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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 12| December 2010| Page o3258
https://doi.org/10.1107/S1600536810047707

(2R,4R)-1-(tert-But­­oxy­carbon­yl)-4-meth­­oxy­pyrrolidine-2-carb­­oxy­lic acid

Jing Yuan,a Zhi-Qiang Cai,a Chang-Jiang Huanga* and Wei-Ren Xua,b

aTianjin Key Laboratory of Molecular Drug Design and Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, People's Republic of China, and bSchool of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China
*Correspondence e-mail: czq0601@gmail.com

(Received 26 October 2010; accepted 17 November 2010; online 20 November 2010)

In the title compound, C11H19NO5, the five-membered pyrrolidine ring adopts an envelope conformation. The dihedral angles between the carboxyl group plane, the pyrrolidine ring and the meth­oxy group are 59.50 (3) and 62.02 (1)°, respectively. In the crystal, inter­molecular O—H⋯O hydrogen bonds link the mol­ecules into chains along [100]. The absolute configuration is assigned in accord with that of (2R,4R)-1-(tert-but­oxy­carbon­yl)-4-hy­droxy­pyrrolidine-2-carb­oxy­lic acid, which was the starting material in the synthesis.

Related literature

The title compound is an inter­mediate in the preparation of the direct FXa inhibitor, eribaxaban {systematic name: (2R,4R)-N1-(4-chlorophenyl)-N2-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-4-methoxypyrrolidine-1,2-dicarboxamide}. For background to the bioactivity and applications of eribaxaban, see: Perzborn (2009[Perzborn, E. (2009). Hamostaseologie, 29, 260-267.]); Kohrt et al. (2007[Kohrt, J. T., et al. (2007). Chem. Biol. Drug Des. 17, 100-112.]). For the synthesis of other derivatives with proline, see: Van Huis et al. (2009[Van Huis, C. A., et al. (2009). Bioorg. Med. Chem. 17, 2501-2511.]); Bigge et al. (2003[Bigge, C. F., et al. (2003). Patent WO 03045912A1. ]).

[Scheme 1]

Experimental

Crystal data

  • C11H19NO5

  • Mr = 245.27

  • Monoclinic, P 21

  • a = 6.4299 (13) Å

  • b = 9.784 (2) Å

  • c = 10.279 (2) Å

  • β = 90.12 (3)°

  • V = 646.7 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 293 K

  • 0.26 × 0.20 × 0.10 mm
Data collection

  • Rigaku Saturn CCD area-detector diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005)[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA.] Tmin = 0.975, Tmax = 0.990

  • 7923 measured reflections

  • 1601 independent reflections

  • 1059 reflections with I > 2σ(I)

  • Rint = 0.059
Refinement

  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.086

  • S = 0.94

  • 1601 reflections

  • 163 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.13 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O3—H3⋯O4i 1.00 (3) 1.68 (4) 2.672 (2) 169 (4)
Symmetry code: (i) x+1, y, z.

Data collection: CrystalClear (Rigaku, 2005)[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]; cell refinement: CrystalClear[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]; data reduction: CrystalClear[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536810047707/kp2285sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810047707/kp2285Isup2.hkl

checkCIF report


Comment top

Eribaxaban is a direct FXa inhibitors and has a high affinity for human FXa. Clinical data with eribaxaban in the prevention of VTE in TKR patients have recently been presented (Perzborn, 2009; Kohrt et al., 2007).

The title compound (Fig. 1), (2R,4R)-1-(tert-butoxycarbonyl)-4-methoxypyrrolidine-2-carboxylic acid is important intermediate in the preparation of Eribaxaban. Some derivatives of Eribaxaban have been reported with high affinity for human FXa (Van Huis et al., 2009; Bigge et al., 2003). Herein, the synthesis and the crystal structure of the title compound are reported; the absolute configuration is assigned by the use of (2R,4R)-1-(tert-butoxycarbonyl)-4- hydroxypyrrolidine-2-carboxylic acid as the starting material for the synthesis.

The pyrrolidine ring of the title compound adopts an envelope conformation with the C3 lying out of the plane. The dihedral angles between the carboxyl group plane, pyrrolidine ring and methoxy system are 120.50 (3)° and 117.98 (1)°, respectively. In the crystal structure, intermolecular O—H···O interactions contribute to the stabilization of the packing. Each molecule is a donor and acceptor for 2 hydrogen bonds (TAble 1).

Related literature top

The title compound is an intermediate in the preparation of the direct FXa inhibitor, e,ribaxaban. For background to the bioactivity and applications of eribaxaban, see: Perzborn (2009); Kohrt et al. (2007). For the synthesis of other derivatives with proline, see: Van Huis et al. (2009); Bigge et al. (2003).

