Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity‐shaped hydrated electron state to a hydrated nucleobase (NB)‐bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron‐induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution‐structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120–200 fs in four aqueous NB solutions, depending on the electron‐binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*‐type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron‐binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure‐fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA‐damage mechanism in solution.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

Slide Fastener Reduction of Graphene‐Oxide Edges by Calcium: Insight from Ab Initio Molecular Dynamics

The reduction of graphene oxide can be used as a simple way to produce graphene on a large scale. However, the numerous edges produced by the oxidation of graphite seriously degrade the quality of the graphene and its carrier transport property. In this work, the reduction of oxygen‐passivated graphene edges and the subsequent linking of separated graphene sheets by calcium are investigated by using first‐principles calculations. The calculations show that calcium can effectively remove the oxygen groups from two adjacent edges. The joining point of the edges serves as the starting point of the reduction and facilitates the reaction. Once the oxygen groups are removed, the crack is sutured. If the joining point is lacking, it becomes difficult to zip the separated fragments. A general electron‐reduction model and a random atom‐reduction model are suggested for these two situations. The present study sheds light on the reduction of graphene‐oxide edges by using reactive metals to give large‐sized graphene through a simple chemical reaction.     

Ab Initio Study of H-Bond Dynamics in Three-Component Crystals Comprising (DABCOH+)n Polycationic Chains

In this work, the dynamic character of hydrogen-bond (H-bond) networks in two three-component crystals comprising polycationic chains was described. The first studied system was 1,4-diazabicyclo[2.2.2]octan-1-ium (DABCOH⁺) sulfamate monohydrate, known for its large negative linear compressibility. The second analyzed material was the newly obtained polar salt co-crystal: 1,4-diazabicyclo[2.2.2]octan-1-ium sulfamate urea. X-ray diffraction measurements enabled us to study the H-bond systems in both crystals using the graph set analysis. Obtained structures served as the initial models for Born-Oppenheimer molecular dynamics computations. A detailed study of intermolecular interactions and power spectra was conducted. The analysis of time and space correlations between the changes in H-bonds enabled the detection of proton transfer occurring in both systems at 300 K. Further study of those dynamic phenomena was done using the Energy Decomposition Analysis for selected trajectory fragments. Our work should improve the understanding of dielectric and ferroelectric properties of hybrid organic-inorganic materials.     

New Insights into the Jahn–Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

The Cu^II hydration shell structure has been studied by means of classical molecular dynamics (MD) simulations including three-body corrections and hybrid quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations at the Hartree–Fock level. The copper(II ) ion is found to be six-fold coordinated and [Cu(H₂O)₆]²⁺ exhibits a distorted octahedral structure. The QM/MM MD approach reproduces correctly the experimentally observed Jahn–Teller effect but exhibits faster inversions (<200 fs) and a more complex behaviour than expected from experimental data. The dynamic Jahn–Teller effect causes the high lability of [Cu(H₂O)₆]²⁺ with a ligand-exchange rate constant some orders of magnitude higher than its neighbouring ions Ni^II and Zn^II. Nevertheless, no first-shell water exchange occurred during a 30-ps simulation. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and various angular distributions and the dynamical properties as librational and vibrational motions and reorientational times were evaluated, which lead to detailed information about the first hydration shell. Second-shell water-exchange processes could be observed within the simulation time scale and yielded a mean ligand residence time of ≈20 ps.     

