Sykesgilbert5650

A novel energy decomposition analysis scheme, named DFTB-EDA, is proposed based on the density functional based tight-binding method (DFTB/TD-DFTB), which is a semi-empirical quantum mechanical method based on Kohn-Sham-DFT for large-scale calculations. In DFTB-EDA, the total interaction energy is divided into three terms frozen density, polarization, and dispersion. Owing to the small cost of DFTB/TD-DFTB, DFTB-EDA is capable of analyzing intermolecular interactions in large molecular systems containing several thousand atoms with high computational efficiency. It can be used not only for ground states but also for excited states. Test calculations, involving the S66 and L7 databases, several large molecules, and non-covalent bonding complexes in their lowest excited states, demonstrate the efficiency, usefulness, and capabilities of DFTB-EDA. Finally, the limits of DFTB-EDA are pointed out.Heavy water or deuterium oxide, D2O, is used as a solvent in various biophysical and chemical experiments. To model such experiments with molecular dynamics simulations, effective pair potentials for heavy water are required, which reproduce the well-known physicochemical differences relative to light water. We present three effective pair potentials for heavy water, denoted SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW. The models were parameterized by modifying the widely used three- and four-site models for light water, with the aim of maintaining the specific characteristics of the light water models. At room temperature, SPC/E-HW and TIP3P-HW capture the modulations relative to light water of the mass and electron densities, heat of vaporization, diffusion coefficient, and water structure. TIP4P/2005-HW captures, in addition, the density of heavy water over a wide temperature range.Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions, or local transport properties from molecular simulations, we show that the variance can be further reduced by considering optimal linear combinations of such estimators. This control variates approach, well known in statistics and already used in other branches of computational physics, has been comparatively much less exploited in molecular simulations. We illustrate this idea on the radial distribution function and the one-dimensional density of a bulk and confined Lennard-Jones fluid, where the optimal combination of estimators is determined for each distance or position, respectively. In addition to reducing the variance everywhere at virtually no additional cost, this approach cures an artifact of the initial force-based estimators, namely, small but non-zero values of the quantities in regions where they should vanish. Beyond the examples considered here, the present work highlights, more generally, the underexplored potential of control variates to estimate observables from molecular simulations.The complex-scaling method can be used to calculate molecular resonances within the Born-Oppenheimer approximation, assuming that the electronic coordinates are dilated independently of the nuclear coordinates. With this method, one will calculate the complex energy of a non-Hermitian Hamiltonian, whose real part is associated with the resonance position and imaginary part is the inverse of the lifetime. In this study, we propose techniques to simulate resonances on a quantum computer. First, we transformed the scaled molecular Hamiltonian to second quantization and then used the Jordan-Wigner transformation to transform the scaled Hamiltonian to the qubit space. To obtain the complex eigenvalues, we introduce the direct measurement method, which is applied to obtain the resonances of a simple one-dimensional model potential that exhibits pre-dissociating resonances analogous to those found in diatomic molecules. Finally, we applied the method to simulate the resonances of the H2 - molecule. The numerical results from the IBM Qiskit simulators and IBM quantum computers verify our techniques.In this work, we provide a nuanced view of electron correlation in the context of transition metal complexes, reconciling computational characterization via spin and spatial symmetry breaking in single-reference methods with qualitative concepts from ligand-field and molecular orbital theories. These insights provide the tools to reliably diagnose the multi-reference character, and our analysis reveals that while strong (i.e., static) correlation can be found in linear molecules (e.g., diatomics) and weakly bound and antiferromagnetically coupled (monometal-noninnocent ligand or multi-metal) complexes, it is rarely found in the ground-states of mono-transition-metal complexes. This leads to a picture of static correlation that is no more complex for transition metals than it is, e.g., for organic biradicaloids. In contrast, the ability of organometallic species to form more complex interactions, involving both ligand-to-metal σ-donation and metal-to-ligand π-backdonation, places a larger burden on a theory's treatment of dynamic correlation. We hypothesize that chemical bonds in which inter-electron pair correlation is non-negligible cannot be adequately described by theories using MP2 correlation energies and indeed find large errors vs experiment for carbonyl-dissociation energies from double-hybrid density functionals. A theory's description of dynamic correlation (and to a less important extent, delocalization error), which affects relative spin-state energetics and thus spin symmetry breaking, is found to govern the efficacy of its use to diagnose static correlation.In the hybrid sulfur (HyS) cycle, the reaction between SO2 and H2O is manipulated to produce hydrogen with water and sulfuric acid as by-products. However, sulfur poisoning of the catalyst has been widely reported to occur in this cycle, which is due to strong chemisorption of sulfur on the metal surface. The catalysts may deactivate as a result of these impurities present in the reactants or incorporated in the catalyst during its preparation and operation of the HyS