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A new 1D coordination polymer of triphenyl lead hydrosulfide: Synthesis and insights into crystal architecture and Hirshfeld surface analyses
Journal of Molecular Structure 1207 (2020) 127801
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Journal of Molecular Structure journal homepage: http://www.elsevier.com/locate/molstruc
A new 1D coordination polymer of triphenyl lead hydrosulfide: Synthesis and insights into crystal architecture and Hirshfeld surface analyses Archisman Dutta a, b, Manoj Trivedi c, Abdullah Alarifi d, Abhinav Kumar a, *, Mohd. Muddassir d, ** a
Department of Chemistry, Faculty of Science, University of Lucknow, Lucknow, 226007, India Chemical Division, Geological Survey of India, Northern Region, Lucknow, 226024, India Department of Chemistry, University of Delhi, Delhi, 110007, India d Catalytic Chemistry Chair, Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia b c
a r t i c l e i n f o
a b s t r a c t
Article history: Received 24 September 2019 Received in revised form 21 January 2020 Accepted 25 January 2020 Available online 30 January 2020
A new Pb(IV)-based coordination polymer having formula [(C6H5)3Pb-SH]n (1) has been synthesized and characterized using microanalyses, multinuclear NMR and single crystal X-ray diffraction. The X-ray crystal structure reveals a distorted square pyramidal geometry (t5 ¼ 0.19) around the central Pb(IV) center. The aromatic p-electron cloud is solely drifted to the anti-bonding s*-orbital of PbeS bond thereby forming intramolecular Pb/C tetrel bonding interaction; intramolecular S/H interaction also occurs in the linear chain of 1. The observed interactions have been discussed in detail and have been addressed critically by Hirshfeld surface analysis and fingerprint plots. © 2020 Elsevier B.V. All rights reserved.
Keywords: Coordination polymer Tetrel bonding Pb/H electrostatic interaction Supramolecular interactions Hirshfeld surface analysis
1. Introduction In last couple of decades weak non-covalent interactions are of prime interest amongst crystal engineers for systematic design of supramolecular architecture for metal-organic frameworks, covalent organic frameworks and organic/inorganic reversible/irreversible single crystal to single crystal transformations in the area of crystal engineering [1e4]. According to Desiraju, Vittal and Ramanan, the presence of large number weak interactions may be more important than a few strong ones thereby playing an important role in crystal packing (Gulliver effect) [4]. According to Desiraju and co-workers, ‘supramolecular synthon’ represents the repeating unit of building block in the supramolecular architecture homologous to organic synthon in the retrosynthetic analysis. The identification of the robust supramolecular synthon provides the
* Corresponding author. ** Corresponding author. E-mail addresses: [email protected] [email protected] (Mohd. Muddassir). https://doi.org/10.1016/j.molstruc.2020.127801 0022-2860/© 2020 Elsevier B.V. All rights reserved.
(A.
Kumar),
guiding tool for strategic crystal design with desired properties. The interaction energy of formation of such kind of robust supramolecular synthon must be more than kT (k ¼ Boltzmann’s constant) for stability of supramolecular synthon and also for its experimental detection. Recently Reddy and co-workers added a concept of ‘shape synthons’ in this context where more robust synthons are developed by shape complementarity that introduces impressive desired properties in the crystals. Thus by modulating the molecular packing in a crystal one can obtain impressive functional properties in solid state of the molecules [3,4]. Self-assembly of such supramolecular synthons mediated through directed weak non-covalent interactions such as hydrogen bonding, halogen bonding, p … p stacking, CeH … p stacking etc. together build up supramolecular structure in the organic or metal-organic crystals. This self-assembly is also a vital tool for molecular recognition, drug encapsulation, protein-protein supramolecular interactions, targeted medication release mechanisms, host-guest interactions, etc. in the context of crystal engineering [5]. The heavier metals of group 14 in the periodic table possess versatile coordination modes of ligation with the soft ligands like S, Se, Br, I etc. by virtue of their high polarisability thereby generating
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covalent character in the ionic bond [6e9]. The relativistic stabilisation and high penetration capacity of the penultimate 6s orbital of lead atom, impart extra stability to the low oxidation state of lead (Inert pair effect). Then the lone pair of electron which is present on 6s orbital governs the geometry of lead complexes which is an active research area of interest of theoretical chemists [6,7]. The electrostatic interaction of type of M$$$X supramolecular synthon plays a vital role in directing the molecular packing in the single crystals of metal organic framework/coordination polymers. The ability to control such kind of interaction in the design strategy is indeed a hard challenge for the crystal engineers. Also, it is very tough to predict the crystal structure of molecules on the basis of ab initio methods due to the limited knowledge of weak interactions dominating in a supramolecular architecture [10]. The elements of group 14e17 are known for the formation of unusual s-hole interactions. The s-hole interactions in elements of tetrel or group 14 family lead to the formation of tetrel bonding while for group 15, 16 and 17 it lead to pnictogen, chalcogen and halogen bonding respectively. The tetrel bonding can be defined as the non-classical interaction between the electrons enriched moieties with the tetrel atom. The s-hole interaction can be explained as the overlapping of electron cloud (may be lone pair, anion or p-electron cloud) of the donor atom to the anti-bonding s*- orbital of acceptor$$$X bond (Scheme 1). This donation becomes very facile when the central tetrel atom having anti-bonding s*- orbital is parallel to incoming electron density. If the overlapping orbitals are mutually orthogonal to each other, such kind of relevant interaction is not possible; the fact similar to negative hyperconjugation. In recent studies of Chattopadhyay et al., it is revealed that the size compactness and high electron deficiency in s-hole account for high polarisability of the tetrel atoms which act as a key factor for apprehending incoming electron density thereby accomplishing s-hole interactions [6]. Such type of unconventional interactions, being guided by the principles of crystal engineering, can be the potential tool for programmed design of supramolecular framework with desired properties and applications. The intramolecular tetrel bonding interaction between the phenyl ring and tetrel atom is indeed a rare observation. Keeping all these aspects in mind and in the quest of rational design of a new coordination polymer with intramolecular tetrel bonding interaction, herein we report the synthesis and characterization of one dimensional coordination polymer [(C6H5)3Pb-SH]n (1) and critically analyse its molecular and supramolecular framework by single crystal X-ray diffraction analysis and Hirshfeld Surface analysis [10]. The study will definitely pave the pathway of understanding how crucial various inter/intra-molecular non-covalent interactions guide in developing supramolecular framework which can help one to design compounds with multi-functional applications.
