Literature DB >> 24454110

N,N,N'-Tris[(1H-indol-3-yl)meth-yl]ethane-1,2-di-amine.

Yan-Jun Li1, De-Ju Wang1.   

Abstract

In the title mol-ecule, C29H29N5, the indole ring systems are essentially planar, with maximum deviations of 0.020 (2), 0.023 (2) and 0.016 (2) Å. The dihedral angles formed between the mean planes of the three indole ring systems are 38.08 (7), 89.64 (8) and 58.28 (8)°. In the crystal, mol-ecules are connected by N-H⋯N hydrogen bonds, forming inversion dimers. An intra-molecular N-H⋯N hydrogen bond is also observed.

Entities:  

Year:  2013        PMID: 24454110      PMCID: PMC3884334          DOI: 10.1107/S1600536813028225

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


Related literature

For applications of indole compounds and for related structures, see: Shimazaki et al.(2009 ▶); Takani et al. (2006 ▶); Munjal et al. (2010 ▶); Zhu et al. (2012 ▶).

Experimental

Crystal data

C29H29N5 M = 447.57 Monoclinic, a = 13.769 (3) Å b = 10.832 (2) Å c = 16.910 (3) Å β = 106.512 (3)° V = 2418.2 (8) Å3 Z = 4 Mo Kα radiation μ = 0.07 mm−1 T = 298 K 0.16 × 0.15 × 0.10 mm

