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Register a new userInconsistencies in ab initio evaluations of non-additive contributions of DNA stacking energies
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We evaluated the non-additive contributions of the inter-molecular interactions in B-DNA stacking by using diffusion Monte Carlo methods with fixed node approximations (FNDMC). For some base-pair steps, we found that their non-additive contributions evaluated by FNDMC significantly differ from those by any other {it ab initio} methods, while there are no remarkable findings on their stacking energies themselves. The apparently unexpected results of non-additivity raise issues in both FNDMC and correlated wavefunction methods. For the latter, it can be partly attributed to the imperfect complete basis set (CBS) correction scheme due to the limitation of the computational costs. On the other hand, the striking contrast between the stacking and non-additivity behaviors was found in FNDMC. This might imply that the error cancellations of the fixed node biases in FNDMC work well for the stacking energies, while not for the non-additivity contributions involving charge transfers caused by hydrogen bonds bridging Watson-Crick base pairs.
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Energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs) decomposes the interaction energy between molecules into physically interpretable components like geometry distortion, frozen interactions, polarization, and charge transfer (CT, also sometimes called charge delocalization) interactions. In this work, a numerically exact scheme to decompose the CT interaction energy into pairwise additive terms is introduced for the ALMO-EDA using density functional theory. Unlike perturbative pairwise charge-decomposition analysis, the new approach does not break down for strongly interacting systems, or show significant exchange-correlation functional dependence in the decomposed energy components. Both the energy lowering and the charge flow associated with CT can be decomposed. Complementary occupied-virtual orbital pairs (COVPs) that capture the dominant donor and acceptor CT orbitals are obtained for the new decomposition. It is applied to systems with different types of interactions including DNA base-pairs, borane-ammonia adducts, and transition metal hexacarbonyls. While consistent with most existing understanding of the nature of CT in these systems, the results also reveal some new insights into the origin of trends in donor-acceptor interactions.
We examined the reliability of exchange-correlation functionals for molecular encapsulations combined by van der Waals forces, comparing their predictions with those of diffusion Monte Carlo method. We established that functionals with D3 dispersion force correction and including sufficient proportion of exact-exchange in long-ranged interaction can comparatively reliably estimate the binding strength. Our finding agrees with a previous ab initio study on argon dimer. However we found that even such functionals may not be able to distinguish the energy differences among different conformations.
Nuclear quantum effects, such as zero-point energy and tunneling, cause significant changes to the structure and dynamics of hydrogen bonded systems such as liquid water. However, due to the current inability to simulate liquid water using an exact description of its electronic structure, the interplay between nuclear and electronic quantum effects remains unclear. Here we use simulations that incorporate the quantum mechanical nature of both the nuclei and electrons to provide a fully ab initio determination of the particle quantum kinetic energies, free energy change upon exchanging hydrogen for deuterium and the isotope fractionation ratio in water. These properties, which selectively probe the quantum nature of the nuclear degrees of freedom, allow us to make direct comparison to recent experiments and elucidate how electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.
Radium compounds have attracted recently considerable attention due to both development of experimental techniques for high-precision laser spectroscopy of molecules with short-lived nuclei and amenability of certain radium compounds for direct cooling with lasers. Currently, radium monofluoride (RaF) is one of the most studied molecules among the radium compounds, both theoretically and recently also experimentally. Complementary studies of further diatomic radium derivatives are highly desired to assess the influence of chemical substitution on diverse molecular parameters, especially on those connected with laser cooling, such as vibronic transition probabilities, and those related to violations of fundamental symmetries. In this article high-precision emph{ab initio} studies of electronic and vibronic levels of diatomic radium monochloride (RaCl) are presented. Recently developed approaches for treating electronic correlation with Fock-space coupled cluster methods are applied for this purpose. Theoretical results are compared to an early experimental investigation by Lagerqvist and used to partially reassign the experimentally observed transitions and molecular electronic levels of RaCl. Effective constants of $mathcal{P}$-odd hyperfine interaction $W_{rm{a}}$ and $mathcal{P,T}$-odd scalar-pseudoscalar nucleus-electron interaction $W_{rm{s}}$ in the ground electronic state of RaCl are estimated within the framework of a quasirelativistic Zeroth-Order Regular Approximation approach and compared to parameters in RaF and RaOH.
We describe a simple method to determine, from ab initio calculations, the complete orientation-dependence of interfacial free energies in solid-state crystalline systems. We illustrate the method with an application to precipitates in the Al-Ti alloy system. The method combines the cluster expansion formalism in its most general form (to model the systems energetics) with the inversion of the well-known Wulff construction (to recover interfacial energies from equilibrium precipitate shapes). Although the inverse Wulff construction only provides the relative magnitude of the various interfacial free energies, absolute free energies can be recovered from a calculation of a single, conveniently chosen, planar interface. The method is able to account for essentially all sources of entropy (arising from phonons, bulk point defects, as well as interface roughness) and is thus able to transparently handle both atomically smooth and rough interfaces. The approach expresses the resulting orientation-dependence of the interfacial properties using symmetry-adapted bases for general orientation-dependent quantities. As a by-product, this paper thus provides a simple and general method to generate such basis functions, which prove useful in a variety of other applications, for instance to represent the anisotropy of the so-called constituent strain elastic energy.
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