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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2012 Aug 23;68(Pt 9):o2744. doi: 10.1107/S1600536812035477

2,2′-{[2-(Pyridin-2-yl)-1,3-diazinane-1,3-diyl]bis(methylene)}diphenol

Adailton J Bortoluzzi a,*, Geovana G Terra a
PMCID: PMC3435756  PMID: 22969627

Abstract

The title compound, C23H25N3O2, was obtained as an inter­mediary in the preparation of non-symmetric tertiary diamines. The mol­ecular structure presents T-shaped spatial form, in which the pyrimidine ring exhibits a chair conformation. The pyridyl ring is almost perpendicular to the phenyl rings with dihedral angles of 80.17 (8) and 76.03 (2)°. The phenol and amine groups are involved in two strong intra­molecular O—H⋯N inter­actions. In the crystal, the mol­ecules are stacked along [010]; however, no inter­molecular inter­actions are observed.

Related literature  

For the synthetic procedure, see: Hureau et al. (2008). For related structures, see: Yokoyama et al. (1995); Xia et al. (2007). For standard bond lengths and angles, see: Bruno et al. (2004).graphic file with name e-68-o2744-scheme1.jpg

Experimental  

Crystal data  

  • C23H25N3O2

  • M r = 375.46

  • Monoclinic, Inline graphic

  • a = 18.7615 (16) Å

  • b = 6.2105 (11) Å

  • c = 19.0407 (12) Å

  • β = 114.594 (8)°

  • V = 2017.3 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 293 K

  • 0.50 × 0.50 × 0.40 mm

Data collection  

  • Enraf–Nonius CAD-4 diffractometer

  • 3711 measured reflections

  • 3595 independent reflections

  • 2038 reflections with I > 2σ(I)

  • R int = 0.079

  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement  

  • R[F 2 > 2σ(F 2)] = 0.052

  • wR(F 2) = 0.146

  • S = 1.01

  • 3595 reflections

  • 253 parameters

  • H-atom parameters constrained

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.22 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: SET4 in CAD-4 Software; data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812035477/lr2078sup1.cif

e-68-o2744-sup1.cif (28KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812035477/lr2078Isup2.hkl

e-68-o2744-Isup2.hkl (172.7KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812035477/lr2078Isup3.mol

Supplementary material file. DOI: 10.1107/S1600536812035477/lr2078Isup4.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
O10—H10⋯N1 1.02 1.69 2.624 (3) 150
O20—H20⋯N5 1.09 1.72 2.705 (3) 148

Acknowledgments

The authors thank the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and the Financiadora de Estudos e Projetos (FINEP) for financial support.

supplementary crystallographic information

Comment

The molecular structure of the title compound (I) shows T-shaped spatial form (Fig. 1). Pyrimidine ring adopts regular chair conformation with square plane formed by N1/C2/C4/C5 atoms (r.m.s. deviation = 0.0111).

The dihedral angles between the mean planes of the rings C31/C36 and C11/C16 of 80.17 (8)° and C31/36 and C211/C26 of 76.03 (8)° demonstrate that pyridil ring is almost perpendicular to phenol groups.

Two strong intramolecular O—H···N hydrogen bonds between phenol and amine groups (Table 1) form additional six-membered rings, which contribute for the rigidity of the structure and avoid the crystal supramolecurity.

The molecules are stacked along [010] direction, however no further intermolecular interactions, such as π-stacking, were observed.

All bond lengths and angles found for (I) are in the expected range for organic compounds (Bruno et al., 2004).

Experimental

Compound (I) was synthesized according to the procedure described by Hureau et al. (2008).

A solution containing 6.0 g of N,N'-bis(2-hydroxybenzyl)-1,3-diamino-propane (21,3 mmol) and 2.39 g (21,3 mmol) of 2-pyridinecarboxaldehyde in 60 ml of MeOH was stirred at temperature of 333,15 K for 1 h. The solvent was evaporated under reduced pressure to afford a white precipitate, which was filtered off and washed with dry diethyl eter. (85% yield = 85%). MP 154.6–154.9 °C, EA for C23H25N3O2: calc C 73,53%; H 7,18%; N 11,27%, found C, 73.57%; H, 6.71%; N, 11.195.

Refinement

H atoms attached to carbon atoms were placed at their idealized positions with distances of 0.98 and 0.97 Å and Uiso fixed at 1.2 times of Ueq of the preceding atom for CH and CH2, respectively. H atoms of the hydroxyl groups were found from difference map and treated with riding model and their Uiso were fixed at 1.2 times of Ueq of the parent atom.

