Coordination of an Amino Alcohol Schiff Base Ligand Toward Cd(II)

Abstract

A potentially tetradentate Schiff base ligand, 2-((2-((pyridin-2-ylmethylene)amino)ethyl)amino)ethan-1-ol (PMAE), and its cadmium(II) complex, [$Cd(PMAE)I_2$] (1), were prepared and characterized by elemental analysis, FT-IR, Raman, $^1H$ and $^{13}C$ NMR spectroscopies and single-crystal X-ray diffraction. In the crystal structure of 1, the cadmium atom has a slightly distorted square-pyramidal geometry and a $CdN_3I_2$ environment in which the PMAE acts as an $N_3$-donor. In the crystal packing of the complex, the alcohol and amine groups of the coordinated ligands participate in hydrogen bonding with iodide ions and form $R^2{_2}(14)$ and $R^2{_2}(8)$ hydrogen bond motifs, respectively. In addition to the hydrogen bonds, the crystal network is stabilized by ${\pi}-{\pi}$ stacking interactions between pyridine rings. The thermodynamic stability of the isolated ligand and its cadmium complex along with their charge distribution patterns were studied by DFT and NBO analysis.

INTRODUCTION

β-Amino alcohols exhibit a broad spectrum of biological activities such as anti-hypertensive,¹ antibacterial agents² and HIV protease inhibitors.³ β-Amino alcohols have been used as intermediates and chiral auxiliaries in organic synthesis,⁴ as well as organocatalysts.⁵ Amino alcohols such as mono- and diethanolamine are known to fix CO₂ and are used as absorbents for the chemical absorption of CO₂. ⁶ Chiral amino alcohol Schiff base ligands⁷ comprise of a group of ligands that are widely employed in asymmetric transformations such as asymmetric oxidations,⁸ asymmetric alkynylations⁹ and enantioselective trimethylsilyl-cyanations.¹⁰ An example of such ligands is 2-((2- ((pyridin-2-ylmethylene)amino)ethyl)amino)ethan-1-ol (PMAE, Scheme 1) which is potentially tetradentate ligand. In this work, in order to extend the chemistry of this class of compounds, microwave-assisted preparation, characterization (elemental analysis, FT-IR, Raman, ¹H and ¹³C NMR spectroscopy) of PMAE ligand and its cadmium(II) complex is presented along with the X-ray structure and theoretical studies.

EXPERIMENTAL

All chemicals and solvents were reagent or analytical grade and used as received. The infrared spectra of KBr pellets in the range 4000–400 cm^–1 were recorded with a FT-IR TENSOR 27 spectrometer. ¹H and ¹³C NMR spectra were recorded on Bruker Aspect 3000 instrument. The carbon, hydrogen and nitrogen contents were determined by a Thermo Finnigan Flash Elemental Analyzer 1112 EA. The melting points were determined with a Barnsted Electrothermal 9200 electrically heated apparatus. The microwave-assisted synthesis of compound was carried out using a Microwave Laboratory Systems MicroSYNTH, Mile stone s.r.l. Raman spectrum was obtained using a Nicolet Model 910 Fourier-transform spectrometer.

Synthesis of 2-((2-((pyridin-2-ylmethylene)amino) ethyl)amino)ethan-1-ol PMAE

A mixture of 1.07 g (10 mmol) pyridine-2-carbaldehyde and 1.04 g (10 mmol) 2-((2-aminoethyl)amino)ethan-1-ol was irradiated inside a microwave oven for 10 min under reflux condition with a power up to 1000 W. After microwave irradiation a brown oily liquid was obtained. All volatile components were removed by rotary evaporation and the resultant was dissolved in water (15 mL) and then washed three times with chloroform (15 mL). The isolated water layer was evaporated to dryness. A viscous brown oil was obtained. Yield 1.00 g, 52%. Anal. calcd for C₁₀H₁₅N₃O (193.25): C 62.15, H 7.82, N 21.74; found C 63.04, H 7.98, N 22.15%. IR (KBr): 3325 (ν O−H), 3254 (ν N−H), 3063 (ν C−H)^ar, 2939 (ν C−H), 1613 (ν C=N), 1574 (ν C=N)^py, 1471 (ν C=C), 1435 (δ_as CH₂), 1366 (δ_s CH₂), 1227 (ν C−O), 1142 (ν C−N), 779 and 664 (γ py) cm⁻¹ . ¹H NMR (250 MHz, CDCl₃, atom numbering as in Scheme 1): δ = 8.33 (d, 1H, C¹H), 8.10 (s, 1H, C⁶H), 6.99– 7.49 (m, 3H, C²H−C⁴H), 5.55 (s, 1H, OH), 2.55–3.43 (m, 9H, C⁷H–C¹⁰H, N³H) ppm. ¹³C NMR (63 MHz, CDCl₃): δ = 122.8–159.0 (C¹ –C⁶), 82.8 (C¹⁰), 53.2–60.20 (C⁷−C⁹) ppm.

