Computational tools, specifically molecular mechanical force field (MM+) and semiempirical (
Previously the theory of transition-metal chemistry has lagged behind the computational theory of organic chemistry because quantitative methods were more complicated [
We selected certain schiff bases and complexes for which X ray crystallographic and IR data were available in the literature. One of the selected series of complexes was that of schiff-base ligands containing salicylaldehyde and amino acids. The crystal and IR studies of this compound were published by Sreenivasulu et al. [
Sreenivasulu et al. had synthesized and characterized three Schiff-base ligands: 2- 2-[(2-hydroxybenzyl) amino] ethanesulfonic acid which abbreviated as Figure
and their Cu complexes by some experimental methods. They gave observed wave numbers for the important infrared spectral bands of the ligands and their metal complexes by using IR spectroscopy. They have reported observed X ray crystallographic bond distances and bond angles.
X-ray crystal structures of complexes thus obtained demonstrated that the schiff-base ligand acts as a tridentate moiety, coordinating through the phenolato oxygen [
The structures of ligand and complex molecules were constructed by HyperChem 8.0 [
We constructed the structure of ligand and complexes by using Hyperchem GUI
The crystallographic model developed by Sreenivasulu et al. [
Crystal structure of [
Reprinted with permission crystal structure of [
Reprinted with permission Crystal Structure of [
Computational structure of [
Computational structure of [Cu2(Saes)2(
Computational structure of [Cu2(Sae)2(
All the molecular mechanics calculations were carried out on Pentium IV 2.46 GHz with the MM+ force field.The search for the lowest energy conformations was performed by Monte Carlo method. This method generated new conformations with randomly varied torsion angle. Monte Carlo search used the temperature Execution of a conformational search by the simulated annealing method with heat time 0.1 ps, run time 0.5 ps, cool time 0.1 ps, starting temperature 100 K, simulation temperature 300 K, and a temperature step 30 K. which was described by Choe et al. [ The structure obtained was minimized with a semiempirical method (PM3) and we verified that there were no negative frequencies in the vibration spectrum [
Semi empirical method is another tool for the determination of stability of molecule by incorporating quantum mechanical parameters into the calculation. We used PM3 method for the semi empirical calculation. The molecule constructed in the hyperchem GUI is initially optimized by using MM+ force field and Polak-Ribiere optimizer, then PM3 method is applied on the molecule. As in MM+ calculations all the parameters refer to isolated molecules in vacuum.
Recently density functional-based methods have been applied to a wide range of chemical problems including coordination compounds. Most successful chemical applications of density functional theory have probably been in the field of organometallic chemistry. A widely used variant of the B3 hybrid functional is termed B3LYP [
The bond distance data and bond angle data obtained from semi empirical, molecular mechanics, and DFT were given in Tables
Bond distances of complex [Cu2(Sams)2(H2O)2] unit in Å.
X-ray | MM+ | PM3 | DFT | |
---|---|---|---|---|
Cu(1)–O(1) | 1.89 | 1.86 | 1.84 | 1.94 |
Cu(1)–O(5) | 1.93 | 2.01 | 1.94 | 1.96 |
Cu(1)–N(1) | 1.93 | 1.91 | 1.88 | 2.01 |
Cu(1)–O(2) | 2.01 | 1.89 | 1.84 | 1.92 |
Cu(1)–O(3)A | 2.39 | 1.84 | 1.92 | 1.89 |
O(3)–Cu(1)A | 2.39 | 1.84 | 1.84 | 1.93 |
N(1)–C(7) | 1.29 | 1.32 | 1.31 | 1.20 |
N(1)–C(8) | 1.45 | 1.50 | 1.45 | 1.51 |
Cu(1)–Cu(1)A | 5.12 | 4.42 | 4.42 | 4.43 |
Bond angles of complex [Cu2(Sams)2(H2O)2] in degrees.
X-ray | MM+ | PM3 | DFT | |
---|---|---|---|---|
S(1)–O(2) –Cu(1) | 117.70 | 125.33 | 113.23 | 118.40 |
S(1)–O(3)–Cu(1)A | 131.60 | 127.41 | 127.47 | 127.00 |
O(1)–Cu(1)–O(5) | 91.36 | 94.96 | 94.08 | 91.08 |
O(1)–Cu(1)–N(1) | 92.20 | 92.20 | 96.60 | 88.50 |
O(5)–Cu(1)–N(1) | 165.60 | 119.10 | 109.97 | 121.52 |
O(1)–Cu(1)–O(2) | 175.60 | 175.60 | 167.89 | 177.09 |
O(1)–Cu(1)–O(3)A | 96.82 | 85.47 | 86.26 | 93.40 |
O(5)–Cu(1)–O(3)A | 89.12 | 92.10 | 92.72 | 94.76 |
N(1)–Cu(1)–O(3)A | 104.10 | 146.00 | 156.77 | 143.00 |
Bond distances of complex [Cu2(Saes)2(H2O)2] unit in Å.
X-ray | MM+ | PM3 | DFT | |
---|---|---|---|---|
Cu(1)–N(1) | 1.96 | 1.92 | 1.92 | 1.91 |
Cu(1)–O(5) | 1.98 | 1.98 | 1.98 | 2.18 |
Cu(1)–O(3)A | 2.41 | 1.91 | 1.91 | 1.59 |
C(7)–N(1) | 1.28 | 1.31 | 1.27 | 1.30 |
N(1)–C(8) | 1.47 | 1.48 | 1.32 | 1.49 |
O(3)–Cu(1)A | 2.41 | 1.92 | 1.96 | 1.92 |
Cu(1)–Cu(1)A | 5.33 | 4.42 | 3.5 | 3.12 |
Bond angles of complex [Cu2(Saes)2(H2O)2] in degrees.
