An Iridium Complex as Bidentate Halogen Bond-Based Anion Receptor Featuring an IncreasedOptical Response

We present a luminescent Ir(III) complex featuring a bidentate halogen bond donor site capable of strong anion binding. The tailor-made Ir(III)(L)2 moiety offers a significantly higher emission quantum yield (8.4 %) compared to previous Ir(III)-based chemo-sensors (2.5 %). The successful binding of chloride, bromide and acetate is demonstrated using emission titrations. These experiments reveal association constants of up to 1.6×105 M-1. Furthermore, a new approach to evaluate the association constant by utilizing the shift of the emission was used for the first time. The experimentally observed characteristics are supported by quantum chemical simulations.

Studies About the Effect of Halogenated Solvents on the Fluorescence Properties of 9-Aryl-Substituted Isoquinolinium Derivatives - A Case Study

It was demonstrated that 9-aryl-substituted isoquinolinium derivatives have significantly increased fluorescence quantum yields in halogenated solvents, mostly pronounced in chloroalkanes, which appears to be specific for this type of solvents. Further analysis with selected halogenated solvents revealed that the type and number of halogen substituents and the dielectric constant of the solvent have a distinct impact on the emission quantum yield. The solvent effect is explained by a solvation of the charge shift (CS) state by attractive halogen-π interactions (halogen bond), which impedes the torsional relaxation of the excited state.

Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines

In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.

Study on the modulating effect of halogen atom substitution on the detection range of water content detection probes in organic solvents

Fluorescence probes based on the variations of aggregation state (Aggregation-Induced Emission (AIE) and Aggregation-Caused Quenching (ACQ)) have received widespread attention due to their simplicity, efficiency and intuitiveness. However, typical probes are highly sensitive to changes in polarity and slight variations in the external environment can cause a complete change in the aggregation state. With the aim of expanding the detection range of the molecular probe, this work adopts a different design strategy from adjusting the molecular backbone but regulates the fluorescence behavior of the Schiff base molecular backbone by introducing different halogen atoms. Systematic studies show that when chlorine serves as substitutional atoms (3,5-Cl Salen), the probe can achieve full-range detection of water content (0-100 vol%) in ethanol and DMF. To our knowledge, the 3,5-Cl Salen represents the best water content probe in organic molecules. Experimental and theoretical studies have shown that the adjustment of halogen atoms can linearly change the charge distribution on the benzene ring and precisely control the strength of intermolecular interactions. At the same time, we developed a fluorescent filter paper based on 3,5-Cl Salen and used smartphones for rapid, sensitive and precise on-site measurement of water content in organic solvents.

The Impact of ortho-substituents on Bonding in Silver(I) and Halogen(I) Complexes of 2-Mono- and 2,6-Disubstituted Pyridines: An In-Depth Experimental and Theoretical Study

The coordination nature of 2-mono- and 2,6-disubstituted pyridines with electron-withdrawing halogen and electron-donating methyl groups for [N-X-N]+ (X=I, Br) complexations have been studied using 15 N NMR, X-ray crystallography, and Density Functional Theory (DFT) calculations. The 15 N NMR chemical shifts reveal iodine(I) and bromine(I) prefer to form complexes with 2-substituted pyridines and only 2,6-dimethylpyridine. The crystalline halogen(I) complexes of 2-substituted pyridines were characterized by using X-ray diffraction analysis, but 2,6-dihalopyridines were unable to form stable crystalline halogen(I) complexes due to the lower nucleophilicity of the pyridinic nitrogen. In contrast, the halogen(I) complexes of 2,6-dimethylpyridine, which has a more basic nitrogen, are characterized by X-crystallography, which complements the 15 N NMR studies. DFT calculations reveal that the bond energies for iodine(I) complexes vary between -291 and -351 kJ mol-1 and for bromine between -370 and -427 kJ mol-1 . The bond energies of halogen(I) complexes of 2-halopyridines with more nucleophilic nitrogen are 66-76 kJ mol-1 larger than those of analogous 2,6-dihalopyridines with less nucleophilic nitrogen. The experimental and DFT results show that the electronic influence of ortho-halogen substituents on pyridinic nitrogen leads to a completely different preference for the coordination bonding of halogen(I) ions, providing new insights into bonding in halogen(I) chemistry.

A Review on Low-Molecular-Weight Gels Driven by Halogen-Effect

As a new type of non-covalent interaction similar to hydrogen bond, halogen bond has become an important supramolecular tool in crystal engineering, material chemistry, biological science, etc., due to its unique properties. In fact, halogen bond has been confirmed on the effect of molecular assemblies and soft materials, and widely used in various functional soft materials including liquid crystals, gels and polymers. In recent years, halogen bonding has aroused strong interest in inducing molecular assembly into low-molecular-weight gels (LMWGs). To the best of our knowledge, there is still a lack of in-depth review of this field. So, in this paper, the recent progress of LMWGs driven by halogen bonding is reviewed. According to the number of components forming halogen bonded gels, the structural characteristics of halogen bonded supramolecular gels, the relationship between halogen bonding and other non-covalent interactions, as well as the application fields of halogen bonded gels are introduced, respectively. In addition, the challenges faced by halogenated supramolecular gels at present and their development prospects in future have been proposed. We believe that the halogen bonded gel will have more impressive applications in the next few years, opening exciting new opportunities for the development of soft materials.

Competition of hydrogen, tetrel, and halogen bonds in COCl2-HOX (X=F, Cl, Br, I) complexes

The present study investigates the competition between hydrogen, halogen, and tetrel bonds from the interaction of COCl₂ with HOX using quantum chemistry simulations at the MP2/aug-cc-pVTZ computational level, in which five configurations were optimized, including adducts I -V. Two hydrogen bonds, two halogen bonds, and two tetrel bonds were obtained for five forms of adducts. The compounds were investigated using spectroscopic, geometry, and energy properties. Adduct I complexes are more stable than others, and adduct V halogen bonded complexes are more stable than adduct II complexes. These results are in agreement with their NBO and AIM results. The stabilization energy of the XB complexes depends on the nature of both the Lewis acid and base. The stretching frequency of the O-H bond in adducts I, II, III, and IV displayed a redshift, and a blue shift was observed in adduct V. The results for the O-X bond showed a blue shift in adducts I and III and a red shift in adducts II, IV, and V. The nature and characteristics of three types of interactions are investigated via NBO analysis and atoms in molecules (AIM).

