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Structural Variations in Manganese Halide Chain Compounds Mediated by Methylimidazolium Isomers
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Synthesis, X-ray Structure, Hirshfeld Analysis of Biologically Active Mn(II) Pincer Complexes Based on s-Triazine Ligands

Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria 21321, Egypt
Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
Authors to whom correspondence should be addressed.
Crystals 2020, 10(10), 931;
Received: 20 September 2020 / Revised: 7 October 2020 / Accepted: 12 October 2020 / Published: 13 October 2020


Herein, the synthesis and antimicrobial activities of [Mn(MorphBPT)(H2O)2NO3]NO3; (1) and [Mn(PipBPT)(H2O)2NO3]NO3; (2) complexes of the pincer-type tridentate ligands MorphBPT; 4-(4,6-di(1H-pyrazol-1-yl)-1,3,5-triazin-2-yl)morpholine and PipBPT; 2-(piperidin-1-yl)-4,6-di(1H-pyrazol-1-yl)-1,3,5-triazine are presented. Both complexes have slightly distorted octahedral coordination geometry. Their molecular packing depends on O–H···O, C–H···O hydrogen bonds and anion–π stacking contacts. Hirshfeld analysis was used to quantify the different contacts. Both complexes exhibited better anti-fungal activity than the standard Fluconazole and comparable antibacterial activity to Gentamycin against Staphylococcus aureus and Escherichia coli microbes. Moreover, complexes 1 and 2 are biologically more active than the free ligands against these microbes.
Keywords: Mn(II); antifungal; s-triazine; DFT; Hirshfeld Mn(II); antifungal; s-triazine; DFT; Hirshfeld

1. Introduction

The use of transition metal complexes as antimicrobial agents, and for their potential applications as inorganic pharmaceuticals and in medicine for diagnostics, has gained great interest from researchers [1,2,3,4]. In this regard, large and rising numbers of mono- and polynuclear complexes of different metals, and with different classes of chelating ligands involving Schiff bases, bipyridine, and phenanthroline with different anions, were presented in literature [5,6,7,8,9,10,11,12,13,14].
Of transition metals, manganese is considered an essential micronutrient in living organisms and has an important role in a broad range of enzyme-catalyzed reactions. There is no doubt about the potential use of Mn(II) complexes as catalytic scavengers for H2O2 against oxidative stress [7,8,9,10,11,12,13,14,15]. From this point of view, an increasing interest with the synthesis of more Mn(II) complexes in order to investigate their catalytic and antimicrobial activities. Mn(II) complexes of bipyridine and phenanthroline ligands were found to have promising antifungal activity comparable to the antifungal drug ketoconazole [15,16]. Mn(II) plays a key role in biology as required enzyme activator, which is responsible for metabolism and apoptosis [17,18]. In addition, a Mn(II) complex of the Schiff base ligand derived from 1,4-diaminobutane and pyridoxal hydrochloride showed a great anticancer activity against breast cancer [19]. More recently, a Mn(II) complex of a Schiff base derived from vitamin B6 was found as an apoptosis inducer in human MCF7 and HepG2 cancer cells [20].
In continuation to our interest with the s-triazine pincer complexes [21,22,23,24], and in light of the interesting recently reported data in literature [25,26,27,28,29,30,31], we are presenting here the synthesis of two new Mn(II) complexes with the s-triazine based NNN-pincer ligands shown in Figure 1. The structural features of both complexes are elucidated. In addition, their antimicrobial activities as antibacterial and antifungal agents are presented.

2. Materials and Methods

Chemicals, reagents, and solvents used in this work were purchased from their commercial suppliers. The CHN analyses were determined using Perkin-Elmer 2400 instrument (PerkinElmer, Inc. 940 Winter Street, Waltham, MA, USA).

2.1. Preparation of the Organic Ligands

The organic ligands were prepared using the method reported in literature [32] (Supplementary data, Method S1, Figures S1 and S2).

