Cooperative effects and optimal halogen bonding motifs for self-assembling systems

Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds

The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.

Triangular Interchalcogen Interactions: A Joint Crystallographic Data Analysis and Theoretical Study

Noncovalent chalcogen-chalcogen interactions are being actively investigated from both crystallographic and theoretical viewpoints in recent years. According to our search of the Cambridge Structural Database (CSD), a huge number of crystal structures containing triangular Ch₃ synthons were extracted. On the basis of the results of the CSD survey, a series of trimeric complexes of organic divalent chalcogen molecules were selected to model such interaction motifs. Similar to that in conventional chalcogen bonds, triangular interchalcogen interactions become gradually stronger along the sequence of Ch = S, Se, Te. Particularly, hydrogen bonds between the chalcogen centers and the H atoms in the substituents occur, which play a significant role in stabilizing the Ch₃ motifs in the trimers. Through multibody energy calculations, the complexes under study exhibit no or only weak cooperativity. Finally, the differences between the Ch₃ interaction motifs and the well-studied windmill X₃ bonding (X means halogen and this is halogen bond) patterns were elucidated.

Halogen bonding controlled 2D self-assembled polymorphism of regioisomeric thienophenanthrene derivatives by coadsorption

5,10-BTD-C14 molecules display self-assembled polymorphism in different bromo-hydrocarbons with different solution concentrations at the liquid/solid interface.

Halogen-bonded haloamine trimers - modelling the X3 synthon

Halogen-halogen bonded haloamine trimers serve as model systems for the X3 synthon present in numerous crystal structures and in two-dimensional self-assembled nanoarchitectures. Halogen bonds forming the synthon are often considered to display cooperativity. Synergy effects were previously found for halogen-halogen bonded bromoamine and iodoamine tetramers. In the present study comparison between haloamine cyclic trimers and tetramers is made. The cooperativity occurring in bromoamine and iodoamine clusters is significantly weaker in the case of the trimers. The present study demonstrates that the bromoamine and iodoamine trimers display weaker cooperativity due to a smaller number of synergy components in comparison to the corresponding tetramers of stronger cooperativity. Moreover, the halogen-halogen interactions in bromoamine and iodoamine dimers with the geometries of the corresponding trimers and tetramers are examined using energy decomposition analysis methods (supermolecular, canonical EDA and SAPT) and the Kohn-Sham molecular orbital model. The results of the analysis indicate that although the interaction energy values for the dimers of the different spatial arrangement are very close to each other, their origin is substantially different. For pairs with the geometry of the trimers orbital interactions and electrostatic attraction are both weaker than for the corresponding dimers with the geometry of the tetramers. This is especially important because both donor-acceptor interactions and electrostatic attraction were previously proven to be responsible for cooperative effects occurring in the bromoamine and iodoamine tetramers.

"Anti-Electrostatic" Halogen Bonding

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

Rigorous Free Energy Simulations in Virtual Screening

Virtual high throughput screening (vHTS) in drug discovery is a powerful approach to identify hits: when applied successfully, it can be much faster and cheaper than experimental high-throughput screening approaches. However, mainstream vHTS tools have significant limitations: ligand-based methods depend on knowledge of existing chemical matter, while structure-based tools such as docking involve significant approximations that limit their accuracy. Recent advances in scientific methods coupled with dramatic speedups in computational processing with GPUs make this an opportune time to consider the role of more rigorous methods that could improve the predictive power of vHTS workflows. In this Perspective, we assert that alchemical binding free energy methods using all-atom molecular dynamics simulations have matured to the point where they can be applied in virtual screening campaigns as a final scoring stage to prioritize the top molecules for experimental testing. Specifically, we propose that alchemical absolute binding free energy (ABFE) calculations offer the most direct and computationally efficient approach within a rigorous statistical thermodynamic framework for computing binding energies of diverse molecules, as is required for virtual screening. ABFE calculations are particularly attractive for drug discovery at this point in time, where the confluence of large-scale genomics data and insights from chemical biology have unveiled a large number of promising disease targets for which no small molecule binders are known, precluding ligand-based approaches, and where traditional docking approaches have foundered to find progressible chemical matter.

Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex

The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.

Cooperativity between hydrogen- and halogen bonds: the case of selenourea

A combined experimental/theoretical investigation on the cooperativity between hydrogen- and halogen bonds is presented. In this study, it is shown that selenourea can interact at the same time with a benzoate anion and a polarized iodine, with the two interactions influencing and enhancing each other.

Halogen-bond driven self-assembly of triangular macrocycles

Halogen bonds drive the self-assembly of 2-iodoethynylpyridine and 2- iodoethynyl-1-methyl-imidazole into discrete supramolecular triangles.

The effect of anions on noncovalent interactions in model clusters of chalcogen-containing (CH3)2X (X = O, S, Se) molecules

A computational study of F⁻⋯(CH₃)₂O⋯CH₃F with F⁻ bound to the protons of the two methyl groups, found significant enhancement of the O⋯C interaction relative to the neutral (CH₃)₂O⋯CH₃F dyad.

Supramolecular nanotubes based on halogen bonding interactions: cooperativity and interaction with small guests

In this manuscript the formation of a series of self-assembled supramolecular nanotubes (SNTs) governed by noncovalent halogen bonding interactions is studied.

Source of Cooperativity in Halogen-Bonded Haloamine Tetramers

Inspired by the isostructural motif in α-bromoacetophenone oxime crystals, we investigated halogen-halogen bonding in haloamine quartets. Our Kohn-Sham molecular orbital and energy decomposition analysis reveal a synergy that can be traced to a charge-transfer interaction in the halogen-bonded tetramers. The halogen lone-pair orbital on one monomer donates electrons into the unoccupied σ*N-X orbital on the perpendicular N-X bond of the neighboring monomer. This interaction has local σ symmetry. Interestingly, we discovered a second, somewhat weaker donor-acceptor interaction of local π symmetry, which partially counteracts the aforementioned regular σ-symmetric halogen-bonding orbital interaction. The halogen-halogen interaction in haloamines is the first known example of a halogen bond in which back donation takes place. We also find that this cooperativity in halogen bonds results from the reduction of the donor-acceptor orbital-energy gap that occurs every time a monomer is added to the aggregate.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.

Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor

Optimization is reported for biaryltriazoles as inhibitors of the tautomerase activity of human macrophage migration inhibitory factor (MIF), a proinflammatory cytokine associated with numerous inflammatory diseases and cancer. A combined approach was taken featuring organic synthesis, enzymatic assaying, crystallography, and modeling including free-energy perturbation (FEP) calculations. X-ray crystal structures for 3a and 3b bound to MIF are reported and provided a basis for the modeling efforts. The accommodation of the inhibitors in the binding site is striking with multiple hydrogen bonds and aryl-aryl interactions. Additional modeling encouraged pursuit of 5-phenoxyquinolinyl analogues, which led to the very potent compound 3s. Activity was further enhanced by addition of a fluorine atom adjacent to the phenolic hydroxyl group as in 3w, 3z, 3aa, and 3bb to strengthen a key hydrogen bond. It is also shown that physical properties of the compounds can be modulated by variation of solvent-exposed substituents. Several of the compounds are likely the most potent known MIF tautomerase inhibitors; the most active ones are more than 1000-fold more active than the well-studied (R)-ISO-1 and more than 200-fold more active than the chromen-4-one Orita-13.

Covalency in resonance-assisted halogen bonds demonstrated with cooperativity in N-halo-guanine quartets

Cooperativity of resonance-assisted halogen bonds is, similar to resonance-assisted hydrogen bonds, shown to originate primarily from charge transfer.