Experimental top

CH3I (22 g, 0.155 mol) and 60%(w/w)NaH (15 g, 0.625 mol) were dissolved in THF(300 ml), and the resulting mixture was cooled to 273 K in an ice bath. (R,R)-4-Hydroxy-pyrrolidine-1,2-dicarboxylic acid, 1-tert-butyl ester(35 g, 0.151 mol)was then added in portions while maintaining a reaction temperature of 278 K or less. The reaction was allowed to warm to 293 K overnight. To the reaction mixture was added H2O (100 ml), 1 N HCl(100 ml) and NaCl(42 g). The layers were separated, and the organic layer was dried over MgSO4, filtered and concentrated to the white solid (37 g). Colourless single crystals suitable for X-ray diffraction were obtained by recrystallisation from methanol.

Refinement top

All H atoms were geometrically positioned (C—H 0.93–0.98 Å) and treated as riding, with Uiso(H) = 1.2Ueq(C).

Structure description top

Eribaxaban is a direct FXa inhibitors and has a high affinity for human FXa. Clinical data with eribaxaban in the prevention of VTE in TKR patients have recently been presented (Perzborn, 2009; Kohrt et al., 2007).

The title compound (Fig. 1), (2R,4R)-1-(tert-butoxycarbonyl)-4-methoxypyrrolidine-2-carboxylic acid is important intermediate in the preparation of Eribaxaban. Some derivatives of Eribaxaban have been reported with high affinity for human FXa (Van Huis et al., 2009; Bigge et al., 2003). Herein, the synthesis and the crystal structure of the title compound are reported; the absolute configuration is assigned by the use of (2R,4R)-1-(tert-butoxycarbonyl)-4- hydroxypyrrolidine-2-carboxylic acid as the starting material for the synthesis.

The pyrrolidine ring of the title compound adopts an envelope conformation with the C3 lying out of the plane. The dihedral angles between the carboxyl group plane, pyrrolidine ring and methoxy system are 120.50 (3)° and 117.98 (1)°, respectively. In the crystal structure, intermolecular O—H···O interactions contribute to the stabilization of the packing. Each molecule is a donor and acceptor for 2 hydrogen bonds (TAble 1).

The title compound is an intermediate in the preparation of the direct FXa inhibitor, e,ribaxaban. For background to the bioactivity and applications of eribaxaban, see: Perzborn (2009); Kohrt et al. (2007). For the synthesis of other derivatives with proline, see: Van Huis et al. (2009); Bigge et al. (2003).

