Pyridine-3-carboxamidinium chloride

Liu, F.; Zhang, F.; Chen, Q.; Zhang, H.

doi:10.1107/S1600536811002704

organic compounds

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ISSN: 2056-9890

Volume 67| Part 4| April 2011| Page o781

doi:10.1107/S1600536811002704

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Pyridine-3-carboxamidinium chloride

Fei Liu,^a ^* Fang Zhang,^a Qifan Chen ^b and Huidong Zhang ^b

^aCollege of Chemical Engineering & Materials, Eastern Liaoning University, No. 325 Wenhua Road, Yuanbao District, Dandong City, Liaoning Province 118003, People's Republic of China, and ^bExperiment Center, Eastern Liaoning University, No. 325 Wenhua Road, Yuanbao District, Dandong City, Liaoning Province 118003, People's Republic of China
^*Correspondence e-mail: berylliu8090@sina.com

(Received 17 November 2010; accepted 20 January 2011; online 5 March 2011)

The title compound, C₆H₈N₃⁺·Cl⁻, crystallizes with two formula units in the asymmetric unit. The cations are non-planar with the –C(NH₂)₂ groups twisted relative to the ring planes by 36.7 (3) and 37.8 (3)°. The cations are linked into chains through N—H⋯N hydrogen bonds. N—H⋯Cl hydrogen bonds link the chains into a three-dimensional network.

Related literature

For structures of pyridine-carboxamidinium chlorides, see: Fan et al. (2009 ); Chen et al. (2010 ).

Experimental

Crystal data

C₆H₈N₃⁺·Cl⁻
M_r = 157.60
Orthorhombic, P n a 2₁
a = 10.9485 (7) Å
b = 33.1581 (14) Å
c = 4.1488 (5) Å
V = 1506.1 (2) Å³
Z = 8
Mo Kα radiation
μ = 0.43 mm⁻¹
T = 293 K
0.40 × 0.35 × 0.17 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.845, T_max = 0.930
14201 measured reflections
3213 independent reflections
2953 reflections with I > 2σ(I)
R_int = 0.033

Refinement

R[F² > 2σ(F²)] = 0.029
wR(F²) = 0.071
S = 1.00
3213 reflections
182 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.18 e Å⁻³
Absolute structure: Flack (1983 ), 1246 Friedel pairs
Flack parameter: 0.0019 (5)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3B⋯N4	0.86	2.07	2.880 (2)	157
N5—H5B⋯Cl2	0.86	2.29	3.1403 (15)	170
N6—H6B⋯Cl1	0.86	2.36	3.1562 (16)	155
N2—H2A⋯N1ⁱ	0.86	2.22	2.990 (2)	149
N2—H2B⋯Cl2ⁱⁱ	0.86	2.31	3.1452 (13)	165
N3—H3A⋯Cl2ⁱⁱⁱ	0.86	2.27	3.1040 (16)	164
N5—H5A⋯Cl1^iv	0.86	2.46	3.2373 (16)	150
N6—H6A⋯Cl1^iv	0.86	2.41	3.2013 (16)	152
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+1]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z+1]$ ; (iii) x, y, z+1; (iv) $[-x+2, -y+1, z-{\script{1\over 2}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 2006 ); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2007 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ); software used to prepare material for publication: WinGX (Farrugia, 1999 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811002704/gk2326sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811002704/gk2326Isup2.hkl

checkCIF report

Comment top

During the last decade, much interest has been focused on the synthesis of pyridine carboximidamidate derivatives because of their very potent antibacterial activities, interesting biological properties and applications in coordination chemistry.

The title compound is an organic salt which crystallizes with two formula units in the asymmetric unit (Fig. 1). The molecules are nonplanar with the C(NH₂)₂ groups twisted out of the ring planes with the twist angles of 36.7 (3) ° and 37.8 (3) °. The bond lengths and angles in title compound are in the normal ranges comparable with those in the related structure (Fan et al., 2009).

