Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Stepwise on-surface dissymmetric reaction to construct binodal organometallic network

Dissymmetric reactions, which enable differentiated functionalization of equivalent sites within one molecule, have many potential applications in synthetic chemistry and materials science, but they are very challenging to achieve. Here, the dissymmetric reaction of 1,4-dibromo-2,5-diethynylbenzene (2Br-DEB) on Ag(111) is realized by using a stepwise activation strategy, leading to an ordered two-dimensional organometallic network containing both alkynyl-silver-alkynyl and alkynyl-silver-phenyl nodes. Scanning tunneling microscopy and density functional theory calculations are employed to explore the stepwise conversion of 2Br-DEB, which starts from the H-passivation of one Br-substituted site at 300 K in accompaniment with an intermolecular reaction to form one-dimensional organometallic chains containing alkynyl-silver-alkynyl nodes. Afterwards, the other equivalent Br-substituted site undergoes metalation reaction at 320-450 K, resulting in transformation of the chains into the binodal networks. These findings exemplify the achievement of the dissymmetric reaction and its practical application for controlled fabrications of complicated yet ordered nanostructures on a surface.

Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design

Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.

The role of halogen substituents and substrate pKa in defining the substrate specificity of 2,6-dichlorohydroquinone 1,2-dioxygenase (PcpA)

2,6-Dichlorohydroquinone 1,2-dioxygenase (PcpA) is a non-heme Fe(II) enzyme that is specific for ortho-dihalohydroquinones. Here we deconvolute the role of halogen polarizability vs. substrate pK_a in defining this specificity, and show how substrate binding compares to the structurally homologous catechol extradiol dioxygenases. The substrates 2,6-dichloro- and 2,6-dibromohydroquinone (polarizable halogens, pK_a1 = 7.3), 2,6-difluorohydroquinone (nonpolarizable halogens, pK_a1 = 7.5), and 2-chloro-6-methylhydroquinone (polarizable halogen, pK_a1 = 9.0) were examined through spectrophotometric titrations and steady-state kinetics. The results show that binding of the substrates to the enzyme decreased [Formula: see text] by about 0.5, except for 2,6-difluorohydroquinone, which showed no change. Additionally, the K_d values of 2,6-dichloro- and 2,6-dibromohydroquinone are about equal to their respective [Formula: see text]. For comparison, with catechol 2,3-dioxygenase (XylE), the substrates 4-methyl- and 3-bromocatechol are bound to the enzyme exclusively in the monoanion form over a wide pH range, indicating a [Formula: see text] of at least - 2.9 and - 1.2, respectively. The steady-state kinetic studies showed that 2,6-difluorohydroquinone is a poor substrate, with [Formula: see text] approximately 40-fold lower and [Formula: see text] 20-fold higher than 2,6-dichlorohydroquinone, despite its similar pK_a1. Likewise, the pH dependence of [Formula: see text] for 2-chloro-6-methylhydroquinone is nearly identical to that of 2,6-dichlorohydroquinone, despite its very different pK_a1. These results show that (1) it is clearly the halogen polarizability and not the lower substrate pK_a that determines the substrate specificity of PcpA, and (2) that PcpA, unlike the catechol extradiol dioxygenases, lacks an active site base that assists with substrate deprotonation, highlighting a key functional difference in what are otherwise similar active sites that defines their different reactivity.

Organopolymer with dual chromophores and fast charge-transfer properties for sustainable photocatalysis

