Environmental theoretical calculation for non-periodic systems

Environmental theoretical calculation aims to use computer simulation assist in solving environmental problems. Herein, we present the guiding principles of for non-periodic systems. A summary is given recent progress towards reveal degradation/transformation mechanisms contaminants reactions. ‘Beyond experiment’ has been gradually accepted as a general concept chemistry discipline. As and science have advanced, it become possible explore close link between macrolevel observations microlevel molecular wave functions, thus providing deep insights into principle chemical phenomena [1.Jensen F. Introduction Computational Chemistry. John Wiley & Sons, 2017Google Scholar]. Chemical reactions an system usually occur complicated ‘box’ involving various oxidation/reduction More specifically, focus on transformation degradation contaminant during reaction because their relationship removal detoxification target contaminant. Therefore, besides conventional experimental evidence, urgently require computational methodology by which examine such detail. new branch defined application Theoretical calculations related research generally comprise two parts: (i) behavior (especially organic compounds) mechanism reactive species (radicals, oxidants, reductants) through finite-scale (molecule level) problem system; (ii) material aimed at revealing physicochemical properties intrinsic interface infinite-scale periodic system. Figure 1 presents overall framework The degradation) most important considered research. For example, advanced oxidation processes (AOPs), highly radicals, are widely applied water treatment [2.Hodges B.C. et al.Challenges prospects using catalytic nanomaterials.Nat. Nanotechnol. 2018; 13: 642-650Crossref PubMed Scopus (614) Google Invariably, typical with degradation, series experiments first conducted obtain essential data (Figure 1, Experimental section), primarily including: determination kinetics products (TPs) contaminant; identification species; (iii) evaluation toxicity variation. underlying mechanism, propose following four-step procedure Calculation section): [based classical frontier orbital (FMO) theory] basic quantum parameters molecules, highest occupied (HOMO), lowest unoccupied (LUMO), electrostatic potential (ESP); electrophilicity/nucleophilicity site analysis conceptual density functional theory (CDFT) natural bond (NBO) [3.Fuentealba P. al.On condensed Fukui function.J. Chem. Phys. 2000; 113: 2544-2551Crossref (346) Scholar,4.Glendening E.D. al.Natural methods.Wiley Interdiscip. Rev. Comput. Mol. 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Reactive radicals can be regarded either electrophiles or nucleophiles depending ability attack sites relatively high/low density. global electrophilicity index (ω) enables electrophilic nucleophilic specific [11.De Vleeschouwer al.Electrophilicity nucleophilicity radicals.Org. Lett. 2007; 9: 2721-2724Crossref (187) according (μ) hardness (η) CDFT. leads absolute scales, solely depend characteristics electrophile therefore independent partner. Higher ω indicates higher electrophilicity. key evaluate reactivity contemporary peracetic acid (PAA)-based AOPs [12.Du al.Hydrogen atom abstraction acetylperoxyl radical Co(II)/peracetic 2022; 212118113Crossref (31) investigates compounds. In practice, CDFT used predict regioselectivity molecule quantifies position number electrons that changed. Moreover, representing (f–), (f+), (f0) calculated from gain loss 2, Section I). Specifically, after geometric optimization molecule, its total local atomic population determined analysis, populations corresponding cationic (−1 electron) anionic (+1 without geometry re-optimization index. Our group pioneered investigate [13.Liu W. al.Visible-light-driven photocatalytic diclofenac carbon dots modified porous g-C3N4: mechanisms, pathway DFT calculation.Water 2019; 151: 8-19Crossref (421) established Peking University Sites Organic Compounds Database (PKU-REOD). Kohn–Sham (K-S) equation one-electron equation) commonly utilized process, accuracy greatly depends selection exchange-correlation [14.Kohn Sham L.J. Self-consistent equations including exchange correlation effects.Phys. 1965; 140: A1133-A1138Crossref (49473) B3LYP, one hybrid generalized-gradient approximation (GGA) functionals, possesses good stability tasks. However, B3LYP 20% Hartree–Fock (HF) composition lack proper description dispersion effects, leading being incapable charge-transfer, vertical excitation Rydberg, large-ring conjugated addition, meta-hybrid GGA functional, M06-2X popularly substitution B3LYP. due moderate HF (54%) accurate weak interaction effects. Meanwhile, requires numerically ultrafine grid (or even superfine grid) guarantee convergence self-consistent field (SCF) optimization, so takes longer time. Gaussian-type selected primary basis solve K-S equation, triple-zeta Pople-style Ahlrichs def2 sets preferred. To achieve compromise result time, B3LYP-D3/6-311G* (6-311+G*) M06-2X/def2-TZVP (def-TZVP) functionals frequently utilized. relates thermodynamics interpret equilibrium direction. It difficult measure experimentally transition state (TS) reaction, TS feature method. assessing three routes considered: single transfer (SET), hydrogen (HAA), adduct formation (RAF) II). Energy estimates parameters: Gibbs free (∆G), difference reactants elementary processes; (ΔG‡), reactant RAF HAA routes. value ΔG‡ SET route Marcus [15.Mayer J.M. Understanding transfer: strengths theory.Acc. 2011; 44: 36-46Crossref (597) kinetics, rate constant may also (TST). further when attacked level, proposed streamlined method species-meditated output this includes: function; profiles (e.g., radicals) attacking via (SET, HAA, RAF); order, spin density, singly orbitals (SOMOs) reactant, TS, intermediate (IM) reaction; details reaction. sense, offers comprehensive integrates preceding sites, change, III). other oxygen (OAT), proton-coupled (PCET), coupling (RCR) provides insight compounds, facilitating regulation processes. core challenge how simulate complex systems more accurately, heavily relying advances computing power. matrix (generally >1000 atoms), upgraded calculation, implicit solvent model needs switched explicit build mid-density low-density boxes Packmol software). CP2K software, performs well large Quickstep approach method, calculation. avenues need explored: construction precise consider variety parameters, solvent, speciation, charge compound, multiple coexisting substances inorganic ions, dissolved matter); suitable (nonrandom) functions polarization function, diffuse pseudopotential) systems; methods overcome compounds weight) combined material, implying contaminant–material adsorption energy, states) obtained straightforwardly than (non-periodic calculation); development finely resolved accounting different species, extending beyond rough classification electrophilic, nucleophilic, attacks; (v) ab initio dynamics precise, unbiased observe process involved degradation. future, expected play significant role screening regulating contaminant-orientated satisfy resource standards. Financial support gratefully acknowledged National Key Research Development Program China (2021YFA1202500), Natural Science Foundation (NSFC) (52270053 52200083), Beijing Nova (20220484215). No interests declared.