organic compounds
Isopropyl 2,5-anhydro-6-azido-3,6-dideoxy-D-xylo-hexonate
aDepartment of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, bDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, and cBiological Chemistry, Division of Biomedical Sciences, Imperial College, London SW7 2AZ, England
*Correspondence e-mail: david.watkin@chem.ox.ac.uk
Determination of the 9H15N3O4, confirmed its relative stereochemistry and validated further work on the use of a derived sugar amino acid (SAA) as a peptidomimetic.
of the title isopropyl azido ester, CComment
Sugar amino acids (SAAs) are et al., 2001; Gruner et al., 2002; Schweizer, 2002; Chakraborty, Srinivasu, Tapadar & Mohan, 2004; Trabocchi et al., 2005). The preference for SAA oligomers (carbopeptoids) to adopt compact conformations as relatively short homooligomers will provide insight into the paradigm of protein folding. SAAs (2,5-O-cis configuration) structurally related to SAA (3) have a high propensity to adopt repeating β-turn conformations (Hungerford et al., 2000; Smith et al., 2003; Chakraborty, Srinivasu, Sakunthala et al., 2004). In contrast, some 2,5-O-trans SAAs have been shown to adopt helical conformations (Claridge et al., 1999; Claridge et al., 2005). The conformational complexity of these dipeptide isosteres is being further explored by preparation of structurally related analogues of the original SAA systems i.e. SAA (3) and corresponding (Watterson et al., 2003).
which contain amine and acid groups; SAAs have been the focus of much interest as dipeptide isosteres, foldamers and library scaffolds (HillThe X-ray ) firmly established the relative stereochemistry of the stereogenic centres in the title compound, (2). The of (2) (see scheme) is determined by the use of D-gulono-1,4-lactone as starting material.
(Fig. 1The crystal packing consists of chains of molecules linked by hydrogen bonds and lying parallel to the a axis (Fig. 2). There are no unusual intermolecular contacts.
Experimental
The title compound, (2), was prepared from the methyl azido ester (1) in good yield by transesterficiation in acidic propan-2-ol, as described by Watterson et al. (2003); subsequent deprotection by hydrolysis and hydrogenation afforded SAA (3). The sample of (2) was crystallized from diethyl ether–hexane.
Crystal data
|
Data collection
Refinement
|
|
Attempted ) parameter gave an inconclusive result, in the absence of Friedel pairs and the presence of only weak effects. The was assigned from the known configuration of the starting material. The H atoms were all located in a difference map, but those attached to C atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H = 0.93–0.98 Å and O—H = 0.82 Å) and Uiso(H) values (in the range 1.2–1.5 times Ueq of the parent atom), after which they were refined with riding constraints.
of the Flack (1983Data collection: CAD-4 EXPRESS, (Straver, 1992); cell CAD-4 EXPRESS; data reduction: RC93 (Watkin et al., 1994); 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
10.1107/S1600536805042133/cf6481sup1.cif
contains datablocks global, 2. DOI:Structure factors: contains datablock 2. DOI: 10.1107/S1600536805042133/cf64812sup2.hkl
The title compound, (2), was prepared from the methyl azido ester (1) in good yield by transesterficiation in acidic propan-2-ol, as described by Watterson et al. (2003); subsequent deprotection by hydrolysis and hydrogenation afforded SAA (3). The sample of (2) was crystallized from diethyl ether/hexane.