Figures

Fig. 1.

Fig. 1.

The molecular structure of the title compound. Ellipsoids are shown at the 40% probability level.

Crystal data

C23H25N3O2 F(000) = 800
Mr = 375.46 Dx = 1.236 Mg m3
Monoclinic, P21/n Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn Cell parameters from 25 reflections
a = 18.7615 (16) Å θ = 5.5–17.4°
b = 6.2105 (11) Å µ = 0.08 mm1
c = 19.0407 (12) Å T = 293 K
β = 114.594 (8)° Block, colorless
V = 2017.3 (4) Å3 0.50 × 0.50 × 0.40 mm
Z = 4

Data collection

Enraf–Nonius CAD-4 diffractometer Rint = 0.079
Radiation source: fine-focus sealed tube θmax = 25.1°, θmin = 1.3°
Graphite monochromator h = −20→22
ω–2θ scans k = −7→0
3711 measured reflections l = −22→0
3595 independent reflections 3 standard reflections every 200 reflections
2038 reflections with I > 2σ(I) intensity decay: 1%

Refinement

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)] = 0.052 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.146 H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0711P)2 + 0.2051P] where P = (Fo2 + 2Fc2)/3
3595 reflections (Δ/σ)max < 0.001
253 parameters Δρmax = 0.17 e Å3
0 restraints Δρmin = −0.22 e Å3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
N1 0.65802 (10) 0.2353 (3) −0.10455 (10) 0.0445 (5)
C2 0.57867 (13) 0.1394 (4) −0.14032 (13) 0.0545 (7)
H2A 0.5828 −0.0130 −0.1492 0.065*
H2B 0.5488 0.2073 −0.1898 0.065*
C3 0.53699 (14) 0.1696 (5) −0.08857 (14) 0.0636 (8)
H3A 0.5285 0.3218 −0.0835 0.076*
H3B 0.4863 0.0989 −0.1109 0.076*
C4 0.58552 (14) 0.0754 (5) −0.01042 (14) 0.0631 (8)
H4A 0.5594 0.0982 0.0235 0.076*
H4B 0.5914 −0.0784 −0.0151 0.076*
N5 0.66299 (10) 0.1781 (3) 0.02244 (11) 0.0481 (5)
C10 0.69848 (14) 0.2035 (4) −0.15583 (14) 0.0528 (6)
H10A 0.6964 0.0521 −0.1691 0.063*
H10B 0.7532 0.2433 −0.1283 0.063*
C11 0.66255 (14) 0.3345 (4) −0.22904 (13) 0.0504 (6)
C12 0.63385 (15) 0.5401 (4) −0.22823 (15) 0.0581 (7)
C13 0.60453 (16) 0.6654 (5) −0.29458 (16) 0.0697 (8)
H13 0.5838 0.8009 −0.2938 0.084*
C14 0.60633 (17) 0.5889 (6) −0.36109 (17) 0.0781 (9)
H14 0.5881 0.6747 −0.4051 0.094*
C15 0.63473 (17) 0.3875 (6) −0.36363 (16) 0.0741 (9)
H15 0.6353 0.3361 −0.4093 0.089*
C16 0.66272 (15) 0.2605 (5) −0.29765 (15) 0.0635 (7)
H16 0.6819 0.1235 −0.2995 0.076*
C20 0.70860 (14) 0.0956 (4) 0.10175 (13) 0.0536 (7)
H20A 0.7614 0.1532 0.1214 0.064*
H20B 0.7121 −0.0600 0.1000 0.064*
C21 0.67202 (13) 0.1560 (4) 0.15583 (13) 0.0479 (6)
C22 0.64091 (15) 0.3595 (5) 0.15448 (14) 0.0564 (7)
C23 0.61059 (16) 0.4140 (5) 0.20724 (16) 0.0689 (8)
H23 0.5892 0.5500 0.2057 0.083*
C24 0.61217 (17) 0.2666 (6) 0.26183 (16) 0.0735 (8)
H24 0.5921 0.3038 0.2974 0.088*
C25 0.64312 (17) 0.0652 (5) 0.26416 (15) 0.0703 (8)
H25 0.6443 −0.0341 0.3012 0.084*
C26 0.67240 (14) 0.0119 (4) 0.21108 (13) 0.0568 (7)
H26 0.6930 −0.1250 0.2125 0.068*
C30 0.70474 (12) 0.1435 (4) −0.02717 (12) 0.0443 (6)
