(3R,4R,5S)-5-(Acetamido­methyl)-N-benzyl-3,4-dihydroxy­tetrahydro­furan-3-carboxamide

Punzo, F.; Watkin, D.J.; Iezzi Simone, M.; Fleet, G.W.J.

doi:10.1107/S1600536805001467

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 61| Part 2| February 2005| Pages o513-o515

https://doi.org/10.1107/S1600536805001467

(3R,4R,5S)-5-(Acetamidomethyl)-N-benzyl-3,4-dihydroxytetrahydrofuran-3-carboxamide

Francesco Punzo,^a ^*‡ David J. Watkin,^b Michela Iezzi Simone ^c and George W. J. Fleet ^c

^aDipartimento di Scienze Chimiche, Facoltà di Farmacia, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy, ^bDepartment of Chemical Crystallography, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, and ^cDepartment of Organic Chemistry, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: francesco.punzo@chemistry.oxford.ac.uk

(Received 10 December 2004; accepted 14 January 2005; online 29 January 2005)

The title compound, C₁₅H₂₀N₂O₅, is the first example of a branched tetrahydrofuran sugar amino acid dipeptide isostere incorporated into a peptidomimetic. The crystal structure contains intermolecular N—H⋯O and O—H⋯O hydrogen bonds.

Comment

δ-Tetrahydrofuran (THF) sugar amino acids (SAA) have been extensively investigated as dipeptide isosteres (Baron et al., 2004 ; Grotenberg et al., 2004 ; Raunkjr et al., 2004 ). Introduction of δ-THF SAA building blocks has been shown to induce secondary structural features such as β-turn-like structures (Chakraborty et al., 2004 ; Smith et al., 2003 ; Hungerford et al., 2000 ) and helices (Claridge et al., 1999 ; Osterkamp et al., 2000 ) in small peptidomimetics. All the previously reported δ-THF SAA scaffolds have linear carbon chains, as in (1), which has been incorporated into peptidomimetics such as (2). The synthesis of branched sugar lactones (Hotchkiss et al., 2004 ) has allowed ready access to a new class of δ-THF SAA building blocks, such as (3), which contain a branched carbon chain. The monomer (3) was prepared as an oil from L-lyxonolactone in a sequence in which the branched carbon chain was introduced by the Ho (1978 , 1985a ,b ) crossed aldol procedure, and the δ-THF ring was subsequently formed by an intramolecular alkylation. The branched scaffold (3) was transformed into the crystalline branched peptidomimetic (4).

The structure of (4) has been determined in order to remove any ambiguity in the stereochemical outcomes of either the aldol or the ring closure reactions. Additionally, the crystal structure of (4) may give some indication of the secondary structural motif likely to be induced by the incorporation of the monomer (3) into peptidomimetics. The molecular structure of (4) is shown in Fig. 1. As usually expected for sugar derivatives, there are intermolecular hydrogen bonds (Table 2 and Fig. 2).

Figure 1
The molecular structure of (4), with displacement ellipsoids drawn at the 50% probability level.

Figure 2
A packing diagram of (4), viewed down the b axis. Hydrogen bonds are indicated by dashed lines.

Experimental

Compound (4) was dissolved in acetone in a small glass cylinder and then crystallized as the solvent evaporated slowly to give colourless needle-like crystals.

Crystal data

C₁₅H₂₀N₂O₅
M_r = 308.33
Orthorhombic, P2₁2₁2₁
a = 15.3802 (6) Å
b = 5.4473 (2) Å
c = 18.0635 (8) Å
V = 1513.37 (10) Å³
Z = 4
D_x = 1.353 Mg m⁻³
Mo Kα radiation
Cell parameters from 3224 reflections
θ = 5–27°
μ = 0.10 mm⁻¹
T = 120 K
Needle, colourless
0.40 × 0.04 × 0.02 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan(DENZO/SCALEPACK; Otwinowski & Minor, 1997 )T_min = 0.820, T_max = 0.998
5747 measured reflections
1973 independent reflections
1594 reflections with I > 2σ(I)
R_int = 0.048
θ_max = 27.4°
h = −19 → 19
k = −7 → 5
l = −23 → 23

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.034
wR(F²) = 0.077
S = 0.93
1973 reflections
200 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + 0.02 + 0.04P], where P = [max(F_o², 0) + 2F_c²]/3
(Δ/σ)_max = 0.001
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.23 e Å⁻³
Extinction correction: Larson (1970 )
Extinction coefficient: 16 (5)

Table 1
Selected bond lengths (Å)