Attempted
of the Flack (1983) parameter gave an inconclusive result, in the absence of Friedel pairs and the presence of only weak effects. The was assigned from the known configuration of the staring material. The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H = 0.93–0.98 Å and O—H = 0.82 Å) and Uiso(H) values (in the range 1.2–1.5 times Ueq of the parent atom), after which they were refined with riding constraints.Data collection: CAD-4 EXPRESS, (Straver, 1992); cell
CAD-4 EXPRESS; data reduction: RC93 (Watkin et al., 1994); 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.C9H15N3O4 | Dx = 1.376 Mg m−3 |
Mr = 229.24 | Cu Kα radiation, λ = 1.54180 Å |
Orthorhombic, P212121 | Cell parameters from 22 reflections |
a = 5.4778 (7) Å | θ = 21–44° |
b = 11.0701 (13) Å | µ = 0.92 mm−1 |
c = 18.2529 (15) Å | T = 190 K |
V = 1106.9 (2) Å3 | Block, colourless |
Z = 4 | 0.60 × 0.40 × 0.40 mm |
F(000) = 488 |
Enraf-Nonius Mach3 diffractometer | Rint = 0.000 |
Graphite monochromator | θmax = 73.9°, θmin = 4.7° |
ω/2θ scans | h = 0→6 |
Absorption correction: ψ scan (North et al., 1968) | k = 0→13 |
Tmin = 0.58, Tmax = 0.69 | l = 0→22 |
1335 measured reflections | 3 standard reflections every 60 min |
1335 independent reflections | intensity decay: 2.2% |
1329 reflections with I > 2σ(I) |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.040 | w = 1/[σ2(F2) + (0.07P)2 + 0.57P], where P = [max(Fo2,0) + 2Fc2]/3 |
wR(F2) = 0.104 | (Δ/σ)max = 0.001 |
S = 0.94 | Δρmax = 0.25 e Å−3 |
1335 reflections | Δρmin = −0.17 e Å−3 |
146 parameters | Extinction correction: Larson (1970), Equation 22 |
0 restraints | Extinction coefficient: 159 (14) |
Primary atom site location: structure-invariant direct methods |
C9H15N3O4 | V = 1106.9 (2) Å3 |
Mr = 229.24 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 5.4778 (7) Å | µ = 0.92 mm−1 |
b = 11.0701 (13) Å | T = 190 K |
c = 18.2529 (15) Å | 0.60 × 0.40 × 0.40 mm |
Enraf-Nonius Mach3 diffractometer | 1329 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.000 |
Tmin = 0.58, Tmax = 0.69 | 3 standard reflections every 60 min |
1335 measured reflections | intensity decay: 2.2% |
1335 independent reflections |
R[F2 > 2σ(F2)] = 0.040 | 0 restraints |
wR(F2) = 0.104 | H-atom parameters constrained |
S = 0.94 | Δρmax = 0.25 e Å−3 |
1335 reflections | Δρmin = −0.17 e Å−3 |
146 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 1.0131 (3) | 0.04582 (14) | 0.13732 (8) | 0.0286 | |
C2 | 0.8763 (4) | 0.07207 (19) | 0.19548 (12) | 0.0265 | |
O3 | 0.7238 (3) | 0.15214 (14) | 0.19695 (9) | 0.0327 | |
C4 | 0.9240 (4) | −0.0150 (2) | 0.25865 (11) | 0.0260 | |
O5 | 0.8152 (3) | 0.03051 (14) | 0.32375 (8) | 0.0283 | |
C6 | 0.9954 (4) | 0.0942 (2) | 0.36612 (11) | 0.0265 | |
C7 | 0.9236 (5) | 0.2241 (2) | 0.37739 (14) | 0.0347 | |
