The ligand 1 was freely optimized without any geometrical constraints and the optimized structure was in good agreement with that established by X-ray diffraction. The bond lengths N3-C1 (1.396 Å) and N2-C4 (1.489 Å) are in close agreement with the experimental values (1.396 Å and 1.490 Å). The bond angles C3-C2-N2 (108.25°) and C2-N2-C1 (109.68°) are in good agreement with the experimental structure (108.02° and 109.68° (109.32°). However the bond angle C1-N1-P1 (145.67 °) showed a significant deviation of 7.65° from the experimental value (138.02°) (Figure 3).
1 1′ 1″
Figure 3: Optimized structures of ligand 1, 1′ and 1″ using HF 3-21G(d) (Hydrogen atoms have been omitted for clarity).
Thus for further investigation ligands 1, 1′ and 1″ were optimized using density functional theory calculations (B3LYP 6-311+G(2d,p)). The optimized structure so obtained was in excellent agreement with experimental one, as the deviation in the bond angle of C1-N1-P1 (136.19°) was reduced to 1.83°. In the DFT optimized structure other bond angles and lengths were also very close to the experimental values. . The calculated bond lengths P1-C19 (1.864 Å) and N2-C2 (1.385 Å) matched with the experimental values (1.861 Å and 1.389 Å). The theoretical bond angles C3-N3-C1 (108.67°) and C1-N1-P1 (136.19°) are also in good agreement
33 with the experimental structure (108.52° and 138.02°).The optimized structures 1 and 1’ are geometrically close whereas 1″ shows distinct differences in bond angles and lengths compared to 1 and 1”. This feature is clearly reflected in the bond angle C1-N1-P1 which is 145.67° and 149.35 ° for ligands 2 and 2’ in the HF optimized structure, but drastically reduces to 129.37° in ligand 1″. Similar trend is observed in the B3LYP optimized structures where the C1-N1-P1 bond angles are 136.19°, 140.78° and 124.25° for ligands 1, 1′ and 1″ respectively. Comparison of all the computed structural parameters with experimental data for ligand 1 are shown in Table 1.
Table 1: Selected bond lengths [Å] and angles[o] of ligand 1 by different methodologies Bond
Length[Å]/angle[o] Experiment HF 3-21G*
B3LYP 6-311+G(2d,p)
P1-N1 1.644 1.654 1.682
P1-C12 1.845 1.839 1.855
P1-C19 1.861 1.841 1.864
N3-C3 1.389 1.401 1.394
N3-C1 1.396 1.396 1.408
N3-C8 1.495 1.492 1.501
N2-C2 1.389 1.397 1.385
N2-C1 1.395 1.389 1.399
N2-C4 1.49 1.489 1.496
N1-C1 1.295 1.275 1.294
C2-C3 1.295 1.322 1.34
N1-P1-C12 101.35 102.29 101.82
N1-P1-C19 101.6 102.95 101.82
C12-P1-C19 97.65 98.89 98.95
C3-N3-C1 108.52 108.79 108.67
C3-N3-C8 123.42 123.06 122.36
C1-N3-C8 127.82 128.12 128.98
C2-N2-C1 109.32 109.68 109.69
C2-N2-C4 125.12 125.16 124.8
34
C1-N2-C4 125.62 125.13 125.49
C1-N1-P1 138.02 145.67 136.19
N3-C1-N2 121.2 122.78 121.37
N3-C1-N1 133.62 132.43 133.9
N2-C1-N3 104.95 104.76 104.64
C3-C2-N2 108.02 108.25 108.22
The calculated geometries of 4 and 5 (Figure 4) by B3LYP/6-311+G(2d,p) were in excellent agreement to that of structural parameters obtained by X-ray diffraction. Furthermore on comparing the optimized structures of 3, 4 and 5 we see that there occurs a increase in the P-X (X=O,S,Se) bond length 1.50 Å (3), 1.99 Å(4), 2.15 Å (5) (Table 2) , which is expected from the increase in size of the chalcogens. Most of the other bond lengths and angles are similar for the three chalcogenides except the C1-N1-P1 angle. C1-N1-P1 angles for 4 (133.8 o) and 5 (133.79o) are almost identical, while for 3 (143.2 o) deviates by approximately 10o.
Figure 3: Optimized structures of 3, 4 and 5 by B3LYP/6-311+G(2d,p)
35 Table 2: Selected bond lengths (Å) and angles (o) from the calculated geometries of 3, 4 and 5 by B3LYP/6-311+G(2d,p) (Experimental values are given in brackets alongside).
