Unprecedented folding in linker based flexible tripodal molecule and their conformational analysis

Journal of Molecular Structure 1134 (2017) 781e788

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Journal of Molecular Structure journal homepage: http://www.elsevier.com/locate/molstruc

Unprecedented folding in linker based flexible tripodal molecule and their conformational analysis Archana Gaurav a, Ranjeet Kumar a, Hariom Gupta b, K. Ravikumar c, B. Sridhar c, Ashish Kumar Tewari a, * a b c

Department of Chemistry, Faculty of Science, Banaras Hindu University, Varanasi, 221005, India Analytical Discipline and Centralized Instrument Facility, CSMCRI, Gijubhai Badheka Marg, Bhavnagar, 364021, Gujarat, India Laboratory of X-ray Crystallography, Indian Institute of Chemical Technology, Hyderabad, 500 607, India

a r t i c l e i n f o

a b s t r a c t

Article history: Received 5 November 2016 Received in revised form 7 January 2017 Accepted 8 January 2017 Available online 10 January 2017

Here, we first time report the flexible tripodal molecules, contained propylene as a linker, thiocyanuric acid as central core and, p-nitro phenol 1 and pyridazinone 2 as terminal for conformational studies. The conformational studies of these tripodal molecules have been carried by X-ray crystallography, 2DNOESY spectra and computational studies. Both the molecules have shown folded conformations in solid and solution state however solid state conformation is not stable in gaseous state. © 2017 Elsevier B.V. All rights reserved.

Keywords: Tripodal molecules X-ray crystallography Intramolecular folding 2D-NOESY DFT calculation

1. Introduction The conformation of tripodal molecule allows the rational control of binding properties such as complex stability and selectivity. Compared to a rigid cyclic system, they can show rapid complexation/decomplexation kinetics and may undergo significant conformational changes upon binding [1]. Further the tripodal molecule can act as receptors for different chemical species: transition metal ions [2], lanthanide ions [3], actinide ions [4], anions [5], or cations [6]. The tripodal molecules are also increasingly applied in the fields of catalysis [7], molecular recognition [8] and biomimetics [9]. These all applications are driven by presence of functional groups [10] as well as heteroaromatic moieties [11] of tripodal molecule. The presence of functional group on tripodal molecules have prone to shown pH sensor [12], metal-binding site [13], and hydrogen bond donors/acceptors [14] which is oriented towards a central cavity enables selective substrate for recognition.

* Corresponding author. E-mail addresses: [email protected], (A.K. Tewari). http://dx.doi.org/10.1016/j.molstruc.2017.01.031 0022-2860/© 2017 Elsevier B.V. All rights reserved.

[email protected]

The tripodal molecule contained heteroaromatic moieties also causes weak interactions [15], metal coordination [16], ionic interactions [17], and hydrophobic interactions [18]. In addition to this, other non-covalent forces, i.e. p-stacking of aromatic units, can be used as a strategic design highly sensitive for solvent employed by p/p and CeH/p interactions regarding for understanding the hostehost and hosteguest interactions [19]. In this article we report the synthesis of two new flexible tripodal molecules (1 and 2) appended with p-nitro phenol and pyridazinone moieties for their conformational studies. These tripodal molecule contained small molecule like thiocyanuric acid as central core, propylene as spacer in middle and, p-nitro phenol 1 and pyridazinone 2 moieties in terminal (Scheme 1). The selection of terminal p-nitro phenol and pyridazinone system have been taken for synthesis of tripodal molecules because these systems are electron deficient systems due to presence of electron withdrawing substituent like nitro, nitrile and amide function in the ring. Electron deficient systems are prone for folding [20]. Conformational studies have been carried out, in solid state by crystal structure, in solution state by 2D-NOESY spectra and in gaseous state by DFT calculations.

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Scheme 1. Synthesis of flexible tripodal molecule.

