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Here, extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events are presented. The species-selective algorithm, where the nanoreactor effectively works for the selected desired reactants, was introduced to the original scheme. Moreover, for efficient simulations of large model systems with the modified approach, the divide-and-conquer linear-scaling density functional tight-binding method was exploited. Two illustrative applications of the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions indicate that species-selective quantum chemical nanoreactor molecular dynamics is a promising method to accelerate the sampling of multicomponent chemical processes proceeding under relatively mild conditions. [ABSTRACT FROM AUTHOR]

Glutaredoxins are small enzymes that catalyze the oxidation and reduction of protein disulfide bonds by the thiol–disulfide exchange mechanism. They have either one or two cysteines in their active site, resulting in different catalytic reaction cycles that have been investigated in many experimental studies. However, the exact mechanisms are not yet fully known, and to our knowledge, no theoretical studies have been performed to elucidate the underlying mechanism. In this study, we investigated a proposed mechanism for the reduction of the disulfide bond in the protein HMA4n by a mutated monothiol Homo sapiens glutaredoxin and the co-substrate glutathione. The catalytic cycle involves three successive thiol–disulfide exchanges that occur between the molecules. To estimate the regioselectivity of the different attacks, classical molecular dynamics simulations were performed and the trajectories analyzed regarding the sulfur–sulfur distances and the attack angles between the sulfurs. The free energy profile of each reaction was obtained with hybrid quantum mechanical/molecular mechanical metadynamics simulations. Since this required extensive phase space sampling, the semi-empirical density functional tight-binding method was used to describe the reactive cysteines. For an accurate description, we used specific reaction parameters fitted to B3LYP energies of the thiol–disulfide exchange and a machine learned energy correction that was trained on coupled-cluster single double perturbative triple [CCSD(T)] energies of thiol–disulfide exchanges. Our calculations show the same regiospecificity as observed in the experiment, and the obtained barrier heights are about 12 and 20 kcal/mol for the different reaction steps, which confirms the proposed pathway. [ABSTRACT FROM AUTHOR]

Nonadiabatic excited state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, and charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamics (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. The nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Furthermore, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well to those obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials. [ABSTRACT FROM AUTHOR]

The clustering, collision, and relaxation dynamics of pristine and doped helium nanodroplets is theoretically investigated in cases of pickup and clustering of heliophilic argon, collision of heliophobic cesium atoms, and coalescence of two droplets brought into contact by their mutual long-range van der Waals interaction. Three approaches are used and compared with each other. The He time-dependent density functional theory method considers the droplet as a continuous medium and accounts for its superfluid character. The ring-polymer molecular dynamics method uses a path-integral description of nuclear motion and incorporates zero-point delocalization while bosonic exchange effects are ignored. Finally, the zero-point averaged dynamics approach is a mixed quantum–classical method in which quantum delocalization is described by attaching a frozen wavefunction to each He atom, equivalent to classical dynamics with effective interaction potentials. All three methods predict that the growth of argon clusters is significantly hindered by the helium host droplet due to the impeding shell structure around the dopants and kinematic effects freezing the growing cluster in metastable configurations. The effects of superfluidity are qualitatively manifested by different collision dynamics of the heliophilic atom at high velocities, as well as quadrupole oscillations that are not seen with particle-based methods, for droplets experiencing a collision with cesium atoms or merging with each other. [ABSTRACT FROM AUTHOR]

The structure of the double-layer formed at the surface of carbon electrodes is governed by the interactions between the electrode and the electrolyte species. However, carbon is notoriously difficult to simulate accurately, even with well-established methods such as electronic density functional theory and molecular dynamics. Here, we focus on the important case of a lithium ion in contact with the surface of graphite, and we perform a series of reference quantum Monte Carlo calculations that allow us to benchmark various electronic density functional theory functionals. We then fit an accurate carbon–lithium pair potential, which is used in molecular density functional theory calculations to determine the free energy of the adsorption of the ion on the surface in the presence of water. The adsorption profile in aqueous solution differs markedly from the gas phase results, which emphasize the role of the solvent on the properties of the double-layer. [ABSTRACT FROM AUTHOR]

