Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron

Journal Pre-proof Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4dichlorodiuron K. Haruna, Veena S. Kumar, Sanja J. Armaković, Stevan Armaković, Y. Sheena Mary, Renjith Thomas, Saheed A. Popoola, A.R. Almohammedi, M.S. Roxy, A.A. AlSaadi PII:

S1386-1425(19)30970-9

DOI:

https://doi.org/10.1016/j.saa.2019.117580

Reference:

SAA 117580

To appear in:

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Received Date: 20 August 2019 Revised Date:

16 September 2019

Accepted Date: 28 September 2019

Please cite this article as: K. Haruna, V.S. Kumar, S.J. Armaković, S. Armaković, Y.S. Mary, R. Thomas, S.A. Popoola, A.R. Almohammedi, M.S. Roxy, A.A. Al-Saadi, Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2019), doi: https://doi.org/10.1016/j.saa.2019.117580. 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.

Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron K. Harunaa, Veena S. Kumarb, Sanja J. Armakovićc,,Stevan Armakovićd, Y. Sheena Marye, Renjith Thomasf*, Saheed A. Popoolag, A.R. Almohammedih, M.S. Roxyb, AA. Al-Saadia, a

Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia b Department of Physics, SN College, Kollam, Kerala, India c University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia d University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia e Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India f Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, 686101, Kerala, India g Department of Chemistry, Islamic University of Madinah, Saudi Arabia h Department of Physics, Islamic University of Madinah, Saudi Arabia Corresponding author- Dr Renjith Thomas, [email protected] Abstract A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT). Keywords: Diuron, DFT; MD; SAPT; DSC/TGA; FT-IR; FT-Raman

1

1. Introduction Diuron is a chloro-substituted derivative of phenyl urea herbicides used for controlling the growth of weeds [1]. Like other phenyl urea herbicides, its toxic action is based on the inhibition of photosynthesis process [1]. It is presented all over the environment like soil, surface water as well as ground water [2]. Its presence in the environment constitutes a major problem, especially in the aquatic environment where it causes water pollution [3]. Diuron is toxic for birds, mammal and aquatic invertebrate, but what is even more dangerous is the fact that its degradation products are even more toxic [3]. It has been reported so far that diuron undergoes environmental transformation ranging from abiotic to biotic degradations [3]. These transformations decrease concentration of diuron in the water. Among the abiotic degradation, hydrolysis is an irreversible reaction, usually catalyzed by OH-, H+ and buffer to give 3,4-dichloroaniline [4]. This product further undergoes aqueous photolysis via solar irradiation and gets converted first into phenolic compound and later into aminophenoxazones [3]. In addition, Photo-Fento system has been applied to reduce diuron concentration in water [5]. Using this method, a prolonged irradiation could result in the total mineralization [3]. Another method is electro-Fento method where the degradation of diuron in water is brought about by the use of electrochemical advanced oxidation [6]. In this process, the hydroxyl radicals that oxidize diuron are catalytically produced. However, due to some constraints on the use of Fento process, attention has been shifted to the use of in situ chemical oxidation methods. In this method, ferrous ion activatedpersulfate was used as an alternative oxidant for the degradation of diuron in both soil and water [2,7]. Energetic electrons produced from dielectric barrier discharge were employed to degrade this halogenophenyl urea in water [8]. On the other hand, the biotic degradation which happened to be the major agent for diuron degradation can occur under both aerobic and anaerobic conditions. For the aerobic, the degradation is assumed to involve two mechanisms, first is Ndemethylation and then the hydrolysis of amide bond [3]. P450 cytochrome monoyxygenase has been suggested to be responsible for the demethylation of diuron while amidase causes the hydrolysis of amide bond to give 3,4dichloroaniline [3]. However, for the anaerobic conditions, sediment micro-organisms were identified to be responsible for the degradation [9]. 2

