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Anion directed supramolecular architecture of benzimidazole-based receptor
Journal of Molecular Structure 1081 (2015) 128–135
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Anion directed supramolecular architecture of benzimidazole-based receptor Udai P. Singh ⇑, Radha Raman Maurya, Sujata Kashyap Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, India
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
Synthesis of five novel
LH44+4ClO44H2O, LH44+4Br4(CH3)2SO, 2LH33+3SiF6214H2O, LH44+4H2PO42H3PO4 and L2CH3 COOH were prepared by the reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2diamine (L) with different inorganic acids and organic acid structurally characterized. In each case the proton was transferred from inorganic acid to the nitrogen of benzimidazole ring. With the variation of anion, different structure was observed due to variation in number and type of interaction and orientation of cation and anion present in the asymmetric unit.
benzimidazole-based salts and cocrystal. These salts/co-crystal show photoluminescence properties in presence of different mineral acids. Crystal structures show different type of hydrogen-bonding.
HClO4
CH3COOH
HBr
H3PO4 HF
a r t i c l e
i n f o
Article history: Received 16 May 2014 Received in revised form 13 September 2014 Accepted 5 October 2014 Available online 12 October 2014 Keywords: Benzimidazole Inorganic acids X-ray structure Co-crystal Supramolecules
⇑ Corresponding author. E-mail address: [email protected] (U.P. Singh). http://dx.doi.org/10.1016/j.molstruc.2014.10.008 0022-2860/Ó 2014 Elsevier B.V. All rights reserved.
a b s t r a c t The reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) with different 4+ inorganic as well as organic acid afford salts viz., LH4+ 4 4ClO4 4H2O (1), LH4 4Br 4(CH3)2SO (2), 2 4+ 2LH3+ 3 3SiF6 14H2O (3), LH4 4H2PO4 2H3PO4 (4) and L2CH3COOH (5) with different structures. The X-ray crystallographic studies revealed that these compounds are all ionic in nature due to proton transfer except 5 and are stabilized in the solid state by networks of hydrogen bonds between their respective components as well as solvent molecules. It also demonstrates that different types of hydrogen bond between protonated ligand and the anions are responsible for the extensive supramolecular frame work. The three dimensional packing is mainly guided by well-balanced primary N–H O, O–H N, O–H O hydrogen bonds and secondary C–H O interactions between benzimidazole and acids. Moreover, the hydrogen bonds, p p and CH p stacking interactions appear to be effective in stabilizing the crystal structures. The colorimetric test showed color change upon the addition of acids in solution of the ligand. The photo-physical experiments suggest that the ligand shows fluorescence properties in the presence of acids. Ó 2014 Elsevier B.V. All rights reserved.
U.P. Singh et al. / Journal of Molecular Structure 1081 (2015) 128–135
Introduction Anion-selected sensing and recognition is of great interest because anions are known to play numerous fundamental roles not only in the supramolecular chemistry but also in environmental, ion exchange, anion separation in nuclear waste, catalysis, water purification and in biological field [1–5]. A variety of new synthetic molecules capable of anion-recognition have been synthesized that offer hydrogen bonding includes, amides [6–8], protonated amine [9], guanidinium [10], indole [11–13], pyrroles [14,15], urea/thiourea [16,17] and benzimidazole [18]. Benzimidazole a hetero-aryl compound is an essential pharmacophore in the drug discovery and is associated with a wide range of biological activities [19–22]. The crystal structures of numerous benzimidazole based ligands, illustrates their potential as excellent hydrogen bond donors for the anions. We are now exploring the anion directed supramolecular architecture of benzimidazole-salts with different inorganic acids and organic acid (acetic acid) to scrutinize the effect of counter anion on structural framework. The present paper reports the synthesis, crystal structure, colorimetric test and photo-physical properties of the benzimidazole based salts.
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evaporation of solvent at room temperature. Anal. Calcd. (%) for C34H36Cl4N10O20 (1046.33) C, 40.47; H, 3.26; N, 12.81. Found: C, 40.25; H, 3.35; N, 12.65. IR (KBr, cm1) 3237, 2927, 1626, 1521, 1453, 1389, 1285, 1146, 951, 753, 625, 466. Synthesis of LH4+ 4 4Br 4(CH3)2SO (2)
To the 5 mL methanol/DMSO solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of HBr was added and the resulting solution was stirred for 4 h. Yield: 73%. Anal. Calcd. (%) for C42H60Br4N10O4S4 (1216.88) C, 41.41; H, 4.93; N, 11.50; S, 10.51. Found: C, 41.21; H, 4.81; N, 11.31; S, 10.36. IR (KBr, cm1) 3417, 3039, 2868, 2642, 1622, 1452, 1386, 1222, 1097, 893. 2 Synthesis of 2LH3+ 3 3SiF6 14H2O (3)
Salt 3 was prepared by same procedure as outlined above for 1 using HF. Yield: 69%. Anal. Calcd. (%) for C68H70F18N20O14Si3 (1817.71) C, 44.90; H, 3.85; N, 15.40. Found: C, 44.65; H, 3.73; N, 15.25. IR (KBr, cm1) 2857, 1625, 1570, 1456, 1388, 1222, 1120, 1023, 955, 783, 618. Synthesis of LH4+ 4 4H2PO4 2H3PO4 (4)
Experimental General All manipulations were performed in air using commercial grade solvents pre-dried by the literature method [23]. N,N,N0 ,N0 -tetrakis(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) was prepared by the procedure reported earlier [24]. Perchloric acid (HClO4, 70%) was purchased from S.D. Fine-Chem limited. Hydrobromic acid (HBr, 40%), hydrofluoric acid (HF, 40%), orthophosphoric acid (H3PO4, 85%), and acetic acid (CH3COOH, 99.8%) were purchased from RENKEM, India. Crystallized salts were carefully dried under vacuum for several hours prior to elemental analysis on Elementar Vario EL III analyzer. IR spectra were obtained on a Thermo Nikolet Nexus FT-IR spectrometer in KBr pellet. Powder XRD data were collected using Bruker Advance D8 XRD diffractometer. The UV–Visible absorption and fluorescence spectra were recorded on Perkin Elmer, Lambda 35, UV–Visible spectrophotometer in 200–800 nm range and RF-5301 PC spectrofluorophotometer Shimadzu respectively.
Salt 4 was prepared by same procedure as outlined above for 1 using H3PO4. Yield: 67%. Anal. Calcd. (%) for C34H49N10O25.88P6 (1199.33) C, 34.03; H, 4.17; N, 11.67. Found: C, 34.21; H, 4.03; N, 11.46. IR (KBr, cm1) 2927, 1625, 1570, 1460, 1405, 1040, 746, 620, 570, 462. Synthesis of L2CH3COOH (5) To the 5 mL methanol/water solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of CH3COOH (v/v%, 5:1) was added and the resulting solution was stirred for 6 h. The colorless crystals of cocrystal 5 in 73% yield, suitable for X-ray data collection were obtained by slow evaporation of solvent at room temperature. Anal. Calcd. (%) for C38H40N10O3.70 (696.06) C, 65.52; H, 6.02; N, 20.11. Found: C, 65.39; H, 6.18; N, 20.25. IR (KBr, cm1) 3173, 2913, 1942, 1677, 1541, 1442, 1268, 1117 1043, 744, 442. Results and discussion
X-ray structure determination The X-ray data collection were performed on a Bruker Kappa Apex four circle-CCD diffractometer using graphite monochromated Mo Ka radiation (k = 0.71070 Å) at 100 K. In the reduction of data Lorentz and polarization corrections, empirical absorption corrections were applied [25]. Crystal structures were solved by Direct methods. Structure solution, refinement and data output were carried out with the SHELXTL program [26,27]. Non-hydrogen atoms were refined anisotropically. Hydrogen atoms were placed in geometrically calculated positions by using a riding model. Images and hydrogen bonding interactions were created in the crystal lattice with DIAMOND and MERCURY software [28,29].
The reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol2ylmethyl)ethane-1,2-diamine (L) with different acids i.e., HClO4, HBr, HF, H3PO4 and CH3COOH in methanol/water/DMSO solution resulted in salts 1–4 and co-crystal 5 (Scheme 1). The crystals suitable for X-ray data collection were obtained by slow evaporation of resultant reaction mixture. The different formulations of these salts and co-crystal were confirmed by elemental analysis, FT-IR, powder XRD and crystallographic structure analysis. The crystallographic data and structure refinement parameters are given in Table 1 and different non-covalent interactions are summarized in Table 2.
Experimental
Salt 1 crystallizes in the triclinic crystal system with P1 space group. The asymmetric unit contains one protonated ligand and four perchlorate anions along with four water molecules (Fig. 1) bonded together through a variety of hydrogen bonds (Fig. S1). Out of four perchlorate anions and water molecule, two are present on the symmetry axis. The proton has been transferred from the acid to the nitrogen bearing lone pair of electron resulting in the formation of salt. Since here four nitrogens are available, therefore
Synthesis of LH4+ 4 4ClO4 H2O (1)
To the 5 mL methanol/water solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of HClO4 (v/v%, 5:1) was added and the resulting solution was stirred for 6 h. The colorless crystals of salt 1 in 71% yield, suitable for X-ray data collection were obtained by slow
Salt 1
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Salt 2 Salt 2 crystallizes in the monoclinic crystal system with P21/c space group. The asymmetric unit consists of a protonated ligand and four molecule of bromide anions and four dimethyl sulfoxide molecules (Fig. 3). The four protonated ligand interacted with each other through C–H p interaction. At one end the p electron density of phenyl ring present on the ligand interact with the phenylic CH of the adjacent ligand molecule (C14–H14 p, 3.986(2) Å), however at the other end the p electron density of other phenyl ring present on the same ligand interact with the hydrogen of dimethyl sulfoxide molecule (C21–H21 p, 3.468(5) Å). The oxygen of the same DMSO molecule interact via., N–H O and C–H O interaction (N1–H3A O2, 1.895(3); C17–H17B O2, 2.429(5) Å) with the neighboring ligand molecule. All the interaction results in the formation of a cavity and is occupied by four molecules of bromide ion and four molecules of dimethyl sulfoxide through various non-covalent interactions (Fig. 4). The three dimensional host–guest packing of the salt 2 is depicted in Fig. 5. Scheme 1.
Salt 3 four protons have been transferred from four acids, hence the asymmetric unit consist of a protonated ligand with four positive charges and four perchlorate anions. We are not able to bind the hydrogen on the oxygen of the water molecule present in the unit cell. In the unit cell, deprotonated perchloric acid and protonated ligand form a cationic–anionic pair where all the imidazolium N– H as well as protonated N–H of ligand are involved in the hydrogen bonding with the oxygen of anion at their respective site. The two wings of the benzimidazole ring of the ligand are bridged by water and perchlorate molecule through N–H O and C–H O interactions on both side (N2–H2B O9, 1.968(5); N4–H4B O8, 1.972(3); C5–H5 O1, 2.680(3); C12–H12 O4, 2.638(3); C8–H8A O3, 2.674(5); C8–H8B O3, 3.476(5 Å) (Fig. S2). The geometry around the chlorine in perchlorate is somewhat distorted tetrahedron with an average bond angle of 111.8 and 107.2° (O4–Cl1–O3, 111.8(26); O2–Cl1–O3, 107.2(49); O4–Cl1–O2, 110.17(22); O1–Cl1–O2, 108.3(49); O5–Cl2–O6, 105.1(17); O5– Cl2–O7, 112.9(17); O5–Cl2–O8, 107.5(27); O6–Cl2–O8, 107.7(27); O7–Cl2–O8, 108.4(17)°). The presence of different non-covalent interactions resulted in a continuous chain of perchlorate and water molecules that runs parallel on either side of the chain formed by the protonated ligands (Fig. 2).
Salt 3 crystallizes in the triclinic crystal system with P1 space group and its molecular structure is shown in Fig. 6. The asymmetric unit consists of two protonated ligands, six hexafluorosilicate anion and fourteen water molecules. The addition of HF to the aqueous-methanolic solution of ligand leads to the formation of SiF2 6 due to the corrosion effect of HF to the glass-vial [30]. We are unable to bind hydrogen on the oxygen of the water molecules present in the unit cell. In salt 3, unlike to the above cases only three protons has been transferred instead of four to three benzimidazole nitrogen bearing lone pair of electron. The geometry around the silicon in hexafluorosilicate ion is distorted octahedron with an average bond angle of 119.9° (F1–Si1–F2, 90.48(47); F1–Si1–F3, 90.40(47); F1–Si1–F4, 174.9(47): F1–Si1–F5, 85.00(60); F1–Si1–F6, 90.14(61); F2–Si1–F3, 102.10(61); F2–Si1– F4, 89.73(23); F2–Si1–F5, 170.40(62); F2–Si1–F6, 85.73(23); F3–Si1–F4, 94.48(12); F3–Si1–F5, 86.29(25); F3–Si1–F6, 172.00; F4–Si1–F5, 94.04(21); F4–Si1–F6, 84.85(45); F5–Si1–F6, 86.29(51)°). Unlike to the salts 1 and 2 the molecular components of salt 3 forms a pseudo cavity for trapping SiF2 6 ions. The distance of C–H p interaction (p electron density of phenyl ring present on the ligand interact with the phenylic CH of the adjacent ligand
Table 1 Crystal data and structure refinement parameters of salts and co-crystal 1–5.
Emprical formula Formula weight Crystal system Space group a (Å) b (Å) c (Å) a (°) b (°) c (°) V (Å3) Z Dcalc (g cm3) l (mm3) Crystal size (mm3) h range (°) Data/Restraints/Parameters R1; wR2 [I > 2r(I)] R1; wR2 (all data)
1
2
3
4
5
C34H36Cl4N10O20 1046.53 Triclinic P1 9.327(3) 11.496(3) 12.090(3) 93.384(16) 90.600(16) 112.474(14) 1195.0(6) 1 1.454 0.332 0.30 0.27 0.21 2.71–31.49 3853/0/307 0.0893; 0.2450 0.1080; 0.2649
C42H60Br4N10O4S4 1216.88 Monoclinic P21/c 9.674(2) 24.767(5) 10.982(2) 90.00 90.232(10) 90.00 2631.2(9) 2 1.536 3.267 0.23 0.20 0.17 2.18–29.73 7003/0/293 0.0313; 0.0969 0.0485; 0.1138
C68H70F18N20O14Si3 1817.71 Triclinic P1 8.9116(3) 14.9883(4) 16.2263(4) 107.941(2) 94.4870(10) 97.4300(10) 2028.56(10) 1 1.488 0.174 0.26 0.18x 0.14 1.92–28.58 7148/0/556 0.0788; 0.2126 0.1109; 0.2436
C34H49N10O25.98P6 1199.33 Monoclinic P21/n 14.2830(4) 16.7711(4) 21.1030(5) 90.00 96.502(2) 90.00 5022.5(2) 4 1.586 0.312 0.31 0.27 0.23 1.39–26.73 12,230/0/699 0.0688; 0.2075 0.0986; 0.2242
C38H40N10O3.70 696.06 Triclinic P1 9.4045(3) 10.1006(4) 10.6257(4) 101.059(2) 100.153(2) 109.647(2) 900.72(6) 1 1.283 0.086 0.31 0.25 0.21 2.87–31.59 3670/0/250 0.0656; 0.1652 0.1394; 0.2066
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U.P. Singh et al. / Journal of Molecular Structure 1081 (2015) 128–135 Table 2 Non-covalent interactions for salts and co-crystal 1–5 (Å and °).
Table 2 (continued) S. No.
S. No.
D–H A
d(D–H)
d(H–A)
d(D–A)
(DHA)
1.
