Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol
Abstract
:Highlights
- The ME molecule has 21 stable configurations.
- For all the tops (except =CH2), the barrier heights are of the same order, while the =CH2 top has a barrier height one order of magnitude higher.
- Like estragole and eugenol, ME also has the same Fermi doublets for the following modes: νs(–CH2) and 2 βs(–CH2); νs(CH3) and 2 δs(CH3).
- The ME molecule has three active sites.
- Vibrational analysis suggests that the solvents affect the internal modes of both OCH3 moieties strongly.
- The methyl-eugenol molecule could be a good choice for the pharmacological applications
- The OCH3 moieties of methyl-eugenol play significant role in interaction with other molecules.
Abstract
1. Introduction
2. Result and Discussion
2.1. Determination of Conformers
2.2. Molecular Geometries
2.3. Barrier Heights
2.4. Bioactive Scores
2.5. APT Charge
2.6. Vibrational Analysis
2.6.1. Methoxy (–OCH3) Group Modes (24)
2.6.2. Allyl (–CH2–CH=CH2) Group Modes (21)
Methylene (–CH2–) Group Modes (6)
Vinyl (–CH=CH2) Group Modes (12)
2.6.3. Phenyl Moiety Modes (30)
Phenyl Ring Modes (12)
C–H Modes (9)
C–O(CH3) and C–C(H2CHCH2) Group Modes (9)
2.7. Conformer Dependent Modes
2.8. Solvent Effects
2.9. MEP Plots
2.10. HOMO-LUMO Plots
3. Experimental Details
4. Computational Detail
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Conformers | Energy (E) | ΔE Relative to the Conformer I | Relative Abundance | |
---|---|---|---|---|
kcal/Mole | kcal/Mole | K | ||
I | −362,794.265 | 0 | 0 | 32.1 |
II | −362,793.860 | 0.405 | 204 | 16.2 |
III | −362,793.644 | 0.622 | 313 | 11.2 |
IV | −362,793.237 | 1.028 | 518 | 5.7 |
V | −362,793.212 | 1.054 | 530 | 5.4 |
VI | −362,792.997 | 1.268 | 638 | 3.8 |
VII | −362,792.978 | 1.287 | 648 | 3.7 |
VIII | −362,792.903 | 1.363 | 685 | 3.2 |
IX | −362,792.881 | 1.384 | 697 | 3.1 |
X | −362,792.871 | 1.395 | 701 | 3.1 |
XI | −362,792.859 | 1.408 | 708 | 3.0 |
XII | −362,792.61 | 1.655 | 833 | 2.0 |
XIII | −362,792.593 | 1.672 | 842 | 1.9 |
XIV | −362,792.517 | 1.748 | 880 | 1.7 |
XV | −362,792.517 | 1.749 | 880 | 1.7 |
XVI | −362,791.789 | 2.477 | 1246 | 0.5 |
XVII | −362,791.74 | 2.525 | 1271 | 0.5 |
XVIII | −362,791.725 | 2.541 | 1279 | 0.4 |
XIX | −362,791.705 | 2.561 | 1289 | 0.4 |
XX | −362,791.302 | 2.963 | 1491 | 0.2 |
XXI | −362,791.301 | 2.964 | 1492 | 0.2 |
Top | Foldness | * ∆EAB | * ∆EBC | * ∆ECD | * ∆EDE | * ∆EEF | * ∆EFG |
---|---|---|---|---|---|---|---|
CHCH2 | 3 | 2.36 | 1.27 | 2.00 | 1.98 | 3.62 | 4.73 |