N8 | 0.7043 (4) | 0.22905 (18) | 0.42600 (11) | 0.0370 | |
N9 | 0.5797 (4) | 0.31992 (19) | 0.41699 (12) | 0.0358 | |
N10 | 0.4495 (5) | 0.3992 (2) | 0.41294 (17) | 0.0538 | |
C11 | 1.2409 (4) | 0.0802 (2) | 0.32561 (12) | 0.0273 | |
C12 | 1.1963 (4) | −0.0296 (2) | 0.27753 (13) | 0.0291 | |
O13 | 1.2826 (3) | 0.18508 (14) | 0.28216 (9) | 0.0319 | |
C14 | 0.9818 (5) | 0.1232 (2) | 0.07308 (11) | 0.0319 | |
C15 | 1.0604 (6) | 0.0491 (2) | 0.00784 (12) | 0.0430 | |
C16 | 1.1340 (6) | 0.2355 (2) | 0.08420 (15) | 0.0458 | |
H41 | 0.8578 | −0.0940 | 0.2460 | 0.0306* | |
H61 | 1.0054 | 0.0554 | 0.4140 | 0.0318* | |
H71 | 1.0540 | 0.2685 | 0.3992 | 0.0425* | |
H72 | 0.8814 | 0.2605 | 0.3297 | 0.0418* | |
H111 | 1.3776 | 0.0681 | 0.3590 | 0.0315* | |
H121 | 1.2259 | −0.1050 | 0.3045 | 0.0333* | |
H122 | 1.2955 | −0.0277 | 0.2341 | 0.0346* | |
H141 | 0.8056 | 0.1442 | 0.0675 | 0.0368* | |
H151 | 1.0365 | 0.0977 | −0.0357 | 0.0639* | |
H152 | 1.2331 | 0.0309 | 0.0141 | 0.0642* | |
H153 | 0.9649 | −0.0252 | 0.0055 | 0.0642* | |
H161 | 1.1211 | 0.2894 | 0.0430 | 0.0688* | |
H162 | 1.3011 | 0.2149 | 0.0890 | 0.0694* | |
H163 | 1.0845 | 0.2801 | 0.1274 | 0.0683* | |
H13 | 1.4026 | 0.1766 | 0.2560 | 0.0476* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0233 (8) | 0.0367 (8) | 0.0259 (7) | 0.0027 (7) | 0.0025 (7) | 0.0002 (6) |
C2 | 0.0200 (10) | 0.0311 (10) | 0.0285 (10) | −0.0031 (9) | 0.0022 (9) | −0.0033 (8) |
O3 | 0.0252 (8) | 0.0400 (8) | 0.0330 (8) | 0.0063 (7) | 0.0068 (7) | 0.0024 (6) |
C4 | 0.0210 (10) | 0.0289 (10) | 0.0279 (10) | −0.0023 (9) | 0.0029 (8) | −0.0010 (8) |
O5 | 0.0174 (7) | 0.0401 (8) | 0.0274 (7) | −0.0041 (7) | 0.0043 (6) | −0.0021 (6) |
C6 | 0.0200 (11) | 0.0351 (11) | 0.0242 (10) | −0.0004 (9) | 0.0003 (9) | 0.0020 (8) |
C7 | 0.0251 (12) | 0.0370 (11) | 0.0421 (12) | −0.0031 (10) | 0.0117 (11) | −0.0067 (10) |
N8 | 0.0306 (10) | 0.0408 (10) | 0.0396 (10) | 0.0029 (10) | 0.0132 (9) | −0.0015 (9) |
N9 | 0.0243 (10) | 0.0402 (10) | 0.0430 (10) | −0.0049 (10) | 0.0035 (9) | −0.0087 (9) |
N10 | 0.0306 (12) | 0.0486 (13) | 0.0823 (18) | 0.0056 (12) | 0.0026 (13) | −0.0082 (13) |
C11 | 0.0155 (10) | 0.0370 (11) | 0.0295 (10) | 0.0030 (9) | 0.0008 (9) | 0.0015 (9) |
C12 | 0.0222 (11) | 0.0335 (11) | 0.0317 (10) | 0.0053 (9) | 0.0048 (9) | 0.0039 (9) |
O13 | 0.0225 (8) | 0.0357 (8) | 0.0375 (8) | −0.0018 (7) | 0.0091 (7) | 0.0008 (7) |
C14 | 0.0299 (12) | 0.0424 (12) | 0.0235 (10) | 0.0058 (11) | 0.0024 (10) | 0.0027 (9) |
C15 | 0.0497 (16) | 0.0508 (13) | 0.0284 (11) | 0.0106 (14) | 0.0050 (12) | −0.0012 (10) |
C16 | 0.0517 (17) | 0.0447 (13) | 0.0410 (12) | −0.0036 (14) | 0.0114 (13) | 0.0049 (11) |
O1—C2 | 1.331 (3) | C11—C12 | 1.519 (3) |
O1—C14 | 1.462 (3) | C11—O13 | 1.424 (3) |
C2—O3 | 1.218 (3) | C11—H111 | 0.974 |
