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

research communications

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ISSN: 2056-9890

Volume 76| Part 1| January 2020| Pages 25-31

https://doi.org/10.1107/S2056989019016153

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

Sang Loon Tan ^a and Edward R. T. Tiekink ^a ^*

^aResearch Centre for Crystalline Materials, School of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
^*Correspondence e-mail: edwardt@sunway.edu.my

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 28 November 2019; accepted 2 December 2019; online 1 January 2020)

The molecular structure of the title bis-pyridyl substituted diamide hydrate, C₁₄H₁₄N₄O₂·H₂O, features a central C₂N₂O₂ residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methylene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intramolecular amide-N—H⋯O(carbonyl) hydrogen bonds are formed, each closing an S(5) loop. Supramolecular tapes are formed in the crystal via amide-N—H⋯O(carbonyl) hydrogen bonds and ten-membered {⋯HNC₂O}₂ synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water molecules via water-O—H⋯N(pyridyl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methylene-C—H⋯O(water) and methylene-C—H⋯π(pyridyl) interactions, give rise to a layer parallel to (10 $[\overline{1}]$ ); the layers stack without directional interactions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding interactions, and to the significant influence of the water molecule of crystallization upon the molecular packing. The analysis also indicates the contribution of methylene-C—H⋯O(carbonyl) and pyridyl-C—H⋯C(carbonyl) contacts to the stability of the inter-layer region. The calculated interaction energies are consistent with importance of significant electrostatic attractions in the crystal.

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

CCDC reference: 1969282

1. Chemical context

Having both amide and pyridyl functionality, bis(pyridin-n-ylmethyl)ethanediamide molecules of the general formula n-NC₅H₄CH₂N(H)C(=O)C(=O)CH₂C₅H₄N-n, for n = 2, 3 and 4, hereafter ⁿLH₂, are attractive co-crystal coformers via conventional hydrogen bonding. In the same way, complexation to metals may also be envisaged. It is therefore not surprising that there is now a wealth of structural information for these molecules occurring in co-crystals, salts and metal complexes, as has been reviewed recently (Tiekink, 2017 ). Complementing hydrogen-bonding interactions, the ⁿLH₂ molecules, for n = 3 (Hursthouse et al., 2003 ; Goroff et al., 2005 ; Jin et al., 2013 ) and n = 4 (Goroff et al., 2005; Wilhelm et al., 2008 ; Tan & Tiekink, 2019c ), are well-known to form N⋯I halogen-bonding interactions and, indeed, some of the earliest studies were at the forefront of pioneering systematic investigations of halogen bonding. It was during the course of on-going studies into co-crystal formation (Tan, Halcovitch et al., 2019 ; Tan & Tiekink, 2019a ,b ,c) and complexation to zinc(II) 1,1-dithiolates (Arman et al., 2018 ; Tiekink, 2018 ; Tan, Chun et al., 2019 ), that the title compound, ³LH₂·H₂O, (I), was isolated. Herein, the crystal and molecular structures of (I) are described along with a detailed analysis of the molecular packing by means of an analysis of the calculated Hirshfeld surfaces, two-dimensional fingerprint plots and the calculation of energies of interaction.

2. Structural commentary

The molecular structures of the two constituents comprising the crystallographic asymmetric unit of (I) are shown in Fig. 1. The ³LH₂ molecule lacks crystallographic symmetry and comprises a central C₂N₂O₂ residue connected at either side to two 3-pyridyl residues via methylene links. The six atoms of the central residue are almost co-planar as seen in their r.m.s. deviation of 0.0205 Å: the maximum deviations above and below the plane are 0.0291 (9) Å for N3 and 0.0321 (11) Å for C8. The N1- and N3-pyridyl rings form dihedral angles of 59.71 (6) and 68.42 (6)°, respectively, with the central plane and lie to the same side of the plane, having a syn-periplanar relationship. The dihedral angle formed between the pyridyl rings is 87.86 (5)°, indicating an almost edge-to-face relationship. The carbonyl-O atoms have an anti disposition enabling the formation of intramolecular amide-N—H⋯O(carbonyl) hydrogen bonds that close S(5) loops, Table 1.