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The structure of C11H19NO5 with all non-H atom-labelling scheme and ellipsoids drawn at the 50% probability level.
(2R,4R)-1-(tert-Butoxycarbonyl)-4-methoxypyrrolidine-2- carboxylic acid top
Crystal data top
C11H19NO5F(000) = 264
Mr = 245.27Dx = 1.260 Mg m−3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P2ybCell parameters from 1953 reflections
a = 6.4299 (13) Åθ = 3.2–27.8°
b = 9.784 (2) ŵ = 0.10 mm−1
c = 10.279 (2) ÅT = 293 K
β = 90.12 (3)°Prism, colorless
V = 646.7 (2) Å30.26 × 0.20 × 0.10 mm
Z = 2
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		1601 independent reflections
Radiation source: rotating anode1059 reflections with I > 2σ(I)
Confocal monochromatorRint = 0.059
ω and φ scansθmax = 27.7°, θmin = 3.2°
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		h = −8→8
Tmin = 0.975, Tmax = 0.990k = −12→12
7923 measured reflectionsl = −13→13
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.086 w = 1/[σ2(Fo2) + (0.0494P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.94(Δ/σ)max < 0.001
1601 reflectionsΔρmax = 0.13 e Å−3
163 parametersΔρmin = −0.16 e Å−3
1 restraintExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.55 (4)
Crystal data top
C11H19NO5V = 646.7 (2) Å3
Mr = 245.27Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.4299 (13) ŵ = 0.10 mm−1
b = 9.784 (2) ÅT = 293 K
c = 10.279 (2) Å0.26 × 0.20 × 0.10 mm
β = 90.12 (3)°
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		1601 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		1059 reflections with I > 2σ(I)
Tmin = 0.975, Tmax = 0.990Rint = 0.059
7923 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0371 restraint
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 0.94Δρmax = 0.13 e Å−3
1601 reflectionsΔρmin = −0.16 e Å−3
163 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.9616 (2)0.74085 (17)0.56702 (14)0.0482 (4)
O21.2349 (3)0.63017 (18)0.30520 (17)0.0550 (5)
O31.1022 (3)0.83878 (17)0.27707 (17)0.0505 (5)
H31.253 (5)0.861 (4)0.262 (3)0.093 (11)*
O40.4931 (2)0.92660 (17)0.24970 (16)0.0472 (5)
O50.6949 (2)0.80182 (16)0.10995 (13)0.0462 (5)
N10.7106 (2)0.7625 (2)0.32240 (16)0.0387 (4)
C11.0873 (3)0.7059 (2)0.2972 (2)0.0383 (5)
C20.8634 (3)0.6534 (2)0.3036 (2)0.0375 (5)
H20.83040.60190.22440.045*
C30.8259 (4)0.5636 (2)0.4235 (2)0.0490 (6)
H3A0.70870.50270.41030.059*
H3B0.94820.50990.44480.059*
C40.7804 (4)0.6680 (2)0.5283 (2)0.0461 (6)
H40.70920.62690.60280.055*
C50.6428 (3)0.7725 (3)0.45841 (19)0.0454 (6)
H5A0.49680.74930.46700.054*
H5B0.66540.86380.49240.054*
C61.1031 (4)0.6610 (3)0.6413 (2)0.0632 (8)
H6A1.02890.61350.70840.095*
H6B1.20570.71970.68010.095*
H6C1.17060.59600.58560.095*
C70.6240 (3)0.8376 (2)0.2284 (2)0.0381 (5)
C80.6706 (4)0.8926 (2)−0.0042 (2)0.0463 (6)
C90.7760 (5)1.0273 (3)0.0251 (3)0.0712 (9)
H9A0.70981.06970.09830.107*
H9B0.76501.0863−0.04930.107*
H9C0.92001.01150.04470.107*
C100.7858 (5)0.8146 (4)−0.1077 (2)0.0734 (9)
H10A0.92560.7975−0.07910.110*
H10B0.78840.8672−0.18650.110*
H10C0.71670.7291−0.12350.110*
C110.4450 (5)0.9100 (4)−0.0410 (3)0.0750 (9)
H11A0.37650.8229−0.03820.113*
H11B0.43560.9469−0.12740.113*
H11C0.37940.97140.01910.113*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0579 (10)0.0464 (10)0.0402 (8)−0.0032 (8)−0.0090 (7)0.0051 (7)
O20.0423 (9)0.0491 (10)0.0735 (11)0.0155 (9)−0.0065 (7)−0.0084 (8)
O30.0326 (9)0.0405 (10)0.0783 (12)0.0026 (8)0.0053 (7)0.0105 (9)
O40.0349 (9)0.0452 (10)0.0614 (10)0.0048 (8)0.0058 (7)0.0067 (7)
O50.0514 (9)0.0497 (10)0.0374 (9)0.0110 (8)−0.0016 (6)0.0051 (7)
N10.0300 (9)0.0469 (11)0.0393 (10)0.0032 (9)0.0017 (7)0.0045 (8)
C10.0368 (13)0.0415 (13)0.0364 (11)0.0045 (10)−0.0013 (9)−0.0039 (9)
C20.0378 (11)0.0365 (12)0.0384 (11)−0.0004 (10)−0.0062 (8)−0.0033 (9)
C30.0561 (16)0.0360 (13)0.0548 (14)−0.0073 (11)−0.0064 (11)0.0074 (10)
C40.0509 (14)0.0451 (15)0.0424 (12)−0.0089 (11)0.0027 (10)0.0084 (10)
