Literature DB >> 21201208

tert-Butyl 2-de-oxy-4,5-O-isopropyl-idene-d-gluconate.

Sarah F Jenkinson, K Victoria Booth, Daniel Best, George W J Fleet, David J Watkin.   

Abstract

The relative configuration of tert-butyl 2-de-oxy-4,5-O-iso-propyl-idene-d-gluconate, C(13)H(24)O(6), an inter-mediate in the synthesis of 2-de-oxy sugars, was determined by X-ray crystallography, and the crystal structure consists of chains of O-H⋯O hydrogen-bonded mol-ecules running parallel to the a axis. There are two mol-ecules in the asymmetric unit. The absolute configuration was inferred from the use of d-erythrono-lactone as the starting material.

Entities:  

Year:  2008        PMID: 21201208      PMCID: PMC2959253          DOI: 10.1107/S160053680803064X

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


Related literature

For background information, see: Granstrom et al. (2004 ▶); Izumori (2002 ▶, 2006 ▶); Rao et al. (2008 ▶); Yoshihara et al. (2008 ▶); Gullapalli et al. (2007 ▶); Jones et al. (2008 ▶). For related structures, see: Booth et al. (2008 ▶); Jenkinson, Booth, Gullapalli et al. (2008 ▶); Jenkinson, Booth, Yoshihara et al. (2008 ▶). For related literature, see: Görbitz (1999 ▶).

Experimental

Crystal data

C13H24O6 M = 276.33 Triclinic, a = 5.9366 (2) Å b = 11.1694 (5) Å c = 12.7530 (6) Å α = 113.413 (2)° β = 100.3696 (19)° γ = 93.783 (2)° V = 754.42 (6) Å3 Z = 2 Mo Kα radiation μ = 0.10 mm−1 T = 150 K 0.50 × 0.05 × 0.05 mm

Data collection

Nonius KappaCCD diffractometer Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ▶) T min = 0.73, T max = 1.00 (expected range = 0.727–0.995) 11759 measured reflections 3441 independent reflections 2788 reflections with I > 2σ(I) R int = 0.045

