Literature DB >> 21583580

Tris{2-[4-(2-pyrid-yl)pyrimidin-2-ylsulfan-yl]eth-yl}amine.

Jian-Quan Wang1, Ya-Wen Zhang, Lin Cheng.   

Abstract

The tripodal character of the title compound, C(33)H(30)N(10)S(3), arises from the three thio-ether arms surrounding a central amine N atom. The three arms have approximately the same conformation but distinct geometries in a trans-trans-cis conformation, resulting in a short pyridine-sulfanyl N⋯S distance of 4.320 (7) Å. The distances of the central N atom to the N atoms of three pyridine rings in the arms are 8.305 (7), 8.032 (7) and 5.076 (9)Å. In the crystal, mol-ecules are joined into a three-dimensional supra-molecular network via effective π-π stacking between adjacent heterocycles [centroid-centroid distances of 3.700 (3)-4.118 (4) Å between adjacent inter-layer pyrimidine rings and 3.676 (4) Å between the pyridine rings].

Entities:  

Year:  2009        PMID: 21583580      PMCID: PMC2977494          DOI: 10.1107/S160053680902741X

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


Related literature

For the use of tripodal ligands in crystal engineering, see: Hammes et al. (1998 ▶); Hiraoka et al. (2005 ▶). For the use of thio­ether ligands in crystal engineering, see: Dong et al. (2008a ▶,b ▶); Zhang et al. (2008 ▶).

Experimental

Crystal data

C33H30N10S3 M = 662.85 Orthorhombic, a = 16.169 (3) Å b = 25.670 (5) Å c = 7.6166 (14) Å V = 3161.3 (10) Å3 Z = 4 Mo Kα radiation μ = 0.28 mm−1 T = 295 K 0.30 × 0.20 × 0.20 mm

Data collection

Bruker SMART CCD diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2000 ▶) T min = 0.922, T max = 0.947 16502 measured reflections 6104 independent reflections 3099 reflections with I > 2σ(I) R int = 0.105