C1—C2	1.551 (2)
C1—C5	1.525 (3)
C1—C12	1.531 (3)
C1—O22	1.421 (2)
C2—C3	1.518 (3)
C2—O11	1.421 (2)
C3—O4	1.438 (2)
C3—C6	1.522 (3)
O4—C5	1.436 (2)
C6—N7	1.453 (2)
N7—C8	1.334 (2)
C8—O9	1.236 (2)
C8—C10	1.501 (3)
C12—N13	1.333 (2)
C12—O21	1.235 (2)
N13—C14	1.454 (2)
C14—C15	1.515 (3)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O22—H6⋯O9ⁱ	0.95	1.75	2.649 (2)	158
N7—H12⋯O21ⁱⁱ	1.00	1.95	2.953 (2)	177
O11—H1⋯O11ⁱⁱⁱ	0.95	1.95	2.886 (2)	166
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iii) $[-x+2, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

In the absence of significant anomalous scattering, Friedel pairs were merged. The absolute configuration of (4) was assigned since the starting material was L-lyxonolactone with known absolute configuration and two of the chiral centres are retained (see scheme). H atoms were located in difference density maps. 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 = 0.98–1.01 Å, O—H = 0.95 Å and N—H = 0.95–1.00 Å), after which they were refined as riding, with U_iso(H) = 1.2U_eq(C), and U_iso(H) = 0.05 Å² for those bonded to N and O atoms.

Data collection: COLLECT (Nonius, 2001 ); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; 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, 4. DOI: https://doi.org/10.1107/S1600536805001467/ob6459sup1.cif

Structure factors: contains datablock 4. DOI: https://doi.org/10.1107/S1600536805001467/ob64594sup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; 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.

(3R,4R,5S)-5-(Acetamidomethyl)-N-benzyl-3,4-dihydroxytetrahydrofuran- 3-carboxamide top

Crystal data top

C₁₅H₂₀N₂O₅	D_x = 1.353 Mg m⁻³
M_r = 308.33	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 3224 reflections
a = 15.3802 (6) Å	θ = 5–27°
b = 5.4473 (2) Å	µ = 0.10 mm⁻¹
c = 18.0635 (8) Å	T = 120 K
V = 1513.37 (10) Å³	Needle, colourless
Z = 4	0.40 × 0.04 × 0.02 mm
F(000) = 656

Data collection top

Nonius KappaCCD diffractometer	1594 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.048
ω scans	θ_max = 27.4°, θ_min = 5.1°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −19→19
T_min = 0.820, T_max = 0.998	k = −7→5
5747 measured reflections	l = −23→23
1973 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.034	w = 1/[σ²(F²) + 0.02 + 0.04P], where P = (max(F_o², 0) + 2F_c²)/3
wR(F²) = 0.077	(Δ/σ)_max = 0.001
S = 0.93	Δρ_max = 0.27 e Å⁻³
1973 reflections	Δρ_min = −0.23 e Å⁻³
200 parameters	Extinction correction: Larson (1970)
0 restraints	Extinction coefficient: 16 (5)
Primary atom site location: structure-invariant direct methods	Absolute structure: see text