C2—C4 | 1.525 (3) | C12—H121 | 0.983 |
C4—O5 | 1.421 (3) | C12—H122 | 0.962 |
C4—C12 | 1.539 (3) | O13—H13 | 0.817 |
C4—H41 | 0.975 | C14—C15 | 1.509 (3) |
O5—C6 | 1.439 (3) | C14—C16 | 1.510 (4) |
C6—C7 | 1.505 (3) | C14—H141 | 0.998 |
C6—C11 | 1.543 (3) | C15—H151 | 0.969 |
C6—H61 | 0.976 | C15—H152 | 0.974 |
C7—N8 | 1.494 (3) | C15—H153 | 0.976 |
C7—H71 | 0.954 | C16—H161 | 0.962 |
C7—H72 | 0.986 | C16—H162 | 0.947 |
N8—N9 | 1.227 (3) | C16—H163 | 0.968 |
N9—N10 | 1.133 (3) | ||
C2—O1—C14 | 116.44 (17) | C6—C11—H111 | 112.6 |
O1—C2—O3 | 124.2 (2) | C12—C11—H111 | 112.0 |
O1—C2—C4 | 111.63 (18) | O13—C11—H111 | 109.7 |
O3—C2—C4 | 124.07 (19) | C4—C12—C11 | 101.61 (18) |
C2—C4—O5 | 109.68 (17) | C4—C12—H121 | 111.2 |
C2—C4—C12 | 113.67 (18) | C11—C12—H121 | 111.4 |
O5—C4—C12 | 104.84 (17) | C4—C12—H122 | 111.1 |
C2—C4—H41 | 108.9 | C11—C12—H122 | 111.6 |
O5—C4—H41 | 111.1 | H121—C12—H122 | 109.7 |
C12—C4—H41 | 108.6 | C11—O13—H13 | 111.1 |
C4—O5—C6 | 109.60 (16) | O1—C14—C15 | 106.30 (18) |
O5—C6—C7 | 111.26 (19) | O1—C14—C16 | 108.05 (19) |
O5—C6—C11 | 106.93 (16) | C15—C14—C16 | 113.3 (2) |
C7—C6—C11 | 112.91 (18) | O1—C14—H141 | 109.4 |
O5—C6—H61 | 107.7 | C15—C14—H141 | 108.8 |
C7—C6—H61 | 108.2 | C16—C14—H141 | 110.9 |
C11—C6—H61 | 109.7 | C14—C15—H151 | 107.9 |
C6—C7—N8 | 109.04 (19) | C14—C15—H152 | 107.3 |
C6—C7—H71 | 110.7 | H151—C15—H152 | 110.1 |
N8—C7—H71 | 109.6 | C14—C15—H153 | 109.9 |
C6—C7—H72 | 109.3 | H151—C15—H153 | 111.1 |
N8—C7—H72 | 108.7 | H152—C15—H153 | 110.5 |
H71—C7—H72 | 109.5 | C14—C16—H161 | 111.4 |
C7—N8—N9 | 113.4 (2) | C14—C16—H162 | 110.4 |
N8—N9—N10 | 173.7 (3) | H161—C16—H162 | 107.0 |
C6—C11—C12 | 102.52 (17) | C14—C16—H163 | 112.0 |
C6—C11—O13 | 108.97 (17) | H161—C16—H163 | 107.4 |
C12—C11—O13 | 110.87 (18) | H162—C16—H163 | 108.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
O13—H13···O3i | 0.82 | 2.08 | 2.897 (2) | 175 |
Symmetry code: (i) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C9H15N3O4 |
Mr | 229.24 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 190 |
a, b, c (Å) | 5.4778 (7), 11.0701 (13), 18.2529 (15) |
V (Å3) | 1106.9 (2) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 0.92 |
Crystal size (mm) | 0.60 × 0.40 × 0.40 |
Data collection | |
Diffractometer | Enraf-Nonius Mach3 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.58, 0.69 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1335, 1335, 1329 |
Rint | 0.000 |
(sin θ/λ)max (Å−1) | 0.623 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.104, 0.94 |
No. of reflections | 1335 |
No. of parameters | 146 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.25, −0.17 |
Computer programs: CAD-4 EXPRESS, (Straver, 1992), CAD-4 EXPRESS, RC93 (Watkin et al., 1994), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996), CRYSTALS.
