Literature DB >> 21201113

3-O-Benzhydryl-2,5-dide-oxy-2,5-imino-2-C-methyl-l-lyxono-1,4-lactone.

Filipa P da Cruz, K Victoria Booth, George W J Fleet, David J Watkin.

Abstract

The title bicyclic lactone, C(19)H(19)NO(3), is an inter-mediate in the synthesis of chiral α-methyl-prolines and branched C-methyl pyrrolidines; the absolute configuration was determined by the use of d-erythronolactone as the starting material. It exhibits no unusual crystal packing features, and each mol-ecule acts as a donor and acceptor for one C-H⋯O hydrogen bond.

Entities: Chemical Disease Gene Species

Year: 2008 PMID： 21201113 PMCID： PMC2959362 DOI： 10.1107/S1600536808027888

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For use of carbohydrates in synthesis see: Monneret & Florent (1994 ▶); Ireland et al. (1983 ▶); Hotchkiss et al. (2006 ▶, 2007a ▶,b ▶); Dukhan et al. (2005 ▶); Rao et al. (2008 ▶); Punzo et al. (2005a ▶,b ▶); Da Cruz et al. (2008 ▶). For related crystallographic literature see: Larson (1970 ▶); Prince (1982 ▶); Watkin (1994 ▶).

Experimental

Crystal data

C19H19NO3 M = 309.36 Orthorhombic, a = 9.0336 (2) Å b = 10.0498 (2) Å c = 17.5941 (4) Å V = 1597.30 (6) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 150 K 0.30 × 0.25 × 0.25 mm

Data collection

Nonius KappaCCD area-detector diffractometer Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ▶) T min = 0.94, T max = 0.98 25603 measured reflections 2071 independent reflections 1411 reflections with I > 2σ(I) R int = 0.053

Refinement

R[F 2 > 2σ(F 2)] = 0.029 wR(F 2) = 0.101 S = 0.86 2071 reflections 212 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.21 e Å−3 Δρmin = −0.21 e Å−3 Data collection: COLLECT (Nonius, 1997-2001 ▶).; 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. Crystal structure: contains datablocks I. DOI: 10.1107/S1600536808027888/cs2089sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808027888/cs2089Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₉H₁₉NO₃	F(000) = 656
M_r = 309.36	D_x = 1.286 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 6711 reflections
a = 9.0336 (2) Å	θ = 5–27°
b = 10.0498 (2) Å	µ = 0.09 mm⁻¹
c = 17.5941 (4) Å	T = 150 K
V = 1597.30 (6) Å³	Block, colourless
Z = 4	0.30 × 0.25 × 0.25 mm

Nonius KappaCCD area-detector diffractometer	1411 reflections with I > 2σ(I)
graphite	R_int = 0.053
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −11→11
T_min = 0.94, T_max = 0.98	k = −13→12
25603 measured reflections	l = −22→22
2071 independent reflections

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.029	Method, part 1, Chebychev polynomial, (Watkin, 1994) [weight] = 1.0/[A₀T₀(x) + A₁T₁(x) ··· + A_n-1]T_n-1(x)] where A_i are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] [1-(deltaF/6*sigmaF)²]² A_i are: 16.5 25.4 13.4 3.97
wR(F²) = 0.101	(Δ/σ)_max = 0.000186
S = 0.86	Δρ_max = 0.21 e Å⁻³
2071 reflections	Δρ_min = −0.21 e Å⁻³
212 parameters	Extinction correction: Larson (1970), Equation 22
0 restraints	Extinction coefficient: 420 (70)
Primary atom site location: structure-invariant direct methods