Scheme 1. The general perspective view of tetrel bonding.
2. Experimental 2.1. Materials and methods The reagents used in the work including, triphenyllead chloride (Ph3PbCl) and sodium hydrosulfide, were of analytical grade purchased from Sigma-Aldrich and Merck, respectively. The solvents used in the reactions were of reagent grade and chemicals were used without further purification. Elemental analyses were performed on a Perkin-Elmer 240 C, H and N analyzer. 1H, 13C and 207Pb NMR spectra were recorded on a BRUKER Advance III FTNMR spectrophotometer. Chemical shifts were reported in parts per million using TMS as internal standard for 1H and 13C NMR and tetramethyllead was used as reference for 207Pb NMR [10(g-j)]. 2.2. Synthesis of [(C6H5)3Pb-SH]n (1) Caution! Lead compounds are highly toxic. Proper experienced handling and disposal methods are adopted while working with lead compounds. To the triphenyllead chloride, (1 mmol, 0.48 g) dissolved in 15 mL dichloromethane, sodium hydrosulfide, (1 mmol, 0.06 g) suspended in 10 mL methanol was added in dropwise manner and the mixture was stirred under inert atmosphere for 5 h at room temperature. The solution was filtered and evaporated to dryness and then residue was dissolved in dichloromethane and methanol mixture (1:1 V/V) to obtain yellow coloured single crystals of 1 in 3e4 days. Yield: 71% (0.35 g). M.W. 471.61; Calcd for 1 (%): C 45.84, H 3.42, S 6.80, Pb 43.94; Found: C 46.12, H 3.43, S 7.01, Pb 43.44. 1H NMR (300.26 MHz, DMSO‑d6): d 7.48 (d, J ¼ 6.9, 6H), 7.52 (t, J ¼ 6.60, 6H), 8.20 (dd, J ¼ 7.2, 3H); 13C NMR (75.50 MHz, DMSO‑d6): d 138.8 (Cph), 133.1 (Cph), 170.9 (Cph). 207Pb-NMR (62.77 MHz, DMSO-D6): d 516.1 ppm. 2.3. X-ray crystallography The single crystal X-ray diffraction data collection were carried out on a “Bruker APEX-II CCD” diffractometer that was equipped with a graphite monochromated Mo-Κa radiation (l ¼ 0.71073 Å) by using an u-scan technique. The diffraction source was fine focus sealed tube. The structure was solved by charge flipping method of Superflip program and refined using the Gauss-Newton procedure based on olex2 refinement technique [11]. The intermediate value of Flack parameter (0.3Flack0.7) suggests that merohedral twin is present in the structure. All the hydrogen atoms were generated geometrically and refined isotropically using the riding model. All the non-hydrogen atoms were refined with anisotropic displacement parameters. As the data has been collected at room temperature, dynamic disorder exists in the crystal structure which is further exaggerated by the presence of heavy atom i.e. lead. In order to address this, a result proper disorder modelling of aromatic rings has been considered while solving the crystal structure by fixing equivalent atomic displacement and similar bond distance constraints in the instructions file of 1. The use of constraints (exact mathematical relationships between certain parameters with zero uncertainty) proved to be superior here than the use of restraints regarding the improvement of data quality. This disorder modelling of aromatic rings led us the betterment of data quality of 1 and validation of CIF. Crystal Data of 1 [(C6H5)3Pb-SH]n, Formula weight ¼ 471.61, Temperature ¼ 298(2) K, Monoclinic, P21, a ¼ 5.2151(16) Å, b ¼ 13.015(4) Å, c ¼ 12.204(4) Å, b ¼ 101.329(4) , V ¼ 812.2(4) Å3, Z ¼ 2, Dcalc ¼ 1.9283 g cm3, F(000) ¼ 444.0, m/mm1 ¼ 10.505, crystal colour- yellow, crystal size 0.06 0.09 0.13 mm, Flack parameter ¼ 0.3(3), reflections collected 3165, independent
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reflections (R(int)) ¼ 0.0393, Final indices [I > 2s(I)] R1 ¼ 0.0419, wR2 ¼ 0.1058, GOF 1.0292, Largest difference peak and hole 1.5741 and 0.8379 eÅ3. CCDC No. 1939860. 2.4. Hirshfeld Surface Analyses The Hirshfeld surfaces are generally constructed by taking into account the electron densities and are concerned about various inter and intramolecular interactions taking place inside the crystal as well as with the atoms in the molecule of interest. The Hirshfeld surfaces are generated by using Crystal Explorer 3.1 software and are mapped with dnorm and 2D fingerprint plots of de (distance from a point on the surface to the nearest nucleus outside the surface; mapped between 0.358 Å to 2.917 Å) with di (distance from a point on the surface to the nearest nucleus inside the surface; mapped between 0.400 Å to 3.149 Å). The combination of de and di helps one to address the fingerprint plots which interpret the extent of intermolecular/intramolecular interactions taking place inside the crystal. The normalised contact distance, dnorm, is based on vdW radii of atom and the sign of dnorm, as per equation (1), may be negative or positive, depending on the regime of intermolecular contacts whether it is shorter or longer than the vdW radii of atoms, respectively. The molecular surfaces are mapped with dnorm in red, blue and white colour schemes (mapped between 1.245 Å to 1.387 Å), shape indices (it is the measure of the shape the surface and is case sensitive to how much extent the change in the surface occurs; mapped between 1.000 and þ1.000) in green, red, yellow and blue colour schemes and surface curvedness (it is the scalar quantity that determines how much is the shape; areas with very sharp curvatures determine high surface curvedness with blue patches while the areas with flat or subtle curvatures elucidate low surface curvedness; mapped between 4.000 and 0.4000) in green colour scheme with blue curvature [12].
