The diamine cation is not a chemical example where density functional theory fails

Theoretical Study of the Thermal Rate Coefficients of the H3+ + C2H4 Reaction: Dynamics Study on a Full-Dimensional Potential Energy Surface

Ion-molecular reactions play a significant role in molecular evolution within the interstellar medium. In this study, the entrance channel reaction, H3+ + C2H4 → H2 + C2H5+, was investigated using classical molecular dynamic (classical MD) and ring polymer molecular dynamic (RPMD) simulation techniques. We developed an analytical potential energy surface function with a permutationally invariant polynomial basis, specifically employing the monomial symmetrized approach. Our dynamic simulations reproduced the rate coefficient of 300 K for H3+ + C2H4 → H2 + C2H5+, aligning reasonably well with the values in the kinetic database commonly utilized in astrochemistry. The thermal rate coefficients obtained using both the classical MD and RPMD techniques exhibited an increase from 100 K to 300 K as the temperature rose. Additionally, we analyzed the excess energy distribution of the C2H5+ fragment with respect to temperature to investigate the indirect reaction pathway of C2H5+ → H2 + C2H3+. This result suggests that the indirect reaction pathway of C2H5+ → H2 + C2H3+ holds minor significance, although the distribution highly depends on the collisional temperature.

Rydberg electron stabilizes the charge localized state of the diamine cation

A previous controversial discussion regarding the interpretation of Rydberg spectra of gaseous dimethylpiperazine (DMP) as showing the co-existence of a localized and delocalized mixed-valent DMP+ radical cation is revisited. Here we show by high-level quantum-chemical calculations that an apparent barrier separating localized and delocalized DMP+ minima in previous multi-reference configuration-interaction (MRCI) calculations and in some other previous computations were due to unphysical curve crossings of the reference wave functions. These discontinuities on the surface are removed in state-averaged MRCI calculations and with some other, orthogonal high-level approaches, which do not provide a barrier and thus no localized minimum. We then proceed to show that in the actually observed Rydberg state of neutral DMP the 3s-type Rydberg electron binds more strongly to a localized positive charge distribution, generating a localized DMP* Rydberg-state minimum, which is absent for the DMP+ cation. This work presents a case where interactions of a Rydberg electron with the underlying cationic core alter molecular structure in a fundamental way.

The Atomic Drill Bit: Precision Controlled Atomic Fabrication of 2D Materials

The ability to deterministically fabricate nanoscale architectures with atomic precision is the central goal of nanotechnology, whereby highly localized changes in the atomic structure can be exploited to control device properties at their fundamental physical limit. Here, an automated, feedback-controlled atomic fabrication method is reported and the formation of 1D-2D heterostructures in MoS₂ is demonstrated through selective transformations along specific crystallographic orientations. The atomic-scale probe of an aberration-corrected scanning transmission electron microscope (STEM) is used, and the shape and symmetry of the scan pathway relative to the sample orientation are controlled. The focused and shaped electron beam is used to reliably create Mo₆ S₆ nanowire (MoS-NW) terminated metallic-semiconductor 1D-2D edge structures within a pristine MoS₂ monolayer with atomic precision. From these results, it is found that a triangular beam path aligned along the zig-zag sulfur terminated (ZZS) direction forms stable MoS-NW edge structures with the highest degree of fidelity without resulting in disordering of the surrounding MoS₂ monolayer. Density functional theory (DFT) calculations and ab initio molecular dynamic simulations (AIMD) are used to calculate the energetic barriers for the most stable atomic edge structures and atomic transformation pathways. These discoveries provide an automated method to improve understanding of atomic-scale transformations while opening a pathway toward more precise atomic-scale engineering of materials.

