Comparative investigation of interactions of hydrogen, halogen and tetrel bond donors with electron-rich and electron-deficient π-systems

Recently, noncovalent interactions in complexes and crystals have attracted considerable interest. The current study was thus designed to gain a better understanding of three seminal types of noncovalent interactions, namely: hydrogen, halogen and tetrel interactions with π-systems. This study was performed on three models of Lewis acids: X₃–C–H, F₃–C–X and F–T–F₃ (where X = F, Cl, Br and I; and T = C, Si, Ge and Sn) and three π-systems as Lewis bases: benzene (BZN), 1,3,5-trifluorobenzene (TFB) and hexafluorobenzene (HFB). Quantum mechanical calculations, including geometrical optimization, molecular electrostatic potential (MEP), maximum positive electrostatic potential (V_s,max), Point-of-Charge (PoC), potential energy surface (PES), quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) calculations, were carried out at the MP2/aug cc-pVDZ level of theory. The binding energies were additionally benchmarked at the CCSD(T)/CBS level. The results showed that: (i) the binding energies of the X₃–C–H⋯π-system complexes were unexpectedly inversely correlated with the V_s,max values on the hydrogen atom but directly correlated with the X atomic sizes; (ii) the binding energies for the F₃–C–X⋯π-system and F–T–F₃⋯π-system complexes were correlated with the σ-hole magnitudes of the X and T atoms, respectively; and (iii) for the F₃–C–F⋯π-system complexes, the binding energy was as strong as the π-system was electron-deficient, indicating the dominating nucleophilic character of the fluorine atom. NCI analysis showed that the unexpected trend of X₃–C–H⋯π-system binding energies could be attributed to additional attractive interactions between the X atoms in the X₃–C–H molecule and the carbon atoms of the π-system. Furthermore, the I₃–Sn–H molecule was employed as a case study of hydrogen, halogen and tetrel interactions with π-systems. It was found that hydrogen and halogen interactions of the I₃–Sn–H molecule correlated with the electron-richness of the π-system. In contrast, tetrel interactions correlated with the electron deficiency of the π-system.

Three seminal types of noncovalent interaction, namely: hydrogen, halogen and tetrel interactions with π-systems, were investigated using quantum mechanical calculations.

Lone pair⋯π interaction versus σ-hole appearance in metal-bonded halogens

Three complexes of N-(2,5-diluorophenyl)-2-pyrazine carboxamide and ZnX₂ have been synthesized. The crystal structures reveal that in all three coordination compounds, metal-bound halides have interacted with π systems through a negative electrostatic region.

Force Fields for Small Molecules

Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.

Salt Bridge in Ligand-Protein Complexes-Systematic Theoretical and Statistical Investigations

Although the salt bridge is the strongest among all known noncovalent molecular interactions, no comprehensive studies have been conducted to date to examine its role and significance in drug design. Thus, a systematic study of the salt bridge in biological systems is reported herein, with a broad analysis of publicly available data from Protein Data Bank, DrugBank, ChEMBL, and GPCRdb. The results revealed the distance and angular preferences as well as privileged molecular motifs of salt bridges in ligand-receptor complexes, which could be used to design the strongest interactions. Moreover, using quantum chemical calculations at the MP2 level, the energetic, directionality, and spatial variabilities of salt bridges were investigated using simple model systems mimicking salt bridges in a biological environment. Additionally, natural orbitals for chemical valence (NOCV) combined with the extended-transition-state (ETS) bond-energy decomposition method (ETS-NOCV) were analyzed and indicated a strong covalent contribution to the salt bridge interaction. The present results could be useful for implementation in rational drug design protocols.

Quantitative Assessment of Tetrel Bonding Utilizing Vibrational Spectroscopy

A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of -1.4 to -26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.

Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor-Ligand Interactions

Here, we predicted the potential halogen bonding interaction between compound 2 and the 5-hydroxytryptamine 2B (5-HT_2B) receptor and systematically assessed this interaction via structure-activity relationship analysis and molecular dynamics simulations. A physics-based computational protocol was then developed to further explore the opportunity of "designing in" halogen bonding interactions in structure-based ligand design for the 5-HT_2B receptor, which not only facilitated the identification of previously uncharacterized halogen bonds in known 5-HT_2B ligands but also enabled the rational design of halogen bonding interactions for the optimization of 5-HT_2B ligands. As a proof-of-concept, a series of halogen-substituted analogues of doxepin was synthesized and evaluated, which showed improved in vitro and in vivo potency.

Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field

Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to R_min provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.

Amino Acid Hot Spots of Halogen Bonding: A Combined Theoretical and Experimental Case Study of the 5-HT7 Receptor

A computational approach combining a structure-activity relationship library of halogenated and the corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was used to search for amino acids frequently targeted by halogen bonding (hot spots) in a 5-HT₇R as a case study. The procedure identified two sets of hot spots, extracellular (D2.65, T2.64, and E7.35) and transmembrane (C3.36, T5.39, and S5.42), which were further verified by a synthesized library of halogenated arylsulfonamide derivatives of (aryloxy)ethylpiperidines. It was found that a halogen bond formed between T5.39 and a bromine atom at 3-position of the aryloxy fragment caused the most remarkable, 35-fold increase in binding affinity for 5-HT₇R when compared to the nonhalogenated analog. The proposed paradigm of halogen bonding hot spots was additionally verified on D₄ dopamine receptor showing that it can be used in rational drug design/optimization for any protein target.

Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases

The new aminoalkyl-substituted derivatives of known CK2 inhibitors 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi) and 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) were synthesized, and their influence on the activity of recombinant human CK2 α, CK2 holoenzyme and PIM1 kinases was evaluated. All derivatives inhibited the activity of studied kinases and the most efficient were aminopropyl-derivatives 8b and 14b. These compounds also exerted inhibition of cancer cell lines - CCRF-CEM (acute lymphoblastoid leukemia), MCF-7 (human breast cancer), and PC-3 (prostate cancer) proliferation and their EC₅₀ is comparable with the value for clinically studied CK2 inhibitor CX-4945. Preliminary structure activity relationship analysis indicated that the spacer length affected antitumor potency, and two to three methylene units were more favorable. The complex of CK2 α^1-335/8b was crystallized, both under high-salt conditions and under low-salt conditions giving crystals which diffracted X-rays to about 2.4 Å resolution, what enabled the determination of the corresponding 3D-structures.

Halogen-Aromatic π Interactions Modulate Inhibitor Residence Times

Prolonged drug residence times may result in longer-lasting drug efficacy, improved pharmacodynamic properties, and "kinetic selectivity" over off-targets with high drug dissociation rates. However, few strategies have been elaborated to rationally modulate drug residence time and thereby to integrate this key property into the drug development process. Herein, we show that the interaction between a halogen moiety on an inhibitor and an aromatic residue in the target protein can significantly increase inhibitor residence time. By using the interaction of the serine/threonine kinase haspin with 5-iodotubercidin (5-iTU) derivatives as a model for an archetypal active-state (type I) kinase-inhibitor binding mode, we demonstrate that inhibitor residence times markedly increase with the size and polarizability of the halogen atom. The halogen-aromatic π interactions in the haspin-inhibitor complexes were characterized by means of kinetic, thermodynamic, and structural measurements along with binding-energy calculations.

A π-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors

Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dibenzo[b,d]furan-3(2H)-one (4a) and (E)-1,3-dichloro-6-[(4-methoxyphenylimino)-methyl]dibenzo[b,d]furan-2,7-diol (5) were tested for inhibition of CK2 and induction of apoptosis in LNCaP cells. Both turned out to be tight binding inhibitors, with IC₅₀ values of 7 nM (4a) and 5 nM (5) and an apparent K_i value of 0.4 nM for both. Compounds 4a and 5 reduced cellular CK2 activity, indicating cell permeability. Cell viability was substantially impaired in LNCaP cells, as well as apoptosis was induced, which was not appearing in non-neoplastic ARPE-19 cells. Co-crystallization of 4a and 5 revealed an unexpected π-halogen bond of the chloro substituent at C9 with the gatekeeper amino acid Phe113, leading to an inverted binding mode in comparison to parent compound 4b, with the Cl at C6 instead, which was co-crystallized as a control. This indicates that the position of the chloro substituent on ring A of the dibenzofuran scaffold is responsible for an inversion of the binding mode that enhances potency.

