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1. Halogen Bonding versus Nucleophilic Substitution in the Co-Crystallization of Halomethanes and Amines

   https://doi.org/10.3390/cryst14020124  

   Grounds, Olivia; Zeller, Matthias; Rosokha, Sergiy V (February 2024, Crystals)

   Haloalkanes and amines are common halogen-bond (XB) donors and acceptors as well as typical reagents in nucleophilic substitution reactions. Thus, crystal engineering using these molecules requires an understanding of the interchange between these processes. Indeed, we previously reported that the interaction of quinuclidine (QN) with CHI3 in acetonitrile yielded co-crystals showing a XB network of these two constituents. In the current work, the interactions of QN with C2H5I or 1,4-diazabicyclo[2.2.2]octane (DABCO) with CH2I2 led to nucleophilic substitution producing I− anions and quaternary ammonium (QN-CH2CH3 or DABCO-CH2I+) cations. Moreover, the reaction of QN with CHI3 in dichloromethane afforded co-crystals containing XB networks of CHI3 with either Cl− or I− anions and QN-CH2Cl+ counter-ions. A similar reaction in acetone produced XB networks comprising CHI3, I− and QN-CH2COCH3+. These distinctions were rationalized through a computational analysis of XB complexes and the transition-state energies for the nucleophilic substitution. It indicated that the outcome of the reactions was determined mostly by the relative energies of the products. The co-crystals obtained in this work showed bonding between the cationic (DABCO-CH2I+, QN-CH2Cl+) or neutral (CHI3) XB donors and the anionic (I−, Cl−) or neutral (CHI3) acceptors. Their analysis showed comparable electron and energy densities at the XB bond critical points and similar XB energies regardless of the charges of the interacting species. 

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2. Shedding Light on the Vibrational Signatures in Halogen‐Bonded Graphitic Carbon Nitride Building Blocks

   https://doi.org/10.1002/cphc.202200812  

   Ellington, Thomas L.; Devore, Daniel P.; Uvin G. De Alwis, W. M.; French, Kirk A.; Shuford, Kevin L. (January 2023, ChemPhysChem)

   Abstract The relative contributions of halogen and hydrogen bonding to the interaction between graphitic carbon nitride monