Literature DB >> 25552984

Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phen-oxy-acetic acid, (4-fluoro-phen-oxy)acetic acid and (4-chloro-2-methyl-phen-oxy)acetic acid.

Graham Smith1.   

Abstract

The structures of the ammonium salts of phen-oxy-acetic acid, NH4 (+)·C8H6O3 (-), (I), (4-fluoro-phen-oxy)acetic acid, NH4 (+)·C8H5FO3 (-), (II), and the herbicidally active (4-chloro-2-methyl-phen-oxy)acetic acid (MCPA), NH4 (+)·C9H8ClO3 (-)·0.5H2O, (III) have been determined. All have two-dimensional layered structures based on inter-species ammonium N-H⋯O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I) and (II) are isomorphous with the core comprising R 1 (2)(5), R 1 (2)(4) and centrosymmetric R 4 (2)(8) ring motifs, giving two-dimensional layers lying parallel to (100). In (III), the water mol-ecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R 4 (4)(12) hydrogen-bonded motif, creating two R 4 (3)(10) rings, which together with a conjoined centrosymmetric R 4 (2)(8) ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100). No π-π ring associations are present in any of the structures.

Entities:  

Keywords:  MCPA; ammonium carboxyl­ates; crystal structure; herbicides; hydrogen bonding; phen­oxy­acetic acid salts

Year:  2014        PMID: 25552984      PMCID: PMC4257399          DOI: 10.1107/S160053681402488X

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


Chemical context

The crystal structures of the ammonium salts of carb­oxy­lic acids are, despite their simple formulae, characterized by the presence of a complex array of hydrogen-bonding inter­actions. From a study of the packing motifs of the these ammonium carboxyl­ate salts from examples in the Cambridge Structural Database (Groom & Allen, 2014 ▶), Odendal et al. (2010 ▶) found that two-dimensional hydrogen-bonded nets, ladders or cubane-type structures could be predicted on the basis of the size and conformation of the anions. These structures are often stabilized by π–π aromatic ring inter­actions. With the benzoic acid analogues, two-dimensional sheet structures are common with inter­actions involving the ammonium cations and the carboxyl­ate anions in N—H⋯O hydrogen bonding, forming core layer structures, with the aromatic rings occupying the inter­stitial cell regions, e.g. with benzoic acid (Odendal et al., 2010 ▶), 3-nitro­benzoic acid (Eppel & Bernstein, 2009 ▶) and 2,4-di­chloro­benzoic acid (Smith, 2014 ▶). Three-dimensional structures are usually only formed when inter­active substituent groups are present on the benzoate rings, inter­linking the layers e.g. with 3,5-di­nitro­benzoic acid (Smith, 2014 ▶). The presence of water mol­ecules of solvation may also produce a similar effect, although these are usually confined to the primary cation–anion layers. With the phen­oxy­acetic acid analogues, which comprise a number of herbicidally active commercial herbicides (Zumdahl, 2010 ▶), this should also be the case. In the only reported structure of an ammonium salt of a phen­oxy­acetic acid [with the commercially important herbicide, the 2,4-di­chloro-substituted analogue (2,4-D) (a hemihydrate) (Liu et al., 2009 ▶)], the expected two-dimensional layered structure is found. Herein are reported the preparation and structures of the anhydrous ammonium salts of the parent phen­oxy­acetic acid, NH4C8H6O3 − (I) and (4-fluoro­phen­oxy)acetic acid, NH4C8H5FO3 − (II) and the hemihydrate salt of the herbicidally active (4-chloro-2-methyl­phen­oxy)acetic acid (MCPA), NH4 +·C9H8ClO3 −·0.5H2O (III). The structure of a hydrated chloro­methyl­ammonium salt of MCPA is known (Pernak et al., 2011 ▶).

Structural commentary

In the structures of the isomorphous ammonium phen­oxy­acetate (I) and (4-fluoro­phen­oxy)acetate (II) (Figs. 1 ▶ and 2 ▶, respectively), the anionic species are essentially planar; the comparative defining torsion angles in the phen­oxy­acetate side chain (C2—C1—O11—C12, C1—O11—C12—C13 and O11—C12—C13O14) are 178.93 (19), −177.48 (18) and −173.58 (18)°, respectively, for (I) and −179.05 (18), −178.98 (17) and −174.13 (17)°, respectively, for (II). This planarity is also found in the MCPA anion in (III) (Fig. 3 ▶) where the corresponding torsion angles are −179.13 (15), −173.34 (14) and −178.71 (15)° and is also the case with the parent acids [for (I): Kennard et al. (1982 ▶), for (II): Smith et al. (1992 ▶) and for (III): Smith & Kennard (1981 ▶); Sieron et al. (2011 ▶)]. In (III), the water mol­ecule of solvation lies on a crystallographic twofold rotation axis.
Figure 1

Mol­ecular conformation and atom labelling for (I), with inter-species hydrogen bonds shown as a dashed lines (see Table 1 ▶ for details). Non-H atoms are shown as 40% probability displacement ellipsoids.