2. Experimental section 2.1. General methods All reactions were performed according to the condition as under at ambient temperature, and reagents were used without further purification. 1H and 13C NMR spectra were recorded on JEOL AL300 and AL500 FT-NMR spectrometer (300 and 500 MHz). TMS was used as internal reference, and chemical shift values were expressed in d ppm units. 2.2. Synthesis Pyridazinone molecules were synthesized according to literature procedure [21]. 2.2.1. Synthesis of compounds (I and II) In a 100 ml round- bottom flask, aromatic and hetero-aromatic compounds (3.4 mmol) were dissolved in minimum amount of dry DMF and to that anhydrous potassium carbonate (3.4 mmol) was added and reaction mixture was stirred for 30 min. Subsequently, 1, 3 dibromopropane (20.4 mmol) was added to the reaction mixture and stirring was continued for next 15e20 h. Completions of the reaction was monitored with TLC (15% Ethyl Acetate and Hexane). After completion of reactions DMF was removed in vacuo and extracted with chloroform and washed with water. The organic layer was dried over sodium sulphate and solvent was evaporated through rotaevaporator after that we obtained crude product. The obtained crude products were purified by column chromatography with mixture of 15% Ethyl Acetate and Hexane as eluent. 2.2.1.1. 1-(3-bromopropoxy)-4-nitrobenzene (I). 1H NMR (500 MHz, CDCl3): d 2.34e2.39 (quint- 2H, eCH2), 3.60e3.62 (t, 2H, eCH2), 4.20e4.23 (t, 2H,eCH2), 6.95e6.99 (m, 2H, AreH), 8.19e8.22 (m, 2H, AreH); 13C NMR (200 MHz, CDCl3) d 29.47, 31.99, 66.18, 114.54,

126.03, 141.76, 163.75; FAB MS: m/258.98 (MþH); Elemental analysis for C9H10BrNO3: Calcd: C, 41.56; H, 3.88; Br, 30.72; N, 5.39; O, 18.45; Found: C, 41.45; H, 3.98; Br, 30.62; N, 5.49; O, 18.46. 2 . 2 .1. 2 . 2 - ( 3 - b r o m o p r o p y l ) - 3 - o x o - 5 , 6 - d i p h e n y l - 2 , 3 dihydropyridazine-4-carbonitrile (II). 1H NMR (500 MHz, CDCl3): d 2.47e2.53 (quint-, 2H, eCH2), 3.50e3.53 (t, 2H, eCH2), 4.46e4.49 (t, 2H, eCH2), 7.08e7.45 (m, 12H, AreH), 13C NMR (75 MHz, CDCl3) d 29.66, 31.13, 51.71, 113.25, 113.89, 120.33, 128.92, 129.01, 129.25, 130.62, 132.52, 134.18, 145.97, 151.14, 156.79; FAB MS: m/714.12 (MþH); Elemental analysis for C20H16BrN3O: Calcd: C, 60.93; H, 4.09; N, 10.66; O, 4.06; Br, 20.27; Found: C, 60.60; H, 4.33; N, 10.45; O, 4.25; Br, 20.37. 2.2.2. Synthesis of compounds (1 and 2) In a 100 ml round- bottom flask, thiocyanuric acid (845.46 mmol) was dissolved in minimum amount of dry DMF and to that anhydrous potassium carbonate (2.54 mmol) was added and reaction mixture was stirred for 30 min. Subsequently, compound I and II (2.54 mmol) was added to the reaction mixture and stirring was continued for next 10e12 h at 60  C. Completions of the reaction were monitored with TLC (25% Ethyl Acetate and Hexane). After completion of reactions DMF was removed in vacuo and extracted with chloroform and washed with water. The organic layer was dried over sodium sulphate and solvent was evaporated through rotaevaporator after that we obtained crude product. The obtained crude products were purified by column chromatography with mixture of 25% Ethyl Acetate and Hexane. 2.2.2.1. 2,4,6-tris((3-(4-nitrophenoxy)propyl)thio)-1,3,5-triazine (1). 1 H NMR (500 MHz, CDCl3): d 2.23e2.28 (quint-, 6H, eCH2), 3.28e3.31 (t, 6H, eCH2), 4.16e4.19 (t, 6H, eCH2), 6.93e6.95 (m, 6H, AreH), 8.17e8.20 (m, 6H, AreH). 13C NMR (125 MHz, CDCl3) d 26.85, 28.75, 66.88, 114.49, 126.03, 141.72, 163.72, 179.39; FAB MS: m/ 393.04 (MþH); Elemental analysis for C30H30N6O9S3: Calcd: C,