Table 1
Hydrogen-bond geometry (Å, °)

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) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) x, y+1, z; (iii) x, y-1, z; (iv) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 1
The molecular structure of the constituents of (I)

showing the atom-labelling scheme and displacement ellipsoids at the 70% probability level. The water-O—H⋯N(pyridyl) hydrogen bond is indicated by the dashed line.

3. Supramolecular features

Significant conventional hydrogen bonding is noted in the crystal of (I) with the geometric parameters characterizing these included in Table 1. The most striking feature of the supramolecular association is the formation of tapes via amide-N—H⋯O(carbonyl) hydrogen bonds leading to a sequence of inter-connected ten-membered {⋯HNC₂O}₂ synthons. Two such tapes are connected by hydrogen bonds provided by the water molecule of crystallization. Thus, alternating water molecules in helical chains of hydrogen-bonded water molecules, being aligned along the b-axis direction and propagated by 2₁ symmetry, connect to ³LH₂ via water-O—H⋯N(pyridyl) hydrogen bonds to form the one-dimensional aggregate shown in Fig. 2(a). The presence of methylene-C—H⋯O(water) and methylene-C—H⋯π(pyridyl) contacts stabilizes a layer lying parallel to (10 $[\overline{1}]$ ). The layers stack without directional interactions between them, Fig. 2(b).

Figure 2
Molecular packing in the crystal of (I)

: (a) one-dimensional chain whereby tapes sustained by amide-N—H⋯O(carbonyl) hydrogen bonds and ten-membered {⋯HNC₂O}₂ synthons are connected, via water-O—H⋯N(pyridyl) hydrogen bonds, by helical chains of hydrogen-bonded water molecules sustained by water-O—H⋯O(water) hydrogen bonds and (b) a view of the unit-cell contents in projection down the b axis, highlighting the stacking of layers. The amide-N—H⋯O(carbonyl) hydrogen bonds are shown as blue dashed lines and hydrogen bonds involving the water molecules, by orange dashed lines. The C—H⋯O and C—H⋯π interactions are shown as green and purple dashed lines, respectively.

4. Hirshfeld surface analysis

The calculations of the Hirshfeld surfaces and two-dimensional fingerprint plots were performed on the crystallographic asymmetric unit shown in Fig. 1, using Crystal Explorer 17 (Turner et al., 2017 ) and based on the procedures as described previously (Tan, Jotani et al., 2019 ). The analysis identified a number of red spots on the d_norm surface of ³LH₂ with varying degrees of intensity indicating the presence of interactions with contact distances shorter than the sum of the respective van der Waals radii (Spackman & Jayatilaka, 2009 ). Referring to the images of Fig. 3, the most intense red spots stem from the amide-N—H⋯O(carbonyl) and water-O—H⋯N(pyridyl) hydrogen bonds, Table 1. Some additional contacts are detected through the Hirshfeld surface analysis for C1—H1⋯O1W, C5–H5⋯N4, C12—H12⋯C7, C6–H6A⋯O2 and C7⋯O1 interactions with the red spots ranging from moderately to weakly intense. The data in Table 2 provide a succinct summary of interatomic contacts revealed in the above analysis; the O2⋯H6A and C7⋯H12 contacts occur in the inter-layer region.

Table 2
Summary of short interatomic contacts (Å) in (I)^a

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	− $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z
C7⋯H12	2.64	−x, −y, 1 − z
O1W⋯H1	2.55	$[{3\over 2}]$ − x, $[{1\over 2}]$ + y, $[{3\over 2}]$ − 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.

