Molecular Dynamics Insights into Electron-Catalyzed Dissociation Repair of Cyclobutane Pyrimidine Dimer

Excess electrons are not only an important source of radiation damage, but also participate in the repair process of radiation damage such as cyclobutane pyrimidine dimer (CPD). Using ab initio molecular dynamics (AIMD) simulations, we reproduce the single excess electron stepwise catalytic CPD dissociation process in detail with an emphasis on the energy levels and molecular structure details associated with excess electrons. On the basis of the AIMD simulations on the CPD aqueous solution with two vertically added excess electrons, we exclude the early-proposed [2+2]-like concerted synchronous dissociation mechanism, and analyze the difference between the symmetry of the actual reaction and the symmetry of the frontier molecular orbitals which deeply impact the mechanism. Importantly, we propose a new model of the stepwise electron-catalyzed dissociation mechanism that conforms to the reality. This work not only provides dynamics insights into the excess electron catalyzed dissociation mechanism, but also reveals different roles of two excess electrons in two bond-cleavage steps (promoting versus inhibiting).     

Full configuration interaction computer simulation study of the thermodynamic and kinetic stability of hydrated dielectrons

The hydrated electron is a unique solvent-supported state comprised of an excess electron that is confined to a cavity by the surrounding water. Theoretical studies have suggested that two-electron solvent-supported states also can be formed; in particular, simulations indicate that two excess electrons could pair up and occupy a single cavity, forming a so-called hydrated dielectron. Although hydrated dielectrons have not been observed directly by experiment, their existence has been posited to explain the lack of an ionic strength effect in hydrated electron bimolecular annihilation [Schmidt, K. H.; Bartels, D. M. Chem. Phys. 1995, 190, 145]. To determine whether dielectrons may be created in the laboratory, we use thermodynamic integration (TI), combined with mixed quantum/classical molecular dynamics simulation, to examine the thermodynamic stability of hydrated electrons and dielectrons. For the dielectron calculations, we solve the two-electron quantum problem using full configuration interaction. Our results suggest that hydrated dielectrons are thermodynamically unstable relative to separated (single) hydrated electrons, although we also show that increasing the pressure could drive the equilibrium toward the formation of dielectrons. Because the simulations suggest that hydrated dielectrons are kinetically stable, we also examine a scenario for creating metstable, nonequilibrium populations of dielectrons, which involves the capture of a newly injected electron by a preexisting, equilibrated hydrated electron. These calculations, which allow for the full nonadiabatic relaxation of the injected electron, show that hydrated electrons may indeed act as trapping sites for unequilibrated electrons, so that capture may be a viable mechanism for creating dielectrons. We suggest possible experimental procedures to create such nonequilibrium hydrated dielectrons using either pulse radiolysis or ultrafast spectroscopic techniques.     

Proton Acidity and Proton Mobility in ECR-40, a Silicoaluminophosphate that Violates Löwenstein's Rule

The silicoaluminophosphate zeotype ECR-40 contains linkages of AlO₄ tetrahedra via a common oxygen atom, thereby violating the famous “Löwenstein's rule”. In this work, a combination of static density functional theory (DFT) calculations and DFT-based ab-initio molecular dynamics (AIMD) simulations were employed to study the acidity and mobility of protons associated with such unusual linkages. It was found that the Al-O-Al linkages are preferentially protonated, as deprotonation causes a local accumulation of negative charge. The protons at these linkages possess a somewhat lower Brønsted acidity than those at Si-O-Al links. AIMD simulations for fully hydrated ECR-40 predicted a partial deprotonation of the Al-O-Al linkages, whereas Si-O-Al linkages were fully deprotonated. Frequently, a coordination of water molecules to framework Al atoms was observed in the vicinity of the Al-O-Al links. Hence, these linkages appear prone to break upon dehydration, potentially explaining why Löwenstein's rule is mostly obeyed in materials formed in aqueous media.     

Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe2+/Fe3+ Redox Reaction**

Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe²⁺/Fe³⁺ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, standard plane-wave based AIMD at that level of theory is typically 150 times slower than GGA for systems containing ∼100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe²⁺/Fe³⁺ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe²⁺/Fe³⁺ system computed from these simulations are compared with the available experimental data for validation.     

