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PAPERYuan Zhuang et al. Structural study on PVA assisted self-assembled 3D hierarchical iron (hydr)oxides

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Conformational variation of ligand in mercury halide complexes; high and low Z' structures Ali Samie and Alireza Salimi*

In this study, five new mercury halide complexes of [Hg(LPy)2Cl2] (1), [Hg(LPy)2Br2] (2), [Hg(LPy)2I2] (3), [Hg(LPz)2Cl2] (4) and [Hg(LPz)2Br2] (5) where LPy is phenyl pyridine-2-carboxylate and LPz is phenyl pyrazine-2-carboxylate, were designed and synthesized. The complexes were characterized using TGA, DSC, CHN-elemental analyses, FT-IR, NMR spectroscopy, PXRD, and SCXRD. The asymmetric unit of compounds 1-3 contains two independent complexes (high Z') and compounds 4 and 5 crystallized with half of complex in the asymmetric unit (low Z′). Interestingly, structural analysis revealed that small change in the ligand molecules (Py to Pz) affect the number of molecules in the asymmetric unit. Indeed, conformational variation of the ligand (LPy) which is related to the rotation of phenyl ring, forms four symmetry-independent (SI) ligands of the complex structures in 1-3. In contrary, there is no conformational change for Lpz in complexes 4 and 5. C−H∙∙∙O, C−H∙∙∙X−M, and C−H∙∙∙π interactions have the major role in the aggregation of molecular structures in titled compounds. The roles of intermolecular interactions in conformational variation of ligands are investigated by theoretical study and Hirshfeld surface analysis on the symmetry-independent (SI) and symmetry-related (SR) molecular pairs. The results show that C−H∙∙∙O/X−M have a key role in the stabilization of SI motifs in 1-3. The conformational variation in complexes are examined based on rmsd of the overlay for molecules in the asymmetric unit for inorganic high and low Z' pairs which presented in CSD. The flexibility of ligands in complexes introduced as an effective factor for structural variation of molecules in the asymmetric unit. In this regard, high Z' complexes of 1-3 belong to essential conformational adjustment between SI molecules. In fact, phenyl ring rotation which was previously reported as a reason for conformational polymorphism in LPy free ligand, is suggested as a reasonable element for high Z' in 1-3. Conversely, pyrazine rotation in LPz free ligand which was previously reported as responsible for making different polymorphs, did not occur in complexes 4-5 due to coordination of this moiety to mercury metal centre and later appeared in low Z' form of structures.

INTRODUCTION High Z′ (packing problem) which refers to the presence of more than one formula unit in the asymmetric unit as a phrase, can have an insight into unusual interaction of the symmetry-independent molecules in the asymmetric unit to stabilize the packing structure.1

In contrary, while the symmetry element of molecule adopts with special position in the space group, low Z′ will be shaped to arrange the supramolecular architecture thorough symmetry-related interactions. In spite of good studies, the origins of high Z′ is not fully understood. The ideal case studies for revealing the mysterious nature of packing problem can be the polymorphic systems with both high and low Z′ crystals concomitantly.2 Some studies on high and low Z′ pairs revealed lots of ideas about this solid state phenomenon.3 Although

multiple Z′ in some cases is more stable4 and in many cases low Z′ analogues even not exist for comparison5 but majority of studies concluded that Z′>1 forms are metastable.6 Many factors such as small-rigid molecules7, resolved chirality8, synthon frustration9, geometrically awkward molecular shape5 and conformational variability10 were introduced as a reason for packing problem by many researchers.11 Indeed, the smaller and less flexible molecules are better choices for crystallization in high Z′ structures.7 In a fascinating study, via the combination of a molecule with at least one resolved chiral centre and strong directional supramolecular synthons with centrosymmetric preference, high Z′ was nicely engineered.8 Synthon frustration as a compromise between close packing requirements and satisfaction of strong intermolecular interactions in the asymmetric unit is one of the most significant reasons for packing problem.9 Since, the real molecules include hollows and bumps, awkwardness is also known as a function to form the structures with Z′>1.5 In the presence of high conformational flexibility, high Z′ crystals are more favourable cases, as well.10 Crystal growth conditions and the crystallization process were also presented as an external role in the appearance of packing problem in some of compounds.12 Upon nucleation period, crystal can build up from any of metastable characters included in the fluid aggregation phase which can be referred to symmetrical

Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. [email protected]. † Neutron normalized interactions geometrical parameters for C−H∙∙∙O/X−M/π with binding energy, FT-IR transmittance plots, CHN-elemental analyses, 1H and 13C-NMR spectrums, TGA plots, DSC plots, PXRD patterns, atom numbering with ortep diagram, Hirshfeld surface analysis, CSD-search results. CCDC 1832638-1832641contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif,or by emailing to the address of [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

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View Article OnlineDOI: 10.1039/C9CE00185A

