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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2120–o2121.
Published online 2009 August 8. doi:  10.1107/S1600536809030815
PMCID: PMC2970119

tert-Butyl N-[1-diazo­acetyl-3-(methyl­sulfan­yl)prop­yl]carbamate

Abstract

In the enanti­omerically pure title compound, C11H19N3O3S, the chain C—N—C(O)—O—C—C (from the asymmetric carbon to a methyl of the tert-butyl group) displays an extended conformation. In the crystal, mol­ecules are linked into chains parallel to the c axis by classical N—H(...)Odiazo­carbon­yl hydrogen bonding and an unusual inter­molecular three-centre inter­action involving the amino acid (aa) carbonyl Oaa and the diazo­carbonyl grouping C(O)—CH—N N, with H(...)Oaa = 2.51 Å and N(...)Oaa = 2.8141 (14) Å.

Related literature

For the applications of α-diazo­carbonyl compounds in organic and, especially, natural product synthesis, see: Padwa & Weingarten (1996 [triangle]). The ready availability, relative stability and facile decomposition of these compounds under various conditions make them useful inter­mediates, see: Doyle et al. (1998 [triangle]). α-Diazo­ketones undergo a variety of transformations, see: Ye & McKervey (1994 [triangle]). Asymmetric versions of diazo­carbonyl reactions have been reported to produce enanti­omerically pure compounds, see: Doyle & McKervey (1997 [triangle]). The Arndt-Eistert synthesis, which consists of conversion of activated carboxylic acids to diazo­ketones by the action of diazo­methane followed by Wolf rearrangement, has become widely used in recent years for the synthesis of β-peptides and β-amino acid derivatives from appropriately protected α-amino acids, see: Müller et al. (1998 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2120-scheme1.jpg

Experimental

Crystal data

  • C11H19N3O3S
  • M r = 273.35
  • Trigonal, An external file that holds a picture, illustration, etc.
Object name is e-65-o2120-efi1.jpg
  • a = 9.7915 (3) Å
  • c = 13.8581 (5) Å
  • V = 1150.62 (6) Å3
  • Z = 3
  • Cu Kα radiation
  • μ = 1.93 mm−1
  • T = 100 K
  • 0.20 × 0.20 × 0.15 mm

Data collection

  • Oxford Diffraction Xcalibur Nova A diffractometer
  • Absorption correction: multi-scan (CrysAlis Pro; Oxford Diffraction, 2009 [triangle]) T min = 0.717, T max = 1.000 (expected range = 0.537–0.749)
  • 16152 measured reflections
  • 3073 independent reflections
  • 3051 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.023
  • wR(F 2) = 0.060
  • S = 1.05
  • 3073 reflections
  • 171 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.14 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1474 Freidel pairs
  • Flack parameter: 0.023 (10)

Data collection: CrysAlis Pro (Oxford Diffraction, 2009 [triangle]); cell refinement: CrysAlis Pro; data reduction: CrysAlis Pro; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP (Siemens, 1994 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809030815/at2855sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809030815/at2855Isup2.hkl

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

Acknowledgments

The authors are grateful to the Department of Chemistry, Quaid-I-Azam University, Islamabad, Pakistan, and the Institute for Inorganic Chemistry, University of Frankfurt, Germany, for providing laboratory and analytical facilities.

supplementary crystallographic information

Comment

α-Diazocarbonyl compounds find widespread applications in organic and, especially, natural product synthesis (Padwa & Weingarten, 1996). The ready availability, relative stability and facile decomposition of these compounds under various conditions (e.g. thermal, photochemical; acid-, base- and transition-metal-catalysis) make them useful intermediates (Doyle et al. 1998). Furthermore, α-diazoketones undergo a variety of transformations such as cyclopropanation, aziridine formation, ylide formation, C–H or C–X insertion reactions and cyclization reactions (Ye & McKervey, 1994). These reactions are chemoselective, and promote the formation of new carbon-carbon and carbon-heteroatom bonds under mild conditions. Asymmetric versions of diazocarbonyl reactions have been reported to produce enantiomerically pure compounds (Doyle & McKervey, 1997). One such method is the Arndt-Eistert synthesis, which consists of conversion of activated carboxylic acids to diazoketones by the action of diazomethane, followed by Wolf rearrangement. The method has become widely used in recent years for the synthesis of β-peptides and β-amino acid derivatives from appropriately protected α-amino acids (Müller et al. 1998). Here we present the structure of an α-diazocarbonyl compound based on methionine.

The structure of the title compound is shown in Fig. 1. Molecular dimensions may be regarded as normal. The two essentially planar groupings N1,O1,O2,C2,4,5,6 and N2,N3,O3,C6,7,8 (r.m.s. deviations 0.04, 0.02 Å) subtend an interplanar angle of 84.75 (3)°. The atom chain C2 to C6 displays an extended conformation (minimum absolute torsion angle 170°).