Comparison of nitrate formation mechanisms from free amino acids and amines during ozonation: a computational study

Nitrate as a potential surrogate parameter for abatement of micropollutants, oxidant exposure, and characterizing oxidant-reactive DON during ozonation has attracted extensive attention, however, understanding of its formation mechanisms is still limited. In this study, nitrate formation mechanisms from amino acids (AAs) and amines during ozonation were investigated by the DFT method. The results indicate that N-ozonation initially occurs to produce competitive nitroso- and N,N-dihydroxy intermediates, and the former is preferred for both AAs and primary amines. Then, oxime and nitroalkane are generated during further ozonation, which are the important last intermediate products for nitrate formation from the respective AAs and amines. Moreover, the ozonation of the above important intermediates is the nitrate yield-controlling step, where the relatively higher reactivity of the CN moiety in the oxime compared to the general C_α atom in the nitroalkane explains why the nitrate yields of most AAs are higher than those from general amines, and it is the larger number of released C_α^- anions, which are the real reaction sites attacked by ozone, that leads to the higher nitrate yield for nitroalkane with an electron-withdrawing group bound to the C_α atom. The good relationship between nitrate yields and activation free energies of the rate-limiting step (ΔG≠rls) and nitrate yield-controlling step (ΔG≠nycs) for the respective AAs and amines verifies the reliability of the proposed mechanisms. Additionally, the bond dissociation energy of C_α-H in the nitroalkanes formed from amines was found to be a good parameter to evaluate the reactivity of the amines. The findings here are helpful for further understanding nitrate formation mechanisms and predicting nitrate precursors during ozonation.

Degradation of mevinphos and monocrotophos by OH radicals in the environment: A computational investigation on mechanism, kinetic, and ecotoxicity

Known organophosphorus pesticides are used widely in agriculture to improve the production of crops. Based on the literature, the degradation of some organophosphorus pesticides was studied theoretically. However, the mechanisms and variation of toxicity during the degradation of mevinphos and monocrotophos are still unclear in the environment, especially in wastewater. In this study, the reaction mechanisms for the degradation of the two representative organophosphorus pesticides (i.e., mevinphos and monocrotophos) in presence of OH radicals in the atmosphere and water are proposed using quantum chemical methods wB97-XD/6-311 + +G(3df,2pd)//wB97-XD/6-311 + +G(d,p). Result shows that the dominant channel is OH-addition to the C atom in CC bond with energy barriers being 15.6 and 14.7 kJ/mol, in the atmosphere and water, respectively, for mevinphos. As for monocrotophos, H-abstraction from NH group via barriers of 8.2 and 10.6 kJ/mol is more feasible in both the atmosphere and water. Moreover, the subsequent reactions of the major products in the atmosphere with NO and O₂ were also studied to evaluate the atmospheric chemistry of mevinphos and monocrotophos. Kinetically, the total rate constant is 2.68 × 10^-9 and 3.86 × 10^-8 cm³ molecule^-1·s^-1 for mevinphos and monocrotophos in the atmosphere and 4.91 × 10¹⁰ and 7.77 × 10¹¹ M^-1 s^-1 in the water at 298 K, thus the lifetime is estimated to be 36.46-364.60 s (2.53-25.31 s) in the atmosphere, and 1.41 × 10^-2 - 1.41 × 10^-1 s (8.92 ×10^-4 - 8.92 ×10^-3 s) in the advanced oxidation processes (AOPs) system. Furthermore, ecotoxic predictions for rats and three aqueous organisms imply their toxicity are reduced during degradation by using ECOSAR and T.E.S.T program based quantitative structure and activity relationship (QSAR) method.

Preparation of a novel iron oxychloride (FeOCl) auxiliary electrode in promoting electrokinetic remediation of Cr(VI) contaminated soil: An experimental and DFT calculation analysis

