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 2| February 2011| Pages o414-o415

5-Fluoro-1,3-di­hydro-2,1-benzoxaborol-1-ol

aWarsaw University of Technology, Faculty of Chemistry, Noakowskiego 3, 00-664 Warszawa, Poland
*Correspondence e-mail: izabela@ch.pw.edu.pl

(Received 23 December 2010; accepted 11 January 2011; online 15 January 2011)

In the crystal structure of the title compound, C7H6BFO2, a broad-spectrum anti­fungal drug (AN2690), the planar [maximum deviation 0.035 (1) Å] mol­ecules form centrosymmetric R22(8) dimers via strong O—H⋯O hydrogen bonds. The dimers are arranged into layers by weak inter­molecular C—H⋯O and C—H⋯F hydrogen bonds. The symmetry of this two-dimensional supra­molecular assembly can be described by the layer group p[\overline{1}] and topologically classified as a simple uninodal four-connected two-dimensional network of a (4.4.4.4.6.6) topology. Further weak C—H⋯O inter­actions build up the three-dimensional structure.

Related literature

For the review of the synthesis, properties and applications of benzoxaboroles, see: Adamczyk-Woźniak et al. (2009[Adamczyk-Woźniak, A., Cyrański, M. K., Żubrowska, A. & Sporzyński, A. (2009). J. Organomet. Chem. 694, 3533-3541.]). For the biological activity of the title compound, see: Baker et al. (2005[Baker, S. J., Hui, X. & Maibach, H. I. (2005). Annu. Rep. Med. Chem. 40, 323-335.], 2006[Baker, S. J., Zhang, Y.-K., Akama, T., Lau, A., Zhou, H., Hernandez, V., Mao, W., Alley, M. R. K., Sanders, V. & Plattner, J. (2006). J. Med. Chem. 49, 4447-4450.]); Hui et al. (2007[Hui, X., Baker, S. J., Wester, R. C., Barbadillo, S., Cashmore, A. K., Sanders, V., Hold, K. M., Akama, T., Zhang, Y.-K., Plattner, J. J. & Maibach, H. I. (2007). J. Pharm. Sci. 96, 2622-2631.]); Rock et al. (2007[Rock, F. L., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou, H., Zhang, Y.-K., Hernandez, V., Akama, T., Baker, S. J., Plattner, J. J., Shapiro, L., Martinis, S. A., Benkovic, S. J., Cusack, S. & Alley, M. R. K. (2007). Science, 316, 1759-1761.]). For the synthesis see: Baker et al. (2006[Baker, S. J., Zhang, Y.-K., Akama, T., Lau, A., Zhou, H., Hernandez, V., Mao, W., Alley, M. R. K., Sanders, V. & Plattner, J. (2006). J. Med. Chem. 49, 4447-4450.]), Gunasekera et al. (2007[Gunasekera, D. S., Gerold, D. J., Aalderks, N. S., Chandra, J. S., Maanu, C. A., Kiprof, P., Zhdankin, V. V. & Reddy, M. V. R. (2007). Tetrahedron, 63, 9401-9405.]). For related structures, see: Adamczyk-Woźniak et al. (2010[Adamczyk-Woźniak, A., Cyrański, M. K., Jakubczyk, M., Klimentowska, P., Koll, A., Kołodziejczak, J., Pojmaj, G., Żubrowska, A., Żukowska, Z. & Sporzyński, A. (2010). J. Phys. Chem. A, 114, 2324-2330.]); Tan et al. (2001[Tan, Y.-L., White, A. J. P., Widdowson, D. A., Wilhelm, R. & Williams, D. J. (2001). J. Chem. Soc. Perkin Trans. 1, pp. 3269-3280.]); Yamamoto et al. (2005[Yamamoto, Y., Ishii, J., Nishiyama, H. & Itoh, K. (2005). J. Am. Chem. Soc. 127, 9625-9631.]); Zhdankin et al. (1999[Zhdankin, V. V., Persichini, P. J. III, Zhang, L., Fix, S. & Kiprof, P. (1999). Tetrahedron Lett. 40, 6705-6708.]). For hydrogen-bond graph-set descriptors and layer symmetry groups, see: Etter (1990[Etter, M. C. (1990). Acc. Chem. Res. 23, 120-126.]) and Inter­national Tables for Crystallography (2006[International Tables for Crystallography (2006). Vol. E, Subperiodic Groups, edited by V. Kopsky & D. B. Litvin. Dordrecht: Kluwer Academic Publishers.]), respectively.

