Crystal structure of 1,1′-(pyridine-2,6-di­yl)bis­[N-(pyridin-2-ylmeth­yl)methanaminium] dichloride dihydrate

In the title compound,the two pyridine side arms are not coplanar, with the terminal pyridine rings subtending a dihedral angle of 26.45 (6)°. In the crystal, hydrogen bonds, inter­molecular C—H...Cl contacts and a weak C—H...O inter­action connect the mol­ecule with neighbouring chloride counter-anions and lattice water mol­ecules. The crystal packing also features by π–π inter­actions.

Key indicators

• Single-crystal X-ray study
• T = 110 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.050
• wR factor = 0.123
• Data-to-parameter ratio = 24.6

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         14 Report
PLAT975_ALERT_2_C Check Calcd Resid. Dens.  0.99A   From O2              0.46 eA-3
PLAT975_ALERT_2_C Check Calcd Resid. Dens.  0.93A   From O1              0.41 eA-3

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          4 Note
PLAT154_ALERT_1_G The s.u.'s on the Cell Angles are Equal ..(Note)      0.003 Degree
PLAT176_ALERT_4_G The CIF-Embedded .res File Contains SADI Records          1 Report
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          1 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          9 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          5 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.         10 Info

   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
   7 ALERT level G = General information/check it is not something unexpected

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

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Computing details

Data collection: APEX3 (Bruker, 2012); cell refinement: APEX3 and SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXT (Sheldrick 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).

1,1'-(Pyridine-2,6-diyl)bis[N-(pyridin-2-ylmethyl)methanaminium] dichloride dihydrate

Crystal data

C19H23N5^2+·2Cl^−·2H2O	Z = 2
Mr = 428.36	F(000) = 452
Triclinic, P1	Dx = 1.416 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.1579 (6) Å	Cell parameters from 4444 reflections
b = 8.8119 (7) Å	θ = 3.2–31.4°
c = 17.4150 (13) Å	µ = 0.35 mm^−1
α = 80.357 (3)°	T = 110 K
β = 80.805 (3)°	Needle, colourless
γ = 68.919 (3)°	0.2 × 0.08 × 0.04 mm
V = 1004.52 (14) Å^3

Data collection

Bruker Kappa APEXII Quazar diffractometer	6970 independent reflections
Radiation source: microfocus sealed tube	4632 reflections with I > 2σ(I)
Multilayer optics monochromator	Rint = 0.097
phi and ω scans	θmax = 32.0°, θmin = 1.2°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −10→10
Tmin = 0.660, Tmax = 0.746	k = −13→13
29584 measured reflections	l = −25→25

Refinement

Refinement on F^2	Primary atom site location: dual
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.05	Hydrogen site location: mixed
wR(F^2) = 0.123	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0518P)^2] where P = (Fo^2 + 2Fc^2)/3
6970 reflections	(Δ/σ)max = 0.002
283 parameters	Δρmax = 0.45 e Å^−3
1 restraint	Δρmin = −0.38 e Å^−3

