Halogen bonding (X-bonding): a biological perspective

Halogen bonding controls selectivity of FRET substrate probes for MMP-9

Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases that catalyze cleavage of extracellular matrix and nonmatrix proteins. MMPs play a role in tissue remodeling, and their uncontrolled activity is associated with number of diseases, including tumor metastasis. Thus, there is a need to develop methods to monitor MMP activity, and number of probes has been previously described. The key problem many probes encounter is the issue of selectivity, since 23 human MMPs, despite playing different physiological roles, have structurally similar active sites. Here, we introduce the halogen bonding concept into the probe design and show that the probe containing iodine exhibits an unprecedented selectivity for MMP-9. We provide structure-based explanation for the selectivity, confirming that it is due to formation of the halogen bond that supports catalysis, and we highlight the value of exploring halogen bonding in the context of selective probe design.

Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl₄, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability.

Probing halogen bonds with solid-state NMR spectroscopy: observation and interpretation of J(77Se,31P) coupling in halogen-bonded PSe⋯I motifs

Intra-halogen bond J couplings measured via NMR spectroscopy and interpreted using natural localized molecular orbitals offer novel insights into this class of non-covalent interaction.

Control of active semiconducting layer packing in organic thin film transistors through synthetic tailoring of dielectric materials

The influence of dielectric material's property on the solid state structure packing of active semiconducting layer in OTFTs has been carefully studied by employing a whole new family of dielectric materials based on the rigid, tetrahedral bulky moleculei.e.adamantane, a smallest cage structure of diamond.

Graded IR Filters: Distinguishing Between Single and Multipoint NO2···I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons)

The NO2···I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2···I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2···I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and R and in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.

Electrochemical controlling and monitoring of halogen bond formation in solution

Cyclic voltammetry has been used for the first time to probe and to activate non-covalent halogen bonding via redox switching in solution.

Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases

Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.

Influence of ring size on the strength of carbon bonding complexes between anions and perfluorocycloalkanes

High level ab initio calculations and Cambridge Structural Database analysis were used to demonstrate the importance of carbon bonding in cyclobutane rings.

Biomolecular halogen bonds

Halogens are atypical elements in biology, but are common as substituents in ligands, including thyroid hormones and inhibitors, which bind specifically to proteins and nucleic acids. The short-range, stabilizing interactions of halogens - now seen as relatively common in biology - conform generally to halogen bonds characterized in small molecule systems and as described by the σ-hole model. The unique properties of biomolecular halogen bonds (BXBs), particularly in their geometric and energetic relationship to classic hydrogen bonds, make them potentially powerful tools for inhibitor design and molecular engineering. This chapter reviews the current research on BXBs, focusing on experimental studies on their structure-energy relationships, how these studies inform the development of computational methods to model BXBs, and considers how BXBs can be applied to the rational design of more effective inhibitors against therapeutic targets and of new biological-based materials.

Exploring the C-X…π halogen bonding motif: an infrared and Raman study of the complexes of CF₃X (X = Cl, Br and I) with the aromatic model compounds benzene and toluene

The formation of halogen bonded complexes formed between the trifluorohalomethanes CF₃Cl, CF₃Br and CF₃I and the Lewis bases benzene and toluene at temperatures below 150K was investigated using FTIR and Raman spectroscopy. Experiments using liquid krypton as solvent show that for both CF₃Br and CF₃I substantial fractions of the monomers can be involved in 1:1 complexes. In addition, weak absorptions illustrating the formation of 2:1 complexes between CF₃I and benzene are observed. Using spectra recorded at temperatures between 120 and 140 K, observed information on the relative stability was obtained for all complexes by determining the complexation enthalpies in solution. The resulting values for CF₃Br.benzene, CF₃I.benzene and (CF₃I)₂.benzene are -6.5(3), -7.6(2) and -14.5(9) kJ mol⁻¹. The values for CF₃Br.toluene and CF₃I.toluene are -6.2(5) and -7.4(5) kJ mol⁻¹. The experimental complexation enthalpies are compared with theoretical data obtained by combining results from MP2/aug-cc-pVDZ(-PP) and MP2/aug-cc-pVTZ(-PP) ab initio calculations, from statistical thermodynamical calculations and from Monte Carlo Free Energy Perturbation simulations. The data are also compared with results derived for other C-X···π halogen bonded complexes involving unsaturated Lewis bases such as ethene and ethyne.