Home Crystal structure of tert-butyl (1S,2R,5R)-2-(hydroxymethyl)-4-(4-methoxyphenyl)-6-oxa-3-azabicyclo[3.1.0]hexane-3-carboxylate, C17H23NO5
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Crystal structure of tert-butyl (1S,2R,5R)-2-(hydroxymethyl)-4-(4-methoxyphenyl)-6-oxa-3-azabicyclo[3.1.0]hexane-3-carboxylate, C17H23NO5

  • Ignez Caracelli EMAIL logo , Julio Zukerman-Schpector , Ariel L. Llanes Garcia , Carlos Roque D. Correia and Edward R.T. Tiekink ORCID logo EMAIL logo
Published/Copyright: August 12, 2020

Abstract

C17H23NO5, monoclinic, P21 (no. 4), a = 6.0479(9) Å, b = 9.7032(10) Å, c = 14.711(2) Å, β = 94.174(9)°, V = 861.0(2) Å3, Z = 2, Rgt(F) = 0.0440, wRref(F2) = 0.1436, T = 293(2) K.

CCDC no.: 2020522

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
Size:0.13 × 0.11 × 0.08 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.09 mm−1
Diffractometer, scan mode:Enraf Nonius TurboCAD4, ω
θmax, completeness:28.0°, >99%
N(hkl)measured, N(hkl)unique:2373, 2177
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 959
N(param)refined:215
Programs:CAD4 [1], [2], SIR2014 [3], SHELX [4], WinGX/ORTEP [5]
Table 2:

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

AtomxyzUiso*/Ueq
O11.0955(5)0.6239(4)0.0462(2)0.0737(10)
O20.5436(4)0.6809(3)0.26247(18)0.0562(8)
O30.8850(4)0.7300(3)0.32798(15)0.0470(7)
O41.0024(6)1.3511(4)0.2627(3)0.0834(11)
O50.5175(6)0.4999(4)0.0060(3)0.0825(11)
H5O0.386(4)0.520(9)−0.005(5)0.124*
N10.8400(5)0.7118(4)0.1783(2)0.0453(8)
C11.0518(6)0.7865(4)0.1710(3)0.0454(9)
H11.1706840.7422740.2093060.055*
C21.0881(7)0.7658(5)0.0721(3)0.0617(12)
H21.1742200.8337750.0402940.074*
C30.8958(7)0.7032(6)0.0251(3)0.0631(13)
H30.8521730.728652−0.0381200.076*
C40.7210(7)0.6772(5)0.0911(2)0.0525(11)
H40.5959570.7403860.0786680.063*
C50.7387(6)0.7058(4)0.2575(2)0.0430(9)
C60.8162(7)0.7445(5)0.4208(2)0.0542(11)
C70.6751(11)0.8712(7)0.4258(4)0.098(2)
H7A0.7480150.9476570.3994070.147*
H7B0.6526110.8911780.4884130.147*
H7C0.5343390.8556840.3929150.147*
C80.6988(11)0.6165(7)0.4494(4)0.095(2)
H8A0.5545850.6117990.4176770.142*
H8B0.6835960.6193600.5139130.142*
H8C0.7833200.5367370.4349550.142*
C91.0359(8)0.7616(8)0.4745(3)0.0879(19)
H9A1.1234760.6799900.4685950.132*
H9B1.0119150.7763310.5375460.132*
H9C1.1126380.8394140.4515700.132*
C101.0365(7)0.9373(4)0.1948(3)0.0455(10)
C110.8468(7)1.0142(5)0.1799(3)0.0547(11)
H110.7190070.9719680.1542780.066*
C120.8402(8)1.1503(5)0.2015(3)0.0634(13)
H120.7095711.1998200.1896660.076*
C131.0254(7)1.2152(5)0.2406(3)0.0545(11)
C141.2181(8)1.1414(6)0.2567(3)0.0659(13)
H141.3453161.1838530.2826060.079*
C151.2205(7)1.0023(5)0.2336(3)0.0566(11)
H151.3508080.9522740.2448590.068*
C161.1937(11)1.4287(6)0.2830(5)0.0895(18)
H16A1.2779341.3884200.3341690.134*
H16B1.1533921.5212800.2977490.134*
H16C1.2815661.4297010.2312590.134*
C170.6391(8)0.5282(5)0.0889(3)0.0656(13)
H17A0.7648690.4662110.0963640.079*
H17B0.5462650.5128170.1389700.079*