Special details

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

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

	x	y	z	Uiso*/Ueq
C1	−0.0133 (3)	1.1436 (2)	0.77592 (11)	0.0187 (4)
H1	−0.057178	1.157686	0.725689	0.022*
C2	−0.0514 (3)	1.2816 (2)	0.81173 (12)	0.0209 (4)
H2	−0.118646	1.387618	0.786614	0.025*
C3	0.0110 (3)	1.2617 (2)	0.88529 (12)	0.0209 (4)
H3	−0.013857	1.353959	0.91186	0.025*
C4	0.1098 (3)	1.1057 (2)	0.91921 (11)	0.0177 (4)
H4	0.15363	1.089007	0.969628	0.021*
C5	0.1446 (3)	0.9729 (2)	0.87872 (10)	0.0141 (3)
C6	0.2661 (3)	0.8058 (2)	0.91424 (10)	0.0154 (3)
H6A	0.405015	0.802589	0.916169	0.018*
H6B	0.20699	0.78592	0.968744	0.018*
C7	0.3958 (3)	0.5088 (2)	0.90648 (10)	0.0152 (3)
H7A	0.32656	0.482715	0.958206	0.018*
H7B	0.528732	0.510415	0.914788	0.018*
C8	0.4252 (3)	0.3788 (2)	0.85503 (10)	0.0123 (3)
C9	0.5158 (3)	0.2141 (2)	0.88081 (10)	0.0159 (4)
H9	0.555649	0.180246	0.93221	0.019*
C10	0.5467 (3)	0.1000 (2)	0.82986 (11)	0.0169 (4)
H10	0.610739	−0.013533	0.84539	0.02*
C11	0.4830 (3)	0.1539 (2)	0.75619 (10)	0.0153 (3)
H11	0.502104	0.078354	0.720177	0.018*
C12	0.3904 (3)	0.3211 (2)	0.73580 (10)	0.0126 (3)
C13	0.3100 (3)	0.3899 (2)	0.65770 (10)	0.0143 (3)
H13A	0.397572	0.323319	0.616689	0.017*
H13B	0.172891	0.385542	0.659994	0.017*
C14	0.2369 (3)	0.6343 (2)	0.55940 (10)	0.0155 (3)
H14A	0.096005	0.640498	0.55942	0.019*
H14B	0.321889	0.562201	0.519947	0.019*
C15	0.2502 (3)	0.8035 (2)	0.53686 (10)	0.0134 (3)
C16	0.2354 (3)	0.8748 (2)	0.45938 (10)	0.0161 (4)
H16	0.225967	0.815293	0.420322	0.019*
C17	0.2348 (3)	1.0342 (2)	0.44024 (11)	0.0186 (4)
H17	0.225559	1.085635	0.387808	0.022*
C18	0.2479 (3)	1.1176 (2)	0.49930 (11)	0.0197 (4)
H18	0.245914	1.227408	0.488339	0.024*
C19	0.2640 (3)	1.0358 (2)	0.57442 (11)	0.0169 (4)
H19	0.273735	1.092671	0.614568	0.02*
N1	0.3620 (2)	0.43202 (17)	0.78433 (8)	0.0120 (3)
N2	0.2743 (2)	0.67297 (17)	0.87003 (9)	0.0127 (3)
N3	0.0822 (2)	0.99031 (18)	0.80798 (9)	0.0160 (3)
N4	0.3036 (2)	0.56233 (17)	0.63771 (8)	0.0129 (3)
N5	0.2668 (2)	0.88122 (17)	0.59397 (8)	0.0146 (3)
Cl1	0.82559 (7)	0.68542 (5)	0.91223 (3)	0.01828 (11)
Cl2	0.76725 (7)	0.49614 (5)	0.62355 (3)	0.01743 (11)
O1	0.9786 (2)	0.76904 (17)	0.72866 (8)	0.0210 (3)
O2	0.4905 (2)	0.76661 (17)	0.73277 (8)	0.0205 (3)
H201	0.592 (4)	0.689 (3)	0.7158 (14)	0.038*
H202	0.389 (4)	0.807 (3)	0.7017 (16)	0.05*
