Synthesis, crystal structures and DFT studies of Co(II) and Zn(II) coordination polymers of terephthalate and 4,4′-trimethylenedipyridyl ligands for removal of dibenzothiophene from a model fuel oil†

Adedibu C. Tella *^ab, Samson O. Owalude ^a, Olanrewaju A. Ameen ^a, Hadley S. Clayton ^b, Quadrat Yusuph ^c, Tendai O. Dembaremba ^d, Eric C. Hosten ^d and Adeniyi S. Ogunlaja *^d
aDepartment of Chemistry, P.M.B.1515, University of Ilorin, Ilorin, Kwara State, Nigeria. E-mail: adedibu@unilorin.edu.ng
^bDepartment of Chemistry, University of South Africa, South Africa
^cDepartment of Chemistry and Biochemistry, University of Mississippi, P.O. Box 1848, MS 38677-1448, USA
^dDepartment of Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth 6031, South Africa. E-mail: adeniyi.ogunlaja@mandela.ac.za

First published on 17th May 2023

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1. Introduction

Several challenges presented by sulfur-containing compounds in the storage, handling, processing, and use of crude oil-based fuel oils compel their removal from fuel oils.¹ Among the several technologies developed for desulfurization of fuel oils, hydrodesulfurization (HDS) has been the most widely used method in industry.² HDS involves the hydrogenation of sulfur compounds into H₂S under high temperature and pressure, and subsequent removal of the H₂S gas. In addition to the large amounts of hydrogen and the high temperature and pressure required, failure of achieving ultra-low sulfur levels through HDS has motivated the continual improvement of alternative or complementary methods such as biodesulfurization, oxidative desulfurization, extractive desulfurization, and adsorptive desulfurization.^3–6 Among these methods, adsorptive desulfurization has been gaining attention over the years especially with the advent of several potential adsorbent materials that offer attractive properties.⁴

Adsorption occurs through a range of mechanisms such as size exclusion, and chemical and physical interactions.^7–9 Essential to selectivity is for these mechanisms to be more prominent only for the target analyte and less so for the other compounds in the fuel oil matrix. Materials such as clay, activated carbon, silica and zeolites which are mesoporous and microporous capitalize on size exclusion to achieve selectivity.^10–12 Organic polymers have organic functional moieties that can interact with analytes through dispersion forces such as electrostatic interactions, hydrogen bonding and van der Waals forces.^13,14 Materials with coordinatively unsaturated sites such as metal oxides and metal ions rely on acid–base interactions and π-complexation.^7–9,15,16 Best performing materials utilize a combination of these mechanisms to achieve good selectivity. Composite materials have also been explored to maximize the benefit of combining these mechanisms.^17–19 Similarly, the use of coordination polymers has been gaining momentum as they allow adsorption to occur through a multifaceted contribution of size exclusion, dispersion forces and acid–base interactions, and they provide a lot of room to manipulate contributions from all these mechanisms.^7–9,20,21

Coordination polymers (CPs) are formed when multidentate organic ligands coordinate to transition-metal clusters or ions to form repeating entities that extend in 1, 2 or 3 dimensions.^4,22–24 The 3-dimensional CPs, commonly known as metal organic frameworks (MOFs), are the most popular in adsorption work due to their porous network. Pioneering work by Cychosz et al.²⁵ showed that MOFs are superior to conventional porous adsorbents such as zeolites and activated carbon in the adsorption of dibenzothiophene and 4,6-dimethyl dibenzothiophene in model fuel oils. Several factors such as dispersion forces, coordination to open metal sites, π-complexation, acid–base interactions, and pore functionality, have been reported to play a vital role in the effective adsorption of sulfur containing compounds by CPs.^4,7–9 Using thiophene, Peralta et al.²⁶ demonstrated the importance of coordinatively unsaturated sites (CUSs) in the MOFs Cu-BTC and CPO-27–Ni in their remarkably higher selectivity when benchmarked against MOFs without CUSs. The benefits of loading MOFs with d-block transition metals such as Cu⁺ and Ag⁺ and Ni²⁺ to encourage high selectivity via π-complexation in the adsorption of dibenzothiophene has been demonstrated.^27,28 The Pearson's hard and soft acid–base theory predicts that sulfur-containing compounds are relatively intermediate to soft (polarizable) and prefer soft Lewis acid sites such as Cu²⁺, Zn²⁺, and Co²⁺.²⁹

The desulfurization of diesel fuel using a 1D coordination polymer of Cu(II) and 4-methoxybenzoate ligand was previously undertaken by our group.³⁰ Effective adsorption of dibenzothiophene sulfoxide using a Zn(II) coordination polymer constructed from 3,3-thiodipropionate and 4,4′-trimethylenedipyridyl ligands was previously reported.³¹ In continuation of our studies and considering that the choice of metal center and ligands play important roles in the selectivity for sulfur-containing compounds during adsorptive separation, this study investigates two materials based on Co(II) and Zn(II), [Co(tmdp)₄Cl₂]_n1 and [Zn(tpa)₂(tmdp)₂·(H₂O)₂]_n2, respectively as potential adsorbents for sulfur-containing compounds in fuel oils. Contributions from trimethylenedipyridine and terephthalic ligands in the adsorption of DBT were also compared.

