Normal Mode Analysis, Electronic Parameters and molecular docking study of 3, 5, 4’-Trihydroxy-6, 7-Dimethoxy-Flavone (Eupalitin) using First Principle
Tanveer Hasan1*, Raza Murad Ghalib2, Sayed Hasan Mehdi3, P. K. Singh4, S. S. R. Baqri5
1Deptt. of Physics, Shia P.G. College, Lucknow, India.
2Deptt. of Chemistry, Faculty of Sciences & Arts, Khulais, University of Jeddah, Jeddah, KSA
3Deptt. of Chemistry, Shia P G College, Lucknow, India
4Deptt. of Applied Physics, SMS Institute, Lucknow, India.
5Deptt. of Zoology, Shia P G College, Lucknow, India
*Corresponding Author E-mail: tanveerhasan09@gmail.com
ABSTRACT:
The quest for novel molecules with therapeutic activity is a happening field and drives a lot of research in the area of chemical synthesis. In this connection, this paper describes the results of detailed spectroscopic investigations along with quantum chemical studies carried out on 3,5,4’-Trihydroxy-6,7-Dimethoxy-Flavone (Eupalitin), a compound which has earlier been shown to possess significant cytotoxicity against colorectal cancer HCT 116 cell line. The density functional method at B3LYP/6-311++G(d,p) level is used to obtain the equilibrium geometries of the title compound. Further, we have performed vibrational analysis of the title compound at its equilibrium geometries and have established complete assignments of the significant vibrational modes. The calculated vibrational frequencies are shown to be in perfect agreement with the experimentally observed FTIR spectra of the molecule under study. The electronic properties of the molecule are discussed with the help of the descriptors like HOMO-LUMO and MEP surface and several electronic parameters are calculated which are closely related to their chemical reactivity and reaction paths. In addition, molecular docking study has also been carried out to get a better insight into such interactions of the molecule that may explain its biological role.
KEYWORDS: 3,5,4’-Trihydroxy-6,7-Dimethoxy-Flavone (Eupalitin); Normal Mode analysis; DFT; NLO; Molecular Docking.
The field of chemical synthesis is always abuzz with activity and the pharmaceutical industry is one of the major contributors to the exponential rise of drugs being synthesized in the lab and used abundantly in clinical trials.
The title compound 3,5,4’-Trihydroxy-6,7-Dimethoxy-Flavone (Eupalitin), which has been taken from the work of Ghalib et al. represents such a synthetic molecule of therapeutic interest as it has been reported to possess significant cytotoxicity against colorectal cancer HCT 116 cell line1. Given the said medicinal properties, it is tempting enough a prospect to explore the various physical and chemical properties of this novel compound which may be of immense help in explaining its biological role and tapping its therapeutic potential. Keeping this in view, the present work was undertaken which deals with a comprehensive investigation of its geometric and electronic structure in ground as well as first excited state. Vibrational spectral features of this molecule have been explained and calculated spectrum has been compared with experimentally recorded FT-IR spectrum by DFT/B3LYP method using 6-311++G(d,p) as basis set. In this regard, VEDA 4 program has been used to carry out the potential energy distribution (PED) analysis2. This work also includes the analysis of HOMO, LUMO and 3-D Molecular Electrostatic Potential (MEP) surface analysis along with calculation of electric moments to predict the NLO properties of the molecule. The molecular docking study of the title compound which is an important prerequisite for predicting its molecular interactions in the living systems was also carried out using Glutathione s-Transferase 1AQW protein as a possible target. The bacterial origin of the target protein chosen for docking correlates well with the reported antimicrobial activity of the title compound.
2. EXPERIMENTAL:
2.1 Structure:
The crystal structure of the title compound Eupalitin is taken from the work of Ghalib et al whereas the molecular structure of the title compound as modelled by Gaussview package 5.0.8 showing number scheme is shown in Figure I3.
2.2 Spectroscopic measurements:
The FT-IR spectrum of the title compound is available online4.
3. RESULT AND DISCUSSION:
All quantum chemical calculations of the title compound Eupalitin are carried out on an AMD dual core/2.71 GHz personal computer using Gaussian 09 program package, invoking gradient geometry optimization and employing the B3LYP/6-311++G (d,p) levels of theory to predict the molecular structure and vibrational wave numbers 5,6. The optimized structural parameters were used to calculate the vibrational wave numbers and the stability of optimized geometry was confirmed by the absence of any negative vibrational wave numbers. The vibrational frequency assignments have been carried out by combining the results of the Gaussview 5.0.8 program, symmetry considerations and the VEDA 4 program.
Fig. 1. Molecular structure of eupalitin as seen by gaussview
3.1 Optimized Molecular Geometry:
The optimized geometry of molecule with labeled atoms is shown in figure I. The optimized structural parameters (bond length, bond angle, dihedral angle etc.) calculated by B3LYP at 6-311++ (d, p) basis set are provided in table I and are compared with the experimental data. The calculated geometrical parameters show a good agreement with the experimental data and they are the basis for calculating vibrational frequencies and electronic properties.
The presence of hetero atom H10 in the molecular structure of the title compound Eupalitin has led to the possibility of intermolecular non-covalent interactions. The hydrogen atom H10 of one molecule is interacting with hydrogen atom of another molecule with bifurcated H-bond distances 0.836 Ĺ, which corresponds with bifurcated H-bond angle 108°.
The title molecule Eupalitin contains three rings R1, R2 and R3 all are six member rings. The ring R1 contains one oxygen atom O1 and one molecule of the compound is attached with the other molecule with H10 of ring R3. The equilibrium geometry optimization of lowest energy has been achieved by energy minimization. The calculated vibration spectrum contains no imaginary wave number which indicates that the optimized geometry of the molecule Eupalitin represents the minima on potential energy surface. The optimized bond length of ν(C-C) in the ring R1, R2, and R3 ranges between 1.365-1.466 Ĺ. The optimized bond length of ν(C-O) varies between 1.357-1.439 Ĺ. As expected, the optimized bond length of ν(O3=C4) attached to R1 is calculated at 1.2168 Ĺ, which is lesser than the other ν(O-C) bond lengths suggesting a double bond structure. The bond lengths of ν(O2-H2), ν(O4-H4) and ν(O7-H3) are calculated as 0.843, 0.864 and 0.836 respectively. The optimized bond length of all ν(C-H) vibrational modes, are calculated as 0.95 Ĺ. The CH3 bond lengths such as ν(C17-H17A), ν(C17-H17B) and ν(C-17-H17C) etc. are calculated in the range 0.98 Ĺ which are in good agreement with the X-ray data.
