Vibrational spectra, hydrogen bonding analysis and herbicidal activity study of mefenacet: A DFT approach

Journal Pre-proof Vibrational spectra, hydrogen bonding analysis and herbicidal activity study of mefenacet: A DFT approach N. Suma, D. Aruldhas, I. Hubert Joe, S. Balachandran, A. Ronaldo Anuf, Arun Sasi, Jesby George PII:

S0022-2860(19)31312-2

DOI:

https://doi.org/10.1016/j.molstruc.2019.127203

Reference:

MOLSTR 127203

To appear in:

Journal of Molecular Structure

Received Date: 23 June 2019 Revised Date:

6 October 2019

Accepted Date: 7 October 2019

Please cite this article as: N. Suma, D. Aruldhas, I. Hubert Joe, S. Balachandran, A.R. Anuf, A. Sasi, J. George, Vibrational spectra, hydrogen bonding analysis and herbicidal activity study of mefenacet: A DFT approach, Journal of Molecular Structure (2019), doi: https://doi.org/10.1016/ j.molstruc.2019.127203. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2019 Published by Elsevier B.V.

Vibrational Spectra, Hydrogen Bonding Analysis and Herbicidal Activity study of Mefenacet: A DFT Approach N. Sumaa, b, D. Aruldhasb, *, I. Hubert Joe c, S. Balachandrand, A. Ronaldo Anuf e, Arun Sasi f , Jesby Georgeg. a

Research

Scholar, Register

Number:

12045,

Manonmaniam

Sundaranar

University,

Abishekapatti, Tirunelveli - 627 012, Tamil Nadu, India, b

Department of Physics & ResearchCentre, Nesamony Memorial Christian College,

Marthandam-629165,TamilNadu, India c

Centre for Molecular and Biophysics Research, Department of Physics, Mar Ivanios College,

Thiruvananthapuram-695015, Kerala, India d

e

NSS College Ottapalam, Palakad-679103, Kerala, India.

Department of Biotechnology, Kamaraj College of Engineering and Technology, Virudhunagar-

626001, Tamilnadu, India. f

Research Scholar, Department of physics, Scott Christian college Nagercoil, Tamilnadu, India

g

Department of physics, Bishop Moore College Mavelikara, Alappuzha, Kerala 690110, India.

* Corresponding author: [email protected],+919976109295 Abstract The present study aims to provide deeper knowledge of structural, spectroscopic conformational analysis and herbicidal activity of the rice paddy herbicide Mefenacet on monomeric (MM) and dimeric (MD) model. The specific solvent effect of MM with water molecule (MM-H2O) has been investigated at the B3LYP/6-311G (d,p) level in order to observe the hydrogen bonding interaction. The fundamental modes of vibration are addressed by experimental FT-IR (4004000cm-1) and FT-Raman (50-3500cm-1) techniques. The vibrational spectrum is performed with normal coordinate analysis (NCA) and the wavenumbers are scaled by using Wavenumber–

1

Linear Scaling (WLS) method in order to identify the herbicidal active mode of vibration. Additionally, Quantum Theory of Atoms in Molecules (QTAIM) describing the electronic structure of the monomer and dimer molecules by means of various topological parameters to scrutinize the herbicidal active region. Potential energy surface (PES) scanning of MM with eight different dihedral angles has been performed to discover the most stable conformer, which leads to the herbicidal activity. The UV and global reactivity descriptors have also been carried out to check the herbicidal activity. Hirshfeld surface analysis of MD is done to confirm the existence of intermolecular interactions. Docking studies are performed to predict the herbicidal active site. Moreover, the stability of MM has been evaluated via Molecular Dynamic Simulations (MDS). Keywords: Mefenacet; FT-Raman; NCA; Hirshfeld Surface; Autodock; MDS. 1. Introduction Mefenacet [2(1, 3-benzothiazole-2yloxy)-N methyl -N-phenyl acetamide] is a herbicide which is used for the control of graminaceous weeds include Beauv, Digitaria sanguuinalis(L)[1]. The compounds containing thiazole or triazole ring, have useful biological properties, and they have been developed as herbicides, fungicides or plant growth regulators (PGRS) [2]. The molecular formula of mefenacet is C16H14N2O2S and its molecular weight is 298.36g/mol. It is one of the top three selling herbicides in Japan [3] with low toxicity (LC50 value 9.04µm) [4] and high activity. It is a member of benzothiazole ring and a phenyl ring linked through the oxyacetamide group with P21/c space group [5]. Oxyacetamides and chloroacetanilides have the same site of herbicidal action [6]. Wei Li et. al [7] have studied the structure and vibrational spectra of novel benzothiazole herbicides. Fedtke suggested that mixed function oxidizes could potentially be a target site for mefenacet [8]. The mode of action of mefenacet (cell division and cell growth) has been studied by Fess H.D et.al [9]. The crystal structure has been reported by S.Cheon et.al [5]. Clemy et.al [10] has reported DFT and vibrational studies of mefenacet. The literature review reveals that the detailed study on monomer, dimer, solvent effect and other bioactive studies for the herbicidal compound mefenacet has not been investigated yet. In the present work, the title compound has been optimized with DFT/B3LYP level using 6-311G (d,p) basis set. Its computational results are compared with the mefenacet dimer (MD). In addition to 2

this the different MM-H2O complexes have been taken into account to analyze various types of H-bonds. IR and Raman spectra of mefenacet monomer (MM) are described both experimentally and theoretically to analyze the bioactive region using hydrogen bondings. NBO analysis of the title molecule has computed to analyze the stabilization and intra and intermolecular charge transfer. Moreover QTAIM analysis and visualization of these results as well as the atomic basins of attraction has been done using AIMALL software. The calculated value of HOMOLUMO energy gap for MM and MD are used to interpret the biological activity of the molecule. Hirshfeld and 2-D finger print plot analyses have been performed to study the nature of the interactions present in the mefenacet molecule. Additionally, molecular dynamic simulations (MDS) are used to investigate which atom of the herbicide molecule has the most pronounced interaction. 2. Experimental techniques The compound Mefenacet in the solid form has purchased from Sigma Aldrich (St.Louis, MO, USA) company with 99% purity and used without further purification. The FT-IR spectrum of the MM has recorded in the wavenumber range 400-4000 cm-1 by the KBr pellet technique using Perkin Elmer Spectrophotometer equipped with mercury lamp and globar as source. The FTRaman spectrum in the wavenumber range 50-3500cm-1 has recorded by the BRUKER RFS 27: FT-Raman spectrophotometer using an Nd: YAG laser at 1064nm as the excitation source with a resolution of 2 cm-1. 3. Computational techniques In computational methods, Gaussian ‘09 software program package is used [11]. The quantum chemical calculations are performed by DFT [12-13] method with the three parameter hybrid functional (B3) for the exchange part and the Lee-Yang-Par (LYP) correlation function with 6311G (d,p) basis set [14-15]. The detailed interpretation of the vibrational spectra is carried out with the aid of Normal Coordinate Analysis (NCA). MOLVIB program version 7.0 is used for NCA calculation [16]. The wave numbers have been scaled down by Wavenumber Linear Scaling method (WLS)[17-18]. Specifically the Quantum Theory of Atoms in Molecules (QTAIM) is performed using AIMALL SOFTWARE [19] and its molecular graph is visualized by multiwfn [20] to provide enhanced insights into the intimate bonding structure of the 3

herbicidal molecule mefenacet. Gauss view 5.0.8 visualization program [21] is used to shape the FMO analysis. UV-visible spectra, electronic transitions, vertical excitation energy and oscillator strengths has been computed by the time dependent DFT method [22]. Gaussum 3.0 is used to evaluate the group contributions of molecular orbitals and identify the TDOS and OPDOS spectra. Molecular Hirshfeld surface analysis and the related 2D finger print plots for the compound is calculated using Crystal explorer 3.1 programs [23]. The docking studies are performed using the molecular docking software, Autodock4.2 [24]. Molecular dynamics simulation (MDS) can also be a powerful tool for analyzing the mechanism of pesticide fate, transport phenomena and evaluating the effect of macromolecule motion on drug-protein interactions [25]. Gromacs (Groningen Machine for Chemical Simulation) 5.1 software is used to perform molecular dynamics analysis [26]. The GROMOS force-field 43a1 is used for the protein selection [27]. 4. Results and discussion 4.1 Structural analysis The optimized geometrical parameters such as bond length, bond angle and dihedral angle of MM, MD, MW1, MW2, MW3, MW4 and MW5 by DFT/B3LYP method with 6-311 G (d,p) basis set are given in supplementary Table S1(a)-S1(c). The corresponding structures together with the labeling of atoms are shown in Fig.1 (a,b). The molecule is made up of aromatic heterocyclic benzothiazole ring (R1) with oxyacetamide and phenylring (R2) having coplanar structure with delocalized π electrons and two nitrogen (N) atom with lone pair of electrons. The thiazole ring with oxyacetamide group plays an important role in the structural analysis of the molecule. The calculated geometrical parameters show good agreement with experimental data [5]. In MM, the ring R1 reveals that the C-C bond lengths are different, which is confirmed by the presence of fused thiazole ring. However the longest C-C bond distance is noticed in C1-C2 (1.414Ǻ) bond because of the delocalization of electron density and fusion of thiazole moiety at these carbons [28]. The bond C1-C2 (1.414Ǻ) and C1-C6 (1.397Ǻ) are altered due to the influence of sulphur and nitrogen in the core structure of thiazole [29]. In R2, the C-C bond lengths lie in the range 1.393Ǻ-1.397Ǻ, which is in good agreement with the reported values [30]. By the 4

influence of electronegative atoms (N and O) present in the ring, the bond distances of the hetero aromatic ring (R1) differ significantly. In MM molecule, the bondlength C12-N13 is increased (1.285Ǻ) from the expected value (1.275Ǻ) [31] due to the possibility of strong C14-H16…N13 hydrogen bonding. In addition the electron donating behavior altered the bond length [29]. The C-S bondlengths are 1.762 Ǻ and 1.771 Ǻ respectively, this slight difference in bond length [32] is due to the presence of oxyacetamide group at C12 carbon atom. The hyperconjugative interactions C14-H15…O35 and C14-H16…O35 affect the bond distances for, C12-O35 (1.333Ǻ) and C14-O35 (1.428Ǻ) bonds. The C20-H23…O18 intramolecular hydrogen bond shortens the bond distance C20-H23 (1.088 Ǻ), however the bond lengths C20-H21 and C20-H22 are increased. In MM the bondlength C17-O18 (1.214 Ǻ) altered from the average distance [33] is due to the C20H23…O18 hydrogen bond. In addition to this the effect of dimer on the same molecule has been studied. In MD, C14-O35 bond length is increased (0.005 Ǻ) when compared with MM due to the influence of C49H51…O35 intermolecular hydrogen bonding. On the other hand, in MD lengthening of the C17O18 bond (0.008Ǻ) and shortening of C17-N19 (0.012 Ǻ) from the monomer clearly indicates the existence of intermolecular hydrogen bonding interactions (C49-H51…O18 and C60-H65…O18). Moreover, in MD the methyl group bondlength is also changed while comparing with MM due to the hyperconjugative interaction, that is C20-H21 (-0.006 Ǻ), C20-H22 (-0.002 Ǻ) and C20-H23 (+0.006 Ǻ). The experimental as well as calculated bond angles of mefenacet MM, MD and MM water complexes are relatively higher due to the steric hindrance offered via mono substitution with bioactive group. In R1, the existence of electron donating substituents, the symmetry of the ring is distorted yielding ring angles altered from 1200 at the point of substitution [34]. At the point C1, the bond angle C6-C1-C2 is 121.70. More distortion in bond parameters is observed in the hetero ring than in the benzene ring. The bond angle C1-S11-C12 is very less (87.40) than the bond angle C2-N13-C12 (110.30) which reveals that the central atom nitrogen has greater electro negativity than sulphur [35]. In R2 the bond angles C24-C25-C26 and C24-C29-C28 exactly show the aromatic character, because the bond angles are 120.00 due to sp2 hybridization [36]. In MM the bond angle C12-O35-C14(1.60) decreases from the reported value [5] due to the hyperconjucative interaction present in the electron withdrawing nature of the lone pair oxygen 5