The main feature of the molecular packing is the classical H bond N1—H1···O3, which links the molecules via the 31 screw operator to form chains parallel to the z axis (Fig. 2). Within the chains, an unusual three-centre interaction is also observed, whereby the carbonyl oxygen O2 is involved in short contacts to H8 and N2 of the diazocarbonyl group of a neighbouring molecule. The former is far from linear (angle 110°) but this is not unusual for three-centre interactions. The latter may be interpreted as a dipole-dipole interaction [dimensions: N2···O2 2.8141 (14) Å, C8—N2···O2 73.5 (1)°]. The remaining "weak" C—H···O interactions (Table 1) link neighbouring chains; H3B···O3 is implicit between the chains of Fig. 2 but is omitted for clarity.

Experimental

10 mmol of BOC-protected methionine was dissolved in 50 ml of dry distilled THF under inert conditions. To maintain basic conditions 12 mmol (1.66 ml) of triethylamine was added. Then 10 mmol (0.95 ml) of ethyl chloroformate was added, and the mixture stirred for 15 min at 248 K. 13 mmol of diazomethane were then added at 268 K and the mixture was further stirred for 30 min. After this temperature was allowed to rise to room temperature over 3 h. The reaction was then quenched with 3–4 drops of glacial acetic acid. The solvent was evaporated under vacuum. The residue was dissolved in ethyl acetate, extracted with aq. solutions of NaHCO3 and NH4Cl and dried over anhydrous MgSO4. The crude product was purified by column chromatography (yield 85%; m.p.326-328 K).

Refinement

The NH hydrogen was refined freely. Methyl H atoms were identified in difference syntheses, idealized and refined as rigid groups with C—H 0.98 Å and H—C—H angles 109.5°, allowed to rotate but not tip. Other H atoms were placed in calculated positions and refined using a riding model with C—H 0.98 Å (methylene) or 0.99 Å (methine); hydrogen U values were fixed at 1.5 × U(eq) of the parent atom for methyl H and 1.2 × U(eq) of the parent atom for other C—H. Data are 100% complete to 2θ 145°. The absolute configuration S at C6 (and thus the space group P31 rather than its enantiomer P32) was determined by the Flack (1983) parameter, which refined to 0.023 (10).

Figures

Fig. 1.
The molecule of the title compound in the crystal. Ellipsoids correspond to 50% probability levels.
Fig. 2.
Packing diagram of the title compound viewed perpendicular to the yz plane. Classical H bonds are represented by thick dashed lines, and the three-centre interaction (see text) by thin dashed lines. H atoms not involved in H bonding are omitted for clarity. ...

Crystal data

C11H19N3O3SDx = 1.183 Mg m3
Mr = 273.35Cu Kα radiation, λ = 1.54184 Å
Trigonal, P31Cell parameters from 14422 reflections
Hall symbol: P 31θ = 3.2–75.7°
a = 9.7915 (3) ŵ = 1.93 mm1
c = 13.8581 (5) ÅT = 100 K
V = 1150.62 (6) Å3Tablet, colourless
Z = 30.20 × 0.20 × 0.15 mm
F(000) = 438

Data collection

Oxford Diffraction Xcalibur Nova A diffractometer3073 independent reflections
Radiation source: Nova (Cu) X-ray Source3051 reflections with I > 2σ(I)
mirrorRint = 0.032
Detector resolution: 10.3543 pixels mm-1θmax = 75.6°, θmin = 5.2°
ω scansh = −12→12
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −12→12
Tmin = 0.717, Tmax = 1.000l = −17→15
16152 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.023H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.060w = 1/[σ2(Fo2) + (0.0342P)2 + 0.1663P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
3073 reflectionsΔρmax = 0.15 e Å3
171 parametersΔρmin = −0.14 e Å3
1 restraintAbsolute structure: Flack (1983), 1474 Freidel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.023 (10)

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.Short contact: 2.8141 (14) N2 - O2_$1; 73.5 (1) C8 - N2 - O2_$1; Operator $1 - x + y+1, -x + 1, z - 1/3
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)

