Interatomic Methods for the Dispersion Energy Derived from the Adiabatic Connection Fluctuation-Dissipation Theorem

Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory (DFT) calculations. However, when applied to more than two atoms, these methods are still frequently perceived to be based on \textit{ad hoc} assumptions, rather than a rigorous derivation from quantum mechanics. Starting from the adiabatic connection fluctuation-dissipation (ACFD) theorem, an exact expression for the electronic exchange-correlation energy, we demonstrate that the pairwise interatomic dispersion energy for an arbitrary collection of isotropic polarizable dipoles emerges from the second-order expansion of the ACFD formula. Moreover, for a system of quantum harmonic oscillators coupled through a dipole--dipole potential, we prove the equivalence between the full interaction energy obtained from the Hamiltonian diagonalization and the ACFD correlation energy in the random-phase approximation. This property makes the Hamiltonian diagonalization an efficient method for the calculation of the many-body dispersion energy. In addition, we show that the switching function used to damp the dispersion interaction at short distances arises from a short-range screened Coulomb potential, whose role is to account for the spatial spread of the individual atomic dipole moments. By using the ACFD formula we gain a deeper understanding of the approximations made in the interatomic pairwise approaches, providing a powerful formalism for further development of accurate and efficient methods for the calculation of the dispersion energy

Electronic Properties of Molecules and Surfaces with a Self\uad-Consistent Interatomic van der Waals Density Functional.

How strong is the effect of van der Waals (vdW) interactions on the electronic properties of molecules and extended systems? To answer this question, we derived a fully self-consistent implementation of the density-dependent interatomic vdW functional of Tkatchenko and Scheffler [Phys. Rev. Lett. 102, 073005 (2009)]. Not surprisingly, vdW self-consistency leads to tiny modifications of the structure, stability, and electronic properties of molecular dimers and crystals. However, unexpectedly large effects were found in the binding energies, distances, and electrostatic moments of highly polarizable alkali-metal dimers. Most importantly, vdW interactions induced complex and sizable electronic charge redistribution in the vicinity of metallic surfaces and at organic-metal interfaces. As a result, a substantial influence on the computed work functions was found, revealing a nontrivial connection between electrostatics and long-range electron correlation effects

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically-relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions---electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters---optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically-relevant molecules. We further focus on hydrogen-bonded complexes---essential but challenging due to their directional nature---where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML in denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.Comment: 15 pages, 9 figure

A Comprehensive Examination of the Post-Conviction Risk Assessment (PCRA) and Risk Prediction Index (RPI) for General Risk Factors, Criminogenic Outcomes, and Risk-Specific Populations

The use of risk assessment instruments has become an increasingly pertinent issue in the realm of reentry. Though sometimes controversial, risk assessment tools provide local, state, and federal governments with actuarial techniques focused on providing unbiased and accurate risk assessments for individuals returning to the community. The present study was focused on the further evaluation of two risk assessment instruments utilized by the Administrative Office of the United States Courts (AOUSC)—the Post-Conviction Risk Assessment (PCRA) and the Risk Prediction Index (RPI). A mixed-methods approach was taken in order to investigate the associations between these tools, general risk factors, criminogenic outcomes, and more riskspecific populations. Utilizing data from a study previously focused on examining a federal reentry program, the results showcased several notable findings. This included the discovery of statistically valid associations between the PCRA and all diverse criminogenic outcomes examined. Among the various risk factors, housing instability stood out due to its association with outcomes, but not with risk assessment instruments. This finding suggests that housing instability may not be adequately integrated within the PCRA or RPI. Furthermore, based on qualitative interviews, federal probation officers possessed a noticeable degree of trust in the PCRA, but they also still believed there was potential for improvement. There were less favorable views of the RPI. Overall, the results of this study suggest the PCRA is a useful tool for federal reentry programming. Despite the progress made in this area of study, there remains ample room for continuing the validation process and expanding the comprehension of complex assessment, supervision, and treatment processes

Crossover from Poisson to Wigner-Dyson Level Statistics in Spin Chains with Integrability Breaking

We study numerically the evolution of energy-level statistics as an integrability-breaking term is added to the XXZ Hamiltonian. For finite-length chains, physical properties exhibit a cross-over from behavior resulting from the Poisson level statistics characteristic of integrable models to behavior corresponding to the Wigner-Dyson statistics characteristic of the random-matrix theory used to describe chaotic systems. Different measures of the level statistics are observed to follow different crossover patterns. The range of numerically accessible system sizes is too small to establish with certainty the scaling with system size, but the evidence suggests that in a thermodynamically large system an infinitesimal integrability breaking would lead to Wigner-Dyson behavior.Comment: 8 pages, 8 figures, Revtex

Report on the sixth blind test of organic crystal-structure prediction methods

The sixth blind test of organic crystal-structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal, and a bulky flexible molecule. This blind test has seen substantial growth in the number of submissions, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and "best practices" for performing CSP calculations. All of the targets, apart from a single potentially disordered Z` = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms

Cdc37 has distinct roles in protein kinase quality control that protect nascent chains from degradation and promote posttranslational maturation

Cdc37 is a molecular chaperone that functions with Hsp90 to promote protein kinase folding. Analysis of 65 Saccharomyces cerevisiae protein kinases (∼50% of the kinome) in a cdc37 mutant strain showed that 51 had decreased abundance compared with levels in the wild-type strain. Several lipid kinases also accumulated in reduced amounts in the cdc37 mutant strain. Results from our pulse-labeling studies showed that Cdc37 protects nascent kinase chains from rapid degradation shortly after synthesis. This degradation phenotype was suppressed when cdc37 mutant cells were grown at reduced temperatures, although this did not lead to a full restoration of kinase activity. We propose that Cdc37 functions at distinct steps in kinase biogenesis that involves protecting nascent chains from rapid degradation followed by its folding function in association with Hsp90. Our studies demonstrate that Cdc37 has a general role in kinome biogenesis