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2 | J. Name., 2012, 00, 1-3 This journal is © The Royal Society of Chemistry 20xx



independent aggregation of more than one molecule in the high Z′ structures.13 Crystallization from solvates which started with structural landscape and followed by nucleation of kinetic clusters can be resulted in thermodynamically stabilized crystals.14 So, initial nuclei are made by kinetic and before nucleation then they are followed by thermodynamic. Crystal engineering15 is the best way for rationalizing the relationship between intermolecular interactions and presence of various Z′ in analogue structures.16 While, in high Z′ compounds the interactions occur between either symmetry-independent (SI) or symmetry-related (SR) motifs, in low Z′ structures, SR interactions are the only choices for the self-assembly of molecules.17 Hence, small systematic change in designed structures can be resulted in different SR and/or SI interactions in the crystal packing. In this regards, five new mercury halide complexes of [Hg(LPy)2Cl2] (1), [Hg(LPy)2Br2] (2), [Hg(LPy)2I2] (3), [Hg(LPz)2Cl2] (4), and [Hg(LPz)2Br2] (5) containing phenyl pyrazine-2-carboxylate (LPz) or phenyl pyridine-2-carboxylate (LPy) were synthesized and fully characterized. Our systematic design on the ligand structures was the exchange of nitrogen in pyrazine ring with C-H in pyridine ring. This apparently small change in the ligand molecules make big difference in crystal structure of halide complexes. While LPz complexes (4 and 5) crystallized in low Z′ (0.5), LPy complexes crystallized with high Z′ (2).

In order to get insight about packing problem the compounds 4,5 were compared with 1,2,3. As far as the ligands have flexible ester bond (COO), conformational changes were structurally and theoretically investigated for both low and high Z′ complexes. The propensity of motifs to form SI and/or SR interactions were energetically determined by DFT-D calculations as well.

RESULTS AND DISCUSSION In this study five new mercuric halide complexes were synthesized and fully characterized. The results of Fourier Transform Infrared Spectroscopy (FTIR), CHN-elemental analyses, Nuclear Magnetic Resonance (1H-NMR and 13C-NMR), Thermal Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), and Powder X-Ray Diffraction (PXRD) can be found in S1-S7 at supporting information (SI), respectively. The atom numbering and ortep diagram for all of compounds with 50% probablity represented in S8. All of the reported interactions are presented in the tables S1-S5. In order to study non-covalent interactions energy for supramolecular architectures, the binding energies for all of the molecular pairs (dimers) were calculated by dispersion corrected M062X level of theory, (S1-S5). Crystallographic data for all of the compounds are given in the table 1.

Table 1. Crystallographic Parameters of 1-5.

1 2 3 4 5 EMP. FORMULA C24H18Cl2Hg N2O4 C24H18Br2HgN2O4 C24H18HgI2N2O4 C22H16Cl2HgN4O4 C22H16Br2HgN4O4 FORMULA WT. 669.89 758.79 852.79 671.88 760.78

CRYSTAL SYSTEM Triclinic Triclinic Monoclinic Monoclinic Monoclinic SPACE GROUP P -1 P -1 P 21/c C 2/c C 2/c

T/K 293(2) 150(2) 150(2) 150(2) 143(2) A/Å 9.449(4) 9.436(5) 22.181(7) 33.59(4) 18.977(13) B/Å 15.591(7) 15.89(1) 10.916(3) 5.376(6) 4.969(3) C/Å 17.606(7) 17.648(10) 27.340(7) 13.679(17) 26.436(17) α/° 99.55(2) 99.93(3) 90.00 90.00 90.00 β/° 97.950(16) 97.67(2) 127.333(18) 112.928(13) 97.967(8) γ/° 107.597(11) 107.083(17) 90.00 90.00 90.00

VOLUME/Å3 2388.6(18) 2443(2) 5264(3) 2275(5) 2469(3) Z 4 4 8 4 4 Z' 2 2 2 0.5 0.5

DCALCD(G.CM−3) 1.863 2.063 2.152 1.962 2.047 μ (MM−1) 6.701 9.603 8.225 7.038 9.506

F(000) 1288.0 1432.0 3152.0 1288.0 1432.0 OBSERVED REF.(I > 2Σ(I)) 16288 17002 34648 35543 75860

TOTAL REF. 10375 10615 11478 2476 2693 UNIQUE REF. 6913 7110 9696 2111 2323 R1 (I > 2Σ(I)) 0.0769 0.0785 0.0494 0.0446 0.0540

WR2 0.1760 0.1828 0.1250 0.1148 0.1210 GOODNESS-OF-FIT 1.067 1.085 1.121 1.149 1.095

2Θ RANGE 1.405-26.999 1.375-26.997 2.088-27.000 2.979-26.995 2.838-26.993 CCDC NO. 1832633 1832634 1832635 1832636 1832637

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(a)

(b)

(c)

Figure 1. representation of the interactions between SI molecules in 1 (a), (b), (c) with calculated energy of dimers; (i) x, -1+y, -1+z, (ii) x, -1+y, z, (iii) 1+x, y, 1+z, (iv) 1-x, 1-y, -z, (v) -1+x, y, z. Complex [Hg(LPy)2Cl2] (1), crystallizes in the triclinic space group P-1, and the asymmetric unit contains two independent complex molecules (Z' = 2), S8(a). The complex containing two chloride counteranion and two phenyl pyridine-2-carboxylate (LPy) ligand. Mercury atoms are located in seesaw style of tetrahedral geometry with τ4 of 0.731 and 0.716. There are two types of interactions (C−H∙∙∙Cl and C−H∙∙∙O) between SI molecules. The C10−H10∙∙∙Cl3 (-7.28 kcal/mol) and C35−H35∙∙∙Cl1 (-8.16 kcal/mol) have grown the structure along b-axis, fig. 1a. The herringbone style of molecule pair made by C21−H21∙∙∙Cl3 and C9−H9∙∙∙Cl4 shows the most stable dimer in this structure with -18.55 kcal/mol interaction energy, 1b. Two more interactions of C3−H3∙∙∙O7 (-4.83 kcal/mol), C27−H27∙∙∙O3 (-4.85 kcal/mol) are also connected SI molecules, 1a. The smallest interaction between SI molecules related to C29−H29∙∙∙O1 with the energy of -2.65 kcal/mol, 1c. Moreover, between two SR molecules made R2