Some of the characteristics bond angles like Ф(C6-O5-C17) , Ф(C7-O6-C18), Ф(O1-C2-C11), Ф(O7-C14-C15) and Ф(O7-C14-C15) are calculated as 118°,119°, 113°, 117° and 123° near the vicinity of ring R1 arise due to decrease in lateral distance between the carbon atoms C2 and C11.
The repulsive interaction between the electrons of the bonds increases thereby causing a decrease in bond angle.
The torsional angles of ring R1, R2 and R3 like τ(C9-O1-C2-C3), τ(C9-O1-C2-C11), τ(C2-O1-C9-C8), τ(C2-O1-C9-C10), τ(H4-O4-C5-C6), τ(H4-O5-O6-C7), τ(H7-O7-C14-C13) and τ(H7-C2-C14-C15) are calculated by DFT as 2.7°, 177.6°, 177°, 1.6°, 179°, 0.385°, 179.87°, and 0.142° respectively, which suggest that ring R1, R2 and R3 nearly lie on the same plane. Several values of torsional angles calculated by DFT method are also shown in table I which could not be found in X-ray method. All other optimized geometrical parameters in the title compound are reasonably matched with experimentally obtained X-ray data and are in accordance with the reported literature 7-10.
Table I Optimized ground state structural parameters of Eupalitin at B3LYP method
|
S .No |
Parameter |
Method |
S. No |
Parameter |
Method |
||
|
Stretching Ĺ |
X-ray |
DFT |
Bending (deg) |
X-ray |
DFT |
||
|
ν(O1-C2) |
1.374 |
1.4026 |
45 |
Ф(C7-O6-C18) |
118.3 |
119.01 |
|
|
2 |
ν(O1-C9) |
1.372 |
1.3924 |
46 |
Ф(H7-O7-C14) |
108 |
112.43 |
|
3 |
ν(O2-H2) |
0.843 |
0.9916 |
47 |
Ф(O1-C2-C3) |
120.1 |
118.36 |
|
4 |
ν(O2-C3) |
1.357 |
1.3893 |
48 |
Ф(O1-C2-C11) |
112.6 |
112.85 |
|
5 |
ν(O3-C4) |
1.268 |
1.2974 |
49 |
Ф(C3-C2-C11) |
127.3 |
128.79 |
|
6 |
ν(O4-H4) |
0.864 |
1.0062 |
50 |
Ф(O2-C3-C2) |
120.4 |
122.93 |
|
7 |
ν(O4-C5) |
1.356 |
1.378 |
51 |
Ф(O2-C3-C4) |
118 |
114.94 |
|
8 |
ν(O5-C6) |
1.38 |
1.3891 |
52 |
Ф(C2-C3-C4) |
121.6 |
122.14 |
|
9 |
ν(O5-C17) |
1.439 |
1.4729 |
53 |
Ф(O3-C4-C3) |
120.8 |
118.73 |
|
10 |
ν(O6-C7) |
1.355 |
1.3801 |
54 |
Ф(O3-C4-C10) |
122.5 |
123.76 |
|
11 |
ν(O6-C18) |
1.436 |
1.4595 |
55 |
Ф(C3-C4-C10) |
116.7 |
117.51 |
|
12 |
ν(O7-H7) |
0.836 |
0.9792 |
56 |
Ф(O4-C5-C6) |
118.9 |
119.71 |
|
13 |
ν(O7-C14) |
1.364 |
1.3953 |
57 |
Ф(O4-C5-C10) |
120.8 |
119.92 |
|
14 |
ν(C2-C3) |
1.365 |
1.381 |
58 |
Ф(C6-C5-C10) |
120.3 |
120.37 |
|
15 |
ν(C2-C11) |
1.466 |
1.4642 |
59 |
Ф(O5-C6-C5) |
119.4 |
123.28 |
|
16 |
ν(C3-C4) |
1.428 |
1.4528 |
60 |
Ф(O5-C6-C7) |
120.9 |
117.84 |
|
17 |
ν(C4-C10) |
1.429 |
1.4402 |
61 |
Ф(C5-C6-C7) |
119.7 |
118.73 |
|
18 |
ν(C5-C6) |
1.37 |
1.4038 |
62 |
Ф(O6-C7-C6) |
114.4 |
115.15 |
|
19 |
ν(C5-C10) |
1.416 |
1.4301 |
63 |
Ф(O6-C7-C8) |
124.2 |
123.29 |
|
20 |
ν(C6-C7) |
1.412 |
1.4314 |
64 |
Ф(C6-C7-C8) |
121.5 |
121.57 |
|
21 |
ν(C7-C8) |
1.388 |
1.4105 |
65 |
Ф(C7-C8-H8) |
121.3 |
122.36 |
|
22 |
ν(C8-H8) |
0.95 |
1.0824 |
66 |
Ф(C7-C8-C9) |
117.5 |
118.33 |
|
23 |
ν(C8-C9) |
1.388 |
1.3962 |
67 |
Ф(H8-C8-C9) |
121.3 |
119.31 |
|
24 |
ν(C9-C10) |
1.393 |
1.4109 |
68 |
Ф(O1-C9-C8) |
116.9 |
117.63 |
|
25 |
ν(C11-C12) |
1.403 |
1.422 |
69 |
Ф(O1-C9-C10) |
120.3 |
120.31 |
|
26 |
ν(C11-C16) |
1.4 |
1.4192 |
70 |
Ф(C8-C9-C10) |
122.8 |
112.06 |
|
27 |
ν(C12-H12) |
0.95 |
1.0839 |
71 |
Ф(C4-C10-C5) |
121.7 |
121.71 |
|
28 |
ν(C12-C13) |
1.384 |
1.3969 |
72 |
Ф(C4-C10-C9) |
120.1 |
119.36 |
|
29 |
ν(C13-H13) |
0.95 |
1.0853 |
73 |
Ф(C5-C10-C9) |
118.1 |
118.93 |
|
30 |
ν(C13-C14) |
1.384 |
1.4089 |
74 |
Ф(C2-C11-C12) |
120.6 |
120 |
|
31 |
ν(C14-C15) |
1.39 |
1.4092 |
75 |
Ф(C2-C11-C16) |
121.4 |
121.57 |
|
32 |
ν(C15-H15) |
0.95 |
1.089 |