cycle. Here, we report a density functional theory investigation of the interaction between S, SO, and SO3 with the Pt (001), (011), and (111) surfaces. First, we have investigated the adsorption of single gas phase molecules on the three Pt surfaces. During adsorption, the 4F hollow sites on the (001) and (011) surfaces and the fcc hollow site on the (111) surface were preferred. S adsorption followed the trend of (001)4F > (011)4F > (111)fcc, while SO adsorption showed (001)4F > (011)bridge/4F > (111)fcc and SO3 adsorption was most stable in a S,O,O bound configuration on the (001)4F > (011)4F > (111)fcc sites. The surface coverage was increased on all the surfaces until a monolayer was obtained. The highest surface coverage for S shows the trend (001)S = (111)S > (011)S, and for SO it is (001)SO > (011)SO > (111)SO, similar to SO3 where we found (001)SO3 > (011)SO3 > (111)SO3. These trends indicate that the (001) surface is more susceptible to S species poisoning. It is also evident that both the (001) and (111) surfaces were reactive toward S, leading to the formation of S2. The high coverage of SO3 showed the formation of SO2 and SO4, especially on the (011) surface. Smad pathway The thermodynamics indicated that an increased temperature of up to 2000 K resulted in Pt surfaces fully covered with elemental S. The SO coverage showed θ ≥ 1.00 on both the (001) and (011) surfaces and θ = 0.78 for the (111) surface in the experimental region where the HyS cycle is operated. Lower coverages of SO3 were observed due to the size of the molecule.Recent studies have indicated that nitramide (NH2NO2) may be formed more plentifully in the atmosphere than previously thought, while also being a missing source of the greenhouse gas nitrous oxide (N2O) via catalyzed isomerization. To validate the importance of NH2NO2 in the Earth's atmosphere, the ground and first electronic excited states of NH2NO2 were characterized and its photochemistry was investigated using multireference and coupled cluster methods. NH2NO2 is non-planar and of singlet multiplicity in the ground state while exhibiting large out-of-plane rotation in the triplet first excited state. One-dimensional cuts of the adiabatic potential energy surface calculated using the MRCI+Q method show low-lying singlet electronic states with minima in their potential along the N-N and N-O bond coordinates. Due to vertical excitation energies in the 225-180 nm region, photochemical processes will not compete in the troposphere, causing N2O production to be the predicted major removal process of NH2NO2. In the upper atmosphere, photodissociation to form NH2NO + O (3P) is suggested to be a major photochemical removal pathway.After exciting scientific debates about its nature, the development of the exclusion zone, a region near hydrophilic surfaces from which charged colloidal particles are strongly expelled, has been finally traced back to the diffusiophoresis produced by unbalanced ion gradients. This was done by numerically solving the coupled Poisson equation for electrostatics, the two stationary Stokes equations for low Reynolds numbers in incompressible fluids, and the Nernst-Planck equation for mass transport. Recently, it has also been claimed that the leading mechanism behind the diffusiophoretic phenomenon is electrophoresis [Esplandiu et al., Soft Matter 16, 3717 (2020)]. In this paper, we analyze the evolution of the exclusion zone based on a one-component interaction model at the Langevin equation level, which leads to simple analytical expressions instead of the complex numerical scheme of previous works, yet being consistent with it. We manage to reproduce the evolution of the exclusion zone width and the mean-square displacements of colloidal particles we measure near Nafion, a perfluorinated polymer membrane material, along with all characteristic time regimes, in a unified way. Our findings are also strongly supported by complementary experiments using two parallel planar conductors kept at a fixed voltage, mimicking the hydrophilic surfaces, and some computer simulations.We propose a route for parameterizing isotropic (generalized) Langevin [(G)LE] thermostats with the aim to correct the dynamics of coarse-grained (CG) models with pairwise conservative interactions. The approach is based on the Mori-Zwanzig formalism and derives the memory kernels from Q-projected time correlation functions. Bottom-up informed (GLE and LE) thermostats for a CG star-polymer melt are investigated, and it is demonstrated that the inclusion of memory in the CG simulation leads to predictions of polymer diffusion in quantitative agreement with fine-grained simulations. Interestingly, memory effects are observed in the diffusive regime. We demonstrate that previously neglected cross-correlations between the "irrelevant" and the CG degree of freedom are important and lie at the origin of shortcomings in previous CG simulations.Two-dimensional (2D) polymers are extended networks of multi-functional repeating units that are covalently linked together but confined to a single plane. The past decade has witnessed a surge in interest and effort toward producing and utilizing 2D polymers. However, facile synthesis schemes suitable for mass production are yet to be realized. In addition, unifying theories to describe the 2D polymerization process, such as those for linear polymers, have not yet been established. Herein, we perform a chemical kinetic simulation to study the recent synthesis of 2D polymers in homogeneous solution with irreversible chemistry. We show that reaction sites for polymerization in 2D always scale unfavorably compared to 3D, growing as molecular weight to the 1/2 power vs 2/3 power for 3D. However, certain mechanisms can effectively suppress out-of-plane defect formation and subsequent 3D growth. We consider two such mechanisms, which we call bond-planarity and templated autocatalysis. In the first, although single bonds can easily rotate out-of-plane to render polymerization in 3D, some double-bond linkages prefer a planar configuration.