Crystal structure of ammonium bis­[(pyridin-2-yl)meth­yl]ammonium dichloride

In the title molecular salt, C₁₂H₁₄N₃⁺·NH₄⁺·2Cl⁻, the central, secondary-amine, N atom is protonated. The bis­[(pyridin-2-yl)meth­yl]ammonium and ammonium cations both lie across a twofold rotation axis. The dihedral angles between the planes of the pyridine rings is 68.43 (8)°. In the crystal, N—H...N and N—H...Cl hydrogen bonds link the components of the structure, forming a two-dimensional network parallel to (010). In addition, weak C—H...Cl hydrogen bonds exist within the two-dimensional network.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.025
• wR factor = 0.066
• Data-to-parameter ratio = 23.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.51 Report
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          2 Report
PLAT915_ALERT_3_C Low Friedel Pair Coverage ......................         78 %

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          3 Note
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Report
PLAT176_ALERT_4_G The CIF-Embedded .res File Contains SADI Records          1 Report
PLAT300_ALERT_4_G Atom Site Occupancy of *H1C    is Constrained at      0.500 Check
PLAT300_ALERT_4_G Atom Site Occupancy of *H1D    is Constrained at      0.500 Check
PLAT790_ALERT_4_G Centre of Gravity not Within Unit Cell: Resd.  #          2 Note
              Cl
PLAT790_ALERT_4_G Centre of Gravity not Within Unit Cell: Resd.  #          3 Note
              H4 N
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          1 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Th(Min) ...          1 Report
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         65 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Chemical context

Atom transfer Radical Addition (ATRA) reactions involve the formation of carbon-carbon bonds through the addition of saturated poly-halogenated hydro­carbons to alkenes (Eckenhoff & Pintauer, 2010). First reported by Kharasch in the 1940s (Kharasch et al., 1945), the reaction incorporates halogen group functionalities within products; which can then be used as starting reagents in further functionalization reactions (Iqbal et al., 1994). Subsequently, ATRA has emerged as some of the most atom economical methods for simultaneously forming C–C and C–X bonds; leading to the production of more attractive molecules with well-defined compositions, architectures, and functionalities (Braunecker & Matyjaszewski , 2007). Structural studies suggest that the type of ligand used in atom transfer radical reactions significantly influence the behavior of catalyst generated due to different steric and electronic inter­actions with the metal center (Matyjaszewski et al., 2001). Copper complexes made with tetra­dentate nitro­gen-based ligands such as 1,4,8,11-tetra­aza-1,4,8,11-tetra­methyl­cyclo­tetra­decane (Me₆CYCLAM), tris(2-pyridyl­methyl)­amine (TPMA), tris(2-(di­methyl­amino)­ethyl)­amine (Me₆TREN), and bis(2-pyridyl­methyl) amine (BPMA) are currently some of the most active multi-dentate structures used in atom transfer radical reactions (Tang et al., 2008). Given the significance of these ligands, we present the crystal structure of a protonated bis(2-pyridyl­methyl)­amine (BPMA) salt.

S2. Structural commentary

The molecular structure of the title compound is shown in Fig 1. The bis­[(pyridin-2-yl)methyl]­ammonium and ammonium cations both lie across a twofold rotation axis. The dihedral angles between the pyridine rings is 68.43 (8)°. This is in contrast to the values of the dihedral anlges in bis­(2-pyridyl­methyl)­ammonium bromide and bis­(2-pyridyl­methyl)­ammonium iodide (Junk et al., 2006) which are 38.47 (13) and 5.17 (9)°, respectively. In the crystal, N—H···N and N—H···Cl hydrogen bonds link the components of the structure forming a two-dimensional network parallel to (010) (Fig. 2). In addition, weak C—H···Cl hydrogen bonds exist within the two-dimensional network.