dnorm ¼
di rvdw i rvdw i
þ
de rvdw e rvdw e
(1)
3. Results and discussions 3.1. Synthesis and spectroscopy The reaction between triphenyllead(IV) chloride and sodium hydrosulfide probably have yielded sodium chloride with the formation of triphenyllead hydrosulfide in situ. Thereafter, the proton is released from the hydrosulfide group in the reaction medium and the generated triphenyllead sulfide anion attacks neighbouring triphenyllead chloride to form a dimer which gradually in presence of proton, polymerizes to linear chain (Scheme 2). The purity and composition of the linear coordination polymer 1 is confirmed by 1 H NMR spectroscopy. The compound displayed well resolved 1H NMR signals which integrate well with the respective hydrogen
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atoms of aromatic ring. The signal at 7.48 ppm corresponds to the hydrogen atoms of ortho carbon atoms of phenyl rings while signals around 7.52 and 8.20 ppm address the hydrogen atoms of meta and para carbon atoms of phenyl ring. The respective ortho, meta and para carbon centers of the aromatic rings show perceptible signals in 13C NMR spectrum at 133.14, 138.77, 170.90 ppm. The upfield shift in 207Pb NMR spectrum at ~ 516.11 ppm is due to coordination of DMSO‑d6 solvent with central Pb(IV) [10(j-k)]. In 1H NMR the signal corresponding to SeH proton was not observed but significant electron density had been observed on sulfur atom while solving the crystal structure. So in order to establish the electroneutral structure, hydrogen atom on sulfur was fixed and had been refined freely.
3.2. Molecular structure description The complex 1 crystallizes in monoclinic crystal system with P21 space group having only one molecule of Ph3PbSH in the asymmetric unit. The three phenyl rings attached with central Pb(IV) are not in the same plane, resembling a propeller shaped molecular arrangement with the angles between two successive planes encompassing the central Pb(IV) and two different aromatic moieties of about 88.92 (planes P1 and P2) and 59.55 (planes P1 and P3) (Fig. 1). The central Pb(IV) atom bears distorted square pyramidal geometry (t5 ¼ 0.19) with one sulfur atom and the disordered aromatic rings having C1, C7 and C13 carbon atoms in a distorted square plane and another sulfur atom in the axial part with bond angles S1ePb1eC1 95.26 (4), S1ePb1eC7 111.4 (4), S1ePb1eC13 109.84 (4). The sulfur centers forms bridge between two adjacent Ph3Pb(IV) moieties as repeating unit to form infinite chain one dimensional coordination polymer (Fig. 2). The PbeC1, PbeC7, PbeC13 bond lengths in the molecule are 2.181(13) Å, 2.192(15) Å and 2.216(14) Å respectively. The m-S between two neighbouring Pb centers is not equidistant as the PbeS1 bond distance is 2.736(2) Å while PbeS10 bond separation is 2.915(2) Å with S1ePbeS10 bite angle 134.69 (7) (Table S2). The most important observation in 1 is the formation of tetrel bonding interaction between the p-electron cloud of aromatic rings with Pb(IV) tetrel center (Fig. 2c). The s-hole opposite to polarisable PbeS bond gets involved in bifurcated tetrel bonding interaction with p-electron cloud of aromatic rings having Pb-Cg bond distances around 3.5 Å (Fig. 2c). The Pb/C tetrel bond distance is significantly longer than Rcov and nearly 0.3 Å shorter than SRvdw of 3.82 Å thereby suggesting a non-covalent interaction. This is so far a rare example where the sole p-electron cloud of aromatic ring polarises the PbeS bond and gets involved in such kind of tetrel supramolecular interaction [8,9]. As a result of this tetrel interaction, where p-electron cloud of aromatic rings donates to antibonding s*- orbital of PbeS bond, two dissimilar PbeS bonds are observed; one with slightly higher covalent bond length than another thereby indulging non-classical interaction character along with classical covalent PbeS bond. Possibly the S atom forms
Scheme 2. Synthetic route of 1.
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Fig. 1. Single molecular unit Ph3PbSePb- of 1 showing interplanar angles between (a) P1 and P2 and (b) P1 and P3; (c) ORTEP representation of 1 with 30% probability ellipsoid density (Hydrogen atoms are omitted for clarity).
Fig. 2. (a) Linear chain of 1; (b) the perspective view of molecule with coordination environment; (c) tetrel bonding interactions between Pb(IV) and centroid of aromatic ring with respective contact distances.
classical covalent bond with one Pb and H atom and a strong two electron coordinate bond with the next Pb atom which has slightly higher bond length due to its inherent weakness compared to a classical two center two electron covalent bond. This may be the probable reason between the dissimilar bond lengths of two PbeS bonds along with metal … chalcogen interaction which is further supported by Hirshfeld surface analysis where Pb$$$S interaction contributes 1.8% of surface coverage [12]. The molecule further displays intramolecular CeH/S hydrogen bonding interactions
with H12/S1 3.031(13) Å,
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Fig. 3. Weak intramolecular S/H hydrogen bonding interaction in 1.