2.2. Syntheses of [Mn(MorphBPT)(H2O)2NO3]NO3; (1) and [Mn(PipBPT)(H2O)2NO3]NO3; (2)

In a 50 mL conical flask, the ligand solution (0.05 mmol) in 10 mL methanol was added to an aqueous solution of the Mn(NO3)2·4H2O (~0.126 g, 0.05 mmol) in 10 mL water. The resulting clear solution was kept at room temperature for slow evaporation. Colorless crystals of the titled complexes were obtained after three days and were collected by filtration.
Yield:C17H26MnN10O9 (1) 80% with respect to the ligand. Anal. Calc. C, 35.86; H, 4.60; N, 24.60%. Found: C, 35.65; H, 4.52; N, 24.48%.
Yield; C18H28MnN10O8 (2) 77% with respect to the ligand. Anal. Calc. C, 38.10; H, 4.97; N, 24.69%. Found: C, 37.91; H, 4.91; N, 24.46%.

2.3. Crystal Structure Determination

The crystal structures of complexes 1 and 2 were determined by using a Bruker D8 Quest (Bruker Corporation, Massachusetts, MA, USA) diffractometer employing SHELXTL and SADABS programs [33,34,35]. Table 1 illustrated the refinement and crystal details. Hirshfeld calculations were performed using the default parameters of the Crystal Explorer 17.5 program [36,37,38,39,40].

2.4. Antimicrobial Studies

The bio-activities of the free MorphBPT and PipBPT ligands, as well as the corresponding Mn(II) complexes against different microbes, were determined [32]. More details regarding the bio-experiments are found in Supplementary data.

2.5. Density Functional Theory (DFT) Calculations

Gaussian 09 (Wallingford, CT, USA) [41] built in MPW1PW91/TZVP method [42] were used for doing charge population [43] and atoms in molecules (AIM) [44] analyses, as previously described [2,21].