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50.41; H, 4.23; N, 11.76; O, 20.15; S, 13.46 Found: C, 50.32; H, 4.46; N, 11.65; O, 20.26; S, 13.31.

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3. Results and discussion 3.1. X-ray crystallography studies

0

00

2.2.2.2. 2,2 ,2 -(((1,3,5-triazine-2,4,6-triyl)tris(sulfanediyl))tris(propane-3,1-diyl))tris(3-oxo-5,6-diphenyl-2,3-dihydropyridazine-4carbonitrile) (2). 1H NMR (500 MHz, CDCl3): d 2.30e2.36 (quint-, 6H, eCH2), 3.18e3.21 (t, 6H, eCH2), 4.41e4.44 (t, 6H, eCH2), 7.06e7.42 (m, 20H, AreH). 13C NMR (75 MHz, CDCl3) d 27.44, 27.96, 51.68, 113.30, 113.76, 128.19, 128.32, 128.77, 128.94, 129.08, 129.19, 130.45, 132.48, 134.14, 145.83, 150.96, 156.68, 179.20; FAB MS: m/ 1117.32 (MþH); Elemental analysis for C63H48N12O3S3: Calcd: C, 67.72; H, 4.33; N, 15.04; O, 4.30; S, 8.61; Found: C, 67.10; H, 4.49; N, 16.00; O, 4.10; S, 8.40. 2.3. X-ray crystallography Single-crystal X-ray data, space groups, unit cell dimensions, and intensity data for compounds 1 and 2 was collected with an Oxford Diffraction X-calibur CCD diffractometer using graphite monochromated Mo Ka radiation (l ¼ 0.71073 Å). The structures were determined by direct methods using SHELXS-97 and refined on F 2 by a full-matrix least-squares technique using SHELXL-97 [22]. Non-hydrogen atoms were refined anisotropically, and hydrogen atoms were geometrically fixed with thermal parameters equivalent to 1.2 times that of the atom to which they are bonded. Molecular diagrams (Figs. S1 and S2) for all compounds were prepared using ORTEP, and the packing diagrams were generated using Mercurry version 3.1 [23]. PLATON was used for the analysis of bond lengths, bond angles, and other geometrical parameters. A crystallographic detail of compounds 1 and 2 has been summarized in Table 1. 2.4. Computational study In order to investigate the conformational stability in gaseous state, single point and optimized energies have been calculated using the DFT-D method equipped in Gaussian 09 [24] through M06-2X/6-31G (d, p) level of theory.

Table 1 Crystallographic detail of compound 1 and 2. Identification code

1

2

Empirical formula Formula weight Crystal system Space group Cell length a (Å) b (Å) c (Å) Cell angle a (0) b (0) g (0) Cell volume, V (Å3) Dcalc (mg/m3) F(000) Measured reflections Indep reflns Theta range (deg) GOF on F2 Z m (mm) Rint R-factor (%) CCDC No.

