Methyl 2,4-an­hydro-5-azido-5,6-di­deoxy-l-altronate

Watkin, D.J.; Johnson, S.W.; Jones, J.H.; Fleet, G.W.J.

doi:10.1107/S1600536804019968

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 60| Part 9| September 2004| Pages o1609-o1610

https://doi.org/10.1107/S1600536804019968

Methyl 2,4-anhydro-5-azido-5,6-dideoxy-L-altronate

David J. Watkin,^a ^* Stephen W. Johnson,^b John H. Jones ^b and George W. J. Fleet ^b

^aDepartment of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, and ^bDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: david.watkin@chem.ox.ac.uk

(Received 5 August 2004; accepted 11 August 2004; online 28 August 2004)

The title compound, C₇H₁₁N₃O₄, was prepared from L-rhamnose as a conformationally restricted dipeptide isostere containing an oxetane ring. Its crystal structure was determined to confirm the synthetic product.

Comment

Sugar amino acids (SAA) are an important class of peptidomimetics (Schweizer, 2002 ; Gruner et al., 2002 ). In particular, D-amino acid scaffolds derived from pyranoses (Kriek et al., 2003 ; El Oualid et al., 2002 ) and furanoses (van Well et al., 2003 ; Chakraborty et al., 2002 ) provide a well established series of conformationally fixed dipeptide isosteres. The azido ester described here, (I), prepared from L-rhamnose, is among the first examples of building blocks for dipeptide isosteres which contain an oxetane ring; it may be viewed as a conformationally restricted dipeptide isostere of L-ala-D-ser, (II).

Fig. 1 shows the asymmetric unit (I). Its absolute structure (C4 R conformation, and C6 and C9 S conformation) was assumed based on the known absolute structure of the starting material.

The crystal packing for (I) consists of slightly pleated ribbons of molecules linked by weak hydrogen bonds, with the sheets stacked in van der Waals contact (Fig. 2).

Figure 1
The asymmetric unit of (I

), with displacement ellipsoids drawn at the 50% probability level. H-atom radii are arbitrary.

Figure 2
Packing diagram of (I

), viewed down the c axis. The weakly hydrogen-bonded pleated ribons in the bc plane are simply stacked along the a axis. Hydrogen bonds are shown as dashed lines.

Experimental

Compound (I) (Johnson et al., 2004 ) was recrystallized from chloroform by solvent diffusion with hexane to give colourless plate-shaped crystals.

Crystal data

C₇H₁₁N₃O₄
M_r = 201.18
Monoclinic, P2₁
a = 4.6318 (2) Å
b = 9.8575 (5) Å
c = 10.6310 (6) Å
β = 92.084 (2)°
V = 485.07 (4) Å³
Z = 2
D_x = 1.377 Mg m⁻³
Mo Kα radiation
Cell parameters from 1439 reflections
θ = 5–32°
μ = 0.11 mm⁻¹
T = 185 K
Plate, colourless
0.50 × 0.40 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997 ) T_min = 0.96, T_max = 0.98
4689 measured reflections
1733 independent reflections
1733 reflections with I > -3σ(I)
R_int = 0.021
θ_max = 32.0°
h = −6 → 6
k = −14 → 8
l = −15 → 15

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.051
wR(F²) = 0.095
S = 1.01
1733 reflections
160 parameters
Only coordinates of H atoms refined
w = 1/[σ²(F) + (0.034P)² + 0.093P], where P = (max(F_o²,0) + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

O1—C2	1.331 (2)
O1—C14	1.445 (3)
C2—O3	1.204 (2)
C2—C4	1.513 (3)
C4—O5	1.439 (2)
C4—C7	1.540 (2)
O5—C6	1.451 (2)
C6—C7	1.533 (2)
C6—C9	1.521 (3)
C7—O8	1.405 (2)
C9—N10	1.486 (3)
C9—C13	1.515 (3)
N10—N11	1.234 (3)
N11—N12	1.132 (4)

C2—O1—C14	116.48 (17)
O1—C2—O3	124.83 (18)
O1—C2—C4	110.25 (15)
O3—C2—C4	124.92 (17)
C2—C4—O5	111.04 (14)
C2—C4—C7	114.58 (14)
O5—C4—C7	91.58 (13)
C4—O5—C6	91.52 (12)
O5—C6—C7	91.38 (13)
O5—C6—C9	110.23 (15)
C7—C6—C9	117.75 (15)
C4—C7—C6	84.73 (13)
C4—C7—O8	114.53 (15)
C6—C7—O8	117.18 (15)
C6—C9—N10	105.37 (17)
C6—C9—C13	111.88 (19)
N10—C9—C13	110.54 (19)
C9—N10—N11	113.4 (2)
N10—N11—N12	174.7 (3)

Table 2
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O8—H5⋯O3ⁱ	0.82 (4)	2.25 (3)	2.990 (2)	150 (3)
O8—H5⋯O5ⁱ	0.82 (4)	2.32 (3)	2.962 (2)	135 (3)
Symmetry code: (i) $[-x,{\script{1\over 2}}+y,1-z]$ .