Data collection

Bruker SMART CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T min = 0.988, T max = 0.993 12582 measured reflections 4486 independent reflections 2785 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.044 wR(F 2) = 0.114 S = 0.99 4486 reflections 319 parameters 4 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.12 e Å−3 Δρmin = −0.17 e Å−3 Data collection: SMART (Bruker, 2001 ▶); cell refinement: SAINT (Bruker, 2001 ▶); 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. Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S1600536813028225/lh5652sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813028225/lh5652Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813028225/lh5652Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C29H29N5F(000) = 952
Mr = 447.57Dx = 1.229 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2164 reflections
a = 13.769 (3) Åθ = 2.4–20.2°
b = 10.832 (2) ŵ = 0.07 mm1
c = 16.910 (3) ÅT = 298 K
β = 106.512 (3)°Block, colourless
V = 2418.2 (8) Å30.16 × 0.15 × 0.10 mm
Z = 4
Bruker SMART CCD diffractometer4486 independent reflections
Radiation source: fine-focus sealed tube2785 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
φ and ω scansθmax = 25.5°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −15→16
Tmin = 0.988, Tmax = 0.993k = −13→8
12582 measured reflectionsl = −19→20
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H atoms treated by a mixture of independent and constrained refinement
S = 0.99w = 1/[σ2(Fo2) + (0.056P)2] where P = (Fo2 + 2Fc2)/3
4486 reflections(Δ/σ)max < 0.001
319 parametersΔρmax = 0.12 e Å3
4 restraintsΔρmin = −0.17 e Å3
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.
xyzUiso*/Ueq
C10.21660 (15)0.20856 (19)−0.00132 (12)0.0548 (5)
H1A0.24230.2468−0.04320.066*
H1B0.15260.1692−0.02870.066*
C20.29084 (15)0.11279 (19)0.04444 (12)0.0560 (5)
H2A0.30450.05380.00580.067*
H2B0.35420.15210.07360.067*
C30.32167 (15)−0.0165 (2)0.16844 (13)0.0572 (6)
H3A0.37820.03770.19320.069*
H3B0.3475−0.08680.14510.069*
C40.27550 (14)−0.06000 (18)0.23321 (12)0.0490 (5)
C50.17503 (15)−0.07432 (19)0.22497 (13)0.0569 (6)
H50.1234−0.05720.17730.068*
C60.25247 (14)−0.13274 (18)0.35366 (12)0.0496 (5)
C70.32704 (14)−0.09563 (17)0.31615 (12)0.0488 (5)
C80.42825 (16)−0.0998 (2)0.36324 (14)0.0646 (6)
H80.4796−0.07580.34080.078*
C90.45039 (17)−0.1402 (2)0.44351 (15)0.0749 (7)
H90.5176−0.14180.47550.090*
C100.37555 (17)−0.1784 (2)0.47800 (14)0.0685 (6)
H100.3934−0.20660.53220.082*
C110.27581 (16)−0.1753 (2)0.43353 (13)0.0599 (6)
H110.2253−0.20120.45650.072*
C120.09756 (14)0.35402 (19)0.03092 (13)0.0559 (6)
H12A0.08110.3816−0.02590.067*
H12B0.09450.42510.06510.067*
C130.02160 (14)0.26081 (19)0.03937 (12)0.0507 (5)
C14−0.04813 (15)0.2018 (2)−0.02227 (13)0.0579 (6)
H14−0.05760.2164−0.07820.069*
C15−0.06722 (15)0.12209 (19)0.09287 (13)0.0537 (5)
C160.01110 (14)0.21007 (18)0.11443 (12)0.0499 (5)
C170.06024 (15)0.2313 (2)0.19794 (13)0.0589 (6)
H170.11340.28740.21350.071*
C180.02882 (18)0.1681 (2)0.25622 (14)0.0696 (7)
H180.06100.18160.31180.084*
C19−0.05100 (19)0.0836 (2)0.23338 (16)0.0726 (7)