CH2CHCH2 | 2 | 2.02 | 1.60 | 1.52 | 1.94 | - | - |
CH3 | 3 | 3.34 | 3.34 | 3.34 | 3.34 | 3.34 | 3.34 |
CH3 | 3 | 3.34 | 3.34 | 3.34 | 3.34 | 3.34 | 3.34 |
8OCH3 | 3 | 1.13 | 1.54 | 7.15 | 7.15 | 1.54 | 1.13 |
9OCH3 | 3 | 2.37 | 1.18 | 2.73 | 2.71 | 1.15 | 2.36 |
=CH2 | 2 | 93.13 | 93.13 | 93.13 | 93.13 | - | - |
Bioactive Acceptors | M-Eugenol |
---|---|
GPCR ligand | −0.81 |
Ion channel modulator | −0.38 |
Kinase inhibitor | −1.06 |
Nuclear receptor ligand | −0.80 |
Protease inhibitor | −1.14 |
Enzyme inhibitor | −0.43 |
Atoms | C-I | C-II | C-III | C-I In Solvent Effect | |
---|---|---|---|---|---|
Water | Ethanol | ||||
C1 | 0.018 | 0.012 | −0.004 | 0.040 | 0.039 |
C2 | −0.159 | −0.119 | −0.117 | −0.200 | −0.198 |
C3 | 0.515 | 0.516 | 0.503 | 0.688 | 0.680 |
C4 | 0.518 | 0.510 | 0.513 | 0.668 | 0.661 |
C5 | −0.096 | −0.072 | −0.088 | −0.131 | −0.129 |
C6 | −0.086 | −0.120 | −0.080 | −0.114 | −0.112 |
H7 | 0.062 | 0.050 | 0.050 | 0.087 | 0.085 |
O8 | −0.863 | −0.891 | −0.869 | −1.135 | −1.121 |
O9 | −0.922 | −0.919 | −0.907 | −1.173 | −1.161 |
H10 | 0.045 | 0.045 | 0.046 | 0.075 | 0.073 |
H11 | 0.027 | 0.042 | 0.027 | 0.040 | 0.039 |
C12 | 0.133 | 0.131 | 0.133 | 0.154 | 0.153 |
H13 | −0.051 | −0.053 | −0.041 | −0.058 | −0.058 |
H14 | −0.028 | −0.032 | −0.035 | −0.039 | −0.038 |
C15 | 0.048 | 0.061 | 0.064 | 0.084 | 0.082 |
H16 | 0.018 | 0.016 | −0.021 | 0.018 | 0.018 |
C17 | −0.141 | −0.142 | −0.149 | −0.200 | −0.196 |
H18 | 0.029 | 0.028 | 0.023 | 0.039 | 0.038 |
H19 | 0.029 | 0.029 | 0.046 | 0.038 | 0.038 |
C20 | 0.552 | 0.542 | 0.545 | 0.653 | 0.648 |
H21 | −0.043 | −0.040 | −0.041 | −0.043 | −0.043 |
H22 | −0.002 | −0.002 | −0.001 | −0.003 | −0.003 |
H23 | −0.042 | −0.041 | −0.041 | −0.042 | −0.042 |
C24 | 0.511 | 0.529 | 0.520 | 0.631 | 0.625 |
H25 | −0.035 | −0.039 | −0.038 | −0.039 | −0.039 |
H26 | 0.000 | −0.001 | 0.000 | 0.000 | 0.000 |
H27 | −0.038 | −0.040 | −0.039 | −0.040 | −0.039 |
Group/Moiety | Modes in Symbolic Form * | Total | |
---|---|---|---|
Phenyl | Ring | 6ν(R) + 3α(R) + 3Φ(R) | 12 |
(Ph)C–O(CH3) | 2ν + 2β + 2γ | 6 | |
(Ph)C–C(H2CHCH2) | ν + β + γ | 3 | |
(Ph)C–H | 3ν + 3β + 3γ | 9 | |
OCH3 | CH3 | 2νs + 4νas + 2δs + 4δas + 2ρ║ + 2ρ┴ + 2τ | 18 |
O–C(H3) | 2ν + 2α + 2τ | 6 | |
Allyl | 2CH2 | 2νs + 2νas + 2βs + 2ρ + 2ω + t + τ | 12 |
C–C | ν + α + τ | 3 | |
C–H | ν + 2δ | 3 | |
C=C | ν + α + τ | 3 |
Gas | Solvent | # Mode | |||
---|---|---|---|---|---|
Water | Ethanol | ||||
(1) | (2) | (3) | (1)–(2) | (1)–(3) | |
