research communications
2,2′:4,4′′:4′,4′′′-Quaterpyridine: synthesis, crystal-structure description, and Hirshfeld surface analysis
aDepartment of Chemistry, Dainton Building, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
*Correspondence e-mail: craig.robertson@sheffield.ac.uk
The title compound, 2,2′:4,4′′:4′,4′′′-quaterpyridine (Qtpy), C20H14N4, crystallizes in the triclinic P and has half of the molecule in the corresponding to 4,4′-bipyridine (4,4′-bpy) that serves as the building block for the molecule. C4,4′-bpy—N—C4,4′-bpy and/or N—C4,4′-bpy—C4,4′-bpy bond-angle parameters show that the 4,4′-bpy ligands are highly rigid, displaying values lower than the linear bond angle of 180°. In the crystal, the 4,4′-bpy units are seen to be facing each other in relatively close proximity. The most important interactions on the Hirshfeld Surface of the compound are C—H⋯N/H⋯N—C interactions (constituting 10.6% and 7.6% of the total surface).
Keywords: crystal structure; quaterpyridine; Hirshfeld surface analysis.
CCDC reference: 2248236
1. Chemical context
2,2′:4,4′′:4′,4′′′-Quaterpyridine (Qtpy) is an important bridging ligand used in synthetic inorganic chemistry for the development of many transition-metal complexes (TMCs) employed as DNA-binding probes (Morgan et al., 1991; Pyle et al., 1989). Previously, bridging ligands that provide low inter-metal communication (due to the absence of conjugation between two ligands subunits connected by saturated carbon chains as experienced in bridging ligands that contain isolated bipyridine) have been obtained by the direct fusion of two bpy moieties. However, there has been a surge in interest in ligands that can electronically and coordinatively link two metal centres. In that context, Qtpy represents one of the only instances of a ligand formed from two fused bpy units whose coordination chemistry has been widely explored (Downard et al., 1991; Cooper et al., 1990).
In fact, the first report of Qtpy dates back to 1938 when Burstall and colleagues obtained the ligand as a by-product of the reaction between 4,4′-bipyridine (4,4′-bpy) and iodine (Burstall, 1938). However, since the 1990s, studies in the use of the ligand as a building block for the construction of oligonuclear supramolecular assemblies of photoactive and redox-active chromophoric sites have multiplied (Gorczyński et al., 2016). Qtpy's suitability for such a role arises from its possession of both a bidentate diimine site that can coordinate through to a metal centre, and also two monodentate imine sites, which can both coordinate to other metal centres (see scheme).
In a number of studies, we have employed Qtpy as a bridging ligand to synthesize novel luminescent TMCs towards therapeutic, diagnostic, theranostic and bioimaging ends. This work has mostly involved RuII and other d6-metal ions (de Wolf et al., 2006; Ghosh et al., 2009; Ahmad et al., 2011, 2013, 2014a,b; Walker et al., 2016) . Despite its structural simplicity and synthetic significance, there is no report of the single-crystal structure of pure crystalline Qtpy.
2. Structural commentary and supramolecular Features
Qtpy (Fig. 1) crystallizes in the triclinic P. The comprises of half of a single molecule, which sits on special position 1g (0.000, 1/2, 1/2). The 2,2′ bipyridine rings are planar within 0.00 (12)° and the mean torsion angle between the 4,4′-bipyridine rings is 34.7 (2)°. Two types of weak intermolecular hydrogen bonds are observed between Qtpy and adjacent molecules (Table 1). A single linear contact between the sp2 hydrogen atom H9 and atom N1 of an adjacent molecule (x + 1, y + 1, z) and a dimeric hydrogen bond between a pair of H11 and N10 atoms in a another adjacent molecule (−x + 1, −y + 2, −z.). Both pyridine rings are engaged in π–π interactions (Fig. 2) between their symmetry-equivalent rings in adjacent molecules, both above and below, packing in π–π-stacked columns parallel to the (100) plane (Fig. 3). The N1/C2–C6 rings pack with a distance between their centroids of 3.779 (1) Å with a shift of 1.629 Å and an angle of 0°. The C7–C9/N10/C11–C12 rings also pack with an intercentroid distance of 3.779 (1) Å, with a shorter shift distance of 1.385 Å and an angle of 0°.
