Notes

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Time-resolved studies have so far relied on rapidly triggering a photo-induced dynamic in chemical or biological ions or molecules and subsequently probing them with a beam of fast moving photons or electrons that crosses the studied samples in a short period of time. Hence, the time resolution of the signal is mainly set by the pulse duration of the pump and probe pulses. In this paper, we propose a different approach to this problem that has the potential to consistently achieve orders of magnitude higher time resolutions than what is possible with laser technology or electron beam compression methods. Our proposed approach relies on accelerating the sample to a high speed to achieve relativistic time dilation. Probing the time-dilated sample would open up previously inaccessible time resolution domains.Encoding the complex features of an energy landscape is a challenging task, and often, chemists pursue the most salient features (minima and barriers) along a highly reduced space, i.e., two- or three-dimensions. Even though disconnectivity graphs or merge trees summarize the connectivity of the local minima of an energy landscape via the lowest-barrier pathways, there is much information to be gained by also considering the topology of each connected component at different energy thresholds (or sublevelsets). We propose sublevelset persistent homology as an appropriate tool for this purpose. Our computations on the configuration phase space of n-alkanes from butane to octane allow us to conjecture, and then prove, a complete characterization of the sublevelset persistent homology of the alkane CmH2m+2 Potential Energy Landscapes (PELs), for all m, in all homological dimensions. We further compare both the analytical configurational PELs and sampled data from molecular dynamics simulation using the united and all-atom descriptions of the intramolecular interactions. In turn, this supports the application of distance metrics to quantify sampling fidelity and lays the foundation for future work regarding new metrics that quantify differences between the topological features of high-dimensional energy landscapes.Gas adsorption is a standard method for measuring pore-size distributions of nanoporous materials. This method is often based on assuming the pores as separate entities of a certain simple shape slit-like, cylindrical, or spherical. Here, we study the effect of interconnections on gas adsorption in materials with spherical pores, such as three-dimensionally ordered mesoporous (3DOm) carbons. We consider interconnected systems with two, four, and six windows of various sizes. We propose a simple method based on the integration of solid-fluid interactions to take into account these windows. We used Monte Carlo simulations to model argon adsorption at the normal boiling point and obtained adsorption isotherms for the range of systems. For a system with two windows, we obtained a remarkably smooth transition from the spherical to cylindrical isotherm. Depending on the size and number of windows, our system resembles both spherical and cylindrical pores. These windows can drastically shift the point of capillary condensation and result in pore-size distributions that are very different from the ones based on a spherical pore model. Our results can be further used for modeling fluids in a system of interconnected pores using Monte Carlo and density functional theory methods.Sequential formation of a poly-cyclic aromatic hydrocarbon (PAH) dication in the H I regions of the interstellar medium (ISM) is proposed to be a function of internal energy of the doubly ionized PAHs, which, in turn, is dependent on the single- and double-ionization potentials of the system. This sets a limit on the single- and double-ionization energies of the system(s) that can further undergo sequential absorption of two photons, leading to a dication (PAH+2). Here, we report the single-ionization (I+1) and double-ionization (I+2) energies and the I+2/I+1 ratio for some selected PAHs and conjugated polyenes obtained using the Fock space coupled cluster technique, enabling simultaneous consideration of several electronic states of different characters. The I+2 to I+1 ratio bears a constant ratio, giving allowance to determine I+2 from the knowledge of single-ionization (I+1) and vice versa. Our observations are in good agreement with the established literature findings, confirming the reliability of our estimates. The measured single- and double-ionization energies further demonstrate that the sequential formation and fragmentation of a PAH dication in the H I regions of the ISM for systems such as benzene and conjugated polyenes such as ethylene and butadiene are quite unlikely because I+2-I+1 for such system(s) is higher than the available photon energy in the H I regions of the ISM. Present findings may be useful to understand the formation and underlying decay mechanisms of multiply charged ions from PAHs and related compounds that may accentuate the exploration of the phenomenon of high-temperature superconductivity.Limitations of the DFT+U approach (e.g., in Dudarev's formulation) applied for accurate evaluation of redox potentials of cathode materials of alkali-ion batteries with U parameters calculated via the linear response (LR) method are