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.104 S = 0.97 3441 reflections 344 parameters 3 restraints H-atom parameters constrained Δρmax = 0.29 e Å−3 Δρmin = −0.37 e Å−3 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. Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680803064X/lh2696sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053680803064X/lh2696Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H24O6Z = 2
Mr = 276.33F(000) = 300
Triclinic, P1Dx = 1.216 Mg m3
Hall symbol: P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.9366 (2) ÅCell parameters from 3172 reflections
b = 11.1694 (5) Åθ = 5–27°
c = 12.7530 (6) ŵ = 0.10 mm1
α = 113.413 (2)°T = 150 K
β = 100.3696 (19)°Plate, colourless
γ = 93.783 (2)°0.50 × 0.05 × 0.05 mm
V = 754.42 (6) Å3
Nonius KappaCCD diffractometer2788 reflections with I > 2σ(I)
graphiteRint = 0.045
ω scansθmax = 27.6°, θmin = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)h = −7→7
Tmin = 0.73, Tmax = 1.00k = −14→14
11759 measured reflectionsl = −16→15
3441 independent reflections
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.040w = 1/[σ2(F2) + (0.05P)2 + 0.04P], where P = [max(Fo2,0) + 2Fc2]/3
wR(F2) = 0.104(Δ/σ)max = 0.009
S = 0.97Δρmax = 0.29 e Å3
3441 reflectionsΔρmin = −0.37 e Å3
344 parametersExtinction correction: Larson (1970), Equation 22
3 restraintsExtinction coefficient: 300 (50)
Primary atom site location: structure-invariant direct methods
xyzUiso*/Ueq
C1−0.0837 (4)0.8713 (3)0.3566 (2)0.0306
C2−0.0148 (4)0.7957 (3)0.2427 (2)0.0322
C30.1598 (5)0.7048 (3)0.2533 (2)0.0300
C40.2288 (4)0.6384 (3)0.1362 (2)0.0296
C50.3854 (4)0.5302 (2)0.1211 (2)0.0297
C60.4988 (4)0.5130 (3)0.2286 (2)0.0338
O70.1033 (3)0.94685 (18)0.43945 (15)0.0333
C80.0854 (5)1.0276 (3)0.5600 (2)0.0342
C9−0.0134 (6)0.9420 (4)0.6127 (3)0.0497
C10−0.0575 (5)1.1357 (3)0.5601 (3)0.0448
C110.3368 (5)1.0859 (3)0.6218 (3)0.0469
O12−0.2796 (3)0.8666 (2)0.37003 (19)0.0434
O130.0757 (3)0.61392 (18)0.29471 (16)0.0330
O140.0195 (3)0.57145 (19)0.04704 (15)0.0335
C150.0657 (5)0.4490 (3)−0.0322 (2)0.0315
C16−0.1538 (5)0.3507 (3)−0.0776 (2)0.0403
C170.1621 (5)0.4644 (3)−0.1296 (2)0.0408
O180.2336 (3)0.41137 (18)0.04004 (16)0.0325
O190.6656 (3)0.4251 (2)0.20259 (18)0.0391
C210.6774 (5)0.7195 (3)0.8287 (2)0.0356
C220.8773 (5)0.7868 (3)0.9330 (2)0.0357
C231.0405 (4)0.8902 (3)0.9222 (2)0.0306
C241.2437 (5)0.9472 (3)1.0283 (2)0.0350
C251.4344 (5)1.0537 (3)1.0373 (2)0.0327
C261.4393 (5)1.0846 (3)0.9321 (2)0.0373
O270.7534 (3)0.6588 (2)0.73097 (16)0.0386
C280.5895 (5)0.5818 (3)0.6156 (2)0.0400
C310.7540 (6)0.5357 (4)0.5339 (3)0.0531
C300.4520 (6)0.4661 (4)0.6211 (3)0.0553
C290.4360 (6)0.6706 (4)0.5831 (3)0.0533
O320.4758 (4)0.7182 (2)0.8340 (2)0.0513
O330.9021 (3)0.9849 (2)0.90964 (19)0.0433
O341.1547 (4)1.0087 (2)1.13082 (17)0.0549
C351.2946 (5)1.1313 (3)1.2071 (2)0.0377
C361.1384 (6)1.2284 (4)1.2579 (3)0.0572
C371.4752 (6)1.1154 (4)1.2987 (3)0.0593
