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The mol­ecule of activated carbamate, (S)-2,5-dioxopyrrolidin-1-yl N-[2-(tert-butoxy­carbonyl­amino)­propyl]­carbamate, tBuOCONHCH(Me)CH2NHCOONC4H4O2 or C13H21N3O6, pre­pared from N-Boc-β3HAla-OH, assumes a folded conformation with the N—C—C—N torsion angle equal to 55.9 (3)°. Both N—H groups are involved in intermolecular hydrogen bonds, forming infinite chains in the crystal.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801002410/ya6006sup1.cif
Contains datablocks I, carbamate

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536801002410/ya6006Isup2.hkl
Contains datablock I

CCDC reference: 159850

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.037
  • wR factor = 0.097
  • Data-to-parameter ratio = 8.7

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
ABSMU_01 Alert C The ratio of given/expected absorption coefficient lies outside the range 0.99 <> 1.01 Calculated value of mu = 0.101 Value of mu given = 0.100 PLAT_353 Alert C Long N-H Bond (0.87A) N(1) - H(1) = 1.01 Ang. PLAT_353 Alert C Long N-H Bond (0.87A) N(2) - H(2) = 1.02 Ang. General Notes
REFLT_03 From the CIF: _diffrn_reflns_theta_max 26.30 From the CIF: _reflns_number_total 1792 Count of symmetry unique reflns 1799 Completeness (_total/calc) 99.61% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
3 Alert Level C = Please check

Comment top

Unnatural biopolymers with a urea backbone, such as N,N-linked oligoureas [N(CONHR)-(CH2)m–]n (Nowick, 1999), N,N'-linked oligoureas [NH-CHR-CH2—NH—CO–]n (Burgess et al., 1995, 1997; Kim et al., 1996; Boeijen & Liskamp, 1999; Guichard et al. 1999, 2000; Tamilarasu et al., 1999), ureidopeptoids [NR—CH2—CH2—NH—CO–]n (Kruijtzer et al., 1997; Wilson & Nowick, 1998) and oligomeric cyclic ureas (Kim et al., 1996) have been described recently as peptide backbone mimetics or as template for the creation of artificial β-sheets. The urea fragment appears particularly promising for drug discovery because of its expected metabolic stability and interesting hydrogen-bonding properties. We have recently reported a simple and effective synthesis of O-succinimidyl 2-(tert-butoxycarbonylamino)-2-subsituted-ethylcarbamate derivatives starting from the corresponding N-protected β-amino acids and their use as activated monomers in the synthesis of di- and trisubstituted ureas and N,N'-linked oligoureas (Guichard et al., 1999). These derivatives are stable compounds that react readily with amines to form substituted ureas. Furthermore, the mild conditions required for their preparation are compatible with most functionalized side chains of amino acids as well as with standard protecting groups used in solid-phase peptide synthesis (Guichard et al., 2000). Herein, we report the crystal structure of (S)—O-succinimidyl N-[2-(tert-butoxycarbonylamino)propyl]carbamate, (I), which was prepared in three steps from Boc-(S)-β3HAla-OH.

Bond distances and angles of the succinimide ring are in good agreement with those recently published by Tenon et al. (2000) and Guichard et al. (1999) for N-methylsuccinimide and O-succinimidyl (2-nitrophenyl)carbamate, respectively. The succinimide ring in (I) is nearly planar, like in the unsubstituted succinimide (Mason, 1961) and O-succinimidyl (2-nitrophenyl)carbamate (Guichard et al., 1999) molecules. Indeed, the puckering parameters of the succinimide ring in the title compound are q = 0.010 Å and ϕ2 = 314.0° for the sequence N3—C10—C11—C12—C13 (Cremer & Pople, 1975).

The molecule (Fig. 1 and Table 1) assumes a folded shape with the gauche conformation about the central C6—C8 bond in the main chain, the N1—C6—C8—N2 torsion angle being equal to 55.9 (3)°. The molecules of the title compound in the crystal are linked into the infinite chains via CO···H—N hydrogen bonds (Table 2). The chains are stretched along the [100] direction and form parallel β sheet-like arrangement. All interactions between the chains are purely van der Waals in nature.

