Excess electron capture by hydrated histidine side-chain group

In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

In the paper, the ORR/OER on graphene-supported nitrogen coordinated Ru-atom (Ru-N-C) is simulated. We discuss nitrogen coordination influences electronic properties, adsorption energies, and catalytic activity in a single-atom Ru active site. The over potentials on Ru-N-C are 1.12 eV/1.00 eV for ORR/OER. We calculate Gibbs-free energy (ΔG) for every reaction step in ORR/OER process. In order to gain a deeper understanding of the catalytic process on the surface of single atom catalysts, the ab initio molecular dynamics (AIMD) simulations show that Ru-N-C has a structural stability at 300 K and that ORR/OER on Ru-N-C can occur along a typical four-electron process of reaction. AIMD simulations of catalytic processes provide detailed information about atom interactions. In this paper, we use density functional theory (DFT) with PBE functional to study the electronic properties and adsorption properties of graphene-supported nitrogen coordinated Ru-atom (Ru-N-C) Gibbs-free energy and Gibbs-free energy for very reaction step. The structural optimization and all the calculations are carried out by Dmol3 package, adopting the PNT basis set and DFT semicore pseudopotential. Ab initio molecular dynamics simulations (AIMD) were run for 10 ps. The canonical (NVT) ensemble, massive GGM thermostat, and a temperature of 300 K are taken into account. The functional of B3LYP and the DNP basis set are chosen for AIMD.

We examine the effect of equilibration methodology and sampling on ab initio molecular dynamics (AIMD) simulations of systems of common solvents and salts found in lithium-oxygen batteries. We compare two equilibration methods: (1) using an AIMD temperature ramp and (2) using a classical MD simulation followed by a short AIMD simulation both at the target simulation temperature of 300 K. We also compare two different classical all-atom force fields: PCFF+ and OPLS. By comparing the simulated association/dissociation behavior of lithium salts in different solvents with the experimental behavior, we find that equilibration with the classical force field that produces more physically accurate behavior in the classical MD simulations, namely, OPLS, also results in more physically accurate behavior in the AIMD runs compared to equilibration with PCFF+ or with the AIMD temperature ramp. Equilibration with OPLS outperforms even the pure AIMD equilibration because the classical MD equilibration is much longer than the AIMD equilibration (nanosecond vs picosecond timescales). These longer classical simulations allow the systems to find a more physically accurate initial configuration, and in the short simulation times available for the AIMD production runs, the initial configuration has a large impact on the system behavior. We also demonstrate the importance of averaging coordination number over multiple starting configurations and Li+ ions, as the majority of Li+ ions do not undergo a single association or dissociation event even in an ∼40 ps long simulation and thus do not sample a statistically significant portion of the phase space. These results show the importance of both equilibration method and sufficient independent sampling for extracting experimentally relevant quantities from AIMD simulations.

We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately.

The shock response of fully-dense and porous crystalline tellurium dioxide (TeO2) to the high-pressure and high-temperature fluid regime was investigated within the framework of density functional theory with Mermin’s generalization to finite temperatures. The principal and porous shock Hugoniot curves were predicted from canonical ab initio molecular dynamics (AIMD) simulations, with the phase space sampled along isotherms up to 80 000 K, for densities ranging from ρ=3 to 17 g/cm3. The polymorphs investigated are α-TeO2 paratellurite (P41212), TeO2 cotunnite (Pnma), and TeO2 post-cotunnite (P21/m). Based on the discontinuity found in the calculated Us−up slope of TeO2 post-cotunnite at a shock velocity of Us≃8.35 km/s and a particle velocity of up≃3.64 km/s, the shock melting temperature and pressure are predicted to be ≃6500 K and ≃170 GPa. Results from the AIMD simulations are in line with the static compression data of TeO2 paratellurite and cotunnite, and with the recent shock Hugoniot data for single-crystal α-TeO2 for pressures up to 85 GPa, obtained using the inclined-mirror method and the velocity interferometer system for any reflector combined with powder gun and two-stage light-gas gun.