S3. Synthesis and crystallization

Bis(2-pyridyl­methyl)­amine salt (BPMA) was synthesized and purified following literature procedures (Carvalho et al., 2006) and the reaction scheme is shown in Fig. 3. A 500 mL round bottom flask was filled with 100 mL of methanol then 2-pyridine­carboxaldehyde (8.90 mL, 94.0 mmol) added. The flask was placed in an ice bath to cool with the solution mixing. After 15 minutes, 2-pyridyl­methyl­amine (9.70 mL, 94.0 mmol) was added to give a dull yellow colored solution. Flask was removed from ice bath and mixture allowed to react at room temperature for 1 hour to give a red colored solution. The flask was placed back in an ice bath and sodium borohydride (3.500 g, 94.0 mmol) was added in small amounts to prevent foaming. After this addition, the flask was removed from the ice bath and the mixture left to stir overnight. Concentrated hydro­chloric acid was added to the mixture drop-wise until a pH of 4 was attained producing an orange mixture. An extraction was performed on the mixture in a separatory funnel with di­chloro­methane until the organic phase became colorless. The aqueous phase was separated and its pH adjusted to 10 with Na₂CO₃. A second extraction was performed with di­chloro­methane on this mixture and the organic layer isolated and dried using MgSO₄. Solvent was removed to produce the desired ligand as a dark-brown colored oil (14.910 g, 80%). ¹H NMR (CDCl₃, 400 MHz): δ3.48 (s, 1H), δ4.01 (s, 4H), δ7.14 (t, J = 7.6 Hz, 2H), δ 7.34 (d, J = 7.6 Hz, 2H), δ 7.63 (t, J = 7.6 Hz, 2H), δ 8.53 (d, J = 4.8 Hz, 2H). ¹³C NMR (CDCl₃, 400 MHz): δ 156.67, 149.20, 136.74, 122.73, 122.48, 53.25. FT—IR (liquid) v (cm^-1): 3283 (b), 3003 (m), 2818 (b), 1587 (s), 1566 (m), 1471 (s), 1429 (s), 1356 (b). Colorless single crystals suitable for X-Ray analysis were obtained from slow cooling of BPMA ligand in the refrigerator.

S4. Refinement

All H atoms, except for those of the ammonium cation, were placed in calculated positions and refined in a riding-model approximation, with C—H = 0.95 - 0.99 Å, N—H = 0.91 Å and U_iso(H) = 1.2U_eq(C,N). The two unique H atoms of the ammonium cation were refined indpendently with isotropic displacement parameters.

Related literature

For background to atom-transfer radical addition reactions, see: Eckenhoff & Pintauer (2010); Kharasch et al. (1945); Iqbal et al. (1994); Braunecker & Matyjaszewski (2007); Matyjaszewski et al. (2001); Tang et al. (2008). For the synthesis, see: Carvalho et al. (2006). For related structures, see: Junk et al. (2006). .

Structure description

Atom transfer Radical Addition (ATRA) reactions involve the formation of carbon-carbon bonds through the addition of saturated poly-halogenated hydro­carbons to alkenes (Eckenhoff & Pintauer, 2010). First reported by Kharasch in the 1940s (Kharasch et al., 1945), the reaction incorporates halogen group functionalities within products; which can then be used as starting reagents in further functionalization reactions (Iqbal et al., 1994). Subsequently, ATRA has emerged as some of the most atom economical methods for simultaneously forming C–C and C–X bonds; leading to the production of more attractive molecules with well-defined compositions, architectures, and functionalities (Braunecker & Matyjaszewski , 2007). Structural studies suggest that the type of ligand used in atom transfer radical reactions significantly influence the behavior of catalyst generated due to different steric and electronic inter­actions with the metal center (Matyjaszewski et al., 2001). Copper complexes made with tetra­dentate nitro­gen-based ligands such as 1,4,8,11-tetra­aza-1,4,8,11-tetra­methyl­cyclo­tetra­decane (Me₆CYCLAM), tris(2-pyridyl­methyl)­amine (TPMA), tris(2-(di­methyl­amino)­ethyl)­amine (Me₆TREN), and bis(2-pyridyl­methyl) amine (BPMA) are currently some of the most active multi-dentate structures used in atom transfer radical reactions (Tang et al., 2008). Given the significance of these ligands, we present the crystal structure of a protonated bis(2-pyridyl­methyl)­amine (BPMA) salt.

