hydrogen-bonded 3d network of d10-metal halide ...profdoc.um.ac.ir/articles/a/1074407.pdf · riety...

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PAPER

Cite this: CrystEngComm, 2019, 21,

2691

Received 20th January 2019,Accepted 5th March 2019

DOI: 10.1039/c9ce00107g

rsc.li/crystengcomm

Hydrogen-bonded 3D network of d10-metal halidecoordination polymer containing N-(3-pyridinyl)nicotinamide: influence of ligand conformation,halide anions and solvent†

Zahra Nezhadali Baghan,a Alireza Salimi, *a

Hossein Eshtiagh-Hosseinia and Allen G. Oliverb

In this study, four new d10-metal halide coordination polymers (CPs), namely [HgCl2 (3-pna)]n (1), [HgBr2Ĳ3-

pna)]n (2), [HgI2Ĳ3-pna)]n CH3OH (3) and [CdI2Ĳ3-pna)]n (4), (3-pna = N-(3-pyridinyl)nicotinamide) were pre-

pared through the reaction of mercuryĲII) or cadmiumĲII) salts with 3-pna by a solution-based method and

structurally characterized via single-crystal X-ray diffraction. Moreover, X-ray crystal structure determina-

tion of 3-pna is reported for the first time. From the viewpoint of green chemistry, solid state reactivity of

the starting materials of compounds 1 and 2 was investigated by mechanochemical and thermal synthesis

methods under solvent-free conditions. Powder X-ray diffraction (PXRD) patterns of the reaction mixture

upon grinding of the starting reactant and powders isolated from heating the reactant materials were suc-

cessfully matched with simulated PXRD patterns of the compounds. According to single-crystal X-ray anal-

ysis, all compounds 1–4 are isostructural CPs as one-dimensional (1D) zigzag chains based on the anti con-

formation of the ligand. The accompanying halogen ions are observed to form C/N–H⋯X (X = Cl, Br, I)

hydrogen bonds resulting in 3D supramolecular architectures. The presence of solvent molecules in the

mercury iodide complex expands the packing structure with the change of halogen-based interactions to

N–H⋯Osolvent and C–H⋯Oamide interactions. Conformational dependence of ligand interactions was inves-

tigated on the reported 3-pna complexes in the Cambridge Structural Database (CSD). The results revealed

that supramolecular synthons of the amide skeleton of the ligand as well as the polymeric architecture of

the complex are significantly influenced by the anti/syn conformation of the ligand.

Introduction

It has been well recognized that intermolecular interactionsplay a crucial role in the self-assembly process for the con-struction of supramolecular architectures. In recent years, re-markable progress in the field of crystal engineering has beenachieved by designed approaches reported by different re-search groups for the prediction and construction of a widerange of coordination compounds.1 Coordination polymers(CPs) are an important class of coordination compounds withmagnetic,2 luminescence3 and antibacterial properties4 andwith extensive applications in various areas such as catalysis,5

gas adsorption6 and selective adsorption of organic dyes.7 In

this regard, numerous coordination polymers with a wide va-riety of metals (such as Ag, Mn, Fe, Co, Ni, Cu, Zn, Cd, andHg) and organic linkers8 have been reported with infinite co-valent frameworks of one, two, and three dimensions. Re-cently, the design of organic linkers has attracted great atten-tion to gain reproducible assembly strategies especiallythrough hydrogen bonds for the coordination networks. Thepropagation of 1D, 2D and 3D supramolecular networks ofCPs depends on the number and nature of hydrogen bondingmoieties of the ligand structure. In the synthesis of coordina-tion networks, an intriguing strategy for the design of CPs isthe utilization of different metal centers and organic ligandswith a variety of coordination geometries, functional groups,spacer groups, coordination sites and flexibilities.9 Differentspacers allow the ligands to participate in different non-covalent interactions and/or in coordination environments,which can significantly affect the crystal structure of thecompounds.

The impact of these factors on the architecture controlcan be explored using different synthetic methodologies. In

CrystEngComm, 2019, 21, 2691–2701 | 2691This journal is © The Royal Society of Chemistry 2019

aDepartment of Chemistry, Faculty of Science, Ferdowsi University of Mashhad,

Mashhad, Iran. E-mail: [email protected] Structure Facility, Department of Chemistry and Biochemistry,