Experimental top

O-succinimidyl carbamate was prepared by homologation of Boc-L-Ala-OH, with subsequent conversion of Boc-(S)-β3HAla-OH [we used the nomenclature proposed by Seebach & Matthews (1997) for β-amino acids] to the corresponding acyl azide and trapping of the intermediate isocyanate, resulting from Curtius rearrangement of the acyl azide, with N-hydroxysuccinimide. Details of the synthetic procedures are available in the CIF file.

Refinement top

The absolute stereochemistry of the title compound is based on the known configuration of Boc-L-Ala-OH (purchased from Neosystem, Strasbourg, France) since the homologation using the Arndt-Eistert reaction is known to proceed without epimerization at the α carbon. The positions of H atoms attached to N atoms were located from a difference map and the N—H bond distance was restrained to 1.03 (1) Å (Taylor & Kennard, 1983). The H atoms connected to carbon were placed in the calculated positions and included in the refinement in the riding model approximation (C—H distances are in the range 0.96–0.98 Å). The isotropic H-atom displacement parameters were restricted to be 30% higher than the equivalent isotropic displacement parameters of the parent atom.

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: COLLECT; data reduction: HKL (Otwinoski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: maXus (Mackay et al., 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with the atom-numbering scheme and 25% probability displacement ellipsoids. Only H atoms at N atoms and at the chiral center are shown.
[Figure 2] Fig. 2. Packing of the molecules showing the infinite chains and the hydrogen-bonding network (in dashed lines).
(S)—O-Succinimidyl N-[2-(tert-butoxycarbonylamino)propyl]carbamate top
Crystal data top
C13H21N3O6F(000) = 336
Mr = 315.33Dx = 1.273 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71070 Å
a = 5.1260 (2) ÅCell parameters from 5236 reflections
b = 8.5650 (4) Åθ = 4.0–26.3°
c = 18.7540 (9) ŵ = 0.10 mm1
β = 91.996 (3)°T = 293 K
V = 822.88 (6) Å3Prismatic, colorless
Z = 20.3 × 0.25 × 0.22 mm
Data collection top
KappaCCD
diffractometer
1436 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.030
Graphite monochromatorθmax = 26.3°, θmin = 4.0°
oscillation scansh = 06
5236 measured reflectionsk = 010
1792 independent reflectionsl = 2323
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.097H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0553P)2 + 0.0391P]
where P = (Fo2 + 2Fc2)/3
1792 reflections(Δ/σ)max < 0.001
