Extending the definition of atomic basis sets to atoms with fractional nuclear charge.

Alchemical transformations showed that perturbation theory can be applied also to changes in the atomic nuclear charges of a molecule. The alchemical path that connects two different chemical species involves the conceptualization of a non-physical system in which an atom possess a non-integer nuclear charge. A correct quantum mechanical treatment of these systems is limited by the fact that finite size atomic basis sets do not define exponents and contraction coefficients for fractional charge atoms.

Molecular Hessian matrices from a machine learning random forest regression algorithm.

In this article, we present a machine learning model to obtain fast and accurate estimates of the molecular Hessian matrix. In this model, based on a random forest, the second derivatives of the energy with respect to redundant internal coordinates are learned individually. The internal coordinates together with their specific representation guarantee rotational and translational invariance.

Alchemical geometry relaxation.

We propose the relaxation of geometries throughout chemical compound space using alchemical perturbation density functional theory (APDFT). APDFT refers to perturbation theory involving changes in nuclear charges within approximate solutions to Schrödinger's equation. We give an analytical formula to calculate the mixed second order energy derivatives with respect to both nuclear charges and nuclear positions (named "alchemical force") within the restricted Hartree-Fock case.

Effects of perturbation order and basis set on alchemical predictions.

Alchemical perturbation density functional theory has been shown to be an efficient and computationally inexpensive way to explore chemical compound space. We investigate approximations made, in terms of atomic basis sets and the perturbation order, introduce an electron-density based estimate of errors of the alchemical prediction, and propose a correction for effects due to basis set incompleteness. Our numerical analysis of potential energy estimates, and resulting binding curves, is based on coupled-cluster single double (CCSD) reference results and is limited to all neutral diatomics with 14 electrons (AlH⋯NN).

Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair?

Reversibly photoswitchable fluorescent proteins (RSFPs) admirably combine the genetic encoding of fluorescence with the ability to repeatedly toggle between a bright and dark state, adding a new temporal dimension to the fluorescence signal. Accordingly, in recent years RSFPs have paved the way to novel applications in cell imaging that rely on their reversible photoswitching, including many super-resolution techniques such as F-PALM, RESOLFT, and SOFI that provide nanoscale pictures of the living matter. Yet many RSFPs have been engineered by a rational approach only to a limited extent, in the absence of clear structure-property relationships that in most cases make anecdotic the emergence of the photoswitching.