76 |
Ф(C12-C11-C16) |
117.9 |
118.42 |
|
33 |
ν(C15-C16) |
1.38 |
1.4015 |
77 |
Ф(C11-C12-H12) |
119.7 |
119.25 |
|
34 |
ν(C16-H16) |
0.95 |
1.0823 |
78 |
Ф(C11-C12-C13) |
120.6 |
121.12 |
|
35 |
ν(C17-H17A) |
0.98 |
1.0921 |
79 |
Ф(H12-C12-C13) |
119.7 |
119.63 |
|
36 |
ν(C17-H17B) |
0.98 |
1.0987 |
80 |
Ф(C12-C13-H13) |
119.7 |
121.49 |
|
37 |
ν(C17-H17C) |
0.98 |
1.0931 |
81 |
Ф(C12-C13-C14) |
120.6 |
119.61 |
|
38 |
ν(C18-H18A) |
0.98 |
1.091 |
82 |
Ф(H13-C13-C14) |
119.7 |
118.9 |
|
39 |
ν(C18-H18B) |
0.98 |
1.0981 |
83 |
Ф(O7-C14-C13) |
118.3 |
116.82 |
|
40 |
ν(C18-H18C) |
0.98 |
1.0984 |
84 |
Ф(O7-C14-C15) |
122.2 |
122.91 |
|
Bending (deg) |
85 |
Ф(C13-C14-C15) |
119.4 |
120.28 |
|||
|
41 |
Ф(C2-O1-C9) |
121.3 |
122.32 |
86 |
Ф(C14-C15-H15) |
119.9 |
120.35 |
|
42 |
Ф(H2-O2-C3) |
111 |
106.87 |
87 |
Ф(C14-C15-C16) |
120.2 |
119.98 |
|
43 |
Ф(H4-O4-C5) |
106 |
109.42 |
88 |
Ф(H15-C15-C16) |
119.9 |
119.67 |
|
44 |
Ф(C6-O5-C17) |
114.6 |
117.95 |
89 |
Ф(C11-C16-C15) |
121.2 |
120.59 |
|
90 |
Ф(C11-C16-H16) |
119.4 |
119.54 |
139 |
τ(C3-C4-C10-C9) |
1.9 |
0.7674 |
|
91 |
Ф(C15-C16-H16) |
119.4 |
119.87 |
140 |
τ(O4-C5-C6-O5) |
5.9 |
3.6437 |
|
92 |
Ф(O5-C17-H17A) |
109.5 |
104.83 |
141 |
τ(O4-C5-C6-C7) |
177.6 |
179.0848 |
|
93 |
Ф(O5-C17-H17B) |
109.5 |
110.16 |
142 |
τ(C10-C5-C6-O5) |
172.7 |
176 |
|
94 |
Ф(O5-C17-H17C) |
109.5 |
110.56 |
143 |
τ(C10-C5-C6-C7) |
3.7 |
0.5637 |
|
95 |
Ф(H17A-C17-H17B) |
109.5 |
109.91 |
144 |
τ(O4-C5-C10-C4) |
2.4 |
0.0312 |
|
96 |
Ф(H17A-C17-H17C) |
109.5 |
110.79 |
145 |
τ(O4-C5-C10-C9) |
179 |
178.6354 |
|
97 |
Ф(H17B-C17-H17C) |
109.5 |
110.46 |
146 |
τ(C6-C5-C10-C4) |
176.1 |
179.62 |
|
98 |
Ф(O6-C18-H18A) |
109.5 |
104.96 |
147 |
τ(C6-C5-C10-C9) |
2.4 |
1.0124 |
|
99 |
Ф(O6-C18-H18B) |
109.5 |
111.02 |
148 |
τ(O5-C6-C7-O6) |
4.69 |
|
|
100 |
Ф(O6-C18-H18C) |
109.5 |
111.13 |
149 |
τ(O5-C6-C7-C8) |
174.6 |
175.42 |
|
101 |
Ф(H18A-C18-H18B) |
109.5 |
109.83 |
150 |
τ(C5-C6-C7-O6) |
178.5 |
179.62 |
|
102 |
Ф(H18A-C18-H18C) |
109.5 |
109.82 |
151 |
τ(C5-C6-C7-C8) |
0.27 |
|
|
103 |
Ф(H18B-C18-H18C) |
109.5 |
109.97 |
152 |
τ(O6-C7-C8-H8) |
0.3308 |
|
|
Torsion(deg) |
153 |
τ(O6-C7-C8-C9) |
178.2 |
179.25 |
|||
|
104 |
τ(C9-O1-C2-C3) |
2.7 |
0.0027 |
154 |
τ(C6-C7-C8-H8) |
179.79 |
|
|
105 |
τ(C9-O1-C2-C11) |
177.6 |
179.99 |
155 |
τ(C6-C7-C8-C9) |
0.6356 |
|
|
106 |
τ(C2-O1-C9-C8) |
177.1 |
179.66 |
156 |
τ(C7-C8-C9-O1) |
175.9 |
179.77 |
|
107 |
τ(C2-O1-C9-C10) |
1.6 |
0.398 |
157 |
τ(C7-C8-C9-C10) |
2.8 |
0.1676 |
|
108 |
τ(H2-O2-C3-C2) |
178.9 |
179.65 |
158 |
τ(H8-C8-C9-O1) |
0.1745 |
|
|
109 |
τ(H2-O2-C3-C4) |
0.2192 |
159 |
τ(H8-C8-C9-C10) |
179.76 |
||
|
110 |
τ(H4-O4-C5-C6) |
179.26 |
160 |
τ(O1-C9-C10-C4) |
0.7861 |
||
|
111 |
τ(H4-O4-C5-C10) |
0.3852 |
161 |
τ(O1-C9-C10-C5) |
177.7 |
179.42 |
|
|
112 |
τ(C17-O5-C6-C5) |
57.31 |
162 |
τ(C8-C9-C10-C4) |
179.4 |
179.28 |
|
|
113 |
τ(C17-O5-C6-C7) |
127.21 |
163 |
τ(C8-C9-C10-C5) |
1 |
0.645 |
|
|
114 |
τ(C6-O5-C17-H17A) |
177.53 |
164 |
τ(C2-C11-C12-H12) |
0.0294 |
||
|
115 |
τ(C6-O5-C17-H17B) |
59.34 |
165 |
τ(C2-C11-C12-C13) |
179.8 |
179.95 |
|
|
116 |
τ(C6-O5-C17-H17C) |
63.03 |
166 |
τ(C16-C11-C12-H12) |
|
179.98 |
|
|
117 |
τ(C6-O6-C7-C6) |
177.91 |
167 |
τ(C16-C11-C12-C13) |
0.8 |
0.004 |
|
|
118 |
τ(C18-O6-C7-C8) |
2.2 |
168 |
τ(C2-C11-C16-C15) |
179.9 |
179.9493 |
|
|
119 |
τ(C16-O6-C18-H18A) |
|
178.95 |
169 |
τ(C2-C11-C16-H16) |
0.0265 |
|
|
120 |
τ(C16-O6-C18-H18B) |
60.34 |
170 |
τ(C12-C11-C16-C15) |
0.9 |
0.0014 |
|
|
121 |