[Scheme 1]

Experimental

Crystal data
  • C7H6BFO2

  • Mr = 151.93

  • Triclinic, [P \overline 1]

  • a = 3.8799 (3) Å

  • b = 6.3077 (5) Å

  • c = 14.0735 (12) Å

  • α = 98.068 (7)°

  • β = 91.564 (7)°

  • γ = 100.473 (7)°

  • V = 334.84 (5) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 1.06 mm−1

  • T = 100 K

  • 0.60 × 0.35 × 0.20 mm

Data collection
  • Oxford Diffraction Gemini A Ultra diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.731, Tmax = 1.000

  • 3451 measured reflections

  • 1193 independent reflections

  • 1147 reflections with I > 2σ(I)

  • Rint = 0.016

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.088

  • S = 1.07

  • 1193 reflections

  • 105 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2⋯O1i 0.83 (2) 1.93 (2) 2.7614 (13) 175 (2)
C7—H7B⋯O2ii 0.99 2.55 3.5325 (15) 172
C5—H5⋯F1iii 0.95 2.58 3.4779 (14) 157
C7—H7A⋯O2iv 0.99 2.66 3.2172 (14) 116
C3—H3⋯O2iv 0.95 2.70 3.4276 (14) 134
Symmetry codes: (i) -x+2, -y+2, -z+1; (ii) x, y-1, z; (iii) -x, -y+2, -z+2; (iv) x-1, y-1, z.

Data collection: CrysAlis PRO (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPIII (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Related literature top

For the review of the synthesis, properties and applications of benzoxaboroles, see: Adamczyk-Woźniak et al. (2009). For the biological activity of the title compound, a broad-spectrum antifungal drug (AN2690), see: Baker et al. (2005, 2006); Hui et al. (2007); Rock et al. (2007). For the synthesis see: Baker et al. (2006), Gunasekera et al. (2007). For related structures, see: Adamczyk-Woźniak et al. (2010); Tan et al. (2001); Yamamoto et al. (2005); Zhdankin et al. (1999). For hydrogen-bond graph-set descriptors and layer symmetry groups, see: Etter (1990) and International Tables for Crystallography (2006), respectively.

Experimental top

5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (I) was synthesized according to Fig. 3.

