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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3079.
Published online 2009 November 14. doi:  10.1107/S1600536809045498
PMCID: PMC2972050

Boc-AzAla-Ala-OMe

Abstract

The title compound (systematic name: tert-butyl 3-{[1-(methoxy­carbon­yl)eth­yl]amino­carbon­yl}-3-methyl­carbazate), C11H21N3O5, is a precursor for the study of a new class of foldamer based on aza/α-dipeptide oligomerization [Abbas et al. (2009 [triangle]). Tetra­hedron Lett. 50, 4158–4160]. The asymmetric unit consists of one mol­ecule in an extended conformation which is stabilized by inter­molecular N—H(...)O and C—H(...)O hydrogen bonding.

Related literature

For the synthesis, see: Majer & Randad (1994 [triangle]); Brosse et al. (2001 [triangle]); Bouillon et al. (2004 [triangle]); Abbas et al. (2009 [triangle]). For the geometry of the aza-residue in aza­peptides, see: Benatalah et al. (1991 [triangle]), André et al. (1996 [triangle]). For Boc-AzAla-Pro-NHiPr, see: André et al. (1997 [triangle]). For the refinement procedure, see: Flack & Schwarzenbach (1988 [triangle]). For hydrogen-bond motifs, see: Etter (1990 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3079-scheme1.jpg

Experimental

Crystal data

  • C11H21N3O5
  • M r = 275.31
  • Tetragonal, An external file that holds a picture, illustration, etc.
Object name is e-65-o3079-efi2.jpg
  • a = 9.3194 (4) Å
  • c = 17.4420 (8) Å
  • V = 1514.86 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 100 K
  • 0.3 × 0.2 × 0.2 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 14534 measured reflections
  • 1847 independent reflections
  • 1806 reflections with I > 2σ(I)
  • R int = 0.049

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.076
  • S = 1.12
  • 1847 reflections
  • 178 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.13 e Å−3

Data collection: COLLECT (Bruker, 2004 [triangle]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO (Otwinowski & Minor, 1997 [triangle]) and SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809045498/dn2501sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809045498/dn2501Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the National Research Agency (ANR) for financial support (No. NT05_4_42848). Support from Nancy Université for the X-ray measurements is gratefully acknowledged

supplementary crystallographic information

Comment

As part of our continuing studies on the synthesis and structure of hydrazino-and N-amino-peptides, we recently described the original and efficient synthesis of aza/α-dipeptides via Mitsunobu and trans-protections protocols starting from N-tert-butyloxycarbonylaminophtalimide (Abbas et al., 2009; Majer & Randad 1994; Brosse et al. 2001; Bouillon et al. 2004). Aza-peptides are pseudopeptides, in which nitrogen has been substituted for at least one of the CHα groups. Here we report the crystal structure of the pseudodipeptide Boc-AzAla-Ala-OMe (Fig. 1).

In the present study, the geometry of the aza-residue is similar to those observed for known azapeptides structures. In most of the cases, the α-nitrogen adopts a non-planar planar structure (André et al., 1996; Benatalah et al. 1991). In the title compound, the deviation of the α-nitrogen out of the plane, defined by the three atoms bonded to it, is 0.268 (2) Å. The greatest difference from standard peptide group concern the bond lengths and bond angles around the α-nitrogen: (i) the N—Nα (N1—N2) and Nα—Cβ (N2—C6) bonds are shorter by about 0.06Å than their homologous bonds in peptides; (ii) the Nα—C' ((N2—C7) bond of 1.392 (3)Å is shorter than the homologous Cα—C' bond and exceeds the dimension of the amide bond; (iii) the bond angles around the α-nitrogen are larger by 5–6° than the bond angles around the α-carbon.

In the solid state, Boc-AzAla-Pro-NHiPr (André et al., 1997) and the title compound Boc-AzAla-Ala-OMe adopt two distinct conformations with the Nα atoms having opposite configurations. In the former, the AzAla residue assumes the R chirality and the pseudodipeptide is folded by an intramolecular hydrogen bond between the (iPr)NH and the Boc(CO) groups. In the crystal of the title compound, the pseudodipeptides adopt an extended conformation which form infinite chains along the four fold axis. The N-H goups of AzaAla and Ala residues are engaged in intermolecular hydrogen bonds with the carbonyl groups of the N-terminal protecting group and the aza-residue, respectively, forming two C(4) chain motifs (Fig. 2, Etter 1990). Combination of these two motifs generates a new R22(12) pattern, shown in the Fig. 2. Finally, the third carbonyl group, C10=O4, is involved in weak CH···O hydrogen bonds forming a threedimensional network structure.

