Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807022799/bx2077sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807022799/bx2077Isup2.hkl |
CCDC reference: 651457
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.002 Å
- R factor = 0.036
- wR factor = 0.089
- Data-to-parameter ratio = 11.9
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3
Alert level G PLAT793_ALERT_1_G Check the Absolute Configuration of C5 = ... R PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 3
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 2 ALERT level G = General alerts; check 1 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 2 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related literature, see: Tramontini (1973); Tramontini & Angliolini (1990); Wozniak et al. (2000).
Urea (12 g, 0.2M), Succinimide (19.8 g, 0.2M) and Benzaldehyde (22 ml, 0.2M) were taken in equimolar ratio. A concentrated aqueous solution of urea and succinimide was prepared. Benzaldehyde was added in drops with continuous stirring of the solution. The mixture first became oily and then slowly turned into a white crystalline mass, which was separated by suction filtration and washed several times with water. The product was dried and recrystallized using acetone by slow evaporation (Tramontini, 1973; Tramontini & Angliolini, 1990).
All the H atoms except those of N atoms were geometrically fixed at chemically meaningful positions. The hydrogen atoms of the phenyl ring were allowed to ride at a distance of 0.93 Å from the parent carbons and their thermal parameter were fixed at 1.2 times that of the parent atom. The secondary CH2 hydrogen were fixed at a distance of 0.97 Å from the parent atom and their thermal parameters were fixed at 1.2 times the parent atom. The H atoms associated with nitrogen atoms were located from the difference fourier map and refined. However, their distances were constrained from the parent atom to avoid abnormal geometry.
Mannich bases- compounds with the general formula R—CH2—N< have been studied extensively, because of their applications in pharmaceutical and polymer chemistry. They are very good model systems for both intermolecular and intramolecular hydrogen bonding and a variety of other effects (Wozniak et al., 2000). In the crystal structure of the title compound, the molecules which are related through center of inversion are linked to each other through N3—H3···O3 hydrogen bonds (2.363 (11) Å, 155.1 (15) °). They form a dimeric pair. These dimeric pairs are linked to its b-translation equivalent through N2—H2···O2 (2.19 Å, 149.4 °) hydrogen bonding. The hydrogen bonded dimer and the translation equivalents form an one dimensional dimeric chain running parallel to the b axis. The one dimensional chains are linked through van der Waals interactions. Succinimide moiety is almost planar with maximum deviation of 0.032 Å for the N atom from the least squares mean plane of atoms. The planarity can be attributed to the sp2 hybridization of C1 and C4 atoms.
For related literature, see: Tramontini (1973); Tramontini & Angliolini (1990); Wozniak et al. (2000).
Data collection: SMART (Bruker–Nonius, 2004); cell refinement: SMART; data reduction: SAINT (Bruker–Nonius, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-32 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
Fig. 1. ORTEP representation of the molecule showing the atom numbering scheme. Thermal ellipsoids are drawn with 30% probability. | |