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator

The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.

Cation-cation and anion-anion complexes stabilized by halogen bonds

Stable minima showing halogen bonds between charged molecules with the same sign have been explored by means of theoretical calculations. The dissociation transition states and their corresponding barriers have also been characterized. In all cases, the results indicate that the complexes are thermodynamically unstable but kinetically stable with respect to the isolated monomers in gas phase. A corrected binding energy profile by removing the charge-charge repulsion of the monomers shows a profile similar to the one observed for the dissociation of analogous neutral systems. The nature of the interaction in the minima and TSs has been analyzed using the symmetry adapted perturbation theory (SAPT) method. The results indicate the presence of local favorable electrostatic interactions in the minima that vanish in the TSs. Natural bond orbital (NBO) and "atoms-in-molecules" (AIM) theories were used to analyze the complexes, obtaining good correlations between Laplacian and electron density values with both bond distances and charge-transfer energy contributions E(2). The largest E(2) orbital interaction energies for cation-cation and anion-anion complexes are 561.2 and 197.9 kJ mol^-1, respectively.

Site specificity of halogen bonding involving aromatic acceptors

Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.

Metabolic Epoxidation Is a Critical Step for the Development of Benzbromarone-Induced Hepatotoxicity

Benzbromarone (BBR) is effective in the treatment of gout; however, clinical findings have shown it can also cause fatal hepatic failure. Our early studies demonstrated that CYP3A catalyzed the biotransformation of BBR to epoxide intermediate(s) that reacted with sulfur nucleophiles of protein to form protein covalent binding both in vitro and in vivo. The present study attempted to define the correlation between metabolic epoxidation and hepatotoxicity of BBR by manipulating the structure of BBR. We rationally designed and synthesized three halogenated BBR derivatives, fluorinated BBR (6-F-BBR), chlorinated BBR (6-Cl-BBR), and brominated BBR (6-Br-BBR), to decrease the potential for cytochrome P450-mediated metabolic activation. Both in vitro and in vivo uricosuric activity assays showed that 6-F-BBR achieved favorable uricosuric effect, while 6-Cl-BBR and 6-Br-BBR showed weak uricosuric efficacy. Additionally, 6-F-BBR elicited much lower hepatotoxicity in mice. Fluorination of BBR offered advantage to metabolic stability in liver microsomes, almost completely blocked the formation of epoxide metabolite(s) and protein covalent binding, and attenuated hepatic and plasma glutathione depletion. Moreover, the structural manipulation did not alter the efficacy of BBR. This work provided solid evidence that the formation of the epoxide(s) is a key step in the development of BBR-induced hepatotoxicity.

A systematic analysis of atomic protein-ligand interactions in the PDB

As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.

Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions

The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π-π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π-π contacts in high-scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand-protein interfaces lies the foundation for the development of type-specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand-protein complexes is available at https://github.com/michal-brylinski/earomatic. The dataset comprising experimental complex structures and computer-generated models is available at https://osf.io/rztha/.

Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding?

Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol^-1) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CH^δ+OH₂ interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol^-1 K^-1) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol^-1 K^-1 consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong interaction potentials with the electron lone pairs of the oxygen atom of the water molecules and thus IXBs provide the most stable hydrated structures of the bromobenzene and iodobenzene radical cations. The results clearly distinguish the hydration behaviors resulting from the ionic hydrogen and halogen bonding interactions of fluorobenzene and iodobenzene cations, respectively, and establish the different bonding and structural features of the two interactions.

Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding?

Halogens are present in a significant number of drugs, contributing favorably to ligand-protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand-protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C-X···HBD orientations. Notably, the orientation dependence of the halogen-HBD (X-HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from -2 to -14 kcal/mol. This contrasts halogen bonds in that X-HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence, such that they make significant, favorable contributions to ligand-protein binding and, therefore, should be actively considered during rational ligand design.

Halogen Bonding in Nucleic Acid Complexes

Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.

