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Effective Adsorption of A-Series Chemical Warfare Agents on Graphdiyne Nanoflake; a DFT Study

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Effective Adsorption of A-Series Chemical Warfare Agents on Graphdiyne Nanoflake; a DFT Study Effective Adsorption of a-series Chemical Warfare Agents on Graphdiyne Nanoake; A DFT Study Hasnain Sajid COMSATS Institute of Information Technology - Abbottabad Campus Sidra Khan COMSATS Institute of Information Technology - Abbottabad Campus Khurshid Ayub COMSATS Institute of Information Technology - Abbottabad Campus Tariq Mahmood ( [email protected] ) COMSATS Institute of Information Technology - Abbottabad Campus https://orcid.org/0000-0001- 8850-9992 Research Article Keywords: Graphdiyne nanoake, Chemical warfare agents, DFT, QTAIM, SAPT, RDG Posted Date: February 10th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-209734/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Journal of Molecular Modeling on April 1st, 2021. See the published version at https://doi.org/10.1007/s00894-021-04730-3. Effective adsorption of A-series chemical warfare agents on graphdiyne nanoflake; a DFT study Hasnain Sajid#, Sidra Khan#, Khurshid Ayub, Tariq Mahmood* Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad-22060, Pakistan *To whom correspondence can be addressed: E-mail: [email protected] (T. M) # Hasnain Sajid & Sidra Khan have equal contributions for first authorship 1 Abstract Chemical warfare agents (CWAs) are highly poisonous and their presence may cause diverse effect not only on living organisms but on environment as well. Therefore, their detection and removal in a short time span is very important. In this regard, here the utility of graphdiyne (GDY) nanoflake is studied theoretically as an electrochemical sensor material for the hazardous CWAs including A-230, A-232, A-234. Herein, we explain the phenomenon of adsorption of A-series CWAs on GDY nanoflake within the density functional theory (DFT) framework. The characterization of adsorption is based on optimized geometries, BSSE corrected energies, SAPT, RDG, FMO, CHELPG charge transfer, QTAIM and UV-Vis analyses. The calculated counterpoise adsorption energies for reported complexes range from -13.70 to -17.19 kcal mol-1. These adsorption energies show that analytes are physiosorbed onto GDY which usually takes place through noncovalent interactions. The noncovalent adsorption of CWAs on GDY is also attributed by the SAPT0, RDG and QTAIM analyses. These properties also reveal that dispersion factors dominate in the complexes among many noncovalent components (exchange, induction, electrostatic, steric repulsion). In order the estimate the sensitivity of GDY, the %sensitivity and average energy gap variations are quantitatively measured by energies of HOMO and LUMO orbitals. In term of adsorption affinity of GDY, UV-Vis analysis, CHELPG charge transfer and DOS analysis depict an appreciable response towards these toxic CWAs. Keywords: Graphdiyne nanoflake; Chemical warfare agents; DFT; QTAIM; SAPT; RDG 2 Introduction Chemical warfare agents (CWAs) are the most destructive, toxic and lethal chemicals being used in the 19th century [1–3]. After World War II, a large quantity of these agents were disposed of in the oceans [4], without keeping in mind that how could it be dangerous for sea life and their dependant species. In the 20th century, these chemicals were used for terrorist attacks to cause more damage [5]. Apart from this, these CWAs have found extensive usage in various industries such as ore refining, metal cleaner, organic synthesis, pharmaceutical, dye and pesticide industries [6, 7]. The concentration of CWAs has gradually increased in the atmosphere due to the easy availability in material industries which may lead to a serious threat to life on earth. Basically, CWAs can be classified in four classes based on their site of actions, these classes include; pulmonary, blood, blistering and nerve agents [8]. Based on the chemical structures, these classes are further divided in four subclasses commonly called as series such as V-series, H-series, G-series and A-series. Among all these classes, A-series nerve agents are considered as fourth generation chemicals, firstly synthesized in 1970s under the Union of Socialist Soviet Republics (U.S.S.R) chemical weapon program [9]. In the beginning A-230 was synthesised by replacing substituting O-isopropyl group of sarin with aceoamydin radical. Later on, Kirpichey et al., synthesized A-232 and A-234 derivatives by introducing methoxy and ethoxy groups in A-230, respectively [10]. A-230 A-232 A-234 O O F F O N P P N N N N N P F O O Fig. 1: Structure of A-series (A-230, A-232m A-234) reported by Mirzayanov [11]. These novel series (A-series) of nerve agents are named as “Novichok” [12]. Even though, the