The molecular structure of the title compound is shown in Fig 1. The bis­[(pyridin-2-yl)methyl]­ammonium and ammonium cations both lie across a twofold rotation axis. The dihedral angles between the pyridine rings is 68.43 (8)°. This is in contrast to the values of the dihedral anlges in bis­(2-pyridyl­methyl)­ammonium bromide and bis­(2-pyridyl­methyl)­ammonium iodide (Junk et al., 2006) which are 38.47 (13) and 5.17 (9)°, respectively. In the crystal, N—H···N and N—H···Cl hydrogen bonds link the components of the structure forming a two-dimensional network parallel to (010) (Fig. 2). In addition, weak C—H···Cl hydrogen bonds exist within the two-dimensional network.

For background to atom-transfer radical addition reactions, see: Eckenhoff & Pintauer (2010); Kharasch et al. (1945); Iqbal et al. (1994); Braunecker & Matyjaszewski (2007); Matyjaszewski et al. (2001); Tang et al. (2008). For the synthesis, see: Carvalho et al. (2006). For related structures, see: Junk et al. (2006). .

Synthesis and crystallization

Bis(2-pyridyl­methyl)­amine salt (BPMA) was synthesized and purified following literature procedures (Carvalho et al., 2006) and the reaction scheme is shown in Fig. 3. A 500 mL round bottom flask was filled with 100 mL of methanol then 2-pyridine­carboxaldehyde (8.90 mL, 94.0 mmol) added. The flask was placed in an ice bath to cool with the solution mixing. After 15 minutes, 2-pyridyl­methyl­amine (9.70 mL, 94.0 mmol) was added to give a dull yellow colored solution. Flask was removed from ice bath and mixture allowed to react at room temperature for 1 hour to give a red colored solution. The flask was placed back in an ice bath and sodium borohydride (3.500 g, 94.0 mmol) was added in small amounts to prevent foaming. After this addition, the flask was removed from the ice bath and the mixture left to stir overnight. Concentrated hydro­chloric acid was added to the mixture drop-wise until a pH of 4 was attained producing an orange mixture. An extraction was performed on the mixture in a separatory funnel with di­chloro­methane until the organic phase became colorless. The aqueous phase was separated and its pH adjusted to 10 with Na₂CO₃. A second extraction was performed with di­chloro­methane on this mixture and the organic layer isolated and dried using MgSO₄. Solvent was removed to produce the desired ligand as a dark-brown colored oil (14.910 g, 80%). ¹H NMR (CDCl₃, 400 MHz): δ3.48 (s, 1H), δ4.01 (s, 4H), δ7.14 (t, J = 7.6 Hz, 2H), δ 7.34 (d, J = 7.6 Hz, 2H), δ 7.63 (t, J = 7.6 Hz, 2H), δ 8.53 (d, J = 4.8 Hz, 2H). ¹³C NMR (CDCl₃, 400 MHz): δ 156.67, 149.20, 136.74, 122.73, 122.48, 53.25. FT—IR (liquid) v (cm^-1): 3283 (b), 3003 (m), 2818 (b), 1587 (s), 1566 (m), 1471 (s), 1429 (s), 1356 (b). Colorless single crystals suitable for X-Ray analysis were obtained from slow cooling of BPMA ligand in the refrigerator.

Refinement details

All H atoms, except for those of the ammonium cation, were placed in calculated positions and refined in a riding-model approximation, with C—H = 0.95 - 0.99 Å, N—H = 0.91 Å and U_iso(H) = 1.2U_eq(C,N). The two unique H atoms of the ammonium cation were refined indpendently with isotropic displacement parameters.

