N,N′-Bis(pyridin-3-ylmeth­yl)ethanedi­amide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

Tan, S.L.; Tiekink, E.R.T.

doi:10.1107/S2056989019016153

N,N′-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

The organic molecule in the title bis-pyridyl-substituted diamide hydrate has a U-shape as the 3-pyridyl rings lie to the same side of the central plane. In the crystal, two supramolecular tapes, each sustained by amide-N—H

O(carbonyl) hydrogen bonds and ten-membered {

HNC₂O}₂ synthons, are connected by a helical chain of hydrogen-bonded water molecules.

Keywords: crystal structure; diamide; hydrogen bonding; Hirshfeld surface analysis; computational chemistry.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989019016153/hb7869sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989019016153/hb7869Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989019016153/hb7869Isup3.cml Supplementary material

CCDC reference: 1969282

checkCIF report

Key indicators

Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.002 Å
R factor = 0.043
wR factor = 0.116
Data-to-parameter ratio = 14.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of        C12 Check
PLAT369_ALERT_2_C Long   C(sp2)-C(sp2) Bond  C7       - C8       .       1.54 Ang.
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.814 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         16 Report

Alert level G
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         52 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 Info

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 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
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXS (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2017 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

N,N'-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate top

Crystal data top

C₁₄H₁₄N₄O₂·H₂O	F(000) = 608
M_r = 288.31	D_x = 1.373 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.54184 Å
a = 12.4784 (4) Å	Cell parameters from 5162 reflections
b = 5.0247 (1) Å	θ = 4.0–75.9°
c = 22.2410 (6) Å	µ = 0.82 mm⁻¹
β = 90.170 (3)°	T = 100 K
V = 1394.51 (6) Å³	Prism, colourless
Z = 4	0.09 × 0.07 × 0.03 mm