Figure 2

Mol­ecular conformation and atom labelling for (II), with inter-species hydrogen bonds shown as dashed lines (see Table 2 ▶ for details). Non-H atoms are shown as 40% probability displacement ellipsoids.

Figure 3

Mol­ecular conformation and atom labelling for (III), with inter-species hydrogen bonds shown as dashed lines (see Table 3 ▶ for details). Non-H atoms are shown as 40% probability displacement ellipsoids.

Supra­molecular features

In the crystals of (I) and (II), two H atoms of the ammonium group give cyclic asymmetric three-centre (bifurcated) N—H⋯(O,O) hydrogen-bonding inter­actions with the anion (Tables 1 ▶ and 2 ▶, respectively). One of these is with two O-atom acceptors of the carboxyl group (O13, O14) [graph set (4)], the other is with the carboxyl and phen­oxy O-atom acceptors (O13ii, O11ii) of an inversion-related anion [graph set (5)]. These, together with a third N1—H13⋯O13ii hydrogen bond, give a cyclic (8) ring motif, forming a series of conjoined rings which extend the structures along c. The other H atom gives structure extension through an N—H⋯O hydrogen bond to a carboxyl O atom (O14iii), forming a two-dimensional sheet-like structure which lies parallel to (100). Present in the crystal are short inversion-related inter­molecular F4⋯F4iv contacts of 2.793 (2) Å [symmetry code: (iv) −x + 2, −y + 1, −z − 1]. The crystal packing and hydrogen-bonding in (I) is identical to that in isostructural (II), as shown in Fig. 4 ▶.
Table 1

Hydrogen-bond geometry (, ) for (I)

DHA DHHA D A DHA
N1H11O130.961.922.849(3)163
N1H11O140.962.553.330(3)138
N1H12O13i 0.852.032.867(3)172
N1H13O11ii 0.902.393.202(3)150
N1H13O13ii 0.902.152.869(3)136
N1H14O14iii 0.841.952.788(3)178

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

Table 2

Hydrogen-bond geometry (, ) for (II)

DHA DHHA D A DHA
N1H11O130.901.952.847(2)177
N1H11O140.902.553.347(2)135
N1H12O13i 0.971.882.847(3)173
N1H13O11ii 0.962.363.172(2)142
N1H13O13ii 0.962.132.892(2)135
N1H14O14iii 0.891.912.793(2)173

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

Figure 4

The two-dimensional hydrogen-bonded network structure of (I), which is equivalent to that of the isomorphous compound (II). Hydrogen bonds are shown as dashed lines and non-associative H-atoms have been omitted [for symmetry codes see Tables 1 ▶ and 2 ▶].

In the crystal of (III), centrosymmetric inter-ion (8) rings are formed between two ammonium cations and two O13 carboxyl O-atom acceptors and are bridged by a third ammonium H donor through O13iii, extending the structure down b (Table 3 ▶ and Fig. 5 ▶). The fourth H atom gives extension along a through N1—H12⋯O14ii forming an enlarged conjoined (12) ring, which is bridged by the water mol­ecule of solvation lying on the twofold rotation axis, through O1W—H11W⋯O14 hydrogen bonds. This link effectively generates two separate (10) ring motifs, extending the structure along a and giving the overall two-dimensional layers lying parallel to (100) (Fig. 6 ▶). In (III), no three-centre (4) or (5) motifs to carboxyl (O,O′) or carboxyl-phen­oxy (O,O 1) acceptors such as are present in (I) and (II) are found. The structure of (III) is essentially isostructural with that of ammonium (2,4-di­chloro­phen­oxy)acetate hemihydrate (Liu et al., 2009 ▶), with isomorphous crystals [a = 37.338 (8), b = 4.388 (9), c = 12.900 (3) Å, β = 103.82 (3)°, V = 2074.7 (8) Å3, Z = 8, space group C2/c].
Table 3

Hydrogen-bond geometry (, ) for (III)

DHA DHHA D A DHA
N1H11O13i 0.822.212.998(4)161
N1H12O14ii 0.822.092.886(4)166
N1H13O13iii 0.842.042.877(4)173
N1H14O130.822.002.798(4)163
O1WH11WO140.881.952.809(4)165

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

Figure 5

A partial extension of the basic cation–anion hydrogen-bonding associations in the structure of (III), showing conjoined cyclic (12), (10) and (8) ring motifs. [Symmetry code: (iv) −x + 1, y, −z + . For other codes, see Table 3 ▶].