University of Notre Dame, Notre Dame, Indiana 46556, USA

† Electronic supplementary information (ESI) available. CCDC 1855819–1855822and 1889063. For ESI and crystallographic data in CIF or other electronic formatsee DOI: 10.1039/c9ce00107g

http://crossmark.crossref.org/dialog/?doi=10.1039/c9ce00107g&domain=pdf&date_stamp=2019-04-11

http://orcid.org/0000-0003-0413-2185

2692 | CrystEngComm, 2019, 21, 2691–2701 This journal is © The Royal Society of Chemistry 2019

this regard, design and synthesis of new CPs with structuraldiversity under different synthetic conditions has also beeninvestigated.10 A principal challenge for synthetic chemists isto develop alternative methods for materials synthesis inwhich problems related to the solvent such as purification,pollution and risk can be resolved. Mechanochemicalmethods without bulk solvents in chemical synthesis haveattracted chemists to perform these techniques as environ-mentally friendly synthetic routes.11 Mechanosyntheticmethods are now a clean and practical alternative to conven-tional solution-based methods and have provided a greenroute for the preparation of various compounds includingcocrystals, pharmaceutical cocrystals,12 metal–organic frame-works (MOFs),13 zeolitic imidazolate frameworks (ZIFs),14 in-organic complexes,15 host–guest compounds,16 nano-particles17 and coordination polymers.18 In addition toadvantages related to lack of solvent in these techniques,these methods reduce the required time and energy for reac-tions and products are obtained in remarkable yields.19a

In the present study, the crystal structure of aconformationally flexible N-(3-pyridinyl) nicotinamide ligand(3-pna) with a CONH spacer for the first time is investigated.Compounds containing bis-(3-pyridyl) ligands with differentspacer groups such as CH2NH, CH–NĲimine), CONHĲamide),N2 (diazene) and alkyl groups have also been reported byreseachers.20a An attractive feature observed in bis-(3-pyridyl)ligands is their ability to adopt different anti/syn conforma-tions resulting in ligating topologies. Singha and co-workersexplored the molecular conformation of 3-pna in solution.21

Kumar and co-workers investigated the gelation propertiesand ligating topologies of 3-pna.22 However, to the best ofour knowledge no report has yet been made on the crystallinestructure of 3-pna and the comparison of amide backbone in-teractions of the ligand with metal complexes to explore theeffect of directional interactions on the stabilization of crystalpacking. Furthermore, a typical solution-based synthesis offour one-dimensional CPs derived from 3-pna is alsoreported. Based on the conformational dependence of ligandinteractions, hydrogen bonding capability of the amide back-bone of 3-pna in the self-assembly process and importantrole of hydrogen-bonding in the final crystalline structure,these compounds are explored. All prepared structures areisostructural and in three of them accompanying halogenions are involved in C/N–H⋯X (X = Cl, Br, I) hydrogen bond-ing to form 3D supramolecular architectures (Scheme 1). The

presence of solvent molecules in the solid state of a fourthcompound led to the change of halogen-based interactions toinclude N–H⋯Osolvent and C–H⋯Oamide interactions. In thesecomplexes, an anti conformation of pyridyl nitrogen atoms ofthe 3pna ligand resulted in zigzag polymeric chains. To ex-plore the impact of reaction conditions on the synthesizedCPs, solid-state reactivity of the starting materials undersolvent-free conditions using thermal and mechanochemicalreactions of a mixture of the N-(3-pyridinyl)nicotinamide li-gand with HgCl2, HgBr2, HgI2 and CdI2 was also investigated.Except in the case of HgI2 and CdI2 which have no reactionwith the ligand, mixing the ligand with HgCl2 and HgBr2 un-der solvent-free reaction conditions successfully producedpure compounds in high yield.

Experimental section

All the reagents and solvents for syntheses and analyses werepurchased from either Aldrich or Merck and used withoutfurther purification. Infrared spectra (4000–250 cm−1) of solidsamples were obtained from a 1% dispersion in KBr pelletsusing a BOMEM-MB102 spectrometer. Elemental analysis wasperformed using a Heraeus CHN-O Rapid analyzer. Meltingpoint was obtained using a Barnstead Electrothermal type9200 melting point apparatus and corrected. X-ray diffractionexperiments were performed at 120 K on a Bruker Apex-II dif-fractometer using Mo-Kα radiation (λ = 0.71073 Å). Data col-lections were performed with the Bruker APEX-3 softwaresuite. Intensities were integrated and absorption correctionswere applied using numerical correction methods. The struc-tures were solved using SHELXS,23 and all of the structureswere refined against F2 in SHELXL24 using WINGX.25a All ofthe non-hydrogen atoms were refined anisotropically. The Hatoms on carbon and nitrogen atoms were placed at calcu-lated positions using a riding model with Uiso(H) = 1.2UeqĲCor N). For L, intensity data revealed twinning by merohedry.The twin law was found by using TwinRotMat implementedin PLATON.25b Due to the moderate quality of the data for 1and 2, two and four EADP constraints had to be used toequalize the guest atoms, respectively. The crystal structureand refinement data are given in Table 1.

Synthesis of the N-(3-pyridinyl) nicotinamide ligand, L

Various methods have been reported for the synthesis of the well-known N-(3-pyridinyl) nicotinamide ligand.21,22 However, no re-port has yet been made on the crystalline structure of this ligand.