Salt 1 N1–H1 O10 N2–H2B O9 N3–H3B O2 N3–H3B O9 C2–H2 O6 C2–H2 O8 C2–H2 O10 C5–H5 O9 C8–H8B O3 C8–H8B O10 C8–H8A O2 C8–H8A O3 C12–H12 O1 C12–H12 O2 C12–H12 O4 C12–H12 O9 C2–H2 Cl2 C8–H8B Cl1
0.860(8) 0.860(8) 0.861(8) 0.861(8) 0.929(12) 0.929(12) 0.929(12) 0.931(10) 0.970(8) 0.970(8) 0.970(11) 0.970(11) 0.930(9) 0.930(9) 0.930(9) 0.930(9) 0.929(12) 0.970(8)
1.902(15) 1.968(16) 2.857(26) 1.972(16) 2.770(4) 3.062(28) 3.549(25) 3.440(9) 2.674(9) 3.542(20) 2.625(12) 3.478(18) 3.194(30) 3.136(32) 3.607(29) 3.680(43) 3.382(25) 3.415(15)
2.758(20) 2.806(1) 3.081(23) 2.832(7) 3.634(33) 3.952(35) 3.989(25) 3.924(10) 3.498(16) 4.081(30) 3.242(21) 3.498(16) 3.599(24) 3.303(35) 4.279(30) 4.122(48) 4.310(34) 3.986(9)
173.50 164.47 96.85 177.49 155.15 161.12 111.77 114.97 142.95 117.33 121.74 83.17 108.48 92.09 131.34 112.19 176.12 119.64
Salt 2 N3–H3A Br2 N4–H4A Br1 C8–H8A Br1 C8–H8B Br1 C8–H8B Br2 C9–H9B Br2 C15–H15 Br1 C17–H17B Br2 C18–H18B Br1 C19–H19B Br1 C20–H20B Br2 C21–H21B Br2
0.860(5) 0.859(4) 0.970(3) 0.971(3) 0.971(3) 0.969(5) 0.929(5) 0.970(3) 0.960(3) 0.960(3) 0.960(4) 0.960(2)
2.380(11) 2.376(11) 3.264(9) 3.308(8) 3.489(11) 3.245(10) 3.540(1) 2.922(2) 2.839(6) 3.257(16) 3.110(1) 2.842(7)
3.233(16) 3.214(14) 3.759(12) 3.759(12) 4.024(15) 4.055(16) 4.115(5) 3.851(12) 3.750(5) 4.070(19) 3.743(7) 3.959(3)
171.56 164.71 113.57 110.45 117.07 142.24 122.58 160.53 158.79 143.52 148.20 156.51
Salt 3 N1–H1 F9 N3–H3B F8 N3–H3B F9 N7–H7 O1 N4–H4A O3 N4–H4A O7 N6–H6 O4 N2–H2B F4 N2–H2B F2 C17–H17A O5 C12–H12 F8 C12–H12 F7 C15–H15 F5 C14–H14 F4 C31–H31 O2 C33–H33A N3 C23–H23 F6 C9–H9A F1 C25–H25A N3 C17–H17A F9
0.860(3) 0.860(2) 0.860(2) 0.860(2) 0.860(3) 0.860(3) 0.860(3) 0.860(3) 0.860(4) 0.970(4) 0.930(3) 0.930(3) 0.930(4) 0.930(5) 0.930(4) 0.970(4) 0.930(5) 0.970(5) 0.970(4) 0.970(4)
1.972(3) 2.754(2) 1.962(2) 1.875(2) 2.100(5) 2.454(7) 1.944(5) 2.324(6) 1.962(7) 2.915(5) 2.718(2) 2.593(2) 2.663(4) 2.778(5) 2.399(3) 2.763(3) 2.554(6) 2.823(5) 2.730(2) 2.748(2)
2.797(4) 3.287(4) 2.822(3) 2.710(3) 2.875(6) 3.118(8) 2.795(7) 3.076(7) 3.602(7) 3.841(6) 3.318(4) 3.415(6) 3.309(6) 3.530(7) 3.314(3) 3.314(5) 3.414(8) 3.768(6) 3.646(4) 3.622(4)
160.42 121.62 177.78 163.30 154.14 134.45 170.07 146.27 131.36 160.07 123.11 147.70 151.48 138.66 167.80 116.74 153.92 164.97 157.70 150.17
Salt 4 O2–H2C O13 O3–H3B O20 O24–H22 O25 C2–H2 O13 C3–H3 O9 O28–H28 O17 O30–H30 O12 N5–H5A O4 N7–H7 O4 O1–H1A O6 N1–H1 O6 N4–H4A O6 O8–H8D O9 O7–H7A O26 O12–H12A O4 O9–H9 O21 O13–H13A O22 C3–H3 O21 O17–H17 O22
0.820(3) 0.820(3) 0.820(3) 0.930(4) 0.930(4) 0.930(4) 0.930(4) 0.860(3) 0.860(3) 0.820(3) 0.860(3) 0.860(3) 0.820(4) 0.820(7) 0.820(3) 0.820(3) 0.820(2) 0.930(4) 0.820(3)
1.876(2) 1.719(3) 1.902(3) 2.898(2) 2.995(3) 2.411(3) 2.742(3) 2.006(2) 2.908(3) 1.807(6) 2.345(2) 1.945(5) 1.883(3) 2.992(5) 1.905(2) 1.718(3) 1.689(3) 2.732(3) 1.811(3)
2.648(3) 2.481(4) 2.667(4) 3.822(5) 3.816(5) 3.288(5) 3.512(5) 2.849(4) 3.337(4) 2.564(7) 3.199(3) 2.783(6) 2.622(5) 3.488(7) 2.689(4) 2.511(4) 2.489(4) 3.621(5) 2.572(4)
156.43 153.73 154.82 172.57 148.09 157.22 140.73 166.48 168.97 152.72 171.99 164.30 149.30 121.19 159.54 162.07 164.38 160.11 153.66
2.
3.
4.
5.
D–H A
d(D–H)
d(H–A)
d(D–A)
(DHA)
C23–H23A O11 N2–H2B O14 C33–H33A O16 C8–H8B O16 N8–H8 O20 C8–H8A O21 C22–H22 O10 C23–H23 O23 C14–H14 O8
0.820(3) 0.860(3) 0.970(3) 0.970(4) 0.860(3) 0.970(4) 0.930(4) 0.930(4) 0.930(5)
1.720(2) 1.849(2) 2.727(3) 2.688(3) 1.851(3) 2.871(3) 2.951(3) 2.921(3) 2.961(5)
2.519(4) 2.700(4) 3.515(4) 3.455(5) 2.709(3) 3.820(5) 3.821(5) 3.807(5) 3.856(7)
164.34 170.86 138.74 136.32 174.80 166.17 156.30 159.87 164.46
Co-crystal 5 O2–H15A N3 N1–H13 O1 N4–H4B N2 C17–H17 N3 C15–H15 O1 C17–H17B O2 C9–H9A N1
0.887(8) 0.860(3) 0.860(3) 0.970(4) 0.930(4) 0.970(3) 0.970(3)
1.806(7) 1.929(5) 2.015(3) 2.866(2) 2.905(3) 2.615(3) 2.923(3)
2.636(8) 2.777(5) 2.851(4) 3.341(4) 3.574(5) 3.499(4) 3.392(4)
154.89 168.46 163.87 111.17 129.96 151.65 110.91
Fig. 1. Molecular structure of salt 1. Color code: C, grey; N, blue; H, orange; O red; Cl, green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
molecule) in salt 3 is found to be in the range of 4.4–4.7 Å (C13–H13 p, 4.764(3); C28–H28 p, 4.421(5) Å), which seems to be too large for the formation of a true cavity. Thus the pseudo cavity formed by ligand entrap single molecule of SiF2 6 through various N–H F and C–H F interactions (N1–H1 F9, 1.972(3); C2–H2 F8, 2.482(3); C17–H17 F9, 2.745(3); C25–H25A F7, 2.693(3); C25–H25A F9, 2.728(3) Å) (Fig. 7). The hexaflourosilicate anion and the water molecule form a continuous chain through F–O interaction (Fig. S3). The cationic host assembly of protonated ligand in salt 3 forms entirely different three dimensional packing as compared to salt 1 and 2 because of different orientation of the protonated ligand and SiF2 ions, having both 6 pseudo cavity as well as alternate channels (Fig. 8). Salt 4 Salt 4 crystallizes in the monoclinic crystal system with the space group P21/n. The asymmetric unit consists of a protonated ligand, three molecules of monohydrogen phosphate anion, three molecules of neutral phosphoric acid and two molecules of crystalline water (Fig. 9). In the unit cell, oxygens of monohydrogen phosphate, neutral phosphoric acids and water molecule are extensively involved in the hydrogen bonding with the protonated
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Fig. 2. Alternate channels of host framework formed by the self-assembly of the cationic protonated Ligand with guest perchlorate anions and water molecules in salt 1.