The Nature of [PdCl2(C2H4)(H2O)] as an Active Species in the Wacker Process: New Insights from Ab Initio Molecular Dynamics Simulations

First‐principles molecular dynamics coupled with metadynamics have been used to gain a deeper insight into the reaction mechanism of the Wacker process by determining the nature of the active species. An explicit and dynamic representation of the aqueous solvent, which was essential for modeling this reaction, was efficiently included into the simulations. Prompted by our earlier results, which showed that the configuration of the catalytically active species [PdCl₂(H₂O)(C₂H₄)] was crucial in the subsequent steps of the Wacker process, herein we focused on the preceding equilibria that led to the formation of both the cis and trans isomers. Starting from the initial catalyst, [PdCl₄]^2?, the free‐energy barriers for the forward and backward reactions were calculated. These results confirmed the relevance of the trans intermediate in the reaction mechanism, whilst conversely, they showed that the cis configuration played no role in it. This sole participation of the trans intermediate has some very important implications; besides the mechanistic interpretation of the initial steps in the Wacker reaction mechanism, the analysis of these equilibria provides additional information about the chemical nature of these ligand‐substitution processes.     

Ab initio molecular dynamics study of the keto-enol tautomerism of acetone in solution.

We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.     

Direct Ab Initio Dynamics Study on the Reaction of CH3CHF2 (HFC‐152a) with the Cl Atom

A direct ab initio dynamics method is used to investigate the hydrogen‐abstraction reaction CH₃CHF₂+Cl. One transition state is located for α‐H abstraction, and two are identified for β‐H abstraction. The potential‐energy surface (PES) is obtained at the G3(MP2)//MP2/6‐311G(d, p) level. Furthermore, the rate constants of the three channels are evaluated by using canonical variational transition‐state theory (CVT) with small‐curvature tunneling (SCT) contributions over a wide temperature range of 200–2500 K. The dynamic calculations show that the reaction proceeds mainly by α‐H abstraction over the whole temperature range. The calculated rate constants and branching ratios are both in good agreement with the available experimental values.     

Ab Initio Study on the Mechanism of the Atmospheric Reaction OH+O3→HO2+O2

The atmospheric reaction (1) OH + O₃→HO₂ + O₂ was investigated theoretically by using MP2, QCISD, QCISD(T), and CCSD(T) methods with various basis sets. At the highest level of theory, namely, QCISD, the reaction is direct, with only one transition state between reactants and products. However, at the MP2 level, the reaction proceeds through a two‐step mechanism and shows two transition states, TS1 and TS2 , separated by an intermediate, Int . The different methodologies employed in this paper consistently predict the barrier height of reaction (1) to be within the range 2.16–5.11 kcal mol^?1, somewhat higher than the experimental value of 2.0 kcal mol^?1.     

乙烯醇钠的从头算研究(英文)

在ＲＨＦ／３－２１Ｇ和ＲＨＦ／６－３１＋Ｇ水平上优化了乙烯醇钠的的平衡构型及过渡态，比较了不同构型的稳定性。在ＲＨＦ／６－３１＋Ｇ水平上探讨了气相中由乙醛和氢氧化钠生成乙烯醇钠的机理。并在ＭＰ２（ｆｕｌ）／６－３１＋Ｇ／／ＭＰ２（ｆｕｌ）／６－３１＋Ｇ水平下计算了反应热     

Exploring the Interfacial Reaction of Nano Al/CuO Energetic Films through Thermal Analysis and Ab Initio Molecular Dynamics Simulation

The effect of the interface layer on energy release in nanoenergetic composite films is important and challenging for the utilization of energy. Nano Al/CuO composite films with different modulation periods were prepared by magnetron sputtering and tested by differential scanning calorimetry. With the increase in the modulation period of the nano Al/CuO energetic composite films, the interface layer contained in the energetic composite film decreased meaningfully, increasing the total heat release meaningfully. Ab initio molecular dynamics (AIMD) simulation were carried out to study the preparation process changes and related properties of the nano Al/CuO energetic composite films under different configurations at 400 K. The results showed that the diffusion of oxygen atoms first occurred at the upper and lower interfaces of CuO and Al, forming AlO_x and Cu_xAl_yO_z. The two-modulation-period structure changed more obviously than the one-modulation-period structure, and the reaction was faster. The propagation rate and reaction duration of the front end of the diffusion reaction fronts at the upper and lower interfaces were different. The Helmholtz free energy loss of the nano Al/CuO composite films with a two-modulation-period configuration was large, and the number of interfacial layers had a great influence on the Helmholtz free energy, which was consistent with the results of the thermal analysis. Current molecular dynamics studies may provide new insights into the nature and characteristics of fast thermite reactions in atomic detail.     