atom(C14-H15…O35 and C14-H16…O35). At N19 position the bond angle C17-N19-C20 is decreased by 0.80 and C17-N19-C24 is increased by 3.40 from 1200, and this is due to the interaction between O18 and the methylene at C14 position. Additionally, the bond angle C17-N19-C20 (119.20) present in the oxyacetamide group lies in a linear manner which exhibits the stable conformer structure. At C17 position the bond angles C14- C17- N19 =115.20 and O18- C17- N19 =123.50, the increase in bond angle O18- C17- N19 clearly indicate the possibility of hydrogen bonding. In MM the dihedral angles N13-C2-C3-C4 (179.7 0), S11-C1-C6-C5 (179.8 0), C3-C2-N13-C12 (180.0 0

) and C1-S11-C12-O35 (-178.5 0) show planar nature. While the dihedral angles C17-N19-C24-C25

(86.70) and C17-N19-C24-C29 (-95.20) show non-planar nature due to the attachment of oxyacetamide group. The van-der Walls repulsion of H21…H22 and H23 causes a steric hindrance in achieving coplanarity for the ring with the oxyacetamide group and thus a twisting of bond angle is noticed. Moreover, in MD, the dihedral angles C17-N19-C24-C25 (100.10) and C17-N19C24-C29 (-81.80) are increases from the monomer due to the intermolecular hydrogen bonding.
Fig. 1 (a, b) The bioactive MM with five different water complexes has been taken to find out the various types of hydrogen bonds. All molecular structures of optimized MM–H2O complexes have been shown in Fig.2 (c, d, e, f, g for MW1, MW2, MW3, MW4 and MW5). The structural parameters of hydrogen bonds in MM–H2O complexes are listed in Table 1. Generally longer X-H bond and shorter H-Y bond indicate the strong interaction and vice versa. In Table 1 hydrogen bond parameter δRH....Y can be defined as δRH....Y =R H VDW + R YVDW - R H….Y Where R H VDW and R YVDW are van der Walls radii of H atoms and Y donor atom are given by Bondi [37] respectively. The distance between H-donor and H-acceptor is R H….Y. In Table 1 the δRH....Y of the intramolecular C20-H23M… O18M hydrogen bond in all MM–H2O complexes is larger than that of the monomer, except MW5 which reveals that the intramolecular hydrogen bond has strengthened in water complexes. The largest ∆RX-H (0.021 Ǻ) value found in all MW complexes except MW1 show the strongest intermolecular (O39-H40W…N13M) H-bond. The Hbond involving thiazole ring nitrogen as H-donor has positive ∆RX-H values influenced red shifted H-bonds. The highest value of ∆RX-H (0.021 Ǻ) is found in MW2, MW3, MW4 and 6

MW5 which seems to be the strongest (O39-H40W…N13M) intermolecular H-bond. The O39H40W…N13M distances in MW2, MW3 and MW4, are 1.916,1.901 and1.907Ǻ respectively, which are shorter than the related van der Waal's radii and the corresponding bond angles are (170.8, 174.0 and173.3o) greater than 90o, this shows that the intermolecular hydrogen bonding interaction is strong. In MW1 the water molecule is added near the benzothiazole ring, the benzene ring has the tendency to form H–bonds because the electron sucking ability of benzene is very strong. Moreover C6-H10M…O36W hydrogen bond shows lengthening of RH....Y, while it is considered as the weakest intermolecular hydrogen bonding. In MW2 the shortest RH....Y (2.283 Ǻ) confirms the strongest intramolecular hydrogen bond because the maximum δRH....Y value (0.618Ǻ) is observed, which seems to be the strongest hydrogen bond. In MW2, the shortest RH....Y (1.916Ǻ) value and maximum δRH....Y value (0.804Ǻ) is observed, which shows the strong intermolecular (O39-H40W…N13M) hydrogen

bonding.

Furthermore the next strongest

intermolecular interaction is C20-H23M… O18M. Moreover C3-H7M…O39W H–bond shows lengthening of RH....Y, so it is considered as the weakest intramolecular H-bond. In MW5 the maximum value of δRH....Y is observed in O39-H40W…N13M (0.815Ǻ) and O48-H50W…O18M (0.758 Ǻ) due to strong intermolecular hydrogen bonding. It is the most stable complex of mefenacet. In addition the N atom is more electronegativity than the carbon atom, so N-H bond is good proton donor than C-H bond. The above strongest intermolecular interaction reveals the herbicidal nature of the compound.
Fig. 2(a,b,c, d, e)
Table 1 4.2 Vibrational Analysis MM molecule consist of 35 atoms, it has 99 normal modes of vibration. The computational and experimental wavenumbers of MM, MD, MW1, MW2, MW3, MW4 and MW5 are listed in Table 2. The recorded and experimental FT-IR spectra of MM are given in Fig.3. Theoretical and experimental FT-Raman spectra are reported in Fig.4. The PED assignments are carried out by normal coordinate analysis and scaled by WLS method. The scaling factors of MM, MD and MM-H2O complexes are listed in supplementary Table S2(a)-S2(g). The definition of internal co-ordinates and local symmetry co-ordinates of mefenacet are listed in supplementary Table S3(a) and S3(b). 7

4.2.1 Benzothiazole ring (R1) Vibrations The thiazole directly connected to a benzene ring suggests that there might be substantial influence in the entire structure. Whereas using standard group frequencies [38] aromatic compounds commonly exhibit multiple weak bands in the range 3000-3100cm-1 [39]. In MM, the C-H stretching vibrations are assigned as a strong IR peak at 3062 cm-1 and very strong Raman band at 3061 cm-1 and the corresponding computed value is observed at 3058 cm-1. The predicted scaled wavenumbers are in very good agreement with the observed bands. The C-H in-plane bending vibrations normally occur in the region 1000-1300cm-1 [40]. In MM benzothiazole ring the C-H in-plane bending vibrations H8C4C3 are calculated as 1467 cm-1 with 45% PED and 1450 cm-1 for H9C5C4 with 48% PED. The corresponding IR values are 1445cm-1 and 1456 cm-1. The C-H out of plane bending vibrations are usually observed in the region 675-1000cm-1[41]. The C-H out of plane bending vibration of MM is assigned as 992, 942cm-1 and 934, 994cm-1 for IR and Raman respectively. The corresponding calculated values at 1002 cm-1 for H8C4C5C3 with 84% PED and 980cm-1 for H9C5C4C6 with 88% PED respectively. Generally the C-C stretching vibrations occur in the range 1200-1650cm-1 [39]. In MM the weak band in IR at 1669 and 1565cm-1 is assigned to a C4-C5 stretching vibration with 67% PED value. The computed values are found as 1575 and 1326cm-1. The C-S stretching vibration is expected in the region 685710cm-1 [42]. The calculated value lies at 708cm-1 and the corresponding experimental values are observed as a very strong IR peak (700cm-1) and a weak band in Raman spectrum (702 cm-1). 4.2.2 C=O vibrations and C-O vibrations. The C=O stretching mode is expected in the region 1700-1780cm-1 [43]. In MM molecule the very strong IR band at 1680cm-1 has been assigned to C17-O18 stretching vibration. However the wavenumber decrease is attributed to the strength of hydrogen bonding due to C20-H23… O18 interaction, moreover red shift occur which leads to the herbicidal active mode of vibration. In addition the C12-O35 stretching mode is assigned to a peak in IR spectrum of wavenumber 1237 cm-1. It agrees with the computational value (1234cm-1). The strong IR band at 1068cm-1 and weak band in Raman spectra at 1069cm-1 are assigned to C14-O35 stretching. The calculated value is found to be 1074cm-1. This variation in wavenumber denotes the influence of C-H…O hyperconjugation.

8

4.2.3 C=N, C-N vibrations.

The C=N stretching vibrations are observed in the range 1566-1672cm−1 [44–46]. Varsanyi [47] has suggested that an IR band at 1626cm−1 for C=N stretching frequency of benzothizaole. The strong IR band at 1540cm−1 and strong Raman band at 1544cm−1 are assigned to C12-N13 stretching vibration of MM molecule. The corresponding calculated value lies at 1561cm−1. The decrease in wavenumber from the expected range causes red shift

which leads to the possibility of strong hydrogen bond interaction (C14-H16…N13) with the interatomic distance 2.489Ǻ as supported by structural analysis. This result clearly reveals that C12-N13 also be the active mode of vibration. The strong IR band at 1249cm-1 and band in Raman spectra at 1247cm-1 are assigned to C17-N19 stretching. The calculated value is assigned to be 1256cm-1. 4.2.4 Methylene Vibrations. Generally the asymmetric and symmetric CH2 stretching appears at 2926cm-1and 2853cm-1 [48] respectively. The asymmetric methylene stretching vibration (C14-H15) is assigned to a weak IR band at 3004cm-1. In MM the computed value lies at 3005cm-1. The symmetric methylene stretching vibration (C14-H16) is assigned as a strong IR peak at 2953cm-1 and a medium intensity Raman peak at 2956cm-1. The calculated value lies at 2956cm-1 with 99% PED contribution. The presence of nitrogen atom adjacent to the methylene group causes electronic effects including back donation. Moreover, due to the hyperconjugative interactions C14-H15…O35 and C14H16…O35, the wavenumber increases while blue shifting occurs [48]. The twisting, wagging and rocking vibrations appear in the region 719-1422cm-1. The medium intensity IR peaks 1397, 1336cm-1 and weak peak (1341cm-1) in Raman spectrum are assigned to CH2 wag. Theoretically, it is calculated as 1394 and 1341cm-1 with 34 and 33% PED contributions. Weak IR band at 1310cm-1 is assigned to CH2 twisting and the corresponding calculated values are 1303, 1285 and 1281 cm-1. The methylene rocking mode is observed as strong IR band at 569cm1

and the calculated values lie at 570cm-1.