H30 0.7115 −0.0114 −0.0321 0.053*
C31 0.78452 (13) 0.2502 (4) 0.00853 (13) 0.0451 (6)
N32 0.84615 (11) 0.1185 (3) 0.03432 (12) 0.0549 (6)
C33 0.91701 (15) 0.2096 (5) 0.06679 (17) 0.0691 (8)
H33 0.9605 0.1195 0.0861 0.083*
C34 0.92949 (17) 0.4257 (6) 0.07337 (17) 0.0740 (9)
H34 0.9801 0.4810 0.0955 0.089*
C35 0.86581 (17) 0.5606 (5) 0.04665 (14) 0.0638 (8)
H35 0.8723 0.7092 0.0505 0.077*
C36 0.79262 (15) 0.4714 (4) 0.01433 (14) 0.0550 (7)
H36 0.7485 0.5592 −0.0037 0.066*
O10 0.63242 (12) 0.6251 (3) −0.16299 (11) 0.0789 (6)
H10 0.6485 0.5027 −0.1240 0.095*
O20 0.63844 (12) 0.5107 (3) 0.10137 (11) 0.0754 (6)
H20 0.6531 0.4237 0.0597 0.090*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
N1 0.0433 (11) 0.0465 (11) 0.0424 (10) 0.0008 (9) 0.0167 (9) 0.0002 (9)
C2 0.0463 (14) 0.0617 (17) 0.0479 (13) −0.0021 (13) 0.0120 (11) 0.0025 (13)
C3 0.0396 (13) 0.093 (2) 0.0531 (15) −0.0052 (14) 0.0141 (12) 0.0054 (15)
C4 0.0490 (15) 0.084 (2) 0.0529 (15) −0.0118 (14) 0.0176 (12) 0.0097 (15)
N5 0.0394 (11) 0.0558 (13) 0.0452 (11) −0.0027 (10) 0.0136 (9) 0.0079 (10)
C10 0.0543 (15) 0.0494 (15) 0.0565 (15) 0.0046 (12) 0.0249 (13) −0.0022 (12)
C11 0.0479 (14) 0.0565 (16) 0.0476 (14) −0.0053 (12) 0.0206 (11) −0.0021 (13)
C12 0.0621 (17) 0.0532 (16) 0.0529 (16) −0.0021 (14) 0.0178 (13) 0.0038 (14)
C13 0.0732 (19) 0.0683 (19) 0.0600 (17) −0.0021 (16) 0.0202 (15) 0.0139 (16)
C14 0.069 (2) 0.100 (3) 0.0585 (19) −0.0141 (19) 0.0190 (15) 0.0212 (19)
C15 0.0710 (19) 0.108 (3) 0.0508 (17) −0.022 (2) 0.0330 (15) −0.0036 (18)
C16 0.0602 (16) 0.078 (2) 0.0611 (17) −0.0102 (15) 0.0337 (14) −0.0119 (16)
C20 0.0468 (14) 0.0567 (16) 0.0479 (14) 0.0035 (12) 0.0104 (11) 0.0101 (13)
C21 0.0412 (13) 0.0541 (15) 0.0392 (13) −0.0039 (12) 0.0076 (10) 0.0041 (12)
C22 0.0530 (15) 0.0593 (17) 0.0517 (15) 0.0035 (14) 0.0167 (12) 0.0081 (14)
C23 0.0653 (18) 0.073 (2) 0.0637 (17) 0.0132 (16) 0.0224 (15) 0.0025 (16)
C24 0.074 (2) 0.094 (2) 0.0539 (17) 0.0093 (19) 0.0283 (15) 0.0021 (18)
C25 0.0755 (19) 0.085 (2) 0.0472 (15) 0.0029 (18) 0.0225 (14) 0.0134 (16)
C26 0.0556 (15) 0.0609 (17) 0.0450 (14) 0.0030 (13) 0.0121 (12) 0.0065 (13)
C30 0.0408 (13) 0.0365 (12) 0.0505 (14) 0.0009 (11) 0.0140 (11) 0.0029 (11)
C31 0.0461 (14) 0.0459 (15) 0.0437 (13) 0.0016 (12) 0.0191 (11) 0.0029 (12)
N32 0.0421 (12) 0.0536 (13) 0.0643 (13) 0.0055 (11) 0.0176 (10) 0.0002 (11)
C33 0.0424 (16) 0.077 (2) 0.078 (2) 0.0063 (15) 0.0156 (14) −0.0024 (17)
C34 0.0540 (17) 0.093 (3) 0.0694 (19) −0.0226 (18) 0.0199 (15) −0.0098 (18)
C35 0.076 (2) 0.0546 (17) 0.0557 (16) −0.0227 (16) 0.0219 (15) −0.0059 (14)
C36 0.0592 (17) 0.0457 (16) 0.0567 (15) 0.0011 (13) 0.0207 (13) 0.0039 (13)
O10 0.1205 (17) 0.0512 (12) 0.0618 (12) 0.0213 (12) 0.0346 (12) 0.0043 (10)
O20 0.0978 (15) 0.0595 (12) 0.0769 (13) 0.0172 (11) 0.0444 (11) 0.0199 (11)

