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Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation.

ABSTRACT: Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution.

SUBMITTER: Danelius E

PROVIDER: S-EPMC5510091 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Preorganization: A Powerful Tool in Intermolecular Halogen Bonding in Solution.

Project description:Preorganization is a powerful tool in supramolecular chemistry which has been utilized successfully in intra- and intermolecular halogen bonding. In previous work, we had developed a bidentate bis(iodobenzimidazolium)-based halogen bond donor which featured a central trifluoromethyl substituent. This compound showed a markedly increased catalytic activity compared to unsubstituted bis(iodoimidazolium)-based Lewis acids, which could be explained either by electronic effects (the electron withdrawal by the fluorinated substituent) or by preorganization (the hindered rotation of the halogen bonding moieties). Herein, we systematically investigate the origin of this increased Lewis acidity via a comparison of the two types of compounds and their respective derivatives with or without the central trifluoromethyl group. Calorimetric measurements of halide complexations indicated that preorganization is the main reason for the higher halogen bonding strength. The performance of the catalysts in a series of benchmark reactions corroborates this finding.

| S-EPMC7011185 | biostudies-literature

Halogen bonding in the co-crystallization of potentially ditopic diiodotetrafluorobenzene: a powerful tool for constructing multicomponent supramolecular assemblies.

Project description:Halogen bonding is emerging as a significant driving force for supramolecular self-assembly and has aroused great interest during the last two decades. Among the various halogen-bonding donors, we take notice of the ability of 1,4-diiodotetrafluorobenzene (1,4-DITFB) to co-crystallize with diverse halogen-bonding acceptors in the range from neutral Lewis bases (nitrogen-containing compounds, N-oxides, chalcogenides, aromatic hydrocarbons and organometallic complexes) to anions (halide ions, thio/selenocyanate ions and tetrahedral oxyanions), leading to a great variety of supramolecular architectures such as discrete assemblies, 1D infinite chains and 2D/3D networks. Some of them act as promising functional materials (e.g. fluorescence, phosphorescence, optical waveguide, laser, non-linear optics, dielectric and magnetism) and soft materials (e.g. liquid crystal and supramolecular gel). Here we focus on the supramolecular structures of multicomponent complexes and their related physicochemical properties, highlight representative examples and show clearly the main directions that remain to be developed and improved in this area. From the point of view of crystal engineering and supramolecular chemistry, the complexes summarized here should give helpful information for further design and investigation of the elusive category of halogen-bonding supramolecular functional materials.

| S-EPMC8288552 | biostudies-literature

Halogen bonding (X-bonding): a biological perspective.

Project description:The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure-energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials.

| S-EPMC3588911 | biostudies-literature

"Anti-Electrostatic" Halogen Bonding.

Project description:Halogen bonding is often described as being driven predominantly by electrostatics, and thus adducts between anionic halogen bond (XB) donors (halogen-based Lewis acids) and anions seem counterintuitive. Such "anti-electrostatic" XBs have been predicted theoretically but for organic XB donors, there are currently no experimental examples except for a few cases of self-association. Reported herein is the synthesis of two negatively charged organoiodine derivatives that form anti-electrostatic XBs with anions. Even though the electrostatic potential is universally negative across the surface of both compounds, DFT calculations indicate kinetic stabilization of their halide complexes in the gas phase and particularly in solution. Experimentally, self-association of the anionic XB donors was observed in solid-state structures, resulting in dimers, trimers, and infinite chains. In addition, co-crystals with halides were obtained, representing the first cases of halogen bonding between an organic anionic XB donor and a different anion. The bond lengths of all observed interactions are 14-21 % shorter than the sum of the van der Waals radii.

| S-EPMC7317790 | biostudies-literature

Activation of a Metal-Halogen Bond by Halogen Bonding.

