Home Physical Sciences Crystal structure of ethyl 4-methyl-2-oxo-5-phenyl-1,3,4-oxadiazinane-3-carboxylate, C13H16N2O4
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Crystal structure of ethyl 4-methyl-2-oxo-5-phenyl-1,3,4-oxadiazinane-3-carboxylate, C13H16N2O4

  • Ignez Caracelli EMAIL logo , Julio Zukerman-Schpector , Alessandro Rodrigues , Elisângela Vinhato , Paulo R. Olivato and Edward R.T. Tiekink ORCID logo EMAIL logo
Published/Copyright: September 1, 2020

Abstract

C13H16N2O4, orthorhombic, P212121 (no. 19), a = 6.7876(2) Å, b = 8.8984(2) Å, c = 22.3399(6) Å, V = 1349.30(6) Å3, Z = 4, Rgt(F) = 0.0384, wRref(F2) = 0.0947, T = 293(2) K.

CCDC no.: 2023861

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colourless irregular prism
Size:0.25 × 0.22 × 0.19 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.10 mm−1
Diffractometer, scan mode:KappaCCD,
θmax, completeness:27.5°, 99%
N(hkl)measured, N(hkl)unique, Rint:7907, 2859, 0.036
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2591
N(param)refined:174
Programs:COLLECT [1], DENZO/SCALEPACK [2], SIR2014 [3], SHELX [4], WinGX/ORTEP [5]
Table 2:

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

AtomxyzUiso*/Ueq
O10.2121(2)−0.21849(18)0.54715(6)0.0556(4)
O2−0.0033(2)−0.3109(2)0.61126(8)0.0658(5)
O3−0.0178(3)−0.0858(2)0.69632(8)0.0713(5)
O40.2812(3)−0.0568(2)0.73833(7)0.0721(5)
N10.4574(2)−0.16094(18)0.63936(7)0.0419(4)
N20.2488(2)−0.15464(19)0.64480(7)0.0429(4)
C10.1373(3)−0.2332(3)0.60243(9)0.0457(5)
C20.3457(3)−0.0930(3)0.53941(10)0.0532(5)
H2A0.2784860.0000340.5492230.064*
H2B0.387762−0.0875460.4979730.064*
C30.5224(3)−0.1118(2)0.57931(9)0.0421(4)
H30.605280−0.1912880.5623340.051*
C40.5267(4)−0.3114(3)0.65494(12)0.0655(7)
H4A0.484998−0.3357720.6948430.098*
H4B0.667895−0.3141870.6528620.098*
H4C0.472633−0.3831320.6273570.098*
C50.1766(3)−0.0954(2)0.69848(9)0.0479(5)
C6−0.1167(5)−0.0279(4)0.74953(13)0.0842(9)
H6A−0.0262660.0354290.7717290.101*
H6B−0.2279890.0333870.7374460.101*
C7−0.1852(5)−0.1481(4)0.78787(13)0.0824(9)
H7A−0.273814−0.2115390.7658980.124*
H7B−0.252629−0.1061710.8217680.124*
H7C−0.074707−0.2061850.8013960.124*
C80.6421(3)0.0319(2)0.58057(9)0.0414(4)
C90.6038(4)0.1439(2)0.62178(10)0.0536(5)
H90.5055630.1300850.6502610.064*
C100.7106(4)0.2765(3)0.62104(12)0.0659(7)
H100.6840850.3511460.6490330.079*
C110.8555(4)0.2977(3)0.57900(12)0.0666(7)
H110.9275310.3866370.5787580.080*
C120.8945(4)0.1882(3)0.53726(13)0.0653(7)
H120.9919340.2032060.5085990.078*
C130.7879(3)0.0552(2)0.53812(11)0.0521(5)
H130.814443−0.0190430.5099470.063*

