Computational tools to study non-covalent interactions and confinement effects in chemical systems

Vargas, Rubicelia; Garza, Jorge; Martínez, Ana; Ibarra, Ilich A.

doi:10.1039/d3cc06347j

Cited by 6 publications

(1 citation statement)

References 119 publications

(211 reference statements)

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“…From the theoretical point of view, many computational studies have been successfully applied to study supramolecular systems, aiming for a more comprehensive understanding of existing materials and rationalizing the novelty of these structures. [13] Herein, we will highlight the use of DFT calculations, molecular dynamics simulations, and machine learning among the various methods to investigate such systems. We highlight the key insights that each of these methods, as well as their combination, can provide for the problems to which they are applied in supramolecular chemistry.…”

Section: Introductionmentioning

confidence: 99%

Supramolecular Chemistry: Exploring the Use of Electronic Structure, Molecular Dynamics, and Machine Learning Approaches

Colaço,

Glitz,

Jacobs

et al. 2024

Eur J Org Chem

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This review aims to highlight the role that computational chemistry has played in advancing the supramolecular chemistry field. We demonstrated recent uses of computational methodologies to elucidate noncovalent interactions in various processes occurring in supramolecular systems. We also emphasized the contributions of these techniques to studying reactions within confined space, showing how computational methodologies help clarify the effects of reactivity and conformational locking. Furthermore, we underscore the utilization of Molecular Dynamics (MD) in elucidating dynamical processes, understanding temperature and pressure effects, and exploring conformational space within supramolecular chemistry. Finally, we highlight the impact that the age of machine learning has on computational chemistry, showing how these universal approximators can enhance existing methods, predict properties, and efficiently explore the chemical space encompassed by these complex systems.

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Section: Introductionmentioning

confidence: 99%

Supramolecular Chemistry: Exploring the Use of Electronic Structure, Molecular Dynamics, and Machine Learning Approaches

Colaço,

Glitz,

Jacobs

et al. 2024

Eur J Org Chem

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The Changing Phases of Bromopentafluorobenzene

Bear,

Cockcroft

2024

Chemistry A European J

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As part of a much larger study on non‐covalent interactions in binary adducts, we have explored the solid‐state structures of bromopentafluorobenzene (C6F5Br) using differential scanning calorimetry (DSC), variable‐temperature powder X‐ray diffraction (VT‐PXRD), and single‐crystal X‐ray diffraction (SXD). DSC data initially indicated a single solid‐state phase below the freezing point, but revealed additional weak transitions upon heating. The crystal structures of three solid‐state phases have been solved. The SXD data showed that phases I and IV are centrosymmetric, whilst phase II is polar. However, the structure of phase III remains elusive due to the changing phase behaviour of C6F5Br that is determined as much as by kinetics as thermodynamics. The results underline the need for multiple analytical techniques to study non‐covalent interactions and offer valuable data for refining computational models in crystal structure prediction and machine learning. A comparison with the iodinated counterpart is also made.

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Interactions involved in the adsorption of ethylene glycol and 2-hydroxyethoxide on the Au(111) surface: a Density Functional Theory study

Avelar,

Hernández-Esparza,

Garza

et al. 2024

J Mol Model

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Context: The monolayers of ethylene glycol and 2-hydroxyethoxide on gold surfaces have been used in hybrid materials as biosensors. In this article, the adsorption of ethylene glycol and 2-hydroxyethoxide on the Au(111) surface was analyzed. For the first system, ethylene glycol on Au(111), there are Au$$\cdot \cdot \cdot $$ · · · O and Au$$\cdot \cdot \cdot $$ · · · H interactions. To the best of our knowledge, the Au$$\cdot \cdot \cdot $$ · · · H interaction has been overlooked until now. However, in this work, there is strong evidence that this interaction is important to stabilize the system. For the second system, the atomic interactions mentioned previously are also predicted, although there is an additional interaction between 2-hydroxyethoxide molecules. Such an interaction induces the link -O-H-O-, with high values of the electron density at the critical points of the corresponding bond path of the O-H interaction. These links suggest the forming of ethylene glycol chains. Methods: The calculations were performed using two exchange-correlation functionals: BEEF-vdW and C09$$_{x}$$ x -vdW; both functionals incorporate dispersion effects within the Kohn-Sham approach in Density Functional Theory as implemented in GPAW code and ASE computational packages. The contacts between the molecules considered in this article and the Au(111) surface were analyzed through the Quantum Theory of Atoms in Molecules implemented in GPUAM code.

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Computational tools to study non-covalent interactions and confinement effects in chemical systems

Abstract: Confinement is a very common phenomenon in chemistry, for example, when molecules are located inside cavities. In these conditions, the electronic structure of atoms and molecules is modified. These changes...

Cited by 6 publications

References 119 publications

Supramolecular Chemistry: Exploring the Use of Electronic Structure, Molecular Dynamics, and Machine Learning Approaches

Supramolecular Chemistry: Exploring the Use of Electronic Structure, Molecular Dynamics, and Machine Learning Approaches

The Changing Phases of Bromopentafluorobenzene

Interactions involved in the adsorption of ethylene glycol and 2-hydroxyethoxide on the Au(111) surface: a Density Functional Theory study

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