Fig. 4. Figure depicting metal Pb/H interactions with respective contact distances.
sum of their van der Waals radii SRvdw (3.220 Å). Here Pb/H interaction is mainly a sort of electrostatic nature of interaction between the involved atoms. Here the bridging sulfur atom is trivalent and as a result of which the electronegative sulfur atom attracts the bonded electron pair of SeH bond towards itself thereby generating partial positive charge density on the hydrogen atom. Due to the presence of tetrel bonding in 1, the electron density on central metal atom increases which provokes electrostatic interaction between the metal (Pb) and electron deficient hydrogen atom. The length of such kind of non-classical interaction is 3.142 Å with
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to identify how weak interactions govern the molecular packing in the crystals [13e15]. The surface of 1 is as translucent as it allows the clear visualization of the propeller shaped slightly disordered aromatic moieties attached with the central Pb atom. The red portions are very faint on the surface which clearly indicates the lack of strong interactions like H-bonding, ion-dipole interactions etc. however, weak interactions play crucial role in determining the molecular structure of the framework as evident from the light colour of the surface; this is consistent with single crystal X-ray diffraction studies. The interactions like CeH/S, H/H, Pb/S interactions which are observed as faintly red area in the dnorm surface are worth-mentionable in developing crystal packing. As confirmed from the crystal packing, there exists no interlayer Pb/S contact but short van der Waals contact of 2.736 Å exists between tetrelchalcogen atoms which exhibit noticeable Hirshfeld surface coverage of 1.8% (Fig. 5). The presence of hydrogen atoms in large number justifies the significant contribution of H/H contacts. The H/H contact contributes 58.9% of Hirshfeld surface coverage. Weak hydrogen bonding interaction of S/HeC(p) also contribute 5.8% of surface coverage that also play significant role in the development of interlocked stacking of molecules in the crystals in one dimensional chain. In the previous section, tetrel bonding interaction has been discussed in detail where p-electron cloud of aromatic ring interacts with s*- orbital of PbeS bond. The supramolecular tetrel Pb/C interaction accounts for 0.1% of Hirshfeld surface coverage. The presence of 2.6% of Hirshfeld surface coverage of Pb/H interaction is very significant that elucidates non-classical electrostatic interaction between the metal-hydrogen atoms. This is so far a rare example where both tetrel and non-classical electrostatic interactions are taking place intramolecularly in the same compound jointly supported SCXRD and Hirshfeld data analyses. Surface curvedness which is the function of root mean square curvature of the surface basically shows flat green surfaces with faint blue patches along the edges which reveal that the interactions taking place inside the crystal of 1 are basically weak and supramolecular architecture is build up by weak isotropic and isoenergetic interactions [15,16]. The curvedness surface is relatively broad and flat which is likewise the fingerprint of isoenergetic interactions. The shape index plot in the Hirshfeld surface coverage also indicates the mode of packing taking place inside the crystal. The yellow ellipses highlight the Pb/S interaction while red ellipses point out the H/H interaction, respectively in 1 (Fig. 6). However, as these interactions are feeble and intramolecular S/H hydrogen bonding is also very weak, sharp tooth are not observed in the fingerprint plot of 1. The Hirshfeld surface thereby elucidates the presence of dominant weak interactions as well as tetrel interactions in the crystal. The crystal void parameter has also been calculated using Crystal Explorer 3.1 software with standard void cluster parameter “unit cell þ5.0 Å”. From crystal void calculation, a promolecule surface including all atoms in the cluster are generated which is capped within the unit cell and provides us an abrupt idea about the voids in the crystal. The promolecule surface is generated by mapping the spherical atoms electron density for the molecule. As weak interactions play dominating role in governing the crystal packing, there is the presence of lot of crystal voids in the crystal structure. Calculations revealed the void volume of crystal as 139.68 Å3 with 324.09 Å2 void surface area. The globularity and asphericity index of crystal void surface have also been calculated and are 0.402 and 0.122 units respectively. Due to lack of strong interactions like hydrogen bonding between hard donor and acceptor groups, the void surface is more aspherical (Fig. 7).
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Fig. 5. Hirshfeld surface analysis and fingerprint plots showing surface coverage of various weak interactions in 1.
Fig. 6. Hirshfeld surfaces of cluster of two molecules mapped with shape index and curvedness where shape index shows H/H and S/H interactions and its complementary highlighted in circles (Hydrogen atoms are omitted for clarity).
4. Conclusion In conclusion, we have successfully demonstrated the synthesis of a new one dimensional linear coordination polymer 1 consisting of [(C6H5)3Pb-SH]n repeating unit and characterized the structure with NMR and single crystal X-ray diffraction techniques. All the interactions discussed here are weak in nature and are addressed critically with Hirshfeld surface analysis. It has been observed that the crystal contains intramolecular Pb/C tetrel interaction and electrostatic non-classical Pb/H interaction, Pb/S metalchalcophilic and S/H interactions in the one dimensional chain; multiple supramolecular interactions are properly articulated by
Hirshfeld surface analysis and crystal void parameter calculation also provided the idea about the presence of lot of voids inside the crystal. The fingerprint plots discourse the detailed study of the involved intermolecular and intramolecular interactions inside the crystal, thereby providing an idea about the category of molecular packing of the crystal system under investigation. The presence of dual tetrel bonding and non-classical electrostatic Pb/H interactions in a single compound, thus modulating the structure of a molecule, can be a potential tool for rational design of supramolecular architecture with desired functional properties in near future.
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[2]
[3]
[4]
Fig. 7. The perspective view of crystal voids present in 1 (incomplete fragments of atoms from voids are omitted for clarity).
Author contribution Abhinav Kumar and Mohd. Muddassir designed the scheme. Archisman Dutta, Abdullah Alarifi and Manoj Trivedi had performed the synthesis and characterization. Archisman Dutta had also performed Hirshfeld Surface Analyses
[5]
[6]
[7]
All the authors had collectively written the paper. Declaration of competing interest Authors declare no competing conflict of financial interests.
[8]
[9]
Acknowledgement [10]
AD acknowledges Geological Survey of India, Northern Region, Lucknow for giving permission of pursuing PhD work at University of Lucknow, India. The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding this work through research group project number RG-1440-076. AK is grateful to Council of Scientific and Industrial Research, New Delhi for the financial support in the form of project no. 01(2899)/17/EMR-II. The authors would like to extend nez, heartfelt acknowledgement to Prof. Pedro S. Valerga Jime diz, Spain for providing fruitful information Universidad de Ca regarding single crystal X-ray diffraction and solving the crystal structure of the compound. Authors are also grateful to the learned reviewers in providing fruitful suggestions for the overall improvement in the paper.
