Implicitly perturbed Hamiltonian as a class of versatile and general-purpose molecular representations for machine learning

Unraveling challenging problems by machine learning has recently become a hot topic in many scientific disciplines. For developing rigorous machine-learning models to study problems of interest in molecular sciences, translating molecular structures to quantitative representations as suitable machine-learning inputs play a central role. Many different molecular representations and the state-of-the-art ones, although efficient in studying numerous molecular features, still are suboptimal in many challenging cases, as discussed in the context of the present research. The main aim of the present study is to introduce the Implicitly Perturbed Hamiltonian (ImPerHam) as a class of versatile representations for more efficient machine learning of challenging problems in molecular sciences. ImPerHam representations are defined as energy attributes of the molecular Hamiltonian, implicitly perturbed by a number of hypothetic or real arbitrary solvents based on continuum solvation models. We demonstrate the outstanding performance of machine-learning models based on ImPerHam representations for three diverse and challenging cases of predicting inhibition of the CYP450 enzyme, high precision, and transferrable evaluation of non-covalent interaction energy of molecular systems, and accurately reproducing solvation free energies for large benchmark sets

Global geometry optimization of clusters using a growth strategy optimized by a genetic algorithm

A new strategy for global geometry optimization of clusters is presented. Important features are a restriction of search space to favorable nearest-neighbor distance ranges, a suitable cluster growth representation with diminished correlations, and easy transferability of the results to larger clusters. The strengths and possible limitations of the method are demonstrated for Si10 using an empirical potential.Comment: accepted by Chem.Phys.Letters; 10 pages text, plus 3 pages for Title, abstract, and figure caption; figures 1a and 1

Differential effects of oligosaccharides on the hydration of simple cations

Changed ion hydration properties near surfaces, proteins, and deoxyribose nucleic acid have been reported before in the literature. In the present work, we extend this work to carbohydrates: We have performed classical-mechanical molecular dynamics simulations to study solvation properties of simple cations of biological relevance (Na(+),K(+),Mg(2+),Ca(2+)) in explicit water, near single and multiple oligosaccharides as glycocalyx models. We find that our oligosaccharides prefer direct contact with K(+) over Na(+), but that the Na(+) contacts are longer lived. These interactions also lead to strong but short-lived changes in oligosaccharide conformations, with oligosaccharides wrapping around K(+) with multiple contacts. These findings may have implications for current hypotheses on glycocalyx functions

Brownian molecular rotors: Theoretical design principles and predicted realizations

We propose simple design concepts for molecular rotors driven by Brownian motion and external photochemical switching. Unidirectionality and efficiency of the motion is measured by explicit simulations. Two different molecular scaffolds are shown to yield viable molecular rotors when decorated with suitable substituents

Indandiazocines: unidirectional molecular switches

We report theoretical investigations on azobenzene-based indandiazocines, novel chiral systems that perform unidirectional cis ↔ trans isomerizations upon photoexcitation. For three different systems of this kind, we have simulated excited-state surface-hopping trajectories for both isomerization directions, using a configuration-interaction treatment based on system-specifically reparametrized semiempirical AM1 theory. Our results are also compared to experimental and theoretical results for the parent system diazocine. We show that, as intended by design, the trans → cis bending of the azo unit in these indandiazocines can only happen in one of the two possible directions due to steric constraints, which is a new feature for photoswitches and a necessary prerequisite for directional action at the nanoscale

Indandiazocines: Unidirectional molecular switches

We report theoretical investigations on azobenzene-based indandiazocines, novel chiral systems that perform unidirectional cis↔trans isomerizations upon photo-excitation. For three different systems of this kind, we have simulated excited-state surface-hopping trajectories for both isomerization directions, using a configuration-interaction treatment based on system-specifically reparametrized semiempirical AM1 theory. Our results are also compared to experimental and theoretical results for the parent system diazocine. We show that, as intended by design, the trans→cis bending of the azo unit in these indandiazocines can only happen in one of the two possible directions due to sterical constraints, which is a new feature for photoswitches and a necessary prerequisite for directional action at the nanoscale