Halogen-π Interactions in the Cytochrome P450 Active Site: Structural Insights into Human CYP2B6 Substrate Selectivity

Numerous cytochrome P450 (CYP) 2B6 substrates including drugs and environmental chemicals are halogenated. To assess the role of halogen-π bonds in substrate selectivity and orientation in the active site, structures of four CYP2B6 monoterpenoid complexes were solved by X-ray crystallography. Bornyl bromide exhibited dual orientations in the active site with the predominant orientation revealing a bromine-π bond with the Phe108 side chain. Bornane demonstrated two orientations with equal occupancy; in both, the C2 atom that bears the bromine in bornyl bromide was displaced by more than 2.5 Å compared with the latter complex. The bromine in myrtenyl bromide π-bonded with Phe297 in CYP2B6, whereas the two major orientations in the active site mutant I114V exhibited bromine-π interactions with two additional residues, Phe108 and Phe115. Analysis of existing structures suggests that halogen-π interactions may be unique to the CYP2B enzymes within CYP family 2 but are also important for CYP3A enzymes.

Development of Halogenase Enzymes for Use in Synthesis

Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.

In silico approach to investigating the adsorption mechanisms of short chain perfluorinated sulfonic acids and perfluorooctane sulfonic acid on hydrated hematite surface

Short chain perfluorinated sulfonic acids (PFSAs) that were introduced as alternatives for perfluorooctane sulfonic acid (PFOS) have been widely produced and used. However, few studies have investigated the environmental process of short chain PFSAs, and the related adsorption mechanisms still need to be uncovered. The water-oxide interface is one of the major environmental interfaces that plays an important role in affecting the adsorption behaviour and transport potential of the environmental pollutant. In this study, we performed molecular dynamics simulations and quantum chemistry calculations to investigate the adsorption mechanisms of five PFSAs and their adsorption on hydrated hematite surface as well. Different to the vertical configuration reported for PFOS on titanium oxide, all PFSAs share the same adsorption configuration as the long carbon chains parallel to the surface. The formation of hydrogen bonds between F and inter-surface H helps to stabilize the unique configuration. As a result, the sorption capacity increases with increasing C-F chain length. Moreover, both calculated adsorption energy and partial density of states (PDOS) analysis demonstrate a PFSAs adsorption mechanism in between physical and chemical adsorption because the hydrogen bonds formed by the overlap of F (p) orbital and H (s) orbital are weak intermolecular interactions while the physical adsorption are mainly ascribed to the electrostatic interactions. This massive calculation provides a new insight into the pollutant adsorption behaviour, and in particular, may help to evaluate the environmental influence of pollutants.

Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)—F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to ansp3-hybridized C atom in the case of A1 and to ansp2hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3—F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4—F1...O1 and 174° at ∠C10—O1...F1) Csp2—F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG–NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine andviceversaprovides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy

The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular docking with binding free-energy calculations was successfully used to reproduce the X-ray geometries of protein–ligand complexes with halogen bonding. The procedure involves quantum-polarized ligand docking (QPLD) to obtain the QM-derived ligand atomic charges in the protein environment at the B3PW91/cc-pVTZ level and the MM/GBSA (generalized-Born/surface area) algorithm to calculate the binding free energies of resultant complexes. The performance was validated using a set of 106 X-ray complexes and compared with the Glide and AutoDock VinaXB scoring functions in terms of RMSD and the reconstruction of halogen-bond geometry (distance and σ-hole angle). The results revealed that docking and scoring using the QPLD–GBSA procedure outperformed the remaining scoring functions in the majority of instances. Additionally, a comparison of the orientation of the top ranked binding poses calculated using the fixed atomic charges of ligands obtained from force-field parameterization and by QM calculations in the protein environment provides strong evidence that the use of QM-derived charges is significant.

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

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

Hydractinia echinata test-system. IV. Toxic synergism of human pharmaceuticals in mixtures with iodoform

The structure-toxicity relationships for a series of singular human stomatological pharmaceuticals preparations and in mixture with Iodoform on Hydractinia echinata were obtained and their synergism was analyzed through the Metamorphosis Reduction Concentration (MRC50) within the "Köln model". The differences manifested between the total and individual components of the samples and mixtures, associated with toxic versus non-toxic synergism, are dependent on three essential factors of synthesis (the nature, the concentration and the number) besides manifested isotoxicity of the given components. The method represents a practical alternative useful for the reduction of experimental tests on animal to the lowest possible level, in accordance to the '3Rs' (reduce, reuse and recycle) integrative concept.