Figure 6

The two-dimensional hydrogen-bonded network structure of (III) in the unit cell, viewed along b.

No π–π inter­actions are found in any of the structures reported here [minimum ring centroid separation = 4.8849 (16) (I), 4.8919 (15) (II) and 4.456 (5) Å (III) (the b unit-cell parameter)].

Synthesis and crystallization

The title compounds were prepared by the addition of excess 5 M aqueous ammonia solution to 1 mmol of either phen­oxy­acetic acid [150 mg for (I)], (4-fluoro­phen­oxy)acetic acid [170 mg for (II)] or (4-chloro-2-methyl­phen­oxy)acetic acid [200 mg for (III)] in 10 mL of 10% ethanolwater. Room-temperature evaporation of the solvent gave colourless plate-like crystals of (I), (II) and (III) from which specimens were cleaved for the X-ray analyses.

Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 4 ▶. Hydrogen atoms potentially involved in hydrogen-bonding inter­actions were located in difference Fourier maps but were subsequently included in the refinements with positional parameters fixed and with U iso(H) = 1.2U eq(N) or = 1.5U eq(O). Other H atoms were included at calculated positions [C—H(aromatic) = 0.95, C—H(methyl­ene) = 0.98, C—H(meth­yl) = 0.97 Å] and also treated as riding, with U iso(H) = 1.5U eq(C) for methyl H atoms and = 1.2U eq(C) for other H atoms. In (III), the methyl group was found to be rotationally disordered, with the H atoms distributed over six equivalent half-sites, and was treated accordingly.
Table 4

Experimental details

 (I)(II)(III)
Crystal data
Chemical formulaNH4 +C8H7O3 NH4 +C8H6FO3 NH4 +C9H8ClNO3 0.5H2O
M r 169.17187.17226.65
Crystal system, space groupMonoclinic, P21/c Monoclinic, P21/c Monoclinic, C2/c
Temperature (K)200200200
a, b, c ()17.824(2), 7.1453(6), 6.7243(7)18.386(2), 7.1223(6), 6.7609(6)38.0396(9), 4.4560(8), 12.944(5)
()90.321(9)93.399(8)104.575(5)
V (3)856.38(15)883.79(14)2123.5(9)
Z 448
Radiation typeMo K Mo K Mo K
(mm1)0.100.120.35
Crystal size (mm)0.35 0.25 0.100.26 0.20 0.050.35 0.35 0.10
 
Data collection
DiffractometerOxford Diffraction Gemini-S CCD detectorOxford Diffraction Gemini-S CCD detectorOxford Diffraction Gemini-S CCD detector
Absorption correctionMulti-scan (CrysAlis PRO; Agilent, 2013)Multi-scan (CrysAlis PRO; Agilent, 2013)Multi-scan (CrysAlis PRO; Agilent, 2013)
T min, T max 0.920, 0.9800.960, 0.9800.913, 0.980
No. of measured, independent and observed [I > 2(I)] reflections5450, 1686, 12185619, 1738, 13046215, 2087, 1771
R int 0.0520.0330.030
(sin /)max (1)0.6170.6170.617
 
Refinement
R[F 2 > 2(F 2)], wR(F 2), S 0.063, 0.163, 1.100.053, 0.116, 1.100.036, 0.091, 1.03
No. of reflections168617382087
No. of parameters109118132
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrained
max, min (e 3)0.29, 0.240.16, 0.220.32, 0.28

