The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths

Lubbe, Stephanie C. C. van der; Guerra, Célia Fonseca

doi:10.1002/asia.201900717

Cited by 148 publications

(85 citation statements)

References 91 publications

(237 reference statements)

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“…(Figure 4). The relatively large deviation from 180 of all three <N…H-C is may be affected by the dispersion interactions, which can have an impact on the geometry of HBs in bulky systems [42]. Unlike in 1, in 3 the XB formation favors I … S interactions.…”

Section: Resultsmentioning

confidence: 99%

A Novel Halogen Bond Acceptor: 1-(4-Pyridyl)-4-Thiopyridine (PTP) Zwitterion

2020

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Sulfur is a widely used halogen bond (XB) acceptor, but only a limited number of neutral XB acceptors with bifurcated sp3-S sites have been reported. In this work a new bidentate XB acceptor, 1-(4-pyridyl)-4-thiopyridine (PTP), which combines sp3-S and sp2-N acceptor sites, is introduced. Three halogen bonded cocrystals were obtained by using 1,4-diiodobenzene (DIB), 1,4-diiodotetrafluorobenzene (DIFB), and iodopentafluorobenzene (IPFB) as XB donors and PTP as acceptor. The structures of the cocrystals showed some XB selectivity between the S and N donors in PTP. However, the limited contribution of XB to the overall molecular packing in these three cocrystals and the results from DSC measurements clearly point out the synergetic influence and interplay of all noncovalent interactions in crystal packing of these compounds.

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Section: Resultsmentioning

confidence: 99%

A Novel Halogen Bond Acceptor: 1-(4-Pyridyl)-4-Thiopyridine (PTP) Zwitterion

2020

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“…The Amsterdam Density Functional (ADF) [76] modelling suite at the B3LYP [71,72]-D3 [73]/TZ2P [74,75] level of theory (no frozen cores) was used for energy decomposition and ‘atoms in molecules’ [77] analyses. Details of the Morokuma-Ziegler inspired energy decomposition scheme used in the ADF-suite have been reported elsewhere [76,78] and the scheme has proven useful to evaluate hydrogen bonding interactions [79].…”

Section: Methodsmentioning

confidence: 99%

Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study

Mooibroek

2019

Molecules

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A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X–CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ –1.5 kcal·mol−1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤–5 kcal·mol−1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol−1 in cationic species like [Me3O+-CH3···OH2]+ (8a).

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“…The acting forces between molecules include hydrogen bonding, van der Waals forces, hydrophobic interaction, electrostatic interaction, p-p stacking and salt bonding (Zhu et al, 2018;Wang et al, 2019c;Wu et al, 2019b;Yasrebi et al, 2019). Hydrogen bonding is produced by the covalent bonding of hydrogen atoms with more electronegative atoms, such as oxygen, nitrogen and sulphur (Cleland, 2010;Liu et al, 2019;van der Lubbe & Fonseca Guerra, 2019). The formation of hydrogen bonding is an interatomic interaction and is generally included in all molecular docking.…”

Section: The Mechanisms Of Interactions Between Moleculesmentioning

confidence: 99%

Recent developments in molecular docking technology applied in food science: a review

Tao

Huang

Wang

et al. 2019

Int J of Food Sci Tech

133

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Molecular docking is a theoretical simulation method based on bioinformatics, which studies the interaction between molecules (such as ligands and receptors), and predicts their binding modes and affinity via a computer platform. This technology acts as a promising mean in medicinal chemistry such as structurebased rational drug design, which is accepted by researchers in the scientific community. During recent years, various fundamental studies involving biomolecular interaction in the food matrix have gradually emerged. The remarkable advantages of molecular docking such as predicting experiments are attracting increasing attention for its application potential in various fields. This review presents the theory and software development of molecular docking, and emphasises its application in the field of food science, including nutritional components and food safety. Moreover, the operational mechanisms of molecular docking are further summarised in this review.

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The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths

Cited by 148 publications

References 91 publications

A Novel Halogen Bond Acceptor: 1-(4-Pyridyl)-4-Thiopyridine (PTP) Zwitterion

A Novel Halogen Bond Acceptor: 1-(4-Pyridyl)-4-Thiopyridine (PTP) Zwitterion

Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study

Recent developments in molecular docking technology applied in food science: a review

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