Interpolating Moving Ridge Regression (IMRR): A machine learning algorithm to predict energy gradients for ab initio molecular dynamics simulations

Recent advances in synthesis and characterization methods have enabled the controllable fabrication of atomically precise metal clusters (AMCs) of subnanometer size that possess unique physical and chemical properties, yet to be explored. Such AMCs have potential applications in a wide range of fields, from luminescence and sensing to photocatalysis and bioimaging, making them highly desirable for further research. Therefore, there is a need to develop innovative methods to stabilize AMCs upon surface deposition, as their special properties are lost due to sintering into larger nanoparticles. To this end, dispersion-corrected density functional theory (DFT-D3) and ab initio molecular dynamics (AIMD) simulations have been employed. Benchmarking against high-level post-Hartree-Fock approaches revealed that the DFT-D3 scheme describes very well the lowest-energy states of clusters of five and ten atoms, Cu5 and Cu10. AIMD simulations performed at 400 K illustrate how intrinsic defects of graphene sheets, carbon vacancies, are capable of confining individual Cu5 clusters, thus allowing for their stabilization. Furthermore, AIMD simulations provide evidence on the dimerization of Cu5 clusters on defect-free graphene, in agreement with the ab initio predictions of (Cu5)n aggregation in the gas phase. The findings of this study demonstrate the potential of using graphene-based substrates as an effective platform for the stabilization of monodisperse atomically precise Cu5 clusters.

The melting curve of the hexagonal close-packed (hcp) phase of lead (Pb) has been determined over a wide pressure range using both ab initio molecular dynamics (AIMD) simulations and classical molecular dynamics (CMD) employing an effective pair potential. The AIMD simulations are based on a density functional theory (DFT) in the generalized gradient approximation (GGA). The Pb melting curve, constructed using a well-established theoretical scheme, is in excellent agreement with the AIMD results. Our calculated equation of state (EOS) of hcp Pb is in excellent agreement with experimental data up to $40\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$. Our melting curve agrees very well with melting temperatures obtained in both shock-wave and diamond-anvil cell (DAC) experiments, but at higher pressures our curve lies between the two data sets.

The performance of water electrolysis is largely limited by the sluggish oxygen evolution reaction (OER). To design and engineer electrocatalysts with higher and higher activity, the first step is to identify catalytic active phases and reaction mechanisms. In this presentation, I will delve into the active phases and reaction mechanics of OER on Ni-based oxyhydroxides in alkaline media. I will show that under extremely oxidative conditions, the active phases are typically not as-prepared precursor phases, as an oxidative phase transition may occur. I identified the atomic-scale structure and electronic structures of active phases through ab initio molecular dynamics simulation and XANES simulation at the O k edge. The predicted structure and electronic structures were confirmed by operando wide-angle X-ray scatting measurement and XNAES measurement at the O k edge. We further found that, under OER conditions, surfaces are not pristine but are in equilibrium with the electrolyte and electrode potential, i.e., they are covered by reaction intermediates. Thus, OER goes through Mars van Krevelen mechanics, rather than traditionally assumed Langmuir-hinshelwood mechanics. Also, active sites can be described by a synergistic dual-metal reaction center. This center is characterized by switching active sites during OER, and through simple surface Fe doping and the formation of dual Fe-Fe centers, they increase OER activity by over two orders of magnitude. This fundamental understanding not only elucidates the high OER activity of Ni (oxy)hydroxides with Fe-doping but also provides principles for developing OER catalysts with further improved performance. If time permits, I will also introduce our recent work in acidic water electrolysis.