dihydrogen phosphate and vice versa) as reported in other cases (Fig. S5-A) [31,32]. Along with dimerization, head-to-tail hydrogen bonding also exists in the same system (O18–H18 O10, 1.707(3) Å) (Fig. S5-B). The oxygen of water molecules bridge the two adjacent phosphate molecule to stabilize the three dimensional herring bone type of packing (Fig. 10). Co-crystal 5
Fig. 3. Molecular structure of salt 2. Color code: C, grey; N, blue; H, orange; O red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
ligand (Fig. S4). The geometry around the phosphorus in phosphate anion is almost regular tetrahedron. The two phosphoric acid selfdimerized in R22(8) motif through O–HO interaction (O9– H9 O21, 1.718(3); O23–H23A O11, 1.719(2) Å, i.e., OH group of one dihydrogen phosphate interact with the oxygen of the other
The co-crystal 5 crystallizes in the triclinic crystal system with P-1 space group and its molecular structure is shown in Fig. 11. The asymmetric unit consists of a neutral ligand (LH) and two acetic acid molecules. In co-crystal 5, unlike to the above cases, no proton has been transferred from the acid to the ligand as a result both the neutral species crystallized simultaneously. The carboxylate oxygens are extensively involved in various C–H O interactions, the phenyl CH forms C–H O interaction with the carboxylate oxygen of acetic acid (C17–H17B 02; 2.615(5) Å) (Fig. S6). Both the imidazolyl NH as well as the protonated NH are involved in N–H O hydrogen bonding with the carboxylate oxygen as well oxygen of water molecules. The four neutral ligand interacts with each other through the p p and C–H p interaction (C3–H3 p, 3.411(4); C4–H4 p, 3.691(7); C14–H14 p, 3.807(49); p p, 3.411(4); p p, 3.668(5) Å, the p electron density of phenyl ring present on ligand and adjacent phenylic CH) results in the formation of a cavity. The methylene C–H is also involved in C–H p interaction (C8–H8 p, 3.040(2) Å) (Fig. S7). This cavity is occupied by two acetic acid molecule through various non-covalent interactions. The three dimensional packing of co-crystal 5 in shown in Fig. 12.
Fig. 4. Different non-covalent interactions in salt 2. Proonated ligand, blue; DMSO, green; water, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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Fig. 5. Host–guest assembly in salt 2. Color code: Proonated ligand, blue; DMSO, green; water, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 8. Host–guest assembly having both pseudo cavity as well as alternate channels.
Fig. 6. Molecular Structure of salt 3. Color code: C, grey; N, blue; F, green; Si Cyan. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 7. Pseudo cavity formed by the protonated ligand for trapping SiF2 6 ions in salt 3. Color code: C, grey; N, blue; H, orange; F, green; Si Pink. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 9. Molecular Structure of salt 4. Color code: C, grey; N, blue; H, orange; P, pink. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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Fig. 10. Three dimensional herring bone type of packing in Salt 4.
Fig. 11. Molecular Structure of co-crystal 5. Color code: C, grey; N, blue; H, orange; O, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Anion selectivity N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) has a strong tendency to forms salts and co-crystal with different anions, therefore an attempt has been made to check the selectivity of this ligand by performing a particular experiment under the same reaction condition in which salts and co-crystal have been prepared. Thus an aqueous methanolic solution containing one equivalent of the ligand was added to a solution containing one equivalent (1.0 mmol) of each HClO4, HBr, HF, H3PO4 and CH3COOH. Suitable crystals were obtained by slow evaporation and subjected to characterization by single crystal X-ray diffraction method. The single crystal X-ray data clearly indicates a = 9.29(3); b = 11.49(3); c = 12.15(4); a = 86.10; b = 89.93; c = 66.99 deg; V = 1173.0(6) Å3 that in the mixture of the acids, the ligand was selective for perchloric acid because of the extensive electrostatic as well as non-covalent interactions [18].
Fig. 12. Three dimensional packing of co-crystal 5. Guest acetic acid molecules are entrapped in the cage formed by the host cationic ligand assembly. Color code: Cage; purple; acetic acid, green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
achieved by the naked eye. One of the most attractive approaches in this field involves the construction of colorimetric chemo-sensors since naked eye detection can offer qualitative and quantitative information [33]. Most of the known colorimetric chemosensors are based on the synthetic receptors generally containing some combination of anion binding unit and signal-reporting group (chromophore), either covalently attached or inter molecularly linked [34]. In the naked eye colorimetric experiment, the ligand undergoes a dramatic color change. The methanolic solution of the ligand is orange–red in color but after addition of the acids the color changes to light blue to dark blue (Fig. 13).
Colorimetric test Powder XRD The signal generated in terms of color change due to the presence of various anions has received a great consideration, because the fluorophore needs no equipment and the detection can be
In solid-state and materials sciences, the application of single-crystal X-ray diffraction is also subject to the limitation of
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Appendix A. Supplementary material CCDC number (981383–981387) contains the supplementary crystallographic data for this paper. These data can be obtained free of charge at www.ccdc.cam.ac.uk/conts/retrieving.html [or from the Cambridge Crystallographic Data Center (CCDC), 12 Union Road, Cambridge CB2 1EZ, UK: fax:+44 (0)1223 336033; email: deposit@ ccdc.cam.ac.uk]. Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/ 10.1016/j.molstruc.2014.10.008. References A
B
C
D
E
F
Fig. 13. Color change after the addition of different acids in the methanolic solution of ligand (A) Ligand (B) Ligand + 0.5 mL HClO4 (C) Ligand + 0.5 mL HBr (D) Ligand + 0.5 mL HF (E) Ligand + 0.5 mL H3PO4 (F) Ligand + 0.5 mL CH3COOH. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
obtaining a suitable structural homogeneity of bulk samples, therefore they were also examined through a comparison of experimental and simulated powder X-ray diffraction (XRD) patterns. The experimental patterns correlate favorably with the simulated ones generated from single-crystal X-ray diffraction (Fig. S8). Fluorescence studies The change in the photo physical properties of the ligand and their respective salts were observed in the UV–Visible absorption and fluorescence spectra. The UV–Visible absorption spectra of ligand show two peaks at 230 and 270 nm. At 270 nm, the trend for the neutral ligand as well as for the co-crystal 5 were found to be same, however drastic change was observed in case of salts 1–4 (Fig. S9). The fluorescence spectra shows similar trend as observed in case of UV–Visible spectra (Fig. S10). Conclusion In this work we have reported the anion directed supramolecular frame work which involves a change in the number and type of interaction and the orientation of the molecules in the three dimensional space. The benzimidazole molecules hold different anions and neutral acid molecule by different type of interactions. Their angle of orientation in the three dimensional space is very important for deciding the formation of cavity or pseudo cavity or alternate channel or herring bone network. In conclusion, we have demonstrated that the variation of anion plays a significant role in controlling the structure of salts and the present ligand is superiorly selective for perchlorate anion. Acknowledgment The authors gratefully acknowledge UGC and CSIR, New Delhi, India for financial assistance.