Figure 3
The d_norm mapping of the Hirshfeld surface for ³LH₂ in (I)

within the range of −0.3259 to 1.0656 arbitrary units, showing the red spots for (a) N2—H2N⋯O1 (intense, connected by green dashed line), N3—H3N⋯O2 (intense, green dashed line) and C6—H6A⋯O2 (diminutive, green dashed line) interactions, (b) O1W—H1W⋯N1 (intense, yellow dashed line), C5—H5⋯N4 (moderately intense, yellow dashed line) and C7⋯O1 (diminutive, blue dashed line) interactions.

To verify the nature of the aforementioned interactions, the ³LH₂ molecule in (I) was subjected to electrostatic potential mapping. The results show that almost all of the interactions identified through the d_norm mapping are electrostatic in nature as can be seen from the distinctive blue (electropositive) and red (electronegative) regions on the surface, albeit with varying intensity, Fig. 4. A notable exception is found for the methylene-C—H⋯π(pyridyl) interaction which is manifested in the pale regions in Fig. 4(a) and (b). This indicates no charge complementarity consistent with the interaction beings mainly dispersive in nature.

Figure 4
The electrostatic potential mapped onto the Hirshfeld surface within the isosurface value of −0.0964 to 0.1012 atomic units for ³LH₂ in (I)

, showing the charge complementarity for (a) C6—H6A⋯O2 (green dashed lines), (b) N2—H2N⋯O1 and N3—H3N⋯O2 (green dashed lines) and (c) C5—H5⋯N4 (yellow dashed line), O1W—H1W⋯N1 (yellow dashed line) and C7⋯O1 (blue dashed lines) interactions. The yellow circles in (a) and (b) highlight the dispersive nature of the methylene-C—H⋯π(pyridyl) interaction with no charge complementarity.

The quantification of the close contacts to the Hirshfeld surface was performed through the analysis of the two-dimensional fingerprint plots for (I) as well as for the individual molecular components. As shown in Fig. 5(a), the overall fingerprint plot of (I) exhibits a bug-like profile with a pair of symmetric spikes. This is in contrast to the asymmetric profile of ³LH₂, with splitting of the spike in the internal region due to the formation of the O—H⋯N hydrogen bond, Fig. 5(e), suggesting a prominent role played by the water molecule in influencing the overall contacts in (I). The observation is very different to that of the benzene solvate of ⁴LH₂ in which the overall surface contacts for ⁴LH₂ are not very much influenced by the benzene molecule as demonstrated by the similar profiles for the solvate and individual ⁴LH₂ molecule (Tan, Halcovitch et al., 2019). The decomposition of the overall profile of (I) shows that the most significant contacts are primarily H⋯H contacts (43.5%), followed by O⋯H/H⋯O (21.1%), C⋯H/H⋯C (19.6%) and N⋯H/H⋯N (9.8%) contacts, with all of these interactions having d_i + d_e distances less than the respective sums of van der Waals radii (vdW), i.e. H⋯H ∼2.26 Å [Σ(vdW) = 2.40 Å], O⋯H/H⋯O ∼1.88 Å [Σ(vdW) = 2.72 Å], C⋯H/H⋯C ∼2.62 Å [Σ(vdW) = 2.90 Å] and N⋯H/H⋯N ∼2.50 Å [Σ(vdW) = 2.75 Å].

Figure 5
(a) The overall two-dimensional fingerprint plots for (I)

and for the individual ³LH₂ and water molecules, and those delineated into (b) H⋯H, (c) H⋯O/O⋯H, (d) H⋯C/C⋯H and (e) H⋯N/N⋯H contacts. The percentage contributions to the surfaces are indicated therein.