Project description:In recent years, the non-covalent interaction of halogen bonding (XB) has found increasing application in organocatalysis. However, reports of the activation of metal-ligand bonds by XB have so far been limited to a few reactions with elemental iodine or bromine. Herein, we present the activation of metal-halogen bonds by two classes of inert halogen bond donors and the use of the resulting activated complexes in homogenous gold catalysis. The only recently explored class of iodolium derivatives were shown to be effective activators in two test reactions and their activity could be modulated by blocking of the Lewis acidic sites. Bis(benzimidazolium)-based halogen bonding activators provided even more rapid conversion, while the non-iodinated reference compound showed little activity. The role of halogen bonding in the activation of metal-halogen bonds was further investigated by NMR experiments and DFT calculations, which support the mode of activation occurring via halogen bonding.

| S-EPMC7540446 | biostudies-literature

Halogen Bonding in Perfluoroalkyl Adsorption.

Project description:Adsorption is a promising technology to remove perfluoroalkyl substances (PFAS), including perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), from contaminated water. Although a large number of materials have been evaluated for PFAS adsorption, guidelines that can facilitate the rational design and selection of adsorbents have not been established due to the lack of a mechanistic understanding on the molecular level. Using a novel interpretation of the Freundlich isotherm, this study identifies halogen bonding as the main mechanism controlling perfluoroalkyl adsorption by using a materiomic approach that compares the electrostatic polarities of a variety of carbon, polymer, and mineral-based materials reported in the literature. Comparisons show that both PFOS and PFOA are favorably adsorbed by materials containing high densities of π electrons, lone electron pairs, and negative charges, consistent with the formation of halogen bonding between the positive σ-hole of fluorine as a Lewis acid and a nucleophilic solid as a Lewis base. The identification of this previously unappreciated noncovalent bonding mechanism offers fresh insight into the search of suitable materials for perfluoroalkyl adsorption.

| S-EPMC11190928 | biostudies-literature

Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding.

Project description:The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin-orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C-At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.

| S-EPMC8347445 | biostudies-literature

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective.

Project description:We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A(-) and the analogous hydrogen-bonded complexes DH⋅⋅⋅A(-) (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A(-) arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO-LUMO interactions between the lone pair of A(-) and the σ* orbital of D-X.

| S-EPMC3922460 | biostudies-literature

Modulation of the Selectivity in Anions Recognition Processes by Combining Hydrogen- and Halogen-Bonding Interactions.

Project description:Most of the halogen bonding receptors for anions described use halogen bonding binding sites solely in the anion recognition process; only a few examples report the study of anion receptors in which the halogen bonding interaction has been used in combination with any other non-covalent interaction. With the aims to extend the knowledge in the behaviour of this kind of mixed receptors, we report here the synthesis and the anion recognition and sensing properties of a new halogen- and hydrogen- bonding receptor which binds anions by the cooperation of both non-covalent interactions. Fluorescence studies showed that the behaviour observed in the anion recognition sensing is similar to the one previously described for the halogen analogue and is quite different to the hydrogen one. On the other hand, the association constants obtained by ¹H-NMR data demonstrate that the mixed halogen- and hydrogen-bonding receptor is more selective for SO?2- anion than the halogen or hydrogen analogues.

| S-EPMC6149874 | biostudies-literature

Hydrogen bonding <i>vs.</i> halogen bonding: the solvent decides.

Project description:Control of intermolecular interactions is integral to harnessing self-assembly in nature. Here we demonstrate that control of the competition between hydrogen bonds and halogen bonds, the two most highly studied directional intermolecular interactions, can be exerted by choice of solvent (polarity) to direct the self-assembly of co-crystals. Competitive co-crystal formation has been investigated for three pairs of hydrogen bond and halogen bond donors, which can compete for a common acceptor group. These competitions have been examined in seven different solvents. Product formation has been determined and phase purity has been examined by analysis of powder X-ray diffraction patterns. Formation of hydrogen-bonded co-crystals is favoured from less polar solvents and halogen-bonded co-crystals from more polar solvents. The solvent polarity at which the crystal formation switches from hydrogen-bond to halogen-bond dominance depends on the relative strengths of the interactions, but is not a function of the solution-phase interactions alone. The results clearly establish that an appreciation of solvent effects is critical to obtain control of the intermolecular interactions.

| S-EPMC5585772 | biostudies-literature

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