Experimental

The title compound was prepared from N-tert-butyloxycarbonylaminophtalimide (Abbas et al., 2009), and was crystallized by slow evaporation of a diethyl ether solution.

Refinement

Because of the lack of any significant anomalous dispersion effects, the absolute configurations of the title compound could not be determined from the diffraction experiments but was known from the method of synthesis. The origin was fixed by floating-origin restraints (Flack & Schwarzenbach, 1988). All H atoms were located in difference Fourier maps. The C/N-bonded H atoms were placed at calculated positions and refined using a riding model, with C—H distances of 0.96–0.98 Å and with N—H distance of 0.86 Å. The H-atom Uiso parameters were fixed at 1.2Ueq(C) for methine C—H, at 1.2Ueq(N) for the N—H group and at 1.5Ueq(C) for methyl C—H.

Figures

Fig. 1.
The molecular structure of the title compound showing the atom-numbering scheme. All non-H atoms are represented by 25% probability displacement ellipsoids.
Fig. 2.
Partial packing view of the title compound showing the formation of the C(4)C(4)[R22(12)] graph set motif paralell to [001]. H atoms not involved in hydrogen bondings have been omitted for clarity. H bonds are shown as dashed lines. [Symmetry code: (i) ...

Crystal data

C11H21N3O5Dx = 1.207 Mg m3
Mr = 275.31Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P41Cell parameters from 14534 reflections
Hall symbol: P 4wθ = 2.5–27.9°
a = 9.3194 (4) ŵ = 0.10 mm1
c = 17.4420 (8) ÅT = 100 K
V = 1514.86 (12) Å3Prism, colorless
Z = 40.3 × 0.2 × 0.2 mm
F(000) = 592

Data collection

Nonis KappaCCD diffractometerRint = 0.049
CCD rotation images, thick slices scansθmax = 27.8°, θmin = 2.5°
14534 measured reflectionsh = −12→12
1847 independent reflectionsk = −12→12
1806 reflections with I > 2σ(I)l = −22→22

Refinement

Refinement on F21 restraint
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.036w = 1/[σ2(Fo2) + (0.0164P)2 + 0.7016P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.076(Δ/σ)max < 0.001
S = 1.12Δρmax = 0.17 e Å3
1847 reflectionsΔρmin = −0.13 e Å3
178 parameters

Special details

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.