Source of material

The title compound (I) was prepared by the carboxylation reaction of (5R)-4-methyl-5-phenyl-1,3,4-oxadiazinan-2-one (II) which was prepared as described in [6]. A solution of BuLi (2.00 M in hexane, 1.45 mL, 2.86 mmol) was added drop-wise to a solution of (II) (500 mg, 2.60 mmol) in dry THF (10 mL) at 195 K. The reaction was stirred for an additional 15 min. An ethyl chloroformate (272 μL, 2.86 mmol) solution in THF (1 mL) was added slowly to the reaction mixture. After 15 min, the light-yellow solution was warmed to RT for a further 30 min. The reaction was quenched with saturated aqueous ammonium chloride solution (5 mL). The mixture was then concentrated under reduced pressure, taken up in water (5 mL) and extracted with CH2Cl2 (3 × 15 mL) then dried (MgSO4). Evaporation of the solvent in vacuo gave the crude product which was purified by flash column chromatography on silica gel with 40% EtOAc in hexane to give the pure product as a white solid (446 mg, 65%). Colourless crystals of (I) were obtained by vapour diffusion from hexane/acetone at 298 K. M. pt.: 394–396 K. [α]D25: + 28.7° (c. 1.07, CHCl3). Anal. calcd. for C13H16N2O4: C, 59.08, H, 6.10, N, 10.60%. Found: C, 58.94, H, 6.01, N, 10.65%. 1H NMR (500 MHz, CDCl3/TMS): δ (p.p.m.): 7.41–7.32 (m, 5H), 4.72 (dd, 2J = 11.4 Hz, 3J = 5.8 Hz, 1H), 4.45 (dd, 2J = 11.4 Hz, 3J = 9.2 Hz, 2H), 4.38–4.28 (m, 2H), 2.82 (s, 3H), 1.33 (t, 3J = 7.1 Hz, 3H). 13C NMR (125 MHz, CDCl3/TMS): δ (p.p.m.): 152.17, 149.74, 135.96, 128.95, 128.51, 126.90, 68.49, 63.63, 63.58, 43.93, 14.24.

Experimental details

The C-bound H atoms were geometrically placed (C—H = 0.93–0.98 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The absolute structure was not determined in the X-ray experiment but, the assignment of stereochemistry at the C3 centre, i.e. R, is based on the chirality of the synthetic precursor employed in the synthesis.

Comment

1,3,4-Oxadiazin-2-one molecules related to the title compound, (I), first attracted interest as stimulants for the central nervous system [7]. Subsequently, there has been interest in employing these molecules as chiral auxiliaries in organic synthesis [8], [9]. Over and above these considerations, these molecules exhibit interesting conformational flexibility [10]. In continuation of previous structural studies on related 1,3,4-oxadiazin-2-ones [11], [12], herein, the crystal and molecular structures of (I) are described.

The molecular structure of (I) is shown in the figure (25% displacement ellipsoids) and is constructed about a 1,3,4-oxadiazin-2-one core. To a first approximation, the six-membered ring has a boat conformation with the N2 and C2 atoms lying out of and to the same side of the plane through the four remaining atoms. In this description, the N1-methyl group occupies an axial position, the N2-bound ethyloxycarbonyl is bisectional as is the C3-phenyl group and, finally, the C2-carbonyl group occupies an equatorial position. Globally, the carbonyl groups are directed to opposite sides of the molecule, and the N-bound methyl group is orientated to the opposite side of the ring to the ethyloxycarbonyl and phenyl substituents. The sum of the angles subtended at the N1 atom amounts to 334° indicating a pyramidal geometry but, that about N2 is planar, with the sum of angles being 359°.

There are crystal structures for two literature precedents for (I) that differ only in the nature of the C(=O)R group [11], [12]. The structures confirm the conformational variability in the six-membered ring [10], so the derivative with R = CH2OPh [11] has a distorted twisted-boat conformation and that with R = CH2Cl has a distorted half-chair conformation [12].

In the molecular packing, methyl-C—H⋯O(carboxylate-carbonyl) [C4—H4b⋯O2i: H4b⋯O2i = 2.42 Å, C4⋯O2i = 3.336(3) Å with angle at H4b = 160° for symmetry operation (i) 1 + x, y, z] interactions link molecules into linear, supramolecular chains along the a-axis. Chains are connected into double-chains via phenyl-C—H⋯π(phenyl) [C12—H12⋯Cg(C8–C13)ii: H12⋯Cg(C8–C13)ii = 2.88 Å with angle at H12 = 164° for (ii) 1/2 + x, 1/2 − y, 1 − z] interactions. The double-chains assemble in the crystal without directional interactions between them. Accordingly, in order to probe further the molecular packing, the Hirshfeld surfaces and of the full and delineated two-dimensional fingerprint plots were calculated using Crystal Explorer 17 [13] and literature methods [14].

Consistent with the above description, H⋯H contacts contribute 54.1% to the overall surface. The fingerprint plot delineated into H⋯O/O⋯H contacts exhibits the characteristic spikes due to the C—H⋯O contact and overall contributes 29.2% of all contacts. The next most significant contributions are from H⋯C/C⋯H contacts [13.0%] followed by O⋯C/C⋯O contacts [2.4%].

Acknowledgements

The Brazilian agencies Coordination for the Improvement of Higher Education Personnel, CAPES, Finance Code 001, the National Council for Scientific and Technological Development (CNPq) are acknowledged for grants (312210/2019–1, 433957/2018–2 and 406273/2015–4) to IC and for a fellowship (303207/2017–5) to JZS and São Paulo Research Foundation (FAPESP) 2003/05520-0 to AR. Sunway University Sdn Bhd is thanked for financial support of this work through Grant No. STR-RCTR-RCCM-001–2019.