Source of material

A 77% solution of m-chloroperbenzoic acid (CPBA; 3.67 g, 16.374 mmol) was dissolved in CH2Cl2 (30 mL). The water contained in the CPBA solution was separated with the aid of a separation funnel. The organic phase was added over a solution of tert-butyl (2S,5S)-2-(hydroxymethyl)-5-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-1-carboxylate (1.0 g, 3.275 mmol) in CH2Cl2 (10 mL), containing anhydrous NaHCO3 (1.65 g, 19.648 mmol) as a buffer. The suspension was stirred for 24 h at room temperature. The reaction was stopped by adding a saturated NaHSO3 (15 mL) solution and the mixture was extracted with EtOAc. The phases were separated and the organic phase was washed with saturated NaHCO3 solution (2 × 15 mL) and NaCl (15 mL). The organic phase was dried with anhydrous Na2SO4, filtered and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel, using an EtOAc/n-hexane elution gradient (1:2, 1:1 and 2:1). The title epoxide (I) was obtained as a white solid in 73% yield (765 mg), with a diastereoselectivity of 100% [6]. M.pt: 380–382 K. Crystals of (I) were obtained by slow evaporation of its CHCl3 solution. The 1H and 13C NMR spectra reflect the presence of conformational rotamers in solution. 1H NMR (300 MHz, CDCl3 r.t.): δ = 7.08 (d, J = 8.8 Hz, 2H); 6.88 (d, J = 8.8 Hz, 2H); 4.91 (s, 1H); 4.20 (dt, J = 6.6 and 2.2 Hz, 1H); 4.08 (dd, J = 12.4 and 2.2 Hz, 1H); 3.96 (dd, J = 12.4 and 6.6 Hz, 1H); 3.84 (m, 1H); 3.83–3.77 (overlapped signal, 1H); 3.80 (s, 3H); 3.43 (d, J = 2.9 Hz, 1H); 1.40 (s, 0.5H); 1.18 (s, 8.5H). 13C{1H} NMR (75 MHz, CDCl3 , r.t.): δ = 159.2; 156.3; 130.9; 127.6 ; 114.0; 80.9; 64.1; 63.7; 62.6; 58.1; 57.6; 55.2; 28.2; 28.0. HRMS Calc for C17H23NO5: 321.15762; found 321.15708.

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 O-bound H atom was refined with O—H = 0.82 ± 0.01 Å, and with 1.5Ueq(O). The absolute structure was not determined in the X-ray experiment but, the assignment of stereochemistry at the four chiral centres is based on the chirality of the synthetic precursor employed in the synthesis.

Comment

The title β-epoxypyrrolidine derivative, (I), is a key precursor for the formation of a salt, 3′-deoxy-radicamine-A hydrochloride [6]. In [6], compound (I) was prepared by the epoxidation reaction of tert-butyl (2S)-2-(hydroxymethyl)-5-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-1-carboxylate with m-chloroperbenzoicacid (CPBA). Subsequently, the opening of (I) in a dioxane/water/H2SO4 mixture (3:2:0.2), at reflux temperature, was totally regioselective. After purification using Dowex-H+, followed by treatment with a 2.5N HCl solution, the desired 3′-deoxy-radicamine-A hydrochloride was obtained in 80% yield. This product is a crucial precursor for the preparation of the (natural product) pyrrolidine alkaloids Radicamines A and B [7] which are of interest as inhibitors of α-glucosidase. The inhibition of α-glucosidase is key for the treatment of type 2 diabetes mellitus but, also for other disease such as cancer [8]. Herein, the crystal and molecular structures of precursor (I) are described.

The molecular structure of (I) is illustrated in the figure (25% displacement ellipsoids) and is constructed about a β-epoxypyrrolidine core. The conformation of the five-membered ring is an envelope with the N1 atom being the flap atom. The r.m.s. deviation of the four constituent carbon atoms is 0.003 Å and the N1 atom lies 0.195(6) Å out of the plane. The dihedral angle between the least-squares plane of the four carbon atoms and the plane through the epoxy ring is 74.4(3)°. The N1 is bound by a tert-butyloxycarbonyl group with the N1—C5—O2—C6 torsion angle of 173.3(3)° indicative of a co-planar system. A close to trigonal geometry about the N1 atom is indicated by the sum of the angles subtended at the N1 atom of 358.2°. The five-membered ring is penta-substituted with the C1 and C4 atoms flanking the N1 atom bearing 4-methoxyphenyl and hydroxymethyl substituents, respectively. The configurations at the C1–C4 atoms are R, R, S and R.