Because the intensity data were collected with molybdenum radiation, there were no measurable anomalous differences, as a consequence of which it was admissible to merge Freidel pairs of reflections. The absolute structure of (I) was assumed to correlate with the known absolute structure of the L-rhamnose starting material. All H atoms were found in difference-density syntheses. They were initially refined with soft restraints on the bonds to regularize their geometry (bond lengths to accepted values, angles either set by symmetry or to accepted values, and U_iso dependent upon the adjacent bonded atom), after which they were refined with riding constraints only.

Data collection: COLLECT (Nonius, 1997–2001 ); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536804019968/hb6077sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804019968/hb6077Isup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1997); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

Methyl 2,4-anhydro-5-azido-5,6-dideoxy-L-altronate top

Crystal data top

C₇H₁₁N₃O₄	F(000) = 212
M_r = 201.18	D_x = 1.377 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1439 reflections
a = 4.6318 (2) Å	θ = 5–32°
b = 9.8575 (5) Å	µ = 0.11 mm⁻¹
c = 10.6310 (6) Å	T = 185 K
β = 92.084 (2)°	Plate, colourless
V = 485.07 (4) Å³	0.50 × 0.40 × 0.20 mm
Z = 2

Data collection top

Nonius KappaCCD diffractometer	1733 reflections with I > −3σ(I)
Graphite monochromator	R_int = 0.021
ω scans	θ_max = 32.0°, θ_min = 5.3°
Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997)	h = −6→6
T_min = 0.96, T_max = 0.98	k = −14→8
4689 measured reflections	l = −15→15
1733 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.051	Only H-atom coordinates refined
wR(F²) = 0.095	w = 1/[σ²(F) + (0.034P)² + 0.093P], where P = (max(F_o²,0) + 2F_c²)/3
S = 1.01	(Δ/σ)_max = 0.000205
1733 reflections	Δρ_max = 0.22 e Å⁻³
160 parameters	Δρ_min = −0.23 e Å⁻³
35 restraints

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

	x	y	z	U_iso*/U_eq
O1	0.1410 (3)	0.40054 (18)	0.21529 (13)	0.0400
C2	0.1392 (4)	0.3140 (2)	0.31133 (17)	0.0307
O3	−0.0147 (3)	0.21590 (17)	0.31663 (13)	0.0401
C4	0.3567 (4)	0.3571 (2)	0.41317 (18)	0.0299
O5	0.4021 (3)	0.25130 (15)	0.50505 (13)	0.0355
C6	0.2570 (4)	0.32935 (18)	0.59975 (18)	0.0320
C7	0.2362 (3)	0.45325 (19)	0.51267 (17)	0.0282
O8	−0.0413 (3)	0.50394 (17)	0.48281 (16)	0.0405
C9	0.4480 (5)	0.3407 (2)	0.71873 (19)	0.0401
N10	0.2816 (5)	0.4247 (2)	0.80673 (19)	0.0545
N11	0.4227 (5)	0.5193 (3)	0.85376 (19)	0.0564
N12	0.5334 (7)	0.6089 (3)	0.9016 (3)	0.0819
C13	0.5152 (8)	0.2029 (3)	0.7759 (3)	0.0665
C14	−0.0618 (5)	0.3739 (3)	0.1117 (2)	0.0501
H41	0.534 (3)	0.390 (2)	0.3796 (16)	0.0374*
H61	0.067 (4)	0.2891 (19)	0.6166 (16)	0.0383*
H71	0.370 (3)	0.5239 (17)	0.5357 (17)	0.0350*
H91	0.626 (4)	0.391 (2)	0.7011 (18)	0.0519*
H131	0.645 (5)	0.216 (3)	0.851 (2)	0.0843*
H132	0.324 (5)	0.168 (3)	0.796 (2)	0.0843*
H133	0.608 (5)	0.147 (3)	0.711 (2)	0.0843*
H141	−0.034 (5)	0.450 (2)	0.056 (2)	0.0677*
H142	−0.261 (4)	0.370 (3)	0.141 (2)	0.0677*
H143	−0.005 (6)	0.289 (2)	0.076 (3)	0.0677*
H5	−0.069 (6)	0.576 (4)	0.519 (3)	0.0610*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0484 (8)	0.0328 (7)	0.0388 (7)	−0.0058 (6)	0.0007 (6)	0.0063 (6)
C2	0.0334 (8)	0.0237 (8)	0.0353 (8)	0.0013 (7)	0.0067 (6)	−0.0004 (7)
O3	0.0482 (7)	0.0302 (7)	0.0419 (7)	−0.0118 (6)	0.0023 (6)	0.0011 (6)
C4	0.0287 (7)	0.0207 (7)	0.0406 (9)	0.0018 (6)	0.0052 (7)	0.0018 (6)
O5	0.0472 (8)	0.0217 (6)	0.0377 (7)	0.0108 (6)	0.0033 (6)	0.0009 (5)
C6	0.0369 (9)	0.0187 (7)	0.0409 (9)	0.0007 (7)	0.0085 (7)	0.0000 (7)
C7	0.0260 (7)	0.0174 (7)	0.0413 (9)	0.0006 (6)	0.0013 (6)	−0.0010 (7)
O8	0.0322 (7)	0.0285 (7)	0.0603 (9)	0.0099 (5)	−0.0043 (6)	−0.0116 (7)
C9	0.0530 (11)	0.0316 (10)	0.0361 (9)	0.0099 (9)	0.0057 (8)	0.0008 (8)
N10	0.0712 (13)	0.0455 (11)	0.0482 (11)	0.0071 (10)	0.0211 (9)	−0.0051 (9)
N11	0.0815 (15)	0.0483 (12)	0.0388 (9)	0.0201 (11)	−0.0043 (9)	−0.0065 (9)
N12	0.101 (2)	0.0691 (18)	0.0741 (17)	0.0172 (16)	−0.0171 (15)	−0.0326 (15)
C13	0.106 (2)	0.0445 (14)	0.0483 (13)	0.0222 (16)	−0.0035 (14)	0.0082 (11)
C14	0.0574 (13)	0.0535 (15)	0.0389 (11)	−0.0018 (12)	−0.0035 (9)	0.0058 (10)