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

xyzUiso*/Ueq
C10.3488 (2)0.0563 (2)0.63461 (13)0.0228 (4)
C20.2822 (3)−0.0204 (3)0.56621 (14)0.0311 (5)
H2A0.19020.0210.55510.047*
H2B0.2706−0.12040.5780.047*
H2C0.3438−0.01030.52240.047*
C30.2529 (3)0.0415 (2)0.70463 (14)0.0279 (5)
H3A0.29950.08370.74820.042*
H3B0.235−0.05820.71450.042*
H3C0.16350.08980.69540.042*
C40.5016 (3)0.0058 (3)0.64752 (15)0.0308 (5)
H4A0.5570.0220.60190.046*
H4B0.5015−0.09480.65940.046*
H4C0.54310.05830.68940.046*
O10.35134 (16)0.20833 (15)0.60837 (9)0.0218 (3)
C50.3987 (2)0.3109 (2)0.65626 (12)0.0193 (4)
O20.43957 (17)0.29435 (17)0.72181 (9)0.0239 (3)
N10.39666 (19)0.44041 (18)0.61993 (11)0.0201 (4)
H10.37530.44640.57210.024*
N20.43006 (19)0.56280 (19)0.66214 (11)0.0200 (4)
C60.3156 (2)0.6117 (2)0.71325 (14)0.0259 (5)
H6A0.23040.630.68390.039*
H6B0.34510.69820.73860.039*
H6C0.29610.53890.75080.039*
C70.5716 (2)0.5760 (2)0.68660 (12)0.0189 (4)
O30.60321 (16)0.65021 (16)0.74280 (8)0.0221 (3)
N30.67193 (19)0.50835 (19)0.64451 (10)0.0209 (4)
H30.64870.46060.60420.025*
C80.8201 (2)0.5181 (2)0.66902 (13)0.0232 (4)
H80.82640.4780.72090.028*
C90.9146 (2)0.4274 (3)0.61671 (14)0.0296 (5)
H9A0.88530.32880.61980.044*
H9B1.01290.43580.63260.044*
H9C0.90520.46050.56480.044*
C100.8773 (2)0.6709 (3)0.67187 (13)0.0244 (4)
O40.97394 (18)0.7060 (2)0.71417 (11)0.0333 (4)
O50.81613 (16)0.75824 (17)0.62089 (9)0.0249 (3)
C110.8685 (3)0.9048 (3)0.62253 (16)0.0310 (5)
H11A0.84240.94870.67030.046*
H11B0.82670.95780.5810.046*
H11C0.9710.90480.61740.046*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0313 (11)0.0171 (9)0.0199 (10)−0.0034 (8)0.0039 (9)0.0017 (8)
C20.0429 (14)0.0269 (12)0.0236 (11)−0.0138 (10)0.0058 (10)−0.0039 (9)
C30.0345 (12)0.0232 (10)0.0261 (11)−0.0033 (9)0.0091 (10)−0.0012 (9)
C40.0339 (11)0.0269 (11)0.0317 (12)0.0044 (9)0.0059 (10)0.0039 (10)
O10.0288 (8)0.0190 (7)0.0178 (7)−0.0036 (6)−0.0026 (6)0.0000 (6)
C50.0183 (9)0.0217 (10)0.0180 (10)−0.0021 (7)0.0011 (8)−0.0017 (8)
O20.0304 (8)0.0240 (8)0.0172 (7)−0.0031 (6)−0.0033 (6)0.0007 (6)
N10.0251 (9)0.0199 (8)0.0155 (8)−0.0020 (7)−0.0033 (7)−0.0001 (7)
N20.0217 (8)0.0204 (8)0.0178 (8)−0.0010 (6)0.0005 (7)−0.0014 (7)
C60.0224 (10)0.0256 (11)0.0295 (12)0.0017 (8)0.0029 (9)−0.0037 (9)
C70.0213 (10)0.0190 (9)0.0164 (10)−0.0028 (8)0.0009 (7)0.0023 (8)
O30.0240 (8)0.0256 (8)0.0165 (7)−0.0023 (6)0.0026 (6)−0.0024 (6)
N30.0197 (8)0.0273 (9)0.0157 (8)−0.0014 (7)0.0003 (7)−0.0035 (7)
C80.0212 (10)0.0306 (11)0.0179 (10)0.0013 (8)−0.0020 (8)0.0005 (9)
C90.0231 (11)0.0413 (13)0.0243 (11)0.0049 (9)0.0008 (9)−0.0043 (10)
C100.0186 (10)0.0357 (12)0.0188 (10)0.0012 (9)0.0007 (8)−0.0009 (9)
O40.0263 (8)0.0421 (10)0.0316 (9)−0.0027 (7)−0.0105 (7)−0.0012 (8)
O50.0228 (8)0.0301 (8)0.0217 (8)−0.0039 (6)−0.0038 (6)0.0018 (7)
C110.0283 (12)0.0330 (12)0.0317 (12)−0.0052 (9)−0.0019 (10)0.0031 (10)

Geometric parameters (Å, °)