O381.4021 (3)1.17115 (18)1.13186 (15)0.0334
O391.2520 (3)1.14885 (18)0.90474 (16)0.0354
H210.05520.86640.22650.0350*
H374−0.15350.74910.18850.0343*
H310.30320.75270.30230.0358*
H410.30720.71130.12410.0318*
H510.51230.55650.09370.0299*
H610.57850.59720.28540.0415*
H620.38420.48670.26760.0379*
H910.00910.99310.69690.0748*
H92−0.17810.90900.57410.0753*
H930.07080.86660.59690.0762*
H101−0.06951.18920.63830.0603*
H1020.01841.19240.53100.0619*
H103−0.21121.09370.50940.0604*
H1110.34901.14320.70560.0638*
H1120.39111.13600.58170.0621*
H1130.43031.01390.61210.0605*
H161−0.13350.2644−0.13560.0533*
H162−0.27100.3893−0.11180.0541*
H163−0.20180.3427−0.01020.0533*
H1710.21040.3825−0.17640.0583*
H1720.04390.4833−0.18090.0615*
H1730.29320.5356−0.09310.0603*
H2210.81350.83091.00280.0370*
H2220.96740.72300.94700.0375*
H2311.10050.84160.84410.0329*
H2411.31490.87251.03240.0438*
H2511.58711.02451.05030.0384*
H2611.58571.14530.95440.0459*
H2621.43081.00160.86390.0418*
H3110.66430.47810.45590.0697*
H3120.84100.60730.52690.0725*
H3130.86020.48480.55750.0711*
H3010.35120.41530.54560.0753*
H3020.36150.50070.67930.0752*
H3030.55650.41290.64240.0755*
H2910.35500.62320.50020.0783*
H2920.32330.69220.63270.0779*
H2930.53420.75080.59610.0786*
H3611.23111.31401.30970.0856*
H3621.05541.19461.30150.0842*
H3631.03131.23541.19540.0846*
H3711.56761.20091.35120.0897*
H3721.39541.07961.34090.0880*
H3731.57441.05531.26000.0883*
H220.60690.34430.17450.0550*
H370.99881.04070.90810.0730*
H49−0.03940.56170.25500.0476*
H51.26941.22330.95970.0500*
U11U22U33U12U13U23
C10.0284 (13)0.0241 (13)0.0345 (13)0.0024 (10)0.0056 (10)0.0082 (11)
C20.0343 (13)0.0255 (13)0.0318 (12)0.0046 (10)0.0077 (10)0.0069 (11)
C30.0297 (12)0.0274 (13)0.0316 (12)0.0024 (10)0.0081 (9)0.0109 (11)
C40.0343 (13)0.0236 (13)0.0312 (12)0.0027 (10)0.0103 (10)0.0110 (11)
C50.0298 (12)0.0228 (13)0.0335 (12)0.0009 (10)0.0102 (10)0.0079 (10)
C60.0298 (12)0.0320 (14)0.0391 (14)0.0067 (11)0.0087 (10)0.0136 (11)
O70.0300 (9)0.0307 (10)0.0312 (9)0.0033 (7)0.0109 (7)0.0030 (8)
C80.0352 (13)0.0356 (15)0.0266 (12)0.0057 (11)0.0112 (10)0.0058 (11)
C90.0574 (19)0.0531 (19)0.0414 (15)0.0020 (15)0.0160 (14)0.0213 (15)
C100.0477 (16)0.0340 (16)0.0424 (16)0.0098 (13)0.0092 (13)0.0053 (13)
C110.0385 (16)0.0500 (19)0.0384 (14)0.0013 (13)0.0060 (12)0.0063 (14)
O120.0297 (10)0.0414 (12)0.0477 (11)0.0036 (8)0.0120 (8)0.0059 (9)
O130.0321 (9)0.0332 (10)0.0339 (9)0.0005 (7)0.0081 (7)0.0147 (8)
O140.0379 (10)0.0288 (10)0.0280 (9)0.0092 (8)0.0063 (7)0.0057 (8)
C150.0414 (15)0.0258 (13)0.0253 (11)0.0103 (11)0.0086 (10)0.0073 (10)
C160.0411 (15)0.0351 (15)0.0359 (14)0.0033 (12)0.0043 (11)0.0080 (12)
C170.0532 (17)0.0378 (16)0.0294 (13)0.0083 (13)0.0126 (12)0.0103 (12)
O180.0370 (10)0.0227 (9)0.0354 (9)0.0049 (7)0.0046 (7)0.0110 (8)
O190.0311 (9)0.0307 (10)0.0510 (11)0.0069 (8)0.0077 (8)0.0129 (9)
C210.0399 (15)0.0298 (15)0.0351 (14)0.0042 (11)0.0074 (11)0.0121 (12)
C220.0425 (15)0.0291 (14)0.0307 (13)0.0038 (11)0.0035 (11)0.0100 (11)