Our literature survey clearly indicates that significant attention is focused to the development of methods for elimination of diuron from environment. Although according to IUPAC this herbicide is moderately toxic to mammals and has low toxicity to honeybees, it has been present in market for almost 70 years, long enough to be accumulated in various water resources. The aim of this work was to understand in details stability, reactive and spectroscopic properties of diuron molecule. Such detailed understanding of diuron’s properties has been made possible by combination of experimental and computational techniques. IR and Raman spectroscopy has been used for characterization of diuron. Thermo-gravimetric analysis was used to analyze the stability of diuron with a temperature increase. Light absorption was studied by UV visible (UV/Vis) spectrometry in a range of 200 nm to 800 nm. Taking into account that there are numerous studies where computations had provided valuable insights into the specific properties of structures relevant for pharmaceutical industry [10-13] and materials science [14-23], in this work we have applied DFT calculations on both isolated molecules and periodic structures. Firstly, DFT calculations enabled us to understand in details the stability, both local and global reactive properties of diuron molecule. DFT calculations were also used in order to reproduce spectroscopic properties obtained by experimental approach. On the other side, periodic DFT calculations helped us to understand band structure of crystal structure of diuron and to address the importance of different atoms to by analyzing the density of states (DOS). Applying DFT calculations, charge transfer rates were studied for the molecular pairs from crystal structure of diuron. Since the influence of hydrolysis to 3,4-dichlorodiuron molecule turned out to be significant, MD simulations were used in order to identify which parts of 3,4-dichlorodiuron molecule have the most pronounced interactions with water molecules by calculating the radial distribution functions (RDF).

2. Experimental and computational details 2.1. FT-IR and FT-Raman spectra The compound under study in the present manuscript is a solid 3-(3,4-dichlorophenyl)-1,1dimethylurea purchased from the Sigma Aldrich. Experimental studies involves the recording of Fourier Transformed Infra Red (FTIR) spectra and FT Raman spectra between the range 4000 400cm-1 using a Nicolet 6700 FT-IR and Nicolet NXR FT-Raman module respectively with a 3

resolution of 4 cm-1. Thermogravimetric analysis (TGA) was performed with SDT Q600 V20.9 Build 20, Module DSC-TGA Standard machine in nitrogen atmosphere at a flow rate of 50 ml/min in a temperature range of 25 to 800 °C. The experimental UV-Visible spectra of 3,4dichlorodiuron recorded between 200-800 nm using a Cary100 series UV/Visible (Agilent Technologies) spectrophotometer. 2.2. Computational details

Two different computational chemistry software packages, Gaussian 09W and Schrödinger Materials Science Suite 2018-4 (SMSS), were used for computational investigations of diuron molecule. Firstly, the Gaussian 09 software program [24] was used for geometrical optimization of diuron molecule. The geometry of the molecule under study was optimises using density functional theory using B3LYP fucntional along with 6-311++G(d,p) basis sets. Frequency calculations were performed to ensure that there are no negative frequencies associated with the molecule, which ensures the global minimal energy optimised structure. Simulated and scaled spectra were visualized and analysed with the help of Gaussview 5 [25] and the potential energy distribution of various vibrational modes was done using GAR2PED suite [26]. A standard scaling factor of 0.9613 was used on the simulated spectra [27] and this is compared with the experimental spectra. Chlorine atoms were replaced by bromine and fluorine atoms in the parent system and the DFT calculations were done at the same level of theory of the parent molecule in order to analyze the effect of other halogens on the physico-chemical properties. There are numerous modules in the SMSS of which Jaguar [28-30] program was engaged for DFT calculations

for estimating average local ionization energy (ALIE), molecular

electrostatic potential (MEP) and bond dissociation energy (BDE), using the same level (B3LYP/6-311++G(d,p)); while the Desmond [31-34] program was used for MD simulations. Maestro [35] helped in the visualization and analysis of results. The usage of Desmond program for MD simulations accounted the extended OPLS3 (OPLS3e) [31, 36-38] force field, with simulation time (10 ns), temperature (300 K), pressure (1.0325 bar) and cut-off radius of 10 Å. The solvation effects are accounted using simple point charge (SPC) model [39]. In order to study the crystal structure of diuron, periodic DFT calculations were performed with QuantumATK 2015.3 modeling suite [40-45]. In case of the periodic DFT calculations a 4

PBE functional with double zeta polarized basis set. Brillouin zone was sampled with the 2×2×2 Monckhorst-Pack scheme [46]. DOS calculations were performed with denser Monckhorst-Pack scheme of 4×4×4. PSI4 modeling program [47, 48] was used for calculations based on symmetry-adapted perturbation theory (SAPT) approach. Specifically, the SAPT0 [49, 50] approach was used together with the jun-cc-pVDZ basis set.

3. Results and discussion 3.1. Structural and conformational analysis

Optimized geometry of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) molecule obtained in this work is presented in Figure 1. The potential energy scan of diuron has being investigated using semi-empirical AM1, PM3 and molecular mechanics methods and the trans conformer was predicted to be more stable than the cis form in all the methods [51]. In this study, diuron was predicted to exist as in its most stable form as planar molecule with the oxygen atom at an antiposition when compared to the N-H bond and forms an N10-C12-O13 angle of 123°, which is in good agreement with previous theoretical conformation studies [52,53].