In this work, we tried to prepare suitable single crystalsfor X-ray single crystallography analysis. An oily solutionobtained from the reaction between 3-aminopyridine and nic-otinic acid was sprayed in dichloromethane solvent. Theresulting powder was filtered and was washed with methanol.Colourless single crystals were isolated after slow evaporationof products in methanol solvent after several days (yield:68%). M.P = 189–191 °C. IR (cm−1): 3243.5, 3066.8, 1678.5s,1608.7, 1587.7, 1548.8s, 1482.3, 1428.2s, 1332.3, 1293.7s,1152.2, 1022.6, 815.7713.

Scheme 1 Schematic representation of complexes [HgCl2ĲL)]n (1),[HgBr2ĲL)]n (2) [HgI2ĲL)]n (3) andĳCdI2ĲL)]n (4).

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Synthesis of [HgCl2 (L)]n (1), [HgBr2ĲL)]n (2), [HgI2ĲL)]nCH3OH (3) and [CdI2ĲL)]n (4)

Solution method. For synthesis of compound 1, to a solu-tion of 3-pna (0.02 g, 0.1 mmol) in 7.0 mL methanol,mercuryĲII) chloride (0.027 g, 0.1 mmol) in 3.0 mL methanolwas added with stirring. The mixture was heated to 70 °C for50 min and the resulting solution was filtered. Upon slowevaporation at room temperature, colorless crystals for suit-able X-ray analysis were obtained after several days. Mp 278–279 °C, IR data (KBr pellet, cm−1): 693, 800, 1052, 1121, 1290,1333, 1426s, 1485, 1529s, 1584, 1603, 1681s, 3332. Anal. calcdfor C11H9HgCl2N3O: C, 28.07; H, 1.93; N, 8.93 found: C, 28.13;H, 1.79; N, 9.08.

A similar procedure was performed for the preparation ofcompound 2, except that mercuryĲII) bromide (0.036 g, 0.1mmol) instead of mercuryĲII) chloride was added to the ligandsolution. Mp 268–269 °C, IR data (KBr pellet, cm−1): 693, 800,1052, 1120, 1288, 1426s, 1482, 1528s, 1584, 1682s, 3344. Anal.calcd for C11H9HgBr2N3O: C, 23.61; H, 1.62; N, 7.51 found: C,23.87; H, 1.43; N, 7.67.

Slow evaporation of the solution obtained from heatingthe mixture of mercuryĲII) iodide and 3-pna at 70 °C resultedin a compound in which the amide moiety was disordered.So, for preparation of compound 3, to a solution of 3-pna(0.02 g, 0.10 mmol) in 7.0 mL methanol, mercuryĲII) iodide(0.045 g, 0.10 mmol) in 3.0 mL methanol was added withstirring at room temperature and then the mixture was leftin a refrigerator for several days. After this time, suitablesingle crystals were isolated. Mp 202–204 °C, IR data (KBrpellet, cm−1): 697, 802, 1048, 1125, 1195, 1334, 1426s, 1481s,1549s, 1590s, 1663s, 3268. Anal. calcd for C11H9HgI2N3O

·CH3OH: C, 21.02; H, 1.91; N, 6.13 found: C, 21.22; H, 1.72;N, 6.71.

Complex (4) was synthesized by layering an ethanolic solu-tion (5.0 mL) of 3-pna (0.02 g, 0.1 mmol) over a 5.0 mL aque-ous solution of CdI2 (0.037 g, 0.1 mmol). After two weeks, sin-gle crystals suitable for X-ray analysis were obtained. Mp315–318 °C, IR data (KBr pellet, cm−1): 693, 802, 1052, 1122,1293s, 1335, 1429s, 1484, 1532s, 1585, 1605, 1684s, 3338.Anal. calcd. for C11H9CdI2N3O: C, 23.37; H, 1.60; N, 7.43Found: C, 23.49; H, 1.52; N, 7.85.

In addition, mechanochemical and thermal synthesis proce-dures were applied for 1 and 2 and are described in the ESI.†

Computational methods. The most stable (probable) synand anti conformations for 3-pna were obtained via full opti-mization using DFT calculations (B3LYP method with the6-311+G(d,p) basis set) without any restriction conditions, andthe frequency analysis showed the absence of imaginary fre-quencies in any state. The electrostatic surface potential (ESP)for conformational forms was obtained based on the full opti-mized structures. Energy of CH⋯X and, NH⋯X interactionsfor compounds 1, 2 and 4 were calculated using the M062Xmethod with the 6-311G(d,p) basis set for C, H, N atoms andLanl2DZ basis set for metal and halogen atoms. The interac-tion energies were corrected for the basis set superposition er-ror (BSSE) in all the complexes. All the calculations wereperformed using the GAMESS program package.26