Geometric parameters (Å, º)

N1—C10 1.478 (3) C20—C21 1.504 (3)
N1—C30 1.480 (3) C20—H20A 0.9700
N1—C2 1.480 (3) C20—H20B 0.9700
C2—C3 1.503 (3) C21—C26 1.379 (3)
C2—H2A 0.9700 C21—C22 1.388 (4)
C2—H2B 0.9700 C22—O20 1.367 (3)
C3—C4 1.503 (3) C22—C23 1.387 (4)
C3—H3A 0.9700 C23—C24 1.376 (4)
C3—H3B 0.9700 C23—H23 0.9300
C4—N5 1.468 (3) C24—C25 1.372 (4)
C4—H4A 0.9700 C24—H24 0.9300
C4—H4B 0.9700 C25—C26 1.376 (4)
N5—C30 1.472 (3) C25—H25 0.9300
N5—C20 1.483 (3) C26—H26 0.9300
C10—C11 1.509 (3) C30—C31 1.515 (3)
C10—H10A 0.9700 C30—H30 0.9800
C10—H10B 0.9700 C31—N32 1.332 (3)
C11—C16 1.386 (3) C31—C36 1.382 (3)
C11—C12 1.388 (4) N32—C33 1.336 (3)
C12—O10 1.360 (3) C33—C34 1.359 (4)
C12—C13 1.388 (4) C33—H33 0.9300
C13—C14 1.366 (4) C34—C35 1.372 (4)
C13—H13 0.9300 C34—H34 0.9300
C14—C15 1.368 (4) C35—C36 1.367 (3)
C14—H14 0.9300 C35—H35 0.9300
C15—C16 1.388 (4) C36—H36 0.9300
C15—H15 0.9300 O10—H10 1.0163
C16—H16 0.9300 O20—H20 1.0857
C10—N1—C30 110.60 (17) N5—C20—C21 112.13 (19)
C10—N1—C2 109.68 (18) N5—C20—H20A 109.2
C30—N1—C2 111.63 (18) C21—C20—H20A 109.2
N1—C2—C3 110.3 (2) N5—C20—H20B 109.2
N1—C2—H2A 109.6 C21—C20—H20B 109.2
C3—C2—H2A 109.6 H20A—C20—H20B 107.9
N1—C2—H2B 109.6 C26—C21—C22 118.3 (2)
C3—C2—H2B 109.6 C26—C21—C20 120.1 (2)
H2A—C2—H2B 108.1 C22—C21—C20 121.5 (2)
C4—C3—C2 109.6 (2) O20—C22—C23 118.1 (3)
C4—C3—H3A 109.8 O20—C22—C21 121.6 (2)
C2—C3—H3A 109.8 C23—C22—C21 120.3 (3)
C4—C3—H3B 109.8 C24—C23—C22 119.9 (3)
C2—C3—H3B 109.8 C24—C23—H23 120.0
H3A—C3—H3B 108.2 C22—C23—H23 120.0
N5—C4—C3 109.7 (2) C25—C24—C23 120.4 (3)
N5—C4—H4A 109.7 C25—C24—H24 119.8
C3—C4—H4A 109.7 C23—C24—H24 119.8
N5—C4—H4B 109.7 C24—C25—C26 119.2 (3)
C3—C4—H4B 109.7 C24—C25—H25 120.4
H4A—C4—H4B 108.2 C26—C25—H25 120.4
C4—N5—C30 111.11 (18) C25—C26—C21 121.8 (3)
C4—N5—C20 109.47 (18) C25—C26—H26 119.1
C30—N5—C20 111.56 (18) C21—C26—H26 119.1
N1—C10—C11 112.53 (19) N5—C30—N1 109.26 (17)
N1—C10—H10A 109.1 N5—C30—C31 109.79 (18)
C11—C10—H10A 109.1 N1—C30—C31 110.09 (18)
N1—C10—H10B 109.1 N5—C30—H30 109.2
C11—C10—H10B 109.1 N1—C30—H30 109.2
H10A—C10—H10B 107.8 C31—C30—H30 109.2
C16—C11—C12 117.9 (2) N32—C31—C36 122.1 (2)
C16—C11—C10 121.1 (2) N32—C31—C30 116.2 (2)
C12—C11—C10 120.8 (2) C36—C31—C30 121.7 (2)
O10—C12—C13 117.6 (3) C31—N32—C33 117.1 (2)
O10—C12—C11 121.5 (2) N32—C33—C34 124.1 (3)
C13—C12—C11 120.9 (3) N32—C33—H33 118.0
C14—C13—C12 119.7 (3) C34—C33—H33 118.0
C14—C13—H13 120.1 C33—C34—C35 118.6 (3)