In the crystal structure, pyridine-3-carboximidamidate cations are linked by N—H···N hydrogen bonds to form one-dimensional supramolecular molecular chain (Fig. 2). Cl1 ion bridges two pyridine carboximidamidate cations through N—H···Cl hydrogen bonding and Cl2 ion triple-bridges three cations through N—H···Cl hydrogen bonding. Thus, one-dimensional chains of cations are linked by N—H···Cl interactions into a three-dimensional network (Fig. 3).

Related literature top

For structures of pyridine-carboxamidinium chlorides, see: Fan et al. (2009); Chen et al. (2010).

Experimental top

To a solution of sodium methoxide (5.15 mmol) in methnol (50 ml) was added 3-cyanopyridine (5.2 g, 4.99 mmol). The mixture was stirred at room temperature for 2 h. Then ammonium chloride (2.9 g, 5.42 mmol) was slowly added to the resulting solution and the mixture was stirred at room temperature for 48 h. The resulting suspension was filtered and the solvent was removed from the filtrate under reduced pressure. Purification by washing with diethylether gave 3-amidinopyridine chloride (5.74 g, 94%) as an off-white solid. Block-shaped crystals suitable for X-ray diffraction were obtained by recrystallization from from ethanol.

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 2006); cell refinement: PROCESS-AUTO (Rigaku, 2006); data reduction: CrystalStructure (Rigaku/MSC, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

	Fig. 1. Structure of the title compound showing 30% probability displacement ellipsoids.
	Fig. 2. View of one-dimensional supramolecular chain in the title compound.
	Fig. 3. The crystal packing of the title compound shown down the x axis. Hydrogen bonds are shown with dashed lines.

Pyridine-3-carboxamidinium chloride top

Crystal data top

C₆H₈N₃⁺·Cl⁻	F(000) = 656
M_r = 157.60	D_x = 1.390 Mg m⁻³
Orthorhombic, Pna2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 3213 reflections
a = 10.9485 (7) Å	θ = 3.1–27.5°
b = 33.1581 (14) Å	µ = 0.43 mm⁻¹
c = 4.1488 (5) Å	T = 293 K
V = 1506.1 (2) Å³	Block, colorless
Z = 8	0.40 × 0.35 × 0.17 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	3213 independent reflections
Radiation source: fine-focus sealed tube	2953 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.033
Detector resolution: 10.0 pixels mm^-1	θ_max = 27.5°, θ_min = 3.1°
ω scans	h = −14→14
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −42→42
T_min = 0.845, T_max = 0.930	l = −4→5
14201 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.029	w = 1/[σ²(F_o²) + (0.0334P)² + 0.3352P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.071	(Δ/σ)_max = 0.002
S = 1.00	Δρ_max = 0.18 e Å⁻³
3213 reflections	Δρ_min = −0.18 e Å⁻³
182 parameters	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.061 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1246 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.0019 (5)

Crystal data top

C₆H₈N₃⁺·Cl⁻	V = 1506.1 (2) Å³
M_r = 157.60	Z = 8
Orthorhombic, Pna2₁	Mo Kα radiation
a = 10.9485 (7) Å	µ = 0.43 mm⁻¹
b = 33.1581 (14) Å	T = 293 K
c = 4.1488 (5) Å	0.40 × 0.35 × 0.17 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	3213 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	2953 reflections with I > 2σ(I)
T_min = 0.845, T_max = 0.930	R_int = 0.033
14201 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.029	H-atom parameters constrained
wR(F²) = 0.071	Δρ_max = 0.18 e Å⁻³
S = 1.00	Δρ_min = −0.18 e Å⁻³
3213 reflections	Absolute structure: Flack (1983), 1246 Friedel pairs
182 parameters	Absolute structure parameter: 0.0019 (5)
1 restraint

