Literature DB >> 22719620

5-Methyl-3,3-bis-(4-methyl-piperazin-1-yl)-1-[2-(4-methyl-piperazin-1-yl)eth-yl]indolin-2-one.

Hui-Hui Lin1, Xiao-Lin Zheng, Sheng-Li Cao.   

Abstract

In the title compound, C(26)H(43)N(7)O, each piperazine ring adopts a chair conformation. Two 1-methyl-piperazine rings bond to one Csp(3) of the pyrrole ring via the piperazine N atoms, while the third one links to the N atom of the indolin-2-one unit through a flexible ethyl group with an almost syn conformation. In the crystal, mol-ecules are connected through methyl-ene-carbonyl C-H⋯O inter-actions into an infinite chain along the c axis. The almost parallel arrays are stacked, forming a three-dimensional framework.

Entities:  

Year:  2012        PMID: 22719620      PMCID: PMC3379422          DOI: 10.1107/S1600536812022416

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


Related literature

For the background to indoline-2,3-dione and its derivatives, see Chiyanzu et al. (2005 ▶); Solomon et al. (2009 ▶); Sriram et al. (2004 ▶). For a related structure, see: Lin et al. (2012 ▶).

Experimental

Crystal data

C26H43N7O M = 469.67 Monoclinic, a = 15.9433 (8) Å b = 14.4097 (6) Å c = 12.5310 (6) Å β = 108.774 (3)° V = 2725.7 (2) Å3 Z = 4 Mo Kα radiation μ = 0.07 mm−1 T = 296 K 0.33 × 0.21 × 0.20 mm

Data collection

Bruker APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2007 ▶) T min = 0.613, T max = 0.746 17378 measured reflections 4785 independent reflections 3332 reflections with I > 2σ(I) R int = 0.036