There is a single literature precedent for (I) which was described only recently [9]. Here, the difference arises as the N1-bound group is ethyloxycarbonyl and the hydroxymethyl group of (I) is no longer present. The five-membered ring is an envelope, as in (I), and the dihedral angle between the rings comprising the β-epoxypyrrolidine core is 78.53(10)° [9].

In the crystal, a linear supramolecular chain along the a-axis is formed through hydroxyl-O—H⋯O(epoxy) hydrogen bonding [O5—H5o⋯O1i: H5o⋯O1i = 2.21(5) Å, O5⋯O1i = 2.921(5) Å with angle at H5o = 145(7)° for symmetry operation (i): −1 + x, y, z]. The chains thus formed, are connected into a supramolecular layer in the ab-plane by methylene-C—H⋯O(carbonyl, hydroxyl) interactions [C1—H1⋯O2ii: H1⋯O2ii = 2.41 Å, C1⋯O2ii = 3.335(5) Å with angle at H1 = 158° and C2—H2⋯O5iii: H2⋯O5iii = 2.59 Å, C2⋯O5iii = 3.545(6) Å with angle at H2 = 164° for (ii) 1 + x, y, z and (iii) 2 − x, 1/2 + y, −z]. The layers inter-digitate along the c-axis direction so the tert-butyl groups are off-set and occupy the space in the inter-layer region.

Further insight into the molecular packing was accomplished by calculating the Hirshfeld surface as well as the full and decomposed two-dimensional fingerprint plots using Crystal Explorer 17 [10] and literature procedures [11]. The most distinctive feature of the overall fingerprint plot were sharp spikes ascribed to the O—H⋯O hydrogen bonding. Indeed, H⋯O/O⋯H contacts contributed 22.4% to the overall surface but, by far, the major contributions come from H⋯H contacts at 70.9%, the large number reflecting to a great extent the occupancy of the inter-layer region by tert-butyl groups. The only other significant contribution to the surface comes from H⋯C/C⋯H contacts at 5.9%.

Acknowledgements

The Brazilian agencies Coordination for the Improvement of Higher Education Personnel, CAPES, Finance Code 001 and 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. Sunway University Sdn Bhd is thanked for financial support of this work through Grant No. STR-RCTR-RCCM-001–2019.

References

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Received: 2020-07-09
Accepted: 2020-08-02
Published Online: 2020-08-12
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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  53. Crystal structure of (μ2-1,1′-bis(diphenylphosphino)hexane-κ2P,P′)-bis[(Z)-N-(3-fluorophenyl)-O-methylthiocarbamato-κS]digold(I), C46H46Au2F2N2O2P2S2
  54. Crystal structure of tetrakis (N-(2-hydroxyethyl)-N-isopropylcarbamodithioato-κS,S′)-(μ2(2-(pyridin-4-yl)vinyl)pyridine-κN,N′)dicadmium(II), C36H58Cd2N6O4S8
  55. Crystal structure of 4-(2-(benzo[b]thiophen-2-yl)-3,3,4,4,5,5-hexafluorocyclopent-1-en-1-yl)-1,5-dimethyl-1H-pyrrole-2-carbonitrile, C20H12F6N2S
  56. Crystal structure of bis(octahydrocyclopenta[c]pyrrolium)pentachlorobismuthate(III), (C7NH14)2BiCl5
  57. The crystal structure of diaqua-tris(nitrato-κ2O,O′)-bis(4,4,5,5-tetramethyl-2-(p-pyridyl)imidazoline-1-oxyl 3-oxide-κN)samarium(III), C24H36N9O15Sm
  58. Synthesis and crystal structure of methyl 2-(2-((tert-butoxycarbonyl)amino)phenyl)-2-(4-oxo-4H-chromen-3-yl)acetate, C23H23NO6
  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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