O1—C2 | 1.331 (3) | C6—C11 | 1.543 (3) |
O1—C14 | 1.462 (3) | C7—N8 | 1.494 (3) |
C2—O3 | 1.218 (3) | N8—N9 | 1.227 (3) |
C2—C4 | 1.525 (3) | N9—N10 | 1.133 (3) |
C4—O5 | 1.421 (3) | C11—C12 | 1.519 (3) |
C4—C12 | 1.539 (3) | C11—O13 | 1.424 (3) |
O5—C6 | 1.439 (3) | C14—C15 | 1.509 (3) |
C6—C7 | 1.505 (3) | C14—C16 | 1.510 (4) |
C2—O1—C14 | 116.44 (17) | C6—C7—N8 | 109.04 (19) |
O1—C2—O3 | 124.2 (2) | C7—N8—N9 | 113.4 (2) |
O1—C2—C4 | 111.63 (18) | N8—N9—N10 | 173.7 (3) |
O3—C2—C4 | 124.07 (19) | C6—C11—C12 | 102.52 (17) |
C2—C4—O5 | 109.68 (17) | C6—C11—O13 | 108.97 (17) |
C2—C4—C12 | 113.67 (18) | C12—C11—O13 | 110.87 (18) |
O5—C4—C12 | 104.84 (17) | C4—C12—C11 | 101.61 (18) |
C4—O5—C6 | 109.60 (16) | O1—C14—C15 | 106.30 (18) |
O5—C6—C7 | 111.26 (19) | O1—C14—C16 | 108.05 (19) |
O5—C6—C11 | 106.93 (16) | C15—C14—C16 | 113.3 (2) |
C7—C6—C11 | 112.91 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
O13—H13···O3i | 0.82 | 2.08 | 2.897 (2) | 175 |
Symmetry code: (i) x+1, y, z. |
Acknowledgements
Financial support from the EPSRC to AAE and MPW is gratefully acknowledged.
References
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Sugar amino acids (SAAs) are carbohydrates which contain amine and acid groups; SAAs have been the focus of much interest as dipeptide isosteres, foldamers and library scaffolds (Hill et al., 2001; Gruner et al., 2002; Schweizer, 2002; Chakraborty, Srinivasu, Tapadar & Mohan, 2004; Trabocchi et al., 2005). The preference for SAA oligomers (carbopeptoids) to adopt compact conformations as relatively short homooligomers will provide insight into the paradigm of protein folding. SAAs (2,5-O-cis configuration) structurally related to SAA (3) have a high propensity to adopt repeating β-turn conformations (Hungerford et al., 2000; Smith et al., 2003; Chakraborty, Srinivasu, Sakunthala et al., 2004). In contrast, some 2,5-O-trans SAAs have been shown to adopt helical conformations (Claridge et al., 1999; Claridge et al., 2005). The conformational complexity of these dipeptide isosteres is being further explored by preparation of structurally related analogues of the original SAA systems i.e. SAA (3) and corresponding diastereoisomers (Watterson et al., 2003).
The X-ray crystal structure (Fig. 1) firmly established the relative stereochemistry of the stereogenic centres in (2). The absolute configuration of (2) (see scheme) is determined by the use of D-gulono-1,4-lactone.
The crystal packing consists of chains of molecules linked by hydrogen bonds and lying parallel to the a axis (Fig. 2). There are no unusual intermolecular contacts.