We study nonideal mixing effects in the regime of warm dense matter (WDM) by computing the shock Hugoniot curves of BN, MgO, and MgSiO3. First, we derive these curves from the equations of state (EOS) of the fully interacting systems, which were obtained using a combination of path integral Monte Carlo calculations at high temperature and density functional molecular dynamics simulations at lower temperatures. We then use the ideal mixing approximation at constant pressure and temperature to rederive these Hugoniot curves from the EOS tables of the individual elements. We find that the linear mixing approximation works remarkably well at temperatures above ∼2 × 105 K, where the shock compression ratio exceeds ∼3.2. The shape of the Hugoniot curve of each compound is well reproduced. Regions of increased shock compression, which emerge because of the ionization of L and K shell electrons, are well represented, and the maximum compression ratio of the Hugoniot curves is reproduced with high precision. Some deviations are seen near the onset of the L shell ionization regime, where ionization equilibrium in the fully interacting system cannot be well reproduced by the ideal mixing approximation. This approximation also breaks down at lower temperatures, where chemical bonds play an increasingly important role. However, the results imply that the equilibrium properties of binary and ternary mixtures in the regime of WDM can be derived from the EOS tables of the individual elements. This significantly simplifies the characterization of binary and ternary mixtures in the WDM and plasma phases, which otherwise requires large numbers of more computationally expensive first-principles computer simulations. [ABSTRACT FROM AUTHOR]

Plane wave basis sets offer many advantages in ab initio molecular dynamics due to their efficiency and simplicity. In combination with hybrid density functionals, they become computationally expensive due to the evaluation of the Hartree-Fock exchange energy. The computational cost can be significantly reduced by screening the Kohn-Sham orbital products after localizing the orbitals in real space. However, such a procedure introduces apparent errors in the wavefunctions and nuclear forces resulting in unstable dynamics. It is shown here that a noise-stabilized dynamics approach can overcome this problem and at the same time permits using insufficiently converged wavefunctions for evaluating atomic forces. In this way, we achieve significant speed up even for a small system containing about 100 atoms. After benchmarking the accuracy and efficiency of this approach, we use it in combination with well-sliced metadynamics to compute the free energy barrier of formamide hydrolysis in alkaline aqueous medium. These results provide insight into the error of the Perdew-Burke-Ernzerhof functional in predicting the free energy barrier for hydrolysis reactions in water. [ABSTRACT FROM AUTHOR]

In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionalsvdW-DF,vdW-DF2, optPBE-vdW, optB88- vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize thewater-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment. [ABSTRACT FROM AUTHOR]

Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD. [ABSTRACT FROM AUTHOR]

The structural properties of a-HfO2/Ge(2 × 1)-(001) and a-ZrO2/Ge(2 × 1)-(001) interfaces were investigated with and without a GeOx interface interlayer using density-functional theory (DFT) molecular dynamics (MD) simulations. Realistic a-HfO2 and a-ZrO2 samples were generated using a hybrid classical-DFT MD "melt-and-quench" approach and tested against experimental properties. The oxide/Ge stacks were annealed at 700 K, cooled to 0 K, and relaxed providing the system withenough freedom toform realistic interfaces. For each high-K/Ge stack type, two systems with single and double interfaces were investigated. All stacks were free of midgap states; however, stacks with a GeOx interlayer had band-edge states which decreased the band gaps by 0%-30%. These band-edge states were mainly produced by under-coordinated Ge atoms in GeOx layer or its vicinity due to deformation, intermixing, and bond-breaking. The DFT-MD simulations show that electronically passive interfaces can be formed either directly between high-K dielectrics and Ge or with a monolayer of GeO2 if the processing does not create or properly passivate under-coordinated Ge atoms and Ge's with significantly distorted bonding angles. Comparison to the charge states of the interfacial atoms from DFT to experimental x-ray photoelectron spectroscopy results shows that while most studies of gate oxide on Ge(001) have a GeOx interfacial layer, it is possible toform an oxide/Ge interface without a GeOx interfacial layer. Comparison to experiments is consistent with the dangling bonds in the suboxide being responsible for midgap state formation. [ABSTRACT FROM AUTHOR]