Results and discussion

X-ray single crystal diffraction analysis of 3-pna demonstratesthat L crystallizes in the monoclinic crystal system with theCc space group. The asymmetric unit of this compound

Table 1 Crystallographic data, data collection and refinement for 1–4

Compound L Compound 1 Compound 2 Compound 3 Compound 4

Formula C11H9N3O C11H9Hg Cl2N3O C11H9HgBr2N3O C12H13HgI2N3O2 C11H9CdI2N3OFormula weight 199.21 470.70 559.62 685.64 565.41T/K 120(2) 120(2) 120(2) 120(2) 120(2)λ/Å 0.71073 0.71073 0.71073 0.71073 0.71073Crystal system Monoclinic Monoclinic Monoclinic Monoclinic MonoclinicSpace group Cc P21/n P21/n P21/n P21/na/Å 3.8737(3) 7.9213(6) 7.9879(14) 10.9713(3) 8.0392(7)b/Å 21.9191(16) 13.4161Ĳ10) 13.791(2) 12.5068(3) 14.4602Ĳ12)c/Å 10.6759(8) 11.9553(9) 12.334(2) 12.1087(3) 12.4285Ĳ10)α/° 90 90 90 90 90β/° 95.751(2) 95.349(2) 93.939(2) 90.4760Ĳ10) 92.449(2)γ/° 90 90 90 90 90V/Å3 901.91(12) 1264.99Ĳ16) 1355.5(4) 1661.45(7) 1443.5(2)Z 2 4 4 4 4Density 1.467 g cm−3 2.472 g cm−3 2.742 g cm−3 2.741 g cm−3 2.602 g cm−3

μ/mm−1 0.099 12.579 17.240 12.984 5.781FĲ000) 416 872 1016 1232 1032θ range for data collection 28.21 to 2.67 2.29 to 26.46 2.22 to 28.54 2.34 to 27.12 2.16 to 28.38GOOF 1.054 1.528 1.421 1.370 1.177Final R indices[I > 2σ(I)]

R1 = 0.0346,wR2 = 0.0789

R1 = 0.0926,wR2 = 0.2072

R1 = 0.0817,wR2 = 0.0.1776

R1 = 0.0552,wR2 = 0.1217

R1 = 0.0601,wR2 = 0.1187

R indices (all data) R1 = 0.0408,wR2 = 0.0817

R1 = 0.0952,wR2 = 0.2081

R1 = 0.0846,wR2 = 0.1787

R1 = 0.0587,wR2 = 0.1229

R1 = 0.0698,wR2 = 0.1242

CCDC no. 1889063 1855821 1855820 1855819 1855822

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consists of one molecule. The molecular structure of 3-pnaindicates that this compound adopts an anti conformation.The dihedral angle between two pyridine rings is 22.42Ĳ8)° in-dicating the non-planar anti conformation. The dihedral an-gles for 3-pna are listed in Table S3.† The crystal packingstructure of 3-pna is depicted in Fig. 1, indicating that hydro-gen bonding R1

2(6) motifs of C8–H8⋯N2 and N3H3A⋯N2and hydrogen bonding R1

2(7) motifs of C1–H1⋯N2 andN3H3A⋯N2 exist between molecules. Moreover, C5H5⋯O1hydrogen bonding occurs between the CH pyridine ring fromone molecule and CO amide group from the adjacent mole-cule. As expected, participation of the amide spacer group asa good hydrogen bonding acceptor and donor has a remark-able role in the formation of these interactions. The hydro-gen bonding parameters for 3-pna are listed in Table 2. Fur-thermore, π–π stacking interactions with a centroid tocentroid distance of 3.874(3) Å exist between two pyridinerings.

X-ray crystallographic analyses for compounds 1–4 revealthat these compounds crystallize in the monoclinic P21/nspace group (Table 1). The asymmetric units of 1, 2 and 4consist of one carboxamide ligand, one metal ion, and twochloride, bromide and iodide anions, respectively. In theasymmetric unit of 3 in addition to one ligand, one metalion, and two iodides, there is one methanol solvent molecule.Coordination geometry around the metal center in com-

pounds 1–4 is similar. According to the τ4 index defined byHouser and co-workers,27 the metal center adopts a distortedtetrahedral geometry with τ values of 0.78 0.79, 0.75 and 0.86,respectively. In these compounds, 3-pna acts as a μ2-bridgingligand and each metal center is four-coordinate.