Refinement

R[F 2 > 2σ(F 2)] = 0.070 wR(F 2) = 0.123 S = 1.06 6104 reflections 415 parameters 1 restraint H-atom parameters constrained Δρmax = 0.41 e Å−3 Δρmin = −0.25 e Å−3 Absolute structure: Flack (1983 ▶), 2750 Friedel pairs Flack parameter: −0.33 (12) Data collection: SMART (Bruker, 2000 ▶); cell refinement: SAINT (Bruker, 2000 ▶); 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: SHELXL97 and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680902741X/si2186sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053680902741X/si2186Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C33H30N10S3F(000) = 1384
Mr = 662.85Dx = 1.393 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 787 reflections
a = 16.169 (3) Åθ = 2.4–28.0°
b = 25.670 (5) ŵ = 0.28 mm1
c = 7.6166 (14) ÅT = 295 K
V = 3161.3 (10) Å3Block, yellow
Z = 40.30 × 0.20 × 0.20 mm
Bruker SMART CCD diffractometer6104 independent reflections
Radiation source: fine-focus sealed tube3099 reflections with I > 2σ(I)
graphiteRint = 0.105
φ and ω scansθmax = 26.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)h = −19→18
Tmin = 0.922, Tmax = 0.947k = −25→31
16502 measured reflectionsl = −9→9
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.070H-atom parameters constrained
wR(F2) = 0.123w = 1/[σ2(Fo2) + (0.0045P)2 + 0.8P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
6104 reflectionsΔρmax = 0.41 e Å3
415 parametersΔρmin = −0.25 e Å3
1 restraintAbsolute structure: Flack (1983), 2750 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.33 (12)
Experimental. A trial to refine the structure by interchanging the C16 and N6 atoms resulted in slightly worse R-values and larger anisotropic displacement parameters. A further trial to treat the N6 pyridine as a rotational disordered group, using EADP and PART instructions did not show any improvement. The large negative Flack parameter may result from an unresolved twinning problem or from tiny intergrown material that contribute to additional intensities in the data set. This may also explain the relatively large Rint and R(sigma) values after absorption correction and data reduction.
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
S10.83661 (8)0.33092 (6)0.0846 (3)0.0824 (6)
S20.41967 (9)0.46398 (6)0.0662 (3)0.0677 (5)
S30.78712 (8)0.58482 (6)0.0894 (3)0.0695 (5)
C10.9379 (3)0.3547 (2)0.1233 (9)0.0600 (19)
C21.0620 (3)0.3334 (3)0.2283 (10)0.071 (2)
H21.09850.30990.27950.085*
C31.0900 (4)0.3824 (2)0.1879 (9)0.0692 (19)
H31.14500.39150.20620.083*
C41.0356 (3)0.4172 (2)0.1206 (7)0.0461 (15)
C51.0572 (3)0.4721 (2)0.0830 (10)0.0564 (15)
C61.1378 (3)0.4874 (3)0.0554 (11)0.077 (2)
H61.17870.46190.05390.092*
C71.1010 (4)0.5729 (3)0.0369 (11)0.093 (3)
H71.11570.60780.02360.112*
C81.0201 (4)0.5610 (2)0.0618 (11)0.080 (2)
H80.98010.58700.06000.096*
C90.9983 (3)0.5105 (2)0.0894 (10)0.0723 (18)
H90.94350.50200.11260.087*
C100.3913 (4)0.4001 (2)0.0151 (8)0.0567 (18)
C110.2849 (4)0.3452 (3)−0.0115 (9)0.074 (2)
H110.22880.3377−0.00330.089*
C120.3360 (4)0.3062 (3)−0.0749 (9)0.0715 (19)
H120.31590.2739−0.10980.086*