An Ab Initio Study on the Mechanism of the Atmospheric Reaction NH2+O3→H2NO+O2

The atmospheric reaction NH₂+O₃→H₂NO+O₂ has been investigated theoretically by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At the MP2 level of theory, the hypersurface of the potential energy (HPES) shows a two step reaction mechanism. Therefore, the mechanism proceeds along two transition states (TS1 and TS2), separated by an intermediate designated as Int. However, when the single‐reference higher correlated QCISD and the multiconfigurational CASSCF methodologies have been employed, the minimum structure Int and TS2 are not found on the HPES, which thus confirms a direct reaction mechanism. Single‐reference high correlated and multiconfigurational methods consistently predict the barrier height of the reaction to be within the range of 3.9 to 6.6 kcal mol^?1, which is somewhat higher than the experimental value. ¹ The calculated reaction enthalpy is ?67.7 kcal mol^?1.     

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.     

Ab Initio Molecular Dynamics Study of Hydrogen Cleavage by a Lewis Base [tBu3P] and a Lewis Acid [B(C6F5)3] at the Mesoscopic Level—Dynamics in the Solute–Solvent Molecular Clusters

With the help of state‐of‐the‐art ab initio molecular dynamics methods, we investigated the reaction pathway of the {tBu₃P + H₂ + B(C₆F₅)₃} system at the mesoscopic level. It is shown that: i) the onset of H₂ activation is at much larger boron???phosphorus distances than previously thought; ii) the system evolves to the product in a roaming‐like fashion because of quasi‐periodic nuclear motion along the asymmetric normal mode of P???H?H???B fragment; iii) transient configurations of a certain type are present despite structural interference from the solvent; iv) transient‐state configurations with sub‐picosecond lifetime have potentially interesting infrared activity in the organic solvent (toluene) as well as in the gas phase. The presented results should be helpful for future experimental and theoretical studies of frustrated Lewis pair (FLP) activity.     

Insight into Markovnikov Reactions of Alkenes in Terms of Ab Initio and Molecular Face Theory

Electrophilic additions of hydrogen halides to alkenes in the gas phase are investigated with a high‐level ab initio method, MP2/6‐311+G(3df,2p). Based on this, the interesting features of these reactions along the IRC routes are characterized by the molecular face (MF) theory. For an alkene at the initial state, if the representative electron density (ED) encoded on the molecular face (MF) of the Markovnikov (M) carbon atom (the carbon with more hydrogen atoms) is larger than that of the anti‐Markovnikov (AM) carbon atom (the carbon with fewer hydrogen atoms), the electrophilic addition reaction is predicted to proceed along the Markovnikov addition route; in the reverse situtation, the anti‐Markovnikov addition route would be slightly preferred. It is then demonstrated that for a series of alkenes, the difference between activation energies of Markovnikov and anti‐Markovnikov addition routes [ΔE^#_(M?AM)] has a good linear correlation with sign(K_ED)K²_ED, where K_ED is characteristic of the electron density (ED) at the π region in the initial state of the alkenes. Interestingly, there is a good linear correlation between our sign (K_ED)K²_ED and the absolute values of difference in the core ionization energy between M and AM carbon atoms obtained by others (L. J. Sæthre, T. D. Thomas, S. Svensson J. Chem. Soc. P2 1997 , 2, 749.) in terms of the experimental study. In addition, the spatial dynamic changing features of the MF faces and interesting pictures of the electron transfer are clearly shown during the course of the electrophilic addition reactions. These results indicate that not only regioselectivity, but also activation energy and reactivity correlate with the π charge distribution in the initial state of the alkenes for electrophilic addition reactions.