The coordination sphere of the metal ion is occupied bytwo halide anions, two pyridine nitrogen atoms from two dif-ferent carboxamide ligands. In the case of compound 4,Cd–N and Cd–I distances of 2.251(9), 2.275(8) Å and 2.677(1),2.688(1) Å are in the range of previously reported covalentbonds for similar cadmium complexes.28 Also in the case ofcompounds 1, 2 and 3 Hg–N and Hg–X (X = halogen atom)distances are in the range of covalent bonds in mercury coor-dination compounds.29

The selected bond distances and angles are listed in TableS1.† Structural analysis of complexes 1, 2, 3 and 4, demon-strates that the self-assembly process in these similar com-pounds creates one-dimensional zigzag chains extendingalong the b-axis. In compounds 1, 2 and 3, 1D coordinationpolymers were generated from mercury-bridged chainextending in the b-direction. As shown in Fig. 2, the connec-tion between the 1D chains in compounds 1, 2 and 4 simi-larly occurs through the R2

2(12) motifs of C–H⋯X, R22(16) mo-

tifs of N–H⋯X (X = Cl, Br, I) and C–H⋯π hydrogen bonds inthe ac plane. In the case of compound 3, polymeric chainsare connected to each other through the R2

2(14) motifs of the

Fig. 1 Representation of crystal packing of 3-pna showing NH⋯N, CH⋯N, and CH⋯O hydrogen bonding interactions and π–π stacking interac-tions with a centroid to centroid distance of 3.874(3) Å between pyridine rings.

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C–H⋯O hydrogen bond between the amide oxygen atomfrom one chain and pyridine hydrogen atom of the other li-gand in the adjacent chain. Furthermore, the presence ofmethanol solvent molecules in compound 3 generates R1

2(7)motifs of N–H⋯O and C–H⋯O hydrogen bonds between themethanol oxygen atom and amide hydrogen and pyridine hy-

drogen atoms, respectively and the O–H⋯I hydrogen bondbetween the methanol and iodine atom (Fig. 3 and Table 2).

Among the different non-covalent interactions, π-based in-teractions such as anion⋯π, cation⋯π, lone-pair⋯π, XH⋯π

(X = B, C, N, O) and π–π interactions have an important rolein the planning and designing of final crystal packing of

Table 2 Hydrogen bonding parameters for 1–4

Compound D–H⋯A (Å) D–H (Å) H⋯A (Å) D⋯A (Å) <D–H⋯A Symmetry

L N3–H3A⋯N2 0.88 2.23 3.086(2) 164 −1/2 + x, 3/2 − y, −1/2 + zC1–H1⋯N2 0.95 2.48 3.310(3) 146 −1/2 + x, 3/2 − y, −1/2 + zC8–H8⋯N2 0.95 2.56 3.368(3) 143 −1/2 + x, 3/2 − y, −1/2 + zC10–H10⋯N1 0.95 2.59 3.477(3) 156 3/2 + x, 3/2 − y, 1/2 + zC5–H5⋯O1 0.95 2.70 3.650(3) 175 −1 + x, 1 − y, −1/2 + z

[HgCl2ĲL)]n (1) C4–H4⋯Cl2 0.95 2.81 3.686(18) 153 −x, 1 − y, 1 − zN3–H3A⋯Cl1 0.88 2.48 3.30(2) 155 1 − x, 1 − y, 2 − zC3–H3⋯πPy–N 0.95 3.06 3.999(24) 171 −1/2 + x, 3/2 − y, −1/2 + zC11–H11⋯O1 0.95 2.30 2.78(3) 110

[HgBr2ĲL)]n (2) C4–H4⋯Br2 0.95 2.96 3.82(2) 151 1 − x, 2 − y, 1 − zN3–H3A⋯Br1 0.88 2.65 3.438(16) 149 1 − x, 1 − y, 1 − zC3–H3⋯ πPy–N 0.95 3.20 4.14(2) 168 −1/2 + x, 1/2 − y, −1/2 + zC3–H3⋯O1 0.95 2.52 2.84(2) 100C11–H11⋯O1 0.95 2.33 2.84(2) 113

[HgI2ĲL)]n meth (3) C9–H9⋯O1 0.95 2.41 3.330(16) 162 1 − x, 1 − y, 1 − zN3–H3A⋯O2 0.88 1.96 2.783(16) 155C3–H3⋯O2 0.95 2.46 3.365(19) 159O2–H2A⋯O1 0.84 2.02 2.835(13) 164 1/2 − x, −1/2 + y, 1/2 − z

[CdI2ĲL)]n (4) C4–H4⋯I1 0.95 3.15 3.989(11) 149 −x, 1 − y, 1 − zN3–H3A⋯I2 0.88 2.86 3.558(10) 138 −x, −y, 1 − zC3–H3⋯πPy–N 0.95 3.44 4.38(1) 169 −1/2 + x, 1/2 − y, −1/2 + zC11–H11⋯O1 0.95 2.34 2.849(13) 113

Fig. 2 Representation of 1-D zigzag chains extending along the b-axis in 1, 2 and 4. (a) NH⋯Cl (b) CH⋯Br and (c) CH⋯π hydrogen bonding inter-actions between the resulting chains in the bc plane in 1, 2 and 4. For clarity, only one synthon was shown for each compound.