Special details top

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. 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.80408 (4)	0.549620 (13)	0.75756 (15)	0.05193 (15)
Cl2	0.82982 (4)	0.318730 (12)	0.22533 (15)	0.04986 (15)
N2	0.49341 (12)	0.25905 (4)	1.1812 (4)	0.0384 (3)
H2A	0.5635	0.2541	1.2661	0.046*
H2B	0.4372	0.2409	1.1835	0.046*
N1	0.17495 (13)	0.28055 (4)	0.6167 (4)	0.0392 (4)
N4	0.56768 (13)	0.39520 (4)	0.6649 (4)	0.0427 (4)
C3	0.30154 (15)	0.34172 (5)	0.9320 (5)	0.0359 (4)
H3	0.3444	0.3622	1.0348	0.043*
C2	0.35090 (13)	0.30307 (5)	0.9096 (4)	0.0294 (3)
N3	0.55529 (14)	0.32232 (5)	1.0408 (6)	0.0540 (5)
H3A	0.6261	0.3181	1.1239	0.065*
H3B	0.5390	0.3451	0.9521	0.065*
C1	0.28379 (13)	0.27351 (4)	0.7498 (5)	0.0321 (3)
H1	0.3164	0.2477	0.7352	0.038*
N5	0.93657 (14)	0.40511 (4)	0.3554 (5)	0.0515 (5)
H5A	1.0143	0.4075	0.3329	0.062*
H5B	0.9030	0.3817	0.3431	0.062*
N6	0.91881 (14)	0.47268 (4)	0.4274 (5)	0.0511 (5)
H6A	0.9965	0.4754	0.4053	0.061*
H6B	0.8739	0.4935	0.4622	0.061*
C7	0.68741 (16)	0.40022 (5)	0.6164 (5)	0.0376 (4)
H7	0.7409	0.3809	0.6971	0.045*
C12	0.86919 (16)	0.43713 (5)	0.4083 (5)	0.0366 (4)
C6	0.47248 (14)	0.29402 (5)	1.0493 (5)	0.0328 (3)
C5	0.12821 (16)	0.31783 (5)	0.6479 (5)	0.0448 (5)
H5	0.0512	0.3228	0.5624	0.054*
C8	0.73540 (15)	0.43301 (4)	0.4505 (4)	0.0332 (4)
C4	0.18844 (16)	0.34905 (5)	0.7998 (5)	0.0440 (5)
H4	0.1533	0.3745	0.8126	0.053*
C9	0.65596 (16)	0.46198 (5)	0.3279 (5)	0.0400 (4)
H9	0.6853	0.4846	0.2198	0.048*
C11	0.49241 (17)	0.42297 (5)	0.5413 (5)	0.0432 (4)
H11	0.4089	0.4196	0.5718	0.052*
C10	0.53172 (17)	0.45609 (5)	0.3720 (5)	0.0433 (4)
H10	0.4757	0.4744	0.2879	0.052*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0348 (2)	0.0464 (2)	0.0746 (4)	0.00362 (16)	0.0023 (3)	−0.0112 (3)
Cl2	0.0345 (2)	0.03388 (19)	0.0812 (4)	0.00596 (15)	−0.0204 (2)	−0.0130 (2)
N2	0.0260 (6)	0.0361 (7)	0.0531 (10)	−0.0005 (5)	−0.0083 (6)	0.0086 (7)
N1	0.0318 (7)	0.0404 (7)	0.0454 (9)	−0.0045 (6)	−0.0117 (6)	0.0005 (7)
N4	0.0342 (7)	0.0342 (6)	0.0597 (11)	−0.0032 (5)	0.0011 (7)	0.0042 (7)
C3	0.0339 (8)	0.0309 (8)	0.0428 (10)	−0.0015 (6)	−0.0054 (7)	−0.0025 (8)
C2	0.0230 (7)	0.0320 (7)	0.0332 (8)	−0.0020 (6)	−0.0022 (6)	0.0043 (7)
N3	0.0291 (7)	0.0421 (8)	0.0907 (14)	−0.0092 (6)	−0.0213 (8)	0.0190 (9)
C1	0.0292 (7)	0.0307 (7)	0.0363 (9)	−0.0015 (5)	−0.0041 (8)	0.0015 (8)
N5	0.0326 (7)	0.0328 (7)	0.0890 (15)	0.0001 (6)	0.0051 (8)	−0.0079 (8)
N6	0.0359 (8)	0.0336 (7)	0.0837 (14)	−0.0037 (6)	0.0103 (8)	−0.0099 (9)
C7	0.0348 (8)	0.0285 (7)	0.0495 (11)	0.0022 (6)	−0.0024 (7)	0.0008 (8)
C12	0.0347 (8)	0.0318 (7)	0.0433 (10)	0.0002 (6)	0.0015 (7)	−0.0025 (8)
C6	0.0239 (7)	0.0348 (8)	0.0396 (9)	−0.0021 (6)	−0.0046 (7)	0.0004 (7)
C5	0.0281 (8)	0.0510 (10)	0.0552 (13)	0.0046 (7)	−0.0141 (8)	0.0008 (9)
C8	0.0324 (8)	0.0276 (7)	0.0397 (10)	−0.0003 (6)	−0.0010 (7)	−0.0046 (7)
C4	0.0364 (8)	0.0391 (8)	0.0565 (13)	0.0098 (7)	−0.0067 (8)	−0.0020 (9)
C9	0.0413 (9)	0.0313 (7)	0.0473 (12)	0.0021 (7)	−0.0011 (8)	0.0036 (7)
C11	0.0306 (8)	0.0410 (9)	0.0580 (12)	−0.0010 (7)	−0.0038 (8)	−0.0026 (9)
C10	0.0400 (9)	0.0383 (9)	0.0516 (11)	0.0076 (7)	−0.0066 (8)	0.0031 (8)

