Relative Position and Relative Rotation in Supramolecular Systems through the Analysis of the Principal Axes of Inertia: Ferrocene/Cucurbit[7]uril and Ferrocenyl Azide/β-Cyclodextrin Case Studies

Abstract

Parameters comprising the relative position and relative rotation of molecules can be evaluated when the principal axes of inertia of the entities in a supramolecular association are employed as reference. Such information applies to the characterization and identification of experimental and theoretical nonbonded systems. The parameters are relevant to geometric comparison (for theory and experiment) and, for instance, to monitoring structures by theoretical simulations. This work introduces a software developed to obtain such parameters through the discussion of some intriguing host−guest systems, the ferrocene/cucurbit[7]uril and ferrocenyl azide/β-cyclodextrin. The ideas within this contribution naturally apply to the study of other nonbonded associations beyond host−guest chemistry. A modified version of the software discussed herein serves to obtain user-defined spatial arrangements for two nonbonded entities. Therefore, with a given geometry, for instance, from X-ray data, the parameters can be derived, and with the parameters, from a theoretical perspective, a spatial arrangement can be obtained.

Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson–Crick/Hoogsteen Base Pairs: A Computational Analysis

“…Computing the strength of individual bonds using quantum mechanics is hostile; hence, several external methods such as bond dissociation energy, valence bond theory, molecular orbital theory, and topology of electron density are widely used. , Atoms in molecule (AIM) analysis is widely used to detect the existence of H-bonds. At the intermolecular bond critical points (BCPs), the electron density (ρ( r bcp )), their Laplacians (∇ 2 ρ( r bcp )), and the energetic properties (H(r bcp )) allow us to categorize the interactions . For hydrogen bonds, ∇ 2 ρ( r bcp ) is positive, V ( r bcp ) is negative, and G ( r bcp ) and H ( r bcp ) are positive values.…”

Structure, stability, and dynamics of the inclusion complexes formed by auranofin derivatives and hydroxypropyl-β-cyclodextrin

“…The structures of the guests optimized at the DFT level were used as starting systems. The supramolecular starting systems were systematically obtained from the UD-APARM software (https://github.com/anconi-lab), in which the axes of inertia of host and guest are used to obtain the starting supramolecular arrangements [28]. This procedure falls under the multi-equilibrium approach [33,34], in which the xTB 6.41 was used to obtain the GFN2-xTB data.…”

“…More recently, the tight-binding QC method (GFN2-xTB) [24,25] has been applied to CD-based systems [26,27]. Within this QC approach, a new form of characterizing and obtaining supramolecular arrangements was proposed [28] in an attempt to account for many equilibria simultaneously [29][30][31][32]. This was employed to treat CDbased systems with the use of the low-cost GFN2-xTB method, known as the multi-equilibrium approach [33].…”

Automated and Efficient Generation of General Molecular Aggregate Structures

“… [1] It is crucial for the association and function of supermolecular dimers and oligomers, [2] the self‐assembly of molecules, [3] or protein‐protein and protein‐ligand complexes[ 4 , 5 ] to name only a few examples. Nowadays, computational studies often complement experimental work to elucidate structure and interaction (free) energies in great detail [6] and finally even predict complex reaction mechanisms. [7] Usually, well‐established wave‐function theory (WFT) or Kohn–Sham (KS) density functional theory (DFT) are used as computational methods for simulating basic molecular properties, but they quickly reach their limits for the structure generation of large oligomer and aggregate systems containing a few hundred atoms due to high computational costs.…”