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Fig. 3 (a) Spacefill representation of methanol molecules between 1-D zigzag chains in 3. (b) CH⋯O and NH⋯O hydrogen bonding interactionsin 3. (c) Hirshfeld surface mapped with dnorm and (d) the two-dimensional fingerprint plot showing the CH⋯O and NH⋯O contacts.

Fig. 4 (a) Representation of π⋯π stacking interactions of πpy–C⋯πpy–N (black dashed line), and (b) C3H3⋯π interactions between πpy–C (red)and πpy–N (blue) rings in 1, 2 and 4 (c) showing π⋯π interactions between πpy–C (red) rings and C3H3⋯O2, N3H3A⋯O2 hydrogen bonding in 3.

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compounds. The term “π–π stacking interactions” refers tothe attractive intermolecular interactions between aromaticmolecules with parallel-stacked, parallel-displaced, edge-to-face or T-shaped geometries. π–π interactions have been stud-ied extensively in molecular recognition, catalysis, supramo-lecular and biomolecular systems.30

Structural analyses of compounds 1, 2 and 4 clearly showthat the intermolecular parallel-displaced head-to-tail π⋯π

stacking interactions occur between pyridine rings in adja-

cent chains. This causes more stability in the crystal packingof these compounds. As shown in Fig. 4a, in these com-pounds πpy–C⋯πpy–N stacking interactions occur between thepyridine ring directly connected to the amide CO group(hereafter denoted as Py–C) and the pyridine ring directlyconnected to the amide N–H group (hereafter denoted as Py–N) with a centroid to centroid distance of 3.720(2), 3.816(4)and 3.893(2) Å for compounds 1, 2 and 4, respectively. Itseems that the CH group of Py–C orientated toward the Py–Nring to create a C–H⋯π interaction while the N–H amidegroup forms a N–H⋯X hydrogen bond with a halide anion(Cl or Br) (Fig. 4b). As shown in Fig. 4c, π–π interactions incompound 3 occurred between two similar Py–C rings so thatPy–N rings don't participate in π–π interactions. The centroidto centroid distance of Py–C rings for compound 3 is 3.545(1)Å and the angle of mean planes is equal to zero (Table S2†).To further study the interactions of the pyridine rings ofthese compounds, we used the harmonic oscillator model ofaromaticity (HOMA) index to determine the local aromaticityof the pyridine rings. HOMA indices for the pyridine rings di-rectly connected to the CO amide group (Py–C) for com-pounds 1, 2, 3 and 4 are 0.857, 0.921, 0.951 and 0.916, respec-tively. The HOMA indices for the Py–N rings are 0.609, 0.985,0.971 and 0.951, respectively. These results indicated that inthe case of compound 1, the (HOMA) index value and subse-quently aromaticity are less than those of compounds 2 and4. This localization in the pyridine ring can be related to thestronger C–H⋯π hydrogen bond in this compound whichleads to various bond distances in the π acceptor pyridine ring(Fig. S2†) (C–C/C–N bond distances of the pyridine ring are1.297(28), 1.42(3), 1.302 (25), 1.37(3), 1.38(3) and 1.38(3) Å).

The main difference in the molecular geometry of com-pound 3 in comparison with compounds 1, 2 and 4 is the sig-nificant angle of the Py–N ring to the amide plane (44.2 (6)°)and the dihedral angle between Py–N and Py–C rings(38.1Ĳ3)°) which are the largest observed (Table S3†). The cor-responding Py–N and amide angles for compounds 1, 2 and

Fig. 5 Representation of various conformers of the N-(3-pyridinyl)nicotinamide ligand (3-pna), electrostatic surface potentials (ESP) as wellas metal coordination sites (M), and total number of amide-backbonehydrogen bonds for each conformer obtained fromCSD study.

Fig. 6 Molecular pairs (a and b) for compounds 1, 2 and 4 with corrected interaction energy (in K cal mol−1).

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4 are in the range of 28.2Ĳ9)–32.7Ĳ12)° while the dihedral an-gles between two pyridine rings for compounds 1, 2 and 4are 4.6Ĳ6)°, 8.2Ĳ5)° and 13.5Ĳ3)°, respectively. Such deviationin compound 3 may be explained by N–H⋯O hydrogen bond-ing between the amide NH group and methanol while noguest molecules were observed in 1, 2 and 4.