Novichok nerve agents are not tested in the battlefield, but the accidental exposure of a worker of Novichok development project induced nerve damage, resulted permanent loss of arm movability, epilepsy, liver cirrhosis and inability to concentrate etc [13, 14]. The structures of Novichok nerve agents have not yet been fully known, however, the two chemists namely; Mirzayanov [13] and Hoenig [15] proposed two different composition with different structures. The Mirzayanov’s structures are displayed in Fig. 1 while the structures of Hoenig are given in supplementary information (Fig. S1). In this study we only focused on the A-230, A-232 and A-234 structures proposed by Mirzayanov because the phosphoramidate nature (Mirzayanov’s structure) is most acceptable by scientific community than phosphorylated oxime nature (Hoenig’s structure) [16]. By virtue of their high toxicity, various experimental and theoretical studies have been performed to find a suitable candidate for even a minute detection of these A-series 3 molecules. In this regard, numerous materials have been tested such as covalent/metal organic frameworks [17–22], zeolites [23], metal oxides [24–26], and other [27–29]. Though, these materials exhibit significant capturing of toxic pollutants, but due to low porosity, small surface area, lack of reproducibility, less active sites and lack of periodicity limit their utility. The desirable properties of sensor materials are have high surface area, high selectivity/sensitivity, rapid response time, low detection limit, less cost, high surface to volume ratio, and minimal impact on environment [30–32]. Recent literature reveals that the two-dimension carbon surfaces are considered to be the best candidate for the effective adsorption of toxic chemical. One of our previous study reveals that graphdiyne (GDY) has superior sensitivity for hazardous materials than graphyne and other 2D carbon surfaces [33]. Moreover, we were failed to find any theoretical study to explain the adsorption sensitivity of GDY towards A-series of CWAs. This motivated us to explore the adsorption mechanism and sensing behaviour of GDY particularly for A-230, A-232 and A-234 analytes. Therefore, we have designed three complexes named as; A-230@GDY, A-232@GDY and A-234@GDY. Our desired results are based on geometric parameters, adsorption energies and other geometric and electronic properties. Computational methodology In this study, ωB97XD/6-31+G(d,p) is used for the optimization of all the structures on Gaussian09 [34]. DFT-ωB97XD is a dispersion corrected long-range functional which is well reported to estimate non-covalent interaction energies [35, 36]. The lowest energy geometries (see Fig. 2) are reported in the main manuscript for detailed analysis while all possible interaction orientations are given in supplementary information (Fig. S2). For these stable geometries of complexes, the counterpoise interaction energies are calculated by using the expression below; Ead = E(ana@GDY) – [E(GDY) + E(ana)] + BSSE ---- (1) Here, Eana@GDY, EGDY and Eana are interaction energies of analytes@graphdiyne complexes, bare graphdiyne and analytes, respectively. The BSSE (basis set superposition error) strategy has be adopted to avoid the error created by overlapping of finite basis set. The accurate determination of noncovalent interactions is mandatory because these play an important role on adsorbing of analytes on graphdiyne surface. For this purpose, the SAPT0 [37] analysis has been performed via Psi4 [38] software. The SAPT0 analysis splits the noncovalent interaction energy in four meaningful components which include exchange, electrostatic, dispersion and induction component. Exchange components attributes the repulsion between completely filled orbitals of interacting moieties whereas, electrostatic, dispersion and induction account the attractive energies between occupied and virtual orbitals of interacting species. The total SAPT energy is accounted by the equation below: ESAPT = (-Eest) + (Eexch) + (-Eind) + (-Edis) ---- (2) 4 Reduced density gradient analysis (RDG) graphs are also plotted with their isosurfaces to understand the role and strength of noncovalent interactions between analytes and graphdiyne nanoflake. RDG exhibits that the interaction mechanism mainly depends on the electronic density (ρ). The expression below defines the relationship between ρ and RDG [39]: ---- (3) 1 |∇ρ| 2 1/3 4/3 푅퐷퐺 = 2(3휋 ) ρ In RDG isosurfaces, the colours such as red, blue and green attributes the type of interactions present. The colours represent the steric repulsion (red), strong (blue) and weak (green) interactions [40]. These RDG plots are generated by MultiWFN [41] software. Literature reveals that the charge transfer is an another important electronic property which reveals the accurate
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