Noncovalent interactions in isolated molecular aggregates: From single molecules to nanostructures

León, Íker; Lesarri, Alberto; Fernández, José A.

doi:10.1016/b978-0-12-817586-6.00005-0

Cited by 3 publications

(2 citation statements)

References 247 publications

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“…Further computational and experimental work should be carried out to assess the generality of the results presented in this work and to gain additional insight into the intermolecular forces driving the formation of the complexes studied [ 75 , 76 ]. The author is currently investigating the ability of the bracelet-like complexes to host small molecules or metal ions.…”

Section: Future Perspectivesmentioning

confidence: 99%

Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study

Parra

2023

Molecules

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Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F interactions. The complex with both interactions is the most stable one, followed by the complex with only N-H⋯F interactions. Doubling the size of the former resulted in a complex with a LiF dimer sandwiched between the model tetraamides. In turn, doubling the size of the latter resulted in a more stable tetramer with bracelet-like geometry having the two LiF molecules also sandwiched but far apart from each other. Additionally, all methods show that the energy barrier to transition to the more stable tetramer is small. The self-assembly of the bracelet-like complex mediated by the interactions of adjacent LiF molecules is demonstrated by all computational methods employed.

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Section: Future Perspectivesmentioning

confidence: 99%

Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study

Parra

2023

Molecules

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“…However, the computational cost of these advanced ab initio methods scales rapidly, rendering them impractical for larger molecular systems, whereas lower-tier methods such as density functional theory (DFT), despite reliance on empirical corrections, often fail to achieve the necessary chemical accuracy [7]. The prototypical homocluster molecules of phenol (PhOH) have been investigated extensively and have earned a place in benchmark databases for biomolecular systems [8], although the computational costs for theoretical CCSD(T) predictions become prohibitive already at the (PhOH) 2 level due to the size of the aromatic fragments [9,10]. The introduction of these aromatic structures facilitates the formation of intermolecular contacts involving the π-electron clouds.…”

Section: Introductionmentioning

confidence: 99%

Self-Association and Microhydration of Phenol: Identification of Large-Amplitude Hydrogen Bond Librational Modes

Mihrin,

Feilberg,

Larsen

2024

Molecules

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The self-association mechanisms of phenol have represented long-standing challenges to quantum chemical methodologies owing to the competition between strongly directional intermolecular hydrogen bonding, weaker non-directional London dispersion forces and C–H⋯π interactions between the aromatic rings. The present work explores these subtle self-association mechanisms of relevance for biological molecular recognition processes via spectroscopic observations of large-amplitude hydrogen bond librational modes of phenol cluster molecules embedded in inert neon “quantum” matrices complemented by domain-based local pair natural orbital-coupled cluster DLPNO-CCSD(T) theory. The spectral signatures confirm a primarily intermolecular O-H⋯H hydrogen-bonded structure of the phenol dimer strengthened further by cooperative contributions from inter-ring London dispersion forces as supported by DLPNO-based local energy decomposition (LED) predictions. In the same way, the hydrogen bond librational bands observed for the trimeric cluster molecule confirm a pseudo-C3 symmetric cyclic cooperative hydrogen-bonded barrel-like potential energy minimum structure. This structure is vastly different from the sterically favored “chair” conformations observed for aliphatic alcohol cluster molecules of the same size owing to the additional stabilizing London dispersion forces and C–H⋯π interactions between the aromatic rings. The hydrogen bond librational transition observed for the phenol monohydrate finally confirms that phenol acts as a hydrogen bond donor to water in contrast to the hydrogen bond acceptor role observed for aliphatic alcohols.

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Inferring the existence of hydrogen bonds directly from statistical analysis of molecular dynamics trajectories

Chuiko,

Ayers

2024

The Journal of Chemical Physics

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As a demonstration of how fundamental chemical concepts can be gleaned from data using machine learning methods, we demonstrate the automated detection of hydrogen bonds by statistical analysis of molecular dynamics trajectories. In particular, we infer the existence and nature of electrostatically driven noncovalent interactions by examining the relative probability of supramolecular configurations with and without electrostatic interactions. Then, using Laplacian eigenmaps clustering, we identify hydrogen bonding motifs in hydrogen fluoride, water, and methanol. The hydrogen bonding motifs that we identify support traditional geometric criteria.

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Noncovalent interactions in isolated molecular aggregates: From single molecules to nanostructures

Cited by 3 publications

References 247 publications

Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study

Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study

Self-Association and Microhydration of Phenol: Identification of Large-Amplitude Hydrogen Bond Librational Modes

Inferring the existence of hydrogen bonds directly from statistical analysis of molecular dynamics trajectories

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