C30H30N6O9S3 714.78 Triclinic P 1

C63H48N12O3S3,CHCl3 1236.72 Triclinic P 1

10.8180(5) 11.5000(5) 15.3940(7)

14.9873(11) 15.7901(11) 16.3198(11)

84.035(1) 74.457(1) 63.231(1) 1647.03(13) 1.441 744.0 19404 8255 2.0e28.4 0.786 2 0.288 0.019 5.18 1504887

114.143(7) 115.976(7) 94.014(6) 3018.6(5) 1.361 1280 24454 13790 3e29.2 1.03 2 0.313 0.031 9.55 1063142

In this section, we shall discuss the crystallographic details of compound 1 and 2 (Fig. 1), the intramolecular interactions that stabilized the folded conformation. Although molecular packing of all the compounds are stabilized by intermolecular CeH/N, CeH/S, CeH/p as well as CeH/O interactions [25,26] except for compounds 2 is also stabilized by p/p interactions (Table S1y), the molecular conformation is mainly controlled by intramolecular interactions. The molecular crystal revealed that compound 1 has shown folded conformation between two arms of terminal moieties and one arm free, showed T-shape p/p stacking while compound 2 has shown folded bowl shape conformations. Compound 1 crystallized in the triclinic crystal system with P-1 space group. The conformation of compounds 1 has stabilized by one Tshape p/p stacking formed between centroid of nitro phenyl ring with centroid of C20eC21 of another nitro phenyl ring. Further, conformation is also stabilized by two CeH$$$p and three CeH/N intramolecular interactions. Compound 2 crystallized in the triclinic crystal system with P-1 space group. The crystal structure revealed that compound 2 possesses folded bowl shaped conformations (Fig. 1). This bowl shaped conformation forming a cavity feature, come out from interplay of weak intramolecular forces such as four CeH/N, three CeH/S and three CeH/O interactions. The folded bowl shaped structure come out due to presence of terminal pyridazinone moieties that provide a heteroatom and p-electron rich environment to favour weak non covalent interaction as well as used of the thiocyanuric moiety also helped for this interaction. It means formation of bowl shaped occurred due to folding properties of pyridazinone moieties because recently our group developed a folded molecule based on pyridazinone molecule linked with polymethylene and diethyleamine linker [27,28]. Due to presence of folded conformation and encapsulation of neutral molecule, the crystal packing studies is important. Crystal packing of compound 2 revealed that it encapsulated chloroform molecule. The encapsulation of chloroform in compound 2, was due to intermolecular CeH/p. Cl/p and CeH/Cl interactions. The crystal packing revealed that two guest molecule was capped by two host molecules which were situated in a very specific manner inside the molecule. The packing also show that the tripodal host and guest molecules are formed C3 symmetry to better fit CHCl3 in its host cavity. The conformation of guest molecule encapsulated in host molecule was fitted like a staggered conformation. The staggered conformation in host-guest cavity was occurred due to the Cl/p interactions found between chlorine atom of chloroform with phenyl centroids of pyridazinone moieties. Further, crystal packing showed intermolecular p/p stacking interaction between two adjacent thiocyanuric ring of tripodal molecule. The distance between thiocyanuric rings with thiocyanuric ring is 3.480 Å. The intermolecular p/p interaction as well some as other non covalent interactions like CeH/p, CeH/N has provide the strongest possible overlapping of the thiocyanuric rings with a stable structure. This p/p interaction between the thiocyanuric rings was found to be extended in all directions during molecular assembly. Apart from p/p interaction between two thiocyanuric rings another intermolecular p/p interaction 4.075 Å exist between centroids of pyridazinone moieties. Furthermore, a careful examination of the crystal packing of the tripodal molecule had shown intermolecular p-stacking interactions 3.384(9) Å, found between phenyl ring of pyridazinone moetioes with adjacent phenyl ring of another pyridazinone moieties of neighbouring tripodal molecule. The packing of folded tripodal 2 was stabilized in such a manner by

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Fig. 1. Crystal structure of compound 1 and 2 showing folded conformation in solid state.