2(12) motif by two symmetric C47−H47∙∙∙Cl3 with -8.4 kcal/mol

energy, S9(a). In addition, there are two symmetric C5−H5∙∙∙O3 and C22−H22∙∙∙Cl1 interactions between SR molecules thorough R2

2(30) and R2

2(10) motifs, S9(b). The calculated energy for these dimers are -3.35 and -8.6 kcal/mol, respectively.

Complex [Hg(LPy)2Br2] (2), crystallizes in the P-1 space group (Z = 4) with two independent molecules in the asymmetric unit (Z' = 2), S8(b). The complex contains two phenyl pyridine-2-carboxylate (LPy) ligand and two bromide counteranion. The molecular structure of this compound is similar to compound 1 in which mercury atom is located in tetrahedral geometry with τ4 of 0.714 and 0.727 (seesaw shape). The crystal packing consists only the interactions of C−H∙∙∙Br and C−H∙∙∙O related to SI and SR molecule pairs. Regarding to aggregation of SI molecular pairs, figure 2a represents C35−H35∙∙∙Br1 (-7.58 kcal/mol) and C27−H27∙∙∙O3 (-2.43 kcal/mol) interactions. There are two more interactions of C15−H15∙∙∙O7 (-4.85 kcal/mol) and C29−H29∙∙∙O1 (-4.47 kcal/mol) between SI molecules in 2a. The other interactions of C45−H45∙∙∙Br2 and C22−H22∙∙∙Br4 between SI molecules have developed the structure along b-axis (-6.96 kcal/mol), 2b. As it is observable in 2c, there are C9−H9∙∙∙Br4 and C21−H21∙∙∙Br3 which have grown the structure along a-axis with the energy of -19.18 kcal/mol. In S10(a), C10−H10∙∙∙Br1 (-7.72 kcal/mol) and C17−H17∙∙∙O1 (-3.38 kcal/mol) make R2

2(10) and R22(30) motifs, respectively. Two

symmetric C47−H47∙∙∙Br4 interaction with the energy of -6.86 kcal/mol makes R2

2(12) motif in one of SR molecule pairs, S10(b). C34−H34∙∙∙Br3 (2e) makes R2

2(10) motif with the energy of -6.54 kcal/mol, S10(b).

(a)

(b)

(c)

Figure 2. representation of the interactions between SI molecules in 2 (a), (b), (c) with calculated energy of dimers; (i)1-x, -y, -z, (ii)1-x, -y, 1-z, (iii)2-x, 1-y, 1-z, (iv)2-x, 1-y, 2-z, (v)1-x, 1-y, 1-z.


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Figure 3 representation of the interactions between SI molecules in 3 (a), (b) with calculated energy of dimers; (i)1-x, -½+y, 1.5-z (ii)2-x, -½+y, 1.5-z (iii)1-x, 2-y, 1-z (iv)x, 1.5-y, ½+z (v) 1-x, ½+y, 1.5-z (vi) 1+x, y, z (vii)1+x, 1.5-y, ½+z. Complex [Hg(LPy)2I2] (3), crystallizes in P21/c (monoclinic) space group with two independent metal iodide complexes in the asymmetric unit, S8(c). The complex contains two phenyl pyridine-2-carboxylate (LPy) ligand and two iodide counteranion. τ4 for mercury metal in the centre of this compound is 0.791 and 0.802 which shows seesaw shape in tetrahedral geometry. In addition to C−H∙∙∙O and C−H∙∙∙X interactions which are represented in the metal halide series of L1 ligand, there exist C−H∙∙∙π interactions between both SI and SR molecular pairs in this complex. In 5a, C23−H23∙∙∙O7 (-5.0 kcal/mol) and C35−H35∙∙∙O1 (-3.0 kcal/mol) occur between two SI molecules. One of the CHX interactions between SI molecules in 3a, is C14−H14∙∙∙I4 with the energy of -7.4 kcal/mol. The SR molecules are connected by symmetric C40−H40∙∙∙I4 (-5.57 kcal/mol) along c-axis with R2

2(24) motif, 3a. The C−H∙∙∙π interaction between two SI molecules is represented in 3b is C47−H47∙∙∙Cgph1 with the energy of -4.92 kcal/mol. In some of the dimers C−H∙∙∙π cooperates with CHI/O interaction. In this regard, the C12−H12∙∙∙CgPh3 along with C11−H11∙∙∙O5 interaction stabilize the one of SI molecular pairs (-5.36 kcal/mol), 3a. Moreover, C42−H42∙∙∙Cgph3 and C41−H41∙∙∙I3 have formed symmetrical

arrangement of four SR molecules along the c-direction with the energy of-17.21 and -2.52 kcal/mol respectively, S11(a). In the same crystallographic direction, C18-H18∙∙∙Cgph1 (3b) exists among the other SR molecules with the energy of -6.02 kcal/mol. C3−H3∙∙∙I2 (-3.89 kcal/mol) makes symmetric motif of R2

2(22) between two SR molecules, S11(b). C2−H2∙∙∙CgPh2 also occur between SR molecules with the energy of -15.75 kcal/mol, S11(b).