2. Experimental section

2.1 Materials

All reagents such as terephthalic acid (tpa) (98%), 4,4-trimethylenedipyridine (tmdp) (99%), Zn(NO₃)₂·6H₂O and CoCl₂·6H₂O were obtained from Sigma Aldrich and used as received.

2.2 Synthesis

2.3 Instrumentation and physical measurements

FT-IR spectra were collected in a single mode with a resolution of 4 cm⁻¹ in the range of 4000 to 400 cm⁻¹ and an average of 32 scans for each sample using a Bruker Tensor 27 platinum ATR-FTIR spectrometer. Elemental analyses of the compounds were carried out on a Carlo Erba Model EA1108 elemental analyzer at Medac Limited UK. Single crystal diffraction data for was obtained at 200 K using a Bruker APEX II CCD diffractometer with graphite monochromated radiation, using APEX2 data collection software and SAINT³² for cell refinement and data reduction. The structures were solved using dual-space methods using SHELXT-2018/2 and refined using least-squares methods using SHELXL-2018/3.^33,34 All non-hydrogen atoms were anisotropically refined, and carbon-bound hydrogen atoms were introduced in idealized geometrical positions in a riding model. The numerical approach implemented in SADABS was used to adjust the data for absorption effects.²² The crystal structure diagrams were drawn using ORTEP-3 for windows.³⁵ An Agilent 7890A gas chromatograph with a flame ionization detector (GC-FID) equipped with a Sigma-Aldrich Supelco SLB®-5 ms column (30 m × 0.25 mm × 0.25 μm) was used to quantify the amount of DBT in samples with initial oven temperature set to 50 °C and ramped to 80 °C at a rate of 15 °C min⁻¹, and then elevated to 300 °C at a rate of 20 °C min⁻¹. Thermogravimetric-differential scanning calorimetry (TG-DSC) analysis of the CPs was performed under a nitrogen atmosphere with a heating rate of 15 °C min⁻¹ in the temperature range 40 to 600 °C. Infrared spectra were acquired on a Bruker Platinum ATR Tensor 27 FT-IR spectrophotometer.

2.4 Adsorption studies

Adsorption studies were carried out by adding measured amounts of activated adsorbent (either 1 or 2) to a 10 mL dibenzothiophene (DBT)/n-hexane solution in a vial (600 mgL⁻¹ being the stock solution). Addition of the adsorbent marked the beginning of each experiment. The studies were generally carried out at room temperature with shaking at 300 rpm. Aliquots were then collected at intervals for analysis using a GC-FID. The following formula was used to compute the adsorption capacity at reaction time t (q_t):

	(1)

where V is volume, W is the amount of CP, C₀ is the initial concentration of DBT in mg L⁻¹ in solution and C_t the concentration of DBT at reaction time (t) in mg L⁻¹.

2.5 Computational calculations

Computational calculations were carried out using Biovia Materials Studio 2020. The Forcite tool was used for pre-optimize the geometry of the drawn structures to ultra-fine quality and for preliminary determination of the position with the lowest total energy when checking the interaction between the CPs and DBT. Geometry optimization was then carried out using the DMol³ module with convergence threshold parameters set to medium; energy = 0.00002, gradient = 0.004 and displacement = 0.005.^36–39 The generalized gradient approximation (GGA) with Perdew–Burke–Ernzerhof (PBE) parametrization functional was applied with Grimme for DFT-D correction. Density functional semi-core pseudopotentials were fitted to all electrons with a double numerical plus (DNP) polarization basis set and 4.4 basis file. A real-space orbital global cut-off of 4.4 Å was applied. The studies were first carried out in gas phase before the conductor-like screening model (COSMO) was applied using n-hexadecane at a dielectric constant of 2.06. The binding energies between each CP and DBT were then determined by subtracting the sum of the total energies of CP and DBT from the total energy of the CP/DBT cluster, i.e.