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.129 S = 1.03 4785 reflections 307 parameters H-atom parameters constrained Δρmax = 0.23 e Å−3 Δρmin = −0.20 e Å−3 Data collection: APEX2 (Bruker, 2007 ▶); cell refinement: APEX2 and SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812022416/zj2076sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812022416/zj2076Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812022416/zj2076Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C26H43N7OF(000) = 1024
Mr = 469.67Dx = 1.145 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 233 reflections
a = 15.9433 (8) Åθ = 2.2–27.0°
b = 14.4097 (6) ŵ = 0.07 mm1
c = 12.5310 (6) ÅT = 296 K
β = 108.774 (3)°Block, colorless
V = 2725.7 (2) Å30.33 × 0.21 × 0.20 mm
Z = 4
Bruker APEXII CCD area-detector diffractometer4785 independent reflections
Radiation source: fine-focus sealed tube3332 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.036
ω scansθmax = 25.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2007)h = −18→12
Tmin = 0.613, Tmax = 0.746k = −15→17
17378 measured reflectionsl = −14→14
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) = 0.129H-atom parameters constrained
S = 1.03w = 1/[σ2(Fo2) + (0.0638P)2 + 0.4418P] P = (Fo2 + 2Fc2)/3
4785 reflections(Δ/σ)max < 0.001
307 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.20 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
O10.61856 (8)0.42163 (9)0.51428 (11)0.0505 (4)
N10.63105 (9)0.48564 (10)0.68622 (13)0.0417 (4)
N20.81475 (9)0.38396 (9)0.65785 (12)0.0382 (4)
N30.84094 (11)0.18704 (11)0.66137 (14)0.0508 (4)
N40.56630 (11)0.10611 (11)0.64539 (14)0.0509 (4)
N50.56530 (10)0.29754 (10)0.71078 (12)0.0445 (4)
N60.78671 (10)0.52537 (10)0.55620 (12)0.0426 (4)
N70.83904 (12)0.65751 (12)0.42139 (14)0.0594 (5)
C10.93336 (16)0.62601 (16)1.02535 (18)0.0685 (7)
H1A0.91810.65081.08780.103*
H1B0.96000.67380.99360.103*
H1C0.97450.57581.05090.103*
C20.85101 (14)0.59104 (13)0.93714 (16)0.0508 (5)
C30.76872 (15)0.59731 (14)0.95242 (18)0.0567 (6)
H3A0.76510.62441.01820.068*
C40.69174 (14)0.56483 (13)0.87348 (17)0.0516 (5)
H4A0.63730.56940.88560.062*
C50.69861 (12)0.52560 (12)0.77654 (15)0.0411 (4)
C60.77938 (12)0.51941 (11)0.75634 (15)0.0385 (4)
C70.85514 (13)0.55156 (12)0.83746 (15)0.0457 (5)
H7A0.90950.54670.82530.055*
C80.76536 (11)0.47217 (12)0.64355 (14)0.0382 (4)
C90.66284 (12)0.45605 (12)0.60356 (15)0.0395 (4)
C100.89282 (18)0.10229 (16)0.6758 (2)0.0817 (8)
H10A0.88370.06590.73520.123*
H10B0.95450.11770.69470.123*
H10C0.87460.06740.60690.123*
C140.80539 (13)0.32577 (12)0.74919 (16)0.0457 (5)
H14A0.74410.30690.73190.055*
H14B0.82200.36110.81880.055*
C120.79338 (14)0.32871 (14)0.55410 (16)0.0529 (5)
H12A0.80120.36630.49380.064*
H12B0.73190.30920.53200.064*
C130.86357 (14)0.24095 (14)0.76392 (16)0.0529 (5)
H13A0.92510.26000.78470.063*
H13B0.85660.20290.82440.063*
C110.85262 (15)0.24454 (14)0.57235 (17)0.0575 (6)
H11A0.83840.20890.50310.069*
H11B0.91400.26410.59240.069*
C210.61197 (17)0.03109 (15)0.6078 (2)0.0715 (7)
H21A0.6241−0.01860.66160.107*
H21B0.66660.05400.60120.107*
H21C0.57510.00870.53580.107*
C190.62220 (14)0.13991 (14)0.75484 (17)0.0523 (5)
H19A0.67960.15740.75000.063*
H19B0.63120.09050.81000.063*
C200.58116 (14)0.22236 (14)0.79314 (16)0.0536 (5)
H20A0.52560.20400.80300.064*
H20B0.62040.24390.86530.064*
C180.54742 (15)0.18231 (14)0.56412 (17)0.0555 (5)
H18A0.50750.16060.49250.067*
H18B0.60210.20190.55250.067*
C170.50618 (13)0.26400 (14)0.60349 (16)0.0526 (5)
H17A0.49480.31330.54790.063*
H17B0.45010.24560.61180.063*
C160.53429 (13)0.38064 (13)0.75112 (18)0.0516 (5)
H16A0.56880.38990.82970.062*