H21	0.345 (3)	0.689 (2)	0.8209 (11)	0.018 (5)*
H22	0.152 (3)	0.676 (2)	0.8706 (11)	0.013 (5)*
H41	0.431 (4)	0.562 (3)	0.6375 (13)	0.026 (6)*
H42	0.216 (4)	0.622 (3)	0.6789 (12)	0.037 (7)*
H101	0.917 (4)	0.721 (3)	0.7716 (15)	0.040 (7)*
H102	1.026 (5)	0.841 (4)	0.7531 (19)	0.084 (11)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0158 (9)	0.0187 (9)	0.0217 (9)	−0.0080 (7)	−0.0011 (7)	0.0014 (7)
C2	0.0147 (9)	0.0153 (8)	0.0302 (10)	−0.0057 (7)	0.0053 (8)	−0.0016 (7)
C3	0.0187 (10)	0.0150 (8)	0.0291 (10)	−0.0080 (7)	0.0087 (8)	−0.0084 (7)
C4	0.0159 (9)	0.0194 (9)	0.0187 (9)	−0.0077 (7)	0.0042 (7)	−0.0068 (7)
C5	0.0121 (9)	0.0145 (8)	0.0164 (8)	−0.0062 (7)	0.0024 (7)	−0.0031 (6)
C6	0.0184 (9)	0.0148 (8)	0.0142 (8)	−0.0053 (7)	−0.0028 (7)	−0.0047 (6)
C7	0.0179 (9)	0.0132 (8)	0.0133 (8)	−0.0039 (7)	−0.0046 (7)	0.0012 (6)
C8	0.0109 (8)	0.0136 (7)	0.0136 (8)	−0.0062 (6)	−0.0010 (6)	−0.0002 (6)
C9	0.0164 (9)	0.0144 (8)	0.0173 (8)	−0.0061 (7)	−0.0060 (7)	0.0032 (6)
C10	0.0135 (9)	0.0112 (8)	0.0240 (9)	−0.0035 (7)	−0.0021 (7)	0.0016 (7)
C11	0.0147 (9)	0.0122 (8)	0.0202 (9)	−0.0061 (7)	0.0005 (7)	−0.0038 (6)
C12	0.0099 (8)	0.0121 (7)	0.0160 (8)	−0.0043 (6)	−0.0005 (6)	−0.0015 (6)
C13	0.0180 (9)	0.0109 (7)	0.0156 (8)	−0.0059 (7)	−0.0022 (7)	−0.0030 (6)
C14	0.0199 (9)	0.0153 (8)	0.0120 (8)	−0.0060 (7)	−0.0053 (7)	−0.0003 (6)
C15	0.0100 (8)	0.0148 (8)	0.0138 (8)	−0.0028 (6)	−0.0017 (6)	−0.0007 (6)
C16	0.0129 (9)	0.0186 (8)	0.0145 (8)	−0.0030 (7)	−0.0016 (7)	−0.0012 (7)
C17	0.0116 (9)	0.0227 (9)	0.0174 (9)	−0.0045 (7)	−0.0013 (7)	0.0052 (7)
C18	0.0141 (9)	0.0163 (8)	0.0270 (10)	−0.0057 (7)	−0.0035 (8)	0.0038 (7)
C19	0.0147 (9)	0.0151 (8)	0.0219 (9)	−0.0062 (7)	−0.0029 (7)	−0.0014 (7)
N1	0.0113 (7)	0.0118 (6)	0.0129 (7)	−0.0042 (5)	−0.0020 (5)	−0.0004 (5)
N2	0.0147 (8)	0.0116 (7)	0.0125 (7)	−0.0044 (6)	−0.0030 (6)	−0.0018 (5)
N3	0.0153 (8)	0.0146 (7)	0.0187 (7)	−0.0069 (6)	0.0005 (6)	−0.0023 (6)
N4	0.0155 (8)	0.0111 (6)	0.0124 (7)	−0.0049 (6)	−0.0030 (6)	−0.0001 (5)
N5	0.0146 (8)	0.0142 (7)	0.0160 (7)	−0.0065 (6)	−0.0029 (6)	0.0004 (5)
Cl1	0.0158 (2)	0.01449 (19)	0.0216 (2)	−0.00422 (16)	−0.00132 (17)	0.00282 (16)
Cl2	0.0160 (2)	0.0182 (2)	0.0178 (2)	−0.00561 (17)	−0.00165 (16)	−0.00182 (16)
O1	0.0217 (8)	0.0225 (7)	0.0175 (7)	−0.0062 (6)	−0.0017 (6)	−0.0028 (5)
O2	0.0234 (8)	0.0193 (7)	0.0194 (7)	−0.0083 (6)	−0.0002 (6)	−0.0040 (5)