4.2.5 Methyl Group Vibrations.

9

The asymmetric and symmetric CH3 stretching modes are expected in the region around 2980 and 2870cm-1[49]. For the title molecule the C20-H23 asymmetric stretching vibration is assigned to a Raman band at 3011cm-1. The corresponding calculated value lies at 3018cm-1 with 100% PED contribution. The increase in wavenumber occur blue shift due to the influence of electronic effect resulting from C20-H23…O18 intramolecular hydrogen bond interaction. The CH3 symmetric stretching vibration is calculated as 2950 and 2903cm-1. The deformation modes of the CH3 group are assigned in IR spectrum at 1416cm-1, 1397cm-1 and Raman band at 1416 cm-1. 4.2.6 Phenyl ring (R2) vibrations The aromatic ring vibrational modes of the mefenacet are analysed based on the Wilson’s Numbering Convention. The selection rule allows five normal modes (2,20a, 7a, 7b, and 20b) for the C-H stretching in mono substituted benzene derivatives. For heavy mono substituted benzene derivatives the normal mode 7b is expected in the range 3000-3060cm1 [47]. The 3036cm-1 peak in IR spectrum has been assigned to vibrational mode 7b and the calculated value lies at 3036cm-1. In mono substituted benzenes there are five C-H in- plane bending vibrations. The aromatic C-H in plane (1015-1300cm-1) and out-of-plane (1000-700cm-1) [47] bending vibrations have substantial overlapping with the ring CCC-in plane and out of plane bending modes respectively. The strong IR band lies at 1124 cm-1 has been assigned to the H32-C27-C26 in plane bending vibration with the calculated value 1129cm-1(58%). There are five normal vibrations of benzene having the character of C-C stretching mode 8a, 8b, 19a 19b and 14 [47]. The fundamental modes 19b is expected in the range 1440-1470cm-1[47]. The strong IR band and weak Raman band lie at 1594 cm-1 has been assigned to the modes 19b vibration with the calculated value 1595cm-1. In addition the ring breathing mode for monosubstituted benzene appears near 1000 cm-1[47]. In MM the strong IR band at 992 cm-1 and weak Raman band at 994 cm-1 are assigned to the ring breathing mode and the corresponding calculated values lie at 1002 cm-1.
Fig. 3&4
Table 2 4.2.7 Modes involved in Hydrogen bonding interactions of Dimer.

10

The Experimental and theoretical bond length(Å) and stretching frequency(cm-1) of modes involved in intermolecular hydrogen bonding for dimer are listed in the Table 3. In MD, due to the influence of C60-H65-…O18 hydrogen bond the C60-H65 stretching vibrations exhibit a bond at 3056cm-1 and 3049cm-1 for symmetric and asymmetric respectively. Moreover the theoretical wavenumber 3017cm-1 has been assigned to C49-H51 asymmetric vibration and 2963 cm-1 to symmetric stretching vibration with slight increase in bond length. In addition the strong IR band observed at 3062cm-1 and strong Raman band observed at 3061cm-1 are assigned to stretching vibrations of C29-H34 and similar mode is calculated at 3048cm-1 for asymmetric and 3055cm-1 for symmetric stretching in MD. Thus the down shift in wavenumber of 8cm-1 in asymmetric and upshift in wavenumber 5cm-1 from monomeric to dimeric model due to the involvement of C29-H34…O53 hydrogen bond. On the other hand strong IR band at 2953cm-1 and 3004cm-1 weak bond as well as 3011cm-1 and 2953cm-1 in Raman spectrum are assigned as C14-H15 stretching vibrations. This mode has been calculated at 3016cm-1 for asymmetric and 2963cm-1 for symmetric stretching vibrations, this result clearly reveals that the wavenumber upshift occurs due to the influence of C14-H15…O70 intermolecular H-bond.
Table 3 4.2.8 MM-H2O complex Vibrations. The X-H bondlength and frequency shift of X-H stretching vibration is a measure of the strength of interaction. If the change in X-H bond length is higher, larger red shift of X-H stretching vibrational frequency in the water complex denotes stronger interaction. Supplementary Table S4 collects the data of the X-H stretching vibrational frequencies of H-bonds in both MM-H2O complexes and monomers. The largest red shifted values (-350 to -540cm-1) are found in O39H40W…N13M intermolecular H-bonds in TW3,TW4 and TW5, which shows hydrogen bond in MM-H2O complexes.

the strongest

However this N13 atom is identified as the most

interactive atom due to the herbicidal nature of the compound. In C20-H23…O18 H-bonds in MW1, MW2, MW3 and MW4 (except MW5) are blue shifted one because of the positive shifts. The interaction in TW5 is due to the presence of O48-H50W…O18M intermolecular hydrogen bond in the oxyacetamide group. The large red shift occurs with negative ∆υX-H (-353, 342 cm-1 for asymmetric and -367 cm-1 for symmetric stretching). The intra and intermolecular hydrogen bonding present in the molecule reduce the O-H stretching band from the normal range (355011

3700cm-1) [50]. In MW1 because of the C6-H10M…O36W, H-bond have smaller blue shift value of about 1cm-1(symmetric stretching) and 3, 2 cm-1 (asymmetric stretching). Also one red shift occurs in asymmetric stretching with negative shift value (-1cm-1). In MW2, the smaller blue shift occurs due to the influence of C6-H10M …O36W, C14-H16M …O39W and C25-H30M … O39W Hbonds. In MW3, O42-H43W…O35M H-bond have large ∆υX-H value (-347cm-1 for asymmetric and 359 cm-1 for symmetric) which produces red shift. In addition O42-H44W…O18M also exhibits a red shifted H-bond with negative ∆υX-H (-347cm-1 and -359 cm-1) value. Moreover, in MW4, O42-H44W…O18M and O42-H43W…O35M also exist the negative shift (-347 and -362) due to the involvement of lone pair (-347 and-362 cm-1) oxygen atom. Another intramolecular interaction C25-H30M … O39W, C27-H32M … O45W and C26-H31M … O45W exhibit the positive shift value (8cm1

for symmetric and 5, 1, 2 cm-1 for asymmetric stretching) while it predicts the blue shift. In

MW5 due to the influence of oxygen atom present in the molecule O42-H44W…O18M,O42H43W…O35M and O48-H50W…O18M H-bonds show red shift because of high negative shift values (-344 and -342cm-1). While it shows the herbicidal activity of oxyacetamide group in the molecule. 4.3 Charge Analysis 4.3.1 Natural Population Analysis The NPA analysis is an important tool to describe the distribution of electrons which helps vibrational spectral analysis [51]. The NPA of MM, MD, MW1, MW2, MW3, MW4, and MW5 are studied by using B3LYP/6-311G (d,p) level which is given in supplementary Table S5. The NPA plot is shown in Sup Fig. 1. The data shows that, the maximum difference is observed at the N and S atoms, which belong to the thiazole ring and N, O atoms in the oxyacetamide group. In MM, MD, MW1, MW2, MW3, MW4 and MW5, C2 atom (0.135, 0.135, 0.133, 0.136, 0.133, 0.133 and 0.131e) behave as electropositive when compared to other carbon atoms due to the influence of N13 and S11 present in the thiazole ring. The other neighbouring carbon atoms like C1, C3, C4, C5 and C6 possess electronegative nature. The atoms C2, C12, C17 and C24 have positive charge. Obviously all other carbon atoms exhibit electronegative nature. The atom C17 shows maximum positive charge due to the influence of O18 (C20-H23…O18 hydrogen bond). In MW5 the charges are highly increased (0.704e) when compared to other structures, which is due to the effect of more intermolecular interaction of water molecules. Direction of the dipole 12

moment vector in a molecule depends on the centers of positive and negative charges. Hydrogen atom exhibits a positive charge which is an acceptor atom in the title molecule. The atom N13 shows more electronegative (-0.557e for MM) charge due to the bioactivity of thiazole ring. Atom O18 shows more electronegativity (-0.612, -0.661, -0.614, -0.619, -0.657, -0.660 and 0.699e), this may be due to the involvement of lone pair electrons present in the nitrogen for extended conjugation due to the hyperconjugative interactions (C20-H21…N19 and C20-H22…N19) as supported by vibrational analysis. Due to the effect of water molecules, the charge values are altered, which reveals the strong intramolecular hydrogen bondings, such as O-H…O, C-H…O and N-H…O. It predicts that the high electronegative nature of O18 and N19 in the oxyacetamide as well as N13 atom in the R1 increases the herbicidal activity of the compound. 4.3.2 NBO Analysis The NBO analysis evaluates the electron delocalization and hybridization of atomic lone pairs from donors to acceptors [52]. NBO analysis has performed on the present molecule using DFT/B3LYP method with 6-311G (d,p) basis set and the possible intensive interactions are given in supplementary Table S6. In MM, the donor (C5-C6) to acceptor (C1-S11) transistion arises with the stabilization energy 25.65 kJ/mol. MD, MW1, MW2, MW3, MW4 and MW5 (25.82, 26.45, 25.57, 26.23, 26.19 and 26.28 kJ/mol) also show the strong stabilization energy due to the attachment of high electronegative atom present in oxyacetamide group and benzothiazole ring. The strong intramolecular hyperconjugative interaction

such as C20-

H21…N19, C20-H22…N19 are observed in MM, MD, MW1, MW2, MW3, MW4 and MW5, and are tabulated in supplementary Table S7. Due to the hyperconjugative interactions, the donor to acceptor transition σ (C24-C29) →σ* (C24-C25) occurred with high stabilization energy (17.53, 18.16, 17.53, 17.74, 18.8, 18.28 and 18.45 kJ/mol). It is supported by vibrational analysis. The NBO result also reveals that another intensive hyperconjugative interactions present in the molecules that are C14-H15…O35 and C14-H16…O35. In MM due to the influence of the above hyperconjugative

interactions, σ(C14-H17)→σ*( C12-O35) the stabilization energy decreases

(3.60kJ/mol) with ED(0.052e) which is substantiated by vibrational analysis and charge analysis. Similarly the second order interaction energies for MD, MW1, MW2, MW3, MW4 and MW5 are 3.60, 3.56, 3.52, 3.64, 3.64,3.56kJ/mol respectively.