28 (0.29) 0.74 | 27 (0.16) 0.75 | 27 (0.21) 0.75 | 1 | 1 | τ(C1–C12) |
64 (1.95) 0.69 | 61 (1.53) 0.75 | 62 (1.63) 0.75 | 3 | 2 | τ(C4–OCH3) |
76 (2.48) 0.71 | 77 (2.24) 0.75 | 78 (2.29) 0.75 | −1 | −2 | τ(C12–C15) |
89 (0.40) 0.74 | 91 (1.31) 0.75 | 91 (1.39) 0.75 | −2 | −2 | τ(C3–OCH3) |
121 (0.36) 0.75 | 122 (0.25) 0.75 | 123 (0.31) 0.75 | −1 | −2 | γ(C1–C12) |
165 (0.17) 0.73 | 169 (0.11) 0.73 | 169 (0.13) 0.73 | −4 | −4 | γ(C3–O8) |
186 (2.23) 0.50 | 187 (2.9) 0.37 | 187 (2.11) 0.37 | −2 | −2 | β(C3–O8) |
204 (0.21) 0.62 | 207 (0.6) 0.68 | 207 (0.8) 0.68 | −3 | −3 | γ(C4–O9) |
225 (0.18) 0.69 | 224 (0.9) 0.75 | 224 (0.12) 0.75 | 1 | 1 | τ(OCH3) |
250 (0.7) 0.68 | 251 (0.3) 0.67 | 251 (0.4) 0.66 | −1 | −1 | τ(OCH3) |
279 (0.3) 0.33 | 282 (0.2) 0.60 | 282 (0.3) 0.60 | −3 | −3 | α(C1–C12–C15) |
345 (0.18) 0.25 | 344 (0.5) 0.58 | 344 (0.7) 0.55 | 2 | 2 | β(C1–C12) |
354 (0.74) 0.11 | 353 (0.44) 0.10 | 353 (0.49) 0.10 | 1 | 1 | β(C1–O10) |
384 (1.12) 0.22 | 383 (1.5) 0.43 | 383 (1.7) 0.42 | 1 | 1 | α(C–O–C)ipc |
398 (2.10) 0.72 | 397 (1.12) 0.73 | 397 (1.14) 0.73 | 1 | 1 | α(C14–C15=C17) |
462 (1.2) 0.69 | 462 (1.2) 0.68 | 462 (1.2) 0.69 | 1 | 1 | Φ(R) 16b |
474 (0.6) 0.61 | 473 (0.3) 0.71 | 473 (0.4) 0.71 | 0 | 0 | α(R) 6b |
534 (1.15) 0.52 | 533 (1.11) 0.46 | 533 (1.13) 0.47 | 1 | 1 | α(R) 6a |
592 (1.5) 0.54 | 590 (1.3) 0.51 | 591 (1.4) 0.52 | 3 | 2 | α(C–O–C)opc |
600 (4.6) 0.72 | 601 (5.3) 0.71 | 601 (5.4) 0.71 | −1 | −1 | τ(C=C) |
642 (6.22) 0.49 | 643 (7.15) 0.46 | 643 (6.19) 0.46 | −1 | −1 | α(R) 12 |
728 (2.15) 0.17 | 730 (3.15) 0.25 | 730 (3.18) 0.24 | −2 | −2 | Φ(R) 4 |
748 (7.30) 0.13 | 748 (9.25) 0.14 | 748 (9.31) 0.14 | 0 | 0 | Φ(R) 16a |
766 (6.47) 0.07 | 762 (6.27) 0.07 | 763 (6.34) 0.07 | 3 | 3 | ν(R) 1 |
799 (12.3) 0.24 | 803 (12.6) 0.57 | 803 (12.7) 0.56 | −5 | −4 | γ(C–H) |
851 (7.2) 0.13 | 854 (8.3) 0.20 | 854 (8.3) 0.19 | −2 | −2 | γ(C2–H7) |
888 (4.6) 0.14 | 887 (4.7) 0.13 | 888 (4.8) 0.13 | 2 | 1 | t(C12–H) |
903 (1.1) 0.44 | 912 (2.0) 0.41 | 911 (2.0) 0.48 | −9 | −9 | γ(C–H) |
920 (12.3) 0.47 | 919 (10.5) 0.67 | 919 (10.5) 0.65 | 1 | 1 | ω(=CH2) |
928 (6.11) 0.48 | 927 (5.10) 0.67 | 927 (6.13) 0.66 | 2 | 1 | ν(C12–C15) |
948 (3.7) 0.05 | 943 (5.9) 0.05 | 943 (5.10) 0.05 | 5 | 5 | ν(C1–C12) 20a |
1005 (6.6) 0.63 | 1004 (5.5) 0.66 | 1004 (5.6) 0.66 | 2 | 1 | δ(=C–H) |
1027 (28.9) 0.22 | 1011 (29.8) 0.13 | 1012 (29.10) 0.13 | 17 | 16 | ν(O9–CH3) |
1042 (3.5) 0.74 | 1023 (6.2) 0.70 | 1023 (6.3) 0.71 | 19 | 19 | ν(O8–CH3) |
1092 (4.8) 0.17 | 1087 (5.4) 0.21 | 1088 (5.5) 0.21 | 6 | 6 | ρ(=CH2) |
