Halogen-Bonded Co-Crystals of Aromatic N-oxides: Polydentate Acceptors for Halogen and Hydrogen Bonds

Comparison of N···I and N···O Halogen Bonds in Organoiodine Cocrystals of Heterocyclic Aromatic Diazine Mono-N-oxides

A series of cocrystals of halogen bond donors 1,4-diiodotetrafluorobenzene (p-F4DIB) and tetraiodoethylene (TIE) with five aromatic heterocyclic diazine mono-N-oxides based on pyrazine, tetramethylpyrazine, quinoxaline, phenazine, and pyrimidine as halogen bonding acceptors were studied. Structural analysis of the mono-N-oxides allows comparison of the competitive occurrence of N···I vs O···I interactions and the relative strength and directionality of these two types of interactions. Of the aromatic heterocyclic diazine mono-N-oxide organoiodine cocrystals examined, six exhibited 1:1 stoichiometry, forming chains that utilized both N···I and O···I interactions. Two cocrystals presented 1:1 stoichiometry with exclusive O···I interactions. Two cocrystals displayed a 2:1 stoichiometry-one characterized solely by O···I interactions and the other solely by N···I interactions. We have also compared these interactions to those present in the corresponding diazines, some of which we report here and some which have been previously reported. In addition, a computational analysis using density functional theory (M062X/def2-SVPD) was performed on these two systems and has been compared to the experimental results. The calculated complex formation energies were, on average, 4.7 kJ/mol lower for the I···O halogen bonding interaction as compared to the corresponding N···I interaction. The average I···O interaction distances were calculated to be 0.15 Å shorter than the corresponding I···N interactions.

N-X⋅⋅⋅O-N Halogen Bonds in Complexes of N-Haloimides and Pyridine-N-oxides: A Large Data Set Study

N-X⋅⋅⋅- O-N+ halogen-bonded systems formed by 27 pyridine N-oxides (PyNOs) as halogen-bond (XB) acceptors and two N-halosuccinimides, two N-halophthalimides, and two N-halosaccharins as XB donors are studied in silico, in solution, and in the solid state. This large set of data (132 DFT optimized structures, 75 crystal structures, and 168 1 H NMR titrations) provides a unique view to structural and bonding properties. In the computational part, a simple electrostatic model (SiElMo) for predicting XB energies using only the properties of halogen donors and oxygen acceptors is developed. The SiElMo energies are in perfect accord with energies calculated from XB complexes optimized with two high-level DFT approaches. Data from in silico bond energies and single-crystal X-ray structures correlate; however, data from solution do not. The polydentate bonding characteristic of the PyNOs' oxygen atom in solution, as revealed by solid-state structures, is attributed to the lack of correlation between DFT/solid-state and solution data. XB strength is only slightly affected by the PyNO oxygen properties [(atomic charge (Q), ionization energy (Is,min ) and local negative minima (Vs,min )], as the σ-hole (Vs,max ) of the donor halogen is the key determinant leading to the sequence N-halosaccharin>N-halosuccinimide>N-halophthalimide on the XB strength.

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Construction of 2D extended cocrystals on the Au(111) surface via IOaldehyde halogen bonds

2D extended organic cocrystals were constructed using 1,4-diiodotetrafluorobenzene and aromatic aldehydes via IOaldehyde halogen bonds on an Au(111) surface. The competition and synergy of halogen bonds and hydrogen bonds in 2D co-crystallization were revealed by scanning tunneling microscopy.

Cocrystal trimorphism as a consequence of the orthogonality of halogen- and hydrogen-bonds synthons

True trimorphic cocrystals, i.e. multi-component molecular crystals of identical composition that exhibit three polymorphic structures, are exceedingly rare and so far no halogen-bonded cocrystal system has been reported to exhibit trimorphism. Here we describe a unique example of a trimorphic cocrystal exhibiting both hydrogen and halogen bonds in which the differences between polymorphs reveal their orthogonality, evident by the apparently independent variation of well-defined hydrogen- and halogen-bonded motifs.

Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C₃ F₆ ), upon its interaction with another same molecule to form (C₃ F₆ )₂ dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C₃ F₆ itself and the (C₃ F₆ )₂ dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C₃ F₆ )₂ dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C₃ F₆ )₂ dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.

Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

New polymorphism and structural sensitivity in triphenylmethylphosphonium trihalide salts

PPh₃MeX₃ (X = I, Br) is studied on the basis of temperature and halide composition revealing new polymorphism structure types.

Tridentate C–I⋯O−–N+ halogen bonds

N-Oxides can act as tridentate halogen bond acceptors, or as tetradentate ligands in a pseudo-μ₄ mode with silver(i).