Figure 1. Optimized geometry of 3-(3,4-dichlorophenyl)-1,1-dimethylurea

The phenyl ring plane and the dimethyl urea moiety plane were predicted to be at angle 179.1o and 0.9o in good agreement with recent computational study [54] which predicted diuronto exist in its most stable form as a planar conformation with the phenyl group and the dimethylurea planes at angle close to 180° and 0°. However, results from solid state X-ray spectroscopic analysis has showed diuron to exist in its most stable form as a non-planar trans 5

conformer with the amide group twisted 29.4o from the ring plane [55]. This non-planar nature of diuron has been explained to be as a result of intermolecular hydrogen bonding between the N-H group of one molecule and C=O group of another which is in consistent with a computational study of diuron clusters and water molecules, where it was revealed that the formation of intermolecular hydrogen bond lead to the loss of planarity of the most stable trans conformer [52]. Potential energy scans (PES) are an effective tool to predict the relative stability of the infinite number of conformations possible for the compound. A relaxed potential energy scan was performed here about about the N10-C12 (Figure 2), C3-N10 (Figure 3) and the C12-N14 (Figure 4) bonds.

Figure 2. Potential energy scan and the optimized structures of the minima the resulting from the rotation of H11N10-C12O13 dihedral angle In Figure 2, there are two minimal conformations (anti and syn forms) due to the internal rotation around the N10–C12 bond. The anti-conformer is more stable than syn by about 2.60 kcal/mol, in agreement with previously reported studies on urea and dimethylurea at the DFT and MP2 levels of theories [56-60]. The high energy conformational interchange gap of about 7 kcal/mol for diuron (Figure 2) is observed , which may be due to the inversion N10 [58]. Repulsive forces between the N10 lone pair (lp) methyl hydrogen atoms also goes along with the reported values of urea [60-63]. 6

Figure 3 shows the PES scan of the rotation of the phenyl ring of the anti-conformer about the C3-N10 bond to examine the effect of the phenyl ring rotation on the overall stability of diuron.

Figure 3. Potential energy scan and the optimized structures of the minima resulting from the rotation of H11N10-C3C2 dihedral angle The rotation about the phenyl group leads to break-up of the conjugation between the phenyl ring and the urea moiety; two minima (A and B) were obtained. The two minima were predicted to be of comparable stability; however, the optimized structure of B conformer was predicted to be slightly more stable A conformer by 0.19 kcal/mol. The relatively low energy conformational interchange barrier of 3.35 kcal/mol could be attributed to the modest electron delocalization across the aliphatic chain of the molecule. Figure 4 shows the PES of the rotation of the dimethyl moiety of the most stable conformer B conformer about C12–N14 bond to examine the effect of its rotation on the overall stability of diuron.

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Figure 4. Potential energy scan and the optimized structures of the minima resulting from the rotation of O13C12-N14C15 dihedral angle PES shows the effect of the LP present in N14 on the stability of the system. Two structures were obtained (B1 and B2) in which B2 is more stable than B1. When the dimethyl group rotates, two identical conformations with dihedral angles 173o and 5o are detected and they are in close proximity with the expected OCNCH3 dihedral of 178o and 9o [57], which means that the methyl substitutions are not much influencing the stabilization pattern of the diurons. 3.2. IR, Raman and VCD spectra This section deals with the detailed spectral analysis of the compound and how various inferences are reached about the structure of the compound. Infra Red (IR), Raman (RS) and VCD spectra are discussed here. Figures 5 and 6 represents experimentally and scaled simulated FTIR and FT-Raman spectra of the molecule under study. The experimental and simulated IR and Raman modes along with detailed potential energy distribution assignments are presented in Table S1 of the Supplementary Materials.