13

In the presence of C20-H23…O18 intramolecular hydrogen bond σ (C14-C17) →σ*(N19-C20) interaction exists with the strong stabilization energy (19.21 kJ/mol for MM and 19.79kJ/mol for MD), which increases the occupancy of the antibonding orbital. However the above interactions proved that, the molecule mefenacet have high herbicidal activity due to the presence of oxyacetamide region. Relatively the interaction energy high means strong ICT interactions leading to stabilization of the molecule. The most important interactions between Lewis type (filled) NBOs and non Lewis (empty) NBOs are reported in supplementary Table S8. In MM the bonding orbital C14-C17 with 1.980e has 51.55% C14 character in a sp2.44 hybrid and has 48.45% C17 character in a sp1.93 hybrid orbital of MM. In addition the bonding orbital for C12-N13 with 1.988e electrons has 40.11% C12 character in a sp1.48 hybrid and has 59.89% N13 character in a sp 1.71 hybrid orbital. Due to the delocalization, MM shows more p character and less s character. Similarly in MD, MW1, MW2, MW3, MW4 and MW5 also the C-C and C-N bonds having more p character than s character. 4.3.3 NBO Analysis of MM-H2O complexes. Generally the second order perturbation energy E(2) larger indicates the stronger charge transfer interaction occurred in the H-bond. The result of NBO MM-H2O complex is listed in supplementary Table S9. The highest E(2) value of 55.35kJ/mol corresponds to O39-H40…N13 Hbond of MW3 is the largest H- bond which indicates the strongest charge transfer interaction. MW2, MW4 and MW5 also confirm the O39-H40…N13 H-bond with energies 52.43, 54.05 and 54.64 kJ/mol .This interaction is highly effective for the herbicidal compound mefenacet. In MW5, the second largest intermolecular interaction exist in the bond O48-H50W…O18M with the energy 12.27 kJ/mol. Moreover C20-H25M…O48W intermolecular interaction (MW5) is found with the E(2) value 11.17 kJ/mol, which confirms the partial covalent character of these H-bonds. Similarly for other hydrogen bonds with lower E(2) energy values indicate the weaker charge transfer interaction occurred. Especially C14-H16M…O39W and C3-H7M…O39W H-bonds in MW2 have no E

(2)

values, which indicates the hydrogen bonds comes from non charge transfer

interaction. Due to the cooperativity between the intra and intermolecular H-bonds the above strong H-bonds have the positive ∆RX-H value which shows the strengthening of the herbicidal activity. The strong charge transfer exists due to the effect of thiazole ring and oxyacetamide group as supported by vibrational analysis. 14

4.3.4 QTAIM analysis Quantum Theory of Atoms in Molecules (QTAIM) is a special practical tool to explain the physical nature of chemical bonds [53-54] and, it is employed to calculate the interactions mainly for intra and intermolecular hydrogen bonding interaction. The electron density (ρ) and Laplacian of electron density ( 2ρ) of Nuclear Attractor Critical Points (NACP) and Bond Critical Point (BCP) are the important factor which determines the topological parameters in AIM analysis. On the basis of a topological parameters Laplacian of total electronic density 2

ρ(r) is expressed as, ¼ 2ρ(r) =2G(r) +V(r)............... (1)

Where G(r) and V(r) are the kinetic and potential electron energy densities of critical points respectively. The Laplacian of electron density 2ρ(r) provided significant information about the nature of the bonds and the type of interaction exist between the atoms in molecule. The energy of the intermolecular conventional H-bonds are evaluated by the Epsina [55] hypothesis based on the electron density distribution at the (3, -1) BCPs of the H-bonds: EHB = 1/2 V(r); where V(r) is the value of a local potential energy at the bond critical point. Analysis of the QTAIM properties, such as electron density and Laplacian of electron density, are performed using AIMALL program [19] and its molecular graph is visualized by Multiwfn [20]. The bond topological parameters of dimer and monomer have been listed in supplementary Table S10, while its various topological parameters responsible for intermolecular hydrogen bonding interaction are tabulated in Table 4. The molecular graph of dimer and monomer showing different bond path at critical points (3,-1) are shown in Fig.5 (a,b).
Fig.5(a,b)
Table 4 For hydrogen bonded interaction

2

ρ(r) is positive which shows depletion of electronic charge

along the bond path. While for covalent bond

2

ρ(r) is negative, which shows the charge

concentration. The electron density ρBCP(r) of the C-C bonds of the aromatic ring nearly 2.02 e˚A−3 and the C14-C17 (supplementary Table S4) bonds exhibit low value due to different environments. The Laplacian values of C2-N13 and C17-N19 bonds lie between -21.20 and -20.72 15

eÅ-5, respectively, which shows the herbicidal active region of the mefenacet molecule. Upon dimerization, noticeable changes have been occurring and lie between -26.50 and -21.68 eÅ-5. The intermolecular C-H…O interaction has been formed by the orbital overlap between n1(O18), n2(O18) with σ*(C49–H51) and σ*(C60–H65) which are further supported by low charge density (0.06 eÅ-3, for O18…H51 and 0.07 eÅ3, for O18…H65) and positive Laplacian density (-0.48 eÅ-5 for O18…H51 and -0.72 eÅ-5 for O18…H65). Similarly for C14-H15 and C29-H34 bond it suffers from a strong attraction (BCP: CH…O) have positive Laplacian (Table 4) and low electron density (ρ < 0.1), indicating the existence of intermolecular hydrogen bonds. These bonding characters in the oxyacetamide region and thiazole ring nitrogen show the herbicidal nature of the compound. 4.4 Potential Energy Surface Scan (PES) Analysis The evaluation of the most stable conformations of MM molecule has performed by the potential energy surface (PES) as a function of eight dihedral angles that are modified independently. Fig.6 shows that the combined PES scans done at the B3LYP 6-311 G (d,p) level for the eight different dihedral angles at every 10o for a 360o rotation from 0

o

around the bond and the

corresponding energy are listed in the supplementary Table S11(a)- S11(h). In this kind of compound rotation occurs, due to the influence of different structural parameters, such as steric, dipolar, mesomeric and hyperconjugative effects including hydrogen bonding interaction [29]. The minimum energy distribution is obtained by choosing the dihedral angle N13-C12-O35-C14. This dihedral angle has the relevant coordinate for conformational flexibility within the molecule. The lowest global minimum energy is obtained at 00 in the potential energy curve with an energy value -3351520.1kJ/mol, which is due to the possibility of strong C14-H16…N13 hydrogen bonding with the interatomic distance H16…N13(2.496Ǻ) which leads to the herbicide active site (N13) as supported by structural, vibrational, NPA, NBO and QTAIM analysis. The maximum energy is obtained at 2200 with the energy value -3351487.2 kJ/mol. High barriers has been noticed as 32.9kJ/mol due to the influence of C14-H16…O35 hyperconjugative interaction. The above rotation is compared with the rotation about S11-C12-O35-C14, due to the electrostatic attraction of sulphur present in the thiazole. The minimum energy is obtained at 500 with energy -3351486.1kJ/mol and the maximum energy is obtained at 2300 with the energy value 3351496.7 kJ/mol, which is due to the possibility of strong C14-H16…O18 hydrogen bonding with the interatomic distance O18…H16 as 2.573Ǻ. Moreover, it is in good agreement with OH 16

distance 2.600Ǻ. In addition the S11-H16 interaction at 3400 and S11-H15 interaction at 3600 are observed as 2.873Ǻ and 2.814 Ǻ respectively. Rotation about C14-C17-N19-C20 shows minimum energy at 1700 with the energy value 3351520.0kJ/mol due to the influence of C20-H21…N19, C20-H22…N19 and C20-H23…N19 hyperconjugations with the N-H interatomic distances 2.075, 2.113 and 2.112 Ǻ respectively. Maximum energy is obtained at 2700 (-3351455.0kJ/mol) due to the involvement of C20H21…N19 hyperconjugation with the distance of 2.084Ǻ (N19… H21). The intensive interactions are identified in this group due to the C-H…N hyperconjugations and van der Walls repulsion. However the separation between the energy curve shows a highest potential barrier ∆E=60 kJ/mol. The rotation about the dihedral angles C29-C24-N19-C20 and C25-C24-N19-C20 show the maximum and minimum energy values at the same angle (1700 and 2500) with same energy. In C29-C24-N19-C20, the H34…H16 interatomic distance has been noticed as 2.669Ǻ with minimum energy -3351519.8kJ/mol at 2500. Obviously the steric strain occurs with the interatomic distance of H34…H16 (1.924 Ǻ) with maximum energy -3351489.5 kJ/mol at 1700. In C25-C24N19-C20 also the H30…H16 interatomic distance is noticed as 1.928Ǻ with minimum energy 3351519.8kJ/mol at 2500 and the maximum energy is obtained at 1700 with the H30…H16 interatomic distance as 2.679Ǻ. Moreover, the rotation about the dihedral angle N19-C17-C14- O35, the minimum energy is obtained at 2700 (-3351513.9kJ/mol) due to the influence of strong C14H15…O18 hydrogen bond with the interatomic distance O18… H15 as 2.488 Ǻ and C20-H23…O18 hydrogen bond with the interatomic distance of O18…H23 as 2.269Ǻ.The maximum energy is obtained at 500 with an energy -3351506.9kJ/mol due to the influence of C14-H16…O18, C17H23…O18 and C14-H16…N13 hydrogen bonds with the interatomic distances 2.453 Ǻ (O18… H16), 2.277Ǻ (O18…H23) and 2.481Ǻ (N13…H16) respectively. The barrier width is calculated as 7kJ/mol. In addition, the rotation about the dihedral angles H23-C20-N19-C17 and H23-C20-N19-C24 show the minimum and maximum energy values at the same angle with same energy. In both dihedral angles the maximum energy is obtained at 500 and 1700 with the energy value 3351517.5kJ/mol and the minimum energy is obtained at 00 and 2300 with an energy value 3351520.0kJ/mol. In H23-C20-N19-C24 the maximum energy is obtained at 2300 due to the possibility of strong hydrogen bonding C20-H21…O18 with the interatomic distance of O18…H21 (2.665Ǻ). The minimum energy is obtained at 500 with the possibility of C20-H22…O18 strong

17

hydrogen bond with an O18…H22 interatomic distance 2.281Ǻ and at 700 there is a possibility of C20-H23…O18 hydrogen bonding with the O18…H22 interatomic distance as 2.281Ǻ.
Fig. 6 4.5 Analysis of structure-activity descriptors 4.5.1. UV absorption spectrum analysis. The UV absorption spectrum of mefenacet is computed theoretically using Time Dependent – Density Functional Theory (TD-DFT) method with B3LYP/6-311G (d,p) as the basis set. The calculations are performed by assuming the title compound in solid phase with water as solvent. The computational absorption maxima (λmax) has depicted in Fig.7. The maximum absorption peak observed in 241.9nm is caused by the π-π* transition and another band is due to n-π* transition [56]. The calculated visible absorption maxima (λmax), excitation energy, band gap energy, oscillator strengths and the major assignments of the title compound are tabulated in Table 5. The band gap energy is calculated using the formula E=hc/λ, here h and c are the Planck’s constant and light velocity, respectively; λ is the cutoff wavelength. The band gap energy of the title molecule calculated from the theoretical λmax value is found to be 5.126eVrespectively. According to the absorption spectra, it is found that the maximum absorption wavelength with high oscillator strength (0.2271) is assigned to the transition from the HOMO-LUMO with 71%, the wavelength with moderate oscillator strength (0.0002) to HOMO → LUMO with 32%.
Fig.7
Table 5 4.5.2 Frontier Molecular Orbital Analysis. The frontier molecular orbital (FMO) explains the way by which the molecule interact with other chemical species. The HOMO-LUMO gap is an important parameter which is used to investigate the chemical stability and reactivity [57]. In mefenacet the HOMO map is located on the benzothiozole ring and oxyacetamide on the other hand, the LUMO orbitals are mainly located on the benzene ring (R2). HOMO-LUMO energy gap of MM and MD (Sup Fig. 2(1)-2(2)) are 5.2110 and 5.0382ev respectively. This low energy gap suggests that the electronic transition 18