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Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc
Anion directed supramolecular architecture of benzimidazole-based receptor Udai P. Singh ⇑, Radha Raman Maurya, Sujata Kashyap Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, India
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
Synthesis of five novel
LH44+4ClO44H2O, LH44+4Br4(CH3)2SO, 2LH33+3SiF6214H2O, LH44+4H2PO42H3PO4 and L2CH3 COOH were prepared by the reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2diamine (L) with different inorganic acids and organic acid structurally characterized. In each case the proton was transferred from inorganic acid to the nitrogen of benzimidazole ring. With the variation of anion, different structure was observed due to variation in number and type of interaction and orientation of cation and anion present in the asymmetric unit.
benzimidazole-based salts and cocrystal. These salts/co-crystal show photoluminescence properties in presence of different mineral acids. Crystal structures show different type of hydrogen-bonding.
HClO4
CH3COOH
HBr
H3PO4 HF
a r t i c l e
i n f o
Article history: Received 16 May 2014 Received in revised form 13 September 2014 Accepted 5 October 2014 Available online 12 October 2014 Keywords: Benzimidazole Inorganic acids X-ray structure Co-crystal Supramolecules
⇑ Corresponding author. E-mail address: [email protected] (U.P. Singh). http://dx.doi.org/10.1016/j.molstruc.2014.10.008 0022-2860/Ó 2014 Elsevier B.V. All rights reserved.
a b s t r a c t The reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) with different 4+ inorganic as well as organic acid afford salts viz., LH4+ 4 4ClO4 4H2O (1), LH4 4Br 4(CH3)2SO (2), 2 4+ 2LH3+ 3 3SiF6 14H2O (3), LH4 4H2PO4 2H3PO4 (4) and L2CH3COOH (5) with different structures. The X-ray crystallographic studies revealed that these compounds are all ionic in nature due to proton transfer except 5 and are stabilized in the solid state by networks of hydrogen bonds between their respective components as well as solvent molecules. It also demonstrates that different types of hydrogen bond between protonated ligand and the anions are responsible for the extensive supramolecular frame work. The three dimensional packing is mainly guided by well-balanced primary N–H O, O–H N, O–H O hydrogen bonds and secondary C–H O interactions between benzimidazole and acids. Moreover, the hydrogen bonds, p p and CH p stacking interactions appear to be effective in stabilizing the crystal structures. The colorimetric test showed color change upon the addition of acids in solution of the ligand. The photo-physical experiments suggest that the ligand shows fluorescence properties in the presence of acids. Ó 2014 Elsevier B.V. All rights reserved.
U.P. Singh et al. / Journal of Molecular Structure 1081 (2015) 128–135
Introduction Anion-selected sensing and recognition is of great interest because anions are known to play numerous fundamental roles not only in the supramolecular chemistry but also in environmental, ion exchange, anion separation in nuclear waste, catalysis, water purification and in biological field [1–5]. A variety of new synthetic molecules capable of anion-recognition have been synthesized that offer hydrogen bonding includes, amides [6–8], protonated amine [9], guanidinium [10], indole [11–13], pyrroles [14,15], urea/thiourea [16,17] and benzimidazole [18]. Benzimidazole a hetero-aryl compound is an essential pharmacophore in the drug discovery and is associated with a wide range of biological activities [19–22]. The crystal structures of numerous benzimidazole based ligands, illustrates their potential as excellent hydrogen bond donors for the anions. We are now exploring the anion directed supramolecular architecture of benzimidazole-salts with different inorganic acids and organic acid (acetic acid) to scrutinize the effect of counter anion on structural framework. The present paper reports the synthesis, crystal structure, colorimetric test and photo-physical properties of the benzimidazole based salts.
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evaporation of solvent at room temperature. Anal. Calcd. (%) for C34H36Cl4N10O20 (1046.33) C, 40.47; H, 3.26; N, 12.81. Found: C, 40.25; H, 3.35; N, 12.65. IR (KBr, cm1) 3237, 2927, 1626, 1521, 1453, 1389, 1285, 1146, 951, 753, 625, 466. Synthesis of LH4+ 4 4Br 4(CH3)2SO (2)
To the 5 mL methanol/DMSO solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of HBr was added and the resulting solution was stirred for 4 h. Yield: 73%. Anal. Calcd. (%) for C42H60Br4N10O4S4 (1216.88) C, 41.41; H, 4.93; N, 11.50; S, 10.51. Found: C, 41.21; H, 4.81; N, 11.31; S, 10.36. IR (KBr, cm1) 3417, 3039, 2868, 2642, 1622, 1452, 1386, 1222, 1097, 893. 2 Synthesis of 2LH3+ 3 3SiF6 14H2O (3)
Salt 3 was prepared by same procedure as outlined above for 1 using HF. Yield: 69%. Anal. Calcd. (%) for C68H70F18N20O14Si3 (1817.71) C, 44.90; H, 3.85; N, 15.40. Found: C, 44.65; H, 3.73; N, 15.25. IR (KBr, cm1) 2857, 1625, 1570, 1456, 1388, 1222, 1120, 1023, 955, 783, 618. Synthesis of LH4+ 4 4H2PO4 2H3PO4 (4)
Experimental General All manipulations were performed in air using commercial grade solvents pre-dried by the literature method [23]. N,N,N0 ,N0 -tetrakis(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) was prepared by the procedure reported earlier [24]. Perchloric acid (HClO4, 70%) was purchased from S.D. Fine-Chem limited. Hydrobromic acid (HBr, 40%), hydrofluoric acid (HF, 40%), orthophosphoric acid (H3PO4, 85%), and acetic acid (CH3COOH, 99.8%) were purchased from RENKEM, India. Crystallized salts were carefully dried under vacuum for several hours prior to elemental analysis on Elementar Vario EL III analyzer. IR spectra were obtained on a Thermo Nikolet Nexus FT-IR spectrometer in KBr pellet. Powder XRD data were collected using Bruker Advance D8 XRD diffractometer. The UV–Visible absorption and fluorescence spectra were recorded on Perkin Elmer, Lambda 35, UV–Visible spectrophotometer in 200–800 nm range and RF-5301 PC spectrofluorophotometer Shimadzu respectively.
Salt 4 was prepared by same procedure as outlined above for 1 using H3PO4. Yield: 67%. Anal. Calcd. (%) for C34H49N10O25.88P6 (1199.33) C, 34.03; H, 4.17; N, 11.67. Found: C, 34.21; H, 4.03; N, 11.46. IR (KBr, cm1) 2927, 1625, 1570, 1460, 1405, 1040, 746, 620, 570, 462. Synthesis of L2CH3COOH (5) To the 5 mL methanol/water solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of CH3COOH (v/v%, 5:1) was added and the resulting solution was stirred for 6 h. The colorless crystals of cocrystal 5 in 73% yield, suitable for X-ray data collection were obtained by slow evaporation of solvent at room temperature. Anal. Calcd. (%) for C38H40N10O3.70 (696.06) C, 65.52; H, 6.02; N, 20.11. Found: C, 65.39; H, 6.18; N, 20.25. IR (KBr, cm1) 3173, 2913, 1942, 1677, 1541, 1442, 1268, 1117 1043, 744, 442. Results and discussion
X-ray structure determination The X-ray data collection were performed on a Bruker Kappa Apex four circle-CCD diffractometer using graphite monochromated Mo Ka radiation (k = 0.71070 Å) at 100 K. In the reduction of data Lorentz and polarization corrections, empirical absorption corrections were applied [25]. Crystal structures were solved by Direct methods. Structure solution, refinement and data output were carried out with the SHELXTL program [26,27]. Non-hydrogen atoms were refined anisotropically. Hydrogen atoms were placed in geometrically calculated positions by using a riding model. Images and hydrogen bonding interactions were created in the crystal lattice with DIAMOND and MERCURY software [28,29].