As for the individual ³LH₂ molecule, the dominance of these contacts follows the order H⋯H (41.1%; d_i + d_e 2.33 Å), C⋯H/H⋯C (21.2%; d_i + d_e 2.60 Å), O⋯H/H⋯O (17.9%; d_i + d_e 1.88 Å) and N⋯H/H⋯N (13.5%; d_i + d_e 1.80 Å). While the aforementioned interactions are almost evenly distributed between the internal and external contacts for (I), some contacts for ³LH₂ are found to either to be inclined towards the internal or external contact region compared with (I), such as that displayed by (internal)-O⋯H-(external) (8.4%) versus (internal)-H⋯O-(external) (9.5%) and (internal)-N⋯H-(external) (8.8%) versus (internal)-H⋯N-(external) (4.6%), respectively, Fig. 5(c)–(e).

The hydrate molecule exhibits a completely different fingerprint profile, which is dominated by three major contacts, namely H⋯H (46.9%; d_i + d_e 2.26 Å), O⋯H/H⋯O (39.4%; d_i + d_e 1.88 Å) and H⋯N (13.7%; d_i + d_e 1.80 Å). In particular, the second most dominant contacts are found to be heavily inclined toward (internal)-O⋯H-(external) (30.5%) as compared to (internal)-H⋯O-(external) (8.9%), presumably due to relatively large contact surface area.

5. Computational chemistry

All associations between molecules in (I), as described in Hirshfeld surface analysis, were subjected to the calculation of the interaction energy using Crystal Explorer 17 (Turner et al., 2017) based on the method described previously (Tan, Jotani et al., 2019) to evaluate the strength of each interaction, Table 3. Among those close contacts, the (³LH₂)₂ dimer connected by a ten-membered {⋯HNC₂O}₂ synthon has the greatest E_int energy of −73.0 kJ mol⁻¹ which is comparable in energy to the classical eight-membered {⋯HOCO}₂ synthon (Tan & Tiekink, 2019a). Perhaps unexpectedly, the C12–H12⋯C7 contact which also sustains a pair of ³LH₂ molecules constitutes the second strongest interaction with E_int = −32.7 kJ mol⁻¹, and this is followed by the C6—H6A⋯O2 (−32.0 kJ mol⁻¹), O1W—H1W⋯N1 (−28.6 kJ mol⁻¹), O1W—H2W⋯O1W (−26.2 kJ mol⁻¹), C7⋯O1 (−20.7 kJ mol⁻¹), C5—H5⋯N4 (−13.0 kJ mol⁻¹) and C1—H1⋯O1W (−10.5 kJ mol⁻¹) interactions. As expected, the N2—H2N⋯O1, N3—H3N⋯O2, O1W—H1W⋯N1 and O1W—H2W⋯O1W interactions are associated with distinct electropositive and electronegative sites and therefore, are mainly governed by electrostatic forces, while the rest of the close contacts are dispersive in nature. The relatively stable nature of the C12—H12⋯C7 and C6—H6A⋯O2 interactions as compared to the O1W—H1W⋯N1 and O1W—H2W⋯O1W interactions could be due to the presence of low repulsion energies in the former as compared to the latter.

Table 3
Summary of interaction energies (kJ mol⁻¹) calculated for (I)

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) $[{3\over 2}]$ − x, $[{1\over 2}]$ + y, $[{3\over 2}]$ − z; (vi) 1 − x, − y, 1 − z; (vii) $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z; (viii) $[{3\over 2}]$ − x, − $[{1\over 2}]$ + y, $[{3\over 2}]$ − z.

The crystal of (I) is mainly sustained by electrostatic forces owing to the strong N2—H2N⋯O1/ N3—H3N⋯O2, O1W—H1W⋯N1 and O1W—H2W⋯O1W hydrogen bonding leading to a barricade-like electrostatic energy framework parallel to ( $[\overline{1}]$ 01), as shown in Fig. 6(a). This is further stabilized by the dispersion forces arising from other supporting interactions which result in another barricade-like dispersion energy framework parallel to (100), Fig. 6(b). The overall energy framework for (I) is shown in Fig. 6(c).