Halogen microregulation in metal-organic frameworks for enhanced adsorption performance of ReO4-/TcO4. JOURNAL OF HAZARDOUS MATERIALS 2023;446:130744. [PMID: 36630874 DOI: 10.1016/j.jhazmat.2023.130744]

Effective and selective removal of ⁹⁹TcO₄^-, one of the most nuisance radionuclides in nuclear waste, is highly desirable but remains a significant challenge. Herein, two isostructural MOFs, NCU-3-X (X = Cl, Br) were constructed by ZnX₂ coordinated to nitrogen-containing neutral ligand tri(4-(1H-imidazole-1-l) phenyl) amine for efficient adsorption ReO₄^-/TcO₄^-. Owning to the twofold interpenetrating structure, both of them exhibit strong alkaline resistance. Consequently, NCU-3-Br exhibited superior adsorption performances with a maximum capacity as high as 483 mg/g, which is 2.23 times larger than that of NCU-3-Cl. The primary reasons accounting for the enhanced adsorption performances of NCU-3-Br are that compared to chlorine atoms, the smaller electronegativity of bromine atoms as halogen bonds donor can facilitate the formation of σ-holes, enhance positively charged skeleton, and reduce the adsorption energy associated with ReO₄^-/TcO₄^-. In addition, the one-dimensional hydrophobic channels in the NCU-3-Br framework enable NCU-3-Br to have highly selective toward ReO₄^-, which has a low relative charge density against interfering ions. The SRS simulation removal experiment further confirmed the excellent adsorption capacity of NCU-3-Br to ReO₄^-/TcO₄^-. This work illustrated that the halogenated new strategy incorporated different halogen atoms into MOF skeletons can dramatically modulate the adsorption performances for ReO₄^-/TcO₄^-.

The "Nitrogen Effect": Complexation with Macrocycles Potentiates Fused Heterocycles to Form Halogen Bonds in Competitive Solvents

Weak intermolecular forces are typically very difficult to observe in highly competitive polar protic solvents as they are overwhelmed by the quantity of competing solvent. This is even more challenging for three-component ternary assemblies of pure organic compounds. In this work, we overcome these complications by leveraging the binding of fused aromatic N-heterocycles in an open resorcinarene cavity to template the formation of a three-component halogen-bonded ternary assembly in a protic polar solvent system.

Unexpectedly significant stabilizing mechanism of iodous acid on iodic acid nucleation under different atmospheric conditions

Iodous acid (HIO₂) has been shown to play a stabilizing role in the nucleation of iodic acid (HIO₃) (He et al., 2021). However, the stabilization effect and specific stabilizing mechanism of HIO₂ on HIO₃ nucleation under different atmospheric conditions remain unclear. Therefore, we studied these two issues under different temperatures and nucleation precursor concentrations using density functional theory combined with the Atmospheric Cluster Dynamics Code. We found that HIO₂ can form clusters with HIO₃ via strong hydrogen bonds, halogen bonds, and proton-transfer, substantially enhancing the stability of HIO₃ clusters and decreasing the energy barrier of HIO₃-based cluster formation at different temperatures and nucleation precursor concentrations. The particle formation rate and cluster concentrations of HIO₃-HIO₂ nucleation were negatively correlated with temperature and positively correlated with HIO₂ concentration. The enhancements by HIO₂ on the particle formation rate and cluster concentration of HIO₃ nucleation were positively correlated with temperature and HIO₂ concentration. Interestingly, even at a low HIO₂ concentration (1.0 × 10⁵ molecules cm^-3), the enhancement on the particle formation rate and cluster concentration of HIO₃ nucleation by HIO₂ were both unexpectedly up to 4.1 × 10⁴-fold at 283 K. Therefore, HIO₃-HIO₂ nucleation can be extremely rapid in cold regions, and the enhancement by HIO₂ can be significant, especially in warm regions even at relatively high HIO₂ concentrations.

The binding affinity of human pediatric respiratory syncytial virus Phosphoprotein's C-terminal tail to nucleocapsid can be improved by a rationally designed halogen-bonded system

Human respiratory syncytial virus (hRSV) is a common contagious virus that causes infections of pediatric pneumonia and specifically impacts infants and small children. The hRSV phosphoprotein is a key component of the viral RNA polymerase, which can interact with nucleocapsid and other partners through its C-terminal tail (CTT) to promote the formation of viral transcriptase complex, where the Phe241 is a key anchor residue. Based on the crystal template-modeled complex structure of hRSV nucleocapsid with a peptidic segment derived from the phosphoprotein's CTT, we successfully introduced a rationally designed halogen-bonded system to the complex interface by substituting para (p)-position of the side-chain phenyl moiety of CTT Phe241 residue with a halogen atom X (X = F, Cl, Br or I). The halogen-bonded system consists of a halogen bond (X-bond) between nucleocapsid Ser131 residue and CTT Phe241 residue as well as a hydrogen bond (H-bond) between nucleocapsid Ser131 residue and nucleocapsid Glu128 residue; the X-bond and H-bond share a common hydroxyl group of nucleocapsid Ser131 residue. High-level theoretical calculations suggested that bromine Br is the best choice that can render strong potency for the X-bond and can confer high affinity to the nucleocapsid-CTT binding. Affinity analysis revealed that the p-brominated CTT ([p]bCTT) exhibited 6.3-fold affinity improvement relative to its nonhalogenated counterpart. In contrast, the Br-substitutions at ortho (o)- and meta (m)-positions, which resulted in two negative controls of o-brominated [o]bCTT and m-brominated [m]bCTT, respectively, were unable to form effective X-bond with nucleocapsid according to theoretical investigation and did not improve the binding affinity essentially relative to native CTT.