3. Results and Discussion

3.1. X-ray Crystal Structure Description

The structure with atomic numbering of [Mn(MorphBPT)(H2O)2NO3]NO3 complex (1) are shown in Figure 2 and list of the most important geometric parameters are given in Table 2. It crystallized in the triclinic crystal system and P-1 space group, and Z = 2. This cationic complex has a hexa-coordinated Mn(II) with one tridentate pincer ligand, one monodentate nitrate ion, and two water molecules in its inner sphere while the outer sphere comprised two halves of nitrate ions. The manganese to nitrogen distance is significantly shorter with s-triazine (2.2170(14) Å) than the corresponding Mn–N(pyrazole) bonds (2.3187(15)–2.3269(14) Å). Moreover, the equatorial Mn–O bond is the shortest (2.1419(13) Å) where the length of the manganese to oxygen distances is in the order of Mn–O(equatorial water) < Mn–O(nitrate) < Mn–O(axial water). The two bite angles of the tridentate chelate are 69.49(5) and 69.09(5)° for N5–Mn1–N1 and N5–Mn1–N7, respectively while the angle between the two trans Mn–N(pyrazole) bonds is 138.55(5)° for N1–Mn1–N7. The O2–Mn1–O3 and O2–Mn1–O1 bond angles of these cis bonds are 90.33(5) and 80.66(6)°, respectively while the O3–Mn1–O1 trans bond angle is 167.72(5)°. The hexa-coordinated Mn(II) has a distorted octahedral configuration with a distorted square comprised the N1N5N7O2 atoms while the O1 and O3 atoms are located at the apexes. Using Shape 2.1 software (Barcelona, Spain), the continuous shape measure (CShM) values of 4.1 and 11.8 relative to perfect octahedron and trigonal prism, respectively were computed. The CShM values revealed slightly distorted octahedral coordination geometry.
The three dimensional structure of 1 is built by O–H···O hydrogen bonds and C–H···O interactions as shown in the left part of Figure 3. The donor-acceptor distances are generally shorter (2.662(3)–2.924(2) Å) in the former than in the latter (3.271(3)–3.455(3) Å) (Table 3). The packing of 1 is shown in the upper part of Figure 4. In addition, anion–π contacts play an important role in the packing of 1 (Figure S3 (Supplementary data) and Table 4).
The structure of [Mn(PipBPT)(H2O)2NO3]NO3 complex 2 is very similar to 1. It also crystallized in the primitive triclinic unit cell with P-1 space group and two of the molecular formula per unit cell. In this case, the asymmetric unit comprised one cationic [Mn(PipBPT)(H2O)2NO3] and one NO3¯ counter anion. In general, the Mn–N and Mn–O bonds are slightly shorter in this complex than those in 1 except one of the Mn–N(pyrazole) bonds as well as one Mn–O(water) bond, which is trans to the Mn–O(nitrate). The hexa-coordinated Mn(II) coordination configuration is slightly less distorted than that in 1 where the continuous shape measure values for 2 were computed to be 3.3 and 11.9 with respect to the perfect octahedron and trigonal prism, respectively. The most important O–H···O and C–H···O hydrogen bond contacts as well as the anion–π stacking contacts in 2 are shown in the right part of Figure 3 and Figure S3, respectively. The packing of 2 could be considered as 1D hydrogen bond polymer (Figure 4) while list of the hydrogen bonds is given in Table 3.
A slight structural difference between complexes 1 and 2 is the deviation of the Mn and coordinated equatorial oxygen atoms from the s-triazine plane. The plane passing through the perfectly planar aromatic s-triazine moiety is nearly passing through the center of Mn atom in complex 2 with only 0.040(2) Å deviation from this mean plane. The corresponding distances in complex 1 is 0.142(2) Å. The equatorial oxygen atom is deviated from this plane by a distance of 0.603(3) and 0.515(3) Å in complexes 1 and 2, respectively. The reason could be simply attributed to the involvement of the s-triazine in larger number of anion–π stacking contacts in 1 compared to 2.
There is another structural difference between complexes 1 and 2. It is the orientation of the nitrate counter anion, with respect to the s-triazine moiety. In complex 1, the nitrate anion is nearly perpendicular to the s-triazine mean plane where the angle between the two planes is 86.67(3)°. It seems that such situation allowed further anion–π stacking interactions in 1 compared to 2. The corresponding angle between the two mean planes in complex 2 is only 26.64(3)°.

3.2. Analysis of Molecular Packing

Hirshfeld surfaces for 1 and 2 are given in Figure S4 (Supplementary data) while all possible contacts are shown in Figure 5. The decomposed dnorm maps of the short and most significant contacts are collected in Figure 6. The H···H, O···H, N···H and C···H interactions are the most frequent in both complexes. In complex 1, these contacts contributed by 38.4, 37.5, 9.9 and 6.1%, respectively from the whole fingerprint area while the corresponding values in complex 2 are 45.2, 32.8, 8.8 and 5.2%, respectively. In addition, both complexes showed comparable amounts of anion–π stacking interactions with net C(s-triazine)···O(nitrate) and N(s-triazine)···O(nitrate) contacts of 2.8 and 2.5% for complexes 1 and 2, respectively. The latter is weaker in complex 2 and not showed the characteristics of short contacts. The shortest C···O contact is C7···O8 (2.982(2) Å) in 2 while in 1 the shortest contact is C8···O9 (2.889(3) Å). Regarding the N···O contacts in complexes 1 and 2, the shortest contact distances are N5···O9 (2.831(3) Å) and N6···O7 (3.077(2) Å), respectively. The N···O interaction in 2 is slightly longer than the vdW radii sum of nitrogen and oxygen indicating weaker interaction than 1. The O···H contacts appeared strong in both complexes where the O11···H1 (1.742 Å) and O7···H1B (1.770 Å) are the shortest in complexes 1 and 2, respectively. The values are different from those obtained from the CIF data given in Table 3 because in the Hirshfeld analysis the X–H (X = C, O) distances are normalized using the default criteria of Crystal Explorer 17.5 program. Many of the O···H contacts appeared as red regions in the dnorm map indicated shorter distance than the vdW radii sum of hydrogen and oxygen. In addition, complex 2 showed H···H and C–H···π interactions as red regions in the dnorm map with remarkable short distances of 1.959 Å (H5B···H5B) and 2.646 Å (C6···H5C). The latter occurred between the C–H of one methyl group from a complex unit with the s-triazine π-system from another complex unit. There are no observable π–π stacking interactions from the shape index and curvedness surfaces in both complexes.