C230.0322 (13)0.0275 (13)0.0321 (12)0.0102 (10)0.0064 (10)0.0121 (11)
C240.0422 (15)0.0286 (14)0.0331 (13)0.0028 (11)0.0042 (11)0.0140 (12)
C250.0325 (13)0.0268 (13)0.0349 (13)0.0068 (10)0.0073 (10)0.0085 (11)
C260.0428 (15)0.0322 (15)0.0400 (14)0.0115 (12)0.0153 (12)0.0146 (12)
O270.0370 (10)0.0368 (11)0.0310 (9)0.0039 (8)0.0019 (8)0.0053 (8)
C280.0374 (14)0.0404 (17)0.0348 (14)−0.0020 (12)0.0015 (11)0.0120 (13)
C310.0525 (19)0.059 (2)0.0333 (14)0.0006 (16)0.0091 (13)0.0060 (14)
C300.066 (2)0.049 (2)0.0388 (16)−0.0109 (16)0.0027 (14)0.0126 (15)
C290.0459 (17)0.065 (2)0.0492 (17)0.0050 (16)−0.0018 (14)0.0293 (17)
O320.0376 (11)0.0576 (15)0.0490 (12)0.0053 (10)0.0111 (9)0.0120 (11)
O330.0349 (10)0.0435 (12)0.0654 (14)0.0144 (9)0.0148 (9)0.0343 (11)
O340.0727 (15)0.0466 (13)0.0281 (10)−0.0250 (11)0.0114 (10)0.0031 (9)
C350.0431 (15)0.0355 (15)0.0299 (13)−0.0060 (12)0.0042 (11)0.0125 (12)
C360.061 (2)0.062 (2)0.0487 (17)0.0073 (17)0.0258 (16)0.0180 (17)
C370.067 (2)0.067 (2)0.0449 (18)0.0006 (18)−0.0012 (16)0.0313 (18)
O380.0384 (10)0.0290 (10)0.0301 (9)0.0022 (8)0.0085 (7)0.0097 (8)
O390.0481 (11)0.0262 (9)0.0302 (9)0.0090 (8)0.0087 (8)0.0096 (8)
C1—C21.508 (3)C21—C221.504 (4)
C1—O71.344 (3)C21—O271.337 (3)
C1—O121.206 (3)C21—O321.210 (4)
C2—C31.524 (4)C22—C231.522 (4)
C2—H210.977C22—H2210.988
C2—H3740.937C22—H2220.971
C3—C41.526 (3)C23—C241.522 (4)
C3—O131.418 (3)C23—O331.423 (3)
C3—H310.940C23—H2311.066
C4—C51.546 (4)C24—C251.542 (4)
C4—O141.445 (3)C24—O341.429 (3)
C4—H410.989C24—H2410.975
C5—C61.504 (4)C25—C261.516 (4)
C5—O181.435 (3)C25—O381.439 (3)
C5—H510.961C25—H2510.992
C6—O191.429 (3)C26—O391.427 (3)
C6—H610.954C26—H2610.988
C6—H621.004C26—H2620.978
O7—C81.469 (3)O27—C281.490 (3)
C8—C91.513 (4)C28—C311.520 (4)
C8—C101.521 (4)C28—C301.514 (5)
C8—C111.521 (4)C28—C291.516 (5)
C9—H910.974C31—H3110.971
C9—H920.985C31—H3120.967
C9—H930.977C31—H3130.962
C10—H1010.956C30—H3010.960
C10—H1020.974C30—H3020.966
C10—H1030.980C30—H3030.964
C11—H1110.990C29—H2910.983
C11—H1120.970C29—H2920.979
C11—H1130.987C29—H2930.973
O13—H490.807O33—H370.827
O14—C151.420 (3)O34—C351.418 (4)
C15—C161.508 (4)C35—C361.499 (5)
C15—C171.520 (4)C35—C371.512 (4)
C15—O181.432 (3)C35—O381.431 (3)
C16—H1610.986C36—H3610.975
C16—H1620.970C36—H3620.967
C16—H1630.987C36—H3630.959
C17—H1710.968C37—H3710.976
C17—H1720.965C37—H3720.955
C17—H1730.974C37—H3730.967
O19—H220.849O39—H50.832
C2—C1—O7110.2 (2)C22—C21—O27110.8 (2)
C2—C1—O12124.6 (2)C22—C21—O32124.2 (2)
O7—C1—O12125.2 (2)O27—C21—O32125.0 (3)
C1—C2—C3112.8 (2)C21—C22—C23113.8 (2)
C1—C2—H21102.3C21—C22—H221108.0
C3—C2—H21110.5C23—C22—H221108.2
C1—C2—H374105.5C21—C22—H222111.0
C3—C2—H374112.2C23—C22—H222108.3
H21—C2—H374112.9H221—C22—H222107.4
C2—C3—C4109.1 (2)C22—C23—C24110.0 (2)
C2—C3—O13111.77 (19)C22—C23—O33105.6 (2)
C4—C3—O13113.4 (2)C24—C23—O33113.9 (2)
C2—C3—H31111.7C22—C23—H231106.9
C4—C3—H31100.9C24—C23—H231110.2
O13—C3—H31109.6O33—C23—H231109.8