H19−0.07180.04330.27430.087*
C20−0.09945 (17)0.0584 (2)0.15233 (16)0.0670 (6)
H20−0.15180.00110.13760.080*
C210.27573 (16)0.40222 (19)0.06586 (12)0.0564 (6)
H21A0.25440.45890.01980.068*
H21B0.33980.36640.06450.068*
C220.29158 (14)0.47297 (19)0.14409 (12)0.0517 (5)
C230.27479 (18)0.5946 (2)0.15314 (15)0.0667 (6)
H230.24510.64830.11020.080*
C240.34721 (16)0.5248 (2)0.28034 (14)0.0588 (6)
C250.33709 (15)0.42618 (19)0.22502 (12)0.0509 (5)
C260.37186 (17)0.3112 (2)0.25615 (14)0.0704 (6)
H260.36580.24390.22100.084*
C270.4153 (2)0.2975 (3)0.33937 (16)0.0852 (8)
H270.43830.22010.36040.102*
C280.42564 (19)0.3970 (3)0.39261 (15)0.0812 (8)
H280.45630.38540.44870.097*
C290.39172 (18)0.5112 (3)0.36443 (15)0.0750 (7)
H290.39810.57780.40030.090*
N10.20034 (11)0.30344 (14)0.05540 (9)0.0476 (4)
N20.24795 (13)0.04946 (16)0.10288 (11)0.0525 (5)
H20.2211 (15)0.1029 (17)0.1248 (12)0.063*
N30.16084 (13)−0.11738 (18)0.29652 (11)0.0610 (5)
H30.1064 (14)−0.135 (2)0.3083 (13)0.073*
N4−0.10242 (13)0.11849 (18)0.00839 (12)0.0606 (5)
H4−0.1491 (16)0.066 (2)−0.0244 (12)0.073*
N50.30761 (17)0.62689 (19)0.23432 (14)0.0758 (6)
H5A0.3038 (18)0.6959 (18)0.2547 (15)0.091*
U11U22U33U12U13U23
C10.0607 (13)0.0539 (13)0.0514 (12)−0.0051 (11)0.0184 (10)−0.0059 (10)
C20.0567 (12)0.0555 (13)0.0594 (13)−0.0005 (11)0.0226 (11)−0.0058 (11)
C30.0540 (12)0.0495 (13)0.0697 (14)0.0061 (10)0.0202 (11)0.0013 (11)
C40.0474 (12)0.0402 (11)0.0601 (13)0.0007 (9)0.0166 (10)−0.0032 (10)
C50.0516 (13)0.0594 (14)0.0579 (14)0.0006 (11)0.0124 (10)−0.0064 (11)
C60.0455 (11)0.0448 (12)0.0587 (13)−0.0032 (10)0.0153 (10)−0.0102 (10)
C70.0474 (11)0.0388 (11)0.0602 (13)0.0012 (9)0.0152 (10)−0.0040 (10)
C80.0466 (12)0.0747 (16)0.0742 (16)0.0027 (11)0.0198 (11)0.0008 (13)
C90.0512 (13)0.100 (2)0.0687 (16)0.0086 (13)0.0087 (11)0.0051 (14)
C100.0651 (15)0.0786 (18)0.0621 (14)0.0072 (13)0.0188 (12)0.0015 (12)
C110.0617 (13)0.0584 (14)0.0629 (15)−0.0043 (12)0.0230 (11)−0.0054 (11)
C120.0572 (13)0.0482 (13)0.0577 (13)0.0010 (11)0.0088 (10)−0.0006 (10)
C130.0462 (11)0.0469 (12)0.0552 (13)0.0008 (10)0.0086 (9)−0.0065 (10)
C140.0528 (12)0.0604 (14)0.0586 (13)0.0011 (11)0.0131 (10)−0.0038 (11)
C150.0482 (12)0.0524 (13)0.0605 (14)0.0021 (10)0.0156 (10)−0.0074 (11)
C160.0452 (11)0.0468 (12)0.0570 (13)0.0059 (10)0.0135 (9)−0.0068 (10)
C170.0527 (12)0.0605 (14)0.0607 (14)0.0054 (11)0.0116 (10)−0.0093 (11)
C180.0697 (15)0.0787 (17)0.0596 (15)0.0148 (14)0.0169 (12)−0.0015 (13)
C190.0759 (16)0.0734 (17)0.0773 (18)0.0112 (14)0.0361 (14)0.0081 (14)
C200.0600 (14)0.0608 (15)0.0851 (18)0.0016 (12)0.0287 (13)−0.0036 (13)
C210.0630 (13)0.0547 (13)0.0535 (13)−0.0103 (11)0.0196 (10)0.0005 (10)
C220.0518 (12)0.0465 (13)0.0583 (13)−0.0074 (10)0.0182 (10)−0.0045 (10)
C230.0782 (16)0.0544 (15)0.0695 (16)0.0008 (12)0.0243 (12)−0.0005 (12)
C240.0567 (13)0.0581 (15)0.0648 (15)−0.0044 (12)0.0224 (11)−0.0143 (12)
C250.0513 (12)0.0481 (13)0.0532 (13)−0.0072 (10)0.0146 (10)−0.0078 (10)
C260.0890 (17)0.0563 (15)0.0599 (15)0.0042 (13)0.0114 (12)−0.0058 (12)
C270.102 (2)0.0800 (19)0.0637 (17)0.0137 (16)0.0079 (14)0.0055 (14)
C280.0788 (17)0.105 (2)0.0564 (15)0.0071 (16)0.0134 (13)−0.0044 (16)