τ(C16-O6-C18-H18C) |
62.4 |
171 |
τ(C12-C11-C16-H16) |
|
179.98 |
|
|
122 |
τ(H7-O7-C14-C13) |
179.87 |
172 |
τ(C11-C12-C13-H13) |
|
179.984 |
|
|
123 |
τ(H7-O7-C14-C15) |
0.142 |
173 |
τ(C11-C12-C13-C14) |
0.4 |
0.0033 |
|
|
124 |
τ(O1-C2-C3-O2) |
177.9 |
179.86 |
174 |
τ(H12-C12-C13-H13) |
|
0.0072 |
|
125 |
τ(O1-C2-C3-C4) |
0.0005 |
175 |
τ(H12-C12-C13-C14) |
|
179.97 |
|
|
126 |
τ(C11-C2-C3-O2) |
1.7 |
0.1481 |
176 |
τ(C12-C13-C14-O7) |
179.5 |
179.99 |
|
127 |
τ(C11-C2-C3-C4) |
178.9 |
179.99 |
177 |
τ(H13-C13-C14-O7) |
0.0132 |
|
|
128 |
τ(O1-C2-C11-C12) |
0.0709 |
178 |
τ(H13-C13-C14-C15) |
|
0.0174 |
|
|
129 |
τ(O1-C2-C11-C16) |
179.98 |
179 |
τ(H15-C14-C13-O7) |
179.99 |
||
|
130 |
τ(C3-C2-C11-C12) |
179.94 |
180 |
τ(H15-C15-C14-O7) |
0.0091 |
||
|
131 |
τ(C3-C2-C11-C16) |
18.7 |
0.0116 |
181 |
τ(C16-C15-C14-O7) |
179.4 |
179.99 |
|
132 |
τ(O2-C3-C4-O3) |
0.232 |
182 |
τ(C13-C14-C15-H15) |
|
179.99 |
|
|
133 |
τ(O2-C3-C4-C10) |
179.74 |
183 |
τ(C13-C14-C15-C16) |
0.3 |
0.0158 |
|
|
134 |
τ(C2-C3-C4-O3) |
179.64 |
184 |
τ(C14-C15-C16-C11) |
0.7 |
0.0084 |
|
|
135 |
τ(C2-C3-C4-C10) |
0.8 |
0.386 |
185 |
τ(C14-C15-C16-H16) |
|
179.97 |
|
136 |
τ(O3-C4-C10-C5) |
3 |
0.6605 |
186 |
τ(H15-C15-C16-C11) |
|
179.99 |
|
137 |
τ(O3-C4-C10-C9) |
178.5 |
179.26 |
187 |
τ(H15-C15-C16-H16) |
|
0.0204 |
|
138 |
τ(C3-C4-C10-C5) |
176.5 |
179.37 |
3.2 Vibrational Analysis:
3.2.1 (O-H) Stretch:
In the vibrational spectra, the strength of hydrogen bond decides the position of O-H band. In general the O-H stretching appears in 3600-3400 cm-1 11,12. In the present study the title molecule exhibits a weak absorption peak in the FTIR spectra at 3520 cm-1 and two calculated vibrational modes are assigned at 3549 and 3365 cm-1 with 100 and 99% PED’s respectively.
3.2.2 (C-H) stretch:
The hetero aromatic structure of ring R1 of the title compound shows the presence of (C-H) stretching vibration in the region 3133-3056 cm-1, which is the characteristic region for ready identification of C-H stretching vibration and is assigned a strong peak at 3270 cm-1 in the FTIR spectra 13. There is a discrepancy in the calculated and observed peaks due to the position of substitution of other moieties. The (C-H) in-plane bending vibrations appear in the range 1500-1000 cm-1 and are very useful for the purpose of characterization. The (C-H) in-plane bending vibrations appearing as strong band in the FTIR spectra at 1470, 1410 and 1360 cm-1 and are well assigned at 1474, 1402 and 1359 cm-1 respectively. These are well supported by literature 14.
3.2.3 Methyl (CH3) Vibrations:
The asymmetric CH3 stretching vibrations are calculated at 3062, 3022, 2994, 2919 and 2909 cm-1 and are assigned to two observed weak absorption peaks at 3220 and 3200 cm-1 respectively in FTIR spectra. These assignments are also supported by literature 15.
3.2.4 (C-C)-Vibrations:
The ν(C-C) aromatic stretching vibrational modes also known as semicircle stretching were calculated at 1666, 1639, 1627, 1594, 1580, 1557, 1522, 1402, 1391, 1370, 1333 and 1324 cm-1 and are assigned to vibrational modes in-plane bending ф(C-C-C) and torsional τ(H-C-C-C) mixed with stretching modes. The corresponding absorption peaks are 1680, 1640, 1630, 1610, 1550, 1410 and 1380 cm-1 respectively in the FTIR spectra. Therefore theoretically calculated values are in good agreement with experimental FTIR spectra. The absorption peak at 1410 cm-1 in the FTIR spectra appears to be one of the characteristics peaks of the title molecule.