3. Database survey
Qtpy is a bridging ligand used in synthetic inorganic chemistry popular for the development of multinuclear TMCs. As such, a search in the Cambridge Structural Database (WebCSD, September 2022; Groom et al., 2016) shows there are 19 reported structures of Qtpy utilized as a ligand: in all cases, the 2,2′-bipyridine has the cis configuration and thus acts as a bidentate chelating ligand. In seven of these structures, the monodentate 4-pyridine coordinates to a different metal centre. There are three crystal structures of modified Qtpy substrates, which are uncoordinated to metal centres. In each of these cases, as we see in our structure of Qtpy, the 2,2′-bipyridine is in the trans configuration, which is the lower energy conformation.
4. Hirshfeld Surface Analysis
A Hirshfeld surface analysis (HSA) was undertaken and fingerprint plots for Qtpy were generated using Crystal Explorer 21.5 (Spackman et al., 2021). HSA is an established technique to understand the various intermolecular interactions present in a compound and quantify weak interactions. In mapping such interactions, internal consistency is highly crucial when comparing structures. As such, all reported Hirshfeld surfaces reported herein have their bond lengths set to hydrogen atoms are set to typical neutron values (C—H = 1.083 Å, N—H = 1.009 Å and O—H = 0.98 3Å). A Hirshfeld surface is unique for a given and a set of spherical atomic electron densities. It can help structural chemists gain additional insight into the intermolecular interactions present in molecular crystals (Spackman & McKinnon, 2002; Spackman & Jayatilaka, 2009). The dnorm values are mapped onto the Hirshfeld surface by using a red–blue–white colour scheme, where red signifies shorter contacts, white represents contacts around the van der Waals separation and blue indicates longer contacts (Montazerozohori et al., 2016). The 2D fingerprint plot presents the decomposition of Hirshfeld surfaces into the contribution of different intermolecular interactions present in a 2D fingerprint plots of Hirshfeld surfaces are usually given as plots of di against de (Montazerozohori et al., 2016).
Hirshfeld surfaces of Qtpy ligand are given in Figs. 4–6 and two-dimensional fingerprint plots in Figs. 7 and 8. To visualize the calculated molecular structure, the surfaces were set to be transparent (Jayendran et al., 2019). The intermolecular interactions (Table 2) are summarized effectively in the spots with large circular depressions (deep red) visible on the dnorm surfaces indicative of hydrogen-bonding contacts and other weak contacts. The major contact points of the intermolecular interactions in the ligand involve H⋯H, as shown by the clearly visible light red spots on the dnorm surface (Hu et al., 2019; Pan et al., 2020). The shape-index is used to identify complementary hollows (red) and bumps (blue) where two molecular surfaces touch one another. On the Hirshfeld surface mapped with the shape-index function, C—H⋯π interactions appear as hollow orange areas (π⋯H) and bulging blue areas (H⋯π). On the Hirshfeld surface mapped with shape-index for the ligand, these interactions manifest as hollow orange areas and bulging blue areas. Curvedness is a function of the root-mean-square curvature of the surface, and maps of curvedness typically show large regions of green (relatively flat) separated by dark blue edges (large positive curvature). The π–π stacking interactions are further evidenced by the appearance of flat surfaces towards the bottom of the compound as clearly visible on the curvedness surface.