Data collection top

XtaLAB Synergy Dualflex AtlasS2 diffractometer	2441 reflections with I > 2σ(I)
Detector resolution: 5.2558 pixels mm^-1	R_int = 0.053
ω scans	θ_max = 76.7°, θ_min = 4.0°
Absorption correction: gaussian (Crysalis PRO; Rigaku OD, 2018)	h = −14→15
T_min = 0.921, T_max = 1.000	k = −6→6
16961 measured reflections	l = −27→28
2871 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.043	Hydrogen site location: mixed
wR(F²) = 0.116	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0553P)² + 0.7659P] where P = (F_o² + 2F_c²)/3
2871 reflections	(Δ/σ)_max < 0.001
202 parameters	Δρ_max = 0.30 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.39488 (9)	−0.1106 (2)	0.53440 (5)	0.0211 (3)
O2	0.28502 (10)	0.4170 (2)	0.45056 (5)	0.0245 (3)
N1	0.51280 (11)	0.8092 (3)	0.72982 (6)	0.0230 (3)
N2	0.40224 (11)	0.3337 (3)	0.55256 (6)	0.0178 (3)
H2N	0.3890 (16)	0.486 (4)	0.5378 (9)	0.021*
N3	0.26914 (11)	−0.0297 (3)	0.43753 (6)	0.0176 (3)
H3N	0.2848 (16)	−0.182 (4)	0.4529 (8)	0.021*
N4	−0.08573 (13)	0.1419 (4)	0.36223 (9)	0.0434 (5)
C1	0.52700 (13)	0.6284 (3)	0.68624 (7)	0.0205 (3)
H1	0.598157	0.573079	0.677719	0.025*
C2	0.44417 (12)	0.5164 (3)	0.65271 (7)	0.0176 (3)
C3	0.34062 (13)	0.6008 (3)	0.66496 (7)	0.0202 (3)
H3	0.281622	0.530908	0.642955	0.024*
C4	0.32438 (13)	0.7884 (3)	0.70976 (7)	0.0224 (3)
H4	0.254145	0.849326	0.718705	0.027*
C5	0.41200 (13)	0.8860 (3)	0.74135 (7)	0.0227 (3)
H5	0.400111	1.012319	0.772402	0.027*
C6	0.47006 (13)	0.3104 (3)	0.60569 (7)	0.0202 (3)
H6A	0.545984	0.329839	0.593668	0.024*
H6B	0.461045	0.130847	0.623270	0.024*
C7	0.37291 (12)	0.1213 (3)	0.52134 (7)	0.0163 (3)
C8	0.30359 (12)	0.1859 (3)	0.46578 (7)	0.0170 (3)
C9	0.20743 (13)	−0.0186 (3)	0.38182 (7)	0.0196 (3)
H9A	0.228818	−0.169871	0.355973	0.024*
H9B	0.225732	0.147561	0.360270	0.024*
C10	0.08770 (13)	−0.0283 (3)	0.39089 (7)	0.0199 (3)
C11	0.02169 (15)	0.1432 (4)	0.35990 (9)	0.0370 (5)
H11	0.054734	0.272529	0.334924	0.044*
C12	−0.13026 (14)	−0.0379 (4)	0.39790 (8)	0.0304 (4)
H12	−0.206194	−0.042293	0.400717	0.036*
C13	−0.07261 (17)	−0.2165 (5)	0.43067 (11)	0.0486 (6)
H13	−0.107827	−0.342052	0.455703	0.058*
C14	0.03821 (16)	−0.2127 (5)	0.42700 (10)	0.0450 (6)
H14	0.079722	−0.336857	0.449325	0.054*
O1W	0.71328 (9)	0.9787 (2)	0.77119 (5)	0.0217 (3)
H1W	0.642 (2)	0.942 (4)	0.7593 (9)	0.033*
H2W	0.7244 (18)	1.141 (5)	0.7574 (10)	0.033*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0241 (6)	0.0137 (5)	0.0254 (6)	0.0006 (4)	−0.0029 (4)	0.0011 (4)
O2	0.0323 (7)	0.0139 (5)	0.0272 (6)	0.0018 (5)	−0.0065 (5)	0.0007 (4)
N1	0.0189 (7)	0.0242 (7)	0.0261 (7)	−0.0010 (5)	−0.0026 (5)	−0.0033 (5)
N2	0.0207 (7)	0.0122 (6)	0.0206 (6)	0.0009 (5)	−0.0012 (5)	0.0013 (5)
N3	0.0192 (7)	0.0131 (6)	0.0205 (6)	0.0005 (5)	−0.0011 (5)	−0.0001 (5)
N4	0.0187 (8)	0.0514 (11)	0.0600 (11)	0.0000 (7)	−0.0009 (7)	0.0268 (9)
C1	0.0160 (7)	0.0205 (8)	0.0248 (8)	0.0001 (6)	−0.0022 (6)	−0.0008 (6)
C2	0.0178 (7)	0.0156 (7)	0.0195 (7)	−0.0013 (6)	−0.0013 (6)	0.0023 (5)
C3	0.0161 (7)	0.0219 (8)	0.0227 (7)	−0.0035 (6)	−0.0016 (6)	0.0002 (6)
C4	0.0170 (8)	0.0263 (8)	0.0239 (7)	−0.0002 (6)	0.0023 (6)	−0.0018 (6)
C5	0.0213 (8)	0.0243 (8)	0.0226 (7)	−0.0008 (6)	−0.0003 (6)	−0.0034 (6)
C6	0.0192 (8)	0.0175 (7)	0.0239 (7)	0.0014 (6)	−0.0037 (6)	−0.0018 (6)
C7	0.0151 (7)	0.0140 (7)	0.0198 (7)	−0.0001 (5)	0.0032 (6)	0.0010 (5)
C8	0.0168 (7)	0.0151 (7)	0.0192 (7)	0.0013 (6)	0.0028 (6)	0.0003 (5)
C9	0.0195 (8)	0.0196 (7)	0.0197 (7)	−0.0003 (6)	−0.0004 (6)	−0.0012 (6)
C10	0.0206 (8)	0.0193 (7)	0.0198 (7)	−0.0013 (6)	0.0000 (6)	−0.0023 (6)
C11	0.0198 (9)	0.0432 (11)	0.0481 (11)	−0.0018 (8)	−0.0005 (8)	0.0262 (9)
C12	0.0187 (8)	0.0370 (10)	0.0355 (9)	−0.0035 (7)	0.0031 (7)	0.0028 (8)
C13	0.0268 (10)	0.0584 (14)	0.0605 (14)	−0.0057 (10)	0.0068 (9)	0.0343 (12)
C14	0.0241 (10)	0.0509 (13)	0.0601 (13)	0.0014 (9)	−0.0001 (9)	0.0345 (11)
O1W	0.0186 (6)	0.0205 (6)	0.0261 (6)	−0.0009 (5)	−0.0027 (4)	0.0012 (5)