Nonadiabatic molecular dynamics simulations of correlated electrons in solution. 1. Full configuration interaction (CI) excited-state relaxation dynamics of hydrated dielectrons

The hydrated dielectron is composed of two excess electrons dissolved in liquid water that occupy a single cavity; in both its singlet and triplet spin states there is a significant exchange interaction so the two electrons cannot be considered to be independent. In this paper and the following paper,we present the results of mixed quantum/classical molecular dynamics simulations of the nonadiabatic relaxation dynamics of photoexcited hydrated dielectrons, where we use full configuration interaction (CI) to solve for the two-electron wave function at every simulation time step. To the best of our knowledge, this represents the first systematic treatment of excited-state solvation dynamics where the multiple-electron problem is solved exactly. The simulations show that the effects of exchange and correlation contribute significantly to the relaxation dynamics. For example, spin-singlet dielectrons relax to the ground state on a time scale similar to that of single electrons excited at the same energy, but spin-triplet dielectrons relax much faster. The difference in relaxation dynamics is caused by exchange and correlation: The Pauli exclusion principle imposes very different electronic structure when the electrons' spins are singlet paired than when they are triplet paired, altering the available nonadiabatic relaxation pathways. In addition, we monitor how electronic correlation changes dynamically during nonadiabatic relaxation and show that solvent dynamics cause electron correlation to evolve quite differently for singlet and triplet dielectrons. Despite such differences, our calculations show that both spin states are stable to excited-state dissociation, but that the excited-state stability has different origins for the two spin states. For singlet dielectrons, the stability depends on whether the solvent structure can rearrange to create a second cavity before the ground state is reached. For triplet dielectrons, in contrast, electronic correlation ensures that the two electrons do not dissociate, even if the dielectron is artificially kept from reaching the ground state. In addition, both singlet and triplet dielectrons change shape dramatically during relaxation, so that linear response fails to describe the solvation dynamics for either spin state. In the following paper (Larsen, R. E.; Schwartz, B. J. J. Phys. Chem. B 2006, 110, 9692), we use these simulations to calculate the pump-probe spectroscopic signal expected for photoexcited hydrated dielectrons and to predict an experiment to observe hydrated dielectrons directly.     

Nonadiabatic molecular dynamics simulations of correlated electrons in solution. 2. A prediction for the observation of hydrated dielectrons with pump-probe spectroscopy

The hydrated dielectron is a highly correlated, two-electron, solvent-supported state consisting of two spin-paired electrons confined to a single cavity in liquid water. Although dielectrons have been predicted to exist theoretically and have been used to explain the lack of ionic strength effect in the bimolecular reaction kinetics of hydrated electrons, they have not yet been observed directly. In this paper, we use the extensive nonadiabatic mixed quantum/classical excited-state molecular dynamics simulations from the previous paper to calculate the transient spectroscopy of hydrated dielectrons. Because our simulations use full configuration interaction (CI) to determine the ground and excited state two-electron wave functions at every instant, our nonequilibrium simulations allow us to compute the absorption, stimulated emission (SE), and bleach spectroscopic signals of both singlet and triplet dielectrons following excitation by ultraviolet light. Excited singlet dielectrons are predicted to display strong SE in the mid infrared and a transient absorption in the near-infrared. The near-infrared transient absorption of the singlet dielectron, which occurs near the peak of the (single) hydrated electron's equilibrium absorption, arises because the two electrons tend to separate in the excited state. In contrast, excitation of the hydrated electron gives a bleach signal in this wavelength region. Thus, our calculations suggest a clear pump-probe spectroscopic signature that may be used in the laboratory to distinguish hydrated singlet dielectrons from hydrated electrons: By choosing an excitation energy that is to the blue of the peak of the hydrated electron's absorption spectrum and probing near the maximum of the single electron's absorption, the single electron's transient bleach signal should shrink or even turn into a net absorption as sample conditions are varied to produce more dielectrons.     

Unraveling the Role of Water in the Stereoselective Step of Aqueous Proline‐Catalyzed Aldol Reactions

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self‐condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First‐principles molecular dynamics simulations were used to study the free‐energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high‐level static first‐principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths.     