Photocatalytic polymers offer an alternative to prevailing organometallics and nanomaterials, and they may benefit from polymer-mediated catalytic and material enhancements. MPC-1, a polymer photoredox catalyst reported herein, exhibits enhanced catalytic activity arising from charge transfer states (CTSs) between its two chromophores. Oligomeric and polymeric MPC-1 preparations both promote efficient hydrodehalogenation of α-halocarbonyl compounds while exhibiting different solubility properties. The polymer is readily recovered by filtration. MPC-1-coated vessels enable batch and flow photocatalysis, even with opaque reaction mixtures, via "backside irradiation." Ultrafast transient absorption spectroscopy indicates a fast charge-transfer process within 20 ps of photoexcitation. Time-resolved photoluminescence measurements reveal an approximate 10 ns lifetime for bright valence states. Ultrafast measurements suggest a long CTS lifetime. Empirical catalytic activities of small-molecule models of MPC-1 subunits support the CTS hypothesis. Density functional theory (DFT) and time-dependent DFT calculations are in good agreement with experimental spectra, spectral peak assignment, and proposed underlying energetics.

Synthesis and Biological Evaluation of (E)-N’-Benzylidene-7-methyl-2-propyl-1H-benzo[d] imidazole-5-carbohydrazides as Antioxidant, Anti-inflammatory and Analgesic agents

(E)-N’-Benzylidene-7-methyl-2-propyl-1H-benzo [d]imidazole-5-carbohydrazides (5a-r) have been synthesized from 7-methyl-2-propyl-1H-benzo[d]imidazole-5-carbohydrazide (3) by condensing with different aromatic aldehydes (4a-r). Title compounds (5a-r) were evaluated for in vitro antioxidant activity and based on their potential for antioxidant property, selected compounds 5d and 5m-p were screened for in vivo anti-inflammatory and analgesic activity. The results indicate that the compound 5o and 5p are effective against anti-inflammatory and analgesic activity. The biological data was further supported by molecular docking studies, which revealed the binding pattern and the affinity of the molecules in the active site of COX-2.

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.

Halogen and Hydrogen Bonding Interplay in the Crystal Packing of Halometallocenes

This paper focuses in the influence of halogen atoms in the design and structural control of the crystal packing of Group VIII halogenated metallocenes. The study is based on the present knowledge on new types of intermolecular contacts such as halogen (X⋯X, C-X⋯H, C-X⋯π), π⋯π, and C-H⋯π interactions. The presence of novel C-H⋯M interactions is also discussed. Crystal packings are analysed after database search on this family of compounds. Results are supported by ab initio calculations on electrostatic charge distributions; Hirshfeld analysis is also used to predict the types of contacts to be expected in the molecules. Special attention is given to the competition among hydrogen and halogen interactions, mainly its influence on the nature and geometric orientations of the different supramolecular motifs. Supramolecular arrangements of halogenated metallocenes and Group IV di-halogenated bent metallocenes are also compared and discussed. Analysis supports halogen bonds as the predominant interactions in defining the crystal packing of bromine and iodine 1,1′-halometallocenes.

The study of interactions with a halogen atom: influence of NH2 group insertion on the crystal structures of meta-bromonitrobenzene derivatives

Halogen atoms in molecular crystals may be involved in various interactions, often playing a very important role in structure stabilization. By introducing electron-donating groups, such as NH₂, the electron density of the molecule is changed and thus interactions with the bromine substituent may alter. Herein, the crystal structures of meta-bromonitrobenzene and its NH₂-substituted derivatives are analyzed. In all four described structures, namely m-bromonitrobenzene [Charlton & Trotter (1963). Acta Cryst. 16, 313], 4-bromo-2-nitroaniline (C₆H₅BrN₂O₂, 1), 2-bromo-6-nitroaniline (2) and 2-bromo-4-nitroaniline [Arshad et al. (2009). Acta Cryst. E65, o480], the Br atom is engaged in different interactions (Br...π, Br...O, Br...Br and C-H...Br, respectively). The Hirshfeld surface analysis (HS) and Reduced Density Gradient NonCovalent Interaction (RDG NCI) plots are used to prove the relevance, directionality and stabilizing nature of these interactions. Their modifications have been associated with the position of the amino group in the molecular structure and its influence on charge distribution analyzed with electrostatic potential surfaces (EPS). The diversification of the interactions has been correlated with a σ-hole potential value that enables a switching of the Br-atom character from electrophilic to nucleophilic.