Static ion structure factor for dense plasmas: Semi-classical and ab initio calculations

Calcium batteries are rapidly emerging as a potential, future energy storage technology; however, their advancement relies heavily on understanding of the liquid electrolyte component in terms of stability and interactions with a calcium metal anode. Tetrahydrofuran, a cyclic ether, is an experimentally common and promising solvent for the preparation of stable and efficient calcium electrolytes. However, insights into the reasons why are lacking, which could unveil key principles to electrolyte design. In this report, we provide a theoretical study employing ab initio molecular dynamics (AIMD) simulations of the interactions of Ca metal with the cyclic ether tetrahydrofuran (THF). The results show that the electrochemical breakdown and decomposition of THF at the Ca surface is highly orientation- and surface-site dependent, thereby significantly reducing the likelihood of its instability in a randomly organized bulk solvent. Likewise, in bulk electrolytes, its likelihood for breakdown is further diminished, in preference for coordination Ca2+ to form solvated structure. Hence, the finding that molecules require such strict conditions for their decomposition is an important selection and design principle for any solvent to prepare suitable calcium electrolytes. These findings are critical to the advancement of the calcium batteries.

The development of sodium ion batteries (NIBs) can provide an alternative to lithium ion batteries (LIBs) for sustainable, low-cost energy storage. However, due to the larger size and higher m/e ratio of the sodium ion compared to lithium, sodiation reactions of candidate electrodes are expected to differ in significant ways from the corresponding lithium ones. In this work, we investigated the sodiation mechanism of a typical transition metal-oxide, NiO, through a set of correlated techniques, including electrochemical and synchrotron studies, real-time electron microscopy observation, and ab initio molecular dynamics (MD) simulations. We found that a crystalline Na2O reaction layer that was formed at the beginning of sodiation plays an important role in blocking the further transport of sodium ions. In addition, sodiation in NiO exhibits a "shrinking-core" mode that results from a layer-by-layer reaction, as identified by ab initio MD simulations. For lithiation, however, the formation of Li antisite defects significantly distorts the local NiO lattice that facilitates Li insertion, thus enhancing the overall reaction rate. These observations delineate the mechanistic difference between sodiation and lithiation in metal-oxide conversion materials. More importantly, our findings identify the importance of understanding the role of reaction layers on the functioning of electrodes and thus provide critical insights into further optimizing NIB materials through surface engineering.

We report investigation of phonons and oxygen diffusion in Bi2O3 and (Bi0.7Y0.3)2O3. The phonon spectra have been measured in Bi2O3 at high temperatures up to 1083 K using inelastic neutron scattering. Ab initio calculations have been used to compute the individual contributions of the constituent atoms in Bi2O3 and (Bi0.7Y0.3)2O3 to the total phonon density of states. Our computed results indicate that as temperature is increased, there is a complete loss of sharp peak structure in the vibrational density of states. Ab initio molecular dynamics simulations show that even at 1000 K in δ-phase Bi2O3, Bi–Bi correlations remain ordered in the crystalline lattice while the correlations between O–O show liquid like disordered behavior. In the case of (Bi0.7Y0.3)2O3, the O–O correlations broadened at around 500 K indicating that oxygen conductivity is possible at such low temperatures in (Bi0.7Y0.3)2O3 although the conductivity is much less than that observed in the undoped high temperature δ-phase of Bi2O3. This result is consistent with the calculated diffusion coefficients of oxygen and observation by quasielastic neutron scattering experiments. Our ab initio molecular dynamics calculations predict that macroscopic diffusion is attainable in (Bi0.7Y0.3)2O3 at much lower temperatures, which is more suited for technological applications. Our studies elucidate the easy directions of diffusion in δ-Bi2O3 and (Bi0.7Y0.3)2O3.

The conformational preference of the glycosidic linkage of methyl-beta-mannose was studied in the gas phase and in aqueous solution by ab initio calculations, and by molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) simulations. MD simulations were performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in solution. This study shows that the trans (t) orientation of the glycosidic linkage of methyl-beta-mannose is preferred over its gauche clockwise (g+) orientation in solution. CPMD simulations clearly indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by MD simulations. This study demonstrates the importance of ab initio molecular dynamics simulations in studying the structural properties of carbohydrate-water interactions.

Collision reactions between the cyano radical (CN) and unsaturated hydrocarbons (C2H2), which occur in the atmosphere of Saturn’s moon Titan, were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short‐time Fourier transform analysis of velocity auto‐correlation functions obtained by the AIMD simulations was performed to examine the non‐equilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states.