C1—O11.489 (2)C6—H6A0.96
C1—C41.517 (3)C6—H6B0.96
C1—C31.520 (3)C6—H6C0.96
C1—C21.523 (3)C7—O31.235 (3)
C2—H2A0.96C7—N31.346 (3)
C2—H2B0.96N3—C81.448 (3)
C2—H2C0.96N3—H30.86
C3—H3A0.96C8—C101.521 (3)
C3—H3B0.96C8—C91.524 (3)
C3—H3C0.96C8—H80.98
C4—H4A0.96C9—H9A0.96
C4—H4B0.96C9—H9B0.96
C4—H4C0.96C9—H9C0.96
O1—C51.344 (2)C10—O41.210 (3)
C5—O21.215 (3)C10—O51.334 (3)
C5—N11.363 (3)O5—C111.450 (3)
N1—N21.393 (2)C11—H11A0.96
N1—H10.86C11—H11B0.96
N2—C71.392 (3)C11—H11C0.96
N2—C61.463 (3)
O1—C1—C4109.01 (17)N2—C6—H6A109.5
O1—C1—C3110.01 (17)N2—C6—H6B109.5
C4—C1—C3113.9 (2)H6A—C6—H6B109.5
O1—C1—C2102.26 (17)N2—C6—H6C109.5
C4—C1—C2110.7 (2)H6A—C6—H6C109.5
C3—C1—C2110.32 (19)H6B—C6—H6C109.5
C1—C2—H2A109.5O3—C7—N3122.0 (2)
C1—C2—H2B109.5O3—C7—N2121.24 (19)
H2A—C2—H2B109.5N3—C7—N2116.72 (18)
C1—C2—H2C109.5C7—N3—C8118.14 (18)
H2A—C2—H2C109.5C7—N3—H3120.9
H2B—C2—H2C109.5C8—N3—H3120.9
C1—C3—H3A109.5N3—C8—C10113.75 (18)
C1—C3—H3B109.5N3—C8—C9109.84 (18)
H3A—C3—H3B109.5C10—C8—C9109.64 (19)
C1—C3—H3C109.5N3—C8—H8107.8
H3A—C3—H3C109.5C10—C8—H8107.8
H3B—C3—H3C109.5C9—C8—H8107.8
C1—C4—H4A109.5C8—C9—H9A109.5
C1—C4—H4B109.5C8—C9—H9B109.5
H4A—C4—H4B109.5H9A—C9—H9B109.5
C1—C4—H4C109.5C8—C9—H9C109.5
H4A—C4—H4C109.5H9A—C9—H9C109.5
H4B—C4—H4C109.5H9B—C9—H9C109.5
C5—O1—C1119.40 (17)O4—C10—O5124.0 (2)
O2—C5—O1126.7 (2)O4—C10—C8122.3 (2)
O2—C5—N1123.66 (19)O5—C10—C8113.58 (18)
O1—C5—N1109.64 (18)C10—O5—C11114.71 (18)
C5—N1—N2118.43 (18)O5—C11—H11A109.5
C5—N1—H1120.8O5—C11—H11B109.5
N2—N1—H1120.8H11A—C11—H11B109.5
C7—N2—N1116.51 (17)O5—C11—H11C109.5
C7—N2—C6118.49 (18)H11A—C11—H11C109.5
N1—N2—C6114.46 (17)H11B—C11—H11C109.5
C4—C1—O1—C5−65.6 (2)C6—N2—C7—N3168.95 (18)
C3—C1—O1—C560.0 (2)O3—C7—N3—C83.2 (3)
C2—C1—O1—C5177.16 (18)N2—C7—N3—C8−179.09 (18)
C1—O1—C5—O2−1.3 (3)C7—N3—C8—C10−60.0 (3)
C1—O1—C5—N1177.86 (17)C7—N3—C8—C9176.65 (19)
O2—C5—N1—N2−6.4 (3)N3—C8—C10—O4153.4 (2)
O1—C5—N1—N2174.45 (17)C9—C8—C10—O4−83.2 (3)
C5—N1—N2—C768.4 (2)N3—C8—C10—O5−30.0 (3)
C5—N1—N2—C6−75.9 (2)C9—C8—C10—O593.5 (2)
N1—N2—C7—O3−156.14 (19)O4—C10—O5—C11−3.6 (3)
C6—N2—C7—O3−13.3 (3)C8—C10—O5—C11179.84 (19)
N1—N2—C7—N326.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.862.182.972 (2)153
N3—H3···O3i0.862.032.850 (2)159
C6—H6A···O4ii0.962.553.303 (3)136
C11—H11B···O4iii0.962.413.346 (3)164

Symmetry codes: (i) y, −x+1, z−1/4; (ii) x−1, y, z; (iii) y, −x+2, z−1/4.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2501).

References

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