1134 (16.2) 0.68 | 1130 (31.3) 0.44 | 1130 (29.3) 0.46 | 4 | 4 | β(C–H) 8a |
1139 (0.6) 0.75 | 1138 (1.2) 0.61 | 1138 (1.3) 0.64 | 1 | 1 | ρ(CH3) a″ |
1139 (0.4) 0.75 | 1139 (1.2) 0.72 | 1139 (1.2) 0.73 | 1 | 1 | ρ(CH3′) a″ |
1148 (41.14) 0.06 | 1141 (30.11) 0.05 | 1141 (31.14) 0.05 | 7 | 7 | β(C–H) |
1175 (1.6) 0.25 | 1174 (1.6) 0.17 | 1174 (1.7) 0.18 | 1 | 1 | ρ(CH3′) a′ |
1180 (2.12) 0.40 | 1179 (2.7) 0.36 | 1179 (2.8) 0.37 | 1 | 1 | ρ(CH3) a′ |
1203 (1.38) 0.39 | 1201 (3.22) 0.43 | 1201 (3.27) 0.43 | 2 | 2 | ρ(–CH2) |
1231 (91.1) 0.63 | 1218 (64.1) 0.41 | 1219 (65.2) 0.42 | 14 | 13 | [ν(C2–O12)+ ν (C1–O10)]op |
1255 (100.36) 0.06 | 1242 (100.50) 0.03 | 1242 (100.60) 0.03 | 13 | 13 | [ν(C2–O12)+ ν(C1–O10)]ip7a |
1269 (1.3) 0.57 | 1272 (1.3) 0.47 | 1272 (1.3) 0.47 | −3 | −3 | β(C–H) 3 |
1287 (1.39) 0.26 | 1283 (1.34) 0.27 | 1283 (1.41) 0.27 | 4 | 4 | δ(=C–H) |
1296 (1.25) 0.39 | 1294 (0.8) 0.41 | 1295 (0.11) 0.41 | 2 | 2 | ω(–CH2) |
1340 (14.71) 0.09 | 1332 (10.52) 0.07 | 1333 (11.64) 0.07 | 8 | 7 | ν(R) 14 |
1407 (12.5) 0.58 | 1404 (11.4) 0.20 | 1405 (11.4) 0.22 | 3 | 2 | ν(R) 19b |
1413 (3.20) 0.39 | 1408 (1.9) 0.44 | 1408 (1.12) 0.43 | 6 | 6 | βs(=CH2) |
1438 (9.8) 0.61 | 1435 (5.5) 0.75 | 1436 (5.6) 0.75 | 3 | 3 | δs(CH3′) a′ |
1439 (1.6) 0.75 | 1437 (5.4) 0.75 | 1437 (4.5) 0.75 | 2 | 2 | βs(–CH2) |
1447 (2.8) 0.49 | 1444 (1.7) 0.54 | 1444 (1.9) 0.54 | 3 | 3 | δs(CH3) a′ |
1454 (2.20) 0.75 | 1447 (3.10) 0.75 | 1447 (2.13) 0.75 | 7 | 6 | δas(CH3) a″ |
1454 (6.17) 0.75 | 1447 (4.9) 0.75 | 1448 (4.11) 0.75 | 8 | 7 | δas(CH3′) a″ |
1467 (20.7) 0.44 | 1459 (22.2) 0.23 | 1459 (22.2) 0.21 | 8 | 7 | δas(CH3) a′ |
1467 (15.10) 0.66 | 1460 (6.6) 0.75 | 1460 (6.8) 0.75 | 8 | 7 | δas(CH3′) a′ |
1508 (82.10) 0.28 | 1499 (66.7) 0.17 | 1500 (67.8) 0.18 | 8 | 8 | ν(R) 19a |
1582 (15.28) 0.75 | 1577 (12.27) 0.74 | 1578 (12.33) 0.74 | 5 | 5 | ν(R) 8a |
1600 (7.92) 0.62 | 1595 (4.68) 0.66 | 1595 (4.84) 0.66 | 5 | 5 | ν(R) 8b |
1653 (7.90) 0.13 | 1645 (7.64) 0.11 | 1646 (7.78) 0.12 | 7 | 7 | ν(C=C) |
2867 (35.60) 0.05 | 2883 (24.22) 0.04 | 2882 (25.29) 0.03 | −15 | −14 | νs(CH3) a′ |
2870 (13.100) 0.02 | 2885 (11.25) 0.05 | 2884 (11.51) 0.03 | −14 | −14 | νs(CH3) a′ |
2878 (11.83) 0.03 | 2885 (8.100) 0.01 | 2885 (9.100) 0.02 | −7 | −6 | νs(–CH2) |
2911 (5.38) 0.73 | 2921 (6.32) 0.71 | 2920 (6.38) 0.71 | −10 | −10 | νas(–CH2) |
2921 (15.35) 0.75 | 2943 (12.19) 0.75 | 2942 (12.23) 0.75 | −21 | −20 | νas(CH3) a″ |
2924 (16.24) 0.75 | 2945 (12.17) 0.75 | 2944 (12.20) 0.75 | −20 | −19 | νas(CH3) a″ |