H16B0.47300.37170.74700.062*
C150.54066 (12)0.46790 (13)0.68498 (17)0.0498 (5)
H15A0.50250.46100.60760.060*
H15B0.51980.52070.71720.060*
C220.73461 (14)0.60954 (14)0.51764 (18)0.0550 (5)
H22A0.75430.65810.57380.066*
H22B0.67250.59730.50610.066*
C250.87969 (13)0.54758 (15)0.57798 (18)0.0558 (5)
H25A0.91600.49380.60860.067*
H25B0.89730.59750.63250.067*
C260.8496 (2)0.68403 (19)0.3141 (2)0.0871 (8)
H26A0.81370.73750.28460.131*
H26B0.83150.63360.26170.131*
H26C0.91070.69850.32540.131*
C240.89265 (16)0.57653 (16)0.4690 (2)0.0669 (6)
H24A0.95470.59080.48230.080*
H24B0.87640.52560.41560.080*
C230.74686 (15)0.63994 (15)0.40848 (18)0.0606 (6)
H23A0.72440.59210.35200.073*
H23B0.71280.69600.38210.073*
U11U22U33U12U13U23
O10.0457 (8)0.0621 (8)0.0380 (8)−0.0015 (6)0.0053 (6)−0.0015 (7)
N10.0393 (8)0.0425 (8)0.0440 (9)0.0020 (7)0.0145 (7)−0.0015 (7)
N20.0452 (9)0.0371 (8)0.0313 (8)0.0021 (6)0.0110 (7)0.0003 (7)
N30.0609 (10)0.0404 (9)0.0488 (10)0.0074 (8)0.0145 (8)−0.0025 (8)
N40.0605 (10)0.0466 (9)0.0479 (10)−0.0058 (8)0.0206 (8)−0.0001 (8)
N50.0497 (9)0.0447 (9)0.0377 (9)−0.0012 (7)0.0122 (7)0.0013 (8)
N60.0429 (9)0.0427 (8)0.0428 (9)0.0008 (7)0.0145 (7)0.0079 (7)
N70.0748 (12)0.0513 (10)0.0556 (11)−0.0103 (9)0.0261 (10)0.0090 (9)
C10.0831 (16)0.0589 (13)0.0493 (13)−0.0106 (12)0.0016 (12)−0.0094 (11)
C20.0689 (14)0.0371 (10)0.0406 (11)−0.0035 (9)0.0097 (10)−0.0022 (9)
C30.0830 (16)0.0438 (11)0.0445 (12)−0.0027 (11)0.0225 (12)−0.0111 (10)
C40.0633 (13)0.0445 (11)0.0530 (12)0.0023 (10)0.0270 (11)−0.0069 (10)
C50.0499 (11)0.0331 (9)0.0404 (11)0.0029 (8)0.0146 (9)−0.0004 (8)
C60.0443 (10)0.0337 (9)0.0366 (10)0.0010 (8)0.0118 (8)0.0000 (8)
C70.0499 (11)0.0401 (10)0.0442 (11)−0.0021 (8)0.0111 (9)−0.0003 (9)
C80.0401 (10)0.0388 (9)0.0353 (10)0.0005 (8)0.0118 (8)−0.0003 (8)
C90.0428 (10)0.0382 (9)0.0358 (10)0.0028 (8)0.0102 (9)0.0049 (9)
C100.109 (2)0.0567 (14)0.0793 (18)0.0317 (14)0.0299 (16)0.0022 (13)
C140.0561 (12)0.0420 (10)0.0409 (11)0.0034 (9)0.0182 (9)0.0005 (9)
C120.0704 (14)0.0486 (11)0.0365 (11)0.0082 (10)0.0125 (10)−0.0037 (10)
C130.0628 (13)0.0489 (11)0.0428 (11)0.0087 (10)0.0113 (10)0.0053 (10)
C110.0729 (14)0.0542 (12)0.0475 (12)0.0109 (11)0.0224 (11)−0.0067 (11)
C210.0855 (17)0.0564 (13)0.0788 (17)−0.0015 (12)0.0349 (14)−0.0081 (13)
C190.0576 (12)0.0496 (11)0.0488 (12)−0.0002 (10)0.0160 (10)0.0078 (10)
C200.0658 (13)0.0564 (12)0.0389 (11)−0.0026 (10)0.0175 (10)0.0048 (10)
C180.0689 (14)0.0559 (12)0.0400 (11)−0.0113 (11)0.0152 (10)−0.0015 (10)
C170.0530 (12)0.0550 (12)0.0439 (11)−0.0058 (10)0.0072 (10)0.0039 (10)
C160.0478 (11)0.0562 (12)0.0568 (13)−0.0028 (9)0.0251 (10)−0.0066 (11)
C150.0408 (11)0.0527 (12)0.0568 (12)0.0077 (9)0.0169 (9)0.0004 (10)
C220.0590 (13)0.0463 (11)0.0610 (14)0.0050 (10)0.0210 (11)0.0112 (11)
C250.0480 (12)0.0617 (13)0.0589 (13)−0.0020 (10)0.0189 (10)0.0096 (11)
C260.121 (2)0.0796 (18)0.0699 (17)−0.0179 (16)0.0443 (16)0.0146 (14)
C240.0666 (14)0.0676 (14)0.0772 (16)−0.0018 (12)0.0379 (13)0.0128 (13)
C230.0716 (15)0.0481 (12)0.0570 (14)−0.0014 (11)0.0136 (11)0.0137 (11)
O1—C91.220 (2)C14—H14A0.9700
N1—C91.360 (2)C14—H14B0.9700
N1—C51.410 (2)C12—C111.509 (3)
N1—C151.459 (2)C12—H12A0.9700
N2—C141.465 (2)C12—H12B0.9700
N2—C121.468 (2)C13—H13A0.9700
N2—C81.476 (2)C13—H13B0.9700
N3—C131.445 (2)C11—H11A0.9700
N3—C111.449 (3)C11—H11B0.9700
N3—C101.453 (3)C21—H21A0.9600
N4—C191.458 (3)C21—H21B0.9600
N4—C181.461 (2)C21—H21C0.9600
N4—C211.464 (3)C19—C201.507 (3)
N5—C161.447 (2)C19—H19A0.9700
N5—C171.454 (2)C19—H19B0.9700
N5—C201.461 (2)C20—H20A0.9700
N6—C251.454 (2)C20—H20B0.9700
N6—C221.462 (2)C18—C171.507 (3)
N6—C81.464 (2)C18—H18A0.9700
