Literature DB >> 23424560

rac-N-Benzyl-isatincreatinine (unknown solvate).

Narsimha Reddy Penthala1, Peter A Crooks.   

Abstract

The title compound, C(19)H(18)N(4)O(3) [systematic name: (RS)-1-benzyl-3-hy-droxy-3-(2-imino-3-methyl-5-oxoimidazolidin-4-yl)-2,3-dihydro-1H-indol-2-one], was prepared as a racemate (RR and SS) by the aldol condensation of N-benzyl-isatin with creatinine in the presence of sodium acetate in acetic acid. The r.m.s. deviation of the isatin ring system is 0.033 Å. The benzyl group is disordered over two orientations, with refined occupancies of 0.847 (7) and 0.153 (7). The dihedral angles between the isatin ring system and the benzene ring (major disorder component) and the imidazole ring are 82.82 (7) and 51.31 (3)°, respectively, In the crystal, mol-ecules are linked into (001) sheets by N-H⋯O and O-H⋯N hydrogen bonds, which incorporate R(2) (2)(9) ring motifs. The crystal was grown from mixed solvents (ethanol, methanol and possibly also ethyl acetate). These solvents are disordered in the crystal and the resulting electron density was found to be uninter-pretable. The solvent contribution to the scattering was removed with the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155]. The formula mass and density do not take account of the solvent.

Entities:  

Year:  2013        PMID: 23424560      PMCID: PMC3569814          DOI: 10.1107/S1600536813000378

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


Related literature

For details on the development of isatin derivatives as anti­cancer agents, see: Penthala et al. (2010a ▶,b ▶). For similar structures, see: Tang et al. (2009 ▶); Penthala et al. (2009a ▶,b ▶).

Experimental

Crystal data

C19H18N4O3 M = 350.37 Orthorhombic, a = 13.4466 (2) Å b = 10.6921 (2) Å c = 27.2057 (5) Å V = 3911.43 (12) Å3 Z = 8 Cu Kα radiation μ = 0.68 mm−1 T = 90 K 0.12 × 0.10 × 0.04 mm

Data collection

Bruker X8 Proteum CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2006 ▶) T min = 0.911, T max = 0.973 55165 measured reflections 3602 independent reflections 3344 reflections with I > 2σ(I) R int = 0.043