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5. Synthesis and crystallization
Qtpy was synthesized (Fig. 9) according to the published method given by Morgan & Baker (1990). 4,4′-bpy (20.42 g, 70.19 mmol) was weighed into a 500 mL two-neck round-bottom flask to which fresh Pd/C (2.20 g) was added. DMF (300 mL) that had been deaerated for ca 15 min was then transferred into the flask. The reaction was left to progress under an N2 atmosphere while being refluxed at 426 K for ca 120 h. Once the reaction was complete and the mixture had cooled down to room temperature, DMF was removed by rotary evaporation to afford a mass of black residue. Chloroform (100 mL) was added to the black residue, and the mixture was allowed to reflux under stirring for a further ca 30 min. Once cooled, the Pd/C catalyst was filtered off through celite to yield a clear yellow solution. Afterwards, chloroform was removed in vacuo and the crude mass obtained was left to stir in acetone (60 mL) for ca 30 min to remove any unreacted 4,4′-bpy. The mixture was filtered under vacuum, and the residue was collected. The filtrate was concentrated by rotary evaporation to yield more portions of the desired product. There were several repetitions of this process, and the various portions of the product were reunited. The compound obtained was then recrystallized from EtOH to yield crystals of Qtpy ligand 6.84 g (33.7%) as a creamy solid but sometimes an off-white solid. 1H NMR (400 MHz, d3-CDCl3): δH = 8.85 (dd, J = 5.1, 2H), 8.81– 8.79 (m, 6H), 7.71 (dd, J = 4.5, 1.6 Hz, 4H), 7.63 (dd, J = 5.1, 1.8 Hz, 2H). ESI–MS, m/z: 311 [MH]+.
6. Refinement
Crystal data, data collection and structure . Hydrogen atoms were placed in calculated positions with idealized geometries C—H = 0.95 Å) and then refined using a riding model and isotropic displacement parameters [Uiso(H) = 1.2Ueq(C)].
details are summarized in Table 3Supporting information
CCDC reference: 2248236
https://doi.org/10.1107/S2056989023002426/zn2024sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023002426/zn2024Isup2.hkl
Data collection: APEX2 (Bruker, 2016); cell
SAINT V8.38A (Bruker, 2016); data reduction: SAINT V8.38A (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015b); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: Olex2 (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 (Dolomanov et al., 2009).C20H14N4 | Z = 1 |
Mr = 310.35 | F(000) = 162 |
Triclinic, P1 | Dx = 1.416 Mg m−3 |
a = 3.7794 (9) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 9.132 (2) Å | Cell parameters from 1538 reflections |
c = 11.115 (3) Å | θ = 2.3–27.1° |
α = 106.477 (2)° | µ = 0.09 mm−1 |
β = 96.768 (2)° | T = 110 K |
γ = 92.720 (2)° | Plate, colourless |
V = 363.98 (15) Å3 | 0.4 × 0.35 × 0.15 mm |
Bruker APEXII CCD diffractometer | 1176 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.036 |