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Figure 5. FTIR spectra of diuron a)

Figure 6. FT-Raman spectra of diuron (a)

experimentally and b) theoretically obtained

experimentally and (b) theoretically obtained

For diuron, the NH modes are assigned at 3307 cm-1 in the (IR), 3309 cm-1 (RS), 3509 cm-1 (SIMULATED) (stretching) and at 1492, 1239, 676 cm-1 (SIMULATED), 1490, 673 cm-1 (RS), 1485, 1238, 675 cm-1 (IR) (deformation) [64,65]. The stretching mode of NH in the IR shows a downshift of 202 cm-1 from the computed value which is due to the intermolecular hydrogen bonding in the condensed phase of diuron. The strong interaction is evident from NBO analysis (n1(O13) to σ*(N10-C12) with energy 26.05 kcal/mol). NH modes are reported at 3462 cm-1 (IR), 3450 cm-1 (RS), 3400 cm-1 (SIMULATED) (stretching), 1508, 1219, 655 cm-1 (SIMULATED) (bending) [66] and 1587, 1250, 650 cm-1 (IR), 1580, 1227, 652 cm-1 (SIMULATED) (bending) [67]. For diuron, CN stretching modes associated with N-CH3 group are assigned at 989 and 857 cm-1 (SIMULATED) and other CN modes at 1237, 1203, 1118 cm-1 (SIMULATED) and modes are observed experimentally at 1197, 978 cm-1 (IR) and at 1237 cm-1 (RS) [68-71]. For diuron, the C=O stretch is assigned at 1660 cm-1 (IR), 1650 cm-1 (RS), 1664 cm-1 (SIMULATED) [72] and literature data at 1694 cm-1 (IR), 1696 cm-1 (RS) and at 1699 cm-1 (SIMULATED) [66].

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The stretching of methyl groups are observed at 3000, 2940, 2885, 2859 cm-1 (IR) and at 3000, 2952, 2930, 2882, 2856 cm-1(RS) [64, 68]. Methyl bending modes are assigned at 1387, 1078, 1043, 1015, 863 cm-1(IR) and at 1470, 1410, 1384, 1078, 1038, 864 cm-1 (RS). Theoretically these modes are at 3039-2867 cm-1 (stretching) and 1468-862 cm-1 (deformation) [64,68]. CCl stretching modes are assigned at 722 and 693 cm-1 (SIMULATION) [73] and bands are observed at 723, 692 cm-1 (IR) and at 724, 691 cm-1 (RS). The phenyl (Ph) CH stretching vibrations are observed at 3080, 3033 cm-1(IR), 3061, 3032 cm-1 (RS) [68].3121-3034 cm-1 (SIMULATION)[68]. The Ph stretching vibrations are in the between 1562-1270 cm-1 and found in 1570, 1536,1440, 1356, 1268 cm-1(IR) and at 1556, 1440, 1358, 1271 cm-1 (RS) [68]. For diruon, phenyl ring breathing mode is assigned at 1096 cm1

theoretically [74] and reported values are 1110, 1129 cm-1 [75] and at 1109, 1100, 1109, 1100

cm-1 [76]. The phenyl CH deformation vibrations are observed at 1238, 1136 cm-1(IR), 1142, 1111 cm-1 (RS) (in-plane) and at 813 cm-1(IR), 947, 815 cm-1 (RS) (out-of-plane) [68]. RMS deviation between the theoretical wavenumbers and experimental bands are 4.50 (RS) and 7.13 (IR). Vibrational circular dichroism (VCD) provides information about the sterogenic centers possible in the molecule and its possible orientation towards the plain polarised light [77]. VCD spectra of the diuron is presented in Figure 7.

Figure 7. VCD spectra of diuron

The different stretching and deformations modes produce VCD signals and these are markers of configuration in the molecular systems. The phenyl stretching at 1552, 1440, 1266 cm-1 (Fig.S6-supporting information) shows left polarization and C=O mode at 1665 cm-1shows right 10

polarization. The other VCD bands at 2892, 1468, 1356 cm-1 and at 2927, 1412, 1378 cm1

corresponding to CH3 groups are good markers showing left and right polarization are good

identifiers. The VCD signals at 1490 cm-1 and 1238 cm-1 shows left and right polarization for NH bending.

3.3.Global stability of diuron: analysis of TG/DTG In this chapter we will refer to some of the quantities that reflect the stability of diuron. Namely, we will summarize the results of TG/DTG, frontier molecular orbitals and H-BDE. The TG/DTG curves have been recorded in the interval between 25 °C to 800 °C and the obtained results indicate significant stability of diuron compound, Figure 8.

Figure 8. TG/DTG results of the diuron

Namely, it can be seen thanks to the TG curve (red curve in Figure 8) that diuron compound is stable up to temperature of around 200 °C. DTG peak (black curve in Figure 8) further characterize the influence of temperature increase and indicate that there are two decomposition stages, one happening at the temperature of 243 °C and the second one happening at the temperature of 286 °C. These results indicate highly significant stability of diuron

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compound as it is stable to temperatures that are far higher than the ones that occur in natural conditions.

