Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes

Fanfrlík, Jindřich; Holub, Josef; Růžičková, Zdeňka; Řezáč, Jan; Lane, Paul D.; Wann, Derek A.; Hnyk, Drahomı́r; Růžička, Aleš; Hobza, Pavel

doi:10.1002/cphc.201600848

Cited by 45 publications

(41 citation statements)

References 36 publications

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“…Therefore, in YBs, as well as in other non-covalent interactions, the importance of the electrostatic interaction term is uppermost [426,437]. Several works have been carried out regarding the tunability of the mentioned σ -holes in different types of interactions, including halogen, chalcogen, and pnicogen [438,439,440,441]. In particular, the effect on the σ -hole upon substitution on aromatic rings has been previously studied [438,442,443,444].…”

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

confidence: 99%

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

confidence: 99%

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

Yunta¹

2017

AJMO

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“…[16][17][18][19][20] However, some aspects of halogen bonds are not yet fully explored. Whereas competition with other inter-or intramolecular interactions, such as hydrogen and chalcogen bonds and C H•••π and lone-pair•••π interactions, has been the subject of numerous studies, [15,[21][22][23][24][25][26][27][28][29][30] in the current study we focus on an aromatic system with no functional groups besides the halogen (halobenzene; see below). Systematic studies on varying halogen-bonded systems may help to increase our knowledge of this fascinating type of non-covalent interaction.…”

Section: Introductionmentioning

confidence: 99%

Halogen bonding in mono‐ and dihydrated halobenzene

Hogan

Mourik

2018

J Comput Chem

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Density functional theory calculations were performed on halogen‐bonded and hydrogen‐bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06‐2X density functional with the 6‐31+G(d) (for C, H, F, Cl, and Br) and aug‐cc‐pVDZ‐PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh‐H2O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••Ow internuclear separation (where Ow is the water oxygen). For all XPh‐H2O systems hydrogen‐bonded systems exist, containing a combination of CH•••Ow and OwHw•••X hydrogen bonds. For all systems except X = At the X•••Hw hydrogen‐bonding interaction is stronger than the X•••Ow halogen bond. In the XPh‐(H2O)2 system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the CH bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as CH•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.

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“…For the calculations of deprotonated Pen ( Pen ‐H) and its complexes with Zn(II) ion, the resolution of identity density functional theory (RI‐DFT) method augmented with empirical dispersion (D3) was combined with the B3LYP/DZVP level for molecular dynamics (MD) and optimisation . All compounds were calculated in the single state.…”

Section: Methodsmentioning

confidence: 99%

Complexation and stability of the fungicide penconazole in the presence of zinc and copper ions

Kovač

Jakl

Fanfrlík

et al. 2020

Rapid Comm Mass Spectrometry

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Rationale:For the risk assessment of penconazole in the environment and the evaluation of the possible consequences of its use, it is important to determine how its reactivity and degradation are influenced by metals commonly found in nature, such as copper and zinc. Methods:Changes in the reactivity of penconazole in the presence of zinc/copper ions were studied using electrospray ionisation mass spectrometry and density functional theory calculations.Results: Many penconazole complexes with copper and zinc ions were created; a comparison of the elements showed that a few complexes were formed analogously (doubly charged complexes with four penconazole molecules, singly charged complexes with chlorine as a counterion and singly charged complexes with deprotonated penconazole as a counterion). The metal complexes with different structures indicated different reactivity of penconazole with copper and zinc. Conclusions:The experimental and computational approaches have revealed different changes in the structure of penconazole. In the Zn(II) complex, penconazole deprotonated to stabilise the bond to Zn(II). In the Cu(II) complex, it loses one chlorine atom, creates an additional ring between the triazole ring and the phenyl ring, and/or creates a double bond in the short aliphatic chain.

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Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes

Cited by 45 publications

References 36 publications

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

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

Halogen bonding in mono‐ and dihydrated halobenzene

Complexation and stability of the fungicide penconazole in the presence of zinc and copper ions

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