Figure 4 representation of the C−H∙∙∙O and C−H∙∙∙Cl interactions in 4 with calculated energy of dimers; (i)x, 1-y, -½+z, (ii)-x, y, ½-z, (iii)-x, 2-y, 1-z, (iv)x, 1+y, -1+z, (v)-x, 1-y, -z, (vi)-x, 1+y, -½-z. Complex [Hg(LPz)2Cl2] (4), with C2/c (monoclinic system) space group shows low Z’ structure in which half of the molecule presented in the asymmetric unit, S8(d). In this structure Hg atom lies in the special position, on a twofold axis. The complex contains two chloride anion and two phenyl pyrazine-2-carboxylate (LPz) ligand. The centric metal of mercury takes seesaw shape (tetrahedral geometry) with τ4 of 0.725. Three interactions are existed in the crystal structure of complex 4, fig 4. C3−H3∙∙∙O1 (-7.16 kcal/mol) interactions have formed R2

2(30) motif in ac-plane. Bifurcated hydrogen bonds of C10−H10∙∙∙Cl1 (-6.58 kcal/mol) and C11−H11∙∙∙Cl1 (-16.26 kcal/mol) have also connected the molecules in the same plane.

(a)

(b)

Figure 5 (a) representation of the C−H∙∙∙O and C−H∙∙∙Br interactions and (b) C−H∙∙∙Br interaction along b-axis in 5 with calculated energy of dimers; (i)1-x, -1-y, -z (ii)1-x, y, ½-z, (iii)-½+x, ½+y, z (iv)-½+x, -½-y, -½+z, (v)½-x, -½-y, -z, (vi)1-x, 1+y, ½-z.


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Complex and [Hg(LPz)2Br2] (5), crystallizes in C2/c space group (monoclinic lattice system) and Z = 4 with half of the molecule in the asymmetric unit (Z' = 0.5), S8(e). In this structure Hg atom lies in the special position, on a twofold axis. The complex contains two bromide counteranion and two phenyl pyrazine-2-carboxylate (LPz) ligand. The molecular structure of this compound is similar to compound 4 in which mercury atom positioned in tetrahedral geometry with τ4 of 0.732 (seesaw shape). Two interactions of C11−H11∙∙∙O1 (-6.05 kcal/mol) and C4−H4∙∙∙Br1 (-3.71 kcal/mol) are presented in the figure 5a. The mentioned interactions occur in a symmetrical arrangement at ac-plane. C9−H9∙∙∙Br1 and C10−H10∙∙∙Br1 have developed the structure along b-axis (-15.8 kcal/mol), 5b.

Figure 6. schematic for dihedral angles of τ1 and τ2 in ligands.

According to crystal engineering concept, five halide complexes were designed to explore the interactional behaviour of the ligands in titled compounds. There is possibility of conformational variations in ligands due to the change in dihedral angles of τ1 and τ2, by rotation around rotatable bonds, figure 6. As previously reported by us, two conformational polymorphs for LPy and LPz ligands were obtained based on rotation around τ1 and τ2, respectively.18 In addition, the halide counteranion in self-assembly process can play a significant role.19 As it is explained, C−H∙∙∙O and C−H∙∙∙X−M are the main interactions in self-assembly of our compounds. One of the specific halogen-based interactions in crystal engineering of inorganic materials is D−H∙∙∙X−M20 (D; C, N, O and X; F, Cl, Br, I).21 C−H∙∙∙O interaction as a weak hydrogen bond is also comparable with the other classical H-bonds which is effective in the stabilization of crystal packing in the absence of strong hydrogen bonds.22

In complexes 1-3 there are two molecules in the asymmetric unit (Z'=2) and each molecule has two ligands, so there are four ligands (L and L' for one of molecules in the asymmetric unit, L'' and L''' for another one) in the asymmetric unit of each compound. Due to the different conformation of ligands, we can formulate them as (MLL' X2) (ML''L''' X2). Complexes 1, 2, and 3 have crystallized with Z'=2 and it have been checked with rmsd of the overlay of SI molecules in the asymmetric unit, S12. For 4 and 5, similar ligands in formulae are symbolized by M(LX)2 which refer to Z'=0.5. Since, the conformational variations might be affected by intermolecular interactions, theoretical studies were performed on all molecular pairs in the crystal packing. DFT-D calculations has shown that in 1 and 2, SI interactions (kinetic function17) is stronger than SR interactions (thermodynamic function17). Indeed, the energy summation for SI dimers (-43.67 kcal/mol for 1 and -45.47 kcal/mol for 2) is more than twice as SR dimers (-19.54 kcal/mol for 1 and -24.51 kcal/mol for 2) which arises from C−H∙∙∙O and C−H∙∙∙X−M