Figure 6
Perspective views of the energy framework of (I)

, showing the (a) electrostatic force, (b) dispersion force and (c) total energy diagram. The cylindrical radius is proportional to the relative strength of the corresponding energies and they were adjusted to the same scale factor of 100 with a cut-off value of 8 kJ mol⁻¹ within 2 × 1 × 2 unit cells.

A comparison of the distribution of contacts on the Hirshfeld surfaces between the ³LH₂ molecule in (I) and in its two polymorphic forms, i.e. Form I and Form II (Jotani et al., 2016 ), with latter having two independent molecules, was performed. This analysis returned the data shown in Table 4 and indicates that ³LH₂ in (I) is relatively closer to Form I as compared to the independent molecules comprising Form II.

Table 4
A comparison of the distribution of contacts (%) to the calculated Hirshfeld surfaces for (I) and for Forms I and II (Jotani et al., 2016)

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

This conclusion is consistent with the analysis of the packing similarity in which a comparison of (I) and Form I exhibits an r.m.s. deviation of 0.895 Å while a comparison with Form II exhibits an r.m.s. deviation of 1.581 Å, despite only one out of 20 molecules displaying some similarity with the reference ³LH₂ molecule in (I), Fig. 7. The packing analysis was performed using Mercury (Macrae et al., 2006 ), with the analysis criteria being set that only molecules within the 20% tolerance for both distances and angles were included in the calculation while molecules with a variation >20% were discarded, and that molecular inversions were allowed during calculation. It is therefore also apparent through this analysis that the water molecules in (I) play a crucial role in influencing the packing of ³LH₂ in (I).

Figure 7
A comparison of the molecular packing of ³LH₂: (a) (I)

(red) and Form I (green) and (b) (I)

(red) and Form II (blue), showing the differences in terms of molecular connectivity of ³LH₂ with r.m.s. deviations of 0.895 and 1.581 Å, respectively.

6. Database survey

The ³LH₂ molecule has been characterized in two polymorphs (Jotani et al., 2016) and in a number of (neutral) co-crystals. A characteristic of these structures is a long central C—C bond and conformational flexibility in terms of the relative disposition of the 3-pyridyl substituents with respect to the central C₂N₂O₂ chromophore (Tiekink, 2017). Indeed, the relatively long length of the central C—C bonds often attracts a level C alert in PLATON (Spek, 2009 ). Of the data included in Table 5 [for the chemical diagrams of (II) and (III), see Scheme 2], the shorter of the C—C bonds is 1.515 (3) Å, found in the co-crystal of ³LH₂ with HO₂CCH₂N(H)C(=O)N(H)CH₂CO₂H (Nguyen et al., 2001 ) and the longest bond of 1.550 (17) Å is found in the co-crystal of ³LH₂ with (III) (Jin et al., 2013). In terms of conformational flexibility, the two polymorphs of ³LH₂ highlight this characteristic of these molecules (Jotani et al., 2016). In Form I, the pyridyl rings lie to the same side of the central C₂N₂O₂ and therefore, have a syn-periplanar relationship, or, more simply, a U-shape. In Form II, comprising two independent molecules, each is disposed about a centre of inversion so the relationship is anti-periplanar, or S-shaped. DFT calculations revealed that the difference in energy between the two conformations is less than 1 kcal⁻¹ (Jotani et al., 2016). Despite this result, most of the ³LH₂ molecules are centrosymmetric, S-shaped. For the U-shaped molecules, the dihedral angles between the central plane and pyridyl rings range from 59.71 (6) to 84.61 (9)°. The comparable range for the S-shaped molecules, for which both dihedral angles are identical from symmetry, is 64.2 (3) to 84.79 (18)°.