Computer programs: CrysAlis PRO (Agilent, 2013 ▶), SIR92 (Altomare et al., 1993 ▶), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▶) within WinGX (Farrugia, 2012 ▶) and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablock(s) global, I, II, III. DOI: 10.1107/S160053681402488X/su5018sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681402488X/su5018Isup2.hkl Structure factors: contains datablock(s) II. DOI: 10.1107/S160053681402488X/su5018IIsup3.hkl Structure factors: contains datablock(s) III. DOI: 10.1107/S160053681402488X/su5018IIIsup4.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S160053681402488X/su5018Isup5.cml Click here for additional data file. Supporting information file. DOI: 10.1107/S160053681402488X/su5018IIsup6.cml Click here for additional data file. Supporting information file. DOI: 10.1107/S160053681402488X/su5018IIIsup7.cml CCDC references: 1033945, 1033946, 1033947 Additional supporting information: crystallographic information; 3D view; checkCIF report
NH4+·C9H8ClNO3·0.5H2OF(000) = 952
Mr = 226.65Dx = 1.418 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1819 reflections
a = 38.0396 (9) Åθ = 4.4–28.1°
b = 4.4560 (8) ŵ = 0.35 mm1
c = 12.944 (5) ÅT = 200 K
β = 104.575 (5)°Plate, colourless
V = 2123.5 (9) Å30.35 × 0.35 × 0.10 mm
Z = 8
Oxford Diffraction Gemini-S CCD-detector diffractometer2087 independent reflections
Radiation source: Enhance (Mo) X-ray source1771 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
Detector resolution: 16.077 pixels mm-1θmax = 26.0°, θmin = 3.2°
ω scansh = −46→46
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)k = −5→5
Tmin = 0.913, Tmax = 0.980l = −15→15
6215 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.091H-atom parameters constrained
S = 1.03w = 1/[σ2(Fo2) + (0.0409P)2 + 1.4504P] where P = (Fo2 + 2Fc2)/3
2087 reflections(Δ/σ)max < 0.001
132 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = −0.28 e Å3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
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. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/UeqOcc. (<1)
Cl40.24818 (1)0.32330 (12)0.36021 (4)0.0372 (2)
O110.39197 (3)0.8996 (3)0.46961 (9)0.0262 (4)
O130.45425 (3)1.2161 (3)0.49906 (10)0.0296 (4)
O140.44789 (4)1.4021 (3)0.65332 (10)0.0339 (4)
C10.35808 (5)0.7686 (4)0.44981 (13)0.0224 (5)
C20.34876 (5)0.5869 (4)0.35836 (13)0.0246 (5)
C30.31491 (5)0.4496 (4)0.33324 (14)0.0269 (5)
C40.29091 (5)0.4918 (4)0.39679 (14)0.0264 (5)
C50.30027 (5)0.6675 (4)0.48684 (14)0.0275 (6)
C60.33390 (5)0.8070 (4)0.51321 (14)0.0258 (5)
C120.40205 (5)1.0812 (4)0.56298 (14)0.0242 (5)
C130.43762 (5)1.2444 (4)0.57156 (14)0.0234 (5)
C210.37517 (5)0.5430 (5)0.29002 (15)0.0370 (6)
O1W0.500001.8306 (4)0.750000.0464 (7)
N10.46781 (3)0.7274 (3)0.37900 (10)0.0156 (4)
H30.308200.328000.273100.0320*
H50.284200.692600.529600.0330*
H60.340300.927100.573800.0310*
H1210.404200.955500.625500.0290*
H1220.383001.227200.561900.0290*
H2110.397000.654500.319800.0550*0.500
H2120.364400.613000.218900.0550*0.500
H2130.380900.333800.287900.0550*0.500
H2140.364600.413000.231300.0550*0.500
H2150.397100.454500.332100.0550*0.500
H2160.380600.733700.263200.0550*0.500
H11W0.483901.712600.708600.0700*
H110.490100.738700.398100.0190*
H120.459700.714700.314500.0190*
H130.462500.573600.409500.0190*
H140.459300.866700.406800.0190*
U11U22U33U12U13U23
Cl40.0264 (3)0.0466 (3)0.0378 (3)−0.0121 (2)0.0064 (2)−0.0044 (2)
O110.0233 (7)0.0335 (7)0.0230 (6)−0.0071 (5)0.0083 (5)−0.0075 (5)