Geometric parameters (Å, º)

C1—N3	1.345 (2)	C12—C13	1.507 (2)
C1—C2	1.380 (3)	C13—N4	1.487 (2)
C1—H1	0.95	C13—H13A	0.99
C2—C3	1.387 (3)	C13—H13B	0.99
C2—H2	0.95	C14—N4	1.480 (2)
C3—C4	1.379 (3)	C14—C15	1.511 (2)
C3—H3	0.95	C14—H14A	0.99
C4—C5	1.393 (2)	C14—H14B	0.99
C4—H4	0.95	C15—N5	1.340 (2)
C5—N3	1.343 (2)	C15—C16	1.393 (2)
C5—C6	1.501 (2)	C16—C17	1.387 (3)
C6—N2	1.485 (2)	C16—H16	0.95
C6—H6A	0.99	C17—C18	1.393 (3)
C6—H6B	0.99	C17—H17	0.95
C7—N2	1.488 (2)	C18—C19	1.384 (2)
C7—C8	1.507 (2)	C18—H18	0.95
C7—H7A	0.99	C19—N5	1.342 (2)
C7—H7B	0.99	C19—H19	0.95
C8—N1	1.331 (2)	N2—H21	0.937 (18)
C8—C9	1.388 (2)	N2—H22	0.86 (2)
C9—C10	1.387 (2)	N4—H41	0.91 (2)
C9—H9	0.95	N4—H42	0.967 (19)
C10—C11	1.381 (2)	O1—H101	0.93 (3)
C10—H10	0.95	O1—H102	1.00 (4)
C11—C12	1.390 (2)	O2—H201	0.85 (3)
C11—H11	0.95	O2—H202	0.91 (3)
C12—N1	1.338 (2)
N3—C1—C2	123.83 (18)	N4—C13—H13A	109.7
N3—C1—H1	118.1	C12—C13—H13A	109.7
C2—C1—H1	118.1	N4—C13—H13B	109.7
C1—C2—C3	118.32 (17)	C12—C13—H13B	109.7
C1—C2—H2	120.8	H13A—C13—H13B	108.2
C3—C2—H2	120.8	N4—C14—C15	111.73 (14)
C4—C3—C2	118.88 (17)	N4—C14—H14A	109.3
C4—C3—H3	120.6	C15—C14—H14A	109.3
C2—C3—H3	120.6	N4—C14—H14B	109.3
C3—C4—C5	119.23 (17)	C15—C14—H14B	109.3
C3—C4—H4	120.4	H14A—C14—H14B	107.9
C5—C4—H4	120.4	N5—C15—C16	122.97 (16)
N3—C5—C4	122.47 (16)	N5—C15—C14	117.68 (14)
N3—C5—C6	119.35 (15)	C16—C15—C14	119.28 (15)
C4—C5—C6	118.09 (16)	C17—C16—C15	118.87 (16)
N2—C6—C5	112.92 (14)	C17—C16—H16	120.6
N2—C6—H6A	109	C15—C16—H16	120.6
C5—C6—H6A	109	C16—C17—C18	118.78 (17)
N2—C6—H6B	109	C16—C17—H17	120.6
C5—C6—H6B	109	C18—C17—H17	120.6
H6A—C6—H6B	107.8	C19—C18—C17	118.13 (17)
N2—C7—C8	110.77 (13)	C19—C18—H18	120.9
N2—C7—H7A	109.5	C17—C18—H18	120.9
C8—C7—H7A	109.5	N5—C19—C18	123.98 (17)
N2—C7—H7B	109.5	N5—C19—H19	118
C8—C7—H7B	109.5	C18—C19—H19	118
H7A—C7—H7B	108.1	C8—N1—C12	118.13 (14)
N1—C8—C9	123.01 (15)	C6—N2—C7	111.76 (13)
N1—C8—C7	116.08 (14)	C6—N2—H21	106.6 (12)
C9—C8—C7	120.90 (15)	C7—N2—H21	105.3 (13)
C10—C9—C8	118.50 (16)	C6—N2—H22	107.3 (13)
C10—C9—H9	120.7	C7—N2—H22	108.9 (13)
C8—C9—H9	120.7	H21—N2—H22	117.1 (18)
C11—C10—C9	118.94 (16)	C5—N3—C1	117.25 (15)
C11—C10—H10	120.5	C14—N4—C13	112.47 (13)
C9—C10—H10	120.5	C14—N4—H41	108.2 (14)
C10—C11—C12	118.65 (16)	C13—N4—H41	107.4 (14)
C10—C11—H11	120.7	C14—N4—H42	112.1 (14)
C12—C11—H11	120.7	C13—N4—H42	106.6 (15)
N1—C12—C11	122.75 (16)	H41—N4—H42	110 (2)
N1—C12—C13	115.14 (14)	C15—N5—C19	117.26 (15)
C11—C12—C13	122.10 (15)	H101—O1—H102	102 (2)
N4—C13—C12	109.75 (13)	H201—O2—H202	115 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H201···Cl2	0.85 (3)	2.41 (3)	3.1844 (15)	152 (2)
O2—H202···N5	0.91 (3)	2.10 (3)	2.947 (2)	155 (2)
N2—H21···O2	0.94 (2)	1.89 (2)	2.804 (2)	165 (2)
N2—H22···Cl1^i	0.86 (2)	2.31 (2)	3.1446 (17)	162.5 (17)
N4—H41···Cl2	0.91 (2)	2.25 (2)	3.1319 (17)	164.1 (19)
N4—H42···O1^i	0.97 (2)	1.90 (2)	2.825 (2)	158 (2)
O1—H101···Cl1	0.93 (3)	2.43 (3)	3.2611 (15)	149 (2)
O1—H102···N3^ii	1.00 (4)	1.93 (4)	2.920 (2)	172 (3)
C3—H3···Cl1^iii	0.95	2.73	3.5702 (19)	148
C6—H6A···Cl1	0.99	2.8	3.751 (2)	161
C7—H7A···Cl1^iv	0.99	2.78	3.7351 (18)	162
C10—H10···Cl1^v	0.95	2.71	3.6469 (18)	168
C17—H17···O1^vi	0.95	2.57	3.437 (2)	151

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