Table 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)

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	$[\overline{1}]$	S	1.5383 (16)	77.29 (4)	0	OWOHAL01	Jotani et al. (2016)
	$[\overline{1}]$	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	$[\overline{1}]$	S	1.515 (3)	81.41 (7)	0	CAJQEK	Nguyen et al. (2001)
HO₂CCH₂N(H)C(=O)C(=O)N(H)CH₂CO₂H	$[\overline{1}]$	S	1.532 (19)	64.2 (3)	0	CAJQAG	Nguyen et al. (2001)
2-NH₂C₆H₄CO₂H	$[\overline{1}]$	S	1.543 (2)	74.64 (4), 74.64 (4)	0	DIDZAT	Arman et al. (2012 )
(II)	$[\overline{1}]$	S	1.533 (3)	79.50 (6)	0	EMACIG	Suzuki et al. (2016 )
C₆F₄I₂	$[\overline{1}]$	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	$[\overline{1}]$	S	1.530 (2)	78.20 (4)	0	PAGFIP	Syed et al. (2016 )
(III)	$[\overline{1}]$	S	1.550 (17)	80.5 (4)	0	REWVUM	Jin et al. (2013)
I—C≡C—C≡C—I	$[\overline{1}]$	S	1.542 (10)	76.6 (2)	0	WANNOP	Goroff et al. (2005)
I—C≡C—C≡C—C≡C—I	$[\overline{1}]$	S	1.548 (11)	84.7 (2)	0	WANPIL	Goroff et al. (2005)
Br—C≡C—C≡C—Br	$[\overline{1}]$	S	1.530 (9)	84.79 (18)	0	WUQQUW	Jin et al. (2015 )

7. Synthesis and crystallization

The precursor, N,N′-bis(pyridin-3-ylmethyl)oxalamide, was prepared according to the literature (Schauer et al., 1997 ). Crystallization of the precursor in a DMF (1 ml) and ethanol (1 ml) mixture resulted in the isolation of the title hydrate, (I); m.p.: 409.4–410.7 K. IR (cm⁻¹): 3578 ν(O—H), 3321 ν(N—H), 3141–2804 ν(C—H), 1687–1649 ν(C=O), 1524–1482 ν(C=C), 1426 ν(C—N), 710 ν(C=C).

8. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 6. The carbon-bound H atoms were placed in calculated positions (C—H = 0.95–0.99 Å) and were included in the refinement in the riding-model approximation, with U_iso(H) set to 1.2–1.5U_eq(C). The oxygen- and nitrogen-bound H atoms were located in a difference-Fourier map and refined with O—H = 0.84±0.01 Å and N—H = 0.88±0.01 Å, respectively, and with U_iso(H) set to 1.5U_eq(O) or 1.2U_eq(N). Owing to poor agreement, one reflection, i.e. (551), was omitted from the final cycles of refinement.

Table 6
Experimental details

Crystal data
Chemical formula	C₁₄H₁₄N₄O₂·H₂O
M_r	288.31
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	100
a, b, c (Å)	12.4784 (4), 5.0247 (1), 22.2410 (6)
β (°)	90.170 (3)
V (Å³)	1394.51 (6)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	0.82
Crystal size (mm)	0.09 × 0.07 × 0.03

Data collection
Diffractometer	XtaLAB Synergy Dualflex AtlasS2
Absorption correction	Gaussian (CrysAlis PRO; Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.921, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	16961, 2871, 2441
R_int	0.053
(sin θ/λ)_max (Å⁻¹)	0.631

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.116, 1.04
No. of reflections	2871
No. of parameters	202
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.30, −0.24
Computer programs: CrysAlis PRO (Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Oxford Diffraction, Yarnton, England.]$ ), SHELXS (Sheldrick, 2015a ), SHELXL2017 (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ), DIAMOND (Brandenburg, 2006 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1969282

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989019016153/hb7869sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989019016153/hb7869Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989019016153/hb7869Isup3.cml

checkCIF report

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)

Funding information

Crystallographic research at Sunway University is supported by Sunway University Sdn Bhd (grant No. STR-RCTR-RCCM-001-2019).

References

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