C12—C13—H13 120.1 C33—C34—H34 120.7
C13—C14—C15 120.7 (3) C35—C34—H34 120.7
C13—C14—H14 119.6 C36—C35—C34 118.4 (3)
C15—C14—H14 119.6 C36—C35—H35 120.8
C14—C15—C16 119.6 (3) C34—C35—H35 120.8
C14—C15—H15 120.2 C35—C36—C31 119.7 (3)
C16—C15—H15 120.2 C35—C36—H36 120.1
C11—C16—C15 121.1 (3) C31—C36—H36 120.1
C11—C16—H16 119.5 C12—O10—H10 105.3
C15—C16—H16 119.5 C22—O20—H20 104.9
C10—N1—C2—C3 179.7 (2) C20—C21—C22—C23 −177.2 (2)
C30—N1—C2—C3 56.7 (3) O20—C22—C23—C24 −179.8 (3)
N1—C2—C3—C4 −56.0 (3) C21—C22—C23—C24 0.8 (4)
C2—C3—C4—N5 57.8 (3) C22—C23—C24—C25 −0.4 (4)
C3—C4—N5—C30 −60.3 (3) C23—C24—C25—C26 −0.2 (4)
C3—C4—N5—C20 176.1 (2) C24—C25—C26—C21 0.5 (4)
C30—N1—C10—C11 −167.62 (19) C22—C21—C26—C25 −0.1 (4)
C2—N1—C10—C11 68.8 (2) C20—C21—C26—C25 176.6 (2)
N1—C10—C11—C16 −148.2 (2) C4—N5—C30—N1 59.5 (2)
N1—C10—C11—C12 36.9 (3) C20—N5—C30—N1 −178.04 (17)
C16—C11—C12—O10 −179.3 (2) C4—N5—C30—C31 −179.67 (19)
C10—C11—C12—O10 −4.3 (4) C20—N5—C30—C31 −57.2 (2)
C16—C11—C12—C13 1.5 (4) C10—N1—C30—N5 179.92 (18)
C10—C11—C12—C13 176.6 (2) C2—N1—C30—N5 −57.7 (2)
O10—C12—C13—C14 178.5 (2) C10—N1—C30—C31 59.3 (2)
C11—C12—C13—C14 −2.3 (4) C2—N1—C30—C31 −178.30 (19)
C12—C13—C14—C15 1.8 (4) N5—C30—C31—N32 111.9 (2)
C13—C14—C15—C16 −0.6 (4) N1—C30—C31—N32 −127.7 (2)
C12—C11—C16—C15 −0.3 (4) N5—C30—C31—C36 −67.7 (3)
C10—C11—C16—C15 −175.4 (2) N1—C30—C31—C36 52.7 (3)
C14—C15—C16—C11 −0.1 (4) C36—C31—N32—C33 0.3 (4)
C4—N5—C20—C21 −64.3 (3) C30—C31—N32—C33 −179.3 (2)
C30—N5—C20—C21 172.29 (19) C31—N32—C33—C34 −1.4 (4)
N5—C20—C21—C26 141.8 (2) N32—C33—C34—C35 1.4 (5)
N5—C20—C21—C22 −41.6 (3) C33—C34—C35—C36 −0.2 (4)
C26—C21—C22—O20 −179.9 (2) C34—C35—C36—C31 −0.7 (4)
C20—C21—C22—O20 3.4 (4) N32—C31—C36—C35 0.7 (4)
C26—C21—C22—C23 −0.5 (4) C30—C31—C36—C35 −179.7 (2)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O10—H10···N1 1.02 1.69 2.624 (3) 150
O20—H20···N5 1.09 1.72 2.705 (3) 148

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LR2078).

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812035477/lr2078sup1.cif

e-68-o2744-sup1.cif (28KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812035477/lr2078Isup2.hkl

e-68-o2744-Isup2.hkl (172.7KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812035477/lr2078Isup3.mol

Supplementary material file. DOI: 10.1107/S1600536812035477/lr2078Isup4.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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