organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 67| Part 9| September 2011| Pages o2531-o2532

6-De­­oxy-3,4-O-iso­propyl­­idene-2-C-methyl-L-galactono-1,5-lactone

aDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, bSummit PLC, 91 Milton Park, Abingdon, Oxfordshire OX14 4RY, England, and cDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England
*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 18 August 2011; accepted 25 August 2011; online 31 August 2011)

X-ray crystallography unequivocally confirmed the stereochemistry of the 2-C-methyl group in the title mol­ecule, C10H16O5, in which the 1,5-lactone ring exists in a boat conformation. The absolute stereochemistry was determined by the use of D-ribose in the synthesis. The crystal exists as O—H⋯O hydrogen bonded chains of mol­ecules running parallel to the a axis with each mol­ecule acting as a donor and acceptor for one hydrogen bond.

Related literature

For branched imino­sugars, see: Håkansson et al. (2007[Håkansson, A. E., Horne, G., Fleet, G. W. J. & Watkin, D. J. (2007). Acta Cryst. E63, o210-o212.], 2008[Håkansson, A. E., van Ameijde, J., Horne, G., Nash, R. J., Wormald, M. R., Kato, A., Besra, G. S., Gurcha, S. & Fleet, G. W. J. (2008). Tetrahedron Lett. 49, 179-184.]); Asano et al. (2000[Asano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymmetry, 11, 1645-1680.]); da Cruz et al. (2011[da Cruz, F. P., Newberry, S., Jenkinson, S. F., Wormald, M. R., Butters, T. D., Alonzi, D. S., Nakagawa, S., Becq, F., Norez, C., Nash, R. J., Kato, A. & Fleet, G. W. J. (2011). Tetrahedron Lett. 52, 219-223.]); Best et al. (2010[Best, D., Jenkinson, S. F., Saville, A. W., Alonzi, D. S., Wormald, M. R., Butters, T. D., Norez, C., Becq, F., Blèriot, Y., Adachi, I., Kato, A. & Fleet, G. W. J. (2010). Tetrahedron Lett. 51, 4170-4174.]) and for branched sugars, see: Booth et al. (2008[Booth, K. V., da Cruz, F. P., Hotchkiss, D. J., Jenkinson, S. F., Jones, N. A., Weymouth-Wilson, A. C., Clarkson, R., Heinz, T. & Fleet, G. W. J. (2008). Tetrahedron Asymmetry, 19, 2417-2424.], 2009[Booth, K. V., Jenkinson, S. F., Best, D., Fernandez Nieto, F., Estevez, R. J., Wormald, M. R., Weymouth-Wilson, A. C. & Fleet, G. W. J. (2009). Tetrahedron Lett. 50, 5088-5093.]); da Cruz et al. (2008[da Cruz, F. P., Horne, G. & Fleet, G. W. J. (2008). Tetrahedron Lett. 49, 6812-6815.]); Hotchkiss et al. (2006[Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315-318.], 2007[Hotchkiss, D. J., Soengas, R., Booth, K. V., Weymouth-Wilson, A. C., Eastwick-Field, V. & Fleet, G. W. J. (2007). Tetrahedron Lett. 48, 517-520.]); Jenkinson et al. (2007[Jenkinson, S. F., Jones, N. A., Moussa, A., Stewart, A. J., Heinz, T. & Fleet, G. W. J. (2007). Tetrahedron Lett. 48, 4441-4445.]); Jones et al. (2007[Jones, N. A., Jenkinson, S. F., Soengas, R., Fanefjord, M., Wormald, M. R., Dwek, R. A., Kiran, G. P., Devendar, R., Takata, G., Morimoto, K., Izumori, K. & Fleet, G. W. J. (2007). Tetrahedron Asymmetry, 18, 774-786.], 2008[Jones, N. A., Rao, D., Yoshihara, A., Gullapalli, P., Morimoto, K., Takata, G., Hunter, S. J., Wormald, M. R., Dwek, R. A., Izumori, K. & Fleet, G. W. J. (2008). Tetrahedron Asymmetry, 19, 1904-1918.]); Rao et al. (2008[Rao, D., Yoshihara, A., Gullapalli, P., Morimoto, K., Takata, G., da Cruz, F. P., Jenkinson, S. F., Wormald, M. R., Dwek, R. A., Fleet, G. W. J. & Izumori, K. (2008). Tetrahedron Lett. 49, 3316-3121.]). For conformations of related 1,5-lactones, see: Baird et al. (1987[Baird, P. D., Dho, J. C., Fleet, G. W. J., Peach, J. M., Prout, K. & Smith, P. W. (1987). J. Chem. Soc. Perkin Trans. 1, pp. 1785-1791.]); Booth et al. (2007a[Booth, K. V., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2007a). Acta Cryst. E63, o1128-o1130.],b[Booth, K. V., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2007b). Acta Cryst. E63, o1759-o1760.]); Bruce et al. (1990[Bruce, I., Fleet, G. W. J., Girdhar, A., Haraldsson, M., Peach, J. M. & Watkin, D. J. (1990). Tetrahedron, 46, 19-32.]); Punzo et al. (2005[Punzo, F., Watkin, D. J., Jenkinson, S. F., Cruz, F. P. & Fleet, G. W. J. (2005). Acta Cryst. E61, o511-o512.], 2006[Punzo, F., Watkin, D. J., Jenkinson, S. F., da Cruz, F. P. & Fleet, G. W. J. (2006). Acta Cryst. E62, o321-o323.]); Dai et al. (2010[Dai, N., Jenkinson, S. F., Fleet, G. W. J. & Watkin, D. J. (2010). Acta Cryst. E66, o406-o407.]).