3.3. AIM Topology Analysis

The nature and strength of Mn–N and Mn–O interactions in the studied complexes were analyzed using atoms in molecules (AIM) calculations [44,45,46,47,48,49,50,51,52,53,54]. The electron density (ρ(r)) of the Mn–O and Mn–N bondings are in the range of 0.028–0.046 and 0.035–0.045 a.u, respectively which are generally lower than 0.1 a.u indicating weak interactions with closed shell characters (Table 5). With the exception of the Mn–N(s-triazine), the positive H(r) and V(r)/G(r) < 1 for the rest of Mn–N and Mn–O interactions are the typical characteristics of the closed shell interactions. The Mn–N(s-triazine) bonds have very slightly small negative H(r) values and V(r)/G(r) very slightly higher than one indicating that the Mn–N(s-triazine) bonds have higher covalent characters than the Mn–N(pyrazole). Among the Mn–O bonds, the equatorial bond which is located trans to the Mn–N(s-triazine) has the highest ρ(r) value and the highest interaction energy. As clearly seen in Figure 7, the Mn–O distances correlate well with the ρ(r) values as well as interaction energies (Eint). Similar observation could be noted for the Mn–N distances where the correlation coefficients (R2) are found to be 0.992 and 0.993, respectively.
Bond orbital analysis (Table 6) of the Mn–N and Mn–O coordination interactions agreed very well with the experimental bond distances observed experimentally. It is clear that the bond order is the highest for Mn–N(s-triazine) compared to the Mn–N(pyrazole). Similarly, the equatorial Mn–O bond has the highest bond order compared to the rest of Mn–O bonds where the order of the Mn–O bond length is Mn–O(equatorial water) < Mn–O(nitrate) < Mn–O(axial water). The correlation coefficients of the Mn–N and Mn–O distances with the calculated bond order values are 0.996 and 0.976, respectively.
Charge calculations of the free ligands allowed us to investigate the charge variations at the coordinating sites due to the chelation with the Mn(II) cation. It is obvious from the natural charges listed in Table 7 that all the coordinated donor atoms have more negative charge than those in the free ligand. The natural charge variation is higher (0.12–0.13 e) for the s-triazine N-site than the pyrazole (0.08–0.09 e) nitrogen atoms. As a conclusion, the coordination of the pincer ligand with the positively charged Mn(II) ion produced further polarization in the electron density towards the donor atom.

3.4. Antimicrobial Activity

In the current study, the bio-activity of MorphBPT and PipBPT as well as their Mn(II) complexes were tested as antibacterial and antifungal agents (Supplementary data, Method S2) [32,55,56,57,58]. The Mn(II) complexes showed good bio-activities against the target pathogenic microbes more than original ligand as illustrated from the inhibition zones (mm), which were measured as indicator for bioactivity of the tested compounds (Table 8) at concentration 200 µg/mL. MorphBPT is completely inactive against all tested microbes while PipBPT showed good activity against Staphylococcus aureus and Candida albicans, while completely inactive against Escherichia coli (Table 8). Both Mn(II) complexes have better antibacterial and antifungal activity than the free ligands against S. aureus, E. coli, and C. albicans. Moreover, complexes 1 and 2 have better antifungal activity than the standard Fluconazole. In addition, the studied complexes have comparable antibacterial activity to Gentamycin against S. aureus and E. coli.
The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of all the tested complexes against S. aureus, E. coli, and C. albicans are reported (Table 9). It is clear that the studied Mn(II) complexes showed good bio-activity against S. aureus and E. coli as well as the fungus C. albicans. The MIC values are less for [Mn(PipBPT)(H2O)2NO3]NO3 than [Mn(MorphBPT)(H2O)2NO3]NO3 against S. aureus, while both compounds showed similar antifungal actions against C. albicans and almost similar bio-activity against E. coli. Similarly, the MBC revealed these results very well.