Refinement

R[F 2 > 2σ(F 2)] = 0.038 wR(F 2) = 0.104 S = 1.04 3602 reflections 287 parameters 222 restraints H-atom parameters constrained Δρmax = 0.28 e Å−3 Δρmin = −0.30 e Å−3 Data collection: APEX2 (Bruker, 2006 ▶); cell refinement: SAINT (Bruker, 2006 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELX97. Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813000378/hb7013sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813000378/hb7013Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813000378/hb7013Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H18N4O3F(000) = 1472
Mr = 350.37Dx = 1.190 Mg m3
Orthorhombic, PbcaCu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ac 2abCell parameters from 9086 reflections
a = 13.4466 (2) Åθ = 4.6–68.9°
b = 10.6921 (2) ŵ = 0.68 mm1
c = 27.2057 (5) ÅT = 90 K
V = 3911.43 (12) Å3Plate, pale yellow
Z = 80.12 × 0.10 × 0.04 mm
Bruker X8 Proteum CCD diffractometer3602 independent reflections
Radiation source: fine-focus rotating anode3344 reflections with I > 2σ(I)
Graded multilayer optics monochromatorRint = 0.043
Detector resolution: 5.6 pixels mm-1θmax = 68.7°, θmin = 4.6°
φ and ω scansh = −16→16
Absorption correction: multi-scan (SADABS; Bruker, 2006)k = −12→12
Tmin = 0.911, Tmax = 0.973l = −32→31
55165 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.104w = 1/[σ2(Fo2) + (0.0555P)2 + 1.5834P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
3602 reflectionsΔρmax = 0.28 e Å3
287 parametersΔρmin = −0.30 e Å3
222 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00043 (9)
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 > 2σ(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*/UeqOcc. (<1)
O10.34991 (6)0.33786 (8)0.64888 (3)0.0243 (2)
C10.41054 (9)0.42315 (12)0.65145 (4)0.0212 (3)
N20.40105 (8)0.53751 (10)0.63017 (4)0.0240 (2)
C30.48704 (9)0.61071 (13)0.63800 (4)0.0252 (3)
C40.50442 (11)0.73157 (14)0.62246 (5)0.0339 (3)
H40.45510.77810.60540.041*
C50.59772 (12)0.78247 (14)0.63292 (6)0.0396 (4)
H50.61200.86570.62290.047*
C60.66974 (11)0.71461 (14)0.65753 (5)0.0359 (3)
H60.73310.75080.66350.043*
C70.64986 (10)0.59308 (13)0.67374 (5)0.0283 (3)
H70.69900.54640.69090.034*
C80.55730 (9)0.54224 (12)0.66432 (4)0.0231 (3)
O90.56962 (6)0.31592 (8)0.66485 (3)0.0238 (2)
H90.54980.25160.67960.036*
C90.51144 (9)0.41884 (11)0.67907 (4)0.0202 (3)
C100.49128 (8)0.41474 (11)0.73572 (4)0.0180 (3)
H100.45920.33390.74530.022*
O110.34262 (6)0.54407 (8)0.74190 (3)0.0234 (2)
C110.42968 (9)0.52621 (11)0.75378 (4)0.0188 (3)
N120.48658 (7)0.60115 (9)0.78275 (4)0.0200 (2)
N130.65376 (7)0.59593 (10)0.80798 (4)0.0228 (2)
H13A0.71130.55670.80860.027*
H13B0.64740.66910.82240.027*
C130.57697 (9)0.54496 (11)0.78532 (4)0.0188 (3)
N140.58264 (7)0.43382 (9)0.76280 (3)0.0185 (2)
C140.66413 (9)0.34513 (12)0.76781 (5)0.0240 (3)
H14A0.71410.36160.74240.036*
H14B0.63860.25980.76400.036*