Fig. 2. Packing diagram of title compound projected down the b axis |
C12H13N3O3 | F(000) = 520 |
Mr = 247.25 | Dx = 1.421 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 3812 reflections |
a = 13.8460 (4) Å | θ = 2.6–26.8° |
b = 5.3527 (1) Å | µ = 0.11 mm−1 |
c = 15.9052 (4) Å | T = 298 K |
β = 101.310 (1)° | Needle, colourless |
V = 1155.90 (5) Å3 | 0.30 × 0.15 × 0.10 mm |
Z = 4 |
Bruker SMART CCD area-detector diffractometer | 2032 independent reflections |
Radiation source: fine-focus sealed tube | 1620 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
phi and ω scans | θmax = 25.0°, θmin = 1.8° |
Absorption correction: multi-scan (Blessing, 1995) | h = −16→15 |
Tmin = 0.894, Tmax = 0.982 | k = −5→6 |
11730 measured reflections | l = −18→16 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0389P)2 + 0.3355P] where P = (Fo2 + 2Fc2)/3 |
2032 reflections | (Δ/σ)max < 0.001 |
171 parameters | Δρmax = 0.13 e Å−3 |
3 restraints | Δρmin = −0.16 e Å−3 |
C12H13N3O3 | V = 1155.90 (5) Å3 |
Mr = 247.25 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 13.8460 (4) Å | µ = 0.11 mm−1 |
b = 5.3527 (1) Å | T = 298 K |
c = 15.9052 (4) Å | 0.30 × 0.15 × 0.10 mm |
β = 101.310 (1)° |
Bruker SMART CCD area-detector diffractometer | 2032 independent reflections |
Absorption correction: multi-scan (Blessing, 1995) | 1620 reflections with I > 2σ(I) |
Tmin = 0.894, Tmax = 0.982 | Rint = 0.031 |
11730 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 3 restraints |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.13 e Å−3 |
2032 reflections | Δρmin = −0.16 e Å−3 |
171 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.42128 (11) | 0.9642 (3) | 0.38640 (9) | 0.0335 (4) | |
C2 | 0.33912 (12) | 0.8629 (3) | 0.42524 (11) | 0.0460 (4) | |
H2A | 0.2851 | 0.9812 | 0.4189 | 0.055* | |
H2B | 0.3619 | 0.8282 | 0.4857 | 0.055* | |
C3 | 0.30687 (12) | 0.6246 (3) | 0.37642 (11) | 0.0422 (4) | |
H3D | 0.3205 | 0.4804 | 0.4138 | 0.051* | |
H3E | 0.2369 | 0.6291 | 0.3523 | 0.051* | |
C4 | 0.36532 (11) | 0.6135 (3) | 0.30708 (10) | 0.0352 (4) | |
C5 | 0.50746 (11) | 0.8393 (3) | 0.26626 (9) | 0.0324 (4) | |
H5 | 0.5056 | 0.6887 | 0.2310 | 0.039* | |
C6 | 0.61091 (11) | 0.8554 (3) | 0.31986 (9) | 0.0315 (4) | |
C7 | 0.67576 (12) | 1.0414 (3) | 0.30768 (11) | 0.0422 (4) | |
H7 | 0.6551 | 1.1672 | 0.2679 | 0.051* | |
C8 | 0.77135 (13) | 1.0423 (4) | 0.35423 (12) | 0.0509 (5) | |
H8 | 0.8144 | 1.1693 | 0.3461 | 0.061* | |
C9 | 0.80266 (13) | 0.8556 (4) | 0.41245 (12) | 0.0494 (5) | |
H9 | 0.8668 | 0.8566 | 0.4439 | 0.059* | |
C10 | 0.73927 (13) | 0.6677 (3) | 0.42410 (11) | 0.0474 (5) | |
H10 | 0.7608 | 0.5399 | 0.4629 | 0.057* | |
C11 | 0.64353 (12) | 0.6676 (3) | 0.37835 (10) | 0.0400 (4) | |
H11 | 0.6007 | 0.5404 | 0.3869 | 0.048* | |
C12 | 0.47214 (10) | 1.0140 (3) | 0.12240 (9) | 0.0324 (4) | |
N1 | 0.43403 (9) | 0.8032 (2) | 0.32059 (8) | 0.0319 (3) | |
N2 | 0.47887 (10) | 1.0439 (2) | 0.20808 (8) | 0.0378 (3) | |
H2 | 0.4659 | 1.1869 | 0.2278 | 0.045* | |
N3 | 0.43973 (10) | 1.2140 (3) | 0.07345 (9) | 0.0404 (4) | |
O1 | 0.46858 (9) | 1.1527 (2) | 0.40438 (7) | 0.0448 (3) | |
O2 | 0.35735 (9) | 0.4659 (2) | 0.24816 (8) | 0.0500 (3) | |
O3 | 0.49252 (9) | 0.8126 (2) | 0.09201 (7) | 0.0461 (3) | |
H3A | 0.4524 (13) | 1.205 (3) | 0.0176 (7) | 0.060 (6)* | |