xyzUiso*/Ueq
S0.08692 (4)−0.10432 (4)0.14682 (2)0.03648 (9)
O10.57182 (11)0.62115 (10)0.24352 (6)0.02868 (19)
O20.57776 (11)0.51506 (10)0.38885 (6)0.02855 (19)
O30.66256 (11)0.16891 (11)0.38136 (6)0.02857 (19)
N10.49938 (13)0.36907 (12)0.25188 (8)0.0259 (2)
H010.4999 (17)0.3757 (17)0.1913 (12)0.021 (3)*
N20.88980 (14)0.31145 (15)0.24685 (9)0.0340 (3)
N31.00277 (17)0.3112 (2)0.25596 (10)0.0492 (4)
C10.76526 (17)0.85794 (16)0.33133 (11)0.0350 (3)
H1A0.76320.79910.38900.052*
H1B0.79070.96470.34990.052*
H1C0.84550.86400.28650.052*
C20.60734 (19)0.86229 (16)0.19163 (11)0.0369 (3)
H2A0.68870.86850.14770.055*
H2B0.63070.96900.20850.055*
H2C0.50420.80590.16000.055*
C30.47294 (18)0.75163 (17)0.35029 (12)0.0364 (3)
H3A0.37140.69140.31720.055*
H3B0.48830.85480.36930.055*
H3C0.47390.69400.40790.055*
C40.60502 (15)0.77449 (14)0.28283 (10)0.0278 (3)
C50.55262 (14)0.50412 (13)0.30286 (9)0.0244 (2)
C60.48307 (14)0.22893 (14)0.29774 (9)0.0240 (2)
H60.43290.21730.36240.029*
C70.64131 (14)0.23513 (13)0.31215 (9)0.0234 (2)
C80.75513 (15)0.31186 (15)0.23793 (10)0.0288 (3)
H80.73560.36090.18470.035*
C90.37572 (14)0.08310 (13)0.23693 (9)0.0257 (2)
H9A0.42200.09570.17180.031*
H9B0.3707−0.01100.26700.031*
C100.20871 (15)0.05652 (15)0.22743 (10)0.0300 (3)
H10A0.21440.15440.20320.036*
H10B0.15880.03390.29200.036*
C110.0623 (2)−0.26955 (18)0.21754 (14)0.0502 (4)
H11A0.1660−0.25590.23310.075*
H11B0.0012−0.36710.18060.075*
H11C0.0062−0.27550.27740.075*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S0.03136 (16)0.03576 (17)0.03360 (17)0.01025 (14)−0.00604 (13)−0.00369 (14)
O10.0426 (5)0.0199 (4)0.0260 (4)0.0176 (4)−0.0038 (4)−0.0017 (3)
O20.0390 (5)0.0245 (4)0.0246 (5)0.0177 (4)−0.0050 (3)−0.0027 (3)
O30.0319 (4)0.0295 (4)0.0243 (4)0.0153 (4)0.0004 (3)0.0041 (3)
N10.0384 (6)0.0196 (5)0.0208 (5)0.0154 (4)−0.0023 (4)−0.0016 (4)
N20.0324 (6)0.0379 (6)0.0292 (6)0.0157 (5)0.0058 (4)0.0081 (4)
N30.0392 (7)0.0717 (10)0.0426 (8)0.0320 (7)0.0095 (6)0.0198 (7)
C10.0336 (7)0.0248 (6)0.0424 (8)0.0115 (5)−0.0030 (6)−0.0028 (5)
C20.0521 (8)0.0249 (6)0.0381 (8)0.0224 (6)−0.0028 (6)0.0013 (5)
C30.0400 (8)0.0309 (7)0.0456 (8)0.0230 (6)0.0044 (6)0.0018 (6)
C40.0334 (6)0.0184 (5)0.0335 (7)0.0145 (5)−0.0017 (5)−0.0019 (5)
C50.0271 (6)0.0203 (5)0.0282 (6)0.0137 (5)−0.0001 (4)−0.0001 (4)
C60.0293 (6)0.0198 (5)0.0239 (6)0.0131 (5)0.0010 (4)0.0005 (4)
C70.0275 (6)0.0170 (5)0.0228 (6)0.0091 (4)−0.0009 (4)−0.0021 (4)
C80.0289 (6)0.0277 (6)0.0289 (6)0.0135 (5)0.0024 (5)0.0051 (5)
C90.0273 (6)0.0199 (5)0.0289 (6)0.0110 (5)−0.0003 (5)−0.0015 (4)
C100.0274 (6)0.0261 (6)0.0356 (7)0.0126 (5)−0.0017 (5)−0.0014 (5)
C110.0479 (9)0.0284 (7)0.0653 (11)0.0124 (7)−0.0165 (8)−0.0071 (7)

Geometric parameters (Å, °)