[Cu2(Saes)2(H2O)2] | X-ray | MM+ | PM3 | DFT |
---|---|---|---|---|
O(1)–Cu(1)–O(2) | 168.87 | 176.80 | 171.77 | 158.00 |
N(1)–Cu(1)–O(5) | 166.9 | 142.60 | 110.77 | 124.00 |
O(1)–Cu(1)–N(1) | 94.08 | 92.41 | 97.31 | 90.30 |
O(2)–Cu(1)–N(1) | 97.04 | 85.86 | 90.24 | 96.04 |
O(1)–Cu(1)–O(5) | 85.74 | 91.70 | 90.88 | 85.06 |
O(2)–Cu(1)–O(5) | 83.56 | 94.80 | 89.43 | 107.00 |
O(1)–Cu(1)–O(3) | 87.32 | 89.00 | 84.28 | 85.00 |
O(2)–Cu(1)–O(3A | 89.54 | 89.10 | 87.49 | 91.00 |
N(1)–Cu(1)–O(3)A | 103.30 | 158.2 | 156.41 | 163.01 |
O(5)–Cu(1)–O(3)A | 89.70 | 88.3 | 92.68 | 88.68 |
Bond distances of complex [Cu2(Sae)2] unit in Å.
X-ray | MM+ | PM3 | DFT | |
---|---|---|---|---|
Cu(1)–O(1)A | 1.93 | 2.10 | 2.11 | 2.01 |
Cu(1)–O(1) | 1.97 | 1.85 | 1.86 | 1.89 |
Cu(1)–N(1) | 1.98 | 1.90 | 1.90 | 1.95 |
Cu(1)–O(2) | 2.00 | 1.87 | 1.87 | 1.89 |
O(1)–Cu(1)A | 1.93 | 2.08 | 2.08 | 2.00 |
Cu(1)–O(1)A | 1.93 | 2.10 | 2.11 | 1.98 |
C(7)–N(1) | 1.49 | 1.51 | 1.51 | 1.50 |
N(1)–C(8) | 1.47 | 1.53 | 1.53 | 1.49 |
Cu(1)–Cu(1)A | 3.03 | 2.22 | 2.21 | 2.11 |
Bond angles of complex [Cu2(Sae)2] in degrees.
X-ray | MM+ | PM3 | DFT | |
---|---|---|---|---|
S(1)–O(2)–Cu(1) | 120.58 | 126.49 | 126.13 | 122.23 |
O(1)a–Cu(1)–O(1) | 78.09 | 87.83 | 87.83 | 81.83 |
O(1)a–Cu(1)–N(1) | 172.15 | 97.99 | 125.69 | 123.09 |
O(1)–Cu(1)–N(1) | 94.31 | 97.99 | 97.99 | 98.96 |
O1)a–Cu(1)–O(2) | 95.32 | 93.92 | 93.92 | 93.90 |
O(1)–Cu(1)–O(2) | 152.72 | 164.24 | 164.24 | 164.04 |
Calculation of energy parameters by using molecular mechanics.
Ligand Sams | Complex | |
---|---|---|
Energy | 0.15 | 68.7 |
Bond | 0.64 | 4.94 |
Angle | 5.22 | 58.92 |
Dihedral | 8.41 | 7.3 |
Vdw | 7.38 | 19.42 |
Stretch-bend | 0.63 | 7.67 |
Electrostatic | 0.03 | |
Ligand Sae | Complex | |
Energy | 1.96 | 55.3 |
Bond | 0.85 | 2.5 |
Angle | 5.7 | 50.61 |
Dihedral | 8.6 | 2.96 |
Vdw | 6.5 | 6.61 |
Stretch-bend | 0.73 | 1.98 |
Electrostatic | 5.85 | 0.32 |
Ligand Saes | Complex | |
Energy | 67.12 | |
Bond | 0.73 | 4.9 |
Angle | 5.33 | 58.9 |
Dihedral | 7.55 | 8.55 |
Vdw | 5.59 | 19.6 |
Stretch-bend | 0.75 | |
Electrostatic | 7.5 | 0.04 |
Units Kcal/mol.
Calculation of energy parameters by using semi empirical methods (PM3) units Kcal/mol.
Sams | Saes | Sae | ||||
Ligand | Complex | Ligand | Complex | Ligand | Complex | |
Total energy | ||||||
Binding energy* | ||||||
Heat of formation |
Another interesting point we analyzed by using the molecular mechanics calculations was the prediction of the stability of this molecule by using MM+ force field and PM3 calculation by hyperchem. The result obtained in this calculation was summarized in Tables
The proposed structures of the samples were optimized and their IR were spectra generated based on PM3 semiempirical calculations using Hyperchem molecular modeling software. The assignment of the calculated wave numbers was aided by the animation option of same program, which gave a visual presentation of the shape of the vibrational modes.
Infrared spectra of ligand and their complexes have been analyzed by FT IR by Sreenivasulu et al. [
The molecular mechanics (MM+) method and semiempirical PM3 and density functional method were used to calculate bond distance, bond angle, and infrared spectra of the titled compounds. It was found that some of the bond lengths and bond angles were in agreement with X ray crystallographic method. But some discrepancy was occurring in Cu–O bond length and Cu–Cu bond lengths. We noticed a big anomaly in the bond angle of O(5)–Cu(1)–N(1) bond angles in all three complexes. But the one discrepancy observed in all three complexes was suggesting the recalibration of X ray crystallographic data. It was found that the simulated IR spectra were in consistence with the experimental data.
The authors thank Head of the Department of Chemistry, University of Calicut, Malabar Christian College Calicut and also the University Grants Commission, New Delhi, for financial assistance. They are thankful to Wiley and Professor Sreenivasaulu for permitting the publication of figures and crystallographic data.