Table I: Frequency assignments for Eupalitin at B3LYP/6-311G (d,p) in cm–1, with PED % in Square Brackets
|
S. No. |
Calc Freq Unscaled |
Scaled |
Exp freq FTIR |
Assignment Modes[PED] |
|
1 |
3705 |
3549 |
3715(m) |
ν(O9-H10)[100] |
|
2 |
3513 |
3365 |
3520(m) |
ν(O2-H3)[99] |
|
3 |
3270 |
3133 |
3270(s) |
ν(C29-H30)[97] |
|
4 |
3262 |
3125 |
ν(C17-H18)[99] |
|
|
5 |
3256 |
3119 |
ν(C22-H23)[76]+ν(C24-H25)[22] |
|
|
6 |
3231 |
3095 |
3220(wsh) |
ν(C24-H25)[77] + ν(C22-H23)[23] |
|
7 |
3196 |
3062 |
ν(C31-H32)[55] + ν(C31-H34)[32]+ ν(C35-H34)[11] |
|
|
8 |
3195 |
3061 |
3200(w) |
ν(O5-H6)[87] |
|
9 |
3190 |
3056 |
ν(C27-H28)[98] |
|
|
10 |
3155 |
3022 |
ν(C31-H32)[22]+ν(C31-H33)[33]+ν(C31-H34)[44] |
|
|
11 |
3125 |
2994 |
2870(m) |
ν(C35-H37)[52]+ν(C35-H38)[48] |
|
12 |
3047 |
2919 |
ν(C31-H33)[66]+ν(C31-H34)[19]+ν(C31-H32)[15] |
|
|
13 |
3037 |
2909 |
ν(C35-H38)[47]+ν(C35-H37)[42]+ν(C35-H36)[11] |
|
|
14 |
1695 |
1624 |
1680(m) |
ν(C1=C12)a[13]+ν(C17=C19)a[10]+ν(C14=C15)[19] |
|
15 |
1667 |
1639 |
1640(s) |
ν(C22=C24)[22]+ν(C1=C12)[13]+ν(C29=C27)[22]+ν(C11=C12)[12] |
|
16 |
1655 |
1627 |
1630(m) |
ν(C11=C12)[29] |
|
17 |
1622 |
1594 |
1610(m) |
ν(C21=C29[11]a + ν(C26=C27)[32] |
|
18 |
1607 |
1580 |
ν(C16=C17)[22]+ν(C19=C20)[24]+φ(C15-C14-C20)[13] |
|
|
19 |
1584 |
1557 |
1550(s) |
ν(C17-C19)[14]+ν(O4-C13)[15]+φ(H6-O5-C14)[17] |
|
20 |
1548 |
1522 |
ν(C21-C29)[10] + φ(H30-C29-C27)[16]+ φ(H28-C27-C29)[16] |
|
|
21 |
1528 |
1502 |
1510(s) |
φ(H33-C31-H34)[53]+ φ(H33-C31-H34)[28]+ τ(H34-C31-O7-C15)[12] |
|
22 |
1518 |
1492 |
φ(H36-C35-H38)[51]+ φ(H36-C35-H37)[10]+ φ(H38-C35-H37)[16]+ τ(H36-C35-O7-C16)[10] |
|
|
23 |
1517 |
1491 |
1500(m) |
φ(H37-C35-H36)[46]+ φ(H38-C35-H37)[23]+τ(H37-C35-O8-C16)[11] |
|
24 |
1511 |
1485 |
φ(H38-C35-H37)[46]+ν(C13-C20)[18] |
|
|
25 |
1503 |
1477 |
φ(H32-C31-H33)[57]+ φ(H33-C31-H34)[16]+ φ(H32-C31-H34)[15] |
|
|
26 |
1499 |
1474 |
1470(s) |
φ(H36-C35-H38)[11]+ φ(H32-C31-H34)[13]+ φ(H37-C35-H36)[10] |
|
27 |
1482 |
1457 |
φ(H38-C35-H37)[12]+ φ(H34-C31-H33)[13]+ φ(H32-C31-H34)[20] |
|
|
28 |
1468 |
1443 |
ν(C22-C24)[14]+ν(C27-C29)[10]+ν(O4-C13)[10] |
|
|
29 |
1465 |
1440 |
ν(O4-C13)[12] |
|
|
30 |
1426 |
1402 |
1410(vs) |
ν(C14-C20)[10]+φ(H6-O5-C14)[19] |
|
31 |
1415 |
1391 |
1380(s) |
ν(C16-C17)[19]+ν(C14-C15)[14]+ν(C17-C19)[12] |
|
32 |
1394 |
1370 |
ν(C24-C26)[16] + ν(C27-C29)[15]+ν(C21-C29)[19]+φ(H10-O9-C26)[11] |
|
|
33 |
1382 |
1359 |
1360(s) |
φ(H30-C29-C27)[12]+φ(H6-O5-C14)[17] |
|
34 |
1356 |
1333 |
ν(C21-C29)[15]+φ(H30-C29-C27)[13] |
|
|
35 |
1347 |
1324 |
ν(C11-C21)[22]+φ(H3-O2-C12)[33] |
|
|
36 |
1345 |
1322 |
ν(O8-C16)[11]+ν(C17-C19)[13] |
|
|
37 |
1296 |
1274 |
ν(O9-C26)[11]+ν(O7-C15)[13]+φ(H3-O2-C12)[16] |
|
|
38 |
1288 |
1266 |
1250(m) |
ν(O9-C26)[30]+φ(H23-C22-C24)[11] |
|
39 |
1242 |
1221 |
ν(O7-C15)[16]+φ(H18-C17-C19)[15] |
|
|
40 |
1227 |
1206 |
1215(m) |
φ(H28-C27-C29)[25]+φ(H18-C17-C19)[17] |
|
41 |
1217 |
1196 |
ν(O8-C16)[26]+φ(H18-C17-C19)[17] |
|
|
42 |
1206 |
1185 |
1190(vs) |
ν(O1-C11)[26]+ν(O8-C16)[20]+τ(H37-C35-O8-C16)[17]+ |
|
τ(H38-C35-O8-C16)[16] |
||||
|
43 |
1193 |
1173 |
φ(H32-C31-H33)[25]+φ(H32-C31-H34)[12]+τ(H33-C31-O7-C15)[29]+ τ(H34-C31-O7-C15)[26] |
|
|
44 |
1177 |
1157 |
1165(w) |
φ(H10-O31-C26)[16]+φ(H25-C24-C22)[17] |
|
45 |
1172 |
1152 |
1150(w) |
R3-brth[33] |
|
46 |
1151 |
1131 |
φ(H36-C35-H38)[13]+φ(H36-C35-H37)[14]+τ(H36-C35-O8-C16)[39]+ |
|
|
τ(H37-C35-O8-C12)[18] |
||||
|
47 |
1149 |
1129 |
φ(H36-C35-H38)[13]+φ(H36-C35-H37)[14]+τ(H36-C35-O8-C16)[39]+ τ(H37-C35-O8-C12)[18] |
|
|
48 |
1141 |
1122 |
1125(w) |
ν(C22-C24)[10]+φ(H10-O9-C26)[26]+φ(H23-C22-C24)[11] |
|
49 |
1117 |
1098 |
1190(vs) |
ν(O8-C35)[10]+φ(O1-C11=C12)[16]+ν(O1-C11)[14] |
|
50 |
1069 |
1051 |
1050(wsh) |
ν(O2-C12)[11]+ ν(O8-C35)[17]+φ(C13-C20-C14)[12] |