forming intermolecular staggered conformation (Fig. 2). The explanation for favoured staggered conformation was found in the crystal packing in solid state due to steric hindrance and intermolecular p/p stacking as well as many weak non covalent forces. 3.2. 2D-NOESY studies In order to study the folded conformations of compound 2 in the solution state, analyzed by the 2D-NOESY NMR spectrum. 2DNOESY has been the best tool for analysing conformation based on the 1He1H space interaction in solutions. Since-molecular rotations in solutions are very fast at room temperature, they may exist in several conformations, but the equilibrium would be greater toward stable conformation. The characteristic inter-residual NOEs interactions supported the folded conformations of compounds 1 and 2 due to interactions between the linker eCH2 protons with nitro-phenyl proton and with phenyl proton of pyridazinone moieties (Figs. 3 and 4). The NOE interactions of compound 1 has

shown that solid and solution state conformation is same while in compound 2 is doubt. However we can say that compound 2 has shown folded conformation either two arms interacted with each other or all three arms interacted continuous form like crystal structure. The presence of NOEs peaks were a direct evidence that interacting protons were below 5 Å in space [29]. The dipolar couplings for compound 1 are indicated with red and blue arrows. The Selected NOEs supported folded conformation of compound 1 can be anticipated for interaction network of phenyl hydrogen of C4 with methylene hydrogen of carbon C1, C2 and C3 i.e. (C4H Vs C1H, C2H and C3H) as well as C5 phenyl hydrogen with C3 methylene hydrogen (C5H Vs C3H). The dipolar couplings are for compound 2 are indicated with red, green and blue arrows. The Selected NOEs supported folded conformation of compound 2 can be anticipated for interaction network of phenyl hydrogen of C5 and C6 with methylene hydrogen of C1, C2 and C3 i.e. (C3H Vs C5H, C6H), (C1H Vs C5H, C6H), and (C2H Vs C5H, C6H) respectively.

Fig. 2. (a) Packing of compound 2 (b) approximate C3 symmetry of both host-guest molecule (c) Staggered conformation of encapsulated host-guest molecule (d) Intermolecular staggered conformation of tripodal compound 2.

Fig. 3. The structure Selected 2D NOE spectra of compound 1 displaying noncovalent interactions (CDCl3, 500 MHz).

Fig. 4. The structure Selected 2D NOE spectra of compound 2 displaying noncovalent interactions (CDCl3, 500 MHz).

Fig. 5. Total electron density mapped with electrostatic potential surface for compound 1 and 2 (views along front, side and back for clarity of electron density).

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A. Gaurav et al. / Journal of Molecular Structure 1134 (2017) 781e788 Table 2 Single pointa and optimized energyb energy of compounds 1 and 2 at M062X/6-31g (d, p) level of theory. Name a

1sp 1ab 1b 1c 1d 1e 2spa 2ab 2b 2c 2d

kcal/mol 2108201.51 2108515.61 2108512.69 2108506.27 2108520.76 2108520.88 2826657.41 2827203.03 2827231.44 2827228.23 2827212.82

3.3. Computational studies The conformational stability in gaseous state such as MEPSs map, single point energy, and optimized structure energy of each molecule were calculated at the M06-2X/6-31G (d, p) level of theory [29(c), 30,31]. The M06-2X method is known to describe both exchange and dispersion corrections reasonably well and it correctly described both bond changes and weak interactions.

To investigate reactive sites for intramolecular interaction we calculated the total electron density mapped with electrostatic potential surface (Fig. 5) of compounds 1 and 2 [32] to support the intramolecular interaction in crystal structure. MEP maps have been used to qualitatively rationalize trends observed in hydrogen bond donors and acceptors through electrophilic and nucleophilic regions. The electrostatic potential increases in the order red < orange < yellow < green < blue. The colors code of the electrostatic potential maps was found to be in the range of 7.273e-2 a.u to 7.273e-2 a.u for compound 1 and -6.750e-2 a.u to 6.750e-2 a.u for compound 2 i.e. (deepest red) to (deepest blue). The red color indicates high electron-density sites i.e. nucleophilic region and blue color indicates low electro-density sites i.e. electrophilic region. According to the MEP surface of the compound (1), the high electron densities i.e. nucleophilic region are observed in the oxygen atom of nitro group and aromatic rings and low electron density i.e. electrophilic region are observed in all hydrogen atoms. Therefore, it can be indicative of intramolecular CeH/p interactions between H21 and H20 with aromatic ring to in their crystal structure. Similarly, in MEP surface of the compound 2, the high electron density located near aromatic ring of triazine ring, nitrogen atom of triazine ring, sulfur atom, carbonyl group as well as on cyano group and low electron density located on all hydrogen