3.4. Frontier molecular orbital analysis and BDE studies

High stability of diuron molecule is also reflected through global stability and reactivity descriptors based on molecular orbital theory. Figure 9 contains visualization of the frontiers molecular orbitals (HOMO and LUMO), where it can be seen that HOMO is delocalized over the larger area of molecule, while LUMO is delocalized over the phenyl ring, indicating that charge transfer mainly occurs between the phenyl ring and nitrogen atoms.

Figure 9. Frontier molecular orbitals

Among the different quantum molecular descriptors relevant for this study, we will refer to the energy difference between frontier molecular orbitals (HOMO-LUMO gap) and electrophilicity index (ω). HOMO-LUMO gap is closely related to the global stability of molecular systems and our DFT calculations indicate that this parameter in case of the diuron has a high value of 5.30 eV, confirming high stability as shown by TG/DTG experiments. On the other side, electrophilicity index, that can be calculated according to the equation ω = µ 2 /2 η , is closely related to the toxicity molecular systems [78, 79]. This descriptor also has a high value of 2.56 eV, indicating toxicity which is known for this molecule. Identification of molecular sites characterized by the lowest H-BDE values is important from biochemical and environmental aspects. Namely, process during which the carbon– hydrogen bonds are broken is very important for the phase I drug metabolism [80,81]. The 12

potential of organic molecules to form degradation products during their storage is also of importance for pharmaceutical industry and this is also the area for which the concept of H-BDE is important [82, 83]. H-BDE and bond dissociation energies for the remaining single acyclic bonds (BDE) of diuron molecule are summarized in Figure 10.

Figure 10.Summarized H-BDE and BDE. H-BDE are provided in black color, while BDE are provided in blue color

Diuron molecule is characterized by the high H-BDE values, indicating its stability towards oxidation, this could explain the high stability of diuron up to 200 oC in the TGA curve. There are no H-BDE values in the range between 70 and 85 kcal/mol[84, 85], explaining the stable storage lifetime. However, the lowest H-BDE value of nearby 94 kcal/mol has been calculated for the hydrogen atom connected to nitrogen atom, thus indicating that oxidation could take place at the central position of the molecule. The hydrogen atoms of methyl groups are having H-BDE values of nearby 96 kcal/mol, while the highest H-BDE values have been calculated for the hydrogen atoms of benzene rings. BDE results also go in favor that the breaking of molecule occur in its central part, since the lowest BDE of ~73 kcal/mol is calculated in for the C10-N12 bond. 3.5.Local reactivity properties of diuron molecule: MEP and ALIE surfaces

Local reactivity properties of title molecule have been considered by calculation of MEP and ALIE descriptors, which are well-known by their abilities to indicate the most important reactive sites of the studied molecules. Both of these descriptors are tightly connected with the electron 13

density, thanks to which they can be considered as fundamental quantum-molecular quantities addressing the reactivity of molecular structures [86, 84]. While MEP descriptor provides information about the charge distribution, ALIE descriptor provides information about the site locations where electrons are least tightly bound. The combination of MEP and ALIE surfaces proved out to be very useful for determination of molecular sites prone to electrostatic interactions and to electrophilic attacks, respectively [34, 88]. The most frequently used visualization method for MEP and ALIE descriptors is certainly the mapping of their values to the electron density surface, which has been applied in this work as well (Figure 11).

Figure 11. MEP and ALIE surfaces of diuron

MEP surface presented in Fig.5 clearly indicates that oxygen atom of diuron molecule might be the most sensitive in terms of electrostatic interactions, as the lowest values of this descriptor are located precisely there. This molecule site might interact with positively charged locations of other molecular species. Regarding the MEP surfaces it can be also seen that two methyl groups are having different charge distribution. As it can be seen in Figure 11, hydrogen atoms of methyl group located in the near vicinity of hydrogen atom connected to the nitrogen atom are characterized to higher extent with the positive charge, in comparison with hydrogen atoms of the other methyl group. Although the same atom is characterized by yellow to reddish color in case of the ALIE descriptor, other sites, such as chlorine atoms and some carbon atoms of benzene ring are characterized by the even lower ALIE values, which designate them to be more sensitive towards the electrophilic attacks.

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3.6. Interactions of diuron with water – an insight through MD simulations

When it comes to the interactivity with water, MD simulations were used in order to discover which atoms of the diuron molecule possess the highest interactivity with water molecules. This has been achieved by calculations of radial distribution functions (RDF), which provide information about the probability to find water molecule at certain distance from the observed atom of diuron molecule. Representative RDFs of atoms interacting with water molecules in case of the diuron have been presented in Figure 12.