interaction energy. In addition to aforementioned interactions, there are C−H∙∙∙π contacts in 3 (the summation is -40 kcal/mol). Interestingly, 80% of C−H∙∙∙π interaction energy is related to SR molecular pairs of 3. That means C−H∙∙∙π interaction did not play important role in the formation of SI molecules. It can be concluded that in all high Z' complexes (1-3), C−H∙∙∙X−M and C−H∙∙∙O has the major role in the formation of SI molecular pairs, and in complex 3 C−H∙∙∙π assembles SR molecular pairs. The considerable point for attention is the comparison of C−H∙∙∙X−M interactions in high Z' complexes. The summation energy of C−H∙∙∙X−M interaction for 1, 2 and 3 is -50.2, -54.8 and -19.4 kcal/mol, respectively. In contrary with our expectation, iodide made weaker interactions compared to chloride and bromide. As previously mentioned, C−H∙∙∙π interactions are likely to compensate the stability energy of crystal packing in 3 by ring rotation which effectively connect the SR molecules. It can be deduced that in all high Z' complexes (1-3), C−H∙∙∙X−M and C−H∙∙∙O have assembled the first clusters in the nucleation process and in complex 3, C−H∙∙∙π contacts have played important role in thermodynamic part of crystal growth. The differences in C−H∙∙∙X−M, C−H∙∙∙O, and C−H∙∙∙π interactions for each monomer of 1-3 in the asymmetric unit were performed separately by Hirshfeld Surface Analysis (HSA) in S13. In the other word, our results have shown that the interaction with a strong tendency to occur between SI molecules is likely to play a significant role in stabilizing crystal-packing arrangements with Z'>1. Besides, SI molecular pairs (kinetic) have stronger interactions than SR (thermodynamic) molecular pairs. In complexes 4 and 5, the SR molecular pairs are the only option due to the location of mercury centre in the special position (low Z'). Theoretical studies on the energies of SR moieties revealed that C−H∙∙∙X−M and C−H∙∙∙O interactions, similar to high Z' structures, have the major role in formation of crystal architecture. The energy summation of C−H∙∙∙X−M is -22.83 and -19.51 kcal/mol for 4 and 5, respectively. The energy summation of C−H∙∙∙O is -7.16 and -6.06 kcal/mol for 4 and 5, respectively. The importance of C−H∙∙∙X−M, C−H∙∙∙O, and C−H∙∙∙π interactions are clarified by HSA, (S14). A big portion of this analysis belong to C−H∙∙∙π interactions but in most of the dimers geometrically it is not suitable interaction. As Desiraju stated, high and low Z' pairs are good candidates for mysterious nature of high Z' phenomenon. It means, if a compound can crystallize in low Z', why it should crystallize in high Z', as well?! Alongside this suggestion, Babu and Nangia deduced that shortening in C−H∙∙∙O/O−H∙∙∙O made high Z' pairs for 26 crystals out of 38 samples which were found in CSD search. Gavezzotti once noticed that each high Z' case study might have its own story.23 Hence, single molecule case studies with high and low Z' pairs clarified good reasons for this phenomenon. However, reaching to a consensus about high Z' foundation has long way to go even with constraining the statistical samples to high and low Z' pairs. This happens due to the fact that, high Z' compounds are not belong to an especial category of materials and barely it is possible to find a group in which high Z' is one of repeatable options thorough it.8b Anyhow, in a unique and careful paper, Steed exemplified main foundations of this


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phenomenon. In some of organic (especially drug) high and low Z' case studies, the conformational variation has introduced as responsible for this phenomenon.4,11 The conformational flexible ligand24 usage in molecular structure of complex may lead to prominent change in crystal architecture.25 Locking the conformation by restriction enforcement is another noteworthy tool for changing the topology.26 Since, the conformational variation in complexes mostly occurs in ligand and conformational polymorphism has been introduced as a reason for high Z' in organic compounds, the criteria for conformational polymorphism27 can be good scales for conformational variation in the asymmetric unit. In order to generalize conformational variation factor in complexes, inorganic high and low Z' pairs were found in CSD version 5.38. The searches were restricted to the structures with Zr = 1 which means it was excluded any salts, solvates, and co-crystals.1 Further constraint were included: R-factor ≤10%; not disordered; no errors; no polymeric; no ions; no powder structures; only organometallics. X−H distances were equal to the average neutron-diffraction value (C−H = 1.089, N−H = 1.015, O−H = 0.993 Å). The applied constraints and all of the pairs are presented in the table S6. The rmsd of SI molecules in the asymmetric unit have been calculated and the results have been divided to four classes, (blue bars in the figure 7). I) rmsd ≤ 0.1 (molecular shake) II) 0.1 < rmsd ≤ 0.225 (partial conformational adjustment) III) 0.225< rmsd ≤ 0.375 (essential conformational adjustment) IV) 0.375 > rmsd (conformational Change). The existence of rotatable bond (τ) in the ligand before or after complexation or in metal-ligand bond direction was considered, table S6. Then, the percentage of compounds containing rotatable bond (τ), determined for each class; I (45.9%), II (82.1%), III (86.5%), and IV (98.6%). The importance of conformational flexibility

presentation in high Z' complexes by simultaneous increase in rmsd and τ is nicely clarified, (purple bars in the figure 7).

Figure 7. four rmsd classes in CSD-study of SI molecules in the asymmetric unit (blue) before (purple) after omitting the non-rotational cases. With exact consideration in the structures of complexes 1, 2, and 3, it was distinguished that conformational variation in ligand is responsible for making different SI molecules in the asymmetric unit. The overlay of ligands in complexes 1, 2 and 3 are represented in the figure 8 (a-c), respectively. The rmsd for 1, 2, and 3 was calculated as 0.2613, 0.2652, and 0.3532, respectively. All of them belong to the class III which is essential conformational adjustment. Consequently, the rotation around τ1 was distinguished as responsible for high Z' in all of the titled compounds. Interestingly, this rotation was introduced as a reason for conformational polymorphism in LPy and LPz ligand which was previously reported by us.18 It seems that the presence of conformational polymorphism in LPy ligand have shown itself in mercury halide complexes of 1, 2, and 3. For more clarification about structural difference of the ligands existed in high Z' structures, the energy profiles of rotation around τ1 have been calculated. By drawing the energy profile for 1-3, the results indicate different but close energy for the mentioned ligands in complexes, figure 8 (a'-c').