ΔE(BE) = ECP+DBT − (ECP + EDBT)	(2)

Data for the HOMO–LUMO diagrams was acquired using GaussView 6.0.16 at 6-311+G** level and the diagrams were then created using Avogadro 2.0.8 at medium resolution and ISO value of 0.02.

3. Results and discussions

3.1 FT-IR

FT-IR spectra of the two CPs [Co(tmdp)₄Cl₂]_n1 and [Zn(tpa)₂(tmdp)₂(H₂O)₂]_n2 (Fig. 1) show the characteristic bands expected for the CPs. Primarily, the ν(Co–N) band expected for 1 was observed at 513 cm⁻¹ while the ν(Zn–N) and ν(Zn–O) expected for 2 were observed at 516 cm⁻¹ and 496 cm⁻¹, respectively.⁴⁰ The band observed at 1096 cm⁻¹ was attributed to the ν(Co–Cl) expected for 1.⁴⁰ Characteristic bands for ν_asymmetric(COO⁻) and ν_symmetric(COO⁻) stretches observed at 1580 cm⁻¹ and 1370 cm⁻¹, respectively, in the spectrum of 2 give an insight into the bridging binding mode of tpa carboxyl to Zn(II).⁴¹ Other bands such as the azomethine stretches [ν(CN)], ν(C–H) and ν(CC) were also observed in both spectra at typical wavenumbers as reported in the literature.⁴⁰

3.2 Thermogravimetric analysis

The thermal decomposition of 1 (Fig. 2) occurred in two steps; firstly, there was 29% mass loss between 100 °C to 270 °C and secondly, a 47% loss in the temperature range between 270 °C and 500 °C. The two respective mass losses add up to 76% which is attributed to the mass of the tmdp ligands (calculated, 75.29%) which were lost in no regular patterns. After the decomposition of the ligands, there is a residual mass of 24% (calculated, 24.33%) which is attributed to CoCl₂.

The thermogram of 2 (Fig. 2) shows the first weight loss between 40 °C and 200 °C that accounts for a 4% mass loss which was attributed to the loss of lattice waters. A further 4% was lost between 200 and 300 °C, and 20% between 300 °C and 410 °C which together accounted for the loss of one tmdp from [Zn(tpa)₂(tmdp)₂]. The succeeding 42% mass loss accounts for the loss of the other tmdp and the two tpa molecules to leave a residue of zinc oxides, ∼30%. Transition between the steps is not well defined.

3.3 Scanning electron microscopy

The SEM image of 1 (Fig. 3A) shows that the particles have no definite shape and are agglomerated into large particles mostly between 10 to 50 μm. The bright spots show the adsorbent's rough and porous surface. The SEM image of 2 (Fig. 3B) shows large straight edged plates >200 μm with wide ranging cracks of no definite shape distributed throughout the surfaces. Pores of varied sizes were observed on the surface of 1 as compared to 2 with no distinct visible pores.

3.4 Single crystal XRD

Single crystals of 1 and 2 were obtained as described in Section 2.2. Data collection parameters, refinement data and selected crystal information for the CPs are provided in Table 1. Selected bond lengths and angles for the structures are presented in Tables 2 and 3, while ORTEP and Mercury representations of the structures are provided in Fig. 4. Structure 1 was refined as a 2 component twin. The nature of the included solvent could not be determined and the residual electron density was removed with Platon's squeeze routine.⁴² In structure 2 one of the pyridine rings and the propane group of the tmdp ligand shows positional disorder with a 0.51:0.49 ratio.

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[Co(tmdp)₄Cl₂] crystallizes in a tetragonal system of space group I41/a. No similar structure has been deposited in the Cambridge Structural Database. There are two Co(II) metal centers in the asymmetric unit cell, each located on a 4-fold rotoinversion axis. Each complex is the inverse of the other and the RMSD is 0.0358 with the largest difference of 0.0711 Å between C11 and C21. Each metal center is coordinated to four symmetrical trimethylenedipyridine (tmdp) ligands coordinated equatorially to the Co(II) metal center via the nitrogens. Two symmetrical chlorides complete the slightly distorted octahedral geometry by coordinating axially to the Co(II) center. The average bond distance between Co(II) and the tmdp nitrogens is 2.168 Å while the distance between Co(II) and the chlorides is 2.451 Å, both typical of theoretical Co(II)–N and Co(II)–Cl bond distances.^40,41,43 The coordination geometry around cobalt is an almost perfect octahedral geometry with the N–Co–Cl bond angles in the range 88.59–91.67°, averaging 90.00°, while the N–Co–N bond angles are in the range 88.29–92.11°, averaging 90.01°. The dihedral angles between the Co–N equatorial planes and the coordinated tmdp pyridine rings are 50.20(17) and 50.4(2)°. The dihedral angles between the pyridine rings in the tmdp ligands are 71.89(12) and 71.98(15)°. The tmdp molecules link the Co centers with Co–Co–Co angles of 78.16 and 127.05° to form an infinite 3-dimensional polymeric structure. The smallest ring consists of six metal centres and tmdp ligands. The packing is composed of four interpenetrating nets, each with a dia; 4/6/c1; sqc6 topology.⁴⁴Fig. 5a shows one of the topographical nets. The structure has isolated void cavities with total volume of 3170 ų per unit cell which is 25.8% of the total unit cell volume.