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

	x	y	z	U_iso*/U_eq
C1	0.88317 (12)	0.7829 (4)	0.87417 (9)	0.0223
C2	0.97505 (11)	0.8760 (3)	0.85276 (9)	0.0218
C3	1.03223 (13)	0.7093 (3)	0.89934 (10)	0.0236
O4	0.98853 (9)	0.4761 (2)	0.90166 (8)	0.0325
C5	0.89837 (13)	0.5078 (4)	0.88312 (11)	0.0253
C6	1.12326 (12)	0.6622 (4)	0.86972 (10)	0.0280
N7	1.17646 (10)	0.8825 (3)	0.87016 (8)	0.0265
C8	1.23146 (13)	0.9302 (4)	0.92556 (10)	0.0277
O9	1.23594 (9)	0.7976 (3)	0.98096 (7)	0.0359
C10	1.28844 (14)	1.1520 (4)	0.91690 (12)	0.0382
O11	0.99245 (8)	0.8649 (2)	0.77563 (6)	0.0260
C12	0.81349 (12)	0.8364 (3)	0.81569 (9)	0.0223
N13	0.76255 (10)	1.0272 (3)	0.83168 (8)	0.0270
C14	0.69186 (12)	1.1100 (4)	0.78430 (10)	0.0302
C15	0.62532 (12)	1.2545 (4)	0.82810 (10)	0.0258
C16	0.59055 (13)	1.4675 (4)	0.79875 (11)	0.0290
C17	0.52648 (15)	1.5955 (4)	0.83627 (11)	0.0364
C18	0.49727 (14)	1.5138 (4)	0.90401 (11)	0.0369
C19	0.53254 (14)	1.3028 (4)	0.93495 (12)	0.0344
C20	0.59632 (13)	1.1732 (4)	0.89712 (11)	0.0308
O21	0.80707 (9)	0.7148 (3)	0.75824 (7)	0.0310
O22	0.86476 (8)	0.9015 (3)	0.94242 (6)	0.0267
H21	0.9824	1.0484	0.8695	0.0249*
H31	1.0346	0.7770	0.9505	0.0275*
H51	0.8628	0.4350	0.9230	0.0314*
H52	0.8863	0.4194	0.8351	0.0314*
H61	1.1528	0.5378	0.9019	0.0351*
H62	1.1197	0.6002	0.8182	0.0351*
H101	1.3496	1.1069	0.9211	0.0460*
H102	1.2828	1.2342	0.8676	0.0460*
H103	1.2789	1.2808	0.9548	0.0460*
H141	0.7154	1.2151	0.7437	0.0369*
H142	0.6659	0.9606	0.7617	0.0369*
H161	0.6108	1.5234	0.7492	0.0370*
H171	0.5021	1.7491	0.8141	0.0440*
H181	0.4517	1.6088	0.9321	0.0440*
H191	0.5124	1.2389	0.9851	0.0400*
H201	0.6219	1.0239	0.9186	0.0366*
H3	0.7724	1.0854	0.8803	0.0500*
H6	0.8250	0.7940	0.9658	0.0500*
H12	1.1800	0.9957	0.8266	0.0500*
H1	0.9932	0.6928	0.7664	0.0500*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0245 (10)	0.0238 (9)	0.0187 (8)	−0.0028 (9)	0.0037 (8)	−0.0028 (8)
C2	0.0248 (10)	0.0213 (8)	0.0192 (8)	−0.0016 (9)	0.0011 (8)	−0.0008 (8)
C3	0.0272 (10)	0.0211 (8)	0.0226 (9)	−0.0026 (9)	−0.0003 (8)	0.0003 (8)
O4	0.0278 (8)	0.0248 (7)	0.0450 (8)	−0.0026 (7)	−0.0068 (7)	0.0071 (7)
C5	0.0249 (10)	0.0249 (10)	0.0263 (10)	−0.0029 (9)	0.0005 (8)	0.0003 (9)
C6	0.0288 (10)	0.0282 (10)	0.0270 (10)	0.0034 (10)	−0.0045 (9)	−0.0033 (9)
N7	0.0221 (8)	0.0322 (8)	0.0252 (8)	−0.0006 (8)	−0.0029 (7)	0.0027 (8)
C8	0.0217 (10)	0.0331 (11)	0.0284 (10)	0.0027 (9)	−0.0032 (8)	0.0007 (10)
O9	0.0339 (8)	0.0421 (9)	0.0316 (7)	−0.0004 (8)	−0.0118 (6)	0.0080 (7)
C10	0.0323 (12)	0.0396 (12)	0.0428 (12)	−0.0034 (11)	−0.0087 (10)	0.0039 (11)
O11	0.0267 (7)	0.0315 (7)	0.0198 (6)	0.0008 (7)	0.0037 (6)	0.0033 (6)
C12	0.0216 (9)	0.0232 (9)	0.0222 (10)	−0.0032 (9)	0.0032 (8)	−0.0013 (8)
N13	0.0239 (8)	0.0292 (8)	0.0278 (8)	0.0028 (8)	−0.0027 (7)	−0.0039 (8)
C14	0.0256 (10)	0.0372 (10)	0.0276 (10)	0.0032 (10)	−0.0002 (8)	0.0000 (9)
C15	0.0228 (10)	0.0295 (9)	0.0252 (9)	−0.0032 (9)	−0.0023 (8)	−0.0022 (9)
C16	0.0284 (11)	0.0308 (10)	0.0279 (10)	0.0009 (10)	−0.0012 (9)	−0.0004 (9)
C17	0.0377 (12)	0.0365 (11)	0.0351 (11)	0.0071 (11)	−0.0083 (10)	−0.0029 (10)
C18	0.0291 (11)	0.0471 (13)	0.0344 (11)	0.0054 (11)	−0.0015 (10)	−0.0111 (11)
C19	0.0324 (11)	0.0405 (11)	0.0304 (10)	−0.0035 (11)	0.0039 (9)	−0.0016 (10)
C20	0.0327 (11)	0.0298 (10)	0.0299 (10)	−0.0009 (9)	−0.0014 (9)	0.0010 (9)
O21	0.0299 (8)	0.0380 (7)	0.0251 (7)	0.0014 (7)	−0.0014 (6)	−0.0076 (7)
O22	0.0281 (7)	0.0316 (7)	0.0204 (6)	−0.0023 (7)	0.0040 (6)	−0.0042 (6)