Geometric parameters (Å, º) top

O1—C7	1.2313 (18)	C4—H4	0.9500
O2—C8	1.2314 (18)	C5—H5	0.9500
N1—C5	1.341 (2)	C6—H6A	0.9900
N1—C1	1.341 (2)	C6—H6B	0.9900
N2—C7	1.3244 (19)	C7—C8	1.541 (2)
N2—C6	1.456 (2)	C9—C10	1.509 (2)
N2—H2N	0.85 (2)	C9—H9A	0.9900
N3—C8	1.323 (2)	C9—H9B	0.9900
N3—C9	1.4579 (19)	C10—C14	1.374 (2)
N3—H3N	0.86 (2)	C10—C11	1.376 (2)
N4—C12	1.326 (2)	C11—H11	0.9500
N4—C11	1.342 (2)	C12—C13	1.361 (3)
C1—C2	1.392 (2)	C12—H12	0.9500
C1—H1	0.9500	C13—C14	1.386 (3)
C2—C3	1.388 (2)	C13—H13	0.9500
C2—C6	1.507 (2)	C14—H14	0.9500
C3—C4	1.387 (2)	O1W—H1W	0.95 (2)
C3—H3	0.9500	O1W—H2W	0.88 (2)
C4—C5	1.387 (2)

C5—N1—C1	117.34 (14)	O1—C7—N2	125.30 (14)
C7—N2—C6	121.32 (13)	O1—C7—C8	120.84 (13)
C7—N2—H2N	118.1 (13)	N2—C7—C8	113.84 (13)
C6—N2—H2N	119.8 (13)	O2—C8—N3	125.51 (14)
C8—N3—C9	122.84 (13)	O2—C8—C7	121.59 (13)
C8—N3—H3N	117.8 (13)	N3—C8—C7	112.89 (13)
C9—N3—H3N	119.4 (13)	N3—C9—C10	113.95 (12)
C12—N4—C11	116.55 (16)	N3—C9—H9A	108.8
N1—C1—C2	124.18 (15)	C10—C9—H9A	108.8
N1—C1—H1	117.9	N3—C9—H9B	108.8
C2—C1—H1	117.9	C10—C9—H9B	108.8
C3—C2—C1	117.51 (14)	H9A—C9—H9B	107.7
C3—C2—C6	123.21 (14)	C14—C10—C11	116.47 (16)
C1—C2—C6	119.28 (14)	C14—C10—C9	123.13 (15)
C2—C3—C4	119.13 (14)	C11—C10—C9	120.31 (15)
C2—C3—H3	120.4	N4—C11—C10	125.07 (17)
C4—C3—H3	120.4	N4—C11—H11	117.5
C5—C4—C3	119.17 (15)	C10—C11—H11	117.5
C5—C4—H4	120.4	N4—C12—C13	123.24 (17)
C3—C4—H4	120.4	N4—C12—H12	118.4
N1—C5—C4	122.66 (15)	C13—C12—H12	118.4
N1—C5—H5	118.7	C12—C13—C14	119.05 (18)
C4—C5—H5	118.7	C12—C13—H13	120.5
N2—C6—C2	112.50 (12)	C14—C13—H13	120.5
N2—C6—H6A	109.1	C10—C14—C13	119.61 (18)
C2—C6—H6A	109.1	C10—C14—H14	120.2
N2—C6—H6B	109.1	C13—C14—H14	120.2
C2—C6—H6B	109.1	H1W—O1W—H2W	103.3 (19)
H6A—C6—H6B	107.8