An alkali-resistant metal-organic framework as halogen bond donor for efficient and selective removing of ReO4-/TcO4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022;29:86815-86824. [PMID: 35794336 DOI: 10.1007/s11356-022-21870-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

⁹⁹Tc is one of the most problematic nuclear fuel products due to its long half-life and high environmental mobility. Direct removal of TcO₄^- from the highly alkaline solution of nuclear fuel is a serious and challenging environmental issue. In this work, the first efficient synthetic approach introducing halogens into a two-dimensional metal-organic framework, named Mn-MOF, is established using MnCl₂·4H₂O coordinating with neutral nitrogen-donor ligand, showing ultrahigh stability in alkaline aqueous even under 1 M NaOH. The luxuriant Mn-Cl bonds and ordered hydrophobic pore channels enable the Mn-MOF to have an efficient adsorption capacity for ReO₄^- with a large capacity (403 mg g^-1), which is higher than most MOF adsorbents. More importantly, the Mn-MOF shows an excellent selectivity toward ReO₄^- in high-density competitive anions, such as NO₃^- and SO₄^2-. Moreover, the outstanding performance of Mn-MOF in removing ReO₄^- endowed it successfully separated ReO₄^- from the simulated Savannah River Site (SRS) high-level waste (HLW) stream with high removal of 66.84% at the phase ratio of 10. The adsorption mechanism is further demonstrated by FT-IR, XPS analysis, and DFT calculation, showing that the ReO₄^- can selectively interact with Mn-Cl bonds and imidazole groups, forming unique halogen bonds Cl-O-Re, and a series of hydrogen bonds, respectively. This work suggests a new approach to the removal of TcO₄^- from nuclear fuel.

The Importance of Electrostatics and Polarization for Noncovalent Interactions: Ionic Hydrogen Bonds vs Ionic Halogen Bonds

A series of 26 hydrogen-bonded complexes between Br⁻ and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6–311 + G(2df,2p) level of theory. Analysis using a model in which Br⁻ is replaced by a point charge shows that the interaction energy (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt) of the complexes is accurately reproduced by the scaled interaction energy with the point charge (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC).This is demonstrated by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}=0.86{\Delta E}_{Int}^{PC}$$\end{document}ΔEInt=0.86ΔEIntPC with a correlation coefficient, R² =0.999. The only outlier is (Br-H-Br)⁻, which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC can be divided rigorously into an electrostatic contribution (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{ES}^{PC}$$\end{document}ΔEESPC) and a polarization contribution (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Pol}^{PC}$$\end{document}ΔEPolPC).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol⁻¹, whereas the latter varies between -1.6 and -11.5 kcal mol⁻¹. Compared to our previous study of halogen-bonded (XB) complexes between Br⁻ and C–Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br⁻···HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt at short distances in this complex to a large extent can be attributed to charge penetration.

The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods

Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH₃, H₂O and NMe₃ partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO₂ (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.

Rationalizing the binding and α subtype selectivity of synthesized imidazodiazepines and benzodiazepines at GABAA receptors by using molecular docking studies

The pharmacological actions exerted by benzodiazepines are dependent on the discrete α protein subunits of the γ-aminobutyric acid type A receptor (GABA_A R). Recent developments via a cryo-EM structure of the α1β3γ2L GABA_A R ion channel provide crucial insights into ligand efficacy and binding affinity at this subtype. We investigated the molecular interactions of diazepam and alprazolam bound GABA_A R structures (6HUP and 6HUO) to determine key binding interaction domains. A halogen bond between the chlorine atoms of diazepam and alprazolam with the group on the backbone of the α1 histidine amino acid 102 is important to the positive allosteric modulatory actions of diazepam and alprazolam in the α1β3γ2L GABA_A R ion channel. In order to gain insight into α subtype selectivity we designed and synthesized close structural analogs of diazepam and alprazolam. These compounds were then docked into the recently publish cryo-EM structures of GABA_A Rs (6HUP and 6HUO). This modeling along with radio-ligand binding data resulted in the conclusion that the non-classical bioisosteric replacement of the chlorine atom at C7 with an ethinyl group (compound 5) resulted in an 11-fold gain in α5 binding selectivity over the α1 subtype. Moreover, the potency of compound 5 resulted in a ligand with less sedation than diazepam, while still maintaining the same anxiolytic potency. These modeling data extend our understanding of the structural requirements for α-subtype-selective compounds that can be utilized to achieve improved medical treatments. It is clear that the ethinyl group in place of a halogen atom decreases the affinity and efficacy of benzodiazepines and imidazodiazepines at α1 subtypes, which results in less sedation and ataxia.

An unprecedented interconversion between non-covalent and covalent interactions driven by halogen bonding

The spontaneous interconversion between covalent forces and noncovalent counterparts remains an unexplained mystery to date. Here we have discovered a marvelous transformation between them through halogen bonding using NI 3 as a prototype. Our results show that the interaction strength of the NI 3 dimer is 7.01 kcal mol -1 , demonstrating it is a quite strong halogen bond. Molecular orbital analyses indicate that the frontier MOs result from strong mixing of the fragment MOs, which may be the electronic structure basis of interconversion. Further studies on a series of NI 3 oligomers (5-, 10-, 15-, 20-, 26-, 30-mer) show that the interconversion occurs approximately at 26-mer on the basis on bond distance, ELF, etc.; the interconversion is a gradual transformation not a sudden one. This study provides more insights into the halogen bonding and the high explosivity of NI 3 containing species.

Molecular conversion of MIG6 hotspot-3 peptide from the nonbinder to a moderate binder of HER2 by rational design of an orthogonal interaction system at the HER2-peptide interface

Human epidermal growth factor receptor 2 (HER2) has been established as an approved druggable target for the treatment of patients with diverse gynecological tumors such as ovarian, cervical and breast cancers. The mitogen-inducible gene 6 (MIG6) protein is a negative regulator of HER2 signaling by using its Seg1 segment to disrupt the allosteric dimerization of HER2 kinase domain. Previous studies found that the Seg1 adopts three separated hotspots to interact with the HER2 dimerization interface, in which the third hotspot (H3) is located at the core region of the interface but its derived H3 peptide (³⁵⁶PKYVS³⁶⁰) and Tyr358Phe mutant (³⁵⁶PKFVS³⁶⁰) cannot bind effectively to the interface in an independent manner. In this study, we demonstrate that the H3 peptide can be converted from nonbinder to a moderate binder of HER2 by just adding an orthogonal noncovalent interaction system (X⋯O┄H) between a halogen bond (X⋯O) and a hydrogen bond (H┄O) involving peptide Phe358 residue and HER2 Val948/Trp951 residues. High-level calculations are utilized to rigorously characterize and rationally design the X⋯O┄H system, which is then optimized with different halogen atoms and at different substituting positions. It is revealed that there is a synergistic effect between the X⋯O and H┄O of the orthogonal interaction system; formation of the halogen bond can enhance the interaction strength of the hydrogen bond. In silico analysis and in vitro assay reach a consistence that Br-substitution at the m-position of peptide Phe358 phenyl moiety is the best choice that can render strong interaction for the X⋯O┄H system, which also makes the peptide 'bindable' to HER2 kinase domain, while F/Cl/I-substitution at the same position can only improve the peptide affinity moderately or modestly. In contrast, the Br-substitution at the o- and p-positions of peptide Phe358 phenyl moiety cannot define effective X⋯O┄H interaction and thus does not confer additional affinity to the HER2-peptide complex.

