A120.9C13—C14—H14A110.1
C2—C1—H1A120.9C15—C14—H14A110.1
C3—C2—C1120.27 (16)C13—C14—H14B110.1
C3—C2—H2A119.9C15—C14—H14B110.1
C1—C2—H2A119.9H14A—C14—H14B108.4
C4—C3—C2120.72 (14)C16—C15—C20119.09 (13)
C4—C3—H3A119.6C16—C15—C14121.16 (12)
C2—C3—H3A119.6C20—C15—C14119.60 (13)
C3—C4—C5120.24 (16)C15—C16—C17120.48 (14)
C3—C4—H4A119.9C15—C16—H16A119.8
C5—C4—H4A119.9C17—C16—H16A119.8
C6—C5—C4117.79 (16)C18—C17—C16118.61 (16)
C6—C5—H5A121.1C18—C17—H17A120.7
C4—C5—H5A121.1C16—C17—H17A120.7
C1—C6—C5122.84 (13)C19—C18—C17122.36 (14)
C1—C6—N1119.32 (12)C19—C18—N6119.06 (17)
C5—C6—N1117.71 (13)C17—C18—N6118.58 (19)
O2—C7—O1120.32 (11)C18—C19—C20118.29 (15)
O2—C7—C8136.17 (13)C18—C19—H19A120.9
O1—C7—C8103.50 (10)C20—C19—H19A120.9
N1—C8—C7105.59 (10)C19—C20—C15121.14 (16)
N1—C8—C9126.62 (10)C19—C20—H20A119.4
C7—C8—C9127.47 (11)C15—C20—H20A119.4
O3—C9—C8122.84 (12)
C8—N1—N2—O1−0.65 (15)C12—N3—C11—N5−3.89 (17)
C6—N1—N2—O1−179.61 (10)N7—N3—C11—N5−176.56 (12)
C13—N4—N5—C11−0.56 (18)C12—N3—C11—S1174.64 (8)
N1—N2—O1—C70.50 (15)N7—N3—C11—S11.97 (14)
C6—C1—C2—C31.2 (3)C10—S1—C11—N5−5.61 (11)
C1—C2—C3—C4−1.7 (3)C10—S1—C11—N3175.82 (8)
C2—C3—C4—C50.9 (3)C11—N3—C12—O4−177.39 (11)
C3—C4—C5—C60.4 (3)N7—N3—C12—O4−5.09 (18)
C2—C1—C6—C50.1 (2)C11—N3—C12—C132.88 (15)
C2—C1—C6—N1−175.51 (14)N7—N3—C12—C13175.17 (11)
C4—C5—C6—C1−0.9 (2)N5—N4—C13—C12−0.10 (18)
C4—C5—C6—N1174.80 (13)N5—N4—C13—C14174.79 (11)
N2—N1—C6—C1124.32 (14)O4—C12—C13—N4179.22 (12)
C8—N1—C6—C1−54.43 (19)N3—C12—C13—N4−1.05 (16)
N2—N1—C6—C5−51.51 (17)O4—C12—C13—C144.33 (18)
C8—N1—C6—C5129.74 (15)N3—C12—C13—C14−175.94 (10)
N2—O1—C7—O2−179.23 (13)N4—C13—C14—C15−92.98 (14)
N2—O1—C7—C8−0.19 (14)C12—C13—C14—C1582.18 (14)
N2—N1—C8—C70.54 (15)C13—C14—C15—C16−94.98 (15)
C6—N1—C8—C7179.29 (12)C13—C14—C15—C2080.63 (16)
N2—N1—C8—C9174.43 (12)C20—C15—C16—C17−1.6 (2)
C6—N1—C8—C9−6.8 (2)C14—C15—C16—C17174.06 (13)
O2—C7—C8—N1178.62 (16)C15—C16—C17—C180.7 (2)
O1—C7—C8—N1−0.19 (13)C16—C17—C18—C190.6 (2)
O2—C7—C8—C94.8 (3)C16—C17—C18—N6−178.61 (14)
O1—C7—C8—C9−174.00 (12)O6—N6—C18—C19−1.9 (3)
N1—C8—C9—O3−0.7 (2)O5—N6—C18—C19176.04 (19)
C7—C8—C9—O3171.92 (13)O6—N6—C18—C17177.31 (17)
N1—C8—C9—C10178.87 (12)O5—N6—C18—C17−4.7 (3)
C7—C8—C9—C10−8.56 (19)C17—C18—C19—C20−1.0 (3)
O3—C9—C10—S110.82 (18)N6—C18—C19—C20178.23 (14)
C8—C9—C10—S1−168.69 (9)C18—C19—C20—C150.1 (2)
C11—S1—C10—C9−88.06 (10)C16—C15—C20—C191.2 (2)
N4—N5—C11—N32.54 (18)C14—C15—C20—C19−174.51 (14)
N4—N5—C11—S1−175.89 (9)
D—H···AD—HH···AD···AD—H···A
N7—H2N7···O4i0.89 (2)2.15 (2)3.0152 (19)163.5 (18)
N7—H1N7···N4ii0.89 (2)2.43 (2)3.1019 (17)133.1 (17)
N7—H1N7···N5ii0.89 (2)2.45 (2)3.0166 (16)122.5 (16)
C3—H3A···O5iii0.932.573.345 (3)141.
C14—H14A···O3iv0.972.533.4443 (18)157.
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N7—H2N7⋯O4i0.89 (2)2.15 (2)3.0152 (19)163.5 (18)
N7—H1N7⋯N4ii0.89 (2)2.43 (2)3.1019 (17)133.1 (17)
N7—H1N7⋯N5ii0.89 (2)2.45 (2)3.0166 (16)122.5 (16)
C3—H3A⋯O5iii0.932.573.345 (3)141
C14—H14A⋯O3iv0.972.533.4443 (18)157

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

  5 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Synthesis and antimicrobial activities of a new series of 4-S-[4(1)-amino-5(1)-oxo-6(1)-substituted benzyl-4(1),5(1)-dihydro-1(1),2(1),4(1)-triazin-3-yl]mercaptoacetyl-3-arylsydnones.

Authors:  Jyothi C Hegde; K S Girisha; Adithya Adhikari; Balakrishna Kalluraya
Journal:  Eur J Med Chem       Date:  2008-03-04       Impact factor: 6.514

3.  4-({[4-Amino-6-(p-bromo-benz-yl)-5-oxo-4,5-dihydro-1,2,4-triazin-3-yl]sulfan-yl}acet-yl)-3-phenyl-sydnone.

Authors:  Hoong-Kun Fun; Ching Kheng Quah; Balakrishna Kalluraya
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-03-31

4.  Convenient access to 1,3,4-trisubstituted pyrazoles carrying 5-nitrothiophene moiety via 1,3-dipolar cycloaddition of sydnones with acetylenic ketones and their antimicrobial evaluation.

Authors:  N Satheesha Rai; Balakrishna Kalluraya; B Lingappa; Shaliny Shenoy; Vedavati G Puranic
Journal:  Eur J Med Chem       Date:  2007-08-30       Impact factor: 6.514

5.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.