[Scheme 1]

Experimental

Crystal data
  • C10H16O5

  • Mr = 216.23

  • Orthorhombic, P 21 21 21

  • a = 6.1132 (2) Å

  • b = 12.2963 (4) Å

  • c = 14.6367 (5) Å

  • V = 1100.24 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 150 K

  • 0.20 × 0.20 × 0.04 mm

Data collection
  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.95, Tmax = 1.00

  • 8628 measured reflections

  • 1454 independent reflections

  • 1131 reflections with I > 2σ(I)

  • Rint = 0.067

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.090

  • S = 0.89

  • 1454 reflections

  • 136 parameters

  • H-atom parameters constrained

  • Δρmax = 0.40 e Å−3

  • Δρmin = −0.29 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O11—H111⋯O1i 0.86 1.93 2.793 (3) 172
Symmetry code: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2].

Data collection: COLLECT (Nonius, 2001[Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON, Chemical Crystallography Laboratory, Oxford, England.]); software used to prepare material for publication: CRYSTALS.

Supporting information


Comment top

2-C-Methyl branched sugars, as well as being chirons for the enantiospecific synthesis of complex targets (Hotchkiss et al., 2006; Hotchkiss et al., 2007; da Cruz et al., 2008; Booth et al., 2009) including 2'-C-methyl nucleosides (Jenkinson et al., 2007), are a class of rare sugars with chemotherapeutic potential (Rao et al., 2008; Jones et al., 2008; Booth et al., 2008). Branched iminosugars have also been shown to exhibit interesting biological activity. For example: 6-C-methyl-swainsonine is a more potent inhibitor of L-rhamnosidase than L-swainsonine (Håkansson et al., 2007; Håkansson et al., 2008; Asano et al., 2000); 4-C-methylDAB and 4-C-methylLAB are both potent and specific α-glucosidase inhibitors (da Cruz et al. 2011) and isoLAB has been shown to partially rescue the defective F508del-CFTR function and therefore may have a role in the study of cyctic fibrosis (Best et al., 2010).

D-ribose 1 was converted by a number of steps to the lactols 2 (Fig. 1). The reaction of 2 with sodium cyanide in water gave a chain extension to afford a single isolated crystalline product 3 (Fig. 2).

3,4-O-Isopropylidene-1,5-lactones, such as 3, invariably crystallize in boat conformations (Baird et al., 1987; Bruce et al., 1990; Punzo et al., 2005). The diastereoselectivity of the reaction may be rationalized by the formation of the lactone 3 with less steric congestion (Punzo et al., 2006; Booth et al., 2007a; Booth et al., 2007b; Dai et al. 2010) with the smaller hydroxy group rather than the methyl group in the flagpole position (Fig. 2). The structure of 3 was confirmed by the X-ray crystallographic analysis. The absolute configuration was assigned from the use of D-ribose as the starting material. The title compound exists as O—H···O hydrogen bonded chains of molecules running parallel to the a-axis (Fig. 3). Each molecule acts as a donor and acceptor for 1 hydrogen bond. Only classical hydrogen bonding has been considered.

Related literature top

For branched iminosugars, see: Håkansson et al. (2007, 2008); Asano et al. (2000); da Cruz et al. (2011); Best et al. (2010) and for branched sugars, see: Booth et al. (2008, 2009); da Cruz et al. (2008); Hotchkiss et al. (2006, 2007); Jenkinson et al. (2007); Jones et al. (2007, 2008); Rao et al. (2008). For conformations of related 1,5-lactones, see: Baird et al. (1987); Booth et al. (2007a,b); Bruce et al. (1990); Punzo et al. (2005, 2006); Dai et al. (2010).