Scheme 1. Structures of the PMAE ligand.

Synthesis of [Cd(PMAE)I₂]

0.19 g (1 mmol) of PMAE dissolved in EtOH (15 mL) was added with stirring to a solution containing 0.37 g (1 mmol) of CdI₂ in ethanol (25 mL). The reaction mixture was refluxed for 6 h and then filtered. Yellow crystals suitable for X-ray diffraction were obtained from the solution after standing for four days. Yield 0.47 g, 84%; m. p. 208 °C. Anal. calcd for C₁₀H₁₅CdI₂N₃O (559.47): C 21.47, H 2.70, N 7.51; found C 21.22, H 2.70, N 7.82%. IR (KBr): 3328 (ν O−H), 3301 (ν N−H), 3063 (ν C−H)^ar, 2939 (ν C−H), 1651 (ν C=N), 1589 (ν C=N)^py, 1443 (δ_as CH2), 1373 (δ_s CH₂), 1219 (ν C−O), 1126 (ν C−N), 772 and 661 (γ py) cm⁻¹. Raman: 3073 (ν C−H)^ar, 2978 (ν C−H), 1630 (ν C=N), 1332 (δ_s CH₂), 1166 (ν C−N), 677 (γ py), 553 (ν Cd−N), 132 (ν Cd−I) cm⁻¹ . ¹H NMR (300 MHz, [D₆]-DMSO, atom numbering as in Scheme 1): δ = 8.85 (s, 1H, C⁶H), 7.83–8.67 (m, 4H, C¹H−C⁴H), 4.80 (s, 1H, OH), 2.82–3.89 (m, 9H, C⁷H–C¹⁰H, N³H) ppm.

Computational Details

All structures were optimized with the Gaussian 09 software¹¹ and calculated for an isolated molecule using Density Functional Theory (DFT)¹² at the B3LYP/6-31G(d,p) level of theory for ligand and B3LYP/LanL2DZ for complex as well as for NBO analysis. The coordination from the cif file of complex 1 was used as input file for theoretical calculations.

Crystal Structure Determination and Refinement

Diffraction data were collected at 150 K on a Rigaku Oxford Diffraction Gemini Ultra diffractometer. Data processing and absorption correction was carried out using Crysalis Pro.¹³ The structures were solved with direct methods and refined with least squares using the OLEX2 package.¹⁴ All hydrogen atoms were placed at their calculated positions. Selected crystallographic data are presented in Table 1. Diagrams of the molecular structure and unit cell were created using Ortep-III¹⁵ and Diamond.¹⁶ Selected bond lengths and angles are displayed in Table 2 and hydrogen bond geometries in Table 3. CCDC 981063 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.

Table 1. Crystal data and structure refinement for complex 1

Table 2. Selected bond lengths (Å) and angles (deg) for complex 1 with estimated standard deviations in parentheses

Table 3. Hydrogen bond dimensions (Å and deg) in complex 1

RESULTS AND DISCUSSION

The PMAE formed in the reaction between 2-((2-aminoethyl)amino)ethan-1-ol and pyridine-2-carbaldehyde under solvent free conditions using microwave irradiation.¹⁷ The reaction between an ethanolic solution of CdI2 with PMAE afforded yellow crystals of 1, which are air-stable and soluble in DMF and DMSO. A study of the literature revealed, that a similar structure to complex 1¹⁸ has been reported previously using a different method than used in this study. We prepared the ligand using microwave irradiation and then used it for preparation of the complex while Purkait et al.¹⁸ prepared the complex by a template reaction without isolating the ligand. Also full spectroscopic data of the ligand and its cadmium complex have not been reported previously and are present at this paper. The temperature of the X-ray data collection in our report (150 K) is different than the previous work (room temperature).