occurs easily in this molecule, and it confirms the herbicidal active nature of the compound. The SCF energy, Zero point vibrational energy and dipole moment are listed in supplementary Table S12. The value of energy gap is decreased while comparing with other structures, therefore dimeric model predicts higher reactivity and softness in comparison to monomeric model. 4.5.3 Global reactivity descriptors. The global chemical reactivity descriptors like ionization potential(A), electron affinity (I), electro negativity (χ), chemical potential (µ), electrophilicity index(ω), Hardness(η) and softness(S) are based on HOMO-LUMO energy values. These chemical descriptors are defined by Koopmans’s theorem [58] moreover the energy of frontier molecular orbitals are used to calculate the global reactivity descriptors. The changes in global reactivity descriptors from monomeric(MM) to dimeric(MD) model explain their reactivity and stability (supplementary Table S13). A high value of electronegativity describes a good electrophile, a small value of electronegativity describes a good nucleophile. The lower value of Electron Affinity (0.8600eV) indicates that the title compound readily accepts electrons to form bonds; this indicates the higher molecular reactivity with nucleophilies. According to Parr et al [59], electrophilicity index (ω) is a global reactivity index which shows a good correlation with toxicity. The electronegativity index of the molecule is ω=µ2/2η. In MM, the ionization potential lies at 6.0710 and the electrophilicity index lies at 2.3047. The highest value of ionization potential and electrophilicity index of mefenacet reveals the highest herbicidal activity. The low value of chemical hardness for dimeric model (η=2.5191) and high value of electrophilicity index (ω =2.4331) suggest that the dimeric model exhibits as electrophile and softer molecule than monomeric model. 4.5.4 Total partial and overlap population density-of-states. The total (TDOS), partial (PDOS) and overlap population (OPDOS) density of states is created to convoluting the molecular orbital information using the Gaussum 3.0 program. The spectra of TDOS, PDOS and OPDOS of MM and MD are plotted in Sup Figs. 3(1)-3(6). The DOS plot illustrates the MO compositions and their contributions to the chemical bonding [60]. The PDOS show the bonding, antibonding and non bonding nature of mefenacet. MM PDOS shows that C16 atom having 96% contribution in LUMO and 72% in HOMO is predicted the bonding 19

interactions with positive values. In dimer C32 atom has 91% contribution for LUMO and 72% for HOMO respectively. From the COOP spectrum, overlap of O2 with N2 for MM and O4 with N4 for MD show the maximum negative peak exhibits strong antibonding interactions with overlap population value. It confirms the bioactivity of the mefenacet herbicide. 4.5.5. Molecular electrostatic potential surface (MEPS) The molecular electrostatic potential relates to the electronic density sites for electrophilic attack and nucleophilic reactions as well as hydrogen bonding interactions [61]. MEPS of MM is obtained at the B3LYP/6-311G (d,p) optimized geometry using ArgusLab software. The negative (red) regions are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity sites as shown in Sup Figs. 4(1)-4(7). The color code of MEPS map is in the range between -0.0500a.u and 0.0500a.u. In MM, a large electropositive potential is found in the vicinity of the phenyl ring and more electrophilic region in thiazole ring and oxyacetamide group. From the MEPS map of MD model it shows that electrophilic reactivity spreads over in monomer part due to incorporation of intermolecular H-bond. In MM-H2O complexes MEPS map shows that the C=N and C=O group lying in the vicinity of most electronegative region of the molecule is prone to electrophilic attack and O-H group of water which localizes in the electropositive region is active towards nucleophilic attack. Therefore, C=N, C=O and O-H groups are strongly involved in intermolecular interactions. In mefenacet molecule, the intramolecular as well as intermolecular hydrogen bonding interactions such as C-H…O, CH…N and O-H…O is resulting the equalization of electrostatic potentials in the molecular system. In addition, the N13 atom in thiazole ring and lone pair of oxygen, nitrogen atom present in the oxyacetamide group exhibit electronegative potential and higher herbicidal activity. 4.6. Hirshfeld surface analysis The Hirshfeld surface is unique and suggests the possibility of gaining additional insight into the intermolecular interaction of molecular crystals [62]. The Hirshfeld analysis and associate 2-D finger print plots of mefenacet are produced using crystal explorer 3.1. In MD the Hirshfeld surfaces are mapped out using the dnorm, which exhibited intermolecular hydrogen bonding as well as the network of intermolecuclar van der Walls interaction. In Fig.8 the red color indicating contacts shorter than the sum of van der Wall radii. The white colour indicates intermolecular 20

distances close to van der Walls contacts with dnorm equal to zero. The dnorm, de, di, curvedness and shape index of the compound is shown in Fig.8. In turn contacts longer than the sum of van der Walls radii are indicated by blue. The O-H and C-H contacts in MD can be seen in bright red areas. The other visible spots on the surface indicate to H-H contacts.
Fig.8 4.6.1 Two dimensional finger print plots. The combination of de (distance from the point to the nearest nucleus external to the surface) and di (distance to the nearest nucleus internal to the surface) represents the 2-D finger plot. The 2-D fingerprint plot of mefenacet all intermolecular contacts is shown in Sup Fig.5. The 2-D fingerprint plot of title molecule revealed that the intermolecular interactions in the molecules are H…H, C…H, H…C, O…H. The H…H interactions reflected in the middle of dispersed point contributes the highest towards the Hirshfeld surfaces with 42.0%. The significant contribution from the C… H…O hydrogen bond visualize as a pair of sharp spikes over the surface of the molecule comprising 13.9% of the total Hirshfeld surfaces. In addition of above contribution the other H…C, O…H, H…O, H…S, N…H and H…N contacts are also observed and have a share of 10.8, 7.1, 6.4, 3.9, 2.9 and 2.6% of the total Hirshfeld surfaces. The C…C contacts appear as distinct spikes (Sup Fig.5). Complementary regions are visible in the fingerprint plots, which shows that one molecule acts as a donor (de>di) and the other as an acceptor (de
Lamarkian Genetic Algorithm method. After docking the ligand protein pose with least binding energy is selected as the best confirmation. The hydrogen bond interaction, bond distance and the interacting aminoacid residues has analysed using PYMOL molecule viewer[65] and tabulated in Table 6. The herbicidal protein targets are docked with mefenacet compound using Autodock 4.0. The compound exhibits significant activity against both the protein targets. The highest interaction has witnessed with protein Enoyl-ACP Reductase (PDB ID: 1ZID) with a binding score of -8.4kcal/mol. The hydrogen bond interaction between the target protein and mefenacet has displayed in Fig.9. The thiazole ring nitrogen atom (N13) exhibited hydrogen bond interaction with the amino acid ALA 191. Similarly, a good interaction between the lead compound and the protein fatty acid amide hydrolase (PDB ID: 2WAP) is observed. The compound exhibits two hydrogen bond interaction in the oxyacetamide region at residues VAL 270 and CYS 269 with a binding affinity of -8.3kcal/mol. This result clearly reveals that N13 and O18 atoms show the herbicidal active site of the mefenacet molecule.
Fig.9
Table 6

4.8 Molecular dynamics simulation (MDS) The stability of the ligand protein complex is analyzed using a Molecular Dynamics simulation approach [25]. The ligand protein complex with maximum number of hydrogen bond interaction and least binding energy are selected for the simulation studies. The experiment has performed using GROMACS 5.1 software. The ligand parameters are evaluated using PRODRG server in GROMOS force-field 43a1framework [27]. Solvation of ligand protein complex is done using water box of 1.0 nm. Charges of ligand protein complex are neutralized using Cl- and Na+ ions. Energy minimization for protein ligand complex is performed using steepest descant method for 50,000 steps. The complex has equilibrated under constant volume, pressure and temperature at 300K for 1000ps. Further, the stability of the protein ligand complex is evaluated under constant pressure, temperature and number of particles for 5ns. The trajectories produced from dynamic simulation studies are further analyzed for the Root Mean Square Deviation (RMSD), Root mean square Fluctuation (RMSF) and Radius of Gyration (Rg) of ligand protein complex using grms, grmsf and ggyrate utilities of GROMACS. The stability of the ligand protein complex is 22

analyzed using molecular dynamics studies. The target proteins 1ZID and 2WAP are docked with the compound mefenacet and simulated. From the results, the best fit is identified based on the stability of interaction. The 3D crystal structures of the target proteins docked with mefenacet are used for the following study. 4.8.1 Root Mean Square Deviation The conformational stability of ligand protein complexes are analysed from equilibrated molecular dynamics trajectories [66]. The RMSD for the ligand protein complex has displayed in Sup Fig.6. Low level of variation in RMSD value is observed in 2WAP, which defines the model to be spatially significant. It is observed that the complex remained more stable compared to the protein complex 1ZID. Only minimum deviations are observed in the protein complex 2WAP, which indicates the model to be more stable and rigid. 4.8.2 Root Mean Square Fluctuations Root mean square fluctuation of backbone atoms of each residue in protein structure is evaluated to understand the flexibility of the protein backbone[67]. Lack of significant variations in RMSF values in 2WAP reflects reduced or limited movements in the protein backbone. The residues in position 200-500 exhibit least fluctuation and are more stable. The RMSF value in protein 1ZID is very less compared to 2WAP. On the contrary the interaction in case of protein 1ZID shows more fluctuations with the ligand molecule. 4.8.3 Radius of Gyration Radius of gyration mentions about the compactness of tertiary structure of proteins. They provide valuable insights on stability of a protein in a biological system. Higher Rg value indicates a very loose packing of protein structure [68]. Gyration experiments are performed for about 5 ns and are depicted in Sup Fig.6. From the graph it is evident that the protein 2WAP is highly significant and exhibit more compact property compared to protein 1ZID. The RMSD, RMSF and Radius of gyration results are shown in Sup Fig.6. 5. Conclusion