The reaction of N,N,N0 ,N0 -tetrakis-(1H,benzimidazol2ylmethyl)ethane-1,2-diamine (L) with different acids i.e., HClO4, HBr, HF, H3PO4 and CH3COOH in methanol/water/DMSO solution resulted in salts 1–4 and co-crystal 5 (Scheme 1). The crystals suitable for X-ray data collection were obtained by slow evaporation of resultant reaction mixture. The different formulations of these salts and co-crystal were confirmed by elemental analysis, FT-IR, powder XRD and crystallographic structure analysis. The crystallographic data and structure refinement parameters are given in Table 1 and different non-covalent interactions are summarized in Table 2.
Experimental
Salt 1 crystallizes in the triclinic crystal system with P1 space group. The asymmetric unit contains one protonated ligand and four perchlorate anions along with four water molecules (Fig. 1) bonded together through a variety of hydrogen bonds (Fig. S1). Out of four perchlorate anions and water molecule, two are present on the symmetry axis. The proton has been transferred from the acid to the nitrogen bearing lone pair of electron resulting in the formation of salt. Since here four nitrogens are available, therefore
Synthesis of LH4+ 4 4ClO4 H2O (1)
To the 5 mL methanol/water solution of ligand (0.58 g, 1.0 mmol), 0.5 mL of HClO4 (v/v%, 5:1) was added and the resulting solution was stirred for 6 h. The colorless crystals of salt 1 in 71% yield, suitable for X-ray data collection were obtained by slow
Salt 1
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Salt 2 Salt 2 crystallizes in the monoclinic crystal system with P21/c space group. The asymmetric unit consists of a protonated ligand and four molecule of bromide anions and four dimethyl sulfoxide molecules (Fig. 3). The four protonated ligand interacted with each other through C–H p interaction. At one end the p electron density of phenyl ring present on the ligand interact with the phenylic CH of the adjacent ligand molecule (C14–H14 p, 3.986(2) Å), however at the other end the p electron density of other phenyl ring present on the same ligand interact with the hydrogen of dimethyl sulfoxide molecule (C21–H21 p, 3.468(5) Å). The oxygen of the same DMSO molecule interact via., N–H O and C–H O interaction (N1–H3A O2, 1.895(3); C17–H17B O2, 2.429(5) Å) with the neighboring ligand molecule. All the interaction results in the formation of a cavity and is occupied by four molecules of bromide ion and four molecules of dimethyl sulfoxide through various non-covalent interactions (Fig. 4). The three dimensional host–guest packing of the salt 2 is depicted in Fig. 5. Scheme 1.
Salt 3 four protons have been transferred from four acids, hence the asymmetric unit consist of a protonated ligand with four positive charges and four perchlorate anions. We are not able to bind the hydrogen on the oxygen of the water molecule present in the unit cell. In the unit cell, deprotonated perchloric acid and protonated ligand form a cationic–anionic pair where all the imidazolium N– H as well as protonated N–H of ligand are involved in the hydrogen bonding with the oxygen of anion at their respective site. The two wings of the benzimidazole ring of the ligand are bridged by water and perchlorate molecule through N–H O and C–H O interactions on both side (N2–H2B O9, 1.968(5); N4–H4B O8, 1.972(3); C5–H5 O1, 2.680(3); C12–H12 O4, 2.638(3); C8–H8A O3, 2.674(5); C8–H8B O3, 3.476(5 Å) (Fig. S2). The geometry around the chlorine in perchlorate is somewhat distorted tetrahedron with an average bond angle of 111.8 and 107.2° (O4–Cl1–O3, 111.8(26); O2–Cl1–O3, 107.2(49); O4–Cl1–O2, 110.17(22); O1–Cl1–O2, 108.3(49); O5–Cl2–O6, 105.1(17); O5– Cl2–O7, 112.9(17); O5–Cl2–O8, 107.5(27); O6–Cl2–O8, 107.7(27); O7–Cl2–O8, 108.4(17)°). The presence of different non-covalent interactions resulted in a continuous chain of perchlorate and water molecules that runs parallel on either side of the chain formed by the protonated ligands (Fig. 2).
Salt 3 crystallizes in the triclinic crystal system with P1 space group and its molecular structure is shown in Fig. 6. The asymmetric unit consists of two protonated ligands, six hexafluorosilicate anion and fourteen water molecules. The addition of HF to the aqueous-methanolic solution of ligand leads to the formation of SiF2 6 due to the corrosion effect of HF to the glass-vial [30]. We are unable to bind hydrogen on the oxygen of the water molecules present in the unit cell. In salt 3, unlike to the above cases only three protons has been transferred instead of four to three benzimidazole nitrogen bearing lone pair of electron. The geometry around the silicon in hexafluorosilicate ion is distorted octahedron with an average bond angle of 119.9° (F1–Si1–F2, 90.48(47); F1–Si1–F3, 90.40(47); F1–Si1–F4, 174.9(47): F1–Si1–F5, 85.00(60); F1–Si1–F6, 90.14(61); F2–Si1–F3, 102.10(61); F2–Si1– F4, 89.73(23); F2–Si1–F5, 170.40(62); F2–Si1–F6, 85.73(23); F3–Si1–F4, 94.48(12); F3–Si1–F5, 86.29(25); F3–Si1–F6, 172.00; F4–Si1–F5, 94.04(21); F4–Si1–F6, 84.85(45); F5–Si1–F6, 86.29(51)°). Unlike to the salts 1 and 2 the molecular components of salt 3 forms a pseudo cavity for trapping SiF2 6 ions. The distance of C–H p interaction (p electron density of phenyl ring present on the ligand interact with the phenylic CH of the adjacent ligand
Table 1 Crystal data and structure refinement parameters of salts and co-crystal 1–5.
Emprical formula Formula weight Crystal system Space group a (Å) b (Å) c (Å) a (°) b (°) c (°) V (Å3) Z Dcalc (g cm3) l (mm3) Crystal size (mm3) h range (°) Data/Restraints/Parameters R1; wR2 [I > 2r(I)] R1; wR2 (all data)
1
2
3
4
5
C34H36Cl4N10O20 1046.53 Triclinic P1 9.327(3) 11.496(3) 12.090(3) 93.384(16) 90.600(16) 112.474(14) 1195.0(6) 1 1.454 0.332 0.30 0.27 0.21 2.71–31.49 3853/0/307 0.0893; 0.2450 0.1080; 0.2649
C42H60Br4N10O4S4 1216.88 Monoclinic P21/c 9.674(2) 24.767(5) 10.982(2) 90.00 90.232(10) 90.00 2631.2(9) 2 1.536 3.267 0.23 0.20 0.17 2.18–29.73 7003/0/293 0.0313; 0.0969 0.0485; 0.1138
C68H70F18N20O14Si3 1817.71 Triclinic P1 8.9116(3) 14.9883(4) 16.2263(4) 107.941(2) 94.4870(10) 97.4300(10) 2028.56(10) 1 1.488 0.174 0.26 0.18x 0.14 1.92–28.58 7148/0/556 0.0788; 0.2126 0.1109; 0.2436
C34H49N10O25.98P6 1199.33 Monoclinic P21/n 14.2830(4) 16.7711(4) 21.1030(5) 90.00 96.502(2) 90.00 5022.5(2) 4 1.586 0.312 0.31 0.27 0.23 1.39–26.73 12,230/0/699 0.0688; 0.2075 0.0986; 0.2242
C38H40N10O3.70 696.06 Triclinic P1 9.4045(3) 10.1006(4) 10.6257(4) 101.059(2) 100.153(2) 109.647(2) 900.72(6) 1 1.283 0.086 0.31 0.25 0.21 2.87–31.59 3670/0/250 0.0656; 0.1652 0.1394; 0.2066
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U.P. Singh et al. / Journal of Molecular Structure 1081 (2015) 128–135 Table 2 Non-covalent interactions for salts and co-crystal 1–5 (Å and °).
Table 2 (continued) S. No.
S. No.
D–H A
d(D–H)
d(H–A)
d(D–A)
(DHA)
1.