Is CYP1B1 involved in the metabolism of dioxins in the pig?

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most difficult to biodegradate and the most toxic dioxin congener. Previously, we demonstrated in silico the ability of pig CYP1A1 to hydroxylate 2,7-dichlorodibenzo-p-dioxin (DiCDD), but not TCDD. To increase our knowledge concerning the low effectiveness of TCDD biodegradability, we analyzed in silico the binding selectivity and affinity between pig CYP1B1 and the two dioxins by means of molecular modeling. We also compared the effects of TCDD and DiCDD on CYP1B1 gene expression (qRT-PCR) and catalytic (EROD) activity in porcine granulosa cells. It was found that DiCDD and TCDD were stabilized within the pig CYP1B1 active site by hydrophobic interactions. The analysis of substrate channel availability revealed that both dioxins opened the exit channel S, allowing metabolites to leave the enzyme active site. Moreover, DiCDD and TCDD increased the CYP1B1 gene expression and catalytic activity in porcine granulosa cells. On the other hand, TCDD demonstrated higher than DiCDD calculated affinity to pig CYP1B1, hindering TCDD exit from the active site. The great distance between CYP1B1's heme and TCDD also might contribute to the lower hydroxylation effectiveness of TCDD compared to that of DiCDD. Moreover, the narrow active site of pig CYP1B1 may immobilize TCDD molecule, inhibiting its hydroxylation. The results of the access channel analysis and the distance from pig CYP1B1's heme to TCDD suggest that the metabolizing potential of pig CYP1B1 is higher than that of pig CYP1A1. However, this potential is probably not sufficiently high to considerably improve the slow TCDD biodegradation.

The structure of 9-(3-bromo-6-chloro-2-hy-droxy-phen-yl)-10-(2-hy-droxy-ethyl)-3,6-diphenyl-3,4,5,6,7,9-hexa-hydro-2H-acridine-1,8-dione

In the structure of the title compound C33H29BrClNO4, (I), the hexa-hydro-2H-acridine ring system has a hy-droxy-ethyl substituent on the N atom and a 3-bromo-6-chloro-2-hy-droxy-phenyl substituent on the central C atom at the 9-position. An unusual feature of the mol-ecule is that the substituents at the 3- and 5-positions of the outer cyclo-hexenone rings are phenyl rings rather than the more common dimethyl substituents. C atoms on both of the cyclo-hexenone rings are disordered over two sites. In the crystal structure, O-H⋯O, C-H⋯O and C-H⋯π(ring) hydrogen bonds combine with an Br-O and unusual C-Br⋯π(ring) halogen bonds to generate a three dimensional network with mol-ecules stacked along the a-axis direction.

Drastic rearrangement of self-assembled hydrogen-bonded tapes in a molecular crystal

A 2 : 1 hydrogen-bonded crystal of 2-pyrrolidone and chloranilic acid shows structural phase transitions accompanied by the drastic rearrangement of hydrogen-bonded tapes. Such a phenomenon is attributed to the selective and directional character of hydrogen bonds.

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.

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.

Aggregation-Induced Emission-Active Ruthenium(II) Complex of 4,7-Dichloro Phenanthroline for Selective Luminescent Detection and Ribosomal RNA Imaging