Tuning the activity of known drugs via the introduction of halogen atoms, a case study of SERT ligands - Fluoxetine and fluvoxamine

The selective serotonin reuptake inhibitors (SSRIs), acting at the serotonin transporter (SERT), are one of the most widely prescribed antidepressant medications. All five approved SSRIs possess either fluorine or chlorine atoms, and there is a limited number of reports describing their analogs with heavier halogens, i.e., bromine and iodine. To elucidate the role of halogen atoms in the binding of SSRIs to SERT, we designed a series of 22 fluoxetine and fluvoxamine analogs substituted with fluorine, chlorine, bromine, and iodine atoms, differently arranged on the phenyl ring. The obtained biological activity data, supported by a thorough in silico binding mode analysis, allowed the identification of two partners for halogen bond interactions: the backbone carbonyl oxygen atoms of E493 and T497. Additionally, compounds with heavier halogen atoms were found to bind with the SERT via a distinctly different binding mode, a result not presented elsewhere. The subsequent analysis of the prepared XSAR sets showed that E493 and T497 participated in the largest number of formed halogen bonds. The XSAR library analysis led to the synthesis of two of the most active compounds (3,4-diCl-fluoxetine 42, SERT K_i = 5 nM and 3,4-diCl-fluvoxamine 46, SERT K_i = 9 nM, fluoxetine SERT K_i = 31 nM, fluvoxamine SERT K_i = 458 nM). We present an example of the successful use of a rational methodology to analyze binding and design more active compounds by halogen atom introduction. 'XSAR library analysis', a new tool in medicinal chemistry, was instrumental in identifying optimal halogen atom substitution.

Direct matrix isolation IR spectroscopic evidence of halogen bonding from a comparative study of complexes of CBr4 and CCl4with acetone and formic acid

Binary complexes of acetone and formic acid with tetrahalomethanes CBr₄ and CCl₄ have been isolated in argon matrix. Spectral shifts in the characteristic ν_C=O region of acetone, as well as in the fingerprint regions, are unambiguously assigned to the formation of halogen bond involving one of the halogen atoms on CBr₄/CCl₄ as donor, and the carbonyl oxygen of acetone as acceptor. The higher magnitude of shifts of ν_C=O and the fingerprint vibrations for the CBr₄ complex, as compared to the CCl₄ complex, is consistent with theoretical predictions of higher value of positive electrostatic potential in the "σ-hole" region of the former, and hence its higher susceptibility to halogen bonding. The formation of halogen bonded complexes involving formic acid as acceptor and CBr₄/CCl₄ as donors is also being reported for the first time. In this case too, distinct shifts are obtained in the ν_C=O as well as ν_C-O regions of formic acid, which again are significantly larger in magnitude for the CBr₄ complex, as compared to the CCl₄ complex. Electronic structure calculations have been carried out using different theoretical methods to identify the various possible structural isomers of the halogen bonded complexes, and to obtain relevant information regarding their energies and intermolecular geometrical parameters. In addition, NBO and AIM analysis have been carried out to understand the role of local interactions at the halogen bonded interface. Such predicted data are found to be consistent with experimental observations, and re-assert the stronger nature of CBr₄ as halogen bond donor, as compared to CCl₄.

Underappreciated Chemical Interactions in Protein-Ligand Complexes

Non-covalent interactions lie at the bases of the molecular recognition process. In medicinal chemistry, understanding how bioactive molecules interact with their target can help to explain structure-activity relationships (SAR) and improve potency of lead compounds. In particular, computational analysis of protein-ligand complexes can help to unravel key interactions and guide structure-based drug design.The literature describing protein-ligand complexes is typically focused on few types of non-covalent interactions (e.g., hydrophobic contacts, hydrogen bonds, and salt bridges). Stacking interactions involving aromatic rings are also relatively well known to medicinal chemistry practitioners. Potency optimization efforts are often focused on targeting these interactions. However, a variety of underappreciated interactions were shown to have a relevant effect on the stabilization of protein-ligand complexes. This chapter aims at listing selected non-covalent interactions and discuss some examples on how they can impact drug design.

Halogen bonding interactions in the XC5H4N···YCF3 (X = CH3, H, Cl, CN, NO2; Y = Cl, Br, I) complexes

The noncovalent interactions between the σ-hole region outside the halogen atom and the nitrogen atom of pyridine and its para-substituted derivatives are the focus of this work. Based on the analyses of the electrostatic potentials, YCF₃ (Y = Cl, Br, I) act as halogen bond donors, XC₅H₄N (X = CH₃, H, Cl, CN, NO₂) act as halogen bond acceptors, and the binary halogen-bonded complexes XC₅H₄N···YCF₃ have been designed and investigated by B3LYP-D3/aug-cc-pVDZ calculations together with the aug-cc-pVDZ-PP basis set for iodine. When the halogen bond acceptor remains unchanged, the interactions between C₅H₅N and YCF₃ (Y = Cl, Br, I) increase with the order of Y = Cl, Br, and I. When the halogen donor ICF₃ is fixed, the halogen bonding interactions decrease along the sequence of X = CH₃, H, Cl, CN, NO₂. Therefore, the halogen bond of the CH₃C₅H₄N···ICF₃ complex is the strongest. The interactions between Lewis acid YCF₃ (Y = Cl, Br, I) and pyridine and para-substituted pyridine are closed-shell and noncovalent interactions. On the one hand, when the halogen bond acceptor XC₅H₄N is fixed, with the increase of halogen atomic number, the strength of halogen bond increases; on the other hand, when the halogen bond donor ICF₃ is fixed, as the electron-withdrawing ability of the electron-withdrawing group (X) increases, the halogen bond gradually weakens.