Experimental top

The title compound was recrystallized by diffusion from a mixture of ethyl acetate and cyclohexane: m.p. 369–371 K; [α]D25 -84.6 (c, 1.03 in CHCl3).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-ribose as the starting 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 in the range 0.93–0.98, O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 timesUeq of the parent atom), after which the positions were refined with riding constraints.

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); 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 (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic Scheme.
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. Packing diagram of the title compound projected along the b-axis. Hydrogen bonds are shown by dotted lines.
6-Deoxy-3,4-O-isopropylidene-2-C-methyl-L-galactono-1,5-lactone top
Crystal data top
C10H16O5F(000) = 464
Mr = 216.23Dx = 1.305 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1433 reflections
a = 6.1132 (2) Åθ = 5–27°
b = 12.2963 (4) ŵ = 0.11 mm1
c = 14.6367 (5) ÅT = 150 K
V = 1100.24 (6) Å3Plate, colourless
Z = 40.20 × 0.20 × 0.04 mm
Data collection top
Nonius KappaCCD
diffractometer
1131 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.067
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 77
Tmin = 0.95, Tmax = 1.00k = 1515
8628 measured reflectionsl = 1819
1454 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.090 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.06P)2 + 0.14P],
where P = [max(Fo2,0) + 2Fc2]/3
S = 0.89(Δ/σ)max = 0.000259
1454 reflectionsΔρmax = 0.40 e Å3
136 parametersΔρmin = 0.29 e Å3
0 restraints
Crystal data top
C10H16O5V = 1100.24 (6) Å3
Mr = 216.23Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.1132 (2) ŵ = 0.11 mm1
b = 12.2963 (4) ÅT = 150 K
c = 14.6367 (5) Å0.20 × 0.20 × 0.04 mm
Data collection top
Nonius KappaCCD
diffractometer
1454 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
1131 reflections with I > 2σ(I)
Tmin = 0.95, Tmax = 1.00Rint = 0.067
8628 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.090H-atom parameters constrained
S = 0.89Δρmax = 0.40 e Å3
1454 reflectionsΔρmin = 0.29 e Å3
136 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.0165 (3)0.80556 (12)0.89995 (10)0.0290
C20.1164 (4)0.75275 (16)0.85712 (12)0.0226
O30.0426 (3)0.68163 (11)0.79561 (10)0.0287
C40.1986 (4)0.60986 (16)0.74843 (14)0.0289
C50.3861 (4)0.67578 (16)0.71001 (14)0.0271
O60.3108 (3)0.73556 (12)0.63264 (9)0.0355
C70.4068 (4)0.84132 (17)0.63637 (13)0.0292
O80.4222 (3)0.86365 (10)0.73198 (9)0.0261
C90.4744 (4)0.76299 (15)0.77626 (13)0.0240
C100.3643 (4)0.76166 (16)0.86972 (13)0.0221
O110.4337 (3)0.66259 (11)0.91228 (10)0.0301
C120.4222 (4)0.86099 (16)0.92581 (13)0.0277
C130.2506 (5)0.92177 (19)0.59465 (16)0.0401
C140.6306 (5)0.8415 (2)0.59246 (16)0.0422
C150.0664 (5)0.55020 (19)0.67809 (16)0.0402
H410.25540.55720.79480.0338*
H510.50680.62600.69260.0337*
H910.63480.75430.78320.0290*
H1210.58030.86270.93630.0432*
H1220.34900.85700.98640.0426*
H1230.37420.92720.89330.0431*
H1310.30820.99610.60140.0583*
H1320.23490.90480.52890.0582*
H1330.10990.91710.62620.0586*
H1410.68680.91610.59340.0627*
H1420.72800.79290.62680.0622*
H1430.61660.81790.52750.0623*
H1530.16160.49990.64650.0610*
H1520.05080.50920.70770.0613*
H1510.00620.60220.63400.0612*
H1110.43610.67160.97080.0460*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0284 (9)0.0329 (8)0.0257 (7)0.0061 (7)0.0025 (7)0.0035 (7)
C20.0264 (11)0.0224 (10)0.0191 (8)0.0006 (10)0.0006 (9)0.0049 (9)
O30.0263 (8)0.0302 (8)0.0295 (8)0.0029 (7)0.0011 (6)0.0051 (6)
C40.0344 (13)0.0224 (10)0.0299 (11)0.0027 (9)0.0008 (10)0.0023 (9)