O130.0293 (7)0.0279 (6)0.0355 (7)−0.0036 (6)0.0155 (6)−0.0015 (6)
O140.0340 (8)0.0378 (7)0.0268 (7)−0.0094 (6)0.0020 (6)−0.0054 (6)
C10.0215 (9)0.0222 (8)0.0224 (9)−0.0010 (7)0.0037 (7)0.0028 (7)
C20.0253 (9)0.0277 (9)0.0198 (8)0.0005 (7)0.0041 (7)0.0002 (7)
C30.0278 (10)0.0287 (9)0.0223 (9)−0.0021 (8)0.0027 (8)−0.0023 (8)
C40.0217 (9)0.0277 (9)0.0277 (9)−0.0031 (7)0.0023 (8)0.0037 (8)
C50.0230 (10)0.0332 (10)0.0282 (9)0.0003 (8)0.0099 (8)0.0017 (8)
C60.0259 (10)0.0281 (9)0.0234 (9)−0.0011 (8)0.0062 (7)−0.0022 (8)
C120.0244 (9)0.0276 (9)0.0208 (8)−0.0026 (7)0.0059 (7)−0.0033 (7)
C130.0247 (9)0.0215 (8)0.0232 (9)0.0029 (7)0.0045 (7)0.0042 (7)
C210.0331 (11)0.0520 (12)0.0278 (10)−0.0083 (10)0.0114 (9)−0.0126 (9)
O1W0.0421 (13)0.0259 (10)0.0667 (15)0.00000.0053 (11)0.0000
N10.0141 (7)0.0159 (6)0.0179 (6)−0.0006 (5)0.0060 (5)−0.0004 (5)
Cl4—C41.744 (3)C3—C41.387 (3)
O11—C11.379 (3)C4—C51.375 (3)
O11—C121.425 (3)C5—C61.386 (3)
O13—C131.263 (3)C12—C131.515 (3)
O14—C131.248 (3)C3—H30.9300
O1W—H11W0.8800C5—H50.9300
O1W—H11Wi0.8800C6—H60.9300
N1—H120.8200C12—H1210.9700
N1—H110.8200C12—H1220.9700
N1—H130.8400C21—H2160.9600
N1—H140.8200C21—H2110.9600
C1—C21.404 (3)C21—H2120.9600
C1—C61.389 (3)C21—H2130.9600
C2—C211.509 (3)C21—H2140.9600
C2—C31.388 (3)C21—H2150.9600
C1—O11—C12115.95 (13)C2—C3—H3120.00
H11W—O1W—H11Wi107.00C4—C3—H3120.00
H12—N1—H14114.00C4—C5—H5120.00
H13—N1—H14104.00C6—C5—H5120.00
H11—N1—H12114.00C5—C6—H6120.00
H11—N1—H13105.00C1—C6—H6120.00
H11—N1—H14108.00C13—C12—H122109.00
H12—N1—H13111.00C13—C12—H121109.00
O11—C1—C2115.26 (16)O11—C12—H121109.00
O11—C1—C6124.41 (15)O11—C12—H122109.00
C2—C1—C6120.33 (17)H121—C12—H122108.00
C1—C2—C21120.32 (17)C2—C21—H211109.00
C1—C2—C3118.30 (17)C2—C21—H212109.00
C3—C2—C21121.37 (16)C2—C21—H213109.00
C2—C3—C4120.77 (16)C2—C21—H214110.00
C3—C4—C5120.76 (18)C2—C21—H215109.00
Cl4—C4—C3119.22 (14)C2—C21—H216109.00
Cl4—C4—C5120.01 (15)H214—C21—H215109.00
C4—C5—C6119.37 (17)H214—C21—H216109.00
C1—C6—C5120.46 (16)H215—C21—H216110.00
O11—C12—C13112.31 (15)H211—C21—H212109.00
O13—C13—O14125.29 (18)H211—C21—H213110.00
O13—C13—C12120.17 (16)H212—C21—H213109.00
O14—C13—C12114.55 (16)
C12—O11—C1—C2−179.13 (15)C1—C2—C3—C40.2 (3)
C12—O11—C1—C61.0 (2)C21—C2—C3—C4179.98 (17)
C1—O11—C12—C13−173.34 (14)C2—C3—C4—Cl4178.25 (14)
O11—C1—C2—C3−179.57 (15)C2—C3—C4—C5−0.8 (3)
O11—C1—C2—C210.6 (2)Cl4—C4—C5—C6−178.13 (14)
C6—C1—C2—C30.3 (3)C3—C4—C5—C60.9 (3)
C6—C1—C2—C21−179.46 (17)C4—C5—C6—C1−0.4 (3)
O11—C1—C6—C5179.67 (16)O11—C12—C13—O131.7 (2)
C2—C1—C6—C5−0.2 (3)O11—C12—C13—O14−178.71 (15)
D—H···AD—HH···AD···AD—H···A
N1—H11···O13ii0.822.212.998 (4)161
N1—H12···O14iii0.822.092.886 (4)166
N1—H13···O13iv0.842.042.877 (4)173
N1—H14···O130.822.002.798 (4)163
O1W—H11W···O140.881.952.809 (4)165
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  5 in total
  3 in total

1.  Crystal structures of the potassium and rubidium salts of (3,5-di-chloro-phen-oxy)acetic acid: two isotypic coordination polymers.

Authors:  Graham Smith
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-09-17

2.  Crystal structures and hydrogen bonding in the morpholinium salts of four phen-oxy-acetic acid analogues.

Authors:  Graham Smith; Daniel E Lynch
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-10-28

3.  Crystal structure of ammonium (3,5-di-chloro-phen-oxy)acetate hemihydrate.

Authors:  Graham Smith
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-09-12
  3 in total

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