Geometric parameters (Å, º) top

C1—C2	1.551 (2)	C10—H103	0.992
C1—C5	1.525 (3)	O11—H1	0.952
C1—C12	1.531 (3)	C12—N13	1.333 (2)
C1—O22	1.421 (2)	C12—O21	1.235 (2)
C2—C3	1.518 (3)	N13—C14	1.454 (2)
C2—O11	1.421 (2)	N13—H3	0.946
C2—H21	0.993	C14—C15	1.515 (3)
C3—O4	1.438 (2)	C14—H141	0.998
C3—C6	1.522 (3)	C14—H142	0.994
C3—H31	0.996	C15—C16	1.383 (3)
O4—C5	1.436 (2)	C15—C20	1.397 (3)
C5—H51	0.988	C16—C17	1.386 (3)
C5—H52	1.009	C16—H161	0.996
C6—N7	1.453 (2)	C17—C18	1.378 (3)
C6—H61	1.001	C17—H171	1.000
C6—H62	0.991	C18—C19	1.388 (3)
N7—C8	1.334 (2)	C18—H181	1.009
N7—H12	1.001	C19—C20	1.389 (3)
C8—O9	1.236 (2)	C19—H191	1.020
C8—C10	1.501 (3)	C20—H201	0.983
C10—H101	0.975	O22—H6	0.947
C10—H102	1.001

C2—C1—C5	102.01 (15)	C8—C10—H102	113.8
C2—C1—C12	113.72 (14)	H101—C10—H102	105.3
C5—C1—C12	111.54 (15)	C8—C10—H103	114.2
C2—C1—O22	104.54 (14)	H101—C10—H103	105.6
C5—C1—O22	112.69 (15)	H102—C10—H103	106.6
C12—C1—O22	111.80 (15)	C2—O11—H1	102.4
C1—C2—C3	101.14 (14)	C1—C12—N13	114.19 (15)
C1—C2—O11	113.85 (14)	C1—C12—O21	122.15 (16)
C3—C2—O11	114.10 (15)	N13—C12—O21	123.65 (17)
C1—C2—H21	109.7	C12—N13—C14	123.60 (16)
C3—C2—H21	109.4	C12—N13—H3	111.7
O11—C2—H21	108.5	C14—N13—H3	124.1
C2—C3—O4	105.93 (15)	N13—C14—C15	111.03 (15)
C2—C3—C6	116.01 (15)	N13—C14—H141	109.7
O4—C3—C6	106.97 (15)	C15—C14—H141	109.4
C2—C3—H31	108.3	N13—C14—H142	106.7
O4—C3—H31	108.5	C15—C14—H142	111.6
C6—C3—H31	110.9	H141—C14—H142	108.3
C3—O4—C5	109.77 (14)	C14—C15—C16	119.78 (17)
C1—C5—O4	106.88 (16)	C14—C15—C20	121.25 (17)
C1—C5—H51	112.7	C16—C15—C20	118.95 (19)
O4—C5—H51	108.5	C15—C16—C17	120.64 (19)
C1—C5—H52	110.5	C15—C16—H161	118.6
O4—C5—H52	108.6	C17—C16—H161	120.7
H51—C5—H52	109.6	C16—C17—C18	120.4 (2)
C3—C6—N7	112.17 (15)	C16—C17—H171	119.5
C3—C6—H61	109.1	C18—C17—H171	120.1
N7—C6—H61	107.5	C17—C18—C19	119.8 (2)
C3—C6—H62	109.7	C17—C18—H181	120.6
N7—C6—H62	108.5	C19—C18—H181	119.6
H61—C6—H62	109.8	C18—C19—C20	119.90 (19)
C6—N7—C8	121.40 (16)	C18—C19—H191	121.4
C6—N7—H12	122.4	C20—C19—H191	118.7
C8—N7—H12	115.7	C15—C20—C19	120.33 (19)
N7—C8—O9	121.84 (19)	C15—C20—H201	119.1
N7—C8—C10	116.61 (17)	C19—C20—H201	120.6
O9—C8—C10	121.55 (18)	C1—O22—H6	103.7
C8—C10—H101	110.7

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O22—H6···O9ⁱ	0.95	1.75	2.649 (2)	158
N7—H12···O21ⁱⁱ	1.00	1.95	2.953 (2)	177
O11—H1···O11ⁱⁱⁱ	0.95	1.95	2.886 (2)	166

Symmetry codes: (i) x−1/2, −y+3/2, −z+2; (ii) −x+2, y+1/2, −z+3/2; (iii) −x+2, y−1/2, −z+3/2.

Footnotes

‡Visiting Scientist at the Department of Chemical Crystallography, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England.

Acknowledgements

Financial support (to MIS) provided through the European Community's Human Potential Programme under contract HPRN-CT-2002-00173 is gratefully acknowledged.

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