(a)

(b)

(c)

(a')

(b')

(c')

Figure 8. overlay of ligands in complexes (a) 1, (b) 2, (c) and Energy profile and in complexes (a') 1, (b') 2, (c') 3.


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Journal Name

ARTICLE




In spite of the presence of conformational polymorphism in LPz, complexes 4 and 5 have crystallized in low Z'! The overlay of ligands in complexes 4 and 5 is represented in the figure 9. The rotation around τ2 was introduced as responsible for making different polymorphs in LPz ligand.18 Since the Pz was engaged to mercury and it was fixed, the overlay has not shown noticeable changes in both of the complexes (rmsd = 0.094).

Figure 9. overlay of ligands in complexes 4 and 5.

While conformational variation in organic compounds was recognized as primary effect, the conformational variation of organic ligand in inorganic complex can be introduced as secondary effect. If the ligand in complex be able to vary in conformational form (especially if it includes conformational polymorphs), this potential ability can become veritable in complexation stage. Thus, the change of conformation in SI molecules can make high Z' structures. So, one of the reasons for high Z' in inorganic complex can be the conformational variation of the ligand. There are lots of good examples in CSD which confirm this hypothesis and some of them exemplified in the following. The organic compound with the refcode of REHLAT have two conformational polymorphs. REHLAT01 is crystallized with Z'=1 and REHLAT is crystallized with Z'=1, S15(a) and (b), respectively. This compound as a ligand made mercury bromide complex of TEFYEK which crystallized with Z'=2 due to the conformational change, S15(c). NICOAM ligand that has polymorohic conformational adjusment, also made QEHIU and SUYCOF complexes with high Z'. The polymorphic ligands of TPEPHO and TPPOSS including three rings and three suitable rotatable bond (τ), constitute lots of high Z' complexes. Some of these complexes have given in the table S6. It should be noted that in mentioned examples the ligand consists conformational polymorphism and this ability has shown itself as high Z' in metal complex. What explained until now was the internal reason for the presence of high and low Z' structures. Indeed, these internal factors are a function of external drivers. Rapid increment in the saturating level can cause a high level of supersaturation and nucleus may assemble on the situation which makes the metastable high Z′ structure as a favoured product.28 In the other word, crystalline matter growth under unbalanced conditions in which the crystal nucleus and fluid phase as the two ends of a thread are related to each other by

supersaturation stabilizing degree. So, initial nuclei make by kinetic and before nucleation then they followed by thermodynamic.13 That means the rate of evaporation was the external reason for obtaining low and high Z′ pairs. High Z' crystals were previously described as “fossil relic from the fastest growing nucleus”29, “crystal on the way”2, or “snapshot picture from different stage of crystallization”14 by different groups. Nicole and Clegg stated that kinetic products12 have bigger portion of high Z’ structures in CSD than thermodynamic structures. In our study, while low Z' structures have obtained after 1 and 2 months of recrystallization, high Z' structures have grown within 1 night to maximum 3 days. The high Z' compounds most probably are rather kinetic than thermodynamic products. Therefore, 1, 2 and 3 were obtained by fast evaporation, instead of 4 and 5 complexes which built by slow evaporation. Complexes 1 and 3 obtained from THF after three days while 2 crystallized in acetonitrile under the hood in one night only. Upon slow evaporation of heptane and ethyl acetate mixture, crystals for complexes 4 and 5 suitable for X-ray analysis were obtained after one and two months, respectively. In fact, the rate of evaporation was controlled by using various solvents and crystallization conditions.

Conclusions In this study, five new mercury halide complexes with small change in the ligand molecules from Py to Pz affected the number of molecules in the asymmetric unit. Complexes 1-3 crystallized high Z' and complexes 4 and 5 crystallized low Z′ structures. Compounds 1- 3 were obtained by fast evaporation, instead of 4 and 5 which are made by slow evaporation. Inorganic complexes with high and low Z' structures which presented in CSD have studied and the flexibility of ligands in complexes introduced as an effective factor for high Z'. On the basis of rmsd, conformational variation in complexes was divided to four groups: I) molecular shake; II) partial conformational adjustment; III) essential conformational adjustment; IV) conformational Change. This criterion showed that 1-3 belong to the third group. Indeed, the rotation of phenyl ring in Lpy was suggested as a logical reason for the presence of high Z' in 1-3. As far as, there is no conformational change for Lpz in complexes 4 and 5, these complexes crystallized with low Z' form. The roles of intermolecular interactions in conformational variation of ligands were discussed by theoretical study on SI and SR dimers. The results indicated to the major role of C−H∙∙∙X−M/O intermolecular interactions in the stabilization of SI and SR motifs in 1-3 and 4-5, respectively.