205 parametersΔρmax = 0.11 e Å3
3 restraintsΔρmin = 0.17 e Å3
Crystal data top
C13H21N3O6V = 822.88 (6) Å3
Mr = 315.33Z = 2
Monoclinic, P21Mo Kα radiation
a = 5.1260 (2) ŵ = 0.10 mm1
b = 8.5650 (4) ÅT = 293 K
c = 18.7540 (9) Å0.3 × 0.25 × 0.22 mm
β = 91.996 (3)°
Data collection top
KappaCCD
diffractometer
1436 reflections with I > 2σ(I)
5236 measured reflectionsRint = 0.030
1792 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0373 restraints
wR(F2) = 0.097H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.11 e Å3
1792 reflectionsΔρmin = 0.17 e Å3
205 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
C10.2288 (4)0.3268 (3)0.57925 (13)0.0505 (6)
C20.0629 (5)0.4397 (4)0.53911 (19)0.0799 (10)
H2A0.02750.38470.50280.104*
H2B0.06170.48790.57160.104*
H2C0.17230.51860.51730.104*
C30.4126 (5)0.2386 (4)0.52903 (14)0.0640 (7)
H3A0.31430.18700.49330.083*
H3B0.53340.31030.50650.083*
H3C0.50710.16240.55540.083*
C40.3705 (6)0.4101 (4)0.63710 (17)0.0717 (8)
H4A0.24700.46590.66710.093*
H4B0.46120.33520.66520.093*
H4C0.49370.48230.61590.093*
O10.0307 (3)0.2195 (2)0.61109 (9)0.0533 (5)
C50.0988 (4)0.1042 (3)0.65552 (13)0.0464 (6)
O20.3204 (3)0.0650 (3)0.66664 (11)0.0680 (6)
N10.1146 (3)0.0388 (3)0.68556 (11)0.0497 (5)
H10.283 (3)0.081 (4)0.6670 (12)0.065*
C60.1006 (4)0.0925 (3)0.73422 (12)0.0487 (6)
H60.07390.09460.75390.063*
C70.1472 (7)0.2466 (4)0.69701 (19)0.0802 (10)
H7A0.01710.26110.65960.104*
H7B0.13690.33030.73080.104*
H7C0.31730.24590.67710.104*
C80.3002 (4)0.0704 (3)0.79532 (12)0.0484 (6)
H8A0.28440.15520.82920.063*
H8B0.47450.07410.77680.063*
N20.2643 (3)0.0775 (3)0.83175 (11)0.0507 (5)
H20.081 (3)0.121 (4)0.8364 (13)0.066*
C90.4632 (5)0.1632 (3)0.85544 (13)0.0507 (6)
O30.6921 (3)0.1383 (3)0.85408 (11)0.0694 (6)
O40.3633 (3)0.2988 (2)0.88774 (10)0.0644 (5)
N30.5616 (4)0.3975 (3)0.91066 (11)0.0584 (6)
C100.6574 (6)0.5138 (4)0.86724 (16)0.0653 (8)
O50.5707 (6)0.5414 (4)0.80823 (12)0.1015 (8)
C110.8740 (5)0.5889 (4)0.90923 (16)0.0725 (8)
H11A0.83810.69900.91610.094*
H11B1.03680.57890.88480.094*
C120.8908 (5)0.5049 (4)0.98018 (15)0.0709 (9)
H12A1.06200.45830.98790.092*
H12B0.86010.57691.01890.092*
C130.6842 (5)0.3813 (4)0.97655 (15)0.0606 (7)
O60.6276 (4)0.2834 (3)1.01994 (12)0.0886 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0311 (10)0.0514 (14)0.0686 (15)0.0023 (10)0.0046 (10)0.0046 (13)
C20.0481 (14)0.079 (2)0.112 (2)0.0056 (15)0.0033 (14)0.042 (2)
C30.0483 (13)0.0763 (19)0.0667 (17)0.0101 (14)0.0066 (11)0.0067 (16)
C40.0622 (16)0.0658 (18)0.087 (2)0.0080 (15)0.0030 (14)0.0172 (18)