Spectroscopic Characterization

In the FT-IR spectrum of the ligand (Supplementary Materials), frequencies above and under 3000 cm⁻¹ which can be assigned to the stretching vibration of the C−H bonds, reveal the aromatic and aliphatic moieties in these structures, respectively. Frequencies near 3300 and 3250 cm⁻¹ can be attributed to the stretching vibrations of the ν(O−H) and ν(N−H), respectively. After complexation, no significant shift was observed for ν(O−H) while ν(N−H) shifted 47 cm⁻¹ to higher frequencies, confirming the coordination of the amine moiety of the ligand. In the FT-IR spectra of the ligand and complex, two peaks are observed near 1600 cm⁻¹ which can be assigned to the ν(C=N) vibrations of the imine and pyridine units. The ν(C=N) of the imine and pyridine in 1 is shifted 38 and 15 cm⁻¹, respectively, to the higher frequencies than the free ligand. Based on these observations we may infer that the PMAE acts as N₃-donor towards the cadmium atom. The ring wagging vibrations of the pyridine ring are also observed at near 770 and 660 cm⁻¹ in both spectra ^17b,19

Information about the low frequency metal-ligand vibrations was obtained by Raman spectroscopy. In this spectrum, the Cd–N stretching vibration appeared at 553 cm⁻¹. The presence of a band at 132 cm⁻¹ can be attributed to the terminal Cd−I stretching vibrations (100−200 cm⁻¹ for M−I^terminal).²⁰

In the ¹H NMR spectra of the ligand and 1 (see Scheme 1 for numbering), the peaks are observed in three regions, 7−9 ppm for aromatic and imine protons, 5 ppm for the alcohol unit and 2.5−4 ppm for aliphatic and amine moieties. Comparison of the ¹H NMR spectra of ligand and complex revealed that all peaks of the ligand are shifted to lower magnetic field after complexation. Among them, the proton of the imine shows the highest shift by 0.75 ppm. In the ¹³C NMR spectrum of the ligand, the imine and aromatic carbon atoms are observed at 120–160 ppm and others at 50−80 ppm. Among the aliphatic carbon atoms, the C10 atom which was attached to the alcohol moiety is observed at the lowest chemical shift.

Description of the Crystal Structure

In the crystal structure of 1 (Fig. 1), the cadmium atom has a Cd(N^py)(N^imine)(N^amine)(I^terminal)₂ environment and is coordinated by one N₃-donor PMAE ligand and two iodide ions with coordination number of five. A penta-coordinate geometry of 1 may adopt either a square pyramidal or a trigonal bipyramidal structure which is determined by applying the formula of Addison et al.. ^19,21 The angular structural parameter, τ = (β – α)/60, was calculated to be 0.05 for the cadmium atom indicating a slightly distorted square pyramidal geometry. Searching the Cambridge Structural Database (CSD)^20a for analogues of 1 containing Cd(N^py) (N^imine)(N^amine)(I^terminal)₂ environments with two five membered chelate rings revealed that there are five examples²² (one structure containing one five-membered and one six membered chelate rings¹⁸ was omitted for precise comparison). The average geometrical parameters for these structures were calculated and are presented in Scheme 2. Comparison of these data with those of 1 revealed that, all geometrical parameters in 1 are comparable with the CSD averages, except that the Cd1−I1 bond length is 0.092 Å longer than the average and also I−Cd−I bond angle in 1 is 6.33° smaller than the average. A study of the crystal packing of 1 revealed that the longest Cd−I has more interactions with adjacent molecules than the other one. For all analogues of 1, the τ value was calculated to be in the range of 0.07−0.32, showing that 1 is closer to ideal square-pyramidal geometry than its analogues.

Figure 1. The ortep diagram of the molecular structure of 1. The ellipsoids are drawn at the 25% probability level.

Scheme 2. CSD average for the Cd(N^py)(N^imine)(N^amine)(I^terminal)₂ environment.

The PMAE ligand forms two five-membered planar and non-planar chelate rings. This ligand does not have a chiral center, but upon coordination a new chiral center at N3 is produced. Although complex 1 has one chiral center, the crystals are racemic. ^17b,c

Each tridentate ligand can coordinate to a metal center in facial or meridional forms. In the mer form there are two angles of 90° and one of 180°, in the fac form there are three angles of 90°.^17a,20b In 1, two of the relevant bond angles of PMAE deviate slightly from 90° due to the chelating bite angle, whilst the third one is 141.4(1)° and thus consistent with the mer form (135° is exactly half way between fac and mer).