The utilization of auxiliary electrode can improve substantially the electrokinetic remediation efficiency of heavy metal contaminated soil. The increase in the auxiliary electrode performance is the key to further promote the electrokinetic remediation efficiency. In this study, two kinds of auxiliary electrodes, pure FeOCl and doped FeOCl with W and S, were prepared and used in the electrokinetic remediation of Cr(VI) contaminated soil. The system equipped with the auxiliary electrode doped FeOCl brought more stable system current (202 mA) and more uniform electric field than blank group (130 mA). The reduction rate of Cr(VI) was increased by 50% due to the presence of Fe²⁺ and S^2-. The accelerating migration of ions by auxiliary electrode was responsible for the improvement in electrokinetic remediation efficiency. Density functional theory (DFT) calculation showed that Cl vacancy formation energies of pure FeOCl, S-doped FeOCl (S/FeOCl) and W-doped FeOCl (W/FeOCl) were 1.29, 1.15 and 1.49 eV respectively, and the ion diffusion barriers were 0.093, 0.099 and 0.148 eV respectively. Calculation results indicated that the doping of S was conducive to the diffusion of Cl ions, and the bonding of W-Cl was stronger than Fe-Cl. The charging and discharging process of auxiliary electrode became easier due to the formation of lower vacancy in S-doped FeOCl, which could bring a higher current for the electrokinetic remediation system. The electrochemical performance of FeOCl doped with W and S was improved obviously. This study provided a further explanation for the positive role of auxiliary electrode in electrokinetic remediation system.

Density functional theory explorations of parathion and paraoxon hydrolysis as a function of the underlying alkaline environment

Parathion, a once commonly used pesticide known for its potential toxicity, can follow several degradation mechanisms in the environment. Given the species stability and persistence, parathion can be washed into waterways from rain, and therefore an atomistic perspective of the hydrolysis of parathion, and its byproduct paraoxon, is required in order to understand its fate in the environment. Experimental studies have determined that pH plays an important role in the calculated hydrolysis rate constants of parathion degradation. In this work, the degradation of parathion into either paraoxon or 4-nitrophenol, and the degradation of paraoxon to 4-nitrophenol are explored through density functional theory using the M06-2X functional. How the level of basicity affects the reaction mechanism is explored through two different hydroxide/water environments. Our calculations support the anticipated mechanisms determined by previous experimental work that the formation of 4-nitrophenol is the predominant pathway in hydrolysis of parathion.

DFT insights into the degradation mechanism of carbendazim by hydroxyl radicals in aqueous solution

Advanced oxidation of carbendazim by OH radicals is a central step in its wastewater remediation. However, the understanding of the degradation mechanism of carbendazim has always been a challenge. In this paper, the degradation mechanism of carbendazim by •OH in aqueous solution has been explored using density functional theory (DFT) calculations. On account of the structural and electronic characteristics analysis, the nucleophilic aromatic substitution, dehydrogenation oxidation, and decarboxylation degradation pathways were mainly investigated. These degradation reactions may produce hydroxyl substitution products, oxidized aldehyde and carboxyl products, and decarboxylated carbamic acid products. Computational studies demonstrated that these possible degradation reactions are facile to take place kinetically and have large thermodynamic driving forces, indicating the feasibility of the relevant degradation pathways. Additionally, the ecological risk of carbendazim and its possible degradation products was evaluated, showing that the acute toxicity of degradation products decreases in varying degrees compared with that of carbendazim. The comprehensive mechanistic studies open an avenue for the understanding on the degradation of organic pollutants such as benzimidazole pollutants on molecular level.

The investigation of influencing factors on the degradation of sulfonamide antibiotics in iron-impregnated biochar-activated urea-hydrogen peroxide system: A QSAR study