Figure 12. Representative RDFs of diuron molecule

RDFs was calculated for different points with change in the distance between atom of diuron molecule and water molecule's oxygen atom. RDFs also indicate the importance of oxygen atom O13, from the aspect of reactivity. Namely, this atom is characterized by the sharpest g(r) whose maximum value is located at the distance somewhere between 2.5 and 3.0 Å. However, there are no hydrogen atoms with maximal g(r) values located at distances lower than 2 Å, indicating that this molecule has limited reactivity with water. This also goes in favor of its stability, because of which it is hard to expect that hydrolysis mechanism might promote its degradation. Although there are some other atoms with relatively sharp g(r) curves, their maximal g(r) values are

15

located at high distances, thus the oxygen atom O13 certainly has the strongest interactions with water molecules.

3.7. Optical properties of the diuron

Optical properties are of high importance for the removal of pollutants such as diuron molecule. To study its optical properties in this work we have employed TD-DFT calculations in order to simulate diuron’s UV/Vis spectra. We have also employed the formalism of natural transition orbitals in order to get a clearer picture of excitations that are principally responsible for its optical absorption properties. Simulated UV/Vis spectrum of diuron is presented in Figure 13.

Figure 13. Simulated UV spectra with the NTO pair corresponding to excitation at 250 nm

UV spectra simulated in Figure 13. has been obtained by employing the M06 [89] functional and 6-311++G(d,p) basis set, while the NTO has been obtained thanks to the approach by [90]which is incorporated in the Jaguar program for DFT calculations. Performed TD-DFT calculations reproduces the UV spectra with excellent agreement to experimental UV spectra reported by Kovács et al. [91]. Experimentally, UV spectrum of diuron is characterized by the absorption peak located at 248 nm, and this optical feature is nicely reproduced by our TD-DFT 16

calculations (250 nm in our calculations). The specific excitation at 250 nm was visualized in terms of NTO orbitals and the corresponding particle-hole NTO is visualized in Figure 13. The role of carbonyl group and one of the chlorine atoms can be seen. Namely, particle NTO is delocalized over the benzene ring, chlorine atoms and carbonyl group. On the other side, the hole NTO is delocalized over just one chlorine atom and over nitrogen atoms. This indicates that charge transfer for this specific and important excitation occurs from carbonyls group to nitrogen atoms, and from one chlorine atom to the other chlorine atom and benzene ring.

3.8. DFT calculations on crystal structure of diuron

Since in its normal form diuron is white crystaline solid, in this work we have decided to perform periodic DFT calculations as well, in order to gain additional insights into its properties. Diuron's crystal structure has been retrieved from PubChem service in form of the corresponding .cif file, which was subjected to periodic DFT calculations with calculation details explained in Computational details section. In this work periodic DFT calculations were used in order to obtain information about the band structure and density of states (DOS), Figure 13.

Figure 14. a) Band structure and b) DOS of diuron's crystal structure

Band structure of diuron's crystal structure presented in Figure 14a clearly goes in favor of its high stability and confirms why this compound is considered to be environmental threat. Namely, band structure of diuron's crystal structure suggests that diuron belongs to a group of 17

wide gap semiconductors, since the calculated band gap according to our DFT calculations is 3.52 eV. Thanks to wide band gap diuron is highly stable in environment and requires catalysts in order to be efficiently decomposed. On the other side, Figure 14b contains information about DOS and partial DOS (PDOS). These results indicated the overall contribution of different atoms to the stability of diuroncompound. In particular, in Figure 14b we have summarized the contributions chlorine, oxygen and nitrogen atoms. It can be seen that chlorine atoms (indicated with red lines) contribute relatively significantly in the conduction zone, while nitrogen and oxygen atoms (indicated with green and blue lines, respectively) contribute relatively significantly in the valence zone. It is also noteworthy to mention that chlorine atoms contribute principally at lower levels, in energy region between –4 and –6 eV.

3.9. Interactions and charge transfer rates between molecules in crystal structure of diuron compound

The fact that crystal structure of diuron is known enabled us to extract possible and most important molecular pairs and to investigate interactions between them. After a brief analysis it has been concluded that there are three most important molecular orientations within diuron crystal structure. Firstly we have studied the noncovalent interactions that form between these pairs of diuron molecules and those results are presented in Figure 15.