Strengthening of halogen bond in XCl∙∙∙FH∙∙∙F- through cooperativity with a strong hydrogen bond and proton transfer

A theoretical calculation has been performed for the ternary complexes XCl∙∙∙FH∙∙∙F^- (X = CCH, CN, OH, NC, and F) and the corresponding binary complexes. The halogen bond in the dyad is very weak with the interaction energy less than 2.5 kcal/mol. Interestingly, the halogen bond gets a big enhancement when it combines with a very strong hydrogen bond in FH∙∙∙F^-, and the largest interaction energy is up to ∼25.6 kcal/mol in FCl∙∙∙FH∙∙∙F^-. The enhancement of halogen bond not only results in a larger elongation of X-Cl bond and a bigger redshift of the bond stretch vibration but also makes the blue-shifting halogen bond in NCCl∙∙∙FH be a red-shifting one in NCCl∙∙∙FH∙∙∙F^-. The halogen bond belongs to a purely close-shell interaction in the dyad, while it becomes a partially covalent interaction in XCl∙∙∙FH∙∙∙F^- (X = OH, NC, and F) with negative energy density. In FH∙∙∙F^-, the proton is shared between the two F atoms, however, this proton transfers towards the F^- end in XCl∙∙∙FH∙∙∙F^-.

Electronic structure of polythiophene gas sensors for chlorinated analytes

Density functional theory studies are performed to investigate the response of polythiophene as a sensor for chlorinated gaseous analytes. Interaction of polythiophene with these analytes is studied from both H-side (dipole-dipole) and Cl-side (halogen bonding) of analyte to get the most stable interaction site. Inferences from interaction energy, natural bond orbital, and Mulliken charge analyses are in line with those from geometric analysis. Interaction energies reveal that polythiophene has specificity and selectivity towards chlorine. Interestingly, the halogen bond in PT-Cl₂ complexes is stronger than ion-dipole bond in the complexes of polythiophene with other analytes. The sensing of polythiophene towards these analytes is also measured by perturbing the electronic properties including ionization potential, electron affinity, λ_max, and H→L gap. The spectroscopic properties (UV absorption spectra) reveal the interaction behavior of polythiophene with these chlorinated analytes. All these parameters including orbital analysis and H→L energies indicate high sensitivity of polythiophene for chlorine. Graphical abstractInteraction of chlorinated gaseous analytes with polythiophene surface.

Understanding the potency of malarial ligand (D44) in plasmodium FKBP35 and modelled halogen atom (Br, Cl, F) functional groups

The present study clearly depicts the understanding of the D44 in Plasmodium FKBP35 around the hinge region. To analyse the binding stability of D44 ligand and to understand the role of halogen bond, hydrogen bond interaction formed between the hinge region amino acids: Isoleucine (Ile74), Phenylalanine (Phe54), Aspartic acid (Asp55) Phenylalanine (Phe64),Tyrosine (Tyr100), Tryptophan (TRP 77) and ligand D44 was portrayed specifically through interaction energy calculations at HF, M062X, MP2 level of theories for different basis set (6-311G**, 6-31+G*, LANL2DZ). The investigation will provide an apparent picture regarding the non-covalent interaction that hold the contact of ligand and amino acids in the hinge region and the implication of modelled functional groups (Br, Cl, F, OSO and NH₂) on ligand, which will help chemist in synthesizing new novel ligands. HOMO, LUMO chart calculated for D44 ligands reveals graphic illustration of orbital's that stimulate for contact. The aim and natural bond orbital analysis identified key contribution of individual hydrogen/halogen bonds that contribute for the binding strength through stabilization energy, ρ and ∇²ρ values. Overall this study finds out that the Stability of D44 in Plasmodium FKBP35 was enhanced by the Halogen atom (Br, Cl, F) functional groups; which provide an innovative pathway for the selection of functional groups that opt for the hinge region side chains on the ligand.

1,3,5-Trifluoro-2,4,6-triiodobenzene: A neglected NIR phosphor with prolonged lifetime by σ-hole and π-hole capture

Room temperature phosphorescence (RTP) materials have become a hot topic in fields of organic light-emitting dioes, biological sensing and imaging. The present work reports firstly that 1,3,5-trifluoro-2,4,6-triiodobenzene (TITFB) can act as a simple pure organic NIR phosphor due to its novel function in promoting n-π∗ transition. Also, TITFB crystal has longer phosphorescence lifetime than other ordinary multiiodoluminophors and TITFB powder. Based on the TITFB crystal structure, σ-hole and π-hole capture mechanism of n-electron is proposed, i.e., the excited state energy is decreased and n-electrons are stabilized to cause slower radiative decay rate due to the restriction of σ-hole and π-hole bond. Both computational and experimental studies support the mechanism. The new electron-capture mode is more conducive to understanding pure organic ultralong lifetime RTP.

Halogen bond in separation science: A critical analysis across experimental and theoretical results

The halogen bond (XB) is a noncovalent interaction involving a halogen acting as electrophile and a Lewis base. In the last decades XB has found practical application in several fields. Nevertheless, despite the pivotal role of noncovalent interactions in separation science, investigations of XB in this field are still in their infancy, and so far a limited number of studies focusing on solid phase extraction, liquid-liquid microextraction, liquid-phase chromatography, and gas chromatography separation have been published. In addition, in the last few years, our groups have been systematically studying the potentiality of XB for HPLC enantioseparations. On this basis, in the present paper up-to-date results emerging from focused experiments and theoretical analyses performed by our laboratories are integrated with a descriptive presentation of XB features and the few studies published until now in separation science. Then, the aim of this article is to provide a comprehensive and critical discussion of the topic, and account for some still open issues in the application of XB to separate chemical mixtures.