C290.0732 (16)0.092 (2)0.0612 (16)−0.0056 (15)0.0221 (12)−0.0276 (14)
N10.0498 (10)0.0429 (10)0.0498 (10)−0.0044 (8)0.0139 (8)−0.0041 (8)
N20.0521 (10)0.0478 (11)0.0598 (11)0.0021 (9)0.0193 (8)−0.0007 (9)
N30.0455 (10)0.0755 (14)0.0633 (12)−0.0074 (10)0.0176 (9)−0.0044 (10)
N40.0521 (10)0.0605 (12)0.0669 (13)−0.0107 (9)0.0129 (9)−0.0135 (10)
N50.0988 (15)0.0515 (13)0.0811 (16)0.0023 (12)0.0318 (12)−0.0176 (12)
C1—N11.466 (2)C15—N41.373 (3)
C1—C21.507 (3)C15—C201.392 (3)
C1—H1A0.9700C15—C161.407 (3)
C1—H1B0.9700C16—C171.401 (3)
C2—N21.459 (2)C17—C181.367 (3)
C2—H2A0.9700C17—H170.9300
C2—H2B0.9700C18—C191.398 (3)
C3—N21.459 (3)C18—H180.9300
C3—C41.491 (3)C19—C201.370 (3)
C3—H3A0.9700C19—H190.9300
C3—H3B0.9700C20—H200.9300
C4—C51.359 (3)C21—N11.466 (2)
C4—C71.433 (3)C21—C221.490 (3)
C5—N31.362 (3)C21—H21A0.9700
C5—H50.9300C21—H21B0.9700
C6—N31.364 (3)C22—C231.354 (3)
C6—C111.376 (3)C22—C251.427 (3)
C6—C71.410 (3)C23—N51.363 (3)
C7—C81.396 (3)C23—H230.9300
C8—C91.375 (3)C24—N51.373 (3)
C8—H80.9300C24—C291.387 (3)
C9—C101.384 (3)C24—C251.400 (3)
C9—H90.9300C25—C261.383 (3)
C10—C111.366 (3)C26—C271.372 (3)
C10—H100.9300C26—H260.9300
C11—H110.9300C27—C281.385 (3)
C12—N11.463 (2)C27—H270.9300
C12—C131.490 (3)C28—C291.360 (3)
C12—H12A0.9700C28—H280.9300
C12—H12B0.9700C29—H290.9300
C13—C141.359 (3)N2—H20.829 (16)
C13—C161.428 (3)N3—H30.849 (16)
C14—N41.365 (3)N4—H40.92 (2)
C14—H140.9300N5—H5A0.832 (17)
N1—C1—C2110.75 (16)C15—C16—C13107.10 (17)
N1—C1—H1A109.5C18—C17—C16118.9 (2)
C2—C1—H1A109.5C18—C17—H17120.5
N1—C1—H1B109.5C16—C17—H17120.5
C2—C1—H1B109.5C17—C18—C19120.9 (2)
H1A—C1—H1B108.1C17—C18—H18119.5
N2—C2—C1108.99 (16)C19—C18—H18119.5
N2—C2—H2A109.9C20—C19—C18121.9 (2)
C1—C2—H2A109.9C20—C19—H19119.1
N2—C2—H2B109.9C18—C19—H19119.1
C1—C2—H2B109.9C19—C20—C15117.3 (2)
H2A—C2—H2B108.3C19—C20—H20121.3
N2—C3—C4111.29 (16)C15—C20—H20121.3
N2—C3—H3A109.4N1—C21—C22113.73 (16)
C4—C3—H3A109.4N1—C21—H21A108.8
N2—C3—H3B109.4C22—C21—H21A108.8
C4—C3—H3B109.4N1—C21—H21B108.8
H3A—C3—H3B108.0C22—C21—H21B108.8
C5—C4—C7106.02 (18)H21A—C21—H21B107.7
C5—C4—C3126.51 (19)C23—C22—C25106.25 (18)
C7—C4—C3127.47 (17)C23—C22—C21127.9 (2)
C4—C5—N3110.30 (19)C25—C22—C21125.62 (18)
C4—C5—H5124.8C22—C23—N5110.2 (2)
N3—C5—H5124.8C22—C23—H23124.9
N3—C6—C11130.32 (19)N5—C23—H23124.9
N3—C6—C7106.97 (18)N5—C24—C29130.9 (2)
C11—C6—C7122.70 (18)N5—C24—C25106.7 (2)
C8—C7—C6118.10 (19)C29—C24—C25122.4 (2)
C8—C7—C4134.7 (2)C26—C25—C24118.3 (2)
C6—C7—C4107.20 (17)C26—C25—C22134.03 (19)
C9—C8—C7118.6 (2)C24—C25—C22107.65 (19)
C9—C8—H8120.7C27—C26—C25119.4 (2)
C7—C8—H8120.7C27—C26—H26120.3
C8—C9—C10121.9 (2)C25—C26—H26120.3
C8—C9—H9119.1C26—C27—C28121.1 (2)
C10—C9—H9119.1C26—C27—H27119.4
C11—C10—C9120.9 (2)C28—C27—H27119.4
C11—C10—H10119.6C29—C28—C27121.2 (2)
C9—C10—H10119.6C29—C28—H28119.4
C10—C11—C6117.8 (2)C27—C28—H28119.4
C10—C11—H11121.1C28—C29—C24117.6 (2)
C6—C11—H11121.1C28—C29—H29121.2
N1—C12—C13111.60 (16)C24—C29—H29121.2
N1—C12—H12A109.3C12—N1—C1113.12 (15)
C13—C12—H12A109.3C12—N1—C21110.83 (16)
N1—C12—H12B109.3C1—N1—C21110.86 (15)
C13—C12—H12B109.3C2—N2—C3114.63 (16)
H12A—C12—H12B108.0C2—N2—H2107.1 (14)