CP 2 crystallizes in a monoclinic system of space group with C2/c. There is one Zn(II) metal center in the asymmetric unit cell. This structure, recorded at room temperature, has been reported by Chen, et al.⁴⁵ The bond lengths and angles are comparable to the structure reported here. Two tmdp ligands are bonded via N at opposite ends to two symmetrical Zn centres with Zn–N bond distances of 2.065 and 2.068 Å (ignoring the minor disorder component).⁴⁶ The tmdp ligand has positional disorder with the ratio 0.51:0.49. Two terephthalic acid (tpa) ligands bind to the Zn to complete the coordination sphere with bond lengths of 1.9669(17) and 1.9940(16) Å to O21 and O11 respectively. Each tpa ligand is symmetrical around an inversion point at the centroid of the benzene ring. The Zn(II) atom has a distorted tetrahedral geometry if one ignores the longer bonds to O12 and O22 of length 2.556(2) and 2.6636(18) Å respectively. If the Zn1–O12 bond is considered coordinating, then one tpa is bonded to the Zn in a bridging mode of 122.03° with Zn–O; bond distances of 1.994 and 2.556 Å while the other tpa is bonded to the opposite end via a deprotonated hydroxy oxygen with a Zn–O bond distance of 1.967 Å.⁴¹ A geometry index (τ₅ = −0.01667α + 0.01667β, where α and β are the two highest valence angles and β > α) with a value of 0.78 was observed, the coordination center is considered a slightly distorted trigonal bipyramidal.⁴⁷ The structure has an infinite 2-dimensional zig-zag polymeric structure with a sql topology (Fig. 5b).⁴⁸ The polymeric structure consists of chains of ring structures with four metal centers with two tmdp and two tpa ligands. There are two alternating rings structures, one with Zn–Zn angles of 76.91 and 103.09°, and another with angles of 87.08 and 92.92° with a dihedral angle of 111.76° between them. There are polymeric nets parallel to each other and at a dihedral angle of 66.2°. There are two solvent water molecules in the asymmetric unit cell that have hydrogen interactions linking adjacent polymeric structures via the tpa ligands. The O–H⋯O interaction distances vary from 2.04(4) to 2.148(19) Å. Without the water molecules, there are small isolated voids in the structure with total volume of 444.6 ų per unit cell (10.7% of the total unit cell volume).

3.5 Adsorption studies

The synthesized CPs 1 and 2 were employed in the adsorption of dibenzothiophene in n-hexane. Considering that SC-XRD (Section 3.4) showed lattice waters in the structure of 2 and the information from thermogravimetric studies (Section 3.2) both CPs were subjected to heat (150 °C) for 2 h to remove lattice waters and activate them for adsorption, prior to the adsorption process.

3.6 Theoretical calculations

Theoretical calculations were carried out to further interpret the adsorption behavior of the CPs. The most plausible model for 1/DBT interaction was where the DBT was sandwiched between neighboring tmdp ligands with one of the DBT benzene rings lying flat closer to the benzene ring of one tmdp ligand to maximize π–π interactions (Fig. 8a). This position agrees with the expected positioning of DBT within the cavities that are in the bulk material. The position allows for maximum exploitation of the π–π interaction with adjacent tmdp ligands resulting in the most minimal energy state. The electron density of the highest occupied molecular orbitals (HOMO) (Fig. 8b) lies predominantly on the adsorbed DBT while the electron density of the lowest unoccupied orbitals (LUMO) (Fig. 8c) lies on the tmdp ligand. This means that DBT is positioned in such a way that the electron density around it is relieved by both adjacent tmdp ligands in the CP. The energy gap between the HOMO and LUMO was calculated to be 0.03624 eV. No direct contribution of the Co(II) metal center to the adsorption of DBT could be immediately established, but its electronic contribution cannot be overstated, particularly creating an electron deficiency that results in a LUMO that lies around tmdp. The binding energies between 1 and DBT were calculated to be −104.68 kJ mol⁻¹ in gas phase and −99.21 kJ mol⁻¹ in n-hexadecane as described in Section 2.5 (Table 6). A negative binding energy reflects exothermic processes, and the calculated binding energy difference is typical of physisorption.^36–39

