1,3-Bis(3-tert-butyl-2-hy­droxy-5-meth­oxy­benz­yl)hexa­hydro­pyrimidin-5-ol monohydrate

Augusto Rivera; Ingrid Miranda-Carvajal; Héctor Jairo Osorio; Jaime Ríos-Motta; Michael Bolte

doi:10.1107/S1600536814010769

. 2014 May 21;70(Pt 6):o687–o688. doi: 10.1107/S1600536814010769

1,3-Bis(3-tert-butyl-2-hydroxy-5-methoxybenzyl)hexahydropyrimidin-5-ol monohydrate

Augusto Rivera ^a,^*, Ingrid Miranda-Carvajal ^a, Héctor Jairo Osorio ^b, Jaime Ríos-Motta ^a, Michael Bolte ^c

PMCID: PMC4051104 PMID: 24940265

Abstract

The asymmetric unit of the title compound, C₂₈H₄₂N₂O₅·H₂O, consists of one half of the organic molecule and one half-molecule of water, both of which are located on a mirror plane which passes through the central C atoms and the hydroxyl group of the heterocyclic system. The hydroxyl group at the central ring is disordered over two equally occupied positions. The six-membered ring adopts a chair conformation, and the 2-hydroxybenzyl substituents occupy the sterically preferred equatorial positions. The aromatic rings make dihedral angles of 75.57 (9)° with the mean plane of the heterocyclic ring. The dihedral angle between the two aromatic rings is 19.18 (10)°. The molecular structure features two intramolecular phenolic O—H⋯N hydrogen bonds with graph-set motif S(6). In the crystal, molecules are connected via O—H⋯O hydrogen bonds into zigzag chains running along the a-axis direction.

Related literature

For related structures, see: Rivera et al. (2012 ▶), Zhang et al. (2012 ▶). For the synthesis, see: Rivera et al. (2013 ▶). For bond-length data, see: Allen et al. (1987 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶). graphic file with name e-70-0o687-scheme1.jpg

Experimental

Crystal data

C₂₈H₄₂N₂O₅·H₂O
M _r = 504.65
Orthorhombic,
a = 8.2629 (5) Å
b = 33.093 (3) Å
c = 10.0877 (6) Å
V = 2758.4 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 173 K
0.25 × 0.23 × 0.16 mm

Data collection

STOE IPDS II two-circle-diffractometer
Absorption correction: multi-scan (X-AREA; Stoe & Cie, 2001 ▶) T _min = 0.975, T _max = 0.982
22328 measured reflections
2464 independent reflections
2228 reflections with I > 2σ(I)
R _int = 0.109

Refinement

R[F ² > 2σ(F ²)] = 0.075
wR(F ²) = 0.140
S = 1.17
2464 reflections
179 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Data collection: X-AREA (Stoe & Cie, 2001 ▶); cell refinement: X-AREA; data reduction: X-AREA (Stoe & Cie, 2001 ▶); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL2013.

Supplementary Material

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S1600536814010769/sj5401sup1.cif

e-70-0o687-sup1.cif^{(854.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814010769/sj5401Isup2.hkl

e-70-0o687-Isup2.hkl^{(135.6KB, hkl)}

Click here for additional data file.^{(10.4KB, cml)}

Supporting information file. DOI: 10.1107/S1600536814010769/sj5401Isup3.cml

CCDC reference: 1002201

Additional supporting information: crystallographic information; 3D view; checkCIF report

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1	0.94 (3)	1.80 (3)	2.671 (2)	153 (3)
O3—H3⋯O1W	0.89 (6)	1.93 (6)	2.813 (4)	174 (5)
O1W—H1W⋯O1ⁱ	0.84	2.19	3.029 (2)	173

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Symmetry code: (i) Inline graphic .

Acknowledgments

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work.

supplementary crystallographic information

1. Comment

Recently our group reported a protocol for the synthesis of a series of 2,2'-(dihydropyrimidine-1,3(2H,4H)-diyldimethanediyl)diphenols via a Mannich-type reaction (Rivera et al., 2013). As an extension of these studies, in this paper we describe the synthesis and crystal structure of the title compound, 1,3-bis(3-tert-butyl-2-hydroxy-5-methoxybenzyl)hexahydropyrimidin-5-ol, C₂₈H₄₂N₂O₅, as a monohydrate. The molecular structure and atom-numbering scheme for the title compound are shown in Fig. 1. The asymmetric unit contains one half-organic molecule and one half water molecule, which are both located on a mirror plane which passes through the central C atoms and the hydroxyl group of the heterocyclic system. In Fig. 1, atoms without labels were generated by the symmetry operator x, 1/2 - y, z. The 1,3-diazinane ring of the title compound adopts a chair conformation with a diequatorial substitution with puckering parameters Q, θ and φ of 0.594 (2) Å, 2.23 (19)°, 60 (4)° (Cremer & Pople, 1975). The aromatic rings make dihedral angles of 75.57 (9)° with the mean plane of the heterocyclic ring. The benzyl groups are located in a 1,3-diequatorial syn arrangement in the heterocyclic ring with a dihedral angle between the planes containing the aromatic rings of 19.18 (10)°. In the molecule of the title compound (Fig. 1), bond lengths (Allen et al., 1987) and angles are normal and comparable to those observed in related structures namely 4,4',6,6'-tetra-tert-butyl-2,2'- [1,3-diazinane-1,3-diylbis(methylene)]diphenol 0.25-hydrate (Zhang et al., 2012) and 6,6'-di-tert-butyl-4,4'-dimethoxy-2,2'- [1,3-diazinane-1,3-diylbis(methylene)]- diphenol 0.19-hydrate (Rivera et al., 2012). The crystal structure shows two intramolecular O—H···N(1,3-diazinane) hydrogen bonds with graph-set motif S(6) (Bernstein et al., 1995) (Table 1), where the N···O distance [N1···O1, 2.671 (2) Å] is shorter in comparison with the values observed in the related structure (Zhang et al. 2012). In contrast to the 4',6'-di-tert-butyl analog, the title compound was found to be more similar to the other related structure (Rivera et al., 2012), indicating that the methoxy substituent slightly influences the strength of the intermolecular hydrogen bonds in these compounds. In the crystal, hydroxyl groups of the 1,3-diazinane ring are linked to water molecules via O—H···O hydrogen bonds, leading to a two-molecule aggregate where the water-O accepts these interactions. These are linked into a zigzag chain along the a axis via O—H···O interactions between the water molecules and the phenolic-O atoms. (Fig. 2 and Table 1).

2. Experimental

The title compound was prepared as follows: In a 50 ml round bottom flask equipped with a magnetic stir bar, 1 equiv. of 1,3-diamino-2-propanol, 3 equiv. of paraformaldehyde, and 2 equiv. of 2-tert-butyl-4-methoxyphenol were combined with 15 ml of methanol. Upon completion of the addition, the reaction mixture was stirred under reflux for 36 h. Then the reflux was stopped, the solvent was removed on a rotary evaporator under vacuum and the residue obtained (Anal. calcd. for C₂₈H₄₂N₂O₅: C 69.14%; H 8.64%; N 5.76%, O 16.46% found C 69.50%; H 8.66%; N 5.77%) was recrystallized from methanol to provide high quality crystals of the title compound (Yield 30.6%. M.p. = 393 K).