	x	y	z	U_iso*/U_eq
O1	0.68597 (16)	0.81026 (14)	0.31734 (9)	0.0272
C2	0.6994 (2)	0.69016 (19)	0.27608 (12)	0.0242
C3	0.7190 (3)	0.5647 (2)	0.32511 (13)	0.0286
O4	0.76321 (17)	0.46691 (14)	0.26720 (9)	0.0310
C5	0.8514 (3)	0.5332 (2)	0.21745 (12)	0.0301
C6	0.8569 (2)	0.6776 (2)	0.24385 (12)	0.0281
N7	0.9525 (2)	0.6653 (2)	0.31282 (12)	0.0325
C8	0.8577 (3)	0.5979 (2)	0.37011 (13)	0.0337
C9	0.9106 (3)	0.7768 (3)	0.18667 (15)	0.0392
O10	0.9132 (2)	0.47855 (18)	0.16574 (10)	0.0420
C11	0.5358 (2)	0.8483 (2)	0.33392 (12)	0.0251
C12	0.5418 (2)	0.9877 (2)	0.36769 (12)	0.0266
C13	0.6550 (3)	1.0751 (2)	0.34846 (13)	0.0315
C14	0.6565 (3)	1.2033 (2)	0.37762 (14)	0.0370
C15	0.5459 (3)	1.2459 (2)	0.42665 (15)	0.0406
C16	0.4328 (3)	1.1595 (2)	0.44577 (15)	0.0402
C17	0.4305 (3)	1.0309 (2)	0.41629 (13)	0.0344
C18	0.4604 (2)	0.74727 (19)	0.38447 (11)	0.0253
C19	0.5194 (3)	0.7164 (2)	0.45543 (12)	0.0322
C20	0.4554 (3)	0.6179 (3)	0.50012 (13)	0.0405
C21	0.3303 (3)	0.5504 (2)	0.47385 (16)	0.0422
C22	0.2698 (3)	0.5832 (2)	0.40451 (16)	0.0397
C23	0.3342 (3)	0.6812 (2)	0.35977 (13)	0.0312
H21	0.6217	0.6791	0.2367	0.0282*
H31	0.6344	0.5365	0.3548	0.0341*
H81	0.8335	0.6581	0.4126	0.0399*
H82	0.9062	0.5176	0.3880	0.0400*
H91	1.0125	0.7635	0.1745	0.0585*
H92	0.9002	0.8665	0.2083	0.0596*
H93	0.8509	0.7721	0.1411	0.0587*
H111	0.4814	0.8523	0.2851	0.0297*
H131	0.7306	1.0474	0.3158	0.0374*
H141	0.7337	1.2628	0.3636	0.0445*
H151	0.5485	1.3315	0.4472	0.0487*
H161	0.3564	1.1873	0.4788	0.0478*
H171	0.3527	0.9733	0.4299	0.0420*
H191	0.6040	0.7642	0.4731	0.0384*
H201	0.4969	0.5968	0.5471	0.0498*
H211	0.2866	0.4832	0.5036	0.0514*
H221	0.1848	0.5371	0.3861	0.0482*
H231	0.2913	0.7017	0.3118	0.0394*
H1	0.980 (4)	0.748 (3)	0.3251 (17)	0.0433*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0237 (7)	0.0228 (7)	0.0350 (7)	0.0012 (6)	0.0009 (6)	−0.0054 (6)
C2	0.0247 (9)	0.0202 (9)	0.0278 (9)	−0.0005 (8)	0.0007 (8)	−0.0031 (8)
C3	0.0329 (11)	0.0225 (9)	0.0303 (10)	0.0008 (8)	0.0044 (9)	−0.0034 (8)
O4	0.0330 (8)	0.0242 (7)	0.0359 (8)	0.0010 (6)	0.0024 (7)	−0.0046 (7)
C5	0.0280 (10)	0.0300 (10)	0.0324 (10)	0.0045 (9)	−0.0011 (9)	−0.0022 (9)
C6	0.0243 (10)	0.0261 (9)	0.0340 (10)	0.0013 (8)	0.0015 (8)	−0.0012 (9)
N7	0.0264 (9)	0.0306 (9)	0.0404 (10)	0.0011 (8)	−0.0073 (8)	−0.0026 (8)
C8	0.0375 (12)	0.0306 (11)	0.0331 (11)	0.0063 (10)	−0.0040 (10)	0.0005 (9)
C9	0.0358 (12)	0.0361 (12)	0.0457 (13)	−0.0005 (10)	0.0122 (11)	0.0078 (11)
O10	0.0462 (10)	0.0399 (9)	0.0398 (9)	0.0087 (8)	0.0086 (8)	−0.0084 (8)
C11	0.0224 (9)	0.0270 (9)	0.0260 (9)	0.0031 (8)	−0.0017 (8)	−0.0001 (8)
C12	0.0285 (10)	0.0247 (9)	0.0265 (9)	0.0045 (8)	−0.0011 (8)	0.0008 (8)
C13	0.0307 (11)	0.0267 (10)	0.0372 (11)	0.0034 (9)	0.0025 (10)	0.0025 (9)
C14	0.0385 (12)	0.0246 (10)	0.0478 (13)	−0.0016 (10)	0.0034 (11)	0.0045 (10)
C15	0.0496 (15)	0.0239 (11)	0.0482 (14)	0.0065 (10)	0.0007 (12)	−0.0049 (9)
C16	0.0421 (14)	0.0335 (12)	0.0452 (13)	0.0062 (11)	0.0100 (11)	−0.0051 (10)
C17	0.0361 (12)	0.0289 (11)	0.0383 (12)	0.0023 (10)	0.0079 (10)	−0.0004 (9)
C18	0.0265 (10)	0.0230 (9)	0.0265 (10)	0.0029 (8)	0.0018 (9)	−0.0030 (8)
C19	0.0408 (13)	0.0287 (10)	0.0272 (10)	0.0053 (11)	−0.0017 (10)	−0.0039 (8)
C20	0.0570 (16)	0.0362 (12)	0.0283 (10)	0.0138 (11)	0.0069 (12)	0.0020 (10)
C21	0.0474 (14)	0.0292 (11)	0.0501 (14)	0.0055 (11)	0.0209 (13)	0.0051 (10)
C22	0.0348 (12)	0.0299 (11)	0.0544 (15)	−0.0019 (10)	0.0093 (12)	−0.0035 (11)
C23	0.0284 (10)	0.0295 (10)	0.0356 (10)	0.0009 (8)	0.0004 (9)	−0.0038 (9)