|
51 |
1058 |
1040 |
ν(O25-C14)[12]+φ(C20-C19-C17)[12] |
|
|
52 |
1032 |
1014 |
1020(m) |
R3-defrm[86] |
|
53 |
1026 |
1009 |
1005(w) |
τ(H23-C22-C24-C26)[25]+τ(H30-C29-C27-C26)[34]+τ(H25-C24-C26-C27)[19] |
|
54 |
1016 |
999 |
984(wsh) |
τ(H23-C22-C24-C26)[26]+τ(H30-C29-C27-C26)[31]+τ(H25-C24-C26-C27)[15] |
|
55 |
978 |
961 |
950(m) |
R2-brth[30]+ν(O7-C31)[52] |
|
56 |
943 |
927 |
ν(O8-C35)[45]+φ(C16-O8-C35)[16] |
|
|
57 |
893 |
878 |
R3-brth[11]+ φ(C19-O1-C11)[10] |
|
|
58 |
882 |
867 |
870(m) |
τ(H23-C22-C24-C26)[24]+τ(H28-C27-C29-C21)[10]+τ(H25-C24-C26-C27)[33]+ ω(O9-C24-C27-C26)[13] |
|
59 |
872 |
857 |
τ(C20-C19-C17-H18)[50]+ ω(O8-C15-C17-C16)[18]+ω(C20-C17-O1-C19)[10] |
|
|
60 |
856 |
841 |
τ(H28-C27-C29-C21)[53]+τ(H30-C29-C27-C26)[17]+τ(H25-C24-C26-C27)[12] |
|
|
61 |
847 |
833 |
τ(H6-O5-C14-C15)[85] |
|
|
62 |
821 |
807 |
R3-def[67] |
|
|
63 |
809 |
795 |
τ(H18-C17-C16-C20)[17]+ω(O5-C15-C20-C14)[12]+ω(O7-C14-C16-C15)[12] |
|
|
64 |
790 |
777 |
845(m) |
τ(H18-C17-C16-C20)[18]+ω(O5-C15-C20-C14)[15]+ω(O7-C14-C16-C15)[12] |
|
65 |
768 |
755 |
τ(C21-C29-C27-C26)[18]+ ω(O4-C20-C12-C13)[11] |
|
|
66 |
758 |
745 |
775(wsh) |
τ(C21-C29-C27-C26)[18]+ω(C20-C17-O1-C19)[10] |
|
67 |
733 |
721 |
φ(O1-C17-C19)[11]+φ(O8-C16-C17)[13] |
|
|
68 |
676 |
665 |
ω(O1-C17-C19-C20)[16]+τ(C1-O1-C19-C17)[18] |
|
|
69 |
674 |
663 |
ω(O1-C17-C19-C20)[20]+τ(C1-O1-C19-C17)[14] |
|
|
70 |
656 |
645 |
φ(C22-C24-C26)[18]+φ(C29-C27-C26)[27]+φ(C21-C29-C27)[19] |
|
|
71 |
638 |
627 |
ω(C12-C21-O1-C11)[23]+ω(O4-C20-C12-C13)[11]+τ(H3-O2-C12-C13)[16] |
|
|
72 |
625 |
614 |
639(m) |
R1&R2-puck[20] |
|
73 |
615 |
605 |
612(wsh) |
ω(O5-C15-C20-C14)[26]+τ(H3-O2-C12-C13)[15]+τ(H18-C17-C19-C20)[12]+ |
|
ω(O8-C15-C17-C16)[11] |
||||
|
74 |
606 |
596 |
τ(H3-O2-C12-C13)[62]+τ(H3-O2-C12-C11)[15] |
|
|
75 |
600 |
590 |
φ(C19-O1-C11)[18]+φ(C12=C11-O1)[20] |
|
|
76 |
562 |
552 |
520(wsh) |
R1R2&R3 Puck[16] |
|
77 |
519 |
510 |
ω(O9-C24-C27-C26)[33]+τ(C29-C27-C26-C24)[10] |
|
|
78 |
498 |
490 |
φ(C15-C14-C20)[15]+φ(C31-O7-C15)[10] |
|
|
79 |
479 |
471 |
φ(C31-O7-C15)[14] |
|
|
80 |
438 |
431 |
430(s) |
τ(C14-C15-C16-C17)[18]+τ(C21-C22-C24-C26)[12] |
|
81 |
429 |
422 |
φ(O9-C26-C27)[28]+φ(C11-C21-C29)[11] |
|
|
82 |
428 |
421 |
τ(C22-C24-C26-C27)[14]+τ(C29-C27-C24-C26)[13] |
|
|
83 |
410 |
403 |
ω(O2-C13-C11-C12)[12]+φ(O9-C26-C27)[10]+φ(C35-O8-C16)[14] |
|
|
84 |
397 |
390 |
ω(O2-C13-C11-C12)[25] |
|
|
85 |
377 |
371 |
360(s) |
τ(H10-O9-C26-C24)[57]+τ(H10-O9-C26-C27)[38]+φ(O5-C14-C20)[12]+ φ(O2-C12-C13)[10] |
|
86 |
352 |
346 |
φ(O4=C13-C12)[25]+φ(O2=C12-C13)[14] +φ(O5-C14-C20)[15] |
|
|
87 |
331 |
325 |
τ(C19-O1-C11-C21)[13] |
|
|
88 |
321 |
316 |
τ(C19-O1-C11-C21)[12] |
|
|
89 |
297 |
292 |
φ(O1-C11-C21)[13]+φ(O2-C12-C13)[25] |
|
|
90 |
288 |
283 |
ω(C13-C14-C19-C20)[12] |
|
|
91 |
279 |
274 |
ω(C13-C14-C19-C20)[14] |
|
|
92 |
255 |
251 |
ω(C13-C14-C19-C20)[11] +ω(C20-C17-O1-C19)[12]+τ(H36-C35-O8-C16)[12]+ ω(O5-C15-C20-C14)[11] |
|
|
93 |
238 |
234 |
ν(C11-C21)[12]+φ(O7-C15-C16)[12] |
|
|
94 |
217 |
213 |
τ(H38-C35-O8-C16)[11]+ω(O8-C15-C17-C16)[12]+τ(H37-C35-O8-C16)[12]+ τ(C16-C17-C19-C20)[20] |
|
|
95 |
205 |
202 |
φ(O7-C15-C16)[13]+φ(C31-O7-C15)[13]+τ(C15-C14-C20-C19)[11] |
|
|
96 |
182 |
179 |
R1,R2&R3-rock[65] |
|
|
97 |
156 |
153 |
τ(C31-H32-H33-H34)[42] |
|
|
98 |
152 |
149 |
τ(C31-H32-H33-H34)[41] |
|
|
99 |
130 |
128 |
ω(C20-C17-O1-C19)[10]+τ(C14-C20-C19-C17)[18]+τ(C19-O1-C11-C21)[10]+ τ(C35-O8-C16-C15)[10] |
|
|
100 |
113 |
111 |
τ(C17-C19-O1-C11)[12]+τ(C35-O8-C16-C15)[45] |
|
|
101 |
82 |
81 |
R1,R2 & R3-rock[49] |
|
|
102 |
79 |
78 |
τ(C17-C19-O1-C11)[13]+τ(C5-C14-C20-C19)[12] |
|
|
103 |
71 |
70 |
τ(C14-C20-C19-C17)[15]+τ(C35-O8-C16-C15)[27] |
|
|
104 |
63 |
62 |
τ(C31-O7-C15-C14)[62] |
|
|
105 |
42 |
41 |
