organic compounds
of ammonium bis[(pyridin-2-yl)methyl]ammonium dichloride
aDepartment of Chemistry & Physics, Saint Marys College, Notre Dame, IN 46556, USA, and bDepartment of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
*Correspondence e-mail: koshin@saintmarys.edu
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.
Keywords: crystal structure; protonated structure; hydrogen bonding; atom transfer radical addition (ATRA) reactions; chirality.
CCDC reference: 1420168
1. 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).
2. Experimental
2.1. Crystal data
|
2.3. Refinement
Data collection: APEX2 (Bruker, 2013); cell SAINT (Bruker, 2013); data reduction: SAINT; 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).
Supporting information
CCDC reference: 1420168
https://doi.org/10.1107/S2056989015015753/lh5782sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015015753/lh5782Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989015015753/lh5782Isup3.cml
Atom transfer Radical Addition (ATRA) reactions involve the formation of carbon-carbon bonds through the addition of saturated poly-halogenated hydrocarbons to
(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 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.
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.
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 Uiso(H) = 1.2Ueq(C,N). The two unique H atoms of the ammonium cation were refined indpendently with isotropic displacement parameters.
Atom transfer Radical Addition (ATRA) reactions involve the formation of carbon-carbon bonds through the addition of saturated poly-halogenated hydrocarbons to
(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 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). .
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.
detailsAll 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 Uiso(H) = 1.2Ueq(C,N). The two unique H atoms of the ammonium cation were refined indpendently with isotropic displacement parameters.
Data collection: APEX2 (Bruker, 2013); cell
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).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. |
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) Å3 | Rod, colourless |
Z = 2 | 0.55 × 0.30 × 0.25 mm |
F(000) = 304 |
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 on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.025 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.066 | w = 1/[σ2(Fo2) + (0.0393P)2 + 0.1504P] where P = (Fo2 + 2Fc2)/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) |
C12H14N3+·H4N+·2(Cl−) | V = 697.47 (14) Å3 |
Mr = 289.20 | Z = 2 |
Orthorhombic, P21212 | Mo Kα radiation |
a = 8.895 (1) Å | µ = 0.45 mm−1 |
b = 17.676 (2) Å | T = 100 K |
c = 4.4360 (5) Å | 0.55 × 0.30 × 0.25 mm |
Bruker APEXII CCD diffractometer | 2126 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2013) | 2088 reflections with I > 2σ(I) |
Tmin = 0.605, Tmax = 0.746 | Rint = 0.016 |
4292 measured reflections |
R[F2 > 2σ(F2)] = 0.025 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.066 | Δρmax = 0.42 e Å−3 |
S = 1.06 | Δρmin = −0.17 e Å−3 |
2126 reflections | Absolute structure: Flack x determined using 748 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
89 parameters | Absolute structure parameter: 0.04 (2) |
1 restraint |
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. |
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* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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 |
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—C1i | 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) | C1i—N1—C1 | 111.59 (15) |
N2—C2—C1 | 117.19 (12) | C1i—N1—H1C | 109.3 |
C3—C2—C1 | 120.23 (12) | C1—N1—H1C | 109.3 |
C4—C3—C2 | 118.84 (13) | C1i—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—C1i | 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. |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1B···Cl1i | 0.99 | 2.80 | 3.7145 (15) | 154 |
C6—H6···Cl1ii | 0.95 | 2.75 | 3.6410 (15) | 157 |
N1—H1C···Cl1iii | 0.91 | 2.23 | 3.1239 (9) | 168 |
N1—H1D···Cl1iv | 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. |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1B···Cl1i | 0.99 | 2.80 | 3.7145 (15) | 153.5 |
C6—H6···Cl1ii | 0.95 | 2.75 | 3.6410 (15) | 156.7 |
N1—H1C···Cl1iii | 0.91 | 2.23 | 3.1239 (9) | 167.7 |
N1—H1D···Cl1iv | 0.91 | 2.23 | 3.1239 (9) | 167.7 |
N4—H4A···N2 | 0.898 (18) | 2.092 (17) | 2.9748 (15) | 167 (2) |
N4—H4B···Cl1 | 0.926 (18) | 2.322 (18) | 3.2362 (12) | 169.5 (18) |
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. |
Acknowledgements
KO would like to thank Dr. Matthias Zeller for crystallographic support and Youngstown State University for instrument support. The X-ray diffractometer was funded by NSF grant No. 1337296, and Project SEED student (AT) was funded by the American Chemical Society. Research funding from The Weber Foundation, Cambridge Isotope Laboratories Inc., and Thermo-Fisher Scientific are also gratefully acknowledged.
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