H14C0.69450.35430.80040.036*
C150.31240 (10)0.58041 (13)0.60432 (5)0.0262 (3)
H15A0.29290.66300.61760.031*
H15B0.25740.52140.61110.031*
C160.3251 (2)0.5920 (3)0.54852 (14)0.0295 (5)0.847 (7)
C170.2898 (2)0.6974 (3)0.52528 (8)0.0565 (8)0.847 (7)
H170.26310.76450.54400.068*0.847 (7)
C180.2932 (3)0.7056 (3)0.47406 (8)0.0724 (11)0.847 (7)
H180.26870.77830.45800.087*0.847 (7)
C190.3315 (2)0.6099 (3)0.44696 (10)0.0573 (8)0.847 (7)
H190.33370.61590.41210.069*0.847 (7)
C200.3668 (3)0.5051 (4)0.46988 (15)0.0397 (7)0.847 (7)
H200.39360.43840.45090.048*0.847 (7)
C210.3636 (3)0.4957 (4)0.52102 (15)0.0313 (7)0.847 (7)
H210.38810.42270.53680.038*0.847 (7)
C16'0.3153 (14)0.5782 (19)0.5524 (9)0.0295 (5)0.153 (7)
C17'0.2496 (12)0.6474 (16)0.5261 (4)0.054 (2)0.153 (7)
H17'0.20470.70020.54330.065*0.153 (7)
C18'0.2450 (13)0.6442 (17)0.4741 (4)0.060 (2)0.153 (7)
H18'0.19820.69350.45650.072*0.153 (7)
C19'0.3107 (13)0.5673 (16)0.4500 (6)0.054 (2)0.153 (7)
H19'0.30980.56320.41510.065*0.153 (7)
C20'0.3770 (18)0.497 (2)0.4756 (9)0.042 (2)0.153 (7)
H20'0.42200.44380.45870.050*0.153 (7)
C21'0.3787 (17)0.503 (2)0.5264 (9)0.033 (2)0.153 (7)
H21'0.42550.45330.54390.040*0.153 (7)
U11U22U33U12U13U23
O10.0232 (4)0.0268 (5)0.0229 (4)−0.0029 (4)−0.0027 (3)0.0017 (4)
C10.0227 (6)0.0254 (6)0.0154 (5)−0.0006 (5)0.0014 (4)0.0013 (5)
N20.0241 (5)0.0277 (6)0.0202 (5)−0.0014 (4)−0.0022 (4)0.0059 (4)
C30.0273 (6)0.0290 (7)0.0193 (6)−0.0040 (5)0.0020 (5)0.0038 (5)
C40.0402 (8)0.0320 (7)0.0295 (7)−0.0029 (6)−0.0008 (6)0.0104 (6)
C50.0493 (9)0.0330 (8)0.0364 (8)−0.0140 (7)0.0008 (7)0.0116 (6)
C60.0373 (8)0.0409 (8)0.0295 (7)−0.0162 (6)0.0000 (6)0.0063 (6)
C70.0280 (7)0.0359 (7)0.0210 (6)−0.0067 (6)0.0015 (5)0.0040 (5)
C80.0257 (6)0.0276 (6)0.0161 (6)−0.0036 (5)0.0023 (5)0.0027 (5)
O90.0236 (4)0.0257 (5)0.0221 (4)0.0010 (3)0.0040 (3)−0.0004 (3)
C90.0199 (6)0.0230 (6)0.0178 (6)−0.0008 (5)0.0006 (4)0.0010 (4)
C100.0172 (6)0.0189 (6)0.0178 (6)−0.0008 (4)−0.0004 (4)0.0016 (4)
O110.0178 (4)0.0229 (4)0.0295 (5)0.0006 (3)−0.0024 (3)0.0009 (3)
C110.0181 (6)0.0203 (6)0.0179 (5)−0.0011 (4)0.0011 (4)0.0040 (4)
N120.0182 (5)0.0209 (5)0.0208 (5)0.0006 (4)−0.0003 (4)−0.0001 (4)
N130.0191 (5)0.0234 (5)0.0258 (5)0.0024 (4)−0.0041 (4)−0.0046 (4)
C130.0196 (6)0.0223 (6)0.0146 (5)−0.0002 (5)0.0007 (4)0.0031 (4)
N140.0181 (5)0.0187 (5)0.0186 (5)0.0014 (4)−0.0015 (4)0.0001 (4)
C140.0198 (6)0.0215 (6)0.0308 (6)0.0028 (5)−0.0044 (5)−0.0001 (5)
C150.0248 (6)0.0340 (7)0.0199 (6)0.0057 (5)0.0006 (5)0.0044 (5)
C160.0267 (10)0.0427 (11)0.0191 (9)0.0057 (7)0.0021 (7)0.0076 (7)
C170.0808 (19)0.0593 (16)0.0294 (9)0.0366 (14)0.0088 (11)0.0144 (10)
C180.106 (2)0.078 (2)0.0330 (10)0.0440 (19)0.0066 (13)0.0227 (12)
C190.0693 (17)0.083 (2)0.0196 (9)0.0199 (15)0.0079 (10)0.0136 (12)
C200.0358 (13)0.0602 (14)0.0230 (14)0.0012 (11)0.0021 (10)−0.0050 (11)
C210.0316 (15)0.0380 (11)0.0243 (14)−0.0012 (10)−0.0027 (9)−0.0008 (9)