C5—N1—C1—C2	−0.1 (2)	O1—C7—C8—O2	−176.62 (15)
N1—C1—C2—C3	0.8 (2)	N2—C7—C8—O2	4.9 (2)
N1—C1—C2—C6	−178.75 (14)	O1—C7—C8—N3	2.8 (2)
C1—C2—C3—C4	−0.5 (2)	N2—C7—C8—N3	−175.72 (13)
C6—C2—C3—C4	178.98 (14)	C8—N3—C9—C10	−94.71 (17)
C2—C3—C4—C5	−0.3 (2)	N3—C9—C10—C14	−48.5 (2)
C1—N1—C5—C4	−0.8 (2)	N3—C9—C10—C11	135.08 (17)
C3—C4—C5—N1	1.0 (3)	C12—N4—C11—C10	0.8 (3)
C7—N2—C6—C2	−146.60 (14)	C14—C10—C11—N4	−0.4 (3)
C3—C2—C6—N2	37.4 (2)	C9—C10—C11—N4	176.3 (2)
C1—C2—C6—N2	−143.09 (14)	C11—N4—C12—C13	−0.6 (3)
C6—N2—C7—O1	3.0 (2)	N4—C12—C13—C14	0.0 (4)
C6—N2—C7—C8	−178.56 (13)	C11—C10—C14—C13	−0.3 (3)
C9—N3—C8—O2	3.0 (2)	C9—C10—C14—C13	−176.9 (2)
C9—N3—C8—C7	−176.35 (12)	C12—C13—C14—C10	0.5 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O2	0.85 (2)	2.36 (2)	2.7279 (18)	107.0 (16)
N3—H3N···O1	0.86 (2)	2.299 (19)	2.6924 (18)	108.0 (15)
O1W—H1W···N1	0.95 (2)	1.86 (2)	2.7958 (18)	169 (2)
O1W—H2W···O1Wⁱ	0.88 (2)	1.97 (2)	2.8364 (15)	166 (2)
N2—H2N···O1ⁱⁱ	0.85 (2)	2.03 (2)	2.8227 (18)	155.2 (18)
N3—H3N···O2ⁱⁱⁱ	0.86 (2)	2.02 (2)	2.8022 (18)	151.6 (17)
C9—H9A···O1W^iv	0.99	2.45	3.3772 (19)	156
C6—H6B···Cg1ⁱⁱⁱ	0.99	2.74	3.7043 (16)	166

Symmetry codes: (i) −x+3/2, y+1/2, −z+3/2; (ii) x, y+1, z; (iii) x, y−1, z; (iv) x−1/2, −y+1/2, z−1/2.

Summary of short interatomic contacts (Å) in (I)^a top

Contact	Distance	Symmetry operation
O2···H3N	1.89	x, 1 + y, z
O1···H2N	1.89	x, -1 + y, z
O2···H6A	2.57	1 - x, 1 - y, 1 - z
N4···H5	2.52	-1/2 + x, 3/2 - y, -1/2 + z
C7···H12	2.64	-x, -y, 1 - z
O1W···H1	2.55	3/2 - x, 1/2 + y, 3/2 - z
C7···O1	3.16	1 - x, - y, 1 - z
N1···H1W	1.83	x, y, z

Notes: (a) The interatomic distances were calculated in Crystal Explorer 17 (Turner et al., 2017) whereby the X—H bond lengths are adjusted to their neutron values.