2-Bromo-5-fluorobenzaldehyde was purchased from Sigma-Aldrich and used as received. 2-Bromo-5-fluorobenzaldehyde (5.00 g, 0.025 mol) and 2.69 g (0.025 mol) of trimethoxymethane was dissolved in 100 ml of methanol in a two-necked vessel. 0.4 ml of concentrated H2SO4 was added. The solution was refluxed for one hour and left to cool down. Then the solution was brought to pH11 with a concentrated solution of NaOMe in methanol. The reaction mixture was distilled under vacuum to give 5.90 g of 1-Bromo-2-(dimethoxymethyl)-4-fluorobenzene as a colorless liquid (yield 96%; 1H NMR (CDCl3, 400 MHz): 7.49 (dd, 1H), 7.34 (dd, 1H), 6.91 (td, 1H), 5.49 (s, 1H), 3.37 (s, 6H) p.p.m.). The product was dissolved in 100 ml of dry Et2O in a three-necked vessel under argon flow. The solution was cooled down to -78°C using dry ice/acetone bath. n-Butyllithium in hexane (2.5 M, 11 ml) was added dropwise to keep the temperature under -70°C. The solution was stirred for one hour, then 3.80 g (0.026 mol, 4.4 ml) of triethyl borate was added slowly, keeping the temperature under -70°C. The dry ice/acetone bath was removed and the solution was stirred for one hour. The solution was brought to pH3 with 3 M aq. HCl. The aqueous layer was separated and extracted with Et2O (2 × 100 ml). The organic layers were combined and the solvent was partially removed under vacuum. The remaining thick solution was dissolved in hot water. Yellowish crystals of 4-fluoro-2-formylphenylboronic acid were filtered after a few hours. Recrystallization from water gave 1.79 g of the product (yield 49%; 1H NMR (CDCl3, 400 MHz): 9.89 (s, 1H), 8.31 (dd, 1H), 7.62 (dd, 1H), 7.40 (td, 1H) p.p.m.). The product (1.79 g, 0.011 mol) was dissolved in 100 ml of methanol in a one-necked vessel. 0.44 g (0.012 mol) of NaBH4 was added in small portions. The solution was mixed for 12 h. Another portion of 0.22 g of NaBH4 was added and the solution was mixed for 3 days. The solvent was removed under vacuum. The crude product was dissolved in water. Crystallization gave 0.82 g of 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (I) as yellowish crystals (yield 51%; 1H NMR (CDCl3, 400 MHz): 7.72 (dd, 1H), 7.06 (m, 2H), 5.08 (s, 2H) p.p.m.; 19F NMR (CDCl3, 376.3 MHz): -113.51 (q) p.p.m.; 11B NMR ((CdD3)2CO, 64.1 MHz): 32.0 p.p.m.; m.p. 135–136°C).

Refinement top

H2 atom bonded to O2 atom was located in a difference map and freely refined. Other H atoms were positioned geometrically and refined using a riding model with C—H = 0.95–0.99 Å and with Uiso(H) = 1.2 times Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2006); cell refinement: CrysAlis PRO (Oxford Diffraction, 2006); data reduction: CrysAlis PRO (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
ORTEP plot of the hydrogen bonded dimer of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Projection on (1 0 2) plane showing layers of molecules linked by O—H···O (dashed lines), C—H···O and C—H···F (dotted lines) H-bonds.

Synthesis of 5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (I).
5-Fluoro-1,3-dihydro-2,1-benzoxaborol-1-ol top
Crystal data top
C7H6BFO2Z = 2
Mr = 151.93F(000) = 156
Triclinic, P1Dx = 1.507 Mg m3
Hall symbol: -P 1Melting point: 408 K
a = 3.8799 (3) ÅCu Kα radiation, λ = 1.5418 Å
b = 6.3077 (5) ÅCell parameters from 3116 reflections
c = 14.0735 (12) Åθ = 3.2–67.1°
α = 98.068 (7)°µ = 1.06 mm1
β = 91.564 (7)°T = 100 K
γ = 100.473 (7)°Prism, light yellow
V = 334.84 (5) Å30.60 × 0.35 × 0.20 mm
Data collection top
Oxford Diffraction Gemini A Ultra
diffractometer
1193 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source1147 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.016
Detector resolution: 10.3347 pixels mm-1θmax = 67.1°, θmin = 3.2°
ω scansh = 44
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
k = 77
Tmin = 0.731, Tmax = 1.000l = 1614
3451 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.088 w = 1/[σ2(Fo2) + (0.0511P)2 + 0.1152P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
1193 reflectionsΔρmax = 0.33 e Å3
105 parametersΔρmin = 0.18 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.046 (5)
Crystal data top
C7H6BFO2γ = 100.473 (7)°
Mr = 151.93V = 334.84 (5) Å3
Triclinic, P1Z = 2
a = 3.8799 (3) ÅCu Kα radiation
b = 6.3077 (5) ŵ = 1.06 mm1
c = 14.0735 (12) ÅT = 100 K
α = 98.068 (7)°0.60 × 0.35 × 0.20 mm
β = 91.564 (7)°
Data collection top
Oxford Diffraction Gemini A Ultra
diffractometer
1193 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
1147 reflections with I > 2σ(I)
Tmin = 0.731, Tmax = 1.000Rint = 0.016
3451 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.088H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.33 e Å3
1193 reflectionsΔρmin = 0.18 e Å3
105 parameters
Special details top