Absorption correction: multi-scan (SADABS; Krause et al., 2016) | θmax = 27.3°, θmin = 1.9° |
Tmin = 0.689, Tmax = 0.746 | h = −4→4 |
6826 measured reflections | k = −11→11 |
1617 independent reflections | l = −14→14 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.047 | H-atom parameters constrained |
wR(F2) = 0.125 | w = 1/[σ2(Fo2) + (0.0544P)2 + 0.0983P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
1617 reflections | Δρmax = 0.32 e Å−3 |
109 parameters | Δρmin = −0.27 e Å−3 |
0 restraints |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
Refinement. A crystal with dimensions 0.1 x 0.3 x 0.3?mm was selected and intensity data was collected on a Bruker SMART APEX-II CCD diffractometer operating with a MoKα sealed-tube X-ray source of the crystal mounted in fomblin oil on a MicroMount (MiTeGen, USA) and cooled to 110?K in a stream of cold nitrogen gas using an Oxford Cryosystems 700 Cryostream. Data were corrected for absorption using empirical methods (SADABS; Bruker, 2016) based upon symmetry equivalent reflections combined with measurements at different azimuthal angles (Krause et al., 2015). The crystal structures were solved and refined against F2 values using ShelXT (Sheldrick, 2015a) for solution and ShelXL (Sheldrick, 2015b) for refinement accessed via the Olex2 program (Dolomanov et al., 2009). Non-hydrogen atoms were refined anisotropically. The Qtpy structure displayed here has been refined anisotropically with Final R indexes [I>2σ (I)] value of 0.0473. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.0725 (4) | 0.34513 (15) | 0.36534 (13) | 0.0199 (3) | |
N10 | 0.5896 (4) | 0.98051 (16) | 0.15939 (14) | 0.0255 (4) | |
C2 | 0.0647 (4) | 0.48982 (18) | 0.43797 (14) | 0.0172 (4) | |
C3 | 0.1688 (4) | 0.61573 (18) | 0.40043 (15) | 0.0181 (4) | |
H3 | 0.163519 | 0.716337 | 0.455210 | 0.022* | |
C4 | 0.2805 (4) | 0.59466 (18) | 0.28298 (15) | 0.0177 (4) | |
C5 | 0.2848 (4) | 0.44507 (18) | 0.20739 (15) | 0.0190 (4) | |
H5 | 0.357380 | 0.425003 | 0.125703 | 0.023* | |
C6 | 0.1820 (4) | 0.32596 (18) | 0.25263 (15) | 0.0206 (4) | |
H6 | 0.189793 | 0.224202 | 0.200326 | 0.025* | |
C7 | 0.3904 (4) | 0.72786 (18) | 0.24004 (15) | 0.0181 (4) | |
C8 | 0.5635 (4) | 0.86115 (18) | 0.32469 (16) | 0.0213 (4) | |
H8 | 0.616125 | 0.868956 | 0.412099 | 0.026* | |
C9 | 0.6585 (5) | 0.98241 (19) | 0.28053 (16) | 0.0238 (4) | |
H9 | 0.779673 | 1.072268 | 0.339663 | 0.029* | |
C11 | 0.4220 (5) | 0.85210 (19) | 0.07885 (17) | 0.0240 (4) | |
H11 | 0.370005 | 0.847837 | −0.007860 | 0.029* | |
C12 | 0.3199 (4) | 0.72498 (19) | 0.11441 (16) | 0.0213 (4) | |
H12 | 0.201979 | 0.636146 | 0.052993 | 0.026* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0216 (8) | 0.0177 (7) | 0.0212 (8) | 0.0007 (6) | 0.0036 (6) | 0.0068 (6) |
N10 | 0.0314 (9) | 0.0205 (8) | 0.0279 (9) | 0.0025 (6) | 0.0094 (7) | 0.0102 (7) |
C2 | 0.0159 (8) | 0.0174 (8) | 0.0187 (9) | 0.0013 (6) | −0.0005 (6) | 0.0073 (7) |