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EXPERIMENTAL DETAILS All the reagents and solvents for syntheses and analyses were purchased from either Aldrich or Merck and used without further purification. General synthetic procedure for Complexes: To a solution of 0.1 mmol mercuric (II) halide (HgX2, X = Cl, Br) in 10 mL acetonitrile, a solution of 0.2 mmol of L in 10 mL acetonitrile was added with stirring. The mixture was stirred for about 24 hours at ambient situation and then filtered. Same procedure was done for HgI2 in acetone as a solvent. All of the solutions were dried on the ambient situation and recrystallized at room temperature but in different solvents and situations upon different evaporation times. Except 3, which was yellow and prism crystal, all of the crystals were somehow colourless and needle-shaped. Theoretical Studies Without any circumscription, the theoretical studies of intermolecular interaction, have assessed with DFT calculations (B3LYP method with 6-311+G (d, p) basis set. With the same circumstances, the binding energies for all of the molecules pairs (dimers) were computed in order to study non-covalent interactions’ energy for supramolecular architectures. For basis set substitution error (BSSE) corrections the counterpoise method has been used.30

The molecular energies for energy profile, were calculated with gas-phase geometry optimizations by density functional theory including dispersion corrections (DFT-d) at the B97-D/ccpVTZ level of theory and functional B97-D includes van der Waals corrections.31 All the calculations were performed in the GAMESS program package.32

Fourier Transform Infrared Spectroscopy (FTIR) spectra (4000 – 400 cm-1) of solid sample were taken as 1% dispersion in KBr pellets were recorded with an Avatar 370 FTIR Thermal Nicolet spectrometer. Elemental Analyses for C, H and N were performed using a Thermo Finning Flash EA1112 CHNO-S Microanalyzer. Differential Scanning Calorimetry (DSC) was recorded on a Mettler Toledo DSC 823e instrument within a range from 25 to 300 °C with a step size of 2 °C/min. Thermal Gravimetric Analysis (TGA) was performed with Mettler Toledo TGA/SDTA 851e within temperature range of 25 to 400 °C. Nuclear Magnetic Resonance (NMR) was gathered in DMSO-d6 as a media by 300MHz Bruker Avance III for both 1H and 13C. Powder X-Ray Diffraction (PXRD) data were collected on PANalytical X-ray powder diffractometer equipped with a X’cellerator detector using Cu Kα (λ = 1.54184 Å) at room temperature with the scan range 2θ = 5 to 50 °C and step size of 0.026 °C. X’Pert HighScore Plus was used to compare the experimental PXRD pattern with the calculated lines from the crystal structure. Single Crystal X-ray Diffraction (SCXRD) data for 1, 2, 3, 4 and 5 crystals were collected on a Rigaku Mercury 375/M CCD (XtaLAB mini) diffractometer using graphite monochromatic Mo(Kα) radiation (0.71075 Å) at 293(2), 150(2), 150(2), 150(2) and 143(2) respectively. The data were processed with the Rigaku Crystal Clear 2.0 software.33 The structures were solved by direct methods34 and subsequent different Fourier maps were used for refinement on F2 by a full-matrix least-square procedure using anisotropic displacement parameters. The structures were checked for higher