Geometric parameters (Å, º) top

O1—C2	1.331 (2)	O8—H5	0.82 (4)
O1—C14	1.445 (3)	C9—N10	1.486 (3)
C2—O3	1.204 (2)	C9—C13	1.515 (3)
C2—C4	1.513 (3)	C9—H91	0.985 (16)
C4—O5	1.439 (2)	N10—N11	1.234 (3)
C4—C7	1.540 (2)	N11—N12	1.132 (4)
C4—H41	0.964 (15)	C13—H131	0.993 (17)
O5—C6	1.451 (2)	C13—H132	0.981 (18)
C6—C7	1.533 (2)	C13—H133	0.996 (18)
C6—C9	1.521 (3)	C14—H141	0.969 (17)
C6—H61	0.986 (15)	C14—H142	0.983 (17)
C7—O8	1.405 (2)	C14—H143	0.962 (17)
C7—H71	0.958 (16)

C2—O1—C14	116.48 (17)	O8—C7—H71	112.1 (10)
O1—C2—O3	124.83 (18)	C7—O8—H5	111 (2)
O1—C2—C4	110.25 (15)	C6—C9—N10	105.37 (17)
O3—C2—C4	124.92 (17)	C6—C9—C13	111.88 (19)
C2—C4—O5	111.04 (14)	N10—C9—C13	110.54 (19)
C2—C4—C7	114.58 (14)	C6—C9—H91	110.1 (11)
O5—C4—C7	91.58 (13)	N10—C9—H91	107.2 (12)
C2—C4—H41	112.6 (10)	C13—C9—H91	111.5 (12)
O5—C4—H41	113.1 (11)	C9—N10—N11	113.4 (2)
C7—C4—H41	112.3 (11)	N10—N11—N12	174.7 (3)
C4—O5—C6	91.52 (12)	C9—C13—H131	108.5 (19)
O5—C6—C7	91.38 (13)	C9—C13—H132	103 (2)
O5—C6—C9	110.23 (15)	H131—C13—H132	113.6 (16)
C7—C6—C9	117.75 (15)	C9—C13—H133	107.9 (18)
O5—C6—H61	110.5 (11)	H131—C13—H133	111.6 (16)
C7—C6—H61	113.2 (11)	H132—C13—H133	111.7 (16)
C9—C6—H61	111.9 (10)	O1—C14—H141	103.0 (17)
C4—C7—C6	84.73 (13)	O1—C14—H142	110.9 (16)
C4—C7—O8	114.53 (15)	H141—C14—H142	111.6 (16)
C6—C7—O8	117.18 (15)	O1—C14—H143	106.2 (17)
C4—C7—H71	112.1 (11)	H141—C14—H143	113.4 (15)
C6—C7—H71	113.5 (11)	H142—C14—H143	111.4 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O8—H5···O3ⁱ	0.82 (4)	2.25 (3)	2.990 (2)	150 (3)
O8—H5···O5ⁱ	0.82 (4)	2.32 (3)	2.962 (2)	135 (3)

Symmetry code: (i) −x, y+1/2, −z+1.

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