SCFit: Software for single-crystal NMR analysis. Free vs constrained fitting

The design and implementation of a software package for the analysis of single-crystal NMR data is presented. The SCFit software can treat spectra arising from various interactions: (i) chemical shift tensor only; (ii) chemical shift tensor and quadrupolar coupling tensor; (iii) dipolar and indirect nuclear spin-spin coupling tensors; (iv) all four interactions. The software is demonstrated on recently reported ¹⁷O and ³¹P single-crystal NMR data for triphenylphosphine oxide and for two of its halogen-bonded cocrystals. The ¹⁷O single-crystal NMR data represent a case where all four above-mentioned interactions simultaneously affect the spectra. SCFit can fit the chemical shift and quadrupolar coupling in two ways: (i) through an unconstrained fitting process where all tensor parameters are freely optimized or (ii) through a constrained fitting process where the principal components of the tensors may be fixed to values known previously with high precision via the analysis of powder samples. The second strategy is explored in an effort to reduce the number of unknowns in the fitting process; an improvement in the precision of the resulting tensor orientations is noted in some cases.

Molecular dynamics investigation of halogenated amyloidogenic peptides

Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.

Fluorinated indole-imidazole conjugates: Selective orally bioavailable 5-HT7 receptor low-basicity agonists, potential neuropathic painkillers

The 5-HT₇ receptor has recently gained much attention due to its involvement in multiple physiological functions and diseases. The insufficient quality of the available molecular probes prompted design of fluorinated 3-(1-alkyl-1H-imidazol-5-yl)-1H-indoles as a new generation of selective 5-HT₇ receptor agonists. A potent and drug-like agonist, 3-(1-ethyl-1H-imidazol-5-yl)-5-iodo-4-fluoro-1H-indole (AGH-192, 35, K_{i 5-HT7R} = 4 nM), was identified by optimizing the halogen bond formation with Ser5.42 as the supposed partner. The compound was characterized by excellent water solubility, high selectivity over related CNS targets, high metabolic stability, oral bioavailability and low cytotoxicity. Rapid absorption into the blood, medium half-life and a high peak concentration in the brain C_max = 1069 ng/g were found after i.p. (2.5 mg/kg) administration in mice. AGH-192 may thus serve as the long-sought tool compound in the study of 5-HT₇ receptor function, as well as a potential analgesic, indicated by the antinociceptive effect observed in a mouse model of neuropathic pain.

Theoretical and conceptual DFT study of pnicogen- and halogen-bonded complexes of PH2X---BrCl

The pnicogen and halogen bonding interactions in the PH₂X---BrCl(X = H, F, OH, OCH₃ and CH₃) complexes have been studied at the MP2/aug-cc-pVTZ level. Analysis of interaction energies shows that the pnicogen-bonded structures are less stable than the corresponding halogen-bonded structures. The pnicogen and halogen bonds were also studied by conceptual DFT reactivity indices. Noncovalent interaction (NCI) and SAPT analysis reveals that the dispersion interactions dominate the pnicogen-bonded complexes of PH₂X---BrCl in nature, while the halogen-bonded complexes are dominantly electrostatic energy. Graphical abstract It is found that the local softness s⁺ or s^-on the basic center P of PH₂X is related to the interaction energies (ΔE^CP) of halogen- or pnicogen-bonded complexes.

Dual function of the boron center of BH(CO)2/BH(N2)2 in halogen- and triel-bonded complexes with hypervalent halogens

The complexes between BH(CO)₂/BH(N₂)₂ and XF₃/XF₅ are stabilized by a halogen bond and a triel bond. The MEP analyses of BH(CO)₂/BH(N₂)₂ indicate that there are both a region with negative MEPs on the B atom in the vertical direction of the molecular plane and a σ-hole at the B-H bond end. Therefore, the boron atom in BH(CO)₂/BH(N₂)₂ plays a dual role of a Lewis base and an acid in the halogen bond and triel bond, respectively. The halogen and triel bonds are stronger in order of IF₃< BrF₃< ClF₃, IF₅< BrF₅< ClF₅, and BH(CO)₂< BH(N₂)₂ in most complexes. These complexes have large stability since the interaction energy varies from -5 to -115 kcal/mol. The halogen bond belongs to a covalent interaction or a partially covalent interaction in most complexes. The subsystems in these complexes have prominent deformation, accompanied with big charge transfer and large polarization.

Halogen bond in high-performance liquid chromatography enantioseparations: Description, features and modelling

Halogen bond (XB)-driven enantioseparations involve halogen-centred regions of electronic charge depletion (σ-hole) as electrophilic recognition sites. The knowledge in this field is still in its infancy. Indeed, although the influence of halogens on enantioseparation have been often considered, only recently the function of electrophilic halogens (Cl, Br, I) as enantioseparations 'drivers' has been demonstrated by our groups. Further to these studies, in this paper we focus on some unexplored issues. First, as XB-driven chiral recognition mechanisms are at an early stage of comprehension, a theoretical investigation based on a series of 32 molecular dynamic (MD) simulations was performed by using polyhalogenated 4,4'-bipyridines and polysaccharide-based polymers as ligands and receptors, respectively. Enantiomer elution orders (EEOs) were derived from calculations and the theoretical model accounted for some analyte- and chiral stationary phase (CSP)-dependent experimental EEO inversions. Then, the function of halogen-centred σ-holes in competitive systems, presenting also hydrogen bond (HB) centres as recognition sites, was considered. In this regard, Pirkle's enantioseparations of halogenated compounds performed on Whelk-O1 were theoretically re-examined and electrostatic potentials (EPs) associated with both σ-holes on halogens and HB centres were computed and compared. Then, the enantioseparation of halogenated 2-nitro-1-arylethanols was performed on cellulose tris(3,5-dimethylphenylcarbamate) (CDMPC) and the influence of halogen substituents on the chromatographic results was evaluated by correlating theoretical and experimental data.

