Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Zou, Jian‐Wei; Huang, Meilan; Hu, Guixiang; Jiang, Yong‐Jun

doi:10.1039/c6ra27590g

Cited by 31 publications

(28 citation statements)

References 80 publications

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“…Correlations between the sum of the electron density (Σ ρ int ) at the BCP and the sum of the stabilization energy can be performed. This allows the partitioning of the atom ··· atom interaction energy, providing insights into the energetic contribution of each interaction (Figure ) . The types of atom ··· atom intramolecular interactions and QTAIM data are listed in the Supporting Information (Table S4).…”

Section: Resultsmentioning

confidence: 99%

Conformer Distribution in Rotaxanes Containing Nonsymmetric Threads: A Systematic Approach

et al. 2018

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Rotaxanes are designated as molecular machines due their different movements. Systematic studies regarding the different conformations adopted by these systems and the factors that lead to the distribution of the conformations, in both solution and the solid state, have not been widely explored, especially for rotaxanes with nonsymmetric stoppers. Therefore, in this study we have investigated three novel [2]rotaxanes containing threads derived from nonsymmetric succinamides [R1R2NC(O)‐CH2CH2‐C(O)NR2R1, with R1/R2 = Bu/Bn, Bu/2‐furylmethyl, and 5‐methylisoxazol‐3‐yl/2‐furylmethyl]. The proportions of rotamers were investigated for threads and rotaxanes by solution and solid‐state NMR spectroscopy as well as by single‐crystal and powder X‐ray diffraction. In solution, the threads present different proportions of conformer, with the E,Z conformation prevailing, whereas only one conformer is observed in the solid state. For the rotaxanes, only one conformer prevails in the single crystal, whereas the solution and solid (bulk) states present more than one rotamer. These proportions are modified when the threads are incorporated into the macrocycle during rotaxane formation. The intramolecular interactions in each rotamer were investigated by QTAIM and variable‐temperature 1H NMR experiments. The changes in conformational population between the threads and respective rotaxanes can be explained by a set of different intramolecular interactions, with trifurcated hydrogen bonds responsible for most of the stabilization energy.

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Section: Resultsmentioning

confidence: 99%

Conformer Distribution in Rotaxanes Containing Nonsymmetric Threads: A Systematic Approach

et al. 2018

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“…An Atoms in Molecules analysis of the topology of the electron density of [Fe(ent) 3 ] 3− obtained from DFT calculations revealed (3, −1) N–H⋯O bond critical points with properties indicative of closed-shell donor-acceptor interactions (ρ = 0.049 au, ∇ 2 ρ = 0.12) (Figure 3). 53,54 …”

Section: Resultsmentioning

confidence: 99%

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography

Johnstone

Nolan

2017

J. Am. Chem. Soc.

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Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

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“…Strong halogen-bonded complexes were found to exhibit different linear correlations from weak halogenbonded and hydrogen-bonded systems [445]. Nevertheless, for the latter two types of system, a uniform regression equation can be constructed.…”

Section: The Importance In Drug Design Of Similar To Hb Bondsmentioning

confidence: 99%

“…The dependence of the BSSE-corrected interaction energy (ΔE cor ) on the interatomic distance (rA /N ) appeared to be nonlinear for both halogen-bonded and hydrogen-bonded systems; the relationship between ΔE cor and the difference between r A/N and the sum of the van der Waals radii (Δr A/N ) can be fitted to a combined quadratic regression equation. Furthermore, it has been demonstrated that the linear correlations between ΔE cor and r b (BCP) (the electron density at bond critical points in the A/N bond) and its Laplacian V 2 r b (BCP) can be used to provide a combined description of hydrogen bonds and halogen bonds [445].…”

Section: The Importance In Drug Design Of Similar To Hb Bondsmentioning

confidence: 99%

“…The relationships between the interaction strengths and various geometric and electronic structures, as well as topological properties, have been established [445], with a particular focus on the uniformity of hydrogen bonds and halogen bonds types of interaction. The dependence of the BSSE-corrected interaction energy (ΔE cor ) on the interatomic distance (rA /N ) appeared to be nonlinear for both halogen-bonded and hydrogen-bonded systems; the relationship between ΔE cor and the difference between r A/N and the sum of the van der Waals radii (Δr A/N ) can be fitted to a combined quadratic regression equation.…”

Section: The Importance In Drug Design Of Similar To Hb Bondsmentioning

confidence: 99%

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It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

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The effect of weak intermolecular interactions on the binding affinity between ligand-protein complexes plays an important role in stabilizing a ligand at the interface of a protein structure. In this review article, we will explore the different ways of taking into account these interactions, mainly intramolecular hydrogen bonds, in docking calculations. Their possible limitations and their suitable application domains are highlighted. Inspection of the outliers of this study probed very stimulating, as it provides opportunities and inspiration to medicinal chemists, being a reminder of the impact that minimal chemical modifications can have on biological activities.

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Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Abstract: Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.

Cited by 31 publications

References 80 publications

Conformer Distribution in Rotaxanes Containing Nonsymmetric Threads: A Systematic Approach

Conformer Distribution in Rotaxanes Containing Nonsymmetric Threads: A Systematic Approach

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

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