2983 (6.26) 0.21 | 2980 (7.9) 0.32 | 2980 (7.11) 0.31 | 4 | 3 | νs(=CH2) |
2991 (2.63) 0.20 | 2989 (2.47) 0.20 | 2989 (2.56) 0.20 | 3 | 2 | ν(=C–H) |
2993 (8.57) 0.48 | 3002 (6.24) 0.53 | 3001 (6.30) 0.53 | −9 | −8 | νas(CH3) a′ |
2994 (11.68) 0.41 | 3003 (7.26) 0.50 | 3002 (7.33) 0.50 | −9 | −8 | νas(CH3) a′ |
3026 (5.38) 0.36 | 3029 (4.28) 0.35 | 3029 (4.34) 0.35 | −3 | −3 | ν(C–H) 7b |
3056 (2.13) 0.20 | 3057 (1.17) 0.23 | 3057 (2.20) 0.23 | −1 | −1 | ν(C–H) 20b |
3063 (4.58) 0.21 | 3064 (6.20) 0.67 | 3064 (6.25) 0.67 | −1 | −1 | ν(C–H) 2 |
3066 (7.42) 0.59 | 3068 (2.38) 0.22 | 3067 (2.47) 0.22 | −2 | −2 | νas(=CH2) |
Conformers | Energy in Unit (eV) | Electronegativity (χ) | Chemical Hardness (η) | ||
---|---|---|---|---|---|
HOMO | LUMO | ΔE | |||
I | −5.6844 | −0.3170 | 5.3674 | 3.0007 | 2.6837 |
II | −5.6447 | −0.3474 | 5.2973 | 2.9961 | 2.6486 |
III | −5.6776 | −0.3132 | 5.3644 | 2.9954 | 2.6822 |
Absorption Bands | Excitation Energies (eV) | Oscillator Strength (f) | * Contributions | |
---|---|---|---|---|
λexp (nm) | λcal (nm) | |||
265 | 247.7 | 5.0047 | 0.0723 | H – 1 → L + 2 (3.4%) H – 1 → L + 4 (3.9%) H – 1 → L + 7 (2.57%) H − 1 → L + 10 (2.87) H → L (2.9%) H → L + 1 (21.98%) H →L + 2 (10.25%) H → L + 3 (45.41%) H → L + 4 (2.64%) H → L + 5 (4.14%) |
219 * | 223.4 | 5.5503 | 0.0902 | H − 1 → L + 3 (3.50%) H → L (54.89%) H → L + 1 (5.63%) H → L + 2 (3.99%) H → L + (14.50%) H → L + 6 (7.42%) H → L + 8 (7.78%) H → L + 10 (2.29%) |
219 * | 220.7 | 5.6169 | 0.1474 | H − 1 → L + 1 (1.82%) H − 1 → L + 3 (2.85%) H → L (7.84%) H → L + 2 (15.89%) H → L + 3 (6.77%) H → L + 4 (4.97%) H → L + 5 (1.30%) H → L + 7 (6.04%) H → L + 8 (2.60%) H → L + 9 (2.43%) H → L + 10 (47.49%) |
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Yadav, R.K.; Yadav, B.; Yadav, R.A.; Kostova, I. Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol. Molecules 2023, 28, 5409. https://doi.org/10.3390/molecules28145409
Yadav RK, Yadav B, Yadav RA, Kostova I. Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol. Molecules. 2023; 28(14):5409. https://doi.org/10.3390/molecules28145409
Chicago/Turabian StyleYadav, Rohit Kumar, Bhoopendra Yadav, R. A. Yadav, and Irena Kostova. 2023. "Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol" Molecules 28, no. 14: 5409. https://doi.org/10.3390/molecules28145409
APA StyleYadav, R. K., Yadav, B., Yadav, R. A., & Kostova, I. (2023). Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol. Molecules, 28(14), 5409. https://doi.org/10.3390/molecules28145409