Cambridge Structural Database (CSD) analysis of previouslyreported compounds containing 3-pna clearly illustrated thatthese compounds have a high tendency to form crystal struc-ture with guest molecules such as solvent and counterions.These moieties are commonly located in such a way that theyparticipate in hydrogen bonding with the amide moiety as agood hydrogen-bonding donor and acceptor. These resultsshow the important role of the spacer amide group in the com-pounds including the title ligand (Table S4†). It is noteworthythat, 31 out of 42 cases have hydrogen bonding synthons inwhich the NH or CO amide group acts as a hydrogen-bondingdonor or acceptor. Among them, CO contributed to only 2 outof 31 cases. The D1

1(2) synthon has the largest contribution (18out of 31 cases (51%)). In these cases, the NH amide group actsas a hydrogen bond donor (in 30 cases the guest molecule(H2O) acts as an acceptor) and only 3 cases create a ringsynthon. Interestingly, in our compounds 1, 2 and 4 all of theamide NH⋯X hydrogen bonds show an R2

2(16) synthon. In or-der to obtain further insight into the nature of these interac-tions, we theoretically investigated the pair of moleculescontaining NH⋯X and CH⋯X interactions of compounds 1, 2and 4 by the DFT-Dmethod. The calculated energies for NH⋯Xinteractions in compounds 1, 2 and 4 are −20.15, −15.72 and−17.47 kcal mol−1 and for CH⋯X interactions are −4.79, −3.82and −2.18 kcalmol−1, respectively.

Interestingly, conformational dependence of 3-pna is alsoconsidered as an important factor in the final crystalline ar-chitecture of these compounds. Indeed, 3-pna can adopt dif-ferent conformations as well as structural diversity in itscomplexes. Different possible conformations of the title li-gand are shown in Fig. 5. In order to gain more insight intothe interactional behaviour of four probable conformations, acomputational study on electrostatic surface potential (ESP)was performed (Fig. 5). The full optimization results showed

that anti conformations are more stable than syn geometrieswhich is consistent with the abundance of 57% for the anticonformation in CSD analysis. The orientation of the nitro-gen atom of the Py–C ring to the amide CO group can taketwo modes described as cis and trans geometries to differenti-ate the two forms of anti and syn conformations. Statisticalanalysis of amide backbone interactions as the total numberof N–H⋯A (A = any hydrogen bond acceptor) and CO⋯D(D = any hydrogen bond donor) in all 3-pna complexes re-vealed that the anti/cis form has the highest number of hy-drogen bonding and the syn/cis has the lowest (Fig. 6).

In compounds 1–4, two pyridyl nitrogen atoms are ob-served in the anti conformation and therefore favourablepolymeric zigzag chains are created. Moreover, 3-pna in com-pound 3 has a cis geometry and displays an anti/cis confor-mation while the ligand shows an anti/trans conformation incompounds 1, 2 and 4 (Fig. 7). Another feature observed inCSD analysis is the disordered structure of the amide back-bone in 3-pna for some of the compounds. It is interesting tonote that we also observed the disordered amide structure forcompound 3. The structure was partially solved from the lowquality X-ray diffraction data of single crystals obtained byslow evaporation at room temperature. Surprisingly, we suc-cessfully prepared suitable single crystals of this compoundby crystallization at low temperature in which no amide dis-order, as well as solvent molecules, is investigated in the crys-tal structure. One other interesting comparison with the CSDis that there are very few examples of 3-pna that are part of acomplex where the metal center is four-coordinate. Most ofthe structures have metal centers that are six coordinate, withsome having five-coordinate metal centers and about 5 thathave four-coordinate metal centers.

Intermolecular interactions in the title compounds werequantified using molecular Hirshfeld surface calculations asa useful tool for visualizing, exploring, and analysing inter-molecular interactions applying the program Crystal Explorer.Three dimensional pictures show close contact in the crystalstructure with red, white and blue colours, where the whitecolour indicates contacts with distances equal to the sum ofvan der Waals radii the involved atoms and the red and blue

Fig. 7 Superimposed asymmetric units of 1 (green), 2 (brown), 3(purple) and 4 (yellow) showing different conformations of the 3-pnaligand in 3 (solvent molecules in the case of 3 are omitted for clarity). Fig. 8 Relative contributions to the Hirshfeld surface area for

intermolecular contacts in L and 1–4.

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regions refer to the shorter and longer contacts, respectively.The dnorm value for red, white and blue regions is negative,zero and positive, respectively (dnorm is the normalized con-tact distance based on de and di and the vdW radii of theatom where the di and de are the distances from the surfaceto the nearest nucleus inside and outside the surface, re-spectively).31 On the dnorm surface of 3-pna, the red area asshown in Fig. S1† indicates CH⋯N and NH⋯N hydrogenbonds and for compounds 1, 2 and 3 reported here, the redarea as seen in Fig. S3† indicates the N–H⋯X (X = I, Cl andBr) hydrogen bond which is one of the most significant con-tacts in these compounds due to the presence of the amidegroup.