[11]
Appendix A. Supplementary data Supplementary data to this article can be found online at https://doi.org/10.1016/j.molstruc.2020.127801. References [1] (a) A. Ma, F. Ke, J. Jiang, Q. Yuan, Z. Luo, J. Liu, A. Kumar, CrystEngComm 19 (2017) 2172;
[12]
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A new 1D coordination polymer of triphenyl lead hydrosulfide: Synthesis and insights into crystal architecture and Hirshfeld surface analyses Archisman Dutta a, b, Manoj Trivedi c, Abdullah Alarifi d, Abhinav Kumar a, *, Mohd. Muddassir d, ** a
Department of Chemistry, Faculty of Science, University of Lucknow, Lucknow, 226007, India Chemical Division, Geological Survey of India, Northern Region, Lucknow, 226024, India Department of Chemistry, University of Delhi, Delhi, 110007, India d Catalytic Chemistry Chair, Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia b c
a r t i c l e i n f o
a b s t r a c t
Article history: Received 24 September 2019 Received in revised form 21 January 2020 Accepted 25 January 2020 Available online 30 January 2020
A new Pb(IV)-based coordination polymer having formula [(C6H5)3Pb-SH]n (1) has been synthesized and characterized using microanalyses, multinuclear NMR and single crystal X-ray diffraction. The X-ray crystal structure reveals a distorted square pyramidal geometry (t5 ¼ 0.19) around the central Pb(IV) center. The aromatic p-electron cloud is solely drifted to the anti-bonding s*-orbital of PbeS bond thereby forming intramolecular Pb/C tetrel bonding interaction; intramolecular S/H interaction also occurs in the linear chain of 1. The observed interactions have been discussed in detail and have been addressed critically by Hirshfeld surface analysis and fingerprint plots. © 2020 Elsevier B.V. All rights reserved.
Keywords: Coordination polymer Tetrel bonding Pb/H electrostatic interaction Supramolecular interactions Hirshfeld surface analysis
1. Introduction In last couple of decades weak non-covalent interactions are of prime interest amongst crystal engineers for systematic design of supramolecular architecture for metal-organic frameworks, covalent organic frameworks and organic/inorganic reversible/irreversible single crystal to single crystal transformations in the area of crystal engineering [1e4]. According to Desiraju, Vittal and Ramanan, the presence of large number weak interactions may be more important than a few strong ones thereby playing an important role in crystal packing (Gulliver effect) [4]. According to Desiraju and co-workers, ‘supramolecular synthon’ represents the repeating unit of building block in the supramolecular architecture homologous to organic synthon in the retrosynthetic analysis. The identification of the robust supramolecular synthon provides the
* Corresponding author. ** Corresponding author. E-mail addresses: [email protected] [email protected] (Mohd. Muddassir). https://doi.org/10.1016/j.molstruc.2020.127801 0022-2860/© 2020 Elsevier B.V. All rights reserved.
(A.
Kumar),
guiding tool for strategic crystal design with desired properties. The interaction energy of formation of such kind of robust supramolecular synthon must be more than kT (k ¼ Boltzmann’s constant) for stability of supramolecular synthon and also for its experimental detection. Recently Reddy and co-workers added a concept of ‘shape synthons’ in this context where more robust synthons are developed by shape complementarity that introduces impressive desired properties in the crystals. Thus by modulating the molecular packing in a crystal one can obtain impressive functional properties in solid state of the molecules [3,4]. Self-assembly of such supramolecular synthons mediated through directed weak non-covalent interactions such as hydrogen bonding, halogen bonding, p … p stacking, CeH … p stacking etc. together build up supramolecular structure in the organic or metal-organic crystals. This self-assembly is also a vital tool for molecular recognition, drug encapsulation, protein-protein supramolecular interactions, targeted medication release mechanisms, host-guest interactions, etc. in the context of crystal engineering [5]. The heavier metals of group 14 in the periodic table possess versatile coordination modes of ligation with the soft ligands like S, Se, Br, I etc. by virtue of their high polarisability thereby generating
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covalent character in the ionic bond [6e9]. The relativistic stabilisation and high penetration capacity of the penultimate 6s orbital of lead atom, impart extra stability to the low oxidation state of lead (Inert pair effect). Then the lone pair of electron which is present on 6s orbital governs the geometry of lead complexes which is an active research area of interest of theoretical chemists [6,7]. The electrostatic interaction of type of M$$$X supramolecular synthon plays a vital role in directing the molecular packing in the single crystals of metal organic framework/coordination polymers. The ability to control such kind of interaction in the design strategy is indeed a hard challenge for the crystal engineers. Also, it is very tough to predict the crystal structure of molecules on the basis of ab initio methods due to the limited knowledge of weak interactions dominating in a supramolecular architecture [10]. The elements of group 14e17 are known for the formation of unusual s-hole interactions. The s-hole interactions in elements of tetrel or group 14 family lead to the formation of tetrel bonding while for group 15, 16 and 17 it lead to pnictogen, chalcogen and halogen bonding respectively. The tetrel bonding can be defined as the non-classical interaction between the electrons enriched moieties with the tetrel atom. The s-hole interaction can be explained as the overlapping of electron cloud (may be lone pair, anion or p-electron cloud) of the donor atom to the anti-bonding s*- orbital of acceptor$$$X bond (Scheme 1). This donation becomes very facile when the central tetrel atom having anti-bonding s*- orbital is parallel to incoming electron density. If the overlapping orbitals are mutually orthogonal to each other, such kind of relevant interaction is not possible; the fact similar to negative hyperconjugation. In recent studies of Chattopadhyay et al., it is revealed that the size compactness and high electron deficiency in s-hole account for high polarisability of the tetrel atoms which act as a key factor for apprehending incoming electron density thereby accomplishing s-hole interactions [6]. Such type of unconventional interactions, being guided by the principles of crystal engineering, can be the potential tool for programmed design of supramolecular framework with desired properties and applications. The intramolecular tetrel bonding interaction between the phenyl ring and tetrel atom is indeed a rare observation. Keeping all these aspects in mind and in the quest of rational design of a new coordination polymer with intramolecular tetrel bonding interaction, herein we report the synthesis and characterization of one dimensional coordination polymer [(C6H5)3Pb-SH]n (1) and critically analyse its molecular and supramolecular framework by single crystal X-ray diffraction analysis and Hirshfeld Surface analysis [10]. The study will definitely pave the pathway of understanding how crucial various inter/intra-molecular non-covalent interactions guide in developing supramolecular framework which can help one to design compounds with multi-functional applications.