C3—C4—C5118.7 (2)C23—C24—C25119.8 (2)
C3—C4—O14107.8 (2)C23—C24—O34108.3 (2)
C5—C4—O14104.06 (19)C25—C24—O34104.3 (2)
C3—C4—H41105.0C23—C24—H241106.4
C5—C4—H41109.2C25—C24—H241108.8
O14—C4—H41112.2O34—C24—H241108.9
C4—C5—C6118.2 (2)C24—C25—C26119.6 (2)
C4—C5—O18103.49 (19)C24—C25—O38103.7 (2)
C6—C5—O18109.7 (2)C26—C25—O38108.4 (2)
C4—C5—H51105.4C24—C25—H251108.9
C6—C5—H51104.5C26—C25—H251101.8
O18—C5—H51116.0O38—C25—H251115.1
C5—C6—O19110.7 (2)C25—C26—O39113.7 (2)
C5—C6—H61107.6C25—C26—H261105.0
O19—C6—H61107.9O39—C26—H261108.5
C5—C6—H62113.0C25—C26—H262108.2
O19—C6—H62112.6O39—C26—H262107.9
H61—C6—H62104.6H261—C26—H262113.6
C1—O7—C8121.33 (19)C21—O27—C28121.5 (2)
O7—C8—C9110.5 (2)O27—C28—C31101.9 (2)
O7—C8—C10109.2 (2)O27—C28—C30109.1 (2)
C9—C8—C10112.6 (2)C31—C28—C30111.3 (3)
O7—C8—C11102.4 (2)O27—C28—C29110.2 (3)
C9—C8—C11110.9 (3)C31—C28—C29111.3 (3)
C10—C8—C11110.7 (3)C30—C28—C29112.6 (3)
C8—C9—H91109.0C28—C31—H311108.8
C8—C9—H92109.5C28—C31—H312113.1
H91—C9—H92112.0H311—C31—H312106.9
C8—C9—H93107.4C28—C31—H313111.9
H91—C9—H93110.2H311—C31—H313106.7
H92—C9—H93108.6H312—C31—H313109.1
C8—C10—H101109.9C28—C30—H301108.4
C8—C10—H102109.8C28—C30—H302108.0
H101—C10—H102108.0H301—C30—H302109.9
C8—C10—H103108.1C28—C30—H303109.6
H101—C10—H103110.7H301—C30—H303110.6
H102—C10—H103110.4H302—C30—H303110.2
C8—C11—H111110.5C28—C29—H291108.4
C8—C11—H112106.6C28—C29—H292109.2
H111—C11—H112111.1H291—C29—H292110.0
C8—C11—H113109.5C28—C29—H293108.0
H111—C11—H113111.5H291—C29—H293111.1
H112—C11—H113107.5H292—C29—H293110.0
C3—O13—H49118.0C23—O33—H37102.0
C4—O14—C15108.28 (18)C24—O34—C35110.3 (2)
O14—C15—C16108.2 (2)O34—C35—C36108.2 (3)
O14—C15—C17111.3 (2)O34—C35—C37110.9 (3)
C16—C15—C17112.9 (2)C36—C35—C37113.5 (3)
O14—C15—O18103.72 (19)O34—C35—O38104.4 (2)
C16—C15—O18109.1 (2)C36—C35—O38108.6 (3)
C17—C15—O18111.1 (2)C37—C35—O38110.6 (2)
C15—C16—H161111.7C35—C36—H361109.6
C15—C16—H162106.1C35—C36—H362107.2
H161—C16—H162111.4H361—C36—H362110.4
C15—C16—H163108.4C35—C36—H363109.2
H161—C16—H163111.4H361—C36—H363110.6
H162—C16—H163107.5H362—C36—H363110.0
C15—C17—H171109.6C35—C37—H371109.8
C15—C17—H172110.2C35—C37—H372107.5
H171—C17—H172107.4H371—C37—H372110.8
C15—C17—H173107.8C35—C37—H373109.1
H171—C17—H173110.7H371—C37—H373109.7
H172—C17—H173111.1H372—C37—H373109.9
C5—O18—C15106.46 (18)C25—O38—C35107.8 (2)
C6—O19—H22113.3C26—O39—H5107.4
D—H···AD—HH···AD···AD—H···A
C2—H21···O34i0.982.463.407 (4)164
C3—H31···O12ii0.942.543.442 (4)161
C9—H91···O39iii0.972.603.502 (4)154
C10—H103···O120.982.403.031 (4)121
C22—H222···O14iv0.972.503.349 (4)147
C30—H302···O320.972.403.009 (4)121
O19—H22···O38v0.852.032.861 (4)165
O33—H37···C260.832.573.231 (4)138
O33—H37···O390.831.882.703 (4)171
O13—H49···O19iii0.812.062.842 (4)162
O39—H5···O18vi0.831.982.771 (4)157
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O19—H22⋯O38i0.852.032.861 (4)165
O13—H49⋯O19ii0.812.062.842 (4)162
O39—H5⋯O18iii0.831.982.771 (4)157