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Received: 2020-07-17
Accepted: 2020-08-18
Published Online: 2020-09-01
Published in Print: 2020-10-27

©2020 Ignez Caracelli et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  59. Crystal structure of O-hexyl benzoylcarbamothioate, C14H19NO2S
  60. Crystal structure of chlorido-(O-methyl phenylcarbamothioamide-κS)-bis(triphenylphosphane-κP)silver(I), C44H39AgClNOP2S
  61. Crystal structure of chlorido-(O-ethyl phenylcarbamothioamide-κS)-bis(triphenylphosphane-κP)-silver(I), C45H41AgClNOP2S
  62. Crystal structure of 4-[(2-methoxyphenyl)carbamoyl]butanoic acid, C12H15NO4
  63. Crystal structure of ethyl 4-methyl-2-oxo-5-phenyl-1,3,4-oxadiazinane-3-carboxylate, C13H16N2O4
  64. Crystal structure of catena-poly[diaqua(μ2-2-(hydroxymethyl)-1H-imidazole-4,5-dicarboxylato)cadmium(II)], C6H8CdN2O7
  65. Crystal structure of (1S)-N-(chloromethyl)-1-((4S,6aR,8aS, 8bR,9aR)-4-methoxy-6a,8a-dimethyl-1,3,4, 5,6,6a,6b,7,8,8a,9a,10,10a,10b-tetradecahydro-8bH-naphtho[2′,1′:4,5] indeno[1,2-b]oxiren-8b-yl)-N-methylethan-1-amine, C24H46ClNO5
  66. Crystal structure of 4-[(3,5-dichlorophenyl)carbamoyl]butanoic acid, C11H11Cl2NO3
  67. Crystal structure of (2Z)-2-amino-3-[(E)-[(2,4-dihydroxyphenyl)methylidene]-amino]but-2-enedinitrile, C11H8N4O2
  68. Crystal structure of 3-methyl-1-[(E)-(4-phenylbutan-2-ylidene)amino]thiourea, C12H17N3S
  69. Crystal structure of carbonyl{hydridotris[3-phenyl-5-methylpyrazol-1-yl]borato-κ3N,N′N′′}copper(I), C31H28BCuN6O
  70. Crystal structure of ethane-1,2-diylbis(diphenylphosphine oxide) – dihydrogenperoxide (1/2), C26H28O6P2
  71. Crystal structure of 2-(pyridin-2-ylamino)pyridinium chloride dibenzyldichlorostannane, [C10H10N3]Cl, C14H14Cl2Sn
  72. Crystal structure of 4-[(3-methoxyphenyl)carbamoyl]butanoic acid, C12H15NO4
  73. Crystal structure of dichlorido-bis(tri-4-tolylphosphane oxide-κO)-di(4-chlorophenyl-κC)tin(IV), C54H50Cl4O2P2Sn
  74. Crystal structure of dichloridodimethylbis(tri-4-tolylphosphane oxide-κO)-tin(IV), C44H48Cl2O2P2Sn
  75. Crystal structure of chlorido(2-methylquinolin-8-olato-κ2N,O)-bis(4-tolyl-κC)tin(IV), C24H22ClNOSn
  76. Crystal structure of (E)-dichloro(1-chloro-3-methoxyprop-1-en-2-yl)(4-methoxyphenyl)-λ4-tellane, C11H13Cl3O2Te
  77. Crystal structure of bis{N-methyl-N′-[3-(4-methoxyphenyl)-1-methylpropane-1-ylidene]carbamohydrazonothioato}zinc(II), C26H36N6O2S2Zn
  78. Crystal structure of (2-carboxy-4-(3-carboxy-5-carboxylatophenoxy)benzoato-κ2O,O′)bis(1,10-phenantroline-κ2N,N′)cobalt(II), C40H24N4O9Co
  79. The crystal structure of (3S,8R,10R,14R)-17-((2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4,4,8,10,14-pentamethyl-12-oxohexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H52O5
  80. Crystal structure of (μ2-1,1′-bis(diphenylphosphino)ferrocene-κ2P,P′)-bis[(Z)N-(3-fluorophenyl)-O-methylthiocarbamato-S]digold(I) chloroform solvate, C50H42Au2F2FeN2O2P2S2, CHCl3
  81. Crystal structure of poly[bis(μ2-1,4-di(1H-imidazol-1-yl)benzene-κ2N:N′)-(μ2-tetraoxidomolybdato(VI)-κ2O:O′)cobalt(II)], C24H20N8O4MoCo
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