Summary of interaction energies (kJ mol^-1) calculated for (I) top

Contact	E_ele	E_pol	E_dis	E_rep	E_tot
N2—H2N···O1ⁱ +
N3—H3N···O2ⁱ	-68.5	-15.0	-49.2	86.4	-73.0
C12—H12···C7ⁱⁱ	-6.7	-2.0	-46.1	26.0	-32.7
C6—H6A···O2ⁱⁱⁱ	-12.9	-2.9	-28.2	13.5	-32.0
O1W—H1W···N1^iv	-51.9	-11.2	-6.5	65.1	-28.6
O1W—H2W···O1W^v	-36.9	-7.1	-3.5	34.3	-26.2
C7···O1^vi	-2.3	-3.0	-31.4	18.4	-20.7
C5—H5···N4^vii	-9.4	-2.0	-8.1	8.7	-13.0
C1—H1···O1W^viii	-8.1	-1.3	-3.9	3.9	-10.5

Symmetry operations: (i) x, 1 + y, z; (ii) -x, -y, 1 - z; (iii) 1 - x, 1 - y, 1 - z; (iv) x, y, z; (v) 3/2 - x, 1/2 + y, 3/2 - z; (vi) 1 - x, - y, 1 - z; (vii) 1/2 + x, 3/2 - y, 1/2 + z; (viii) 3/2 - x, -1/2 + y, 3/2 - z.

A comparison of the distribution of contacts to the calculated Hirshfeld surfaces for (I) and for Forms I and II (Jotani et al., 2016) top

Contact	(I)	Form I	Form IIa	Form IIb
H···H	41.1	44.1	35.8	36.9
C···H/H···C	21.2	16.7	31.4	22.4
O···H/H···O	17.9	15.7	14.2	19.6
N···H/H···N	13.5	16.7	18.0	19.5
C···O/O···C	2.3	2.1	0.1	0.1
Other	3.9	4.7	0.5	1.5

Geometric data, i.e. central C—C bond lengths (Å) and dihedral angles (°), for ³LH₂ in its polymorphs, solvates and (neutral) co-crystals; see Scheme 2 for the chemical diagrams of (II) and (III) top

Compound	Symmetry	Conformation	C—C	C₂N₂O₂/(3-py)	(3-py)/(3-py)	REFCODE	Reference
Polymorphs
Form I	–	U	1.544 (4)	74.98 (10), 84.61 (9)	88.40 (7)	OWOHAL	Jotani et al. (2016)
Form II^a	1	S	1.5383 (16)	77.29 (4)	0	OWOHAL01	Jotani et al. (2016)
	1	S	1.5460 (16)	75.93 (3)	0
Solvate
(I)	–	U	1.541 (2)	59.71 (6), 68.42 (6)	87.86 (5)	–	this work
Co-crystals of ³LH₂ with
HO₂CCH₂N(H)C(═O)N(H)CH₂CO₂H	1	S	1.515 (3)	81.41 (7)	0	CAJQEK	Nguyen et al. (2001)
HO₂CCH₂N(H)C(═O)C(═O)N(H)CH₂CO₂H	1	S	1.532 (19)	64.2 (3)	0	CAJQAG	Nguyen et al. (2001)
2-NH₂C₆H₄CO₂H	1	S	1.543 (2)	74.64 (4), 74.64 (4)	0	DIDZAT	Arman et al. (2012)
(II)	1	S	1.533 (3)	79.50 (6)	0	EMACIG	Suzuki et al. (2016)
C₆F₄I₂	1	S	1.544 (4)	70.72 (9)	0	IPOSIP	Hursthouse et al. (2003)
2-HO₂CC₆H₄SSC₆H₄CO₂-2	–	U	1.543 (3)	61.22 (5), 69.43 (5)	72.12 (8)	KUZSOO	Arman et al. (2010)
4-NO₂C₆H₄CO₂H	1	S	1.530 (2)	78.20 (4)	0	PAGFIP	Syed et al. (2016)
(III)	1	S	1.550 (17)	80.5 (4)	0	REWVUM	Jin et al. (2013)
I—C≡C—C≡C—I	1	S	1.542 (10)	76.6 (2)	0	WANNOP	Goroff et al. (2005)
I—C≡C—C≡C—C≡C—I	1	S	1.548 (11)	84.7 (2)	0	WANPIL	Goroff et al. (2005)
Br—C≡C—C≡C—Br	1	S	1.530 (9)	84.79 (18)	0	WUQQUW	Jin et al. (2015)

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N,N′-Bis(pyridin-3-ylmeth­yl)ethanedi­amide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

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N,N′-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate: crystal structure, Hirshfeld surface analysis and computational study