C14—C13—C16105.83 (18)C3—N2—H2107.7 (15)
C14—C13—C12127.4 (2)C5—N3—C6109.50 (17)
C16—C13—C12126.69 (17)C5—N3—H3130.0 (15)
C13—C14—N4111.3 (2)C6—N3—H3120.5 (15)
C13—C14—H14124.3C14—N4—C15107.88 (18)
N4—C14—H14124.3C14—N4—H4123.2 (13)
N4—C15—C20130.3 (2)C15—N4—H4128.7 (13)
N4—C15—C16107.87 (19)C23—N5—C24109.17 (19)
C20—C15—C16121.8 (2)C23—N5—H5A127.4 (18)
C17—C16—C15119.16 (19)C24—N5—H5A123.4 (18)
C17—C16—C13133.73 (19)
N1—C1—C2—N263.4 (2)C16—C15—C20—C19−0.8 (3)
N2—C3—C4—C519.5 (3)N1—C21—C22—C23−118.0 (2)
N2—C3—C4—C7−160.79 (18)N1—C21—C22—C2568.3 (3)
C7—C4—C5—N3−0.6 (2)C25—C22—C23—N50.5 (3)
C3—C4—C5—N3179.15 (19)C21—C22—C23—N5−174.18 (19)
N3—C6—C7—C8178.42 (18)N5—C24—C25—C26179.86 (19)
C11—C6—C7—C8−1.6 (3)C29—C24—C25—C260.8 (3)
N3—C6—C7—C4−1.3 (2)N5—C24—C25—C220.9 (2)
C11—C6—C7—C4178.67 (18)C29—C24—C25—C22−178.12 (19)
C5—C4—C7—C8−178.5 (2)C23—C22—C25—C26−179.6 (2)
C3—C4—C7—C81.8 (4)C21—C22—C25—C26−4.7 (4)
C5—C4—C7—C61.2 (2)C23—C22—C25—C24−0.9 (2)
C3—C4—C7—C6−178.60 (19)C21—C22—C25—C24173.95 (18)
C6—C7—C8—C90.3 (3)C24—C25—C26—C27−0.4 (3)
C4—C7—C8—C9179.8 (2)C22—C25—C26—C27178.2 (2)
C7—C8—C9—C101.1 (4)C25—C26—C27—C28−0.5 (4)
C8—C9—C10—C11−1.2 (4)C26—C27—C28—C291.0 (4)
C9—C10—C11—C6−0.2 (4)C27—C28—C29—C24−0.5 (4)
N3—C6—C11—C10−178.5 (2)N5—C24—C29—C28−179.1 (2)
C7—C6—C11—C101.6 (3)C25—C24—C29—C28−0.3 (3)
N1—C12—C13—C14−108.4 (2)C13—C12—N1—C168.4 (2)
N1—C12—C13—C1667.8 (2)C13—C12—N1—C21−166.40 (16)
C16—C13—C14—N40.6 (2)C2—C1—N1—C12−147.38 (16)
C12—C13—C14—N4177.40 (18)C2—C1—N1—C2187.41 (19)
N4—C15—C16—C17−179.86 (17)C22—C21—N1—C1276.6 (2)
C20—C15—C16—C172.1 (3)C22—C21—N1—C1−156.94 (17)
N4—C15—C16—C130.5 (2)C1—C2—N2—C3−161.54 (17)
C20—C15—C16—C13−177.50 (18)C4—C3—N2—C2170.19 (16)
C14—C13—C16—C17179.8 (2)C4—C5—N3—C6−0.2 (2)
C12—C13—C16—C172.9 (3)C11—C6—N3—C5−179.0 (2)
C14—C13—C16—C15−0.6 (2)C7—C6—N3—C50.9 (2)
C12—C13—C16—C15−177.50 (18)C13—C14—N4—C15−0.3 (2)
C15—C16—C17—C18−1.7 (3)C20—C15—N4—C14177.6 (2)
C13—C16—C17—C18177.8 (2)C16—C15—N4—C14−0.2 (2)
C16—C17—C18—C190.0 (3)C22—C23—N5—C240.1 (3)
C17—C18—C19—C201.4 (3)C29—C24—N5—C23178.3 (2)
C18—C19—C20—C15−1.0 (3)C25—C24—N5—C23−0.6 (3)
N4—C15—C20—C19−178.2 (2)
D—H···AD—HH···AD···AD—H···A
N4—H4···N2i0.92 (2)2.03 (2)2.953 (3)176 (2)
N2—H2···N10.83 (2)2.45 (2)2.889 (2)114 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N4—H4⋯N2i 0.92 (2)2.03 (2)2.953 (3)176 (2)
N2—H2⋯N10.83 (2)2.45 (2)2.889 (2)114 (2)

Symmetry code: (i) .

  3 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.  Rare-earth metal complexes having an unusual indolyl-1,2-dianion through C-H activation with a novel η1:(μ2-η1:η1) bonding with metals.

Authors:  Xiancui Zhu; Shuangliu Zhou; Shaowu Wang; Yun Wei; Lijun Zhang; Fenhua Wang; Shaoyin Wang; Zhijun Feng
Journal:  Chem Commun (Camb)       Date:  2012-12-21       Impact factor: 6.222

3.  Indole rings in palladium(II) complexes. Dual mode of metal binding and aromatic ring stacking causing syn-anti isomerism.

Authors:  Masako Takani; Takeshi Takeda; Tatsuo Yajima; Osamu Yamauchi
Journal:  Inorg Chem       Date:  2006-07-24       Impact factor: 5.165

  3 in total

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