C50.0315 (12)0.0276 (10)0.0222 (9)0.0034 (10)0.0012 (10)0.0035 (9)
O60.0500 (11)0.0332 (8)0.0234 (7)0.0145 (8)0.0068 (7)0.0026 (7)
C70.0354 (13)0.0305 (12)0.0216 (10)0.0092 (11)0.0011 (10)0.0005 (9)
O80.0326 (8)0.0250 (7)0.0208 (7)0.0002 (7)0.0006 (6)0.0007 (6)
C90.0220 (11)0.0253 (10)0.0248 (9)0.0032 (9)0.0000 (9)0.0009 (9)
C100.0246 (11)0.0198 (10)0.0220 (9)0.0042 (9)0.0017 (9)0.0009 (8)
O110.0405 (9)0.0267 (7)0.0233 (7)0.0089 (7)0.0047 (7)0.0023 (6)
C120.0300 (12)0.0288 (11)0.0243 (10)0.0005 (10)0.0028 (10)0.0022 (9)
C130.0453 (16)0.0394 (13)0.0355 (12)0.0026 (13)0.0080 (13)0.0110 (12)
C140.0470 (16)0.0480 (14)0.0316 (11)0.0057 (14)0.0137 (12)0.0004 (12)
C150.0509 (17)0.0330 (12)0.0368 (12)0.0104 (12)0.0011 (13)0.0088 (10)
Geometric parameters (Å, º) top
O1—C21.214 (2)C9—H910.992
C2—O31.334 (2)C10—O111.433 (2)
C2—C101.530 (3)C10—C121.514 (3)
O3—C41.472 (3)O11—H1110.864
C4—C51.512 (3)C12—H1210.979
C4—C151.501 (3)C12—H1220.995
C4—H411.000C12—H1230.987
C5—O61.426 (2)C13—H1310.985
C5—C91.543 (3)C13—H1320.989
C5—H510.992C13—H1330.978
O6—C71.428 (3)C14—H1410.979
C7—O81.429 (2)C14—H1420.982
C7—C131.505 (3)C14—H1430.997
C7—C141.512 (3)C15—H1530.967
O8—C91.433 (2)C15—H1520.977
C9—C101.525 (3)C15—H1510.980
O1—C2—O3118.2 (2)C2—C10—O11106.55 (17)
O1—C2—C10124.18 (18)C9—C10—O11105.58 (16)
O3—C2—C10117.60 (18)C2—C10—C12110.78 (18)
C2—O3—C4119.38 (17)C9—C10—C12112.01 (17)
O3—C4—C5110.13 (15)O11—C10—C12112.40 (15)
O3—C4—C15105.41 (19)C10—O11—H111109.1
C5—C4—C15114.54 (18)C10—C12—H121109.5
O3—C4—H41107.1C10—C12—H122109.8
C5—C4—H41109.7H121—C12—H122107.8
C15—C4—H41109.6C10—C12—H123109.5
C4—C5—O6109.09 (18)H121—C12—H123110.5
C4—C5—C9113.83 (17)H122—C12—H123109.7
O6—C5—C9104.69 (15)C7—C13—H131110.0
C4—C5—H51109.2C7—C13—H132108.5
O6—C5—H51110.7H131—C13—H132109.2
C9—C5—H51109.3C7—C13—H133109.2
C5—O6—C7107.85 (16)H131—C13—H133108.7
O6—C7—O8103.85 (15)H132—C13—H133111.2
O6—C7—C13108.81 (18)C7—C14—H141108.2
O8—C7—C13108.23 (18)C7—C14—H142109.3
O6—C7—C14110.92 (18)H141—C14—H142110.5
O8—C7—C14110.89 (19)C7—C14—H143109.1
C13—C7—C14113.65 (18)H141—C14—H143108.4
C7—O8—C9106.95 (14)H142—C14—H143111.3
C5—C9—O8103.77 (15)C4—C15—H153108.4
C5—C9—C10113.70 (17)C4—C15—H152110.1
O8—C9—C10108.47 (15)H153—C15—H152108.9
C5—C9—H91109.6C4—C15—H151109.6
O8—C9—H91111.1H153—C15—H151109.1
C10—C9—H91110.1H152—C15—H151110.7
C2—C10—C9109.25 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C13—H131···O11i0.992.593.536 (3)161
O11—H111···O1ii0.861.932.793 (3)172
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x+1/2, y+3/2, z+2.

Experimental details

Crystal data
Chemical formulaC10H16O5
Mr216.23
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)6.1132 (2), 12.2963 (4), 14.6367 (5)
V3)1100.24 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.20 × 0.20 × 0.04
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.95, 1.00
No. of measured, independent and
observed [I > 2σ(I)] reflections
8628, 1454, 1131
Rint0.067
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.090, 0.89
No. of reflections1454
No. of parameters136
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.40, 0.29

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O11—H111···O1i0.861.932.793 (3)172
Symmetry code: (i) x+1/2, y+3/2, z+2.
 

References

First citationAltomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.  CrossRef Web of Science IUCr Journals Google Scholar
First citationAsano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymmetry, 11, 1645–1680.  Web of Science CrossRef CAS Google Scholar
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Volume 67| Part 9| September 2011| Pages o2531-o2532
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