C50.0411 (12)0.0557 (15)0.0393 (12)−0.0021 (12)0.0076 (9)0.0029 (11)
C60.0698 (17)0.073 (2)0.0469 (15)0.0031 (16)−0.0158 (12)0.0085 (13)
C70.0270 (10)0.0422 (13)0.0451 (12)−0.0051 (10)0.0012 (9)0.0042 (10)
C80.0563 (15)0.0457 (14)0.0367 (12)−0.0018 (11)−0.0070 (10)0.0064 (9)
C90.100 (2)0.0617 (19)0.0519 (16)−0.0284 (18)0.0041 (15)0.0033 (13)
C100.103 (2)0.076 (2)0.0412 (14)0.0196 (19)0.0010 (14)0.0007 (14)
C110.072 (2)0.076 (2)0.078 (2)0.0082 (17)−0.0301 (15)0.0039 (16)
Geometric parameters (Å, º) top
O1—C61.421 (3)C4—H40.9800
O1—C41.422 (3)C5—H5A0.9700
O2—C11.206 (3)C5—H5B0.9700
O3—C11.320 (3)C6—H6A0.9600
O3—H31.00 (3)C6—H6B0.9600
O4—C71.231 (3)C6—H6C0.9600
O5—C71.347 (3)C8—C101.506 (3)
O5—C81.480 (3)C8—C111.508 (4)
N1—C71.335 (3)C8—C91.512 (4)
N1—C21.464 (3)C9—H9A0.9600
N1—C51.469 (3)C9—H9B0.9600
C1—C21.530 (3)C9—H9C0.9600
C2—C31.533 (3)C10—H10A0.9600
C2—H20.9800C10—H10B0.9600
C3—C41.513 (3)C10—H10C0.9600
C3—H3A0.9700C11—H11A0.9600
C3—H3B0.9700C11—H11B0.9600
C4—C51.530 (3)C11—H11C0.9600
C6—O1—C4113.5 (2)O1—C6—H6A109.5
C1—O3—H3108 (2)O1—C6—H6B109.5
C7—O5—C8121.67 (18)H6A—C6—H6B109.5
C7—N1—C2125.79 (17)O1—C6—H6C109.5
C7—N1—C5121.89 (19)H6A—C6—H6C109.5
C2—N1—C5112.03 (17)H6B—C6—H6C109.5
O2—C1—O3123.9 (2)O4—C7—N1123.01 (19)
O2—C1—C2122.1 (2)O4—C7—O5125.3 (2)
O3—C1—C2113.93 (19)N1—C7—O5111.70 (19)
N1—C2—C1113.13 (18)O5—C8—C10101.8 (2)
N1—C2—C3101.81 (17)O5—C8—C11111.5 (2)
C1—C2—C3112.11 (17)C10—C8—C11110.7 (2)
N1—C2—H2109.8O5—C8—C9108.62 (19)
C1—C2—H2109.8C10—C8—C9111.2 (2)
C3—C2—H2109.8C11—C8—C9112.5 (2)
C4—C3—C2102.49 (18)C8—C9—H9A109.5
C4—C3—H3A111.3C8—C9—H9B109.5
C2—C3—H3A111.3H9A—C9—H9B109.5
C4—C3—H3B111.3C8—C9—H9C109.5
C2—C3—H3B111.3H9A—C9—H9C109.5
H3A—C3—H3B109.2H9B—C9—H9C109.5
O1—C4—C3112.24 (19)C8—C10—H10A109.5
O1—C4—C5105.62 (19)C8—C10—H10B109.5
C3—C4—C5103.28 (17)H10A—C10—H10B109.5
O1—C4—H4111.7C8—C10—H10C109.5
C3—C4—H4111.7H10A—C10—H10C109.5
C5—C4—H4111.7H10B—C10—H10C109.5
N1—C5—C4103.27 (19)C8—C11—H11A109.5
N1—C5—H5A111.1C8—C11—H11B109.5
C4—C5—H5A111.1H11A—C11—H11B109.5
N1—C5—H5B111.1C8—C11—H11C109.5
C4—C5—H5B111.1H11A—C11—H11C109.5
H5A—C5—H5B109.1H11B—C11—H11C109.5
C7—N1—C2—C185.8 (2)C7—N1—C5—C4179.02 (19)
C5—N1—C2—C1−100.3 (2)C2—N1—C5—C44.8 (2)
C7—N1—C2—C3−153.7 (2)O1—C4—C5—N189.6 (2)
C5—N1—C2—C320.2 (2)C3—C4—C5—N1−28.4 (2)
O2—C1—C2—N1166.64 (19)C2—N1—C7—O4178.7 (2)
O3—C1—C2—N1−16.0 (2)C5—N1—C7—O45.3 (3)
O2—C1—C2—C352.2 (3)C2—N1—C7—O5−0.3 (3)
O3—C1—C2—C3−130.4 (2)C5—N1—C7—O5−173.6 (2)
N1—C2—C3—C4−37.2 (2)C8—O5—C7—O418.7 (3)
C1—C2—C3—C484.0 (2)C8—O5—C7—N1−162.41 (18)
C6—O1—C4—C3−71.9 (2)C7—O5—C8—C10175.9 (2)
C6—O1—C4—C5176.29 (19)C7—O5—C8—C11−65.9 (3)
C2—C3—C4—O1−72.3 (2)C7—O5—C8—C958.5 (3)
C2—C3—C4—C540.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O4i1.00 (3)1.68 (4)2.672 (2)169 (4)
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC11H19NO5
Mr245.27
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)6.4299 (13), 9.784 (2), 10.279 (2)
β (°) 90.12 (3)
V (Å3)646.7 (2)
Z2
Radiation typeMo Kα
µ (mm−1)0.10
Crystal size (mm)0.26 × 0.20 × 0.10
Data collection
DiffractometerRigaku Saturn CCD area-detector
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2005)
Tmin, Tmax0.975, 0.990
No. of measured, independent and
observed [I > 2σ(I)] reflections		7923, 1601, 1059
Rint0.059
(sin θ/λ)max (Å−1)0.655
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.086, 0.94
No. of reflections1601
No. of parameters163
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.13, −0.16

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O4i1.00 (3)1.68 (4)2.672 (2)169 (4)
Symmetry code: (i) x+1, y, z.
 

Acknowledgements

The authors thank the State Key Laboratory of Elemento-organic Chemistry, Nankai University, for the data collection.

References

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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 66| Part 12| December 2010| Page o3258
https://doi.org/10.1107/S1600536810047707
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