C16'0.0267 (10)0.0427 (11)0.0191 (9)0.0057 (7)0.0021 (7)0.0076 (7)
C17'0.068 (4)0.064 (4)0.030 (3)0.024 (4)0.005 (4)0.012 (4)
C18'0.081 (5)0.072 (5)0.026 (3)0.031 (4)−0.002 (4)0.019 (4)
C19'0.069 (4)0.075 (5)0.019 (4)0.014 (4)−0.001 (4)0.008 (4)
C20'0.044 (4)0.059 (4)0.023 (4)0.005 (4)0.000 (4)0.001 (4)
C21'0.029 (4)0.051 (4)0.020 (4)−0.003 (4)−0.001 (4)0.004 (4)
O1—C11.2253 (15)C14—H14A0.9800
C1—N21.3588 (16)C14—H14B0.9800
C1—C91.5516 (16)C14—H14C0.9800
N2—C31.4124 (17)C15—C16'1.41 (2)
N2—C151.4582 (16)C15—C161.533 (4)
C3—C41.3796 (19)C15—H15A0.9900
C3—C81.3933 (18)C15—H15B0.9900
C4—C51.397 (2)C16—C211.374 (3)
C4—H40.9500C16—C171.377 (3)
C5—C61.383 (2)C17—C181.397 (3)
C5—H50.9500C17—H170.9500
C6—C71.398 (2)C18—C191.362 (4)
C6—H60.9500C18—H180.9500
C7—C81.3821 (18)C19—C201.368 (4)
C7—H70.9500C19—H190.9500
C8—C91.5107 (17)C20—C211.396 (3)
O9—C91.4046 (15)C20—H200.9500
O9—H90.8400C21—H210.9500
C9—C101.5654 (16)C16'—C17'1.357 (16)
C10—N141.4468 (14)C16'—C21'1.368 (17)
C10—C111.5322 (16)C17'—C18'1.418 (13)
C10—H101.0000C17'—H17'0.9500
O11—C111.2295 (14)C18'—C19'1.373 (15)
C11—N121.3597 (16)C18'—H18'0.9500
N12—C131.3576 (15)C19'—C20'1.359 (16)
N13—C131.3204 (15)C19'—H19'0.9500
N13—H13A0.8800C20'—C21'1.385 (17)
N13—H13B0.8800C20'—H20'0.9500
C13—N141.3392 (16)C21'—H21'0.9500
N14—C141.4555 (15)
O1—C1—N2125.66 (11)N14—C14—H14B109.5
O1—C1—C9125.97 (11)H14A—C14—H14B109.5
N2—C1—C9108.37 (10)N14—C14—H14C109.5
C1—N2—C3110.95 (10)H14A—C14—H14C109.5
C1—N2—C15124.43 (11)H14B—C14—H14C109.5
C3—N2—C15124.59 (11)C16'—C15—N2117.0 (8)
C4—C3—C8122.34 (12)N2—C15—C16114.35 (15)
C4—C3—N2127.69 (12)C16'—C15—H15A112.9
C8—C3—N2109.96 (11)N2—C15—H15A108.7
C3—C4—C5117.03 (13)C16—C15—H15A108.7
C3—C4—H4121.5C16'—C15—H15B101.4
C5—C4—H4121.5N2—C15—H15B108.7
C6—C5—C4121.55 (13)C16—C15—H15B108.7
C6—C5—H5119.2H15A—C15—H15B107.6
C4—C5—H5119.2C21—C16—C17119.6 (3)
C5—C6—C7120.43 (13)C21—C16—C15121.4 (3)
C5—C6—H6119.8C17—C16—C15118.9 (3)
C7—C6—H6119.8C16—C17—C18119.8 (3)
C8—C7—C6118.64 (13)C16—C17—H17120.1
C8—C7—H7120.7C18—C17—H17120.1
C6—C7—H7120.7C19—C18—C17120.4 (2)
C7—C8—C3119.95 (12)C19—C18—H18119.8
C7—C8—C9131.44 (12)C17—C18—H18119.8
C3—C8—C9108.58 (11)C18—C19—C20120.0 (3)
C9—O9—H9109.5C18—C19—H19120.0
O9—C9—C8112.56 (10)C20—C19—H19120.0
O9—C9—C1112.14 (10)C19—C20—C21120.2 (3)
C8—C9—C1101.67 (9)C19—C20—H20119.9
O9—C9—C10110.23 (9)C21—C20—H20119.9
C8—C9—C10110.90 (9)C16—C21—C20120.0 (3)
C1—C9—C10109.04 (9)C16—C21—H21120.0
N14—C10—C11100.73 (9)C20—C21—H21120.0
N14—C10—C9110.50 (9)C17'—C16'—C21'117.0 (18)
C11—C10—C9112.80 (9)C17'—C16'—C15120.0 (18)
N14—C10—H10110.8C21'—C16'—C15123.0 (16)
C11—C10—H10110.8C16'—C17'—C18'122.8 (14)
C9—C10—H10110.8C16'—C17'—H17'118.6
O11—C11—N12126.63 (11)C18'—C17'—H17'118.6
O11—C11—C10123.45 (11)C19'—C18'—C17'117.6 (12)
N12—C11—C10109.88 (10)C19'—C18'—H18'121.2
C13—N12—C11105.83 (10)C17'—C18'—H18'121.2