H3B | 0.4387 (13) | 1.371 (2) | 0.0985 (9) | 0.054 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0360 (9) | 0.0376 (9) | 0.0259 (8) | 0.0048 (7) | 0.0037 (7) | −0.0015 (7) |
C2 | 0.0442 (10) | 0.0562 (11) | 0.0409 (10) | −0.0012 (8) | 0.0166 (8) | −0.0043 (8) |
C3 | 0.0367 (9) | 0.0413 (9) | 0.0505 (10) | 0.0018 (7) | 0.0134 (8) | 0.0046 (8) |
C4 | 0.0325 (9) | 0.0344 (8) | 0.0357 (9) | 0.0040 (7) | −0.0005 (7) | −0.0001 (8) |
C5 | 0.0394 (9) | 0.0327 (8) | 0.0265 (8) | 0.0032 (7) | 0.0097 (7) | −0.0020 (7) |
C6 | 0.0352 (9) | 0.0336 (8) | 0.0277 (8) | 0.0023 (7) | 0.0114 (7) | −0.0028 (7) |
C7 | 0.0463 (10) | 0.0413 (10) | 0.0413 (10) | −0.0002 (8) | 0.0144 (8) | 0.0030 (8) |
C8 | 0.0407 (11) | 0.0563 (11) | 0.0585 (12) | −0.0110 (9) | 0.0167 (9) | −0.0083 (10) |
C9 | 0.0336 (9) | 0.0679 (13) | 0.0461 (11) | 0.0056 (9) | 0.0065 (8) | −0.0133 (10) |
C10 | 0.0467 (11) | 0.0560 (11) | 0.0387 (10) | 0.0143 (9) | 0.0062 (8) | 0.0045 (8) |
C11 | 0.0399 (10) | 0.0406 (9) | 0.0406 (10) | 0.0011 (7) | 0.0108 (8) | 0.0062 (8) |
C12 | 0.0269 (8) | 0.0441 (9) | 0.0265 (9) | 0.0002 (7) | 0.0059 (6) | −0.0018 (7) |
N1 | 0.0325 (7) | 0.0373 (7) | 0.0263 (7) | −0.0005 (6) | 0.0068 (5) | −0.0048 (6) |
N2 | 0.0518 (8) | 0.0374 (8) | 0.0243 (7) | 0.0110 (6) | 0.0079 (6) | −0.0018 (6) |
N3 | 0.0483 (9) | 0.0452 (9) | 0.0280 (8) | 0.0062 (7) | 0.0086 (6) | 0.0034 (7) |
O1 | 0.0525 (7) | 0.0405 (7) | 0.0427 (7) | −0.0049 (5) | 0.0128 (6) | −0.0095 (5) |
O2 | 0.0503 (7) | 0.0463 (7) | 0.0516 (8) | −0.0043 (6) | 0.0055 (6) | −0.0172 (6) |
O3 | 0.0653 (8) | 0.0462 (7) | 0.0287 (6) | 0.0074 (6) | 0.0141 (6) | −0.0046 (5) |
C1—O1 | 1.2064 (18) | C6—C11 | 1.384 (2) |
C1—N1 | 1.3933 (19) | C7—C8 | 1.384 (3) |
C1—C2 | 1.498 (2) | C7—H7 | 0.9300 |
C2—C3 | 1.514 (2) | C8—C9 | 1.374 (3) |
C2—H2A | 0.9700 | C8—H8 | 0.9300 |
C2—H2B | 0.9700 | C9—C10 | 1.371 (3) |
C3—C4 | 1.492 (2) | C9—H9 | 0.9300 |
C3—H3D | 0.9700 | C10—C11 | 1.381 (2) |
C3—H3E | 0.9700 | C10—H10 | 0.9300 |
C4—O2 | 1.2139 (18) | C11—H11 | 0.9300 |
C4—N1 | 1.380 (2) | C12—O3 | 1.2364 (18) |
C5—N2 | 1.4381 (19) | C12—N3 | 1.348 (2) |
C5—N1 | 1.4703 (19) | C12—N2 | 1.3571 (19) |
C5—C6 | 1.519 (2) | N2—H2 | 0.8600 |
C5—H5 | 0.9800 | N3—H3A | 0.940 (9) |
C6—C7 | 1.379 (2) | N3—H3B | 0.929 (9) |
O1—C1—N1 | 123.52 (14) | C6—C7—C8 | 120.52 (16) |
O1—C1—C2 | 128.73 (14) | C6—C7—H7 | 119.7 |
N1—C1—C2 | 107.72 (13) | C8—C7—H7 | 119.7 |
C1—C2—C3 | 105.34 (13) | C9—C8—C7 | 120.03 (17) |
C1—C2—H2A | 110.7 | C9—C8—H8 | 120.0 |
C3—C2—H2A | 110.7 | C7—C8—H8 | 120.0 |
C1—C2—H2B | 110.7 | C10—C9—C8 | 119.93 (16) |
C3—C2—H2B | 110.7 | C10—C9—H9 | 120.0 |
H2A—C2—H2B | 108.8 | C8—C9—H9 | 120.0 |
C4—C3—C2 | 105.34 (13) | C9—C10—C11 | 120.18 (17) |
C4—C3—H3D | 110.7 | C9—C10—H10 | 119.9 |
C2—C3—H3D | 110.7 | C11—C10—H10 | 119.9 |
C4—C3—H3E | 110.7 | C10—C11—C6 | 120.44 (16) |
C2—C3—H3E | 110.7 | C10—C11—H11 | 119.8 |
H3D—C3—H3E | 108.8 | C6—C11—H11 | 119.8 |
O2—C4—N1 | 123.70 (15) | O3—C12—N3 | 122.85 (14) |
O2—C4—C3 | 128.05 (15) | O3—C12—N2 | 121.29 (14) |
N1—C4—C3 | 108.25 (13) | N3—C12—N2 | 115.85 (14) |
N2—C5—N1 | 110.08 (12) | C4—N1—C1 | 112.77 (13) |
N2—C5—C6 | 115.35 (12) | C4—N1—C5 | 122.71 (12) |
N1—C5—C6 | 111.24 (12) | C1—N1—C5 | 124.36 (12) |
N2—C5—H5 | 106.5 | C12—N2—C5 | 120.83 (13) |
N1—C5—H5 | 106.5 | C12—N2—H2 | 119.6 |
C6—C5—H5 | 106.5 | C5—N2—H2 | 119.6 |
C7—C6—C11 | 118.88 (15) | C12—N3—H3A | 113.7 (11) |
C7—C6—C5 | 122.03 (14) | C12—N3—H3B | 120.0 (10) |
C11—C6—C5 | 118.91 (13) | H3A—N3—H3B | 118.2 (12) |