discussed. In contrast to our previous studies, where redox potentials of several cathode materials have been calculated in a good agreement with experiment (e.g., NaMnO2, LiFePO4, and LiTiS2), herein, we analyze other cathode materials, such as LiNiO2 and Ni- and V-containing phosphates for which this method provides much underestimated redox voltages. We ascribe this limited predictive power of the DFT+U method, parameterized via LR, to the absence of corrections of Coulomb interactions between the electrons with opposite spins. Using the recently proposed extended DFT+U+U↑↓ functional, which includes the aforementioned corrections, we show how redox potentials of Ni- and V-based compounds could be calculated in a much better agreement with experiment, also proposing a procedure of parameterization of such calculations. Thus, our extended method allows us to calculate redox potentials of several important materials more accurately while retaining good agreement with experiment for structures where the standard DFT+U method also accurately predicts electrochemical properties.We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. These species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.We show how to construct a linearly independent set of antisymmetrized geminal power (AGP) states, which allows us to rewrite our recently introduced geminal replacement models as linear combinations of non-orthogonal AGPs. This greatly simplifies the evaluation of matrix elements and permits us to introduce an AGP-based selective configuration interaction method, which can reach arbitrary excitation levels relative to a reference AGP, balancing accuracy and cost as we see fit.Ultra-fast and multi-dimensional spectroscopy gives a powerful looking glass into the dynamics of molecular systems. In particular, two-dimensional electronic spectroscopy (2DES) provides a probe of coherence and the flow of energy within quantum systems, which is not possible with more conventional techniques. While heterodyne-detected (HD) 2DES is increasingly common, more recently fluorescence-detected (FD) 2DES offers new opportunities, including single-molecule experiments. However, in both techniques, it can be difficult to unambiguously identify the pathways that dominate the signal. Therefore, the use of numerically modeling of 2DES is vitally important, which, in turn, requires approximating the pulsing scheme to some degree. Here, we employ non-perturbative time evolution to investigate the effects of finite pulse width and amplitude on 2DES signals. In doing so, we identify key differences in the response of HD and FD detection schemes, as well as the regions of parameter space where the signal is obscured by unwanted artifacts in either technique. Mapping out parameter space in this way provides a guide to choosing experimental conditions and also shows in which limits the usual theoretical approximations work well and in which limits more sophisticated approaches are required.Physically motivated and mathematically robust atom-centered representations of molecular structures are key to the success of modern atomistic machine learning. They lie at the foundation of a wide range of methods to predict the properties of both materials and molecules and to explore and visualize their chemical structures and compositions. Recently, it has become clear that many of the most effective representations share a fundamental formal connection. Phenol Red sodium They can all be expressed as a discretization of n-body correlation functions of the local atom density, suggesting the opportunity of standardizing and, more importantly, optimizing their evaluation. We present an implementation, named librascal, whose modular design lends itself both to developing refinements to the density-based formalism and to rapid prototyping for new developments of rotationally equivariant atomistic representations. As an example, we discuss smooth overlap of atomic position (SOAP) features, perhaps the most widely used member of this family of representations, to show how the expansion of the local density can be optimized for any choice of radial basis sets. We discuss the representation in the context of a kernel ridge regression model, commonly used with SOAP features, and analyze how the computational effort scales for each of the individual steps of the calculation. By applying data reduction techniques in feature space, we show how to reduce the total computational cost by a factor of up to 4 without affecting the model's symmetry properties and without significantly impacting its accuracy.In this Note, we study the total conservative force instead of pure electrostatic force as it was carried out in the work by Gavrilov [J. Chem. Phys. 152, 164101 (2020)] acting on two charges in a polar liquid using dissipative particle dynamics and coarse-grained molecular dynamics simulations. We show that such force (instead of the electrostatic force) obeys Coulomb's law at large distances between the charges. Apparently, the dielectric response of a polar liquid (at least, within such coarse-grained models) can be decomposed into two contributions the reorientation of the dipoles (i.e., electrostatic contribution) and the density redistribution (i.e., volume interaction contribution).
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