C130.4198 (4)0.3189 (2)−0.0827 (7)0.0521 (16)
C140.4821 (4)0.2805 (3)−0.1415 (9)0.0622 (18)
C150.4630 (5)0.2367 (3)−0.2312 (10)0.084 (2)
H150.40770.2298−0.25500.101*
C160.5189 (7)0.2033 (4)−0.2863 (13)0.105 (3)
H160.50440.1741−0.35160.126*
C170.5973 (8)0.2132 (4)−0.2445 (14)0.130 (4)
H170.63640.1889−0.28050.155*
C180.5641 (5)0.2892 (3)−0.1054 (10)0.083 (2)
H180.57850.3194−0.04520.099*
C190.7194 (3)0.6319 (2)0.0044 (7)0.0524 (16)
C200.7130 (4)0.7117 (2)−0.1116 (8)0.0663 (18)
H200.73840.7419−0.15170.080*
C210.6267 (3)0.7084 (2)−0.1158 (8)0.0607 (17)
H210.59460.7356−0.15880.073*
C220.5919 (3)0.6642 (2)−0.0549 (7)0.0412 (13)
C230.5002 (3)0.6563 (2)−0.0429 (7)0.0412 (13)
C240.4472 (4)0.6917 (2)−0.1183 (9)0.0606 (17)
H240.47030.7185−0.18420.073*
C250.3355 (3)0.6511 (3)−0.0095 (9)0.069 (2)
H250.27840.64940.00510.082*
C260.3812 (3)0.6136 (2)0.0675 (9)0.0636 (17)
H260.35660.58660.13020.076*
C270.4666 (3)0.6166 (2)0.0496 (8)0.0523 (16)
H270.50040.59150.10080.063*
C280.7832 (3)0.3846 (2)−0.0206 (9)0.0719 (19)
H28A0.82320.4102−0.06030.086*
H28B0.75320.3719−0.12220.086*
C290.7245 (3)0.4093 (2)0.1049 (9)0.0671 (17)
H29A0.69290.38240.16390.080*
H29B0.75540.42830.19320.080*
C300.5859 (3)0.4472 (2)0.1069 (8)0.0635 (17)
H30A0.56980.41270.14620.076*
H30B0.58930.46990.20850.076*
C310.5245 (3)0.4676 (2)−0.0191 (8)0.0654 (19)
H31A0.52780.4478−0.12730.078*
H31B0.53760.5036−0.04610.078*
C320.7063 (3)0.4951 (2)−0.0204 (7)0.0576 (17)
H32A0.67120.5140−0.10190.069*
H32B0.75870.4889−0.07870.069*
C330.7220 (3)0.5299 (2)0.1391 (8)0.066 (2)
H33A0.74790.50940.23090.079*
H33B0.66950.54250.18370.079*
N10.9562 (2)0.40316 (17)0.0839 (7)0.0566 (12)
N20.9844 (3)0.31788 (18)0.1973 (7)0.0644 (15)
N31.1603 (3)0.5370 (2)0.0307 (9)0.097 (2)
N40.4466 (3)0.36629 (19)−0.0387 (6)0.0526 (13)
N50.3090 (3)0.39190 (19)0.0383 (7)0.0636 (15)
N60.6259 (4)0.2555 (3)−0.1540 (10)0.121 (3)
N70.6377 (2)0.62430 (16)0.0073 (6)0.0452 (12)
N80.7597 (3)0.6734 (2)−0.0528 (7)0.0618 (14)
N90.3649 (3)0.6902 (2)−0.1038 (8)0.0729 (16)
N100.6680 (3)0.44486 (18)0.0158 (6)0.0588 (14)
U11U22U33U12U13U23
S10.0393 (8)0.0613 (10)0.1466 (17)0.0050 (7)−0.0129 (14)0.0014 (14)
S20.0528 (9)0.0678 (11)0.0827 (12)−0.0013 (7)0.0077 (11)−0.0170 (12)
S30.0376 (7)0.0688 (10)0.1021 (13)0.0047 (7)−0.0071 (11)0.0067 (13)
C10.033 (3)0.055 (4)0.092 (6)−0.002 (3)−0.011 (3)−0.011 (4)
C20.044 (4)0.057 (4)0.112 (6)0.012 (3)−0.017 (4)0.015 (4)
C30.041 (4)0.067 (5)0.100 (6)0.000 (3)−0.017 (4)0.009 (4)
C40.039 (3)0.051 (4)0.048 (4)0.008 (3)0.000 (3)0.005 (3)
C50.046 (3)0.057 (4)0.066 (4)0.007 (3)0.002 (4)0.005 (4)
C60.048 (4)0.074 (4)0.109 (6)0.004 (3)0.010 (5)0.027 (5)
C70.082 (5)0.064 (5)0.134 (8)−0.002 (4)−0.012 (5)0.028 (5)
C80.049 (4)0.063 (4)0.129 (7)0.011 (3)−0.005 (5)0.019 (5)
C90.047 (3)0.067 (4)0.103 (5)0.001 (3)0.002 (4)0.027 (5)
C100.054 (4)0.051 (4)0.065 (5)0.006 (3)−0.002 (3)−0.004 (3)
C110.045 (4)0.070 (5)0.106 (6)−0.005 (4)−0.009 (4)0.012 (4)
C120.065 (5)0.055 (4)0.094 (6)−0.001 (4)0.004 (4)0.007 (4)
C130.052 (4)0.060 (5)0.044 (4)0.013 (3)−0.001 (3)0.014 (3)
C140.069 (5)0.055 (5)0.063 (5)0.007 (4)0.003 (4)0.014 (4)
C150.100 (6)0.053 (5)0.100 (7)0.008 (5)0.013 (5)−0.002 (5)