Structural determinants influencing halogen bonding: a case study on azinesulfonamide analogs of aripiprazole as 5-HT1A, 5-HT7, and D2 receptor ligands

A series of azinesulfonamide derivatives of long-chain arylpiperazines with variable-length alkylene spacers between sulfonamide and 4-arylpiperazine moiety is designed, synthesized, and biologically evaluated. In vitro methods are used to determine their affinity for serotonin 5-HT_1A, 5-HT₆, 5-HT₇, and dopamine D₂ receptors. X-ray analysis, two-dimensional NMR conformational studies, and docking into the 5-HT_1A and 5-HT₇ receptor models are then conducted to investigate the conformational preferences of selected serotonin receptor ligands in different environments. The bent conformation of tetramethylene derivatives is found in a solid state, in dimethyl sulfoxide, and as a global energy minimum during conformational analysis in a simulated water environment. Furthermore, ligand geometry in top-scored complexes is also bent, with one torsion angle in the spacer (τ₂) in synclinal conformation. Molecular docking studies indicate the role of halogen bonding in complexes of the most potent ligands and target receptors.

The interaction of CCl4 with Ng (Ng = He, Ne, Ar), O2, D2O and ND3: rovibrational energies, spectroscopic constants and theoretical calculations

This investigation generated rovibrational energies and spectroscopic constants for systems of CCl₄ with Ng (Ng = He, Ne, Ar), O₂, D₂O and ND₃ from scattering experimental data, and the results presented are of interest for microwave spectroscopy studies of small halogenated molecules. The rovibrational spectra were obtained through two different approaches (Dunham and DVR) within the improved Lennard Jones (ILJ) model. Spectra were also generated within ordinary Lennard Jones and deviations suggest that the ILJ model should be preferred due to interactions beyond dispersion forces presented in these systems. Data from the literature and additional high level quantum mechanical calculations presented in this work show that these systems should not be considered as van der Waals complexes due to halogen bonding (HB) interactions, and this is especially true for the CCl₄-D₂O and CCl₄-ND₃ complexes. The charge displacement from the latter systems are one order of magnitude higher than the values from literature for CCl₄ and He, Ne, Ar and O₂ systems, and show significant deviations between DFT and Hartree-Fock values not previously reported in the literature.

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions

A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the 'sigma hole.' Empirical force fields in which the electrostatic interactions are represented by atom-centered point charges cannot capture this effect because halogen atoms usually carry a negative charge and therefore interact unfavorably with other electronegative atoms. A strategy to overcome this problem is to attach a positively charged virtual particle to the halogen. In this work, we extend the additive CHARMM General Force Field (CGenFF) to include such interactions in model systems of phenyl-X, with X being Cl, Br or I including di- and trihalogenated species. The charges, Lennard-Jones parameters, and halogen-virtual particle distances were optimized to reproduce the orientation dependence of quantum mechanical interaction energies with water, acetone, and N-methylacetamide as well as experimental pure liquid properties and relative hydration free energies with respect to benzene. The resulting parameters were validated in molecular dynamics simulations on small-molecule crystals and on solvated protein-ligand complexes containing halogenated compounds. The inclusion of positive virtual sites leads to better agreement across experimental observables, including preservation of ligand binding poses as a direct result of the improved representation of halogen bonding.

Insights into halogen bond-driven enantioseparations

Although the halogen bond (XB) has been so far mainly studied in silico and in the solid state, its potential impact in solution is yet to be fully understood. In this study, we describe the first systematic investigation on the halogen bond in solvated environment by high-performance liquid chromatography (HPLC). Thirty three atropisomeric polyhalogenated-4,4'-bipyridines (HBipys), containing Cl, Br and I as substituents, were selected and used as potential XB donors (XBDs) on two cellulose-based chiral stationary phases (CSPs) containing potential XB acceptors (XBAs). The impact of the halogens on the enantiodiscrimination mechanism was investigated and iodine showed a pivotal role on the enantioseparation in non-polar medium. Electrostatic potentials (EPs) were computed to understand the electrostatic component of CSP-analyte interaction. Moreover, van't Hoff studies for ten HBipys were performed and the thermodynamic parameters governing the halogen-dependent enantioseparations are discussed. Finally, a molecular dynamic (MD) simulation is proposed to model halogen bond in polysaccharide-analyte complexes by inclusion of a charged extra point to represent the positive 'σ-hole' on the halogen atom. On the basis of both experimental results and theoretical data, we have profiled the halogen bond as a chemo-, regio-, site- and stereoselective interaction which can work in HPLC environment besides other known interactions based on the complementarity between selector and selectand.

AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina

Background

Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don’t account for halogen bonding in their scoring functions and are not able to utilize this new approach. In this study a new and improved halogen bonding scoring function (XBSF) is presented along with its implementation in the AutoDock Vina molecular docking software. This new improved program is termed as AutoDock VinaXB, where XB stands for the halogen bonding parameters that were added.

Results

XBSF scoring function is derived based on the X···A distance and C–X···A angle of interacting atoms. The distance term was further corrected to account for the polar flattening effect of halogens. A total of 106 protein-halogenated ligand complexes were tested and compared in terms of binding affinity and docking poses using Vina and VinaXB. VinaXB performed superior to Vina in the majority of instances. VinaXB was closer to native pose both above and below 2 Å deviation categories almost twice as frequently as Vina.

Conclusions

Implementation of XBSF into AutoDock Vina has been shown to improve the accuracy of the docking result with regards to halogenated ligands. AutoDock VinaXB addresses the issues of halogen bonds that were previously being scored unfavorably due to repulsion factors, thus effectively lowering the output RMSD values.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-016-0139-1) contains supplementary material, which is available to authorized users.

Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand

The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.

Comparison of the directionality of the halogen, hydrogen, and lithium bonds between HOOOH and XF (X = Cl, Br, H, Li)

Detailed electrostatic potential (ESP) analyses were performed to compare the directionality of halogen bonds with those of hydrogen bonds and lithium bonds. To do this, the interactions of HOOOH with the molecules XF (X = Cl, Br, H, Li) were investigated. For each molecule, the percentage of the van der Waals (vdW) molecular surface that intersected with the ESP surface was used to roughly quantify the directionality of the halogen/hydrogen/lithium bond associated with the molecule. The size of the region of intersection was found to increase in the following order: ClF < BrF < HF < LiF. The maximum ESP in the region of intersection, V S, max, was observed to become more positive according to the sequence ClF < BrF < HF < LiF. For ClF and BrF, the positive electrostatic potential was concentrated in a very small region of the vdW molecular surface. On the other hand, for HF and LiF, the positive electrostatic potential was more diffusely scattered across the vdW surface than for ClF and BrF. Also, the optimized geometries of the dipolymers HOOOH··· XF (X = Cl, Br, H, Li) indicated that halogen bonds are more directional than hydrogen bonds and lithium bonds, consistent with the results of ESP analyses.