Iron-impregnated biochar-activated urea-hydrogen peroxide (FB-activated UHP) is a potential in-situ technology for simultaneously reducing soil sulfonamide antibiotic contaminants and improving soil fertility. To better understand the degradation of sulfonamide antibiotics by FB-activated UHP, a two-dimensional quantitative structure-activity relationship (2D-QSAR) model based on quantum chemical parameters and a three-dimensional QSAR (3D-QSAR) model based on molecular force field were developed to investigate the factors influencing the removal efficiencies (Re%). The optimal 2D-QSAR model was Re%= 0.858-8.930 E-5 E_B3LYP-0.175 f(+)_x with the evaluation indices of R²= 0.732, q²= 0.571, and Q_ext²= 0.673. The given 2D-QSAR model indicated that the molecular size (E_B3LYP) and Fukui index with respect to nucleophilic attack (f(+)) were intrinsic factors influencing Re%. Three degradation pathways were subsequently proposed based on the f(+) distribution. Compared to the 2D-QSAR model, the developed 3D-QSAR model exhibited a better predictive ability, with the evaluation indices of R²= 0.989, q²= 0.696, and SEE= 0.001. The analysis of field contribution rates suggested that electrostatic field (48.2%), hydrophobic field (25.3%), and hydrogen-bond acceptor field (12.7%) were the main factors influencing Re%. These findings generated critical information for evaluating the degradation mechanisms/rules and provided theoretical bases for initially estimating the Re% of sulfonamide antibiotics undergoing FB-activated UHP process.

Seeking the Optimal Descriptor for SN2 Reactions through Statistical Analysis of Density Functional Theory Results

Bimolecular nucleophilic substitution is one of the fundamental reactions in organic chemistry, yet there is still knowledge to be gained on the role of the nucleophile and the substrate. A statistical treatment of over 600 density functional theory (DFT)-computed barriers for bimolecular nucleophilic substitution at methyl derivatives (S_N2@C) leads to the identification of numerical descriptors that best represent the entering and leaving ability of 26 different nucleophiles. The treatment is based on singular value decomposition (SVD) of a matrix of computed energy barriers. The current work represents the extension to a problem of reactivity of the hidden descriptor methodology that we had previously developed for the thermodynamic problem of bond dissociation energies in transition-metal complexes. The analysis of the results shows that a single descriptor is sufficient. This hidden descriptor has different values for nucleophilic and leaving abilities and, contrary to expectation, does not correlate especially well with either frontier molecular orbital descriptors or solvation descriptors. In contrast, it correlates with other thermodynamic and geometric parameters. This statistical procedure can be in principle extended to additional chemical fragments and other reactions.

Open-shell extensions to closed-shell pCCD

The pair coupled cluster doubles (pCCD) ansatz represents an inexpensive but accurate single-reference method to describe multi-reference problems. By construction, pCCD remains, however, applicable to closed-shell systems. For the first time, we present extensions to pCCD that allow us to target open-shell molecules with up to 4 unpaired electrons. Although requiring only modest computational cost, our methods approach chemical accuracy for some challenging cases, while their performance is comparable to more expensive models like DMRG or CCSD(T).

Kinetics and mechanisms of phenolic compounds by Ferrate(VI) assisted with density functional theory

In this paper, Phenol, 4-Chlorophenol (4-CP), 2,4-Dichlorophenol (2,4-DCP) and 2,4,6-Trichlorophenol (2,4,6-TCP) were selected as model pollutants to explore the oxidant mechanism by ferrate (Fe(VI)). The reactions between ferrate (1000 μM) and four phenolic compounds (100 μM) were conformed to the second-order reaction kinetics at pH 9.2, and the order of k_obs followed as: k_4-CP (129 M^-1 s^-1) > k_2,4-DCP (96 M^-1 s^-1) > k_2,4,6-TCP (44 M^-1 s^-1) > k_Phenol (12 M^-1 s^-1). Meanwhile, the degradation rates of all four compounds by Fe(VI) increased with increased pH (3.1-9.2). A total of 14 degradation products were identified by Liquid chromatography-Time-of-Flight-Mass Spectrometry (LC-TOF-MS), and two pathways including hydroxylation of benzene ring and substitution of chlorine atom were proposed. Hydroxyl radicals, played a vital role during the degradation of phenolic compounds. Moreover, density functional theory calculations were used to explore the degradation mechanisms. The results showed that the hydroxyl radical was more favorable to substitute chlorine atom than hydrogen atom, and the substitution on ortho-position was more favorable than para-position for all four compounds. The findings of this study could greatly improve our understanding on the degradation mechanism of chlorophenol-like compounds by Fe(VI) for environmental remediation.