Scheme 1. The general perspective view of tetrel bonding.
2. Experimental 2.1. Materials and methods The reagents used in the work including, triphenyllead chloride (Ph3PbCl) and sodium hydrosulfide, were of analytical grade purchased from Sigma-Aldrich and Merck, respectively. The solvents used in the reactions were of reagent grade and chemicals were used without further purification. Elemental analyses were performed on a Perkin-Elmer 240 C, H and N analyzer. 1H, 13C and 207Pb NMR spectra were recorded on a BRUKER Advance III FTNMR spectrophotometer. Chemical shifts were reported in parts per million using TMS as internal standard for 1H and 13C NMR and tetramethyllead was used as reference for 207Pb NMR [10(g-j)]. 2.2. Synthesis of [(C6H5)3Pb-SH]n (1) Caution! Lead compounds are highly toxic. Proper experienced handling and disposal methods are adopted while working with lead compounds. To the triphenyllead chloride, (1 mmol, 0.48 g) dissolved in 15 mL dichloromethane, sodium hydrosulfide, (1 mmol, 0.06 g) suspended in 10 mL methanol was added in dropwise manner and the mixture was stirred under inert atmosphere for 5 h at room temperature. The solution was filtered and evaporated to dryness and then residue was dissolved in dichloromethane and methanol mixture (1:1 V/V) to obtain yellow coloured single crystals of 1 in 3e4 days. Yield: 71% (0.35 g). M.W. 471.61; Calcd for 1 (%): C 45.84, H 3.42, S 6.80, Pb 43.94; Found: C 46.12, H 3.43, S 7.01, Pb 43.44. 1H NMR (300.26 MHz, DMSO‑d6): d 7.48 (d, J ¼ 6.9, 6H), 7.52 (t, J ¼ 6.60, 6H), 8.20 (dd, J ¼ 7.2, 3H); 13C NMR (75.50 MHz, DMSO‑d6): d 138.8 (Cph), 133.1 (Cph), 170.9 (Cph). 207Pb-NMR (62.77 MHz, DMSO-D6): d 516.1 ppm. 2.3. X-ray crystallography The single crystal X-ray diffraction data collection were carried out on a “Bruker APEX-II CCD” diffractometer that was equipped with a graphite monochromated Mo-Κa radiation (l ¼ 0.71073 Å) by using an u-scan technique. The diffraction source was fine focus sealed tube. The structure was solved by charge flipping method of Superflip program and refined using the Gauss-Newton procedure based on olex2 refinement technique [11]. The intermediate value of Flack parameter (0.3Flack0.7) suggests that merohedral twin is present in the structure. All the hydrogen atoms were generated geometrically and refined isotropically using the riding model. All the non-hydrogen atoms were refined with anisotropic displacement parameters. As the data has been collected at room temperature, dynamic disorder exists in the crystal structure which is further exaggerated by the presence of heavy atom i.e. lead. In order to address this, a result proper disorder modelling of aromatic rings has been considered while solving the crystal structure by fixing equivalent atomic displacement and similar bond distance constraints in the instructions file of 1. The use of constraints (exact mathematical relationships between certain parameters with zero uncertainty) proved to be superior here than the use of restraints regarding the improvement of data quality. This disorder modelling of aromatic rings led us the betterment of data quality of 1 and validation of CIF. Crystal Data of 1 [(C6H5)3Pb-SH]n, Formula weight ¼ 471.61, Temperature ¼ 298(2) K, Monoclinic, P21, a ¼ 5.2151(16) Å, b ¼ 13.015(4) Å, c ¼ 12.204(4) Å, b ¼ 101.329(4) , V ¼ 812.2(4) Å3, Z ¼ 2, Dcalc ¼ 1.9283 g cm3, F(000) ¼ 444.0, m/mm1 ¼ 10.505, crystal colour- yellow, crystal size 0.06 0.09 0.13 mm, Flack parameter ¼ 0.3(3), reflections collected 3165, independent
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reflections (R(int)) ¼ 0.0393, Final indices [I > 2s(I)] R1 ¼ 0.0419, wR2 ¼ 0.1058, GOF 1.0292, Largest difference peak and hole 1.5741 and 0.8379 eÅ3. CCDC No. 1939860. 2.4. Hirshfeld Surface Analyses The Hirshfeld surfaces are generally constructed by taking into account the electron densities and are concerned about various inter and intramolecular interactions taking place inside the crystal as well as with the atoms in the molecule of interest. The Hirshfeld surfaces are generated by using Crystal Explorer 3.1 software and are mapped with dnorm and 2D fingerprint plots of de (distance from a point on the surface to the nearest nucleus outside the surface; mapped between 0.358 Å to 2.917 Å) with di (distance from a point on the surface to the nearest nucleus inside the surface; mapped between 0.400 Å to 3.149 Å). The combination of de and di helps one to address the fingerprint plots which interpret the extent of intermolecular/intramolecular interactions taking place inside the crystal. The normalised contact distance, dnorm, is based on vdW radii of atom and the sign of dnorm, as per equation (1), may be negative or positive, depending on the regime of intermolecular contacts whether it is shorter or longer than the vdW radii of atoms, respectively. The molecular surfaces are mapped with dnorm in red, blue and white colour schemes (mapped between 1.245 Å to 1.387 Å), shape indices (it is the measure of the shape the surface and is case sensitive to how much extent the change in the surface occurs; mapped between 1.000 and þ1.000) in green, red, yellow and blue colour schemes and surface curvedness (it is the scalar quantity that determines how much is the shape; areas with very sharp curvatures determine high surface curvedness with blue patches while the areas with flat or subtle curvatures elucidate low surface curvedness; mapped between 4.000 and 0.4000) in green colour scheme with blue curvature [12].