23

In the present approach, quantum chemical techniques have been used to calculate the geometrical parameters of the optimized structure for MM, MD and MM-H2O complexes. The lengthening of C12-N13 bond length shows a red shift in the wavenumber due to C14-H16…N13 intramolecular hydrogen bond in mefenacet monomer. The largest red shifted values (-350 to 540) are found in the O39-H40W…N13M intermolecular H-bond. The N13 (-0.557e) atom shows high electronegative nature, which acts as herbicidal active site. The highest stabilization energy corresponds to O39-H40…N13 H-bond of MW3 exhibits highest herbicidal activity. The Laplacian values show that oxyacetamide and thiazole ring nitrogen are the herbicidal active regions. The most stable conformer (N13-C12-O35-C14) is determined by PES analysis and stabilized by 3351520.1kJ/mol. The band gap energy of the UV spectrum (5.126eV) shows good agreement with the energy gap calculated from the HOMO-LUMO (5.2110eV). The molecular electrostatic potential surface (MEPS) map of mefenacet shows that N13 atom and oxyacetamide group exhibit electronegative potential and large herbicidal activity. Hirshfeld surface analysis for H.....H interaction of mefenacet exhibits 42.0% contribution. Molecular docking predicts a stable complex with the proteins, as evident from the highest binding energy. The molecular docking simulation of MM with target proteins (1ZID, 2WAP) reveals the biological characteristics as well as its herbicidal nature. References [1] HESS.F. D, HOLMSEN. J. D. and FEDTKE. C, The influence of the herbicide mefenacet on cell division and cell enlargement in plants, Weed Research, 30 (1990) 21-27. [2] HE. H.W., MENG.L.P, HU.L.U, LIU.Z.J, Plant growth regulatory activity of 1-(1- phenyl1,2,4triazole-3-oxyacetoxy)alkylphosphonates, Chin. J. Pest. Sci., 4 (2002) 14–18. [3] CARL FEDTKE, Mode of Action Studies with Mefenacet, Pestic. Sci., 33 (1991) 421-426. [4] MASAHIRO SAKA, Acute toxicity of rice paddy herbicides simetryn, mefenacet, and thiobencarb to Silurana tropicalis tadpoles, Ecotoxicology and environmental safety, 73 (2010) 1165-1169. [5]CHEON.S, KIM.T.H, MOON.S, KIM.J, Mefenacet[2-(1,3-benzothiazol-2-yloxy)-N-methyl-Nphenylacetamide], Acta Cryst.E66 (2010) 03153. [6] HESS. F.D, Herbicide effects on the cell cycle of meristematic plant cells, Reviews of Weed Science, 3 (1987) 183-203. [7] WEI LI, QIAOFENG WU, YONG YE, MINDAO LUO, LING HU, YINGHONG GU, FEINIU, JIMING HU, Density Functional Theory and ab initio studies of geometry, electronic structure and vibrational spectra of novel benzothiazole and enzotriazole herbicides, Spect.chem.acta partA, 60 (2004) 2343-2354. 24

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cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic 28

simulation studies, International journal of biological macromolecules, 111 (2018) 548-560. Figures caption Fig. 1(a,b) Optimized geometrical structures of mefenacet monomer (MM) and dimer(MD) Fig. 2(a,b,c,d,e) Optimized geometrical structures of mefenacet-water complexes (MW1, MW2, MW3, MW4 and MW5) Fig.3 Combined FT-IR spectrum of mefenacet (MM) Fig.4 Combined FT-Raman spectrum of mefenacet (MM) Fig. 5(a,b) Molecular graph of MM and MD of different bond critical points at (3,-1) Fig.6 Combined Potential Energy Surface Scan of mefenacet (MM) Fig.7 Computational UV spectrum of mefenacet (MM) Fig.8 dnorm, de,di, curvedness and shape index of mefenacet (MD) Fig.9 Interaction of mefenacet with a) Enoyl-ACP Reductase (PDB ID : 1ZID) , b) Fatty acid amide hydrolase (PDB ID : 2WAP) Tables caption Table 1: Structural parameters (bond lengths in Ǻ and bond angles in degree) of H-bonds in mefenacet-H2O complexes calculated at the B3LYP/6-311G (d,p)level. Table 2: Detailed assignment, fundamental vibrations of mefenacet by Normal Co-ordinate Analysis and scaled wavenumbers by WLS method. Table 3: The observed and calculated bond length and stretching frequency of modes involved in inter molecular hydrogen bonding for dimer. Table 4: Topological parameters for bonds of interacting atoms of monomer and dimer: electron density (ρr), Laplacian of electron density (∇2ρr), electron kinetic energy density (G), electron potential energy density (V), total electron energy density (H), delocalization index (DI) at bond critical point (BCP). Table 5: Calculated absorption spectrum of mefenacet with water solvent at PCM-TDDFT basis set. Table 6: Binding affinity, Hydrogen bond interaction and Number of hydrogen bond residues of mefenacet with the target protein.

29

Supplementary figures caption Sup Fig. 1 The histogram of calculated Natural charges for MM, MD, MW1, MW2, MW3, MW4 and MW5. Sup Fig. 2(1)-2(2) HOMO-LUMO plot of both monomer and dimer of mefenacet with orbitals involved in electronic transitions in isolated (gaseous) phase calculated using B3LYP/ 6311G(D,P) level. Sup Figs. 3(1)-3(6) TDOS, PDOS and OPDOS spectrum of both MM and MD structures Sup Figs. 4(1)-4(7) Molecular electrostatic potential surface (MEPS) formed by mapping of total density over electrostatic potential in gas phase for monomeric, dimeric and MM-H2O complexes of mefenacet molecule. Sup Fig. 5 The de (y axis) and di (x axis) values are the closest external and internal distances from given points on the Hirsfeld contacts are (a)H…H 42.0%, (b)C…H 13.9%, (c)H…C 10.8%, (d) O...H 7.1%, (e) H…O 6.4%, (f) H...S 3.9%, (g) N...H 2.9%, (h) C…C 1.3% Sup Fig. 6 RMSD, RMSF and Radius of gyration of mefenacet Supplementary Tables caption Table S1(a)- S1(c): Optimized geometrical parameters of MM, MD, MW1, MW2, MW3, MW4 and MW5 at B3LYP/ 6-311G (D,P) level Table S2(a): The magnitudes of scaling factors of MM by WLS method Table S2(b): The magnitudes of scaling factors of MD by WLS method Table S2(c): The magnitudes of scaling factors of MW1 by WLS method Table S2(d): The magnitudes of scaling factors of MW2 by WLS method Table S2(e): The magnitudes of scaling factors of MW3 by WLS method Table S2(f): The magnitudes of scaling factors of MW4 by WLS method Table S2(g): The magnitudes of scaling factors of MW5 by WLS method Table S3(a): Definition of internal co-ordinates of mefenacet Table S3(b): Definition of local symmetry co-ordinates of mefenacet Table S4: The X-H stretching vibrational frequencies (strength) of H-bonds in both mefenacet H2O complexes and monomers. Table S5: Natural Charges of MM, MD, MW1, MW2, MW3, MW4 and MW5 Table S6: Second order Perturbation theory analysis of MM, MD, MW1, MW2, MW3, MW4 and MW5 Table S7: Possible Hyper conjugation of MM, MD, MW1, MW2, MW3, MW4 and MW5 30

Table S8: NBO results showing the formation of Lewis and Non Lewis orbitals of MM, MD, MW1, MW2, MW3, MW4 and MW5 Table S9: The second order perturbation energies E(2) (in kJ/mol) of H-bonds in both mefenacetH2O complexes obtained by NBO analysis Table S10: Topological parameters for bonds of interacting atoms of monomer and dimer: electron density (ρr), Laplacian of electron density (∇2ρr), electron kinetic energy density (G), electron potential energy density (V), total electron energy density (H) at bond critical point (BCP). Table S11(a)- S11(h): Potential Energy Surface Scan Analysis of mefenacet with eight different dihedral angles Table S12: Zeropoint vibrational energy,dipole moment and self consistant field energy of MM,MD,MW1,MW2,MW3,MW4 and MW5. Table S13: Global reactive parameters energy band gap (∆ ‫)ܧ‬, electronegativity (χ), chemical potential (µ), global hardness (η), global softness (S) and electrophilicity index (ω), of monomer and dimer of mefenacet molecule explaining their reactivity.

31

Table 1: Structural parameters (bond lengths in Ǻ and bond angles in degree) of H-bonds in mefenacet-H2O complexes calculated at the B3LYP/6-311G (d,p)level. Complex

H-bond

MW1

C6-H10 …O36

M

W

M

C20-H23 … O18 MW2

M

M

W

RH....Y

δRH....Y

< X-H....Y

1.083

0.000

2.454

0.446

139.7

1.087

-0.001

2.283

0.618

105.1

1.083

0.000

2.449

0.451

138.0

W

1.090

0.000

2.614

0.286

143.9

M

M

1.087

-0.001

2.278

0.622

105.2

W

M

0.978

0.021

1.916

0.804

170.8

1.084

-0.001

3.011

-0.111

124.3

1.086

0.002

2.325

0.575

153.8

1.085

0.000

2.322

0.578

146.7

C20-H23 … O18 O39-H40 …N13 M

C3-H7 …O39

W

M

C25-H30 … O39

W

M

W

C25-H30 … O39 M

M

1.087

-0.001

2.286

0.614

104.3

W

M

0.978

0.021

1.901

0.819

174.0

W

M

0.962

0.005

2.454

0.266

118.7

1.083

0.000

2.507

0.393

134.4

0.969

0.012

2.063

0.657

159.9

1.082

-0.001

2.543

0.357

133.3

C20-H23 … O18 O39-H40 …N13 O42-H43 …O35 M

C6-H10 …O36

W

W

O42-H44 …O18

MW4

∆RX-H

M

C6-H10 …O36

C14-H16 …O39

MW3

RX-H

M

C6-H10 …O36

M

W

C25-H30 … O39

M

W

1.084

0.000

2.362

0.538

145.4

M

W

1.083

-0.001

2.603

0.297

124.4

1.087

-0.001

2.286

0.614

104.5

0.977

0.020

1.907

0.813

173.3

1.083

-0.001

2.664

0.236

121.9

0.969

0.012

2.053

0.667

160.2

0.961

0.004

2.476

0.244

118.1

C27-H32 … O45 M

M

W

M

C20-H23 … O18 O39-H40 …N13 M

C26-H31 … O45

W

W

M

W

M

O42-H44 …O18 O42-H43 …O35

MW5

M

C6-H10 …O36

W

2.491

0.409

134.2

M

W

1.084

0.000

2.355

0.545

148.0

M

W

1.083

-0.001

2.626

0.274

122.4

0.968

0.011

2.122

0.598

160.4

0.962

0.005

2.408

0.312

119.6

0.969

0.012

1.962

0.758

159.8

0.978

0.021

1.905

0.815

174.3

1.084

0.001

2.963

-0.063

124.9

1.089

0.000

2.622

0.278

149.2

1.088

0.000

2.340

0.380

171.2

1.083

-0.001

2.597

0.303

123.5

W

M

W

M

W

M

W

M

O42-H44 …O18 O42-H43 …O35 O48-H50 …O18 O39-H40 …N13 M

C3-H7 …O39

W

M

W

M

W

M

W

C14-H16 …O39 C20-H23 …O48 C27-H32 …O45

H2O

0.000

C25-H30 … O39 C26-H31 … O45

monomer

1.083

C6-H10 C20-H23 C14-H16 C3-H7 C25-H30 C27-H32 C26-H31

1.083 1.088 1.089 1.083 1.084 1.084 1.084

OH

0.957

Table 2: Detailed assignment, fundamental vibrations of mefenacet by Normal Co-ordinate Analysis and scaled wavenumbers by WLS method Observed Frequency(cm-1) IR

3062(s)

RAM AN

3061 (vs)

Calculated

MM

MD

MW 1

MW 2

MW 3

MW 4

MW 5

3058

3060

3059

3068

3063

3067

3064

IR Rama Intens n ity Intens ity

3

5

Characterization of normal modes with PED(%)

υsymCHR1(99)

3036(w)

3011( vw) 3004(w) 2953(s)

2953( m)

1680(vs)

1669( w)

3056

3059

3056

3063

3055

3061

3056

2

5

υsym2CHR2(99)