Geometric parameters (Å, º) top

N2—C6	1.303 (2)	N5—H5A	0.8600
N2—H2A	0.8600	N5—H5B	0.8600
N2—H2B	0.8600	N6—C12	1.300 (2)
N1—C1	1.334 (2)	N6—H6A	0.8600
N1—C5	1.344 (2)	N6—H6B	0.8600
N4—C7	1.337 (2)	C7—C8	1.390 (2)
N4—C11	1.338 (2)	C7—H7	0.9300
C3—C4	1.376 (2)	C12—C8	1.482 (2)
C3—C2	1.394 (2)	C5—C4	1.380 (3)
C3—H3	0.9300	C5—H5	0.9300
C2—C1	1.393 (2)	C8—C9	1.392 (2)
C2—C6	1.483 (2)	C4—H4	0.9300
N3—C6	1.305 (2)	C9—C10	1.386 (3)
N3—H3A	0.8600	C9—H9	0.9300
N3—H3B	0.8600	C11—C10	1.373 (3)
C1—H1	0.9300	C11—H11	0.9300
N5—C12	1.311 (2)	C10—H10	0.9300

C6—N2—H2A	120.0	C8—C7—H7	118.6
C6—N2—H2B	120.0	N6—C12—N5	120.60 (16)
H2A—N2—H2B	120.0	N6—C12—C8	119.31 (15)
C1—N1—C5	117.47 (14)	N5—C12—C8	120.08 (14)
C7—N4—C11	117.45 (16)	N2—C6—N3	121.94 (15)
C4—C3—C2	118.99 (16)	N2—C6—C2	120.16 (14)
C4—C3—H3	120.5	N3—C6—C2	117.88 (15)
C2—C3—H3	120.5	N1—C5—C4	123.50 (16)
C1—C2—C3	118.31 (14)	N1—C5—H5	118.2
C1—C2—C6	121.15 (14)	C4—C5—H5	118.2
C3—C2—C6	120.54 (14)	C7—C8—C9	118.99 (16)
C6—N3—H3A	120.0	C7—C8—C12	120.30 (15)
C6—N3—H3B	120.0	C9—C8—C12	120.71 (15)
H3A—N3—H3B	120.0	C3—C4—C5	118.66 (15)
N1—C1—C2	123.03 (14)	C3—C4—H4	120.7
N1—C1—H1	118.5	C5—C4—H4	120.7
C2—C1—H1	118.5	C10—C9—C8	117.87 (16)
C12—N5—H5A	120.0	C10—C9—H9	121.1
C12—N5—H5B	120.0	C8—C9—H9	121.1
H5A—N5—H5B	120.0	N4—C11—C10	123.61 (17)
C12—N6—H6A	120.0	N4—C11—H11	118.2
C12—N6—H6B	120.0	C10—C11—H11	118.2
H6A—N6—H6B	120.0	C11—C10—C9	119.20 (17)
N4—C7—C8	122.86 (16)	C11—C10—H10	120.4
N4—C7—H7	118.6	C9—C10—H10	120.4