Salt 1 N1–H1 O10 N2–H2B O9 N3–H3B O2 N3–H3B O9 C2–H2 O6 C2–H2 O8 C2–H2 O10 C5–H5 O9 C8–H8B O3 C8–H8B O10 C8–H8A O2 C8–H8A O3 C12–H12 O1 C12–H12 O2 C12–H12 O4 C12–H12 O9 C2–H2 Cl2 C8–H8B Cl1
0.860(8) 0.860(8) 0.861(8) 0.861(8) 0.929(12) 0.929(12) 0.929(12) 0.931(10) 0.970(8) 0.970(8) 0.970(11) 0.970(11) 0.930(9) 0.930(9) 0.930(9) 0.930(9) 0.929(12) 0.970(8)
1.902(15) 1.968(16) 2.857(26) 1.972(16) 2.770(4) 3.062(28) 3.549(25) 3.440(9) 2.674(9) 3.542(20) 2.625(12) 3.478(18) 3.194(30) 3.136(32) 3.607(29) 3.680(43) 3.382(25) 3.415(15)
2.758(20) 2.806(1) 3.081(23) 2.832(7) 3.634(33) 3.952(35) 3.989(25) 3.924(10) 3.498(16) 4.081(30) 3.242(21) 3.498(16) 3.599(24) 3.303(35) 4.279(30) 4.122(48) 4.310(34) 3.986(9)
173.50 164.47 96.85 177.49 155.15 161.12 111.77 114.97 142.95 117.33 121.74 83.17 108.48 92.09 131.34 112.19 176.12 119.64
Salt 2 N3–H3A Br2 N4–H4A Br1 C8–H8A Br1 C8–H8B Br1 C8–H8B Br2 C9–H9B Br2 C15–H15 Br1 C17–H17B Br2 C18–H18B Br1 C19–H19B Br1 C20–H20B Br2 C21–H21B Br2
0.860(5) 0.859(4) 0.970(3) 0.971(3) 0.971(3) 0.969(5) 0.929(5) 0.970(3) 0.960(3) 0.960(3) 0.960(4) 0.960(2)
2.380(11) 2.376(11) 3.264(9) 3.308(8) 3.489(11) 3.245(10) 3.540(1) 2.922(2) 2.839(6) 3.257(16) 3.110(1) 2.842(7)
3.233(16) 3.214(14) 3.759(12) 3.759(12) 4.024(15) 4.055(16) 4.115(5) 3.851(12) 3.750(5) 4.070(19) 3.743(7) 3.959(3)
171.56 164.71 113.57 110.45 117.07 142.24 122.58 160.53 158.79 143.52 148.20 156.51
Salt 3 N1–H1 F9 N3–H3B F8 N3–H3B F9 N7–H7 O1 N4–H4A O3 N4–H4A O7 N6–H6 O4 N2–H2B F4 N2–H2B F2 C17–H17A O5 C12–H12 F8 C12–H12 F7 C15–H15 F5 C14–H14 F4 C31–H31 O2 C33–H33A N3 C23–H23 F6 C9–H9A F1 C25–H25A N3 C17–H17A F9
0.860(3) 0.860(2) 0.860(2) 0.860(2) 0.860(3) 0.860(3) 0.860(3) 0.860(3) 0.860(4) 0.970(4) 0.930(3) 0.930(3) 0.930(4) 0.930(5) 0.930(4) 0.970(4) 0.930(5) 0.970(5) 0.970(4) 0.970(4)
1.972(3) 2.754(2) 1.962(2) 1.875(2) 2.100(5) 2.454(7) 1.944(5) 2.324(6) 1.962(7) 2.915(5) 2.718(2) 2.593(2) 2.663(4) 2.778(5) 2.399(3) 2.763(3) 2.554(6) 2.823(5) 2.730(2) 2.748(2)
2.797(4) 3.287(4) 2.822(3) 2.710(3) 2.875(6) 3.118(8) 2.795(7) 3.076(7) 3.602(7) 3.841(6) 3.318(4) 3.415(6) 3.309(6) 3.530(7) 3.314(3) 3.314(5) 3.414(8) 3.768(6) 3.646(4) 3.622(4)
160.42 121.62 177.78 163.30 154.14 134.45 170.07 146.27 131.36 160.07 123.11 147.70 151.48 138.66 167.80 116.74 153.92 164.97 157.70 150.17
Salt 4 O2–H2C O13 O3–H3B O20 O24–H22 O25 C2–H2 O13 C3–H3 O9 O28–H28 O17 O30–H30 O12 N5–H5A O4 N7–H7 O4 O1–H1A O6 N1–H1 O6 N4–H4A O6 O8–H8D O9 O7–H7A O26 O12–H12A O4 O9–H9 O21 O13–H13A O22 C3–H3 O21 O17–H17 O22
0.820(3) 0.820(3) 0.820(3) 0.930(4) 0.930(4) 0.930(4) 0.930(4) 0.860(3) 0.860(3) 0.820(3) 0.860(3) 0.860(3) 0.820(4) 0.820(7) 0.820(3) 0.820(3) 0.820(2) 0.930(4) 0.820(3)
1.876(2) 1.719(3) 1.902(3) 2.898(2) 2.995(3) 2.411(3) 2.742(3) 2.006(2) 2.908(3) 1.807(6) 2.345(2) 1.945(5) 1.883(3) 2.992(5) 1.905(2) 1.718(3) 1.689(3) 2.732(3) 1.811(3)
2.648(3) 2.481(4) 2.667(4) 3.822(5) 3.816(5) 3.288(5) 3.512(5) 2.849(4) 3.337(4) 2.564(7) 3.199(3) 2.783(6) 2.622(5) 3.488(7) 2.689(4) 2.511(4) 2.489(4) 3.621(5) 2.572(4)
156.43 153.73 154.82 172.57 148.09 157.22 140.73 166.48 168.97 152.72 171.99 164.30 149.30 121.19 159.54 162.07 164.38 160.11 153.66
2.
3.
4.
5.
D–H A
d(D–H)
d(H–A)
d(D–A)
(DHA)
C23–H23A O11 N2–H2B O14 C33–H33A O16 C8–H8B O16 N8–H8 O20 C8–H8A O21 C22–H22 O10 C23–H23 O23 C14–H14 O8
0.820(3) 0.860(3) 0.970(3) 0.970(4) 0.860(3) 0.970(4) 0.930(4) 0.930(4) 0.930(5)
1.720(2) 1.849(2) 2.727(3) 2.688(3) 1.851(3) 2.871(3) 2.951(3) 2.921(3) 2.961(5)
2.519(4) 2.700(4) 3.515(4) 3.455(5) 2.709(3) 3.820(5) 3.821(5) 3.807(5) 3.856(7)
164.34 170.86 138.74 136.32 174.80 166.17 156.30 159.87 164.46
Co-crystal 5 O2–H15A N3 N1–H13 O1 N4–H4B N2 C17–H17 N3 C15–H15 O1 C17–H17B O2 C9–H9A N1
0.887(8) 0.860(3) 0.860(3) 0.970(4) 0.930(4) 0.970(3) 0.970(3)
1.806(7) 1.929(5) 2.015(3) 2.866(2) 2.905(3) 2.615(3) 2.923(3)
2.636(8) 2.777(5) 2.851(4) 3.341(4) 3.574(5) 3.499(4) 3.392(4)
154.89 168.46 163.87 111.17 129.96 151.65 110.91
Fig. 1. Molecular structure of salt 1. Color code: C, grey; N, blue; H, orange; O red; Cl, green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
molecule) in salt 3 is found to be in the range of 4.4–4.7 Å (C13–H13 p, 4.764(3); C28–H28 p, 4.421(5) Å), which seems to be too large for the formation of a true cavity. Thus the pseudo cavity formed by ligand entrap single molecule of SiF2 6 through various N–H F and C–H F interactions (N1–H1 F9, 1.972(3); C2–H2 F8, 2.482(3); C17–H17 F9, 2.745(3); C25–H25A F7, 2.693(3); C25–H25A F9, 2.728(3) Å) (Fig. 7). The hexaflourosilicate anion and the water molecule form a continuous chain through F–O interaction (Fig. S3). The cationic host assembly of protonated ligand in salt 3 forms entirely different three dimensional packing as compared to salt 1 and 2 because of different orientation of the protonated ligand and SiF2 ions, having both 6 pseudo cavity as well as alternate channels (Fig. 8). Salt 4 Salt 4 crystallizes in the monoclinic crystal system with the space group P21/n. The asymmetric unit consists of a protonated ligand, three molecules of monohydrogen phosphate anion, three molecules of neutral phosphoric acid and two molecules of crystalline water (Fig. 9). In the unit cell, oxygens of monohydrogen phosphate, neutral phosphoric acids and water molecule are extensively involved in the hydrogen bonding with the protonated
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Fig. 2. Alternate channels of host framework formed by the self-assembly of the cationic protonated Ligand with guest perchlorate anions and water molecules in salt 1.