Assessment of DFT Functionals for QTAIM Topological Analysis of Halogen Bonds with Benzene

Halogen bonding, a noncovalent interaction between a halogen atom and a nucleophilic site, is receiving a growing attention in the chemical community stimulating a large number of theoretical investigations. The density functional theory (DFT) approach revealed to be one of the most suitable methods owing to its accuracy and low computational cost. We report here a detailed analysis of the performance of an extensive set of DFT functionals in reproducing accurate binding energies and topological properties for the halogen-bonding interaction of either NCX or PhX molecules (X = F, Cl, Br, I) with the aromatic system of benzene in the T-shaped configuration. It was found that the better performance for both sets of properties is provided by a small subset of functionals able to take into account, implicitly or explicitly (by inclusion of an additive pairwise potential), the dispersion contribution, that is, ωB97X, M06-2X, M11, mPW2PLYP-D, and B2PLYP-D3.

Exploring the (Very Flat) Potential Energy Landscape of R-Br⋅⋅⋅π Interactions with Accurate CCSD(T) and SAPT Techniques

Halogen bonds involving an aromatic moiety as an acceptor, otherwise known as R-X⋅⋅⋅π interactions, have increasingly been recognized as being important in materials and in protein-ligand complexes. These types of interactions have been the subject of many recent investigations, but little is known about the ways in which the strengths of R-X⋅⋅⋅π interactions vary as a function of the relative geometries of the interacting pairs. Here we use the accurate CCSD(T) and SAPT2+3δMP2 methods to investigate the potential energy landscapes for systems of HBr, HCCBr, and NCBr complexed with benzene. It is found that only the separation between the complexed molecules have a strong effect on interaction strength while other geometric parameters, such as tilting and shifting R-Br⋅⋅⋅π donor relative to the benzene plane, affect these interactions only mildly. Importantly, it is found that the C_6v (T-shaped) configuration is not the global minimum for any of the dimers investigated.

The Important Role of Halogen Bond in Substrate Selectivity of Enzymatic Catalysis

The use of halogen bond is widespread in drug discovery, design, and clinical trials, but is overlooked in drug biosynthesis. Here, the role of halogen bond in the nitrilase-catalyzed synthesis of ortho-, meta-, and para-chlorophenylacetic acid was investigated. Different distributions of halogen bond induced changes of substrate binding conformation and affected substrate selectivity. By engineering the halogen interaction, the substrate selectivity of the enzyme changed, with the implication that halogen bond plays an important role in biosynthesis and should be used as an efficient and reliable tool in enzymatic drug synthesis.

Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F)

Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.

Repositioning organohalogen drugs: a case study for identification of potent B-Raf V600E inhibitors via docking and bioassay

Drug repositioning has been attracting increasingly attention for its advantages of reducing costs and risks. Statistics showed that around one quarter of the marketed drugs are organohalogens. However, no study has been reported, to the best of our knowledge, to aim at efficiently repositioning organohalogen drugs, which may be attributed to the lack of accurate halogen bonding scoring function. Here, we present a study to show that two organohalogen drugs were successfully repositioned as potent B-Raf V600E inhibitors via molecular docking with halogen bonding scoring function, namely D(3)DOCKxb developed in our lab, and bioassay. After virtual screening by D(3)DOCKxb against the database CMC (Comprehensive Medicinal Chemistry), 3 organohalogen drugs that were predicted to form strong halogen bonding with B-Raf V600E were purchased and tested with ELISA-based assay. In the end, 2 of them, rafoxanide and closantel, were identified as potent inhibitors with IC50 values of 0.07 μM and 1.90 μM, respectively, which are comparable to that of vemurafenib (IC50: 0.17 μM), a marketed drug targeting B-Raf V600E. Single point mutagenesis experiments confirmed the conformations predicted by D(3)DOCKxb. And comparison experiment revealed that halogen bonding scoring function is essential for repositioning those drugs with heavy halogen atoms in their molecular structures.