dnorm ¼
di rvdw i rvdw i
þ
de rvdw e rvdw e
(1)
3. Results and discussions 3.1. Synthesis and spectroscopy The reaction between triphenyllead(IV) chloride and sodium hydrosulfide probably have yielded sodium chloride with the formation of triphenyllead hydrosulfide in situ. Thereafter, the proton is released from the hydrosulfide group in the reaction medium and the generated triphenyllead sulfide anion attacks neighbouring triphenyllead chloride to form a dimer which gradually in presence of proton, polymerizes to linear chain (Scheme 2). The purity and composition of the linear coordination polymer 1 is confirmed by 1 H NMR spectroscopy. The compound displayed well resolved 1H NMR signals which integrate well with the respective hydrogen
3
atoms of aromatic ring. The signal at 7.48 ppm corresponds to the hydrogen atoms of ortho carbon atoms of phenyl rings while signals around 7.52 and 8.20 ppm address the hydrogen atoms of meta and para carbon atoms of phenyl ring. The respective ortho, meta and para carbon centers of the aromatic rings show perceptible signals in 13C NMR spectrum at 133.14, 138.77, 170.90 ppm. The upfield shift in 207Pb NMR spectrum at ~ 516.11 ppm is due to coordination of DMSO‑d6 solvent with central Pb(IV) [10(j-k)]. In 1H NMR the signal corresponding to SeH proton was not observed but significant electron density had been observed on sulfur atom while solving the crystal structure. So in order to establish the electroneutral structure, hydrogen atom on sulfur was fixed and had been refined freely.
3.2. Molecular structure description The complex 1 crystallizes in monoclinic crystal system with P21 space group having only one molecule of Ph3PbSH in the asymmetric unit. The three phenyl rings attached with central Pb(IV) are not in the same plane, resembling a propeller shaped molecular arrangement with the angles between two successive planes encompassing the central Pb(IV) and two different aromatic moieties of about 88.92 (planes P1 and P2) and 59.55 (planes P1 and P3) (Fig. 1). The central Pb(IV) atom bears distorted square pyramidal geometry (t5 ¼ 0.19) with one sulfur atom and the disordered aromatic rings having C1, C7 and C13 carbon atoms in a distorted square plane and another sulfur atom in the axial part with bond angles S1ePb1eC1 95.26 (4), S1ePb1eC7 111.4 (4), S1ePb1eC13 109.84 (4). The sulfur centers forms bridge between two adjacent Ph3Pb(IV) moieties as repeating unit to form infinite chain one dimensional coordination polymer (Fig. 2). The PbeC1, PbeC7, PbeC13 bond lengths in the molecule are 2.181(13) Å, 2.192(15) Å and 2.216(14) Å respectively. The m-S between two neighbouring Pb centers is not equidistant as the PbeS1 bond distance is 2.736(2) Å while PbeS10 bond separation is 2.915(2) Å with S1ePbeS10 bite angle 134.69 (7) (Table S2). The most important observation in 1 is the formation of tetrel bonding interaction between the p-electron cloud of aromatic rings with Pb(IV) tetrel center (Fig. 2c). The s-hole opposite to polarisable PbeS bond gets involved in bifurcated tetrel bonding interaction with p-electron cloud of aromatic rings having Pb-Cg bond distances around 3.5 Å (Fig. 2c). The Pb/C tetrel bond distance is significantly longer than Rcov and nearly 0.3 Å shorter than SRvdw of 3.82 Å thereby suggesting a non-covalent interaction. This is so far a rare example where the sole p-electron cloud of aromatic ring polarises the PbeS bond and gets involved in such kind of tetrel supramolecular interaction [8,9]. As a result of this tetrel interaction, where p-electron cloud of aromatic rings donates to antibonding s*- orbital of PbeS bond, two dissimilar PbeS bonds are observed; one with slightly higher covalent bond length than another thereby indulging non-classical interaction character along with classical covalent PbeS bond. Possibly the S atom forms
Scheme 2. Synthetic route of 1.
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Fig. 1. Single molecular unit Ph3PbSePb- of 1 showing interplanar angles between (a) P1 and P2 and (b) P1 and P3; (c) ORTEP representation of 1 with 30% probability ellipsoid density (Hydrogen atoms are omitted for clarity).
Fig. 2. (a) Linear chain of 1; (b) the perspective view of molecule with coordination environment; (c) tetrel bonding interactions between Pb(IV) and centroid of aromatic ring with respective contact distances.
classical covalent bond with one Pb and H atom and a strong two electron coordinate bond with the next Pb atom which has slightly higher bond length due to its inherent weakness compared to a classical two center two electron covalent bond. This may be the probable reason between the dissimilar bond lengths of two PbeS bonds along with metal … chalcogen interaction which is further supported by Hirshfeld surface analysis where Pb$$$S interaction contributes 1.8% of surface coverage [12]. The molecule further displays intramolecular CeH/S hydrogen bonding interactions
with H12/S1 3.031(13) Å,
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Fig. 3. Weak intramolecular S/H hydrogen bonding interaction in 1.