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Figure 15. Formed intermolecular interactions between molecules in crystal structure of diuron compound: a) configuration 1, b) configuration 2 and c) configuration 3

Analysis of electron density according to works [92, 93] enabled us to identify the noncovalent interactions that form between molecules in diuron’s crystal structure. The information about strengths of these interactions in terms of electron density [electron/bohr3] are provided in Table 1.

Table 1. Strengths of noncovalent interactions for configurations visualized in Figure 15 NCI# 1 2 3 4

NCI strength [electron/bohr3] Configuration 1 Configuration 2 Configuration 3 –0.0045 –0.0040 –0.0120 –0.0042 –0.0038 –0.0240 –0.0042 –0.0038 –0.0089 –0.0046 –0.0079 –0.0046

Results in Table 1.indicate that the strongest noncovalent interactions are formed in case of the configuration 3. While all configurations are characterized by four intermolecular noncovalent interactions, in case of the configuration 3 two noncovalent interactions are order of magnitude higher in comparison to all other noncovalent interactions visualized by dotted lines

19

in Figure 15. Another specificity of this configuration is the fact that oxygen atom is involved in three out of four noncovalent interactions. Another specificity of configuration 3 is related to charge transfer rates. Namely, in this case the charge transfer rates of holes are the highest in comparison with charge transfer rates of holes for configurations 1 and 2. , in order to obtain information about charge transfer rates, we had to firstly calculate the electron and hole reorganization energies according to the following equations:

( ) ( ) = E (G ) − E (G )

λ1 = E 0 G* − E 0 G 0 λ2

*

0

*

(1)

*

(2)

λi = λ1 + λ2

(3)

The information on reorganization energies were used in order to calculate charge transfer rates according to the Marcus semi-empiric approach following expression [94, 95]:

k ET =

4π2 h

 −λ  1 t 2 exp . 4 π λ kB T  4 kB T 

(4)

In equation λ denotes the reorganization energy of electrons ( λ− ) and holes ( λ+ ), while t is the charge transfer integral which is in this case calculated within the framework of dimmer splitting approximation. Brief analysis of equation (4) clearly indicates that the higher charge transfer rates are obtained for the lower values of reorganization energy and the higher values of charge transfer integral. Reorganization energies and charge transfer rates for different configurations have been summarized in Table 2. Table 2. Reorganization energies of diuron and charge transfer rates for configurations selected from crystal structure Diuron Configuration 1 Configuration 2 Configuration 3

λ– [eV] 2.90 -

λ+ [eV] 0.35 -

e− k ET [s–1]

h+ k ET [s–1]

3.59 36.91 42.10

4.87×1011 1.54×1013 8.90×1013

Results presented in Table 2 indicate that the charge transfer rates of holes, in case of the diuron molecule, will be having much higher values in comparison with charge transfer rates of electrons, since the reorganization energies of holes are much lower than reorganization energies 20

of electrons. Indeed, by calculations of charge transfer integrals in dimmer splitting approximation it is clear that charge transfer rates of electrons are 10 or 11 orders of magnitudes lower. Actually, charge transfer rates of electrons are insignificant in comparison with charge transfer rates of holes. On the other side, charge transfer rates of holes can be regarded to as significant, since the order of magnitude of this parameter is 1011 s–1 for the configuration 1 and 1013 s–1 for the configurations 2 and 3. Certainly the highest value of charge transfer rates of holes has been calculated in case of the configuration 3, for which this parameter takes value of 8.90×1013s–1. In this work interactions between diuron molecules in its crystal structure have been studied from one more aspect. Employing the approach of symmetry adapted perturbation theory (SAPT) interaction energy has been decomposed into the components [49, 50, 96, 97]. Aside of providing us with the information about the interaction energies between molecules, this approach also allowed us to check which of the physically meaningful components are principally responsible for the interactions between molecules. The SAPT0 variant has been applied within the PSI4 molecular modeling program and the components: electrostatic (EL), exchange (EX), induction (I) and dispersion (D), and their values are summarized in Table 3.