The development of red emissive aggregation-induced emission (AIE) active probes for organelle-specific imaging is of great importance. Construction of metal complex-based AIE-active materials with metal-to-ligand charge transfer (MLCT), ligand-to-metal charge transfer (LMCT) emission together with the ligand-centered and intraligand (LC/ILCT) emission is a challenging task. We developed a red emissive ruthenium(II) complex, 1[PF₆]₂, and its perchlorate analogues of the 4,7-dichloro phenanthroline ligand. 1[PF₆]₂ has been characterized by spectroscopic and single-crystal X-ray diffraction. Complex 1 showed AIE enhancement in water, highly dense polyethylene glycol media, and also in the solid state. The possible reason behind the AIE property may be the weak supramolecular π···π, C-H···π, and C-Cl···H interactions between neighboring phen ligands as well as C-Cl···O halogen bonding (XB). The crystal structures of the two perchlorate analogues revealed C-Cl···O distances shorter than the sum of the van der Waals radii, which confirmed the XB interaction. The AIE property was supported by scanning electron microscopy, transmission electron microscopy, dynamic light scattering, and atomic force microscopy studies. Most importantly, the probe was found to be low cytotoxicity and to efficiently permeate the cell membrane. The cell-imaging experiments revealed rapid staining of the nucleolus in HeLa cells via the interaction with nucleolar ribosomal ribonucleic acid (rRNA). It is expected that the supramolecular interactions as well as C-Cl···O XB interaction with rRNA is the origin of aggregation and possible photoluminescence enhancement. To the best of our knowledge, this is the first report of red emissive ruthenium(II) complex-based probes with AIE characteristics for selective rRNA detection and nucleolar imaging.

High-Affinity Peptidomimetic Inhibitors of the DCN1-UBC12 Protein-Protein Interaction

The Cullin-RING ligases (CRLs) regulate the turnover of approximately 20% of the proteins in mammalian cells and are emerging therapeutic targets in human diseases. The activation of CRLs requires the neddylation of their cullin subunit, which is controlled by an activation complex consisting of Cullin-RBX1-UBC12-NEDD8-DCN1. Herein, we describe the design, synthesis, and evaluation of peptidomimetics targeting the DCN1-UBC12 protein-protein interaction. Starting from a 12-residue UBC12 peptide, we have successfully obtained a series of peptidomimetic compounds that bind to DCN1 protein with K_D values of <10 nM. Determination of a cocrystal structure of a potent peptidomimetic inhibitor complexed with DCN1 provides the structural basis for their high-affinity interaction. Cellular investigation of one potent DCN1 inhibitor, compound 36 (DI-404), reveals that it effectively and selectively inhibits the neddylation of cullin 3 over other cullin members. Further optimization of DI-404 may yield a new class of therapeutics for the treatment of human diseases in which cullin 3 CRL plays a key role.

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.

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.

SAR Studies of Indole-5-propanoic Acid Derivatives To Develop Novel GPR40 Agonists

G-protein coupled receptor 40 (GPR40) has been considered to be an attractive drug target for the treatment of type 2 diabetes because of its role in free fatty acids-mediated enhancement of glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells. A series of indole-5-propanoic acid compounds were synthesized, and their GPR40 agonistic activities were evaluated by nuclear factor of activated T-cells reporter assay and GSIS assay in the MIN-6 insulinoma cells. Three compounds, 8h (EC₅₀ = 58.6 nM), 8i (EC₅₀ = 37.8 nM), and 8o (EC₅₀ = 9.4 nM), were identified as potent GPR40 agonists with good GSIS effects.

Probing halogen-halogen interactions in solution

Halogen-halogen interactions are a particularly interesting class of halogen bonds that are known to be essential design elements in crystal engineering. In solution, it is likely that halogen-halogen interactions also play a role, but the weakness of this interaction makes it difficult to characterize or even simply detect. We have designed a supramolecular balance that allows detecting BrBr interactions between CBr₃ groups in solution and close to room temperature. The sensitivity and versatility of the chosen platform have allowed accumulating consistent data. In halogenoalkane solvents, we propose estimates for the free energy of these weak halogen bond interactions. In toluene solutions, we show that the interactions between Br atoms and the solvent aromatic groups dominate over the BrBr interactions.