dihydrogen phosphate and vice versa) as reported in other cases (Fig. S5-A) [31,32]. Along with dimerization, head-to-tail hydrogen bonding also exists in the same system (O18–H18 O10, 1.707(3) Å) (Fig. S5-B). The oxygen of water molecules bridge the two adjacent phosphate molecule to stabilize the three dimensional herring bone type of packing (Fig. 10). Co-crystal 5
Fig. 3. Molecular structure of salt 2. Color code: C, grey; N, blue; H, orange; O red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
ligand (Fig. S4). The geometry around the phosphorus in phosphate anion is almost regular tetrahedron. The two phosphoric acid selfdimerized in R22(8) motif through O–HO interaction (O9– H9 O21, 1.718(3); O23–H23A O11, 1.719(2) Å, i.e., OH group of one dihydrogen phosphate interact with the oxygen of the other
The co-crystal 5 crystallizes in the triclinic crystal system with P-1 space group and its molecular structure is shown in Fig. 11. The asymmetric unit consists of a neutral ligand (LH) and two acetic acid molecules. In co-crystal 5, unlike to the above cases, no proton has been transferred from the acid to the ligand as a result both the neutral species crystallized simultaneously. The carboxylate oxygens are extensively involved in various C–H O interactions, the phenyl CH forms C–H O interaction with the carboxylate oxygen of acetic acid (C17–H17B 02; 2.615(5) Å) (Fig. S6). Both the imidazolyl NH as well as the protonated NH are involved in N–H O hydrogen bonding with the carboxylate oxygen as well oxygen of water molecules. The four neutral ligand interacts with each other through the p p and C–H p interaction (C3–H3 p, 3.411(4); C4–H4 p, 3.691(7); C14–H14 p, 3.807(49); p p, 3.411(4); p p, 3.668(5) Å, the p electron density of phenyl ring present on ligand and adjacent phenylic CH) results in the formation of a cavity. The methylene C–H is also involved in C–H p interaction (C8–H8 p, 3.040(2) Å) (Fig. S7). This cavity is occupied by two acetic acid molecule through various non-covalent interactions. The three dimensional packing of co-crystal 5 in shown in Fig. 12.
Fig. 4. Different non-covalent interactions in salt 2. Proonated ligand, blue; DMSO, green; water, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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Fig. 5. Host–guest assembly in salt 2. Color code: Proonated ligand, blue; DMSO, green; water, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 8. Host–guest assembly having both pseudo cavity as well as alternate channels.
Fig. 6. Molecular Structure of salt 3. Color code: C, grey; N, blue; F, green; Si Cyan. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 7. Pseudo cavity formed by the protonated ligand for trapping SiF2 6 ions in salt 3. Color code: C, grey; N, blue; H, orange; F, green; Si Pink. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 9. Molecular Structure of salt 4. Color code: C, grey; N, blue; H, orange; P, pink. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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Fig. 10. Three dimensional herring bone type of packing in Salt 4.
Fig. 11. Molecular Structure of co-crystal 5. Color code: C, grey; N, blue; H, orange; O, red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Anion selectivity N,N,N0 ,N0 -tetrakis-(1H,benzimidazol-2ylmethyl)ethane-1,2-diamine (L) has a strong tendency to forms salts and co-crystal with different anions, therefore an attempt has been made to check the selectivity of this ligand by performing a particular experiment under the same reaction condition in which salts and co-crystal have been prepared. Thus an aqueous methanolic solution containing one equivalent of the ligand was added to a solution containing one equivalent (1.0 mmol) of each HClO4, HBr, HF, H3PO4 and CH3COOH. Suitable crystals were obtained by slow evaporation and subjected to characterization by single crystal X-ray diffraction method. The single crystal X-ray data clearly indicates a = 9.29(3); b = 11.49(3); c = 12.15(4); a = 86.10; b = 89.93; c = 66.99 deg; V = 1173.0(6) Å3 that in the mixture of the acids, the ligand was selective for perchloric acid because of the extensive electrostatic as well as non-covalent interactions [18].
Fig. 12. Three dimensional packing of co-crystal 5. Guest acetic acid molecules are entrapped in the cage formed by the host cationic ligand assembly. Color code: Cage; purple; acetic acid, green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
achieved by the naked eye. One of the most attractive approaches in this field involves the construction of colorimetric chemo-sensors since naked eye detection can offer qualitative and quantitative information [33]. Most of the known colorimetric chemosensors are based on the synthetic receptors generally containing some combination of anion binding unit and signal-reporting group (chromophore), either covalently attached or inter molecularly linked [34]. In the naked eye colorimetric experiment, the ligand undergoes a dramatic color change. The methanolic solution of the ligand is orange–red in color but after addition of the acids the color changes to light blue to dark blue (Fig. 13).
Colorimetric test Powder XRD The signal generated in terms of color change due to the presence of various anions has received a great consideration, because the fluorophore needs no equipment and the detection can be
In solid-state and materials sciences, the application of single-crystal X-ray diffraction is also subject to the limitation of
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Appendix A. Supplementary material CCDC number (981383–981387) contains the supplementary crystallographic data for this paper. These data can be obtained free of charge at www.ccdc.cam.ac.uk/conts/retrieving.html [or from the Cambridge Crystallographic Data Center (CCDC), 12 Union Road, Cambridge CB2 1EZ, UK: fax:+44 (0)1223 336033; email: deposit@ ccdc.cam.ac.uk]. Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/ 10.1016/j.molstruc.2014.10.008. References A
B
C
D
E
F
Fig. 13. Color change after the addition of different acids in the methanolic solution of ligand (A) Ligand (B) Ligand + 0.5 mL HClO4 (C) Ligand + 0.5 mL HBr (D) Ligand + 0.5 mL HF (E) Ligand + 0.5 mL H3PO4 (F) Ligand + 0.5 mL CH3COOH. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
obtaining a suitable structural homogeneity of bulk samples, therefore they were also examined through a comparison of experimental and simulated powder X-ray diffraction (XRD) patterns. The experimental patterns correlate favorably with the simulated ones generated from single-crystal X-ray diffraction (Fig. S8). Fluorescence studies The change in the photo physical properties of the ligand and their respective salts were observed in the UV–Visible absorption and fluorescence spectra. The UV–Visible absorption spectra of ligand show two peaks at 230 and 270 nm. At 270 nm, the trend for the neutral ligand as well as for the co-crystal 5 were found to be same, however drastic change was observed in case of salts 1–4 (Fig. S9). The fluorescence spectra shows similar trend as observed in case of UV–Visible spectra (Fig. S10). Conclusion In this work we have reported the anion directed supramolecular frame work which involves a change in the number and type of interaction and the orientation of the molecules in the three dimensional space. The benzimidazole molecules hold different anions and neutral acid molecule by different type of interactions. Their angle of orientation in the three dimensional space is very important for deciding the formation of cavity or pseudo cavity or alternate channel or herring bone network. In conclusion, we have demonstrated that the variation of anion plays a significant role in controlling the structure of salts and the present ligand is superiorly selective for perchlorate anion. Acknowledgment The authors gratefully acknowledge UGC and CSIR, New Delhi, India for financial assistance.
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