3052

3054

3055

3054

3054

3055

3054

5

2

υsymCHR1(99)

3050

3050

3050

3046

3047

3054

3046

4

0

υsym20aCHR2(99)

3044

3044

3045

3044

3045

3045

3045

3

1

υsym7aCHR2(99)

3042

3043

3044

3037

3041

3044

3037

2

2

υsymCHR1(99)

3036

3042

3036

3032

3036

3038

3034

0

2

υasym7bCHR2 (99)

3032

3032

3031

3031

3033

3032

3032

0

1

υasymCHR1 (99)

3030

3031

3030

3026

3030 3030

3020

0

0

υsym 20bCHR2 (99)

3018

3018

3018

3021

3026

3024

3010

0

1

υasym(CH3)C20H 23 (100)

3005

2969

3005

3009

3008

3010

2977

0

1

υasym(CH2)C14H 15 (99)

2956

2964

2956

2959

2963

2961

2961

8

2

υsym(CH2)C14H 16 (99)

2950

2958

2951

2956

2959

2960

2945

5

1

υasym(CH3)C20H 22 (100)

2903

2900

2903

2907

2910

2910

2909

11

3

υsym(CH3)C20H 21 (100)

1732

1730

1731

1723

1698

1696

1700

88

0

υC17=O18 (75),θ O18C17-C14 (9), υN19-C17 (7)

1617

1649

1616

1612

1610

1611

1611

15

0

υ R1C4-C5 ( 51), υN13-C12( 13), βa R1 C2-N13-C12 ( 13),T C5C4-C3 ( 6)

1609

1594

1609

1610

1609

1609

1608

6

2

υ R2 C26-C27 ( 66), αR2 ,H32-C27-C28 ( 21), T C28-C29-C24 ( 8)

1594(vs)

1594( m)

1595

1593

1597

1601

1597

1598

1598

1

1

υ R2C27-C28 ( 69), α R2 H30-C25-C24 ( 18), T C26-C27-C28 ( 7)

1565( w)

1575

1570

1575

1596

1577

1594

1594

1

3

υ R1C4-C5 ( 67), α R1 H8-C4-C3 ( 19), T

C6-C5-C4 ( 7)

1540(s)

1544( s)

1561

1565

1563

1578

1546

1577

1577

80

12

υN13-C12 ( 39), υ R1 C5-C6 ( 19), υC12-O35 ( 17), βa R1 C2-N13C12 ( 6)

1503

1502

1503

1558

1507

1504

1507

15

0

α R2 H34-C29-C24 ( 52), υR2 C28-C29 ( 33), υN19-C24 ( 10)

1488

1496

1488

1507

1490

1488

1497

2

1

MH21-C20-H22 ( 46), M H23-C20-H21( 24), γN19-C20-H21 ( 11), ωN19-C20-H22 ( 9)

1477

1488

1477

1487

1477

1477

1484

3

1

MH23-C20-H21 ( 63), M H21-C20-H22 ( 28), θ N19-C20-H21 ( 6)

1467

1442

1467

1478

1467

1466

1467

4

1

αR1 H8-C4-C3 ( 45), υ R1 C4-C5( 35), αS11C1-C6 ( 6), βsC1-C2N13 ( 6)

1457

1435

1458

1467

1459

1457

1458

1

0

α R2 H32-C27-C26 ( 58), υ R2C26-C27 ( 36)

1445(w)

1450

1431

1453

1459

1457

1455

1451

16

1

α R1 H9-C5-C4 ( 48), υ R1C6-C1 ( 35)

1428(vw )

1434

1409

1436

1458

1449

1449

1445

8

3

wH15-C14-H16 ( 78), wH15-C14-H16 ( 6)

1420

1406

1420

1449

1425

1424

1413

6

1

γ H22-C20-H23 ( 65), M H21-C20-H22 ( 9), w H15-C14-H16 ( 7)

1394

1373

1395

1421

1403

1403

1366

19

1

d H15-C14-C17 ( 34), υN19-C24 ( 24), γH21C20-H22 ( 10), υ C24C25 ( 10)

1341

1343

1341

1395

1346

1345

1341

9

2

d H15-C14-C17 ( 33), υN19-C17 ( 33), ωN19-C20-H22 ( 8)

1328

1337

1328

1345

1343

1339

1327

0

0

α R2 H32-C27-C26 (

1493(m)

1456( vw)

1416(vw )

1416( w)

1397(m)

1336(m)

1341( vw)

62), υR2 C27-C28 ( 34)

1310(w)

1296( m)

1326

1330

1326

1341

1327

1327

1304

3

0

υ C4-C5( 72), α R1 H7C3-C4 ( 15), υ N13C2-C3( 5)

1303

1301

1302

1326

1304

1303

1300

1

4

υ C24-C25R1 ( 31), e H15-C14-C17 ( 27), α H30-C25-C24 ( 15), υ N19-C24 ( 9)

1297

1291

1297

1304

1300

1300

1282

0

1

υ C24-C25 R1 ( 71), α H34-C29-C24 ( 18)

1285

1284

1285

1302

1281

1281

1279

10

2

υ N13-C2 ( 26), eH15C14-C17 ( 22), α R1 H9-C5-C4 ( 19), υ R1 C3-C4 ( 8)

1281

1281

1282

1284

1278

1279

1263

4

1

υN13C12 ( 31), eH15C14-O35 ( 20), αH7C3-C2 ( 11), υ C2-C3 ( 8)

1249(w)

1247( m)

1256

1234

1260

1281

1262

1262

1263

47

7

υ-N19C17 ( 26), αH10C6-C5 ( 20), υ C4-C5 ( 17), βsC1-C2-N13 ( 8)

1237(w)

1234

1230

1233

1265

1232

1233

1233

100

1

υC12O15 ( 41), υ C1S11,C12-S11 ( 9), υ N13-C2( 8), υ C3-C4( 8)

1219(m)

1182( vw)

1157(m) 1137( vw)

1180

1183

1180

1240

1193

1184

1187

1

0

αH34-C29-C28 ( 78), υ C28-C29 ( 20)

1170

1171

1171

1192

1171

1170

1170

0

0

αH32-C27-C26 ( 79), υ R2 C27-C28 ( 20)

1170

1169

1170

1171

1170

1166

1167

1

0

αH9-C5-C6 ( 76), υ R1C5-C6 ( 19)

1137

1160

1137

1170

1139

1137

1144

1

0

ωN19-C20-H22 ( 36), υN19C20 ( 16), υ C1C2 ( 13), E N19-C17O18 ( 6)

1124(vs)

1068(vs)

1020(s)

992(s)

1069( vw)

1020( m)

994(w )

1133

1117

1132

1137

1137

1136

1137

1

2

θN19-C20-H22( 74), ω N19-C20-H23 ( 14)

1129

1100

1128

1131

1133

1132

1134

45

1

αH32-C27-C26 ( 53), υ C29-C24 ( 34)

1086

1084

1087

1095

1096

1093

1093

2

0

υ C29-C24 ( 50), αH32C27-C26 ( 45)

1074

1079

1073

1071

1072

1071

1071

11

2

υC14O35 ( 25), υ C27C28 ( 15), υ N19-C17 ( 14), T C3-C2-C1 ( 13)

1063

1043

1061

1060

1061

1060

1058

2

1

T C5-C4-C3 ( 27), υ R1C3-C4 ( 17), υ C1S11,C12-S11 ( 11), υ N19-C24 ( 10)

1037

1040

1037

1039

1039

1038

1040

6

1

υ C28-C29R2 ( 57), αH34-C29-C28 R2 ( 21), T C29-C24-C25 ( 11), υ C14-O35 ( 6)

1031

1032

1032

1034

1033

1033

1033

3

4

υR1 C1-C2 ( 69), αR1 H9-C5-C4 ( 23)

1022

1020

1023

1026

1028

1028

1030

0

0

D ( 50), h C14-C17O18-N19 ( 19), e ( 7), tC12-O35-C14-C17 ( 7)

1014

1016

1015

1018

1017

1014

1014

4

2

T C28-C29-C24 ( 54), υC14O35 ( 18), υ C27C28 ( 9), υ N19-C20( 9)

1005

1000

1005

1010

1007

1003

1003

13

4

υC28-C29 R2 ( 35), υC14O35 ( 26), υ N19C20, ( 19), T C27-C28C29 ( 8)

1002

992

1002

1001

1002

999

1001

0

0

πH8-C4-C5-C3 ( 84), ψ C25-C26-C27-C28 ( 12)

980

986

993

994

993

991

994

0

0

πH9-C5-C4-C6 ( 88), ψC25-C26-C27-C28 ( 9)

976

986

981

990

990

964

968

0

0

π H9-C5-C4-C6 ( 87), t C2-C1-C6-C5 ( 9)

942(vw)

937

953

960

967

967

954

956

0

0

π H7-C3-C2-C4 ( 66), tC2-C1-C6-C5 ( 9)

935

952

935

946

946

924

927

0

0

πH8-C4-C5-C3 ( 91), t C26-C27-C28-C29 ( 6)

922

910

922

923

925

905

905

1

1

υC28-C29 ( 34), E N19C17-O18 ( 15), υ N19C24 ( 11), ωN19-C20H22 ( 11)

900(v w)

901

889

902

907

905

883

885

2

0

T C5-C4-C3 ( 31), υ R1C1-C2 ( 15), αO35C12-N13 ( 9), υC12O35 ( 7)

867(v w)

858

887

879

885

884

875

877

0

0

π R1 H7-C3-C2-C4 ( 77), ψC3-C2-C1-C6 ( 9), πN19-C24-C29-C25 ( 9)

834(v w)

852

885

852

863

862

802

803

0

0

πH10-C6-C1-C5 ( 84), ψC25-C26-C27-C28

934(v w) 920(m)

893(m)

( 7)

817(v w)

790

807

791

791

791

788

789

2

0

πH7-C3-C2-C4 ( 33), π N19-C24-C29-C25 ( 29), ψC24-C25-C26-C27 ( 22)

769(vs)

778

789

779

787

788

775

776

3

1

wO35-C14-C17 ( 19), υC14-C17 ( 13), θN19-C17-C14 ( 9), υ N19-C17 ( 9)

764

748

776

776

774

773

775

11

0

π R1 H10-C6-C1-C5 ( 25), ψC5-C4-C3-C2 ( 23), π N19-C24-C29C25 ( 10), υC1S 11 ( 7)

759(vs)

755(w )

755

741

755

755

759

758

758

2

5

ψC1-C6-C5-C4 ( 29), πH10-C6-C1-C5 ( 24), πN19-C24-C29-C25 (

12), υC1-S11 ( 6)

730(s)

730

701

735

736

733

733

734

4

0

ψC2-C1-C6-C5( 62), πH9-C5-C4-C6 ( 19), δC1-C2-N13-C12 ( 17)

714

700

715

720

718

727

728

12

0

π R1 H9-C5-C4C6(62),ψR1 C29-C24C25-C26 ( 14), πN19C24-C29-C25 ( 10)

700(vs)

702(w )