Symmetry codes: (i) ; (ii) ; (iii) .

  7 in total

1.  What is the best crystal size for collection of X-ray data? Refinement of the structure of glycyl-L-serine based on data from a very large crystal.

Authors: 
Journal:  Acta Crystallogr B       Date:  1999-12-01

2.  Izumoring: a strategy for bioproduction of all hexoses.

Authors:  Ken Izumori
Journal:  J Biotechnol       Date:  2006-05-23       Impact factor: 3.307

3.  Bioproduction strategies for rare hexose sugars.

Authors:  Ken Izumori
Journal:  Naturwissenschaften       Date:  2002-03

4.  Izumoring: a novel and complete strategy for bioproduction of rare sugars.

Authors:  Tom Birger Granström; Goro Takata; Masaaki Tokuda; Ken Izumori
Journal:  J Biosci Bioeng       Date:  2004       Impact factor: 2.894

5.  1-De-oxy-d-galactitol (l-fucitol).

Authors:  Sarah F Jenkinson; K Victoria Booth; Akihide Yoshihara; Kenji Morimoto; George W J Fleet; Ken Izumori; David J Watkin
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-07-09

6.  6-De-oxy-α-l-talopyran-ose.

Authors:  K Victoria Booth; Sarah F Jenkinson; George W J Fleet; Pushpakiran Gullapalli; Akihide Yoshihara; Ken Izumori; David J Watkin
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-07-05

7.  1-De-oxy-l-mannitol (6-de-oxy-l-mannitol or l-rhamnitol).

Authors:  Sarah F Jenkinson; K Victoria Booth; Pushpakiran Gullapalli; Kenji Morimoto; Ken Izumori; George W J Fleet; David J Watkin
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-08-06
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  1 in total

1.  (4R)-4-(2-Allyl-2H-1,2,3-triazol-4-yl)-1,2-O-isopropyl-idene-l-threose.

Authors:  Sarah F Jenkinson; Daniel Best; Francis X Wilson; George W J Fleet; David J Watkin
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-11-13
  1 in total

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