4. Conclusions

[Mn(MorphBPT)(H2O)2NO3]NO3; (1) and [Mn(PipBPT)(H2O)2NO3]NO3; (2) were synthesized using self-assembly of the pincer MorphBPT and PipBPT ligands with Mn(NO3)2·4H2O in water-alcohol mixture. The molecular and supramolecular structures of complexes 1 and 2 were investigated using X-ray single crystal diffraction combined with Hirshfeld calculations. Their anti-microbial activities were compared with the free ligands and with Fluconazole and Gentamycin as standard agent. Both complexes showed better anti-fungal activity than the standard Fluconazole. Complexes 1 and 2 are biologically more active than the free ligands against S. aureus, E. coli, and C. albicans microbes.

Supplementary Materials

The following are available online at Method S1. General method for preparation of ligands. Figure S1. 1H NMR and 13C NMR of compound ligand MorphBPT. Figure S2. 1H NMR and 13C NMR of compound ligand PipBPT. Method S2. Antimicrobial studies. Figure S3. Anion–π interactions in 1 and 2. Figure S4. Hirshfeld surfaces mapped over dnorm, shape index and curvedness.

Author Contributions

Conceptualization, S.M.S.; formal analysis, S.M.S., H.H.A.-R. and A.E.-F.; funding acquisition, A.E.-F.; investigation, S.M.S. and H.H.A.-R.; resources, S.M.S. and A.E.-F.; software, S.M.S.; supervision, S.M.S.; writing—original draft, S.M.S., H.H.A.-R. and A.E.-F.; writing—review editing, S.M.S. All authors contributed to the first draft and the final version. All authors have read and agreed to the published version of the manuscript.


Deanship of Scientific Research, King Saud University, Saudi Arabia, grant number: RGP-1441-234.


The authors extend their thanks to the Deanship of Scientific Research at King Saud University for funding this work through research group no. (RGP-1441-234, Saudi Arabia).

Conflicts of Interest

The authors declare no conflict of interest.