The two-dimensional fingerprint plots complementary tothe surfaces can provide a summary of the nature and typesof various intermolecular interactions in the crystal struc-tures. These plots show quantitative contribution of closecontacts, and they can be decomposed to give the relativecontribution of each type of interaction for better under-standing of intermolecular contacts.32 The Hirshfeld surfaceanalysis for compounds 3-pna and 1–4 shows the significantcontributions of some important close contacts of H⋯H,H⋯X, C⋯O, and O⋯H. In this regard, the H⋯H contact isthe most significant interaction in compounds 3-pna and 1–3with contributions of 42.4, 24.5, 22.2 and 24.2%, respectively.However, the H⋯I contact has the largest contribution of20.8% in 4, the H⋯X contact for 1 and 2 is in second order(20% and 20.6%, respectively) and for 3, this contact has aproportion of 11.2%. In the case of 3-pna, the N⋯H contactis in second order (18%). The C–H⋯X and N–H⋯X hydrogenbonds refer to the aforementioned contacts in fingerprintplots where the N–H⋯X hydrogen bond is shown as a sharpspike and C–H⋯X is shown as wings. Also, a larger propor-tion of the O⋯H contact in compound 3 related to others re-fers to N–H⋯O and C–H⋯O interactions in this compound.A histogram comparison of percentage contributions of com-pounds 1–4 is shown in Fig. 8. Further investigation to iden-tify aromatic π⋯π stacking interactions was performed withthe shape index and curvedness in which the shape index is

the measurement of “shape type” and curvedness is the mea-surement of “shape size”.33 The presence of alternating adja-cent red (concave regions) and blue (convex regions) triangleson the same region of the shape index of these compoundscorresponds to the π⋯π stacking interactions between pyri-dine rings. Moreover, large flat green areas separated fromeach other by a dark blue outline on the Hirshfeld surfacemapped with the curvedness correspond to the π⋯π stackinginteractions in these compounds.34 The Hirshfeld surfacesmapped with the shape index and curvedness anddecomposed 2D finger print plots for compounds 3-pna and1–4 are shown in Fig. S1 and S4,† respectively. The resultsshow that in compound 3, only one ring of Py–C participatesin the π⋯π stacking interactions. As mentioned above, crystalstructure analysis of compounds 1, 2 and 4 clearly demon-strates that the accompanying anion affects the 3D supramo-lecular networks resulting from the cooperation of C/N–H⋯X(X = Cl, Br, I) hydrogen bonds to link the resulting 1-D zigzagchains. The comparison of compound 3 with these com-pounds clearly shows that the amide (CO–NH) group in thepresence of solvent molecules has a key role in the formationof N–H⋯Osolvent and C–H⋯Oamide interactions instead ofhalogen-based interactions.

In order to investigate the effect of reaction conditions onthe final structure of the title compounds, we synthesizedcompounds [HgCl2ĲL)]n (1) and [HgBr2ĲL)]n (2) using mecha-nochemical and thermal methods under solvent-free condi-tions. Powder X-ray diffraction has been utilized to investi-gate the structure of the products. The results indicated thatPXRD patterns of the solid reaction mixture of the mentionedcompounds are similar to simulated PXRD patterns derivedfrom the single crystal structure of these compounds. Thesame results were obtained for powders isolated from thethermal synthetic method (Fig. 9).

Conclusion

To summarize, we have presented the synthesis and struc-tural analysis of four new d10-metal halide coordination poly-mers containing a conformationally flexible N-(3-pyridinyl)nicotinamide ligand (3-pna). The crystal structures of studiedcompounds are determined as one-dimensional (1D) zigzagchains derived from the anti conformation of the ligandwhich are in contact with each other by C/N–H⋯X (X = Cl,Br, I) hydrogen bonds and π⋯π interactions to form 3D su-pramolecular architectures. The presence of solvent mole-cules in the mercury iodide complex causes the amide (CO–

NH) group to form N–H⋯Osolvent and C–H⋯Oamide interac-tions instead of halogen-based interactions. The CambridgeStructural database study of complexes including 3-pna re-vealed that non-covalent interactions of the amide skeletonof the ligand is significantly influenced by different forms ofconformations of the ligand. The Hirshfeld surface analysisclearly showed that the hydrogen bonded 3D network of thetitle compounds is due to the specific interaction of the am-ide backbone in these compounds.

Fig. 9 Comparison of simulated (green plot) and experimental PXRDpatterns of mechanochemical grinding (blue plot) and thermal (redplot) synthesis for compounds 1 and 2 from bottom to top.

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Conflicts of interest

There are no conflicts to declare.

Acknowledgements

The authors respectfully acknowledge the Ferdowsi Universityof Mashhad, Research Council for the financial support ofthe project Code Number 3/33376. The authors appreciativelywould like to thank the Cambridge Crystallographic Data Cen-tre for access to the CSD Enterprise.

Notes and references

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