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Inverse design strategies have proven highly useful for the discovery of interaction potentials that prompt self-assembly of a variety of interesting structures. However, often the optimized particle interactions do not have a direct relationship to experimental systems. In this work, we show that Relative Entropy minimization is able to discover physically meaningful parameter sets for a model interaction built from depletion attraction and electrostatic repulsion that yield self-assembly of size-specific clusters. We then explore the sensitivity of the optimized interaction potentials with respect to deviations in the underlying physical quantities, showing that clustering behavior is largely preserved even as the optimized parameters are perturbed.Confinement has been shown to contribute to the dynamics of small molecules within nanoscale hydrophobic or hydrophilic cavities. Enclosure within a confined space can also influence energy transfer pathways, such as the enhancement of fluorescence over thermal relaxation. In this paper, the effect of confinement on the thermodynamic properties and reaction kinetics of small hydrophobic molecules confined in a soft polymeric template is detailed. A quasi-elastic neutron scattering experiment identified a substantial decrease in translational diffusion of pyrrole after solubilization within a hydrophobic cavity. This decrease in mobility is due to pyrrole's closer packing and increased density under confinement vs the bulk liquid. The decreased mobility and increased density explain the spontaneous polymerization reaction of pyrrole observed within the cavity. The precise characterization of the polymerization kinetics under confinement found that the reaction is independent of pyrrole concentration, consistent with the close packing density. Kinetic data also show that confinement dimensionality finds a thermodynamic expression in the transition state entropy. The dynamics and kinetics experiments reported here offer rare empirical insight into the important influence that cavity geometry places on the reactions they host.Microcanonical ensemble (NVE) Molecular Dynamics (MD) computer simulations are performed with negligible energy drift for systems incorporating Coulomb interactions and complex constraint schemes. In principle, such systems can now be simulated in the NVE ensemble for millisecond time scales, with no requirement for system thermostatting. Numerical tools for assessing drift in MD simulations are outlined, and drift rates of 10-6 K/μs are demonstrated for molten salts, polar liquids, and room temperature ionic liquids. Such drift rates are six orders of magnitude smaller than those typically quoted in the literature. To achieve this, the standard Ewald method is slightly modified so the first four derivatives of the real space terms go smoothly to zero at the truncation distance, rc. New methods for determining standard Ewald errors and the new perturbation errors introduced by the smoothing procedure are developed and applied, these taking charge correlation effects explicitly into account. The shadow Hamiltonian, Es, is shown to be the strictly conserved quantity in these systems, and standard errors in the mean of one part in 1010 are routinely calculated. Expressions for the shadow Hamiltonian are improved over previous work by accounting for O(h4) terms, where h is the MD time step. These improvements are demonstrated by means of extreme out-of-equilibrium simulations. Using the new methodology, the very low diffusion coefficients of room temperature 1-hexyl-3-methyl-imidazolium chloride are determined from long NVE trajectories in which the equations of motion are known to be integrated correctly, with negligible drift.Under numerous circumstances, many soft and hard materials are present in a puzzling wealth of non-equilibrium amorphous states, whose properties are not stationary and depend on preparation. They are often summarized in unconventional "phase diagrams" that exhibit new "phases" and/or "transitions" in which time, however, is an essential variable. This work proposes a solution to the problem of theoretically defining and predicting these non-equilibrium phases and their time-evolving phase diagrams, given the underlying molecular interactions. We demonstrate that these non-equilibrium phases and the corresponding non-stationary (i.e., aging) phase diagrams can indeed be defined and predicted using the kinetic perspective of a novel non-equilibrium statistical mechanical theory of irreversible processes. This is illustrated with the theoretical description of the transient process of dynamic arrest into non-equilibrium amorphous solid phases of an instantaneously quenched simple model fluid involving repulsive hard-sphere plus attractive square well pair interactions.Atomistic simulations based on the first-principles of quantum mechanics are reaching unprecedented length scales. This progress is due to the growth in computational power allied with the development of new methodologies that allow the treatment of electrons and nuclei as quantum particles. In the realm of materials science, where the quest for desirable emergent properties relies increasingly on soft weakly bonded materials, such methods have become indispensable. In this Perspective, an overview of simulation methods that are applicable for large system sizes and that can capture the quantum nature of electrons and nuclei in the adiabatic approximation is given. In addition, the remaining challenges are discussed, especially regarding the inclusion of nuclear quantum effects (NQEs) beyond a harmonic or perturbative treatment, the impact of NQEs on electronic properties of weakly bonded systems, and how different first-principles potential energy surfaces can change the impact of NQEs on the atomic structure and dynamics of weakly bonded systems.The anisotropy of molecular polarizability in liquid crystals is linked to the birefringence in these substances. The classic methods to compute the