O1—C2	1.414 (2)	C12—C13	1.390 (3)
O1—C11	1.439 (2)	C12—C17	1.389 (3)
C2—C3	1.538 (3)	C13—C14	1.387 (3)
C2—C6	1.537 (3)	C13—H131	0.935
C2—H21	0.992	C14—C15	1.388 (4)
C3—O4	1.471 (2)	C14—H141	0.951
C3—C8	1.519 (3)	C15—C16	1.382 (4)
C3—H31	0.968	C15—H151	0.934
O4—C5	1.358 (3)	C16—C17	1.393 (3)
C5—C6	1.524 (3)	C16—H161	0.945
C5—O10	1.200 (3)	C17—H171	0.941
C6—N7	1.495 (3)	C18—C19	1.393 (3)
C6—C9	1.497 (3)	C18—C23	1.389 (3)
N7—C8	1.486 (3)	C19—C20	1.390 (4)
N7—H1	0.89 (3)	C19—H191	0.954
C8—H81	0.986	C20—C21	1.397 (4)
C8—H82	0.971	C20—H201	0.932
C9—H91	0.955	C21—C22	1.377 (4)
C9—H92	0.983	C21—H211	0.942
C9—H93	0.968	C22—C23	1.389 (4)
C11—C12	1.523 (3)	C22—H221	0.954
C11—C18	1.512 (3)	C23—H231	0.952
C11—H111	0.990

C2—O1—C11	114.34 (15)	C12—C11—C18	113.84 (17)
O1—C2—C3	114.94 (16)	O1—C11—H111	107.6
O1—C2—C6	109.83 (16)	C12—C11—H111	108.5
C3—C2—C6	91.88 (16)	C18—C11—H111	108.3
O1—C2—H21	113.2	C11—C12—C13	120.81 (19)
C3—C2—H21	112.4	C11—C12—C17	120.2 (2)
C6—C2—H21	112.8	C13—C12—C17	119.0 (2)
C2—C3—O4	100.99 (16)	C12—C13—C14	120.3 (2)
C2—C3—C8	101.98 (17)	C12—C13—H131	119.9
O4—C3—C8	106.51 (17)	C14—C13—H131	119.8
C2—C3—H31	116.9	C13—C14—C15	120.6 (2)
O4—C3—H31	113.0	C13—C14—H141	119.7
C8—C3—H31	115.7	C15—C14—H141	119.7
C3—O4—C5	106.11 (16)	C14—C15—C16	119.4 (2)
O4—C5—C6	106.84 (17)	C14—C15—H151	120.5
O4—C5—O10	122.5 (2)	C16—C15—H151	120.2
C6—C5—O10	130.6 (2)	C15—C16—C17	120.2 (2)
C2—C6—C5	99.24 (16)	C15—C16—H161	120.3
C2—C6—N7	104.02 (17)	C17—C16—H161	119.5
C5—C6—N7	100.82 (17)	C16—C17—C12	120.6 (2)
C2—C6—C9	119.55 (18)	C16—C17—H171	119.2
C5—C6—C9	116.07 (19)	C12—C17—H171	120.3
N7—C6—C9	114.42 (19)	C11—C18—C19	120.3 (2)
C6—N7—C8	104.77 (16)	C11—C18—C23	120.47 (19)
C6—N7—H1	106 (2)	C19—C18—C23	119.2 (2)
C8—N7—H1	115 (2)	C18—C19—C20	120.4 (2)
C3—C8—N7	102.82 (18)	C18—C19—H191	119.1
C3—C8—H81	110.3	C20—C19—H191	120.5
N7—C8—H81	111.3	C19—C20—C21	119.7 (2)
C3—C8—H82	111.0	C19—C20—H201	119.8
N7—C8—H82	109.7	C21—C20—H201	120.5
H81—C8—H82	111.3	C20—C21—C22	119.9 (2)
C6—C9—H91	111.7	C20—C21—H211	120.3
C6—C9—H92	108.6	C22—C21—H211	119.9
H91—C9—H92	107.9	C21—C22—C23	120.4 (3)
C6—C9—H93	110.2	C21—C22—H221	120.3
H91—C9—H93	110.1	C23—C22—H221	119.3
H92—C9—H93	108.2	C18—C23—C22	120.4 (2)
O1—C11—C12	106.90 (17)	C18—C23—H231	120.5
O1—C11—C18	111.45 (16)	C22—C23—H231	119.1

D—H···A	D—H	H···A	D···A	D—H···A
C20—H201···O10ⁱ	0.93	2.36	3.293 (3)	174
N7—H1···O10ⁱⁱ	0.89 (2)	2.52 (3)	3.395 (3)	168

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C20—H201⋯O10ⁱ	0.93	2.36	3.293 (3)	174

Symmetry code: (i) .

1 in total

1. Synthesis of 2'-C-methyl-4'-thio ribonucleosides.

Authors: D Dukhan; E Bosc; J Peyronnet; R Storer; G Gosselin
Journal: Nucleosides Nucleotides Nucleic Acids Date: 2005 Impact factor: 1.381

1 in total