Bond
Length[Å]/angle[o] 3 4 5
P1-N1 1.62 1.62(1.60) 1.63(1.61)
O1-P1 1.50 - -
S1-P1 - 1.99(1.96) -
Se1-P1 - - 2.15(2.12)
P1-C12 1.83 1.84(1.83) 1.84(1.83)
P1-C18 1.83 1.85(1.83) 1.85(1.83)
N1-C1 1.30 1.31(1.33) 1.31(1.33)
N3-C1 1.39 1.39(1.37) 1.39(1.38)
N3-C4 1.50 1.50(1.50) 1.50(1.50)
N2-C2 1.39 1.39(1.38) 1.39(1.39)
N2-C1 1.39 1.39(1.37) 1.39(1.37)
N2-C8 1.51 1.51(1.50) 1.51(1.50)
C2-C3 1.34 1.34 (1.34) 1.34(1.33)
N1-P1-C12 104.72 105.03(106.63) 105.30(105.68)
N1-P1-C18 106.64 107.30(105.81) 107.72(106.95)
C12-P1-C18 103.91 100.48(101.19) 100.02(101.28)
O1-P1-C12 111.21 - -
S1-P1-C12 - 112.96(111.73) -
Se1-P1-C12 - - 112.97(111.73)
O1-P1-C18 108.38 - -
S1-P1-C18 - 110.30(110.64) -
Se1-P1-C18 - - 110.55(110.64)
O1-P1-N1 120.67 - -
S1-P1-N1 - 119.02(119.12) -
Se1-P1-N1 - - 118.54(118.97)
C3-N3-C1 109.33 109.33(108.90) 109.32(109.20)
36 Scheme 1 depicts the protonation of three ligands at nitrogen. The energies have been calculated using only B3LYP method without including thermal correction; the difference between these two methods is approximately 10 kcal/mol, and there is no change in trend towards being protonated.
Scheme 1: Protonationof synthesized ligand 1 and model systems1′and 1″.
On protonation of the ligands, the exocyclic nitrogen is most probable to pick up the proton than phosphorous, where the protonation energy of 1 is 248.05 as compared to 252.88 kcal/mol (Scheme 2).
C3-N3-C4 124.47 123.81(123.61) 123.67(127.23)
C2-N2-C1 108.56 108.74(109.20) 108.77(108.89)
C2-N2-C8 121.60 118.40(124.26) 118.22(123.71)
C1-N1-P1 143.20 133.86(130.90) 133.79(130.72)
N3-C1-N2 105.32 105.25(105.93) 105.30(105.72)
N3-C1-N1 122.88 124.26(127.90) 124.59(126.23)
N2-C1-N1 131.68 130.39(125.98) 130.01(127.82)
37 .
Scheme 2: Protonation of phosphorus
Our calculations only reveal a slight difference in the protonation energies between three compounds. Tamm et al [12] reported that protonation affinities were not the best descriptors of basicity. From the calculated protonation energies we can infer that these are inconclusive in comparing the basicity of the three systems.
Furthermore on calculating the NBO charges on ligand 1 the nitrogens on the imidazole ring have charges of -.0458 and -0.469; the exocyclic nitrogen has a charge of -1.011, whereas the phosphorus has a charge of +1.024. Thus the exocylcic nitrogen having the highest negative charge is most likely to get protonated. Thus NBO charges on the exocyclic nitrogen were also calculated at DFT level (B3LYP/6-311+G(2d,p). A pronounced difference was found between 1(-1.011), its saturated analogue 1′ (-0.975) and acyclic 1″ (0.921). Hence the NBO charges clearly indicate that ligand 1 is more basic compared to model systems 1′and 1″.
. NBO Charges on exocyclic N X=CH -1.011
X=CH2 -0.975 X=CH3 -0.921
Scheme 3: Calculated NBO charges on exocylcic Nitrogen for ligand 1 and model systems 1′and 1″.
38 The higher negative charge on exocyclic nitrogen of 1 can be attributed to the stabilization of the zwitterionic form by the imidazolin ring.
Thereafter we decided to computationally explore the chalcogenides 1(a), 1(b) and 1(c).The NBO charges on the exocyclic nitrogen for 1a, 1b and 1c are -1.075, -1.076 and -1.087 respectively. For the sulphur and selenide derivative the chalcogens have a charge of -0.642 and -0.591 respectively and thus the exocylcic nitrogen having the highest negative charge is most likely to get protonated and we calculated the corresponding protonation energies (by the combined method) which were 244.91 kcal/mol and 243.97 kcal/mol respectively (Scheme 4).
242.78 244.91 243.97
Scheme 4: Protonation of 1(a), 1(b) and 1(c) . Energies are reported in kcal/mol.
However for the oxygen derivative (1(a)) oxygen has a higher negative charge (-1.139) than exocyclic nitrogen (-1.075). Protonation at oxygen (Scheme 5) lead to a protonation energy (243.34 kcal/mol) approximately 0.6 kcal/mol higher than the protonated form where exocyclic nitrogen bears the H+. Thus while the protonation energies does not always give a clear idea, the NBO analysis clearly indicate that for 1(a) the more electronegative oxygen is likely to get protonated.
39 243.34
Scheme 5: Protonation at oxygen for 1(a). Energies are reported in kcal/mol.
The NBO charges were also calculated using B3LYP method and a similar trend was observed.
For 1(a) oxygen had a higher negative charge (-1.130) as compared to exocyclic nitrogen (- 1.077). From Table 3 it is evident that occurs a decrease on the negative charge on exocyclic nitrogen ( -1.077, -1.090 and -1.095 for 1(a),1(b) and 1(c) respectively)as we go from oxygen to selenium, thus there occurs a decrease in the tendency of the exocylcic nitrogen to accept a proton, as the electronegativity of the chalcogenide bonded to phosphorus increases.
Table 3: Charge distribution in 1(a), 1(b) and 1(c).
Ligand Chalcogenide
HF/B3LYP B3LYP/B3LYP
Charges on exocyclic N
atom
Charge on chalcogenide
Charges on exocyclic
N atom
Charge on chalcogenide
1(a) O -1.075 -1.139 -1.077 -1.130
1(b) S -1.076 -0.642 -1.090 -0.653
1(c) Se -1.087 -0.591 -1.095 -0.593
40