PHOTOIONIZATION OF TRYPTOPHAN: AN ELECTRON SPIN RESONANCE INVESTIGATION

The photoionization of tryptophan has been studied by ESR spectroscopy using the free radical scavenger 5, 5 dimethyl-1-pyrroline-l-oxide as a spin trap for hydrated electrons. A special set-up has been devised to irradiate more than one aliquot of the bubbled aqueous solutions in the cavity without removing the ESR cell out of the cavity.
Quantum yields of electrons production have been estimated as a function of irradiation wavelength. No photoionization threshold has been observed in these experiments.     

Instrumental neutron activation analysis of ferromanganese oxide encrustations of Indian Ocean by the k0 NAA method

Hot electron injection into aqueous electrolyte solution was studied with electrochemiluminescence and electron paramagnetic resonance (EPR) methods. Both methods provide further indirect support for the previously proposed hot electron emission mechanisms from thin insulating film-coated electrodes to aqueous electrolyte solution. The results do not rule out the possibility of hydrated electron being as a cathodic intermediate in the reduction reactions at cathodically pulse-polarized thin insulating film-coated electrodes. However, no direct evidence for electrochemical generation of hydrated electrons could be obtained with EPR, only spin-trapping experiments could give information about the primary cathodic steps.     

The structure of the hydrated electron. Part 2. A mixed quantum/classical molecular dynamics embedded cluster density functional theory: single-excitation configuration interaction study

Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess electron density with the frontier orbitals of the first-shell solvent molecules cannot explain the observed magnetic, vibrational, and electronic properties of this species. Despite the need for multielectron effects to explain these important properties, the ensemble-averaged radial wavefunctions and energetics of the highest occupied and three lowest unoccupied orbitals of the hydrated electrons in our hybrid model are close to the s- and p-like states obtained in one-electron models. Thus, one-electron models can provide a remarkably good approximation to the multielectron picture of the hydrated electron for many applications; indeed, the two approaches appear to be complementary.     

Thin‐Layer Cyclic Voltammetric and Scanning Electrochemical Microscopic Study of Antioxidant Activity of Ascorbic Acid at Liquid/Liquid Interface

An electron transfer reaction between ascorbic acid (H₂A) in an aqueous solution and oxidizing agent in an organic solution immiscible with water has been studied by thin‐layer cyclic voltammetry (TLCV) for charge transfer at the interface between two immiscible electrolyte solutions (ITIES). As an antioxidant, H₂A provide electrons through the aqueous/organic interface to reduce Fc⁺ and the procedure has been proved to be a one electron process again. In this work, the first combination of TLCV and scanning electrochemical microscopy (SECM) was achieved and showed a reasonable agreement between the results from the two different approaches. Otherwise, lower concentration ratios Kr of aqueous to organic reactants was adopted, which is given as evidence to the proposed procedure of Barker.     

Computing the 7Li NMR chemical shielding of hydrated Li+ using cluster calculations and time-averaged configurations from ab initio molecular dynamics simulations

Ab initio molecular dynamics (AIMD) simulations have been used to predict the time-averaged Li NMR chemical shielding for a Li(+) solution. These results are compared to NMR shielding calculations on smaller Li(+)(H(2)O)(n) clusters optimized in either the gas phase or with a polarizable continuum model (PCM) solvent. The trends introduced by the PCM solvent are described and compared to the time-averaged chemical shielding observed in the AIMD simulations where large explicit water clusters hydrating the Li(+) are employed. Different inner- and outer-coordination sphere contributions to the Li NMR shielding are evaluated and discussed. It is demonstrated an implicit PCM solvent is not sufficient to correctly model the Li shielding, and that explicit inner hydration sphere waters are required during the NMR calculations. It is also shown that for hydrated Li(+), the time averaged chemical shielding cannot be simply described by the population-weighted average of coordination environments containing different number of waters.     