polarizabilities of liquid crystals assume an average number density of molecules that is equal in all directions. In the present work, a new model is proposed for the anisotropic molar polarization based on a virtual anisotropy of the number density of molecules in the liquid-crystalline material. This new strategy hence allows for the computation of both the anisotropic polarizabilities and the anisotropic thermal-expansion coefficients of liquid crystals. The model is applied to the liquid crystals 4-n-pentyl-4'-cyanobiphenyl and N-(4-methoxybenzylidene)-4-butylaniline, yielding polarizabilities similar to those reported for these materials. For these nematic liquid crystals, the results imply the existence of a positive thermal-expansion coefficient in the direction perpendicular to the director vector throughout the entire nematic temperature range and a negative thermal-expansion coefficient parallel to the director vector near the temperature of the nematic-isotropic transition. At the isotropization temperature, there exists divergent and critical behavior of the anisotropic thermal-expansion coefficients, consistent with the typical discontinuity of volume in first-order transitions.A Heisenberg uncertainty relation is derived for spatially-gated electric ΔE and magnetic ΔH field fluctuations. The uncertainty increases for small gating sizes, which implies that in confined spaces, the quantum nature of the electromagnetic field must be taken into account. Optimizing the state of light to minimize ΔE at the expense of ΔH and vice versa should be possible. Spatial confinements and quantum fields may alternatively be realized without gating by interaction of the field with a nanostructure. Possible applications include nonlinear spectroscopy of nanostructures and optical cavities and chiral signals.Magnesium and calcium play an essential role in the folding and function of nucleic acids. To correctly describe their interactions with DNA and RNA in biomolecular simulations, an accurate parameterization is crucial. In most cases, the ion parameters are optimized based on a set of experimental solution properties such as solvation free energies, radial distribution functions, water exchange rates, and activity coefficient derivatives. However, the transferability of such bulk-optimized ion parameters to quantitatively describe biomolecular systems is limited. Here, we extend the applicability of our previous bulk-optimized parameters by including experimental binding affinities toward the phosphate oxygen on nucleic acids. In particular, we systematically adjust the combination rules that are an integral part of the pairwise interaction potentials of classical force fields. This allows us to quantitatively describe specific ion binding to nucleic acids without changing the solution properties in the most simple and efficient way. We show the advancement of the optimized Lorentz combination rule for two representative nucleic acid systems. For double-stranded DNA, the optimized combination rule for Ca2+ significantly improves the agreement with experiments, while the standard combination rule leads to unrealistically distorted DNA structures. For the add A-riboswitch, the optimized combination rule for Mg2+ improves the structure of two specifically bound Mg2+ ions as judged by the experimental distance to the binding site. Including experimental binding affinities toward specific ion binding sites on biomolecules, therefore, provides a promising perspective to develop a more accurate description of metal cations for biomolecular simulations.Single-atom alloys (SAAs) have recently gained considerable attention in the field of heterogeneous catalysis research due to their potential for novel catalytic properties. While SAAs are often examined in reactions of reductive atmospheres, such as hydrogenation reactions, in the present work, we change the focus to AgPd SAAs in oxidative environments since Pd has the highest catalytic activity of all metals for oxidative reactions. Here, we examine how the chemical reactivity of AgPd SAAs differs from its constituent Pd in an oxidative atmosphere. For this purpose, electronic structure changes in an Ag0.98Pd0.02 SAA foil in 1 mbar of O2 were studied by in situ x-ray photoemission spectroscopy and compared with the electronic structure of a Pd foil under the same conditions. When heated in an oxidative atmosphere, Pd in Ag0.98Pd0.02 partly oxidizes and forms a metastable PdOx surface oxide. By using a peak area modeling procedure, we conclude that PdOx on Ag0.98Pd0.02 is present as thin, possibly monolayer thick, PdOx islands on the surface. In comparison to the PdO formed on the Pd foil, the PdOx formed on AgPd is substantially less thermodynamically stable, decomposing at temperatures about 270 °C lower than the native oxide on Pd. Acalabrutinib nmr Such behavior is an interesting property of oxides formed on dilute alloys, which could be potentially utilized in catalytic oxidative reactions such as methane oxidation.The development of a single-atom iron catalyst (Fe©SiO2) for the direct conversion of methane to olefins, aromatics, and hydrogen is a breakthrough in the field of nonoxidative conversion of methane (NCM). However, the optimization of the catalyst remains desirable for industrial applications. Herein, 25 transition metals, including Sc, Ti, V, Cr, Mn, Co, Ni, Cu, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Hf, Ta, W, Re, Os, Ir, Pt, and Au, are selected to replace the central Fe atom for screening out better single-atom catalysts for the NCM. Using the performance on the activation of methane, such as the adsorption energy of methane, the dissociation energy, and the barrier of methane as the screening descriptors, Mn©SiO2, Fe©SiO2, W©SiO2, and Re©SiO2 are first screened out. The remarkable performance of the four catalysts on methane activation is attributed to the unique geometric structure and the dz 2 orbitals of the central metal crossing over the Fermi level, which can benefit the interaction between methane and the catalysts.