C160.147 (9)0.075 (7)0.094 (7)0.015 (7)0.007 (8)0.004 (5)
C170.196 (12)0.086 (8)0.107 (9)0.075 (9)0.048 (9)0.005 (6)
C180.082 (5)0.068 (5)0.098 (6)0.034 (4)0.021 (5)0.008 (4)
C190.048 (4)0.050 (4)0.059 (5)0.001 (3)0.000 (3)−0.007 (3)
C200.055 (4)0.046 (4)0.098 (5)−0.014 (3)0.009 (4)0.006 (4)
C210.037 (3)0.054 (4)0.090 (5)0.004 (3)0.006 (3)0.012 (4)
C220.040 (3)0.043 (4)0.041 (4)−0.001 (3)0.005 (3)0.001 (3)
C230.041 (3)0.044 (4)0.039 (4)0.002 (3)0.002 (3)0.001 (3)
C240.053 (4)0.042 (4)0.087 (5)−0.006 (3)−0.001 (4)0.010 (4)
C250.031 (3)0.087 (5)0.088 (6)0.000 (4)0.001 (3)−0.008 (4)
C260.044 (3)0.071 (4)0.076 (5)−0.010 (3)0.001 (4)−0.005 (5)
C270.042 (3)0.058 (4)0.057 (4)0.000 (3)−0.003 (3)0.005 (4)
C280.045 (3)0.082 (5)0.088 (5)0.009 (3)−0.012 (4)0.001 (4)
C290.070 (4)0.059 (4)0.072 (5)0.008 (3)0.004 (4)0.004 (4)
C300.059 (4)0.073 (4)0.058 (4)0.012 (3)−0.004 (4)0.008 (4)
C310.061 (4)0.066 (4)0.069 (5)−0.005 (3)0.013 (4)−0.002 (4)
C320.045 (4)0.081 (5)0.047 (4)0.020 (3)−0.005 (3)−0.003 (4)
C330.044 (4)0.068 (4)0.085 (6)0.004 (3)0.001 (3)0.020 (4)
N10.039 (2)0.053 (3)0.078 (4)0.003 (2)0.000 (3)−0.018 (3)
N20.043 (3)0.049 (3)0.101 (4)0.007 (3)−0.010 (3)0.007 (3)
N30.062 (4)0.081 (4)0.148 (7)−0.002 (3)0.017 (4)0.030 (5)
N40.048 (3)0.054 (3)0.056 (3)0.006 (3)0.004 (3)0.000 (3)
N50.044 (3)0.065 (3)0.082 (5)0.003 (2)0.001 (3)0.006 (3)
N60.103 (5)0.120 (6)0.139 (7)0.053 (5)0.029 (5)0.007 (5)
N70.031 (2)0.040 (3)0.064 (4)0.001 (2)−0.003 (2)0.001 (2)
N80.033 (3)0.056 (3)0.097 (4)−0.008 (3)0.003 (3)−0.004 (3)
N90.039 (3)0.071 (4)0.109 (5)0.009 (3)−0.009 (3)0.002 (4)
N100.051 (3)0.052 (3)0.073 (4)0.009 (3)0.002 (3)0.003 (3)
S1—C11.773 (5)C17—H170.9300
S1—C281.812 (6)C18—N61.372 (8)
S2—C101.747 (6)C18—H180.9300
S2—C311.818 (6)C19—N81.324 (6)
S3—C191.754 (6)C19—N71.334 (6)
S3—C331.799 (5)C20—N81.318 (6)
C1—N11.312 (6)C20—C211.399 (7)
C1—N21.333 (7)C20—H200.9300
C2—N21.336 (6)C21—C221.348 (7)
C2—C31.372 (8)C21—H210.9300
C2—H20.9300C22—N71.350 (6)
C3—C41.356 (7)C22—C231.500 (7)
C3—H30.9300C23—C271.353 (7)
C4—N11.361 (6)C23—C241.373 (7)
C4—C51.479 (7)C24—N91.337 (7)
C5—C91.371 (7)C24—H240.9300
C5—C61.378 (7)C25—N91.323 (7)
C6—N31.338 (7)C25—C261.350 (7)
C6—H60.9300C25—H250.9300
C7—N31.331 (7)C26—C271.389 (6)
C7—C81.358 (8)C26—H260.9300
C7—H70.9300C27—H270.9300
C8—C91.359 (7)C28—C291.489 (7)
C8—H80.9300C28—H28A0.9700
C9—H90.9300C28—H28B0.9700
C10—N41.312 (6)C29—N101.459 (7)
C10—N51.358 (6)C29—H29A0.9700
C11—N51.317 (7)C29—H29B0.9700
C11—C121.385 (8)C30—C311.477 (7)
C11—H110.9300C30—N101.499 (6)
C12—C131.394 (7)C30—H30A0.9700
C12—H120.9300C30—H30B0.9700
C13—N41.335 (7)C31—H31A0.9700
C13—C141.479 (8)C31—H31B0.9700
C14—C151.352 (8)C32—N101.457 (7)
C14—C181.372 (8)C32—C331.530 (7)
C15—C161.314 (10)C32—H32A0.9700
C15—H150.9300C32—H32B0.9700
C16—C171.331 (12)C33—H33A0.9700
C16—H160.9300C33—H33B0.9700
C17—N61.367 (12)
C1—S1—C28104.5 (3)C21—C22—N7122.1 (5)
C10—S2—C31102.3 (3)C21—C22—C23123.2 (5)
C19—S3—C33104.6 (3)N7—C22—C23114.7 (5)
N1—C1—N2129.9 (5)C27—C23—C24117.8 (5)
N1—C1—S1119.8 (4)C27—C23—C22122.0 (5)
N2—C1—S1110.3 (5)C24—C23—C22120.1 (5)