Ab initio QM/MM molecular dynamics study on the excited-state hydrogen transfer of 7-azaindole in water solution

Ab initio molecular dynamics (AIMD) simulations for the excited-state hydrogen transfer (ESHT) reaction of 7-azaindole (7AI-(H2O)n; n = 1, 2) clusters in the gas phase and in water are presented. The effective fragment potential (EFP) is employed to model the surrounding water molecules. The AIMD simulations for 7AI-H2O and 7AI-(H2O)2 clusters show an asynchronous hydrogen transfer at t approximately 50 fs after the photoexcitation. While the ESHT mechanism for 7AI-H2O in water does not change appreciably compared with that in the gas phase, the AIMD simulations on 7AI-(H2O)2 in water solution exhibit two different mechanisms. Since the tautomer form is lower in energy compared to the normal form in the S1 state, 7AI and (H2O) n fragments separate from each other after the ESHT. With the use of the results of the AIMD trajectories, the minimum energy conical intersection point in the tautomer region has also been located.     

Intrinsic and 1-aminonaphthalene-4-sulfonate-specific extrinsic lyoluminescences of X-ray irradiated sodium chloride

1-Aminonaphthalene-4-sulfonate (ANS)-specific extrinsic lyoluminescence (LL) of X-ray irradiated sodium chloride is observed at 425 nm when the irradiated salt is dissolved in an aqueous solution of ANS. The paper discusses, in detail, the mechanism of the ANS-specific LL and its analytical applicability. Also, the intrinsic LL of X-ray irradiated sodium chloride is studied. Hydrated electron as well as hole scavenger experiments support the proposal that in the case of the intrinsic LL of X-ray irradiated sodium chloride, trapped electrons (mainly F-center electrons) are released and hydrated whereas trapped holes (V-centers) remain surface-bound and are only partially hydrated before recombination occurs. These hydrated electrons and dissolving solid surface-bound hole centers, which are probably only partially hydrated, are able to act as reducing and oxidizing agents, respectively, in the luminophore oxidation-initiated reductive excitation pathway of ANS. Solution additives (halides and pseudohalides) show that in the chemiluminescence processes in question, oxidizing agents will follow the Marcus theory of electron transfer reactions. The LL method described allows the determination of ANS in the concentration range ≈10⁻¹¹ − 10⁻⁷ M. This suggests that aminonaphthalene derivatives can be used as label molecules in high sensitivity lyoluminobioaffinity assays.     

稀醋酸/水溶液中单个醋酸与水分子的氢键结构

在醋酸/水体系的工业分离中,溶液中的氢键对分离效率有很大影响.本文采用两种第一性原理方法,即从头算分子动力学模拟(AIMD)和量子化学计算(QCC),对由单个醋酸和不同水分子所组成聚合体的氢键相互作用进行了研究,采用极化统一模型和自洽反应场模型计算得到了聚合体在水溶液中的热力学数据.从QCC计算的气相和水溶液中的聚合自由能表明六元环在两种状态下都为最优结构,热力学数据反映出的各种结构的相对稳定性与AIMD模拟的环分布符合得相当一致.研究表明,由于存在醋酸和水分子间的氢键作用,稀醋酸/水溶液中的醋酸分离要比在浓醋酸溶液中困难得多.     

Dye-sensitized solar cells based on TiO2-B nanobelt/TiO2 nanoparticle sandwich-type photoelectrodes with controllable nanobelt length

The TiO(2)-B nanobelt (NB)/TiO(2) nanoparticle (NP) sandwich-type structure photoelectrode, with controllable nanobelt length, has been used to fabricate high-efficiency dye-sensitized solar cells (DSSCs), which combine the advantages of the rapid electron transport in TiO(2)-B NBs and the high surface area of TiO(2) NPs. The results indicate that the sandwich-type photoelectrode achieves higher photoelectrical conversion efficiency when compared with the TiO(2) nanoparticulate electrode. Increasing the length of TiO(2)-B NBs has been demonstrated to improve the photoelectric conversion efficiency (η). DSSCs with the longest (10 μm) TiO(2)-B NBs yield the highest η of 7.94%. The interfacial electron transport of DSSCs with different lengths of TiO(2)-B NBs has been quantitatively investigated using the photovoltage transient and the electrochemical impedance spectra, which demonstrates that the DSSCs with longest TiO(2)-B NBs display the highest electron collection efficiency and the fastest interfacial electron transfer.     