Experimental. Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. (Oxford Diffraction, 2006)

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O20.9636 (2)1.22613 (14)0.60638 (7)0.0189 (3)
F10.0385 (2)0.70856 (13)0.93059 (5)0.0282 (3)
O10.7364 (2)0.84381 (13)0.56821 (6)0.0171 (3)
C30.2566 (3)0.6725 (2)0.77652 (9)0.0185 (3)
H30.16240.52070.76600.022*
C40.2168 (3)0.8036 (2)0.86129 (9)0.0200 (3)
C20.4422 (3)0.7757 (2)0.70750 (9)0.0162 (3)
C10.5825 (3)0.9983 (2)0.72234 (9)0.0167 (3)
C50.3485 (3)1.0251 (2)0.87950 (9)0.0207 (3)
H50.31211.10830.93880.025*
C60.5346 (3)1.1237 (2)0.80968 (9)0.0186 (3)
H60.62911.27540.82100.022*
B10.7783 (3)1.0404 (2)0.63011 (10)0.0164 (3)
C70.5248 (3)0.6711 (2)0.61026 (9)0.0170 (3)
H7B0.65620.55260.61640.020*
H7A0.30640.60960.57010.020*
H21.061 (5)1.212 (3)0.5545 (15)0.040 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O20.0245 (5)0.0147 (5)0.0169 (5)0.0025 (4)0.0053 (4)0.0011 (3)
F10.0329 (5)0.0323 (5)0.0196 (4)0.0035 (4)0.0106 (3)0.0065 (3)
O10.0208 (5)0.0145 (5)0.0154 (5)0.0019 (3)0.0046 (3)0.0017 (3)
C30.0178 (6)0.0188 (6)0.0193 (7)0.0037 (5)0.0009 (5)0.0033 (5)
C40.0181 (6)0.0273 (7)0.0160 (6)0.0052 (5)0.0038 (5)0.0061 (5)
C20.0149 (6)0.0174 (6)0.0168 (6)0.0055 (5)0.0004 (4)0.0014 (5)
C10.0154 (6)0.0174 (6)0.0178 (7)0.0051 (5)0.0011 (5)0.0021 (5)
C50.0212 (6)0.0256 (7)0.0155 (6)0.0083 (5)0.0008 (5)0.0016 (5)
C60.0187 (6)0.0179 (6)0.0188 (6)0.0049 (5)0.0001 (5)0.0007 (5)
B10.0162 (6)0.0162 (7)0.0172 (7)0.0055 (5)0.0011 (5)0.0009 (5)
C70.0197 (6)0.0135 (6)0.0174 (6)0.0017 (5)0.0036 (5)0.0021 (5)
Geometric parameters (Å, º) top
O2—B11.3483 (18)C2—C11.3948 (18)
O2—H20.83 (2)C2—C71.5025 (17)
F1—C41.3562 (15)C1—C61.4013 (17)
O1—B11.3922 (17)C1—B11.5522 (18)
O1—C71.4471 (15)C5—H50.9500
C3—H30.9500C5—C61.3856 (18)
C3—C41.3822 (19)C6—H60.9500
C3—C21.3897 (18)C7—H7B0.9900
C4—C51.3829 (19)C7—H7A0.9900
O2—B1—O1121.51 (12)C2—C3—H3121.9
O2—B1—C1130.25 (12)C2—C1—C6119.16 (12)
F1—C4—C3117.85 (12)C2—C1—B1104.93 (11)
F1—C4—C5118.27 (12)C2—C7—H7B110.7
O1—B1—C1108.24 (11)C2—C7—H7A110.7
O1—C7—C2105.45 (9)C1—C2—C7110.88 (11)
O1—C7—H7B110.7C1—C6—H6120.2
O1—C7—H7A110.7C5—C6—C1119.66 (12)
C3—C4—C5123.88 (12)C5—C6—H6120.2
C3—C2—C1122.36 (12)C6—C1—B1135.86 (12)
C3—C2—C7126.75 (11)C6—C5—H5120.6
C4—C3—H3121.9B1—O2—H2115.3 (13)
C4—C3—C2116.12 (12)B1—O1—C7110.46 (10)
C4—C5—H5120.6H7B—C7—H7A108.8
C4—C5—C6118.82 (12)
F1—C4—C5—C6179.28 (10)C2—C1—B1—O2179.25 (12)
C3—C4—C5—C60.58 (19)C2—C1—B1—O10.71 (13)
C3—C2—C1—C60.23 (17)C1—C2—C7—O12.08 (13)
C3—C2—C1—B1177.60 (11)C6—C1—B1—O22.0 (2)
C3—C2—C7—O1177.19 (11)C6—C1—B1—O1178.00 (12)
C4—C3—C2—C10.24 (18)B1—O1—C7—C21.57 (13)
C4—C3—C2—C7179.42 (11)B1—C1—C6—C5177.18 (12)
C4—C5—C6—C10.57 (18)C7—O1—B1—O2179.45 (10)
C2—C3—C4—F1179.69 (9)C7—O1—B1—C10.59 (13)
C2—C3—C4—C50.17 (19)C7—C2—C1—C6179.53 (10)
C2—C1—C6—C50.19 (17)C7—C2—C1—B11.70 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···O1i0.83 (2)1.93 (2)2.7614 (13)175 (2)
C7—H7B···O2ii0.992.553.5325 (15)172
C5—H5···F1iii0.952.583.4779 (14)157
C7—H7A···O2iv0.992.663.2172 (14)116
C3—H3···O2iv0.952.703.4276 (14)134
Symmetry codes: (i) x+2, y+2, z+1; (ii) x, y1, z; (iii) x, y+2, z+2; (iv) x1, y1, z.