N2—C2—C3122.9 (6)N9—C24—C23124.6 (6)
N2—C2—H2118.5N9—C24—H24117.7
C3—C2—H2118.5C23—C24—H24117.7
C4—C3—C2118.4 (5)N9—C25—C26125.5 (6)
C4—C3—H3120.8N9—C25—H25117.3
C2—C3—H3120.8C26—C25—H25117.3
C3—C4—N1120.9 (5)C25—C26—C27117.5 (6)
C3—C4—C5123.3 (5)C25—C26—H26121.2
N1—C4—C5115.8 (5)C27—C26—H26121.2
C9—C5—C6117.3 (5)C23—C27—C26119.5 (5)
C9—C5—C4120.9 (5)C23—C27—H27120.3
C6—C5—C4121.6 (5)C26—C27—H27120.3
N3—C6—C5123.3 (5)C29—C28—S1110.1 (5)
N3—C6—H6118.3C29—C28—H28A109.6
C5—C6—H6118.3S1—C28—H28A109.6
N3—C7—C8122.9 (6)C29—C28—H28B109.6
N3—C7—H7118.6S1—C28—H28B109.6
C8—C7—H7118.6H28A—C28—H28B108.2
C7—C8—C9119.1 (6)N10—C29—C28111.6 (6)
C7—C8—H8120.4N10—C29—H29A109.3
C9—C8—H8120.4C28—C29—H29A109.3
C8—C9—C5120.0 (5)N10—C29—H29B109.3
C8—C9—H9120.0C28—C29—H29B109.3
C5—C9—H9120.0H29A—C29—H29B108.0
N4—C10—N5127.4 (5)C31—C30—N10108.0 (5)
N4—C10—S2120.7 (4)C31—C30—H30A110.1
N5—C10—S2111.9 (4)N10—C30—H30A110.1
N5—C11—C12125.6 (6)C31—C30—H30B110.1
N5—C11—H11117.2N10—C30—H30B110.1
C12—C11—H11117.2H30A—C30—H30B108.4
C11—C12—C13115.2 (6)C30—C31—S2112.1 (4)
C11—C12—H12122.4C30—C31—H31A109.2
C13—C12—H12122.4S2—C31—H31A109.2
N4—C13—C12121.2 (5)C30—C31—H31B109.2
N4—C13—C14117.4 (5)S2—C31—H31B109.2
C12—C13—C14121.3 (6)H31A—C31—H31B107.9
C15—C14—C18117.2 (7)N10—C32—C33116.0 (4)
C15—C14—C13123.4 (7)N10—C32—H32A108.3
C18—C14—C13119.4 (6)C33—C32—H32A108.3
C16—C15—C14123.1 (8)N10—C32—H32B108.3
C16—C15—H15118.4C33—C32—H32B108.3
C14—C15—H15118.4H32A—C32—H32B107.4
C15—C16—C17117.0 (10)C32—C33—S3112.8 (4)
C15—C16—H16121.5C32—C33—H33A109.0
C17—C16—H16121.5S3—C33—H33A109.0
C16—C17—N6126.5 (10)C32—C33—H33B109.0
C16—C17—H17116.8S3—C33—H33B109.0
N6—C17—H17116.8H33A—C33—H33B107.8
C14—C18—N6123.1 (8)C1—N1—C4114.6 (5)
C14—C18—H18118.4C1—N2—C2113.1 (5)
N6—C18—H18118.4C7—N3—C6117.3 (5)
N8—C19—N7127.6 (5)C10—N4—C13117.3 (5)
N8—C19—S3111.6 (4)C11—N5—C10113.1 (5)
N7—C19—S3120.8 (4)C17—N6—C18113.0 (8)
N8—C20—C21122.4 (5)C19—N7—C22115.2 (5)
N8—C20—H20118.8C20—N8—C19115.5 (5)
C21—C20—H20118.8C25—N9—C24115.1 (6)
C22—C21—C20117.2 (5)C32—N10—C29112.0 (4)
C22—C21—H21121.4C32—N10—C30115.4 (4)
C20—C21—H21121.4C29—N10—C30111.4 (5)
  5 in total

1.  Quantitative dynamic interconversion between Ag(I)-mediated capsule and cage complexes accompanying guest encapsulation/release.

Authors:  Shuichi Hiraoka; Koji Harano; Motoo Shiro; Mitsuhiko Shionoya
Journal:  Angew Chem Int Ed Engl       Date:  2005-04-29       Impact factor: 15.336

2.  A short history of SHELX.

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

3.  Anion-modulated reversible conversion of molecular assembly between a macrocycle and a linear chain.

Authors:  Huaze Dong; Juan Yang; Xia Liu; Shaohua Gou
Journal:  Inorg Chem       Date:  2008-04-21       Impact factor: 5.165

4.  Poly[{μ(2)-1,2-bis-[4-(3-pyrid-yl)pyrimidin-2-ylsulfan-yl]ethane}di-μ(2)-cyanido-dicopper(I)].

Authors:  Ya-Wen Zhang; Hua-Ze Dong; Lin Cheng
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-06-07

5.  Structure validation in chemical crystallography.

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

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