τ(O1-C11-C21-C2)[81] |
|
|
106 |
34 |
33 |
τ(C14-C20-C19-C17)[14]+τ(C19-O1-C11-C21)[35]+ω(C11-C22-C29-C21)[14] |
Abbreviations:- ν: Stretching; s: symmetric stretching; as: asymmetric stretching; asi: asymmetric in plane, def: deformation; φ: bending in-plane; ω: bending out-of-plane; τ: torsion/twisting; R: ring; puck: puckering; roc: in plane rocking; breth:breathing.
3.2.5 (C-O) Vibration:
In the present study the ν(C-O) stretching vibrational mode is calculated in the frequency range of 1322-1190 cm-1 which is in good coherence with the experimental FTIR values. The various bending and torsional modes assigned in this study are also supported by the literature12. The absorption peak at 1190 cm-1 in the FTIR spectra is very strong and seems to be one of the characteristics peaks of the present compound.
3.2.6 Low-Frequency Region Modes:
The lower frequency vibrational modes are of great importance as it provides the information about the weak intermolecular interactions, which occurs in enzyme reactions and it is also useful for interpretation of the effect of e-m radiation on biological systems 16,17. In the present study several out of plane modes namely torsional, wagging, ring deformation, ring puckering and ring-rocking modes are calculated in the range 875-33 cm-1 and are in coherence with the experimental FTIR spectra. Two peaks calculated at 431 and 371 cm-1 are assigned to 430 and 360 cm-1 to the experimental values are also the characteristics peaks of the title molecule. Some discrepancies are seen in the experimental and theoretical intensity in lower range of frequencies
Which, are possibly due to impurity of the sample used, the intermolecular interactions, an harmonicity and probable mixing of different modes of vibrations.
3.3 Electronic Properties:
The frontier molecular orbital not only take part in chemical reactions but also the energy gap between them tells about the quantitative chemical reactivity of the molecule 18. HOMO-LUMO energy gap is an important indicator of the stability of the compound. Small energy gap suggests that the molecule is more polarizable, is generally associated with high chemical reactivity and low kinetic stability, and is termed as soft molecule 19,20. In present DFT study, the plots of LUMO and HOMO are shown in figure II and III respectively, and their values are given in table III. From 2D plot of HOMO (-5.95734 eV), it is clear that HOMO is distributed on all three rings R1, R2 and R3 except the atoms C16 and O8. The 2D plot of LUMO (-2.394688 eV) of the title molecule is spread on all three rings R1, R2 and R3 except again the C16 and O8 atoms. The frontier orbital energy band gap is calculated by the difference of LUMO and HOMO values and is found to be 3.56 eV.
The molecular electrostatic potential (MEP) surface plot mapped on to the iso electron density surface, shows the molecular shape, size and electrostatic potential values in terms of color coding and is an experimental tool in the identification of correlation between molecular structure and the physiochemical property relationship of molecules including bio molecules 21-26. The MEP map of the title molecule is shown in fig IV, with color coding ranging from -4.003 e-4 to 4.003 e-4. Various electronic parameters viz, ionization potential (I), electron affinity (A), absolute electro negativity (χ) and chemical hardness (η) etc. at B3LYP/6-311++ G(d,p) level are calculated as the negative energy eigen values of HOMO and LUMO respectively. These parameters are often used to describe the chemical reactivity of the molecules. All the parameters are presented in table III and it is evident that the value of electro negativity (χ) is high for the present molecule (4.176016 eV).
