Low-Energy Transformation Pathways between Naphthalene Isomers

Salomon, Grégoire; Tarrat, Nathalie; Schön, J. Christian; Rapacioli, Mathias

doi:10.3390/molecules28155778

Cited by 3 publications

(2 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Regarding the energy function, full quantum mechanical evaluations of the energy are computationally very expensive and thus always a stretch for global landscape exploration. Nevertheless, energy functions with a good balance between accuracy and computational efficiency, e.g., based on density functional-based tight-binding (DFTB) [46], are available and have been successfully employed to globally explore energy landscapes of chemical systems [47].…”

Section: Discussionmentioning

confidence: 99%

IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules

Margerit,

Charpentier,

Maugis-Rabusseau

et al. 2023

Algorithms

Self Cite

View full text Add to dashboard Cite

The exploration of the energy landscape of a chemical system is essential for understanding and predicting its observable properties. In most cases, this is a challenging task due to the high complexity of such landscapes, which often consist of multiple, possibly hierarchical basins that are difficult to locate and thoroughly explore. In this study, we introduce a novel method, called IGLOO (Iterative Global Exploration and Local Optimization), which aims to achieve a more efficient global exploration of the conformational space compared to existing techniques. The method utilizes a tree-based exploration inspired by the Rapidly exploring Random Tree (RRT) algorithm originating from robotics. IGLOO dynamically adjusts its exploration strategy to both homogeneously scan the landscape and focus on promising regions, avoiding redundant exploration. We evaluated IGLOO using models of two polypeptides and compared its performance to the traditional basin-hopping method and a hybrid method that also incorporates the RRT algorithm. We find that IGLOO outperforms both alternative methods in terms of efficiently and comprehensively exploring the molecular conformational space. This approach can be easily generalized to other chemical systems such as molecules on surfaces or crystalline systems.

show abstract

Section: Discussionmentioning

confidence: 99%

IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules

Margerit,

Charpentier,

Maugis-Rabusseau

et al. 2023

Algorithms

Self Cite

View full text Add to dashboard Cite

show abstract

“…Despite the high accuracy in predicting the structure, energy, and NMR parameters, the ab initio CASTEP calculations were computationally too expensive to perform the Molecular Dynamics (MD) simulations using them. Therefore, for this purpose, we have chosen the DFTB semi-empirical method, which has been proven to provide accurate results at an affordable computational cost [33].…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates

Napiórkowska,

Szeleszczuk,

Milcarz

et al. 2023

Molecules

View full text Add to dashboard Cite

Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the form of hydrates with varying degrees of hydration, depending on the air humidity. Although experimental characterization of the THCL hydrates has been described in the literature, the questions raised in previously published works suggest that additional research and in-depth analysis of THCL dehydration behavior are still needed. Therefore, the main aim of this study was to characterize, by means of quantum chemical calculations, the behavior of thiamine hydrates and explain the previously obtained results, including changes in the NMR spectra, at the molecular level. To achieve this goal, a series of DFT (CASTEP) and DFTB (DFTB+) calculations under periodic boundary conditions have been performed, including molecular dynamics simulations and GIPAW NMR calculations. The obtained results explain the differences in the relative stability of the studied forms and changes in the spectra observed for the samples of various degrees of hydration. This work highlights the application of periodic DFT calculations in the analysis of various solid forms of APIs.

show abstract

Energy landscapes—Past, present, and future: A perspective

Schön

2024

The Journal of Chemical Physics

View full text Add to dashboard Cite

Energy landscapes and the closely related cost function landscapes have been recognized in science, mathematics, and various other fields such as economics as being highly useful paradigms and tools for the description and analysis of the properties of many systems, ranging from glasses, proteins, and abstract global optimization problems to business models. A multitude of algorithms for the exploration and exploitation of such landscapes have been developed over the past five decades in the various fields of applications, where many re-inventions but also much cross-fertilization have occurred. Twenty-five years ago, trying to increase the fruitful interactions between workers in different fields led to the creation of workshops and small conferences dedicated to the study of energy landscapes in general instead of only focusing on specific applications. In this perspective, I will present some history of the development of energy landscape studies and try to provide an outlook on in what directions the field might evolve in the future and what larger challenges are going to lie ahead, both from a conceptual and a practical point of view, with the main focus on applications of energy landscapes in chemistry and physics.

show abstract

Low-Energy Transformation Pathways between Naphthalene Isomers

Cited by 3 publications

References 55 publications

IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules

IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules

Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates

Energy landscapes—Past, present, and future: A perspective

Contact Info

Product

Resources

About