Electrochemical Behavior of Alkali Metal Alcoholates (Alcoxides) on Mercury

Alkali metal alcoholates (alcoxides), which occur as admixtures to fresh samples of alkali borohydrides, cause catalytic evolution of hydrogen of the “presodium type” from aqueous solutions at mercury electrodes. The catalytically active form is presumably a short‐lived, particularly hydrated form of the alcoholate anion, adsorbed in a favorable orientation in the interface between negatively charged mercury and aqueous electrolyte solution. The atom, transferring hydrogen ions from the solution to the electrode, is here negatively charged oxygen, a rare case in electrolytic hydrogen evolution catalysis. The catalytic activity of alcoxides gradually dies out, as they are slowly hydrolyzed by air moisture.     

Dynamics of the Bulk Hydrated Electron from Many‐Body Wave‐Function Theory

The structure of the hydrated electron is a matter of debate as it evades direct experimental observation owing to the short life time and low concentrations of the species. Herein, the first molecular dynamics simulation of the bulk hydrated electron based on correlated wave‐function theory provides conclusive evidence in favor of a persistent tetrahedral cavity made up by four water molecules, and against the existence of stable non‐cavity structures. Such a cavity is formed within less than a picosecond after the addition of an excess electron to neat liquid water, with less regular cavities appearing as intermediates. The cavities are bound together by weak H?H bonds, the number of which correlates well with the number of coordinated water molecules, each type of cavity leaving a distinct spectroscopic signature. Simulations predict regions of negative spin density and a gyration radius that are both in agreement with experimental data.     

Independent pairs and Monte-Carlo simulations of the geminate recombination of solvated electrons in liquid-to-supercritical water

Independent pairs (IP) and Monte Carlo (MC) simulations are employed to model experimental femtosecond time-resolved pump-probe spectroscopic data on the geminate recombination dynamics of solvated electrons in liquid-to-supercritical water. The hydrated electron was created by two-photon ionization of the neat fluid with a total ionization energy of 9.3 eV. In both numerical approaches, the ejection length, , (i.e. the distance from the ionization core, at which the electron is thermally and spatially localized) is used as the primary adjustable fitting parameter that can bring both model simulations into quantitative agreement with the ultrafast kinetic experiment. The influence of the thermodynamic conditions on the ejection length and on the recombination mechanism is discussed. Whereas in the compressed liquid associated with a high dielectric constant (ε ≥ 20), the electron recombines predominantly with the OH radical, the dissociative recombination via charge neutralization with the hydronium cation takes over at small dielectric constants (ε < 20). The importance of charge-dipole interactions for Monte-Carlo simulations of the recombination reactions of the hydrated electrons in the low-permittivity region is stressed.     

Electrogenerated chemiluminescence induced by sequential hot electron and hole injection into aqueous electrolyte solution

Hole injection into aqueous electrolyte solution is proposed to occur when oxide-coated aluminum electrode is anodically pulse-polarized by a voltage pulse train containing sufficiently high-voltage anodic pulses. The effects of anodic pulses are studied by using an aromatic Tb(III) chelate as a probe known to produce intensive hot electron-induced electrochemiluminescence (HECL) with plain cathodic pulses and preoxidized electrodes. The presently studied system allows injection of hot electrons and holes successively into aqueous electrolyte solutions and can be utilized in detecting electrochemiluminescent labels in fully aqueous solutions, and actually, the system is suggested to be quite close to a pulse radiolysis system providing hydrated electrons and hydroxyl radicals as the primary radicals in aqueous solution without the problems and hazards of ionizing radiation. The analytical power of the present excitation waveforms are that they allow detection of electrochemiluminescent labels at very low detection limits in bioaffinity assays such as in immunoassays or DNA probe assays. The two important properties of the present waveforms are: (i) they provide in situ oxidation of the electrode surface resulting in the desired oxide film thickness and (ii) they can provide one-electron oxidants for the system by hole injection either via F- and F⁺-center band of the oxide or by direct hole injection to valence band of water at highly anodic pulse amplitudes.