Computing details

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015) and SHELXLE (Hübschle et al., 2011); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures

	Fig. 1. The molecular structure, shown with 50% probability ellipsoids for non-H atoms and circles of arbitrary size for H atoms [symmetry code: (i) -x+2, -y+2, z].
	Fig. 2. Part of the crystal structure with hydrogen bonds shown as dashed lines.

Ammonium bis[(pyridin-2-yl)methyl]ammonium dichloride

Crystal data

C12H14N3^+·H4N^+·2(Cl^−)	Dx = 1.377 Mg m^−3
Mr = 289.20	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P21212	Cell parameters from 3559 reflections
a = 8.895 (1) Å	θ = 2.3–31.8°
b = 17.676 (2) Å	µ = 0.45 mm^−1
c = 4.4360 (5) Å	T = 100 K
V = 697.47 (14) Å^3	Rod, colourless
Z = 2	0.55 × 0.30 × 0.25 mm
F(000) = 304

Data collection

Bruker APEXII CCD diffractometer	2126 independent reflections
Radiation source: fine focus sealed tube	2088 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
ω and φ scans	θmax = 31.9°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2013)	h = −12→12
Tmin = 0.605, Tmax = 0.746	k = −25→20
4292 measured reflections	l = −6→5

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.025	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.066	w = 1/[σ^2(Fo^2) + (0.0393P)^2 + 0.1504P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max = 0.001
2126 reflections	Δρmax = 0.42 e Å^−3
89 parameters	Δρmin = −0.17 e Å^−3
1 restraint	Absolute structure: Flack x determined using 748 quotients [(I^+)-(I^-)]/[(I^+)+(I^-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.04 (2)

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	0.92866 (15)	0.93964 (7)	1.2090 (3)	0.0121 (2)
H1A	0.8529	0.9629	1.3436	0.015*
H1B	1.0064	0.9156	1.3367	0.015*
C2	0.85420 (16)	0.88021 (7)	1.0170 (3)	0.0110 (2)
C3	0.93696 (16)	0.81886 (8)	0.9096 (4)	0.0149 (3)
H3	1.0412	0.8146	0.9525	0.018*
C4	0.86432 (17)	0.76416 (8)	0.7391 (4)	0.0169 (3)
H4	0.9174	0.7210	0.6683	0.020*
C5	0.71328 (17)	0.77338 (8)	0.6736 (4)	0.0164 (3)
H5	0.6615	0.7375	0.5526	0.020*
C6	0.63891 (16)	0.83632 (8)	0.7888 (4)	0.0168 (3)
H6	0.5351	0.8424	0.7442	0.020*
N1	1.0000	1.0000	1.0188 (4)	0.0103 (3)
H1C	1.0711	0.9787	0.8982	0.012*	0.5
H1D	0.9289	1.0213	0.8982	0.012*	0.5
N2	0.70678 (14)	0.88881 (7)	0.9597 (3)	0.0134 (2)
Cl1	0.73444 (4)	1.08251 (2)	1.69586 (8)	0.01425 (9)
N4	0.5000	1.0000	1.2452 (4)	0.0142 (3)
H4A	0.558 (2)	0.9696 (11)	1.131 (5)	0.021*
H4B	0.563 (2)	1.0295 (11)	1.363 (5)	0.021*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0123 (5)	0.0129 (5)	0.0112 (5)	−0.0025 (4)	0.0005 (5)	0.0010 (5)
C2	0.0108 (6)	0.0111 (5)	0.0111 (5)	−0.0015 (4)	0.0004 (5)	0.0024 (5)
C3	0.0109 (6)	0.0145 (6)	0.0194 (6)	0.0008 (5)	0.0020 (5)	−0.0002 (5)
C4	0.0163 (6)	0.0136 (5)	0.0208 (7)	0.0005 (5)	0.0044 (6)	−0.0024 (5)
C5	0.0165 (6)	0.0151 (5)	0.0176 (6)	−0.0034 (5)	−0.0001 (6)	−0.0038 (5)
C6	0.0126 (6)	0.0152 (6)	0.0225 (7)	−0.0001 (5)	−0.0036 (6)	−0.0016 (6)
N1	0.0099 (7)	0.0105 (6)	0.0104 (7)	−0.0006 (6)	0.000	0.000
N2	0.0118 (5)	0.0118 (4)	0.0167 (6)	0.0002 (4)	−0.0006 (4)	−0.0007 (4)
Cl1	0.01141 (14)	0.01526 (14)	0.01608 (15)	0.00146 (10)	−0.00198 (11)	0.00017 (11)
N4	0.0120 (7)	0.0136 (7)	0.0170 (9)	0.0008 (6)	0.000	0.000