708

689

708

707

710

709

709

1

3

TC6-C5-C4 ( 47), υ C12S 11 ( 23), υC2C 3 ( 10), βC2-N13-C12 ( 9)

661(m)

668(v w)

670

675

671

671

671

670

672

1

0

T C26-C27-C28( 27), w O35-C14-C17 ( 13), E N19-C17-C14 ( 13), T C24-C25-C26 ( 8)

651(v w)

650

655

650

657

657

657

658

3

1

T C4-C3-C2 ( 37), βsC2-N13-C12 ( 23), υ C3-C4 ( 7), υ C1-S11 ( 7)

635(v w)

633

602

633

632

632

634

634

0

2

T C26-C27-C28 ( 60), TC29-C24-C25 ( 20), υ C29-C24 ( 7)

620

600

623

624

625

625

626

0

1

πO35-C12-N13-S11 ( 53), δC1-C2-N13-C12 ( 25), t C12-O35-C14-H15

638(m)

( 8)

585(v w)

569(vs)

577

583

577

582

578

580

585

4

0

tC24-C25-C26-C27 ( 24), ψC5-C4-C3-C2 ( 23), πN19-C24-C29-C25 ( 19), πH9-C5-C4-C6 ( 11)

570

567

572

572

568

570

582

2

0

h C14-C17-O18-N19( 43), t C12-O35-C14-C17 ( 16), θ H15-C14-C17 ( 10), t H15-C14-C17 ( 8)

558

557

559

558

557

558

558

0

0

π O35-C12-N13-S11 ( 30), t C5-C4-C3-C2 (

17), ψC3-C2-C1-C6 ( 9), πH9-C5-C4-C6 ( 9)

515(s)

514

505

515

515

517

516

516

1

3

t C6-C5-C4-C3 ( 20), α S11-C1-C2 ( 12), qC1S11 ( 10), βsS11-C1-C2 ( 7)

501(w)

502(w )

504

504

504

503

501

502

502

4

2

t C26-C27-C28-C29 ( 19), αS11-C1-C2 ( 13), βaC2-N13-C12 ( 11), βsC1-C2-N13 ( 11)

477(m)

483(v w)

483

499

482

487

487

488

487

2

4

t C2-C1-C6-C5 ( 24), υ C12S 11 ( 9), αC14O35-C12 ( 8), T C4-C3C2( 7)

438(m)

450(v w)

438

446

446

448

431

431

436

1

0

t C5-C4-C3-C2 ( 23), T C1-C6-C5 ( 12), πN19C24-C29-C25 ( 8), t H15-C14-C17-O18 ( 6)

423

425

425

428

427

429

430

0

0

t C28-C29-C24-C2 ( 37), t C24-C25-C26-C27 ( 33), πH10-C6-C1-C5 ( 14)

421

419

422

427

425

427

421

1

2

αN19-C24-C25 ( 41), h C17-N19-C20-C24 ( 21), t H15-C14-C17-N19 ( 8)

415(w)

417(v w)

418

403

419

419

403

404

404

3

2

E N19-C17-O18 ( 24), υN19-C24 ( 18), T C26C27-C28 ( 10), T C24C25-C26 ( 8)

384(v w)

391

401

394

396

382

377

380

1

1

αS11-C1-C2 ( 20), tC2C1-C6-C5 ( 12), T C4C3-C2 ( 10), υ C1-S11 ( 7)

351(v w)

354

362

355

349

355

355

349

0

1

t C5-C4-C3-C2 ( 18), G O18-C17-C14 ( 12), t C24-C25-C26-C27 ( 10),

w O35-C14-C17 ( 8) 340

344

342

340

343

335

333

2

2

t C12-O35-C14-C17 ( 40), δC12-S11-C1-C2 ( 11), t C26-C27-C28-C29 ( 7), w H15-C14-H16( 5)

320

318

321

322

322

310

330

1

1

θ O18-C17-C14 ( 29), w H15-C14-H16 ( 12), π O35-C12-N13-S11 ( 9), t C5-C4-C3-C2 ( 9)

268(v w)

268

268

269

275

261

272

272

0

1

t C12-O35-C14-H16 ( 28), t H15-C14-C17-O18 ( 13), w H15-C14-H16 ( 11), t C5-C4-C3-C2 ( 7)

214(v w)

218

228

221

219

227

206

213

1

4

πN19-C24-C29-C25 ( 23), t C12-O35-C14-C17 ( 19), ω C20-N19-C24 ( 8)

192(v w)

143(w )

194

184

198

199

198

197

199

0

1

t C12-O35-C14-C17 ( 30), tO35-C14-C17-N19 ( 27), t O18-C17-N19C24 ( 14), αO35-C12S11 ( 10)

183

181

184

190

165

183

182

1

3

t C27-C28-C29-C24 ( 25), δ C1-C2-N13-C12 ( 25), δ C1-C2-N13-C12 ( 19)

137

138

136

143

141

140

133

0

1

t C17-N19-C24-C29 ( 45), h C17-N19-C20C24 ( 24), t H23-C20N19-C17 ( 8)

121

122

120

121

123

120

122

0

7

t C4-C3-C2-C1( 27), t C17-N19-C24-C25 ( 27), t C12-O35-C14H16 ( 9)

113

114

114

108

108

113

118

0

0

t C20-N19-C24-C25 ( 28), t C14-C17-N19-C20 ( 25), t H22-C20-N19-

C24 ( 19), h C17N19-C20-C24( 17)

71(vs)

84

83

84

82

87

82

84

0

5

t C12-O35-C14-H16 ( 60), δN13-C12-S11-C1 ( 6), t C14-C17-N19C24 ( 6),

73

76

76

78

71

69

74

0

14

h C17-N19-C20-C24 ( 32), t O18-C17-N19-C20 ( 26), t O35-C14-C17O18 ( 26)

33

31

32

35

34

33

38

0

55

tN13-C12-O35-C14 ( 51), t O35-C14-C17-O18 ( 17), π N19-C24-C29C25 ( 10)

28

27

24

28

27

29

31

0

75

tO35-C14-C17-N19 ( 49), tC12-O35-C14-C17( 28), tC17-N19-C24-C25 ( 15)

26

25

19

23

25

26

26

0

32

tH21-C20-N19-C24 ( 61), t O18-C17-N19-C24 ( 17)

11

13

11

18

19

16

15

0

35

t C17-N19-C24-C25 ( 58),t C14-C17-N19-C24 ( 18)

Abbreviations: R1: Ring1 ; R2: Ring2 ; υ: stretching; α : bending; sym: symmetric ; asym: asymmetric ; T: trigonal deformation ; γ: symmetric deformation; βs: symmetric bending;βa: asymmetric bending ; vw-very weak, w-weak, m-medium, s-strong, vs-very strong; ψ-PUCKER ; θ : rocking ; w: scissoring ; h: wagging; e: twisting; t: torsion Table 3: The observed and calculated bond length and stretching frequency of modes involved in intermolecular hydrogen bonding for dimer.

Molecule

C60-H65...O18 Bondlength

Stretching frequency

C49-H51...O35 Bond length

Stretching frequency

IR

Raman

IR

Raman

-

-

Experimental Monomer(MM)

-

Dimer(MD)

0.950

-

-

0.991

Computational Monomer(MM)

-

Dimer(MD)

1.084

3056(sym)3049(asym)

1.089

C29-H34...O53 Molecule

Bondlength

3017(asym)2963(sym) C14-H15...O70

Stretching frequency IR

Bond length

Raman

Stretching frequency IR

Raman

0.991

3004(w)

3011(vw)

0.990

2953(s)

2953(m)

Experimental Monomer(MM)

0.951

Dimer(MD)

0.951

3062(s)

3061(vs)

Computational Monomer(MM)

1.084

3056(asym)3050(sym)

1.090

3005(asym)2956(sym)

Dimer(MD)

1.085

3048(asym)3055(sym)

1.089

3016(asym)2963(sym)

Table 4: Topological parameters for bonds of interacting atoms of monomer and dimer: electron density (ρr), Laplacian of electron density (∇2ρr), electron kinetic energy density (G), electron potential energy density (V), total electron energy density (H), delocalization index (DI) at bond critical point (BCP) Bond

ρ(r)

∇2ρ(r)

V

G

H15…O70

0.06

-0.48

-0.02

O18…H51

0.06

-0.48

O35…H51

0.06

O18…H65 O53…H34

H

IHB

0.03

0.01

-6.28

-0.03

0.04

0.01

-9.41

-0.48

-0.02

0.03

0.01

-6.28

0.07

-0.72

-0.06

0.07

0.01

-18.83

0.06

-0.72

-0.05

0.07

0.02

-15.68

1 au of ρ(r) = 6.7483 eÅ-3, and 1 au of ∇2ρ(r) = 24.099 eÅ-5. The units of V, G, and H are in au, and IHB is in kcal/mol. Table 5: Calculated absorption spectrum of mefenacet with water solvent at PCM-TDDFT basis set Assignments

TD-DFT/B3LYP-6311G(d,p) (λcal)nm

Bandgap

Energy (cm-1)

(eV)

Oscillator

Major contributions

strength(f)

241.9

5.126

41341.846

0.2271

HOMO->LUMO (71%), HOMO-> LUMO +3 (11%)

237.9

5.211

42029.035

0.0039

HOMO -2-> LUMO +1 (12%), HOMO-> LUMO +1 (75%)

236.9

5.234

42216.964

0.0023

HOMO -1-> LUMO +4 (11%), HOMO-> LUMO +2 (10%), HOMO-> LUMO +4 (65%)

233.9

5.300

42746.873

0.0002

HOMO -4-> LUMO +1 (14%), HOMO -3-> LUMO +2 (11%), HOMO -2-> LUMO +1 (16%), HOMO-> LUMO +2 (32%)

232.33

5.337

43042.074

0.0003

HOMO -2-> LUMO +1 (52%), HOMO-> LUMO +2 (15%)

Table 6: Binding affinity, Hydrogen bond Interaction and Number of hydrogen bond residues of Mefenacet with the target protein Protein

Number of Hydrogen Interacting Bond Interaction with Residues distance

Enoyl-ACP Reductase (PDB ID : 1ZID

1

(2.3 Ǻ)

ALA 191

Binding energy (kcal/mol) -8.4

Fatty acid amide hydrolase PDB ID : 2WAP

2

(1.8 and 2.6 Ǻ)

VAL 270, CYS 269

-8.3

Highlights
Structural analysis of Mefenacet monomer and dimer has been performed.
Solvent effect (MM-H2O) reveals the hydrogen bonding.
A complete vibrational spectral analysis has been carried out using NCA.
PES, NBO, QTAIM and Hirshfeld surface analysis show the nature of the herbicide.
Molecular docking studies and MDS exhibit the herbicidal activity.

Declaration of interests ☐The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

We have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper “Vibrational Spectra, Hydrogen Bonding Analysis and Herbicidal Activity study of Mefenacet : A DFT Approach”.

N. Suma,D. Aruldhas,I. Hubert Joe, S. Balachandran, A. Ronaldo Anuf , Arun Sasi, Jesby George. Corresponding author: [email protected]