Interplay between H⋯O, H⋯X, X⋯O and X⋯X interactions in the complex pairing of formyl halides with hypohalous acids

Ab initio study of the complexes formed by hypohalous acids (HOX, X=F, Cl, Br and I) with formyl halides (HCOY, Y=F, Cl, Br and I) has been carried out at the MP2/aug-cc-pVDZ computational level. These molecules can do a vast kind of H⋯O, H⋯X, X⋯O and X⋯Y interactions. The nature of the halogen atom in HOX is more important than HCOY in the X⋯Y interactions. Red shift of H-O bonds and blue shift of C-H bonds were observed frequently which are in line with the elongation (weakening) and contraction (strengthening) of related bonds, respectively. The interactions were analyzed with atoms in molecules (AIM) and natural bond orbital (NBO) theories. Results are showing good correlations between structural properties and AIM parameters.

Synergistic and diminutive effects between halogen bond and lithium bond in complexes involving aromatic compounds

Quantum chemical calculations have been performed to study the interplay between halogen bond and lithium bond in the ternary systems FX-C6H5CN-LiF, FLi-C6H5CN-XF, and FLi-C6H5X-NH3 (X = Cl, Br, and I) involving aromatic compounds. This effect was studied in terms of interaction energy, electron density, charge transfer, and orbital interaction. The results showed that both FX-C6H5CN-LiF and FLi-C6H5CN-XF exhibit diminutive effects with the weakening of halogen bond and lithium bond, while FLi-C6H5X-NH3 displays synergistic effects with the strengthening of halogen bond and lithium bond. The nature of halogen bond and lithium bond in the corresponding binary complexes has been unveiled by the quantum theory of atoms in molecules methodology and energy decomposition analysis.

Modulation of the Interaction between a Peptide Ligand and a G Protein-Coupled Receptor by Halogen Atoms

Systematic halogenation of two native opioid peptides has shown that halogen atoms can modulate peptide-receptor interactions in different manners. First, halogens may produce a steric hindrance that reduces the binding of the peptide to the receptor. Second, chlorine, bromine, or iodine may improve peptide binding if their positive σ-hole forms a halogen bond interaction with negatively charged atoms of the protein. Lastly, the negative electrostatic potential of fluorine can interact with positively charged atoms of the protein to improve peptide binding.

Orthogonal hydrogen/halogen bonding in 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione-I2 adduct: an experimental and theoretical study

The molecular complex between 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (Hmim(OMe)) and iodine (I2) was investigated. Single crystal of [(Hmim(OMe))I2] adduct was grown by slow evaporation technique from chloroform at room temperature. Spectroscopic techniques such as FT-IR and Raman techniques, as well as elemental and thermal analysis were used to characterize the complex. The crystal structure shows that the formed adduct stabilized by two noncovalent interactions, namely, hydrogen bond (HB) and halogen bond (XB). Orthogonal HB/XB associated with iodine atom (I) was observed and fully characterized. The ability of iodine to behave as hydrogen bond acceptor and halogen bond donor was held responsible for the orthogonal HB/XB presence. In addition, the structure of Hmim(OMe)I2 was investigated theoretically using MP2/aug-cc-pVDZ level of theory. Natural bond orbital analysis (NBO) was used to investigate the molecular orbitals interactions and orbitals stabilization energies.

Prediction and characterization of halogen bonds involving formamidine and its derivatives

Ab initio calculations have been carried out for the complexes of formamidine (FA) and some representative halogenated molecules XY (X=Cl, Br, and I; Y=F, CCH, CF3, CN, and NC). The FA-(Z) complex combines with the halogenated molecule through a halogen bond, while the FA-(E) complex is stabilized jointly by both a halogen bond and a X⋯H interaction. The FA-(E) complex is more stable than the FA-(Z) counterpart, with the interaction energy of -3.4 to -23.4kcal/mol, indicating that FA is a good electron donor in halogen bonding. The methyl substituent particularly one at the imino nitrogen atom of FA has an enhancing effect on the strength of halogen bond. The similar effect is found for the phenyl and pyridyl substituents, depending on the FA conformation and substitution position of pyridyl. The stability of stronger halogen bonding is mainly attributed to electrostatic and polarization energies, which is different from the weak one with an electrostatic nature.

Halogen vs hydrogen bonding in thiazoline-2-thione stabilization with σ- and π-electron acceptors adducts: theoretical and experimental study

Molecular charge-transfer complexes (CT) between thiazoline-2-thione (THZ) and different σ- (I2) and π-acceptors (Tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and 2,3,5,6-tetrachloro-1,4-benzoquinone (CHL)) were investigated. UV-Vis absorption spectroscopy and theoretical calculations using both MP2/aug-cc-pVDZ-PP and B3LYP/6-311++G(d,p) level of theory were corroborated to study the nature of the stabilizing forces for THZ-I2, THZ-DDQ, THZ-TCNE, and THZ-CHL. Halogen bonding (XB) was the stabilizing attractive force in THZ-I2 and THZ-CHL whereas; hydrogen bonding (HB) was dominated in both THZ-TCNE, and THZ-DDQ complexes. Formation constant (K), extinction coefficient (ɛ), thermodynamic parameters such as enthalpy change (ΔH), entropy (ΔS), and Gibbs free energy (ΔG) were measured in different solvents.

Cooperative effects in FH/Li⋯HCCX⋯OH2 complexes (X=F, Cl, Br, H)

The dimers with general formula FH/FLi⋯HCCX and HCCX⋯OH2, and the trimers FH⋯HCCX⋯OH2 (X=F, Cl, Br, H), were optimized computationally to stable structures. These model systems derive their strength from a combination of H⋯π (or Li⋯π) electrostatic interactions in the T-shaped FH/FLi⋯HCCX dimers and halogen bonding between the X and the O atom of H2O (or CH⋯O hydrogen-bonding in HCCH complexes). These cooperative interactions in the trimer clusters yield a non-additive energy which enhances the stability by between 7% and 10%. The variation in the interaction energies, as well as other selected properties, for different X is rationalized and discussed.

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X=Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The O-H and O-X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.