Experimental details

Crystal data
Chemical formulaC7H6BFO2
Mr151.93
Crystal system, space groupTriclinic, P1
Temperature (K)100
a, b, c (Å)3.8799 (3), 6.3077 (5), 14.0735 (12)
α, β, γ (°)98.068 (7), 91.564 (7), 100.473 (7)
V3)334.84 (5)
Z2
Radiation typeCu Kα
µ (mm1)1.06
Crystal size (mm)0.60 × 0.35 × 0.20
Data collection
DiffractometerOxford Diffraction Gemini A Ultra
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
Tmin, Tmax0.731, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
3451, 1193, 1147
Rint0.016
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.088, 1.07
No. of reflections1193
No. of parameters105
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.18

Computer programs: CrysAlis PRO (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPIII (Burnett & Johnson, 1996), OLEX2 (Dolomanov et al., 2009), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···O1i0.83 (2)1.93 (2)2.7614 (13)175 (2)
C7—H7B···O2ii0.992.553.5325 (15)172
C5—H5···F1iii0.952.583.4779 (14)157
C7—H7A···O2iv0.992.663.2172 (14)116
C3—H3···O2iv0.952.703.4276 (14)134
Symmetry codes: (i) x+2, y+2, z+1; (ii) x, y1, z; (iii) x, y+2, z+2; (iv) x1, y1, z.
 

Acknowledgements

The authors acknowledge financial support by the Ministry of Science and Higher Education (grant No. N204 127938).

References

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Volume 67| Part 2| February 2011| Pages o414-o415
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