O1—C1—C2—C3 | 179.13 (16) | O2—C4—N1—C1 | 173.20 (15) |
N1—C1—C2—C3 | 1.05 (17) | C3—C4—N1—C1 | −7.39 (17) |
C1—C2—C3—C4 | −5.12 (17) | O2—C4—N1—C5 | −2.4 (2) |
C2—C3—C4—O2 | −173.04 (16) | C3—C4—N1—C5 | 176.96 (13) |
C2—C3—C4—N1 | 7.57 (17) | O1—C1—N1—C4 | −174.25 (14) |
N2—C5—C6—C7 | −5.8 (2) | C2—C1—N1—C4 | 3.96 (17) |
N1—C5—C6—C7 | −132.05 (15) | O1—C1—N1—C5 | 1.3 (2) |
N2—C5—C6—C11 | 179.07 (13) | C2—C1—N1—C5 | 179.52 (13) |
N1—C5—C6—C11 | 52.79 (18) | N2—C5—N1—C4 | 103.21 (15) |
C11—C6—C7—C8 | −1.1 (2) | C6—C5—N1—C4 | −127.66 (14) |
C5—C6—C7—C8 | −176.22 (15) | N2—C5—N1—C1 | −71.93 (17) |
C6—C7—C8—C9 | 0.7 (3) | C6—C5—N1—C1 | 57.21 (18) |
C7—C8—C9—C10 | 0.3 (3) | O3—C12—N2—C5 | −1.7 (2) |
C8—C9—C10—C11 | −1.0 (3) | N3—C12—N2—C5 | 176.62 (13) |
C9—C10—C11—C6 | 0.6 (3) | N1—C5—N2—C12 | −126.47 (14) |
C7—C6—C11—C10 | 0.4 (2) | C6—C5—N2—C12 | 106.66 (15) |
C5—C6—C11—C10 | 175.74 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2i | 0.86 | 2.19 | 2.9600 (18) | 149 |
N3—H3B···O3i | 0.93 (1) | 2.49 (1) | 3.2867 (19) | 144 (1) |
N3—H3A···O3ii | 0.94 (1) | 2.04 (1) | 2.9655 (17) | 169 (2) |
Symmetry codes: (i) x, y+1, z; (ii) −x+1, −y+2, −z. |
Experimental details
Crystal data | |
Chemical formula | C12H13N3O3 |
Mr | 247.25 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 298 |
a, b, c (Å) | 13.8460 (4), 5.3527 (1), 15.9052 (4) |
β (°) | 101.310 (1) |
V (Å3) | 1155.90 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.30 × 0.15 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector |
Absorption correction | Multi-scan (Blessing, 1995) |
Tmin, Tmax | 0.894, 0.982 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 11730, 2032, 1620 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.089, 1.04 |
No. of reflections | 2032 |
No. of parameters | 171 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.13, −0.16 |
Computer programs: SMART (Bruker–Nonius, 2004), SMART, SAINT (Bruker–Nonius, 2004), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-32 (Farrugia, 1997), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2i | 0.86 | 2.19 | 2.9600 (18) | 149.4 |
N3—H3B···O3i | 0.929 (9) | 2.489 (13) | 3.2867 (19) | 144.1 (13) |
N3—H3A···O3ii | 0.940 (9) | 2.037 (9) | 2.9655 (17) | 169.0 (16) |
Symmetry codes: (i) x, y+1, z; (ii) −x+1, −y+2, −z. |
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Mannich bases- compounds with the general formula R—CH2—N< have been studied extensively, because of their applications in pharmaceutical and polymer chemistry. They are very good model systems for both intermolecular and intramolecular hydrogen bonding and a variety of other effects (Wozniak et al., 2000). In the crystal structure of the title compound, the molecules which are related through center of inversion are linked to each other through N3—H3···O3 hydrogen bonds (2.363 (11) Å, 155.1 (15) °). They form a dimeric pair. These dimeric pairs are linked to its b-translation equivalent through N2—H2···O2 (2.19 Å, 149.4 °) hydrogen bonding. The hydrogen bonded dimer and the translation equivalents form an one dimensional dimeric chain running parallel to the b axis. The one dimensional chains are linked through van der Waals interactions. Succinimide moiety is almost planar with maximum deviation of 0.032 Å for the N atom from the least squares mean plane of atoms. The planarity can be attributed to the sp2 hybridization of C1 and C4 atoms.