N7—C231.448 (3)C18—H18B0.9700
N7—C241.456 (3)C17—H17A0.9700
N7—C261.459 (3)C17—H17B0.9700
C1—C21.505 (3)C16—C151.527 (3)
C1—H1A0.9600C16—H16A0.9700
C1—H1B0.9600C16—H16B0.9700
C1—H1C0.9600C15—H15A0.9700
C2—C31.388 (3)C15—H15B0.9700
C2—C71.393 (3)C22—C231.508 (3)
C3—C41.387 (3)C22—H22A0.9700
C3—H3A0.9300C22—H22B0.9700
C4—C51.376 (3)C25—C241.505 (3)
C4—H4A0.9300C25—H25A0.9700
C5—C61.393 (2)C25—H25B0.9700
C6—C71.384 (2)C26—H26A0.9600
C6—C81.519 (2)C26—H26B0.9600
C7—H7A0.9300C26—H26C0.9600
C8—C91.565 (2)C24—H24A0.9700
C10—H10A0.9600C24—H24B0.9700
C10—H10B0.9600C23—H23A0.9700
C10—H10C0.9600C23—H23B0.9700
C14—C131.509 (3)
C9—N1—C5111.34 (14)N3—C11—C12110.32 (17)
C9—N1—C15123.09 (16)N3—C11—H11A109.6
C5—N1—C15125.23 (15)C12—C11—H11A109.6
C14—N2—C12109.19 (14)N3—C11—H11B109.6
C14—N2—C8113.78 (13)C12—C11—H11B109.6
C12—N2—C8113.39 (13)H11A—C11—H11B108.1
C13—N3—C11108.67 (15)N4—C21—H21A109.5
C13—N3—C10111.86 (17)N4—C21—H21B109.5
C11—N3—C10111.54 (17)H21A—C21—H21B109.5
C19—N4—C18109.32 (15)N4—C21—H21C109.5
C19—N4—C21109.44 (17)H21A—C21—H21C109.5
C18—N4—C21110.04 (16)H21B—C21—H21C109.5
C16—N5—C17113.91 (16)N4—C19—C20111.48 (17)
C16—N5—C20111.57 (15)N4—C19—H19A109.3
C17—N5—C20108.67 (15)C20—C19—H19A109.3
C25—N6—C22108.43 (15)N4—C19—H19B109.3
C25—N6—C8116.32 (14)C20—C19—H19B109.3
C22—N6—C8115.95 (14)H19A—C19—H19B108.0
C23—N7—C24110.28 (16)N5—C20—C19110.71 (16)
C23—N7—C26110.92 (19)N5—C20—H20A109.5
C24—N7—C26111.1 (2)C19—C20—H20A109.5
C2—C1—H1A109.5N5—C20—H20B109.5
C2—C1—H1B109.5C19—C20—H20B109.5
H1A—C1—H1B109.5H20A—C20—H20B108.1
C2—C1—H1C109.5N4—C18—C17111.87 (16)
H1A—C1—H1C109.5N4—C18—H18A109.2
H1B—C1—H1C109.5C17—C18—H18A109.2
C3—C2—C7118.01 (18)N4—C18—H18B109.2
C3—C2—C1121.10 (19)C17—C18—H18B109.2
C7—C2—C1120.9 (2)H18A—C18—H18B107.9
C4—C3—C2122.57 (19)N5—C17—C18109.94 (16)
C4—C3—H3A118.7N5—C17—H17A109.7
C2—C3—H3A118.7C18—C17—H17A109.7
C5—C4—C3117.70 (19)N5—C17—H17B109.7
C5—C4—H4A121.1C18—C17—H17B109.7
C3—C4—H4A121.1H17A—C17—H17B108.2
C4—C5—C6121.85 (18)N5—C16—C15113.69 (16)
C4—C5—N1128.26 (17)N5—C16—H16A108.8
C6—C5—N1109.88 (15)C15—C16—H16A108.8
C7—C6—C5118.97 (17)N5—C16—H16B108.8
C7—C6—C8131.72 (17)C15—C16—H16B108.8
C5—C6—C8109.27 (15)H16A—C16—H16B107.7
C6—C7—C2120.87 (18)N1—C15—C16112.12 (15)
C6—C7—H7A119.6N1—C15—H15A109.2
C2—C7—H7A119.6C16—C15—H15A109.2
N6—C8—N2107.37 (13)N1—C15—H15B109.2
N6—C8—C6117.46 (14)C16—C15—H15B109.2
N2—C8—C6111.11 (14)H15A—C15—H15B107.9
N6—C8—C9107.98 (13)N6—C22—C23108.37 (17)
N2—C8—C9111.87 (14)N6—C22—H22A110.0
C6—C8—C9100.97 (14)C23—C22—H22A110.0
O1—C9—N1125.35 (17)N6—C22—H22B110.0
O1—C9—C8126.21 (16)C23—C22—H22B110.0
N1—C9—C8108.44 (15)H22A—C22—H22B108.4
N3—C10—H10A109.5N6—C25—C24108.67 (17)
N3—C10—H10B109.5N6—C25—H25A110.0
H10A—C10—H10B109.5C24—C25—H25A110.0
N3—C10—H10C109.5N6—C25—H25B110.0
H10A—C10—H10C109.5C24—C25—H25B110.0
H10B—C10—H10C109.5H25A—C25—H25B108.3
N2—C14—C13110.23 (15)N7—C26—H26A109.5
N2—C14—H14A109.6N7—C26—H26B109.5
C13—C14—H14A109.6H26A—C26—H26B109.5
N2—C14—H14B109.6N7—C26—H26C109.5
C13—C14—H14B109.6H26A—C26—H26C109.5
H14A—C14—H14B108.1H26B—C26—H26C109.5
N2—C12—C11110.25 (16)N7—C24—C25111.09 (19)
N2—C12—H12A109.6N7—C24—H24A109.4
C11—C12—H12A109.6C25—C24—H24A109.4
N2—C12—H12B109.6N7—C24—H24B109.4
C11—C12—H12B109.6C25—C24—H24B109.4
H12A—C12—H12B108.1H24A—C24—H24B108.0
N3—C13—C14111.04 (16)N7—C23—C22111.87 (18)
N3—C13—H13A109.4N7—C23—H23A109.2
C14—C13—H13A109.4C22—C23—H23A109.2
N3—C13—H13B109.4N7—C23—H23B109.2
C14—C13—H13B109.4C22—C23—H23B109.2
H13A—C13—H13B108.0H23A—C23—H23B107.9
D—H···AD—HH···AD···AD—H···A
C19—H19B···O1i0.972.643.388 (2)135
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C19—H19B⋯O1i0.972.643.388 (2)135