Comprehensive Understanding of Fluoroacetate Dehalogenase-Catalyzed Degradation of Fluorocarboxylic Acids: A QM/MM Approach

Fluorochemicals are persistent, bioaccumulative, and toxic compounds that are widely tributed in the environment. Developing efficient biodegradation strategies to decompose the fluorochemicals via breaking the inert C-F bonds presents a holistic challenge. As a promising biodegradation enzyme candidate, fluoroacetate dehalogenase (FAcD) has been reported as the only non-metallic enzyme to catalyze the cleavage of the strong C-F bond. Here, we systematically investigated the catalytic actions of FAcD toward its natural substrate fluoroacetate using molecular dynamics simulations and quantum mechanism/molecular mechanism calculations. We propose that the enzymatic transformation involves four elementary steps, (I) C-F bond activation, (II) nucleophilic attack, (III) C-O bond cleavage, and (IV) proton transfer. Our results show that nucleophilic attack is the rate-determining step. However, for difluoroacetate and trifluoroacetate, C-F bond activation, instead of nucleophilic attack, becomes the rate-determining step. We show that FAcD, originally recognized as α-fluorocarboxylic acid degradation enzyme, can catalyze the defluorination of difluoroacetate to glyoxylate, which is captured by our high-resolution mass spectrometry experiments. In addition, we employed amino acid electrostatic analysis method to screen potential mutation hotspots for tuning FAcD's electrostatic environment to favor substrate conversion. The comprehensive understanding of catalytic mechanism will inform a rational enzyme engineering strategy to degrade fluorochemicals for benefits of environmental sustainability.

Ultrafast X-ray scattering offers a structural view of excited-state charge transfer

Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon-carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon-carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

Localized and Delocalized States of a Diamine Cation: Resolution of a Controversy

Recent Rydberg spectroscopy measurements of a diamine molecule, N,N'-dimethylpiperazine (DMP), indicate the existence of a localized electronic state as well as a delocalized electronic state. This implies that the cation, DMP⁺, can similarly have its positive charge either localized on one of the N atoms or delocalized over both. This interpretation of the experiments has, however, been questioned based on coupled cluster calculations. In this article, results of high-level multireference configuration interaction calculations are presented where a localized state of DMP⁺ is indeed found to be present with an energy barrier separating it from the delocalized state. The energy difference between the two states is in excellent agreement with the experimental estimate. The results presented here, therefore, support the original interpretation of the experiments and illustrate a rare shortcoming of CCSD(T), the "gold standard" of quantum chemistry. These results have implications for the development of density functionals, as most functionals fail to produce the localized state.

C13 – a new empirical force field to characterize the mechanical behavior of carbyne chains

The C13 empirical potential is developed for accurate modeling of mechanical properties of carbyne specifically taking in account bond alternation.

Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach

Widely distributed fluorocarboxylic acids have aroused worldwide environmental concerns due to its toxicity, persistence, and bioaccumulation. Enzyme-based eco-friendly biodegradation techniques have become increasingly important in treating fluorocarboxylic acids. Here we utilized in silico and in vitro approaches to investigate the defluorination mechanism of fluoroacetate dehalogenase (FAcD) toward monofluoropropionic acids at atomic-level. The experimentally determined k_cat and k_M for defluorination of 2-fluoropropionic acid are 330 ± 60 min^-1 and 6.12 ± 0.13 mM. The in silico results demonstrated positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) under different enzymatic conformations. We also screened computationally and tested in vitro (enzyme assay and kinetic study) the catalytic proficiency of FAcD toward polyfluoropropionic acids and perfluoropropionic acids which are known to be challenging for enzymatic degradation. The results revealed potential degradation activity of FAcD enzyme toward 2,3,3,3-tetrafluoropropionic acids. Our work will initiate the development of a new "integrated approach" for enzyme engineering to degrade environmentally persistent fluorocarboxylic acids.