C3 | 0.0179 (9) | 0.0161 (8) | 0.0205 (9) | −0.0001 (6) | 0.0010 (7) | 0.0068 (7) |
C4 | 0.0150 (8) | 0.0174 (8) | 0.0212 (9) | −0.0003 (6) | 0.0003 (6) | 0.0073 (7) |
C5 | 0.0190 (9) | 0.0210 (9) | 0.0178 (9) | 0.0001 (7) | 0.0028 (7) | 0.0071 (7) |
C6 | 0.0235 (9) | 0.0163 (8) | 0.0215 (9) | 0.0016 (7) | 0.0037 (7) | 0.0042 (7) |
C7 | 0.0175 (9) | 0.0174 (8) | 0.0218 (9) | 0.0032 (6) | 0.0058 (7) | 0.0082 (7) |
C8 | 0.0234 (9) | 0.0207 (9) | 0.0210 (9) | 0.0018 (7) | 0.0041 (7) | 0.0076 (7) |
C9 | 0.0266 (10) | 0.0188 (9) | 0.0253 (9) | −0.0003 (7) | 0.0049 (7) | 0.0051 (7) |
C11 | 0.0293 (10) | 0.0227 (9) | 0.0220 (9) | 0.0031 (7) | 0.0065 (7) | 0.0085 (7) |
C12 | 0.0246 (9) | 0.0186 (9) | 0.0212 (9) | −0.0003 (7) | 0.0041 (7) | 0.0067 (7) |
N1—C2 | 1.343 (2) | C5—C6 | 1.379 (2) |
N1—C6 | 1.333 (2) | C6—H6 | 0.9500 |
N10—C9 | 1.336 (2) | C7—C8 | 1.387 (2) |
N10—C11 | 1.333 (2) | C7—C12 | 1.383 (2) |
C2—C2i | 1.482 (3) | C8—H8 | 0.9500 |
C2—C3 | 1.385 (2) | C8—C9 | 1.381 (2) |
C3—H3 | 0.9500 | C9—H9 | 0.9500 |
C3—C4 | 1.384 (2) | C11—H11 | 0.9500 |
C4—C5 | 1.388 (2) | C11—C12 | 1.381 (2) |
C4—C7 | 1.486 (2) | C12—H12 | 0.9500 |
C5—H5 | 0.9500 | ||
C6—N1—C2 | 117.10 (13) | C5—C6—H6 | 118.0 |
C11—N10—C9 | 116.52 (14) | C8—C7—C4 | 121.35 (15) |
N1—C2—C2i | 116.76 (17) | C12—C7—C4 | 121.41 (15) |
N1—C2—C3 | 122.60 (15) | C12—C7—C8 | 117.23 (14) |
C3—C2—C2i | 120.64 (18) | C7—C8—H8 | 120.4 |
C2—C3—H3 | 120.1 | C9—C8—C7 | 119.30 (15) |
C4—C3—C2 | 119.86 (15) | C9—C8—H8 | 120.4 |
C4—C3—H3 | 120.1 | N10—C9—C8 | 123.72 (16) |
C3—C4—C5 | 117.50 (14) | N10—C9—H9 | 118.1 |
C3—C4—C7 | 120.90 (15) | C8—C9—H9 | 118.1 |
C5—C4—C7 | 121.60 (14) | N10—C11—H11 | 118.2 |
C4—C5—H5 | 120.5 | N10—C11—C12 | 123.68 (16) |
C6—C5—C4 | 119.02 (15) | C12—C11—H11 | 118.2 |
C6—C5—H5 | 120.5 | C7—C12—H12 | 120.2 |
N1—C6—C5 | 123.91 (15) | C11—C12—C7 | 119.54 (16) |
N1—C6—H6 | 118.0 | C11—C12—H12 | 120.2 |
Symmetry code: (i) −x, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
C9—H9···N1ii | 0.95 | 2.60 | 3.420 (2) | 144 |
C11—H11···N10iii | 0.95 | 2.62 | 3.410 (2) | 141 |
Symmetry codes: (ii) x+1, y+1, z; (iii) −x+1, −y+2, −z. |
Inside Atom | Outside Atom | Total Contributions | ||
N | C | H | ||
C | 3.2 | 15.5 | 6.7 | 25.5 |
H | 7.6 | 4.2 | 48.5 | 60.4 |
N | 0.4 | 3.1 | 10.6 | 14.2 |
Total Contributions | 11.2 | 22.8 | 65.8 |
Inside Atom | Outside Atom | Total Contributions | |||
N | C | H | |||
C | 3.2 | 15.5 | 6.7 | 25.4 | |
H | 7.6 | 4.2 | 48.5 | 60.3 | |
N | 0.4 | 3.1 | 10.6 | 14.1 | |
Total Contributions | 11.2 | 22.8 | 65.8 |
Acknowledgements
We are grateful for funding from the University of Sheffield's Faculty of Science and Doctoral Academy for a studentship for SA, as well as the University of Sheffield Institutional Open Access Fund.
Funding information
Funding for this research was provided by: University of Sheffield (studentship to Stephen O. Aderinto).
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