Geometric parameters (Å, º)

C1—N1	1.5010 (16)	C5—C6	1.392 (2)
C1—C2	1.5060 (19)	C5—H5	0.9500
C1—H1A	0.9900	C6—N2	1.3418 (19)
C1—H1B	0.9900	C6—H6	0.9500
C2—N2	1.3442 (18)	N1—C1^i	1.5010 (16)
C2—C3	1.3944 (19)	N1—H1C	0.9100
C3—C4	1.387 (2)	N1—H1D	0.9100
C3—H3	0.9500	N4—H4A	0.898 (18)
C4—C5	1.384 (2)	N4—H4B	0.926 (18)
C4—H4	0.9500
N1—C1—C2	111.33 (12)	C4—C5—C6	118.59 (14)
N1—C1—H1A	109.4	C4—C5—H5	120.7
C2—C1—H1A	109.4	C6—C5—H5	120.7
N1—C1—H1B	109.4	N2—C6—C5	123.12 (13)
C2—C1—H1B	109.4	N2—C6—H6	118.4
H1A—C1—H1B	108.0	C5—C6—H6	118.4
N2—C2—C3	122.57 (13)	C1^i—N1—C1	111.59 (15)
N2—C2—C1	117.19 (12)	C1^i—N1—H1C	109.3
C3—C2—C1	120.23 (12)	C1—N1—H1C	109.3
C4—C3—C2	118.84 (13)	C1^i—N1—H1D	109.3
C4—C3—H3	120.6	C1—N1—H1D	109.3
C2—C3—H3	120.6	H1C—N1—H1D	108.0
C5—C4—C3	118.98 (13)	C6—N2—C2	117.87 (12)
C5—C4—H4	120.5	H4A—N4—H4B	108.0 (19)
C3—C4—H4	120.5
N1—C1—C2—N2	−94.13 (14)	C4—C5—C6—N2	0.3 (2)
N1—C1—C2—C3	86.76 (15)	C2—C1—N1—C1^i	178.68 (13)
N2—C2—C3—C4	−0.5 (2)	C5—C6—N2—C2	1.1 (2)
C1—C2—C3—C4	178.53 (13)	C3—C2—N2—C6	−0.9 (2)
C2—C3—C4—C5	1.9 (2)	C1—C2—N2—C6	179.97 (13)
C3—C4—C5—C6	−1.7 (2)

Symmetry code: (i) −x+2, −y+2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1B···Cl1^i	0.99	2.80	3.7145 (15)	154
C6—H6···Cl1^ii	0.95	2.75	3.6410 (15)	157
N1—H1C···Cl1^iii	0.91	2.23	3.1239 (9)	168
N1—H1D···Cl1^iv	0.91	2.23	3.1239 (9)	168
N4—H4A···N2	0.90 (2)	2.09 (2)	2.9748 (15)	167 (2)
N4—H4B···Cl1	0.93 (2)	2.32 (2)	3.2362 (12)	170 (2)

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