O10.0290 (7)0.0590 (11)0.0718 (11)0.0008 (7)0.0004 (7)0.0189 (10)
C50.0313 (12)0.0510 (15)0.0566 (13)0.0035 (10)0.0002 (9)0.0027 (12)
O20.0287 (8)0.0807 (14)0.0947 (13)0.0057 (9)0.0038 (8)0.0272 (12)
N10.0289 (8)0.0587 (13)0.0614 (12)0.0017 (9)0.0021 (8)0.0118 (11)
C60.0411 (11)0.0487 (14)0.0564 (13)0.0054 (11)0.0004 (10)0.0034 (13)
C70.103 (2)0.0571 (19)0.079 (2)0.0039 (17)0.0194 (17)0.0078 (17)
C80.0413 (11)0.0508 (15)0.0531 (13)0.0011 (11)0.0014 (9)0.0025 (12)
N20.0334 (10)0.0598 (14)0.0589 (12)0.0016 (9)0.0003 (8)0.0079 (11)
C90.0413 (13)0.0609 (17)0.0498 (13)0.0011 (12)0.0015 (10)0.0048 (12)
O30.0344 (9)0.0810 (14)0.0929 (14)0.0008 (9)0.0027 (8)0.0244 (12)
O40.0463 (9)0.0648 (13)0.0819 (12)0.0027 (9)0.0021 (8)0.0224 (11)
N30.0545 (12)0.0590 (14)0.0613 (13)0.0045 (11)0.0046 (10)0.0099 (12)
C100.0690 (17)0.0602 (19)0.0667 (18)0.0091 (15)0.0035 (13)0.0066 (16)
O50.130 (2)0.099 (2)0.0745 (14)0.0048 (16)0.0167 (14)0.0116 (15)
C110.0668 (17)0.065 (2)0.086 (2)0.0044 (15)0.0131 (14)0.0089 (18)
C120.0575 (15)0.091 (2)0.0638 (17)0.0073 (16)0.0008 (12)0.0215 (18)
C130.0527 (14)0.072 (2)0.0568 (15)0.0036 (14)0.0036 (12)0.0066 (16)
O60.0862 (14)0.108 (2)0.0720 (14)0.0075 (14)0.0033 (11)0.0133 (15)
Geometric parameters (Å, º) top
C1—O11.479 (3)C7—H7B0.9600
C1—C41.507 (4)C7—H7C0.9600
C1—C21.507 (4)C8—N21.454 (3)
C1—C31.511 (3)C8—H8A0.9700
C2—H2A0.9600C8—H8B0.9700
C2—H2B0.9600N2—C91.321 (3)
C2—H2C0.9600N2—H21.016 (10)
C3—H3A0.9600C9—O31.194 (3)
C3—H3B0.9600C9—O41.415 (3)
C3—H3C0.9600O4—N31.379 (3)
C4—H4A0.9600N3—C131.374 (3)
C4—H4B0.9600N3—C101.387 (4)
C4—H4C0.9600C10—O51.202 (4)
O1—C51.346 (3)C10—C111.486 (4)
C5—O21.210 (3)C11—C121.513 (4)
C5—N11.336 (3)C11—H11A0.9700
N1—C61.451 (3)C11—H11B0.9700
N1—H11.010 (10)C12—C131.498 (4)
C6—C71.516 (4)C12—H12A0.9700
C6—C81.521 (3)C12—H12B0.9700
C6—H60.9800C13—O61.210 (4)
C7—H7A0.9600
O1—C1—C4110.2 (2)H7A—C7—H7B109.5
O1—C1—C2102.08 (17)C6—C7—H7C109.5
C4—C1—C2110.5 (3)H7A—C7—H7C109.5
O1—C1—C3110.2 (2)H7B—C7—H7C109.5
C4—C1—C3112.3 (2)N2—C8—C6111.7 (2)
C2—C1—C3111.1 (2)N2—C8—H8A109.3
C1—C2—H2A109.5C6—C8—H8A109.3
C1—C2—H2B109.5N2—C8—H8B109.3
H2A—C2—H2B109.5C6—C8—H8B109.3
C1—C2—H2C109.5H8A—C8—H8B107.9
H2A—C2—H2C109.5C9—N2—C8122.2 (2)
H2B—C2—H2C109.5C9—N2—H2118.2 (17)
C1—C3—H3A109.5C8—N2—H2119.5 (17)
C1—C3—H3B109.5O3—C9—N2129.9 (2)
H3A—C3—H3B109.5O3—C9—O4121.8 (2)
C1—C3—H3C109.5N2—C9—O4108.29 (19)
H3A—C3—H3C109.5N3—O4—C9111.27 (17)
H3B—C3—H3C109.5C13—N3—O4121.8 (2)
C1—C4—H4A109.5C13—N3—C10116.2 (2)
C1—C4—H4B109.5O4—N3—C10121.9 (2)
H4A—C4—H4B109.5O5—C10—N3123.7 (3)
C1—C4—H4C109.5O5—C10—C11130.4 (3)