Fig. 6. Optimization and other possible low energy conformers for compounds 1 and 2. Only flexible interactions are shown in the Fig. 6. Hydrogen atoms have been omitted for clarity.

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atom. Therefore, intramolecular CeH/N, CeH/S and CeH/O interactions observed in their crystal structure, occurred between propylene linker hydrogen atom with nitrogen atom of triazine ring, sulfur atom and oxygen atom of carbonyl group. The MEP surface of compound 2 has been shown along front view, side view and back view for clearness of electron density. Furthermore, conformational studies have also been investigating in gaseous state with several possible conformers of compounds 1 and 2. The conformations of compounds 1 and 2 have already been proposed in solid state. Optimized energy of these compounds provided further idea about conformational preferences. The single point energy and optimized energy for all compounds in all possible conformer of these were shown in Table 2. The compounds 1 optimized in five and compound 2 optimized in four possible conformations. The compound 1 show lowest energy in conformers (i.e. 1e ¼ 2108520.88 and 1d ¼ 2108520.76) in spite of crystal structure conformation. The energy of other three conformers of molecule 1 (i.e. 1a, 1b and 1c) were 5.27 kcal/mol, 8.19 and 14.61 kcal/mol higher than 1e, respectively. The energy of conformer 1e and 1d are comparatively same. The compound 2 show lowest energy in conformer (i.e. 2b ¼ 2827231.44) which is in open conformation in spite folded crystal conformation. The energy of other three conformers of molecule 2 (i.e. 2a, 2c and 2d) were 28.41 kcal/mol, 3.21 kcal/mol and 18.62 kcal/mol higher than 2b, respectively. Thus, it was expected that conformation of molecule 1 and 2 in solid state occurred due to geometrical constraint and lattice forces (Table S2). Fortunately the optimization showed the no persistence of solid state geometry in molecule 1 and 2, it revealed that these molecules felt to force of conformational deformation during crystallization. The conformer 1e was stabilized by one p/p, four CeH/N and one CeH/O interactions. The stability of conformer 2b was stabilized by one CeH/S, and two CeH/N and one CeH/O intramolecular interactions. The remaining conformers which was higher in energy than 1e and 2b were also stabilized due to extensive intramolecular CeH/p, CeH/S, CeH/O and CeH/N interactions (Fig. 6). 4. Conclusion We have synthesized new flexible tripodal molecules for their conformational studies. The crystal structure of compound 1 in solid state has shown folded conformation between two arms stacked with each other and one arm free while compound 2 showed the bowl shape folded conformation. The folded conformation of 1 and 2 was also supported by 2D-NOESY studies in solution state where intramolecular NOEs interactions observed between the linker-CH2 protons with phenyl proton. The optimization energy by computational studies in gaseous state revealed that solid state geometry for compounds 1 and 2 were not the most stable geometry. Acknowledgements We acknowledge DST India Grant SR/S1/381 OC-42/2012 for its financial support of this work. The Department of Chemistry, Faculty of Science of Banaras Hindu University is acknowledged for departmental facilities. A. Gaurav thanks to RGNF UGC, New Delhi, for SRF. Appendix A. Supplementary data Supplementary data related to this article can be found at http:// dx.doi.org/10.1016/j.molstruc.2017.01.031.

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