In the packing of 1, there are C–H···I, N–H···I, O–H···I and O–H···N interactions (Fig. 2). Among them, the O– H···I hydrogen bonds participate in the formation of R² ₂(14) hydrogen bond motifs (two acceptors, two donors with degree of 14)^17f between two molecules of 1. Another hydrogen bond motif (R²₂(8)) is formed between two adjacent complexes connected by two N–H···I hydrogen bonds. In addition to the hydrogen bonds, the network is stabilized by π–π stacking interactions between pyridine rings of the ligands of adjacent complexes. The pyridine rings are exactly parallel to each other (dihedral angle between planes: 0°) and nitrogen atoms of the pyridine rings have anti direction. The centroid–centroid distance and the perpendicular distance between the pyridine planes are 3.719 and 3.527 Å, respectively. Thus the slippage of pyridine rings was calculated to be 1.180 Å.²³

Figure 2. Packing of the 1, showing the hydrogen bonds.​​​​​​​

The total intermolecular interactions energy²⁴ for one complex unit of 1 was calculated using the CSD-materials tool in Mercury²⁵ (Fig. 3).²⁶ For this aim, the sum of intermolecular interactions energies in a molecular packing shell containing 100 molecules around one molecule of 1 was calculated to be −293.3 kJ/mol. In 1, 56 and 95 % of the calculated stabilization energy corresponds to the interactions with 6 and 18 surrounding molecules, respectively.

Figure 3. Variation diagram of total intermolecular interactions energy (E) for 1 with increasing number of surrounding molecules.​​​​​​​

Computational Studies

For comparing the structure of the complex 1 in solid state with an isolated one, DFT calculations were performed and optimized structures are presented in Fig. 4. For the optimized structure 1^opt, the τ was calculated to 0.17, showing that the square-pyramidal geometry in solid phase is different from that in an isolated molecule. Com paring the geometrical parameters of 1 with 1^opt revealed that in solid phase, the coordinated bond lengths formed by donor atoms that do not participate in hydrogen bonding (N1, N2) are similar to those of the isolated ones (Table 2) while others are different. In 1^opt, similarly to 1, two of the coordinated bond angles of the PMAE deviate slightly from 90°, whilst the third one is 139.37° and thus in the mer form. In the optimized structure of the ligand, the PMAE has E configuration and all nitrogen atoms have same direction as observed in the structure of the complex.

Figure 4. Optimized structures of the PMAE and its cadmium complex.​​​​​​​

For studying the charge distribution pattern of ligand before and after coordination an NBO analysis was performed (Table 4). The results reveal that the calculated charge on the carbon atom of the imine moiety is positive while other carbon atoms have a negative charge. Among the three nitrogen atoms, the amine nitrogen has higher electronegativity than the others. In the complex, the calculated charge on the metal atom (+1.07) is lower than the formal charge (+2) owing to electron donation of the ligand upon complexation. After coordination of the PMAE, the variation of charge on the hydrogen atoms is not significant while the charges on the carbon atoms are positive compared to the free ligand as well as iodide ligands, showing that these atoms play an important role in electron donation toward metal atom and decreasing the charge of it. The nitrogen atoms of the ligand show the highest charge variation after coordination. The charge on these atoms are negative compared to the free ligand and the nitrogen atom of the imine moiety has the highest variation.

Table 4. The NBO analysis results for PMAE and complex 1. The values are the average of charge on similar atoms​​​​​​​

In the optimized structure of PMAE, the LUMO is mainly delocalized on the aromatic and imine portions whilst the HOMO is delocalized on the aliphatic and partially on the imine unit (Table 5). In 1^opt, the LUMO has similar pattern with PMAE while the HOMO delocalized on the iodide ions. The cadmium atom does not have any quota in the frontier orbitals of the complex. DFT calculations reveal that the HOMO/LUMO energy gap in complex is 4.73 eV higher than the free ligand (Table 5).

Table 5. HOMO and LUMO orbitals for optimized structures of two DFPT isomers​​​​​​​

CONCLUSION

In this work, a Schiff base ligand, 2-((2-((pyridin-2- ylmethylene)amino)ethyl)amino)ethan-1-ol (PMAE), and its cadmium complex, [Cd(PMAE)I₂] (1), were synthesized and their spectral (IR, Raman, ¹H and ¹³C NMR) and structural properties were investigated. In the structure of 1, the cadmium atom has slightly distorted square-pyramidal geometry and CdN₃I₂ environment by coordination of the one mer-(N^py)(N^imine)(N^amine)-donor PMAE and two non-bridging iodide ions. The complex contains one chiral center on an amine nitrogen atom with racemic mixture of isomers. In the crystal packing of the complex, the alcohol and amine groups along with the iodide ions have important roles in the hydrogen bonding map. The O–H···I and N–H···I hydrogen bonds form R²₂(14) and R²₂(8) hydrogen bond motifs, respectively. In addition to the hydrogen bonds, the crystal network is stabilized by π–π stacking interactions between pyridine rings of the PMAE ligands on the adjacent complexes. The DFT calculations revealed that among different atoms of the ligand, the carbon atoms have significant role in electron donation toward cadmium atom. Based on the theoretical studies, the HOMO/LUMO energy gap in complex is 4.73 eV higher than the free ligand.