Table 3. SAPT components [kcal/mol] for molecular configurations obtained from crystal structure of diuron Diuron_1 Diuron_2 Diuron_3

EL –1.3037 –2.1675 –13.5111

EX 5.5985 4.0710 14.0270

I –0.5033 –0.6170 –4.4567

D –8.3271 –4.7547 –9.4971

TSAPT0 –4.5357 –3.4683 –13.4378

Overall interaction energy based on SAPT0 approach (TSAPT0) clearly indicates that the interaction energy is the highest in case of the configuration 3. In this particular case the total interaction energy was calculated to be –13.44 kcal/mol, which is much higher than the interaction energies calculated for the configurations 1 and 2 (–4.54 kcal/mol and –3.47 kcal/mol). Analysis of SAPT contributions indicate that the highest attracting contribution in case of the configuration 3 comes from the EL component (–13.51 kcal/mol), whose contribution is based on the Coulombicmultipole-multipole interactions and the overlap between monomeric charge distributions. However, the repulsing contribution comes from the EX component (having 21

value of 14.03 kcal/mol in case of the configuration 3), which is consequence of the spatial overlap of the wavefunctions of monomer and the antisymmetry demand of the dimer wavefunction after exchange of electronic coordinates. EX components practically cancels with EL component, however, the I and D components have values favoring strong attraction (with

values of –4.46 kcal/mol and –9.50 kcal/mol, respectively). The I contribution results from polarization of the response of monomers to each other’s electric field and also depends on the charge transfer between monomers. D comes from the correlation between electrons of monomers. In cases of configurations 1 and 2, results in Table 3 show that electrostatic interactions are not so important as in case of the configuration 3. I component in these systems is also much lower than in case of the configuration 3, while D component remains highly significant for attraction.

4. Conclusion In this work the combined experimental and computational techniques were applied in order to understand structural, reactive, optical and transport properties of diuron. The spectroscopic properties of the title compound are examined experimentally and computationaly and the vibrational assignments are done by means of potential energy distribution used the simulated and scaled IR and Raman spectra. The stretching mode of NH in the IR shows a downshift from the values due to the strong interaction as evident from NBO analysis. The influence of the two chlorine substituent on attached to the benzene ring of diuron on the conformational stability was investigated and PES were carried out about the N10–C12 bond and the C12–N14 bond. Positive and negative regions suitable for nucleophilic and electrophilic attacks are identified by means of MEP plot analysis. MEP descriptor indicated that the oxygen atom O13 might be the most sensitive towards electrostatic interactions with other molecules. On the other side ALIE descriptor indicated that the various locations at benzene ring might be sensitive towards the electrophilic attacks. The lowest H-BDE value was calculated for the hydrogen atom belonging to nitrogen atom in the central part of the molecule. All hydrogen atoms have H-BDE values higher than 90 kcal/mol, indicating high stability towards the autoxidation mechanism. On the other side, BDE also indicate that bond in the central part of the molecule might be the weakest. 22

RDF indicate that the oxygen atom O13 is the most reactive towards solvent water molecules, however all RDFs have the highest g(r) values located well beyond 2 Å. Investigation of optical absorption properties indicated the importance of carbonyl group. Crystal structure of diuron was also studied by means of DFT calculations and the results showed that this compound belongs to a group of wide band gap semiconductors. The DOS indicated the contributions of different atoms and it was found that chlorine atoms contribute to the conduction zone, while nitrogen and oxygen atoms contribute to the valence zone. Crystal structure of diuron was also used in order to extract all relevant molecular pairs that were used for studying the noncovalent interactions, charge transfer rates. The most important noncovalent interactions formed in case of the configuration (configuration 3) where oxygen atom is involved in noncovalent interactions. In this particular case the highest charge transfer rates for holes were calculated as well. Finally, the interaction energy and its decomposition to different contributions were performed on the basis of SAPT approach. Again, the highest interaction energy was calculated in case of the configuration 3, thanks to the highest contributions of EL, I and D components. Other configurations have significantly lower interaction energies, mainly due to the lower contributions of EL and I. Obtained results clearly emphasize the importance of the oxygen atom for the overall reactivity of diuron. This atom is recognized as important by MEP descriptor, RDFs, it has the strongest interactions with water molecules, it is involved in the most important noncovalent interactions and calculated charge transfer rates, and finally, it is involved in the configuration which has the highest values components as obtained by decomposition of interaction energy by SAPT approach.

Acknowledgment Authors thanks King Fahd University of Petroleum and Minerals (KFUPM) for supporting this work. This study was conducted within the project supported by the Ministry of Education, Science and Technological Development of Serbia, grant number III41017.

23

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Highlights • FT-IR, FT-Raman, TG/DTG UV spectra are investigated • The hyperpolarizability values give the NLO properties. • Periodic DFT SAPT studies reported • Conformational Studies predicts structural preferences • Molecular dynamics studies predicts behavior in water atmosphere