Fig. 2. Homo of Eupalitin as seen by gaussview 5.0
Fig. 3. Lumo of eupalitin as seen by gaussview 5.0
Fig. 4. 2D MEPS plot of Eupalitin as seen by Gaussview 5.0
Table III: Electronic Parameters and Thermo Chemistry of Eupalitin calculated at 6-311++(d,p)
|
S. No. |
Parameter |
DFT Values (eV) |
|
1 |
eHOMO |
5.957344 |
|
2 |
eLUMO |
2.394688 |
|
3 |
Δ(eHOMO–eLUMO) |
3.562656 |
|
4 |
µx |
2.9542 |
|
5 |
µy |
2.9542 |
|
6 |
µz |
1.4829 |
|
7 |
µ |
4.222 |
|
8 |
Ionization Potential(I) |
5.957344 |
|
9 |
Electron Affinity(A) |
2.394688 |
|
10 |
Electronegativity |
4.176016 |
|
Index (χ) |
||
|
11 |
Chemical Hardness(η) |
1.781328 |
|
12 |
Global Hardness (S) |
0.280689 |
|
13 |
Electrophilicity (ω) |
62.129 |
Table IV: Polarizability and first static hyperpolarizability for Eupalitin calculated at B3LYP/6-311++G(d,p) level
|
Compo-nents |
Polarizability |
Compo-nents |
Hyperpolarizability |
|
a.u |
a.u. |
||
|
αxx |
-126.9198 |
βXXX |
172.879 |
|
αxy |
-16.1837 |
βXXY |
-83.5488 |
|
αyy |
-127.5581 |
βXYY |
-44.2854 |
|
αxz |
-8.3936 |
βYYY |
73.7869 |
|
αyz |
-1.3139 |
βxxz |
49.4112 |
|
αzz |
-141.7956 |
βXYZ |
4.2988 |
|
<α> |
-132.091 |
βYYZ |
-1.1632 |
|
βXZZ |
-22.2741 |
||
|
βYZZ |
-3.4601 |
||
|
βZZZ |
0.3716 |
||
|
β1 |
11303.83608 |
||
|
β2 |
174.821284 |
||
|
β3 |
2363.865504 |
||
|
βtotal |
117.6542514 |
3.4 Dipole Moment, Polarizability and First-Satic Hyperpolarizability:
The dipole moment, polarizability and hyperpolarizabilty are important non-linear optical (NLO) response properties for organic molecules. With the help of polarizabilty and hyperpolarizability one can estimate the stability of chemical bonds and characteristics of interactions27,28. The value of dipole moment is calculated as 4.22 Debye for the title molecule. The components αXX, αYY and αZZ of the mean polarizability <α> are calculated as -126.9198 as -127.5581 and -141.795 a.u. which suggest that title molecule is elongated maximum along Z-axis. The largest βXXX component (172.879 a.u) hyperpolarizability βtotal suggest that the charge delocalization occurs maximum along the X-axis and the molecule is more optically along the X-axis. The β components of the title molecule are shown in table IV in atomic units where 1 a.u.= 8.3693* 10-33 e.s.u. The calculated value of βtotal for Eupalitin was found to be 117.6543 a.u. (0.984* 10-30 esu) which is nearly five times to that of urea (0.1947* 10-30 esu).
3.5 Molecular Docking:
Molecular docking is a method to predict the manner in which two molecules, such as a drug (protein) and a receptor (ligand or molecule) fit together and dock to each other. Molecular docking is an important technique in structure based drug design and is often the starting point in our search for a drug against a given target molecule. In order to perform a theoretical study for inhibition of protein “Glutathione s-Transferase 1AQW” by the title ligand “Eupalitin”, we have carried out molecular docking studies using HEX program 8.0. The target protein has been obtained from the protein data bank (PDB) database with PDB ID =1AQW 29. The choice of target protein was made keeping in view the documented anti-microbial activity of the title compound which motivated us to perform random screening of bacterial proteins for binding with Eupalitin and eventually led to identification of the protein as 1AQW as the one giving the best binding score. Fig V shows the docked conformation of the protein 1AQW showing the interaction with the residues in the binding site of the target ligand Eupalitin.
Fig. 5. 2D Docking of Eupalitin with IAQW Protein
The overall docking score can be obtained as function of the six degrees of freedom in a rigid body docking search just by writing expressions for the overlap of pairs of parametric functions. The docking score thus obtained can be approximated to an interaction energy “e-value” which is minimized successively. The higher the negative e-value, the better is the docking. In the present study the total e-value is calculated as -138.26 for 1AQW, which suggest that the title compound Eupalitin can inhibit the 1AQW protein.
CONCLUSIONS:
In the present work, we have carried out os comprehensive study on 3,5,4’-Trihydroxy-6,7-Dimethoxy-Flavone (Eupalitin), which has been a synthetic molecule of enough pharmacological interest ever since it was implicated in carcenogenic activity. The molecular geometry, vibrational wave numbers, and NLO behavior , of title molecule have been calculated using DFT (B3LYP) method adopting 6-311++(d,p) basis set. A good coherence between experimental and calculated normal modes of vibrations is achieved. The nonlinear optical (NLO) behviour of the title molecule has been investigated by the dipole moment, the polarizability and first hyperpolarizability measurements. The frontier orbital energy gap is calculated 3.56 eV. Dipole moment μ, molecular polarizability <α> and total first static hyperpolarizability βtotal are computed as 4.22 D, -132.091 a.u. and 117.654 respectively. Lower value of frontier orbital energy gap and a higher value of dipole moment suggest that the nature of the title compound is highly reactive. The value of βtotal is nearly five times to that of urea indicating that Euaplitin possesses nonlinear optical properties and is a potential candidate for nonlinear optical applications. The molecular orbitals and MEPS map may lead to the understanding of properties and activity of Eupalitin. The results of molecular docking studies speculate that this biologically active molecule might emerge as a potential candidate for the inhibition to protein “Glutathione s-Transferase 1AQW” thereby indicating its possible pharmacological importance. Thus, the present study provides a comprehensive vibrational analysis, structural information and electronic properties of the title compound. Although the molecular docking studies have led to the identification of a target protein of bacterial origin which may satisfactorily explain the molecular basis of antimicrobial activity of the title compound, yet it furnishes no clue as to how the same compound might exert an anticancer effect. Besides, the sequence of molecular events triggered by the binding of Eupalitin with the target protein 1AQW that results in cytotoxicity action remains to be explored and is likely to form the basis of future studies about the therapeutic potential of the title compound.
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Received on 25.08.2017 Modified on 19.09.2017
Accepted on 28.10.2017 © AJRC All right reserved
Asian J. Research Chem. 2017; 10(6):789-797.
DOI: 10.5958/0974-4150.2017.00132.8