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In the case of 2, sandwiching DBT between the tmdp and tpa ligands resulted in the lowest energy state (Fig. 9a). The HOMO (Fig. 9b) in the 2/DBT cluster was found to be predominantly around DBT while the LUMO (Fig. 9c) was found to be predominantly around the tpa ligand. Considering that the LUMO was predominantly on the tpa ligand, an attempt was made to place DBT in a position biased towards the tpa ligand during pre-optimization to establish whether tpa would result in better adsorption and a lower energy state (Fig. 10). The initial model where DBT is sandwiched in-between tpa and tmdp was found to be more favorable with a total binding energy of −29.33 Hartree (gas phase) compared to −23.22 Hartree from the later. It is clear that sandwiching DBT between the tmdp and tpa ligands to allow it to experience effective π–π interactions with both ligands is more favorable compared to π–π stacking between one of the DBT rings and the tpa ring. The binding energies between 2 and DBT were calculated to be −65.36 kJ mol⁻¹ and −70.30 kJ mol⁻¹ in the gas phase and in n-hexadecane, respectively (Table 6). The energy difference between the HOMO and the LUMO was calculated to be 0.09005 eV. No direct contribution of the Zn(II) metal center to the adsorption of DBT could be established.

Findings from these theoretical studies corroborate analytical data from adsorption studies as it reveals that thermodynamically, adsorption of DBT on 1 is more favorable compared to 2, as interpreted from the more negative binding energy obtained for the former compared to the latter (Table 6). The results agree with findings from adsorption isotherm studies where the monolayer physisorption is expected (Section 3.5.2).

3.7 Reusability and recyclability studies

The reusability and recyclability of the two adsorbents were investigated to confirm their industrial applications as shown in Fig. 11 and Table 7. After each cycle run, the adsorbent was regenerated by simple washing with methanol several times and dried at 100 °C for 6 hours. It was observed that after five cycle run, the percentage of removal efficiency decreased by only 2.21% by both 1 and 2. This prove that both 1 and 2 are effective for removal of DBT from model fuel but also can be used many times which make them excellent reusing adsorption materials.

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4. Conclusions

Two novel three-dimensional (3D) coordination polymers 1 and 2 were synthesized and characterized using single crystal X-ray diffraction, infrared spectroscopy, thermal analysis, and scanning electron microscopy. Potential application of the materials in adsorptive desulfurization was investigated by carrying out adsorption studies using a model fuel sample (dibenzothiophene dissolved in n-hexane). The experimental results obtained indicated that the Co and Zn coordination polymers could be used for adsorptive desulphurization. Experimental parameters such as initial concentration of dibenzothiophene and contact time were varied to understand the mechanism of adsorption of dibenzothiophene using the coordination polymers. Adsorption kinetics data better fitted the pseudo-second order model while equilibrium data fitted better to Freundlich isotherm with strong indication for physisorption being the primary mechanism of adsorption. DFT studies also pointed in that direction with binding energies between [Co(tmdp)₄Cl₂] and DBT being ∼−100 kJ mol⁻¹ and the binding energies between [Zn(tpa)₂(tmdp)₂·(H₂O)₂]_n and DBT being ∼−70 kJ mol⁻¹. The more negative binding energy calculated for [Co(tmdp)₄Cl₂]/DBT is also in agreement with the higher adsorption capacity (49 mg g⁻¹) observed for 1 compared to 2 (44 mg g⁻¹). Considering that adsorption and DFT studies hinted towards physisorption that negates the direct contribution of metal centers to the adsorption of DBT in both CPs. However, the electronic influence of the metal centers within the CPs cannot be negated. DFT studies also showed that interaction of DBT with both tmdp and tpa in 2 results in a lower energy state compared to just tmdp alone. Overall, it is clear that the ligands play the determining role in the adsorption of DBT in the investigated CPs with two tmdp ligands resulting in better adsorption of DBT compared to a combination of tmdp and tpa.

Conflicts of interest

There are no conflicts to declare.

Acknowledgements

A. C. Tella and S. O. Owalude are grateful to the Royal Society of Chemistry for the RSC Research Fund grant (R21-4029415773) award. Centre for High Performance Computing (CHPC), Cape Town, South Africa facilities were used for computational studies.

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Footnote

† CCDC 2245306 and 2245307. For crystallographic data in CIF or other electronic format see DOI: https://doi.org/10.1039/d3ce00236e

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