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Figure 1. Structure of the pincer ligands [32].
Figure 1. Structure of the pincer ligands [32].
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Figure 2. Structure and atomic numbering of the symmetric unit of 1 and 2. Thermal ellipsoids were drawn at 50% probability level. Moreover, the nitrate counter ions were omitted for better clarity.
Figure 2. Structure and atomic numbering of the symmetric unit of 1 and 2. Thermal ellipsoids were drawn at 50% probability level. Moreover, the nitrate counter ions were omitted for better clarity.
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Figure 3. Important H–bond contacts in 1 and 2. The green and blue colored contacts refer to the C–H···O and O–H···O interactions, respectively.
Figure 3. Important H–bond contacts in 1 and 2. The green and blue colored contacts refer to the C–H···O and O–H···O interactions, respectively.
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Figure 4. H–bond networks in 1 (a) and 2 (b).
Figure 4. H–bond networks in 1 (a) and 2 (b).
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Figure 5. Summary of the intermolecular interactions in 1 and 2.
Figure 5. Summary of the intermolecular interactions in 1 and 2.
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Figure 6. The dnorm maps of the most important contacts in 1 and 2.
Figure 6. The dnorm maps of the most important contacts in 1 and 2.
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Figure 7. Correlation between ρ(r); (a) and interaction energies (Eint); (b) with Mn–O distances.
Figure 7. Correlation between ρ(r); (a) and interaction energies (Eint); (b) with Mn–O distances.
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Table 1. Crystal and refinement data of 1 and 2.
Table 1. Crystal and refinement data of 1 and 2.
Empirical formulaC17H26MnN10O9C18H28MnN10O8
Formula weight (g/mol)569.42567.44
Temperature (K)124(2)117(2)
λ (Mo-Kα, Å)0.710730.71073
Crystal systemTriclinicTriclinic
Space groupP-1P-1
Unit cell dimensionsa = 8.2794(5) Åa = 7.830(5) Å
b = 12.1167(7) Åb = 12.951(7) Å
c = 12.1738(7) Åc = 13.990(7) Å
α = 88.3660(19)°α = 116.533(10)°
β = 89.605(2)°β = 94.832(14)°
γ = 79.184(2)°γ = 101.694(16)°
Volume (Å3)1199.08(12)1217.9(12)
Density (calc. g/cm3)1.5771.547
Absorption coefficient (mm−1)0.6210.608
Crystal size (mm3)0.29 × 0.21 × 0.110.31 × 0.23 × 0.19
θ range for data collection2.36 to 26.34°2.71 to 25.31°
Index ranges−10 ≤ h ≤ 10, −15 ≤ k ≤ 15, −15 ≤ l ≤ 15−9 ≤ h ≤ 9, −15 ≤ k ≤ 15, −16 ≤ l ≤ 16
Reflections collected21,45119,570
Independent reflections4863 [R(int) = 0.0315]4437 [R(int) = 0.0554]
Completeness to θ99.30%99.80%
Refinement methodFull-matrix least-squares on F2
Goodness-of-fit on F20.8941.06
Final R indices [I>2sigma(I)]R1 = 0.0275, wR2 = 0.0671R1 = 0.0298, wR2 = 0.0732
R indices (all data)R1 = 0.0341, wR2 = 0.0721R1 = 0.0371, wR2 = 0.0775
Extinction coefficient0.0100(8)0.0157(17)
Largest diff. peak and hole0.371 and −0.3180.409 and −0.308
Table 2. The most important bond distances and angles of 1 and 2.
Table 2. The most important bond distances and angles of 1 and 2.
Table 3. The Geometric parameters of the H–bonds in 1 and 2.
Table 3. The Geometric parameters of the H–bonds in 1 and 2.
AtomsD–H (Å)H···A (Å)D···A (Å)D–H···A (°)
Symmetry Code: (i) 1-x,1-y,2-z; (ii) -x,2-y,1-z; (iii) 1+x,y,z; (iv) -1+x,y,z; (v) -x,1-y,2-z
Symmetry Code: (i) 1-x,1-y,-z; (ii) 1-x,1-y,1-z; (iii) 1+x,y,z; (iv) -x,1-y,-z
Table 4. Anion–π contacts in complexes 1 and 2.
Table 4. Anion–π contacts in complexes 1 and 2.
Symmetry Code: (i) x,y,z in 1 (ii) 1-x,1-y,-z in 2
Table 5. Atoms in molecules (AIM) indices (a.u.) for the Mn–O and Mn–N bonds.
Table 5. Atoms in molecules (AIM) indices (a.u.) for the Mn–O and Mn–N bonds.
BondΡ(r)G(r)V(r)Eint aH(r) bV(r)/G(r) c
1 (MPW1PW91)
1 (WB97XD)
2 (MPW1PW91)
2 (WB97XD)
a kcal/mol; b total energy density; c potential to kinetic energy density.
Table 6. Bond order analysis of the Mn–N and Mn–O coordination interactions.
Table 6. Bond order analysis of the Mn–N and Mn–O coordination interactions.
Table 7. The calculated natural charge at the N-sites of the free and coordinated pincer ligands using MPW1PW91(WB97XD) methods.
Table 7. The calculated natural charge at the N-sites of the free and coordinated pincer ligands using MPW1PW91(WB97XD) methods.
Table 8. Inhibition zones at 200 µg of the tested compounds by agar well diffusion method.
Table 8. Inhibition zones at 200 µg of the tested compounds by agar well diffusion method.
CompoundS. aureusE. coliC. albicans
Table 9. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of complexes 1 and 2.
Table 9. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of complexes 1 and 2.
MIC (µg/mL)MBC (µg/mL)MIC (µg/mL)MBC (µg/mL)
S. aureus8.316.56.513.5
E. coli8.316.58.316.8
C. albicans18.510018.5100
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