A one-dimensional HgII coordination polymer based on bis-(pyridin-3-ylmeth-yl)sulfane

The reaction of mercury(II) chloride with bis-(pyridin-3-ylmeth-yl)sulfane (L, C12H12N2S) in methanol afforded the title crystalline coordination polymer catena-poly[[di-chlorido-mercury(II)]-μ-bis-(pyridin-3-ylmeth-yl)sulfane-κ2N:N'], [HgCl2L] n . The asymmetric unit consists of one HgII cation, one L ligand and two chloride anions. Each HgII ion is coordinated by two pyridine N atoms from separate L ligands and two chloride anions. The metal adopts a highly distorted tetra-hedral geometry, with bond angles about the central atom in the range 97.69 (12)-153.86 (7)°. Each L ligand bridges two HgII ions, forming an infinite -(Hg-L) n - zigzag chain along the b axis, with an Hg⋯Hg separation of 10.3997 (8) Å. In the crystal, adjacent chains are connected by inter-molecular C-H⋯Cl hydrogen bonds, together with Hg-Cl⋯π inter-actions [chloride-to-centroid distance = 3.902 (3) Å], that form between a chloride anion and the one of the pyridine rings of L, generating a two-dimensional layer extending parallel to (101). These layers are further linked by inter-molecular C-H⋯π hydrogen bonds, forming a three-dimensional supra-molecular network.

Molecular basis of selective resistance of the bumblebee BiNav1 sodium channel to tau-fluvalinate

Insecticides are widely used to control pests in agriculture and insect vectors that transmit human diseases. However, these chemicals can have a negative effect on nontarget, beneficial organisms including bees. Discovery and deployment of selective insecticides is a major mission of modern toxicology and pest management. Pyrethroids exert their toxic action by acting on insect voltage-gated sodium channels. Honeybees and bumblebees are highly sensitive to most pyrethroids, but are resistant to a particular pyrethroid, tau-fluvalinate (τ-FVL). Because of its unique selectivity, τ-FVL is widely used to control not only agricultural pests but also varroa mites, the principal ectoparasite of honeybees. However, the mechanism of bee resistance to τ-FVL largely remains elusive. In this study, we functionally characterized the sodium channel BiNa_v1-1 from the common eastern bumblebee (Bombus impatiens) in Xenopus oocytes and found that the BiNa_v1-1 channel is highly sensitive to six commonly used pyrethroids, but resistant to τ-FVL. Phylogenetic and mutational analyses revealed that three residues, which are conserved in sodium channels from 12 bee species, underlie resistance to τ-FVL or sensitivity to the other pyrethroids. Further computer modeling and mutagenesis uncovered four additional residues in the pyrethroid receptor sites that contribute to the unique selectivity of the bumblebee sodium channel to τ-FVL versus other pyrethroids. Our data contribute to understanding a long-standing enigma of selective pyrethroid toxicity in bees and may be used to guide future modification of pyrethroids to achieve highly selective control of pests with minimal effects on nontarget organisms.

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.

Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances

We dissected halogen-aryl π interactions experimentally using a bicyclic N-arylimide based molecular torsion balances system, which is based on the influence of the non-bonded interaction on the equilibria between folded and unfolded states. Through comparison of balances modulated by higher halogens with fluorine balances, we determined the magnitude of the halogen-aryl π interactions in our unimolecular systems to be larger than -5.0 kJ mol^-1 , which is comparable with the magnitude estimated in the biomolecular systems. Our study provides direct experimental evidence of halogen-aryl π interactions in solution, which until now have only been revealed in the solid state and evaluated theoretically by quantum-mechanical calculations.

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.

Three closely related 1-(naphthalen-2-yl)prop-2-en-1-ones: pseudosymmetry, disorder and supramoleular assembly mediated by C-H...π and C-Br...π interactions