S—C111.8015 (17)C1—H1A0.9800
S—C101.8089 (13)C1—H1B0.9800
O1—C51.3450 (14)C1—H1C0.9800
O1—C41.4727 (14)C2—H2A0.9800
O2—C51.2107 (16)C2—H2B0.9800
O3—C71.2323 (15)C2—H2C0.9800
N1—C51.3528 (15)C3—H3A0.9800
N1—C61.4468 (15)C3—H3B0.9800
N2—N31.1145 (18)C3—H3C0.9800
N2—C81.3264 (18)C6—H61.0000
C1—C41.5163 (19)C8—H80.9500
C2—C41.5223 (19)C9—H9A0.9900
C3—C41.5189 (19)C9—H9B0.9900
C6—C71.5330 (17)C10—H10A0.9900
C6—C91.5340 (16)C10—H10B0.9900
C7—C81.4237 (17)C11—H11A0.9800
C9—C101.5276 (17)C11—H11B0.9800
N1—H010.842 (16)C11—H11C0.9800
C11—S—C10100.36 (7)H2A—C2—H2B109.5
C5—O1—C4120.53 (10)C4—C2—H2C109.5
C5—N1—C6120.23 (11)H2A—C2—H2C109.5
N3—N2—C8178.84 (15)H2B—C2—H2C109.5
O1—C4—C1110.78 (10)C4—C3—H3A109.5
O1—C4—C3109.87 (10)C4—C3—H3B109.5
C1—C4—C3112.46 (12)H3A—C3—H3B109.5
O1—C4—C2101.65 (10)C4—C3—H3C109.5
C1—C4—C2110.15 (11)H3A—C3—H3C109.5
C3—C4—C2111.43 (11)H3B—C3—H3C109.5
O2—C5—O1126.21 (10)N1—C6—H6108.5
O2—C5—N1124.23 (11)C7—C6—H6108.5
O1—C5—N1109.57 (11)C9—C6—H6108.5
N1—C6—C7112.93 (10)N2—C8—H8121.7
N1—C6—C9109.93 (10)C7—C8—H8121.7
C7—C6—C9108.48 (9)C10—C9—H9A109.1
O3—C7—C8123.12 (12)C6—C9—H9A109.1
O3—C7—C6120.91 (11)C10—C9—H9B109.1
C8—C7—C6115.84 (11)C6—C9—H9B109.1
N2—C8—C7116.62 (12)H9A—C9—H9B107.8
C10—C9—C6112.51 (10)C9—C10—H10A109.1
C9—C10—S112.65 (9)S—C10—H10A109.1
C5—N1—H01117.4 (10)C9—C10—H10B109.1
C6—N1—H01120.3 (10)S—C10—H10B109.1
C4—C1—H1A109.5H10A—C10—H10B107.8
C4—C1—H1B109.5S—C11—H11A109.5
H1A—C1—H1B109.5S—C11—H11B109.5
C4—C1—H1C109.5H11A—C11—H11B109.5
H1A—C1—H1C109.5S—C11—H11C109.5
H1B—C1—H1C109.5H11A—C11—H11C109.5
C4—C2—H2A109.5H11B—C11—H11C109.5
C4—C2—H2B109.5
C5—O1—C4—C166.13 (15)C9—C6—C7—O3−89.46 (13)
C5—O1—C4—C3−58.74 (14)N1—C6—C7—C8−35.64 (15)
C5—O1—C4—C2−176.85 (11)C9—C6—C7—C886.47 (12)
C4—O1—C5—O2−9.28 (19)O3—C7—C8—N2−0.93 (19)
C4—O1—C5—N1170.45 (10)C6—C7—C8—N2−176.76 (11)
C6—N1—C5—O2−5.96 (19)N1—C6—C9—C10−62.16 (13)
C6—N1—C5—O1174.30 (10)C7—C6—C9—C10173.92 (10)
C5—N1—C6—C7−76.13 (14)C6—C9—C10—S174.67 (9)
C5—N1—C6—C9162.57 (10)C11—S—C10—C969.91 (11)
N1—C6—C7—O3148.43 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H01···O3i0.842 (16)2.027 (16)2.8465 (14)164.1 (14)
C8—H8···O2i0.952.512.9686 (16)110
C11—H11B···O2ii0.982.523.457 (2)160
C3—H3B···O3iii0.982.673.5693 (17)152
C1—H1C···Siv0.982.953.9281 (16)177

Symmetry codes: (i) −x+y+1, −x+1, z−1/3; (ii) −x+y, −x, z−1/3; (iii) x, y+1, z; (iv) x+1, y+1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2855).

References

  • Doyle, M. P. & McKervey, M. A. (1997). J. Chem. Soc. Chem. Commun. pp. 983–989.
  • Doyle, M. P., McKervey, M. & Ye, T. (1998). In Modern Catalytic Methods for Organic Synthesis with Diazo compounds from Cyclopropanone to Ylides New York: Wiley-Interscience.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Müller, A., Vogt, C. & Sewald, N. (1998). Synthesis, pp. 837–841.
  • Oxford Diffraction (2009). CrysAlis Pro Oxford Diffraction Ltd, Yarnton, England.
  • Padwa, A. & Weingarten, M. (1996). Chem. Rev.96, 223–269. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Siemens (1994). XP Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
  • Ye, T. & McKervey, M. A. (1994). Chem. Rev.94, 1091–1160.

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