C13—N13—H13A120.0C20'—C19'—C18'120.5 (16)
C13—N13—H13B120.0C20'—C19'—H19'119.8
H13A—N13—H13B120.0C18'—C19'—H19'119.8
N13—C13—N14122.37 (11)C19'—C20'—C21'119.9 (19)
N13—C13—N12122.79 (11)C19'—C20'—H20'120.0
N14—C13—N12114.84 (10)C21'—C20'—H20'120.0
C13—N14—C10108.04 (9)C16'—C21'—C20'122.2 (19)
C13—N14—C14125.31 (10)C16'—C21'—H21'118.9
C10—N14—C14126.52 (10)C20'—C21'—H21'118.9
N14—C14—H14A109.5
O1—C1—N2—C3−176.47 (11)O11—C11—N12—C13−179.47 (11)
C9—C1—N2—C33.04 (13)C10—C11—N12—C13−1.45 (12)
O1—C1—N2—C155.67 (19)C11—N12—C13—N13175.47 (11)
C9—C1—N2—C15−174.83 (10)C11—N12—C13—N14−4.15 (13)
C1—N2—C3—C4−179.33 (13)N13—C13—N14—C10−171.44 (10)
C15—N2—C3—C4−1.5 (2)N12—C13—N14—C108.18 (13)
C1—N2—C3—C81.47 (14)N13—C13—N14—C1412.39 (18)
C15—N2—C3—C8179.33 (11)N12—C13—N14—C14−167.99 (10)
C8—C3—C4—C51.9 (2)C11—C10—N14—C13−7.92 (11)
N2—C3—C4—C5−177.19 (13)C9—C10—N14—C13111.54 (10)
C3—C4—C5—C60.3 (2)C11—C10—N14—C14168.19 (10)
C4—C5—C6—C7−1.5 (2)C9—C10—N14—C14−72.35 (14)
C5—C6—C7—C80.5 (2)C1—N2—C15—C16'−101.9 (9)
C6—C7—C8—C31.71 (19)C3—N2—C15—C16'80.6 (9)
C6—C7—C8—C9−176.14 (13)C1—N2—C15—C16−109.52 (19)
C4—C3—C8—C7−3.0 (2)C3—N2—C15—C1672.9 (2)
N2—C3—C8—C7176.26 (11)C16'—C15—C16—C21−62 (8)
C4—C3—C8—C9175.30 (12)N2—C15—C16—C2150.4 (3)
N2—C3—C8—C9−5.45 (14)C16'—C15—C16—C17113 (8)
C7—C8—C9—O9−55.07 (17)N2—C15—C16—C17−134.8 (2)
C3—C8—C9—O9126.90 (11)C21—C16—C17—C180.11 (19)
C7—C8—C9—C1−175.25 (13)C15—C16—C17—C18−174.8 (2)
C3—C8—C9—C16.72 (12)C16—C17—C18—C19−0.1 (2)
C7—C8—C9—C1068.94 (17)C17—C18—C19—C200.0 (4)
C3—C8—C9—C10−109.09 (11)C18—C19—C20—C210.1 (4)
O1—C1—C9—O953.15 (15)C17—C16—C21—C200.0 (3)
N2—C1—C9—O9−126.36 (11)C15—C16—C21—C20174.8 (2)
O1—C1—C9—C8173.61 (11)C19—C20—C21—C16−0.1 (4)
N2—C1—C9—C8−5.89 (12)N2—C15—C16'—C17'−161.4 (9)
O1—C1—C9—C10−69.22 (15)C16—C15—C16'—C17'−91 (8)
N2—C1—C9—C10111.28 (11)N2—C15—C16'—C21'22.3 (12)
O9—C9—C10—N1467.00 (12)C16—C15—C16'—C21'93 (8)
C8—C9—C10—N14−58.33 (12)C21'—C16'—C17'—C18'−0.1 (3)
C1—C9—C10—N14−169.48 (10)C15—C16'—C17'—C18'−176.5 (14)
O9—C9—C10—C11178.88 (9)C16'—C17'—C18'—C19'−0.1 (3)
C8—C9—C10—C1153.55 (13)C17'—C18'—C19'—C20'0.2 (7)
C1—C9—C10—C11−57.60 (12)C18'—C19'—C20'—C21'−0.2 (9)
N14—C10—C11—O11−176.13 (11)C17'—C16'—C21'—C20'0.1 (7)
C9—C10—C11—O1166.08 (14)C15—C16'—C21'—C20'176.5 (14)
N14—C10—C11—N125.78 (12)C19'—C20'—C21'—C16'0.0 (10)
C9—C10—C11—N12−112.01 (11)
D—H···AD—HH···AD···AD—H···A
O9—H9···N12i0.841.972.8065 (13)175
N13—H13A···O11ii0.882.242.9321 (13)135
N13—H13B···O1iii0.881.972.8410 (14)173
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O9—H9⋯N12i 0.841.972.8065 (13)175
N13—H13A⋯O11ii 0.882.242.9321 (13)135
N13—H13B⋯O1iii 0.881.972.8410 (14)173

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

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Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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