It has been observed that when electron-rich naphthyl rings are present in chalcones they can participate in π-π stacking interactions, and this can play an important role in orientating inhibitors within the active sites of enzymes, while chalcones containing heterocyclic substituents additionally exhibit fungistatic and fungicidal properties. With these considerations in mind, three new chalcones containing 2-naphthyl substituents were prepared. 3-(4-Fluorophenyl)-1-(naphthalen-2-yl)prop-2-en-1-one, C₁₉H₁₃FO, (I), crystallizes with Z' = 2 in the space group P-1 and the four molecules in the unit cell adopt an arrangement which resembles that in the space group P2₁/a. Although 3-(4-bromophenyl)-1-(naphthalen-2-yl)prop-2-en-1-one, C₁₉H₁₃BrO, (II), with Z' = 1, is not isostructural with (I), the molecules of (I) and (II) adopt very similar conformations. In 1-(naphthalen-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one, C₁₇H₁₂OS, (III), the thiophene unit is disordered over two sets of atomic sites, with occupancies of 0.780 (3) and 0.220 (3), which are related by a near 180° rotation of the thiophene unit about its exocyclic C-C bond. The molecules of compound (I) are linked by three independent C-H...π(arene) hydrogen bonds to form centrosymmetric octamolecular aggregates, whereas the molecules of compound (II) are linked into molecular ladders by a combination of C-H...π(arene) and C-Br...π(arene) interactions, and those of compound (III) are linked into centrosymmetric dimers by C-H...π(thiophene) interactions.

Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY

Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.

Halogen-π Interactions between Benzene and X2/CX4 (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)

Various types of interactions between halogen (X) and π moiety (X-π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X₂ and CX₄ (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Møller-Plesset second-order perturbation theory (MP2), and various flavors of density functional theory (DFT) methods, we study complexes of benzene (Bz) with halogen-containing molecules X₂ and CX₄ (X = Cl/Br) and analyze various components of the interaction energy using symmetry adapted perturbation theory (SAPT). As for the lowest energy conformers (S1), X₂-Bz is found to have the T-shaped structure where the electropositive X atom-end of X₂ is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX₄-Bz has the stacked structure. In addition to this CX₄-Bz (S1), other low energy conformers of X₂-Bz (S2/S3) and CX₄-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X₂-Bz (S1), whereas the deviations are relatively small for CX₄-Bz where the dispersion is more important. The halogen bond shows highly anisotropic electron density around halogen atoms and the DFT results are very sensitive to basis set. The unsatisfactory performance of many density functionals could be mainly due to less accurate exchange. This is evidenced from the good performance by the dispersion corrected hybrid and double hybrid functionals. B2GP-PLYP-D3 and PBE0-TS(Tkatchenko-Scheffler)/D3 are well suited to describe the X-π interactions adequately, close to the CCSD(T)/CBS binding energies (within ∼1 kJ/mol). This understanding would be useful to study diverse X-π interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers.

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.

Crystal structure of an HgII coordination polymer with an unsymmetrical dipyridyl ligand: catena-poly[[[di-chlorido-mercury(II)]-μ-N-(pyridin-4-ylmeth-yl)pyridin-3-amine-κ2N:N'] chloro-form hemisolvate]

The asymmetric unit of the title compound, {[HgLCl2]·0.5CHCl3} n (L = N-(pyridin-4-ylmeth-yl)pyridin-3-amine, C11H11N3), contains one HgII ion, one bridging L ligand, two chloride ligands and a chloro-form solvent mol-ecule with half-occupancy that is disordered about a crystallographic twofold rotation axis. Each HgII ion is coordinated by two pyridine N atoms from two symmetry-related L ligands and two chloride anions in a highly distorted tetra-hedral geometry with bond angles falling in the range 99.05 (17)-142.96 (7)°. Each L ligand bridges two HgII ions, forming polymeric zigzag chains propagating in [010]. In the crystal, the chains are linked by inter-molecular N/C-H⋯Cl hydrogen bonds together with weak C-H⋯π inter-actions, resulting in the formation of a three-dimensional supra-molecular network, which is further stabilized by C-Cl⋯π inter-actions between the solvent chloro-form mol-ecules and the pyridine rings of L [chloride-to-centroid distances = 3.442 (11) and 3.626 (13) Å]. In addition, weak Cl⋯Cl contacts [3.320 (5) Å] between the chloro-form solvent mol-ecules and the coordinating chloride anions are also observed.