Symmetry code: (i) .

  6 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.  Design, synthesis and anti-plasmodial evaluation in vitro of new 4-aminoquinoline isatin derivatives.

Authors:  Idan Chiyanzu; Cailean Clarkson; Peter J Smith; Julie Lehman; Jiri Gut; Philip J Rosenthal; Kelly Chibale
Journal:  Bioorg Med Chem       Date:  2005-05-02       Impact factor: 3.641

3.  Design, synthesis and biological evaluation of novel non-nucleoside HIV-1 reverse transcriptase inhibitors with broad-spectrum chemotherapeutic properties.

Authors:  Dharmarajan Sriram; Tanushree Ratan Bal; Perumal Yogeeswari
Journal:  Bioorg Med Chem       Date:  2004-11-15       Impact factor: 3.641

4.  Hybrid pharmacophore design and synthesis of isatin-benzothiazole analogs for their anti-breast cancer activity.

Authors:  V Raja Solomon; Changkun Hu; Hoyun Lee
Journal:  Bioorg Med Chem       Date:  2009-09-15       Impact factor: 3.641

5.  5-Methyl-3,3-bis-(morpholin-4-yl)-1-[2-(morpholin-4-yl)eth-yl]-2,3-dihydro-1H-indol-2-one.

Authors:  Hui-Hui Lin; Wei-Yao Wu; Jing-Jing Zhang; Sheng-Li Cao
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-02-24

6.  Structure validation in chemical crystallography.

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

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