H4A—C4—H4C109.5N3—C10—C11105.9 (2)
H4B—C4—H4C109.5C10—C11—C12106.2 (3)
C5—O1—C1121.10 (16)C10—C11—H11A110.5
O2—C5—N1124.8 (2)C12—C11—H11A110.5
O2—C5—O1125.1 (2)C10—C11—H11B110.5
N1—C5—O1110.03 (17)C12—C11—H11B110.5
C5—N1—C6122.14 (18)H11A—C11—H11B108.7
C5—N1—H1113.6 (17)C13—C12—C11106.1 (2)
C6—N1—H1123.9 (17)C13—C12—H12A110.5
N1—C6—C7111.9 (2)C11—C12—H12A110.5
N1—C6—C8109.31 (19)C13—C12—H12B110.5
C7—C6—C8110.0 (2)C11—C12—H12B110.5
N1—C6—H6108.5H12A—C12—H12B108.7
C7—C6—H6108.5O6—C13—N3124.2 (3)
C8—C6—H6108.5O6—C13—C12130.1 (3)
C6—C7—H7A109.5N3—C13—C12105.7 (3)
C6—C7—H7B109.5
O1—C5—N1—C6177.9 (2)O3—C9—O4—N34.7 (3)
C5—N1—C6—C8139.7 (2)C9—O4—N3—C1386.4 (3)
N1—C6—C8—N255.9 (3)C13—N3—C10—O5179.8 (3)
C6—C8—N2—C9141.7 (2)O4—N3—C10—O52.8 (4)
C8—N2—C9—O4179.76 (19)C13—N3—C10—C110.6 (3)
N2—C9—O4—N3177.1 (2)O4—N3—C10—C11177.5 (2)
C9—O4—N3—C1090.4 (3)O5—C10—C11—C12179.4 (3)
C4—C1—O1—C558.6 (3)N3—C10—C11—C120.2 (3)
C2—C1—O1—C5176.0 (2)C10—C11—C12—C130.8 (3)
C3—C1—O1—C565.8 (3)O4—N3—C13—O61.5 (4)
C1—O1—C5—O29.5 (4)C10—N3—C13—O6178.4 (3)
C1—O1—C5—N1170.7 (2)O4—N3—C13—C12178.0 (2)
O2—C5—N1—C61.9 (4)C10—N3—C13—C121.1 (3)
C5—N1—C6—C798.2 (3)C11—C12—C13—O6178.3 (3)
C7—C6—C8—N2179.2 (2)C11—C12—C13—N31.1 (3)
C8—N2—C9—O32.2 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i1.01 (1)2.04 (2)2.938 (2)147 (2)
N2—H2···O3ii1.02 (1)2.04 (1)3.022 (3)162 (3)
Symmetry codes: (i) x+1, y, z; (ii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC13H21N3O6
Mr315.33
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)5.1260 (2), 8.5650 (4), 18.7540 (9)
β (°) 91.996 (3)
V3)822.88 (6)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.3 × 0.25 × 0.22
Data collection
DiffractometerKappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5236, 1792, 1436
Rint0.030
(sin θ/λ)max1)0.623
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.097, 1.03
No. of reflections1792
No. of parameters205
No. of restraints3
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.11, 0.17

Computer programs: COLLECT (Nonius, 1998), COLLECT, HKL (Otwinoski & Minor, 1997), SIR92 (Altomare et al., 1994), SHELXL97 (Sheldrick, 1997), maXus (Mackay et al., 1999).

Selected torsion angles (º) top
O1—C5—N1—C6177.9 (2)C8—N2—C9—O4179.76 (19)
C5—N1—C6—C8139.7 (2)N2—C9—O4—N3177.1 (2)
N1—C6—C8—N255.9 (3)C9—O4—N3—C1090.4 (3)
C6—C8—N2—C9141.7 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i1.010 (10)2.037 (18)2.938 (2)147 (2)
N2—H2···O3ii1.016 (10)2.038 (14)3.022 (3)162 (3)
Symmetry codes: (i) x+1, y, z; (ii) x1, y, z.
 

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