symmetry with the help of the program PLATON35, and Mercury 3.9 was utilized for molecular representations and packing diagrams. For titled compounds, the non-H atoms were refined anisotropically and H-atoms were placed in the ideal positions. The structural resolution procedure was performed using WinGX crystallographic software package.36 Compound 1: m.p. 174.9oC; IR (KBr disc) νcm-1: 2920.73, 2847.17 (C−H stretching in aromatic rings), 1742.22 (C=O symmetric stretching), 1597.73, 1489.71 (two couple of peaks for C=C in aromatic rings), 1284.03, 1200.24(C=O asymmetric stretching); 1H NMR (300.81 MHz, DMSO-d6, 25oC, ppm) δ 7.335 (tt, 1H, H4, 4J = 0.9 Hz with H2, H6; 3J = 1.8 Hz with H3, H5), 7.3655 (td, 2H, H2, H6, 3J = 3.6 Hz with H3, H5, 4J = 0.9 Hz with H4), 7.513 (td, 2H, H3, H5, 3J = 3.6 Hz with H2, H6, 3J = 1.8 Hz with H4), 7.696 (dd, 1H, H11, 3J = 4.8 Hz with H10, 3J = 7.8 Hz with H12), 8.507 (dt, 1H, H12, 3J = 7.8 Hz with H11, 4J = 1.8 Hz with H9, H10,), 8.9275 (d, 1H, H10, 3J = 3.3 Hz with H11,), 9.295 (s, 1H, H9); 13C NMR (75.65 MHz, DMSO-d6, 25oC, ppm): 122.352 (C2, C6), 124.688 (C11), 125.769 (C4), 126.727 (C8), 130.104 (C3, C5), 138.190 (C12), 150.835 (C9), 150.953 (C1), 154.606 (C10), 164.024 (C7). Compound 2: m.p. 162.6oC; IR (KBr disc) νcm-1: 2928.91, 2851.26 (C−H stretching in aromatic rings), 1742.17 (C=O symmetric stretching), 1597.48, 1489.28 (two couple of peaks for C=C in aromatic rings), 1283.24, 1200.54 (C=O asymmetric stretching); 1H NMR (300.81 MHz, DMSO-d6, 25oC, ppm) δ 7.335 (tt, 1H, H4, 4J = 0.9 Hz with H2, H6; 3J = 1.8 Hz with H3, H5), 7.3645 (td, 2H, H2, H6, 3J = 3.6 Hz with H3, H5, 4J = 0.9 Hz with H4), 7.512 (td, 2H, H3, H5, 3J = 3.6 Hz with H2, H6, 3J = 1.8 Hz with H4), 7.703 (dd, 1H, H11, 3J = 4.8 Hz with H10, 3J = 7.8 Hz with H12), 8.512 (dt, 1H, H12, 3J = 7.8 Hz with H11, 4J = 1.8 Hz with H9, H10,), 8.9245 (d, 1H, H10, 3J = 3.3 Hz with H11,), 9.293 (s, 1H, H9); 13C NMR (75.65 MHz, DMSO-d6, 25oC, ppm): 122.349 (C2, C6), 124.729 (C11), 125.804 (C4), 126.731 (C8), 130.105 (C3, C5), 138.268 (C12), 150.829 (C9), 150.910 (C1), 154.552 (C10), 163.994 (C7). Compound 3: m.p. 116.3oC; IR (KBr disc) νcm-1: 2916.65, 2847.17 (C−H stretching in aromatic rings), 1742.49 (C=O symmetric stretching), 1597.49, 1484.19 (two couple of peaks for C=C in aromatic rings), 1281.78, 1188.99 (C=O asymmetric stretching); 1H NMR (300.81 MHz, DMSO-d6, 25oC, ppm) δ 7.334 (s, 1H, H4), 7.3645 (d, 2H, H2, H6, 3J = 2.4 Hz with H4), 7.506 (t, 2H, H3, H5, 3J = 7.8 Hz with H2, H6), 7.718 (m, 1H, H11), 8.512 (d, 1H, H12, 3J = 7.8 Hz with H11), 8.945 (d, 1H, H10), 9.319 (s, 1H, H9); 13C NMR (75.65 MHz, DMSO-d6, 25oC, ppm): 122.337 (C2, C6), 124.9 (C11), 125.804 (C4), 126.731 (C8), 130.103 (C3, C5), 138.361 (C12), 150.814 (C9), 150.910 (C1), 154.394 (C10), 163.949 (C7). Compound 4: m.p. 123.6oC; IR (KBr disc) νcm-1: 2932.99, 2855.34 (C−H stretching in aromatic rings), 1762.82 (C=O symmetric stretching), 1625.22 (C=N in pyrazine ring), 1587.57, 1486.60, 1454.69 (two couple of peaks for C=C in aromatic rings), 1277.45, 1194.83 (C=O asymmetric stretching); 1H NMR (300.81 MHz, DMSO-d6, 25oC, ppm) δ: 7.3615 (m, 3H, H2, H6, H4), 7.50 (t, 2H, H3, H5, 3J=4.8 Hz with H2, H6), 8.926 (s, 1H, H11), 8.987 (s, 1H, H10), 9.402 (s, 1H, H9);


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13C NMR (75.65 MHz, DMSO-d6, 25oC, ppm) δ: 122.198 (C2, C6), 126.812 (C4), 130.165 (C3, C5), 143.046 (C8), 145.479 (C11), 146.641 (C9), 148.969 (C10), 150.841 (C1), 162.811 (C7). Compound 5: m.p. 107.7oC; IR (KBr disc) νcm-1: 2929.40, 2847.67 (C−H stretching in aromatic rings), 1751.56 (C=O symmetric stretching), 1629.97 (C=N in pyrazine ring), 1588.87, 1484.26, 1454.65 (two couple of peaks for C=C in aromatic rings), 1280.58, 1176.46 (C=O asymmetric stretching); 1H NMR (300.81 MHz, DMSO-d6, 25oC, ppm) δ: 7.363 (m, 3H, H2, H6, H4), 7.513 (t, 2H, H3, H5, 3J=7.8 Hz with H2, H6), 8.926 (s, 1H, H11), 8.984 (s, 1H, H10), 9.402 (s, 1H, H9); 13C NMR (75.65 MHz, DMSO-d6, 25oC, ppm) δ: 122.198 (C2, C6), 126.812 (C4), 130.165 (C3, C5), 143.046 (C8), 145.479 (C11), 146.641 (C9), 148.969 (C10), 150.841 (C1), 162.811 (C7).

Conflicts of interest There are no conflicts to declare.

Acknowledgements The authors respectfully acknowledge the Ferdowsi University of Mashhad, Research Council for the financial support of the project Code Number 3/33540. The authors appreciatively would like to thank Indian Institute of Science (IISc) for the helpful supports. They also gratefully thank the Cambridge Crystallographic Data Centre for access to the CSD Enterprise.

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6 (a) S. Long, S. Parkin, M. Siegler, C. P. Brock, A. Cammers and T. Li, Cryst. Growth Des., 2008, 8, 3137-3140; (b) S. Long, S. Parkin, M. A. Siegler, A. Cammers, and T. Li, Cryst. Growth Des., 2008, 8, 4006-4013; (c) S. Roy, R. Banerjee, A. Nangia and G. J. Kruger, Chem. Eur. J. 2006, 12, 3777-3788. (d) V. S. S. Kumar, A. Addlagatta, A. Nangia, W. T. Robinson, C. K. Broder, R. Mondal, I. R. Evans, J. A. K. Howard and F. H. Allen, Angew. Chem. Int. Ed. 2002, 41, 3848-3851.

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https://doi.org/10.1039/C8CE02107D


Table of Contents

Small change in the ligand resulted in conformational variation of LPy to LPz which led to high and low Z' structures in corresponding metal complexes.


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