Fig. 4. Figure depicting metal Pb/H interactions with respective contact distances.
sum of their van der Waals radii SRvdw (3.220 Å). Here Pb/H interaction is mainly a sort of electrostatic nature of interaction between the involved atoms. Here the bridging sulfur atom is trivalent and as a result of which the electronegative sulfur atom attracts the bonded electron pair of SeH bond towards itself thereby generating partial positive charge density on the hydrogen atom. Due to the presence of tetrel bonding in 1, the electron density on central metal atom increases which provokes electrostatic interaction between the metal (Pb) and electron deficient hydrogen atom. The length of such kind of non-classical interaction is 3.142 Å with
5
to identify how weak interactions govern the molecular packing in the crystals [13e15]. The surface of 1 is as translucent as it allows the clear visualization of the propeller shaped slightly disordered aromatic moieties attached with the central Pb atom. The red portions are very faint on the surface which clearly indicates the lack of strong interactions like H-bonding, ion-dipole interactions etc. however, weak interactions play crucial role in determining the molecular structure of the framework as evident from the light colour of the surface; this is consistent with single crystal X-ray diffraction studies. The interactions like CeH/S, H/H, Pb/S interactions which are observed as faintly red area in the dnorm surface are worth-mentionable in developing crystal packing. As confirmed from the crystal packing, there exists no interlayer Pb/S contact but short van der Waals contact of 2.736 Å exists between tetrelchalcogen atoms which exhibit noticeable Hirshfeld surface coverage of 1.8% (Fig. 5). The presence of hydrogen atoms in large number justifies the significant contribution of H/H contacts. The H/H contact contributes 58.9% of Hirshfeld surface coverage. Weak hydrogen bonding interaction of S/HeC(p) also contribute 5.8% of surface coverage that also play significant role in the development of interlocked stacking of molecules in the crystals in one dimensional chain. In the previous section, tetrel bonding interaction has been discussed in detail where p-electron cloud of aromatic ring interacts with s*- orbital of PbeS bond. The supramolecular tetrel Pb/C interaction accounts for 0.1% of Hirshfeld surface coverage. The presence of 2.6% of Hirshfeld surface coverage of Pb/H interaction is very significant that elucidates non-classical electrostatic interaction between the metal-hydrogen atoms. This is so far a rare example where both tetrel and non-classical electrostatic interactions are taking place intramolecularly in the same compound jointly supported SCXRD and Hirshfeld data analyses. Surface curvedness which is the function of root mean square curvature of the surface basically shows flat green surfaces with faint blue patches along the edges which reveal that the interactions taking place inside the crystal of 1 are basically weak and supramolecular architecture is build up by weak isotropic and isoenergetic interactions [15,16]. The curvedness surface is relatively broad and flat which is likewise the fingerprint of isoenergetic interactions. The shape index plot in the Hirshfeld surface coverage also indicates the mode of packing taking place inside the crystal. The yellow ellipses highlight the Pb/S interaction while red ellipses point out the H/H interaction, respectively in 1 (Fig. 6). However, as these interactions are feeble and intramolecular S/H hydrogen bonding is also very weak, sharp tooth are not observed in the fingerprint plot of 1. The Hirshfeld surface thereby elucidates the presence of dominant weak interactions as well as tetrel interactions in the crystal. The crystal void parameter has also been calculated using Crystal Explorer 3.1 software with standard void cluster parameter “unit cell þ5.0 Å”. From crystal void calculation, a promolecule surface including all atoms in the cluster are generated which is capped within the unit cell and provides us an abrupt idea about the voids in the crystal. The promolecule surface is generated by mapping the spherical atoms electron density for the molecule. As weak interactions play dominating role in governing the crystal packing, there is the presence of lot of crystal voids in the crystal structure. Calculations revealed the void volume of crystal as 139.68 Å3 with 324.09 Å2 void surface area. The globularity and asphericity index of crystal void surface have also been calculated and are 0.402 and 0.122 units respectively. Due to lack of strong interactions like hydrogen bonding between hard donor and acceptor groups, the void surface is more aspherical (Fig. 7).
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Fig. 5. Hirshfeld surface analysis and fingerprint plots showing surface coverage of various weak interactions in 1.
Fig. 6. Hirshfeld surfaces of cluster of two molecules mapped with shape index and curvedness where shape index shows H/H and S/H interactions and its complementary highlighted in circles (Hydrogen atoms are omitted for clarity).
4. Conclusion In conclusion, we have successfully demonstrated the synthesis of a new one dimensional linear coordination polymer 1 consisting of [(C6H5)3Pb-SH]n repeating unit and characterized the structure with NMR and single crystal X-ray diffraction techniques. All the interactions discussed here are weak in nature and are addressed critically with Hirshfeld surface analysis. It has been observed that the crystal contains intramolecular Pb/C tetrel interaction and electrostatic non-classical Pb/H interaction, Pb/S metalchalcophilic and S/H interactions in the one dimensional chain; multiple supramolecular interactions are properly articulated by
Hirshfeld surface analysis and crystal void parameter calculation also provided the idea about the presence of lot of voids inside the crystal. The fingerprint plots discourse the detailed study of the involved intermolecular and intramolecular interactions inside the crystal, thereby providing an idea about the category of molecular packing of the crystal system under investigation. The presence of dual tetrel bonding and non-classical electrostatic Pb/H interactions in a single compound, thus modulating the structure of a molecule, can be a potential tool for rational design of supramolecular architecture with desired functional properties in near future.
A. Dutta et al. / Journal of Molecular Structure 1207 (2020) 127801
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Fig. 7. The perspective view of crystal voids present in 1 (incomplete fragments of atoms from voids are omitted for clarity).
Author contribution Abhinav Kumar and Mohd. Muddassir designed the scheme. Archisman Dutta, Abdullah Alarifi and Manoj Trivedi had performed the synthesis and characterization. Archisman Dutta had also performed Hirshfeld Surface Analyses
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All the authors had collectively written the paper. Declaration of competing interest Authors declare no competing conflict of financial interests.
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Acknowledgement [10]
AD acknowledges Geological Survey of India, Northern Region, Lucknow for giving permission of pursuing PhD work at University of Lucknow, India. The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding this work through research group project number RG-1440-076. AK is grateful to Council of Scientific and Industrial Research, New Delhi for the financial support in the form of project no. 01(2899)/17/EMR-II. The authors would like to extend nez, heartfelt acknowledgement to Prof. Pedro S. Valerga Jime diz, Spain for providing fruitful information Universidad de Ca regarding single crystal X-ray diffraction and solving the crystal structure of the compound. Authors are also grateful to the learned reviewers in providing fruitful suggestions for the overall improvement in the paper.
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