C4—C3—C2—C1	0.8 (3)	N4—C7—C8—C12	179.21 (18)
C4—C3—C2—C6	−179.98 (18)	N6—C12—C8—C7	−141.6 (2)
C5—N1—C1—C2	−1.7 (3)	N5—C12—C8—C7	37.8 (3)
C3—C2—C1—N1	0.2 (3)	N6—C12—C8—C9	37.8 (3)
C6—C2—C1—N1	−178.99 (18)	N5—C12—C8—C9	−142.8 (2)
C11—N4—C7—C8	1.2 (3)	C2—C3—C4—C5	−0.4 (3)
C1—C2—C6—N2	−36.7 (3)	N1—C5—C4—C3	−1.2 (3)
C3—C2—C6—N2	144.10 (19)	C7—C8—C9—C10	−1.4 (3)
C1—C2—C6—N3	144.72 (19)	C12—C8—C9—C10	179.20 (17)
C3—C2—C6—N3	−34.5 (3)	C7—N4—C11—C10	−0.6 (3)
C1—N1—C5—C4	2.1 (3)	N4—C11—C10—C9	−1.0 (3)
N4—C7—C8—C9	−0.2 (3)	C8—C9—C10—C11	1.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3B···N4	0.86	2.07	2.880 (2)	157
N5—H5B···Cl2	0.86	2.29	3.1403 (15)	170
N6—H6B···Cl1	0.86	2.36	3.1562 (16)	155
N2—H2A···N1ⁱ	0.86	2.22	2.990 (2)	149
N2—H2B···Cl2ⁱⁱ	0.86	2.31	3.1452 (13)	165
N3—H3A···Cl2ⁱⁱⁱ	0.86	2.27	3.1040 (16)	164
N5—H5A···Cl1^iv	0.86	2.46	3.2373 (16)	150
N6—H6A···Cl1^iv	0.86	2.41	3.2013 (16)	152

Symmetry codes: (i) x+1/2, −y+1/2, z+1; (ii) x−1/2, −y+1/2, z+1; (iii) x, y, z+1; (iv) −x+2, −y+1, z−1/2.

Experimental details

Crystal data
Chemical formula	C₆H₈N₃⁺·Cl⁻
M_r	157.60
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	293
a, b, c (Å)	10.9485 (7), 33.1581 (14), 4.1488 (5)
V (Å³)	1506.1 (2)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.43
Crystal size (mm)	0.40 × 0.35 × 0.17

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.845, 0.930
No. of measured, independent and observed [I > 2σ(I)] reflections	14201, 3213, 2953
R_int	0.033
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.071, 1.00
No. of reflections	3213
No. of parameters	182
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.18
Absolute structure	Flack (1983), 1246 Friedel pairs
Absolute structure parameter	0.0019 (5)

Computer programs: PROCESS-AUTO (Rigaku, 2006), CrystalStructure (Rigaku/MSC, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3B···N4	0.86	2.07	2.880 (2)	157
N5—H5B···Cl2	0.86	2.29	3.1403 (15)	170
N6—H6B···Cl1	0.86	2.36	3.1562 (16)	155
N2—H2A···N1ⁱ	0.86	2.22	2.990 (2)	149
N2—H2B···Cl2ⁱⁱ	0.86	2.31	3.1452 (13)	165
N3—H3A···Cl2ⁱⁱⁱ	0.86	2.27	3.1040 (16)	164
N5—H5A···Cl1^iv	0.86	2.46	3.2373 (16)	150
N6—H6A···Cl1^iv	0.86	2.41	3.2013 (16)	152

Symmetry codes: (i) x+1/2, −y+1/2, z+1; (ii) x−1/2, −y+1/2, z+1; (iii) x, y, z+1; (iv) −x+2, −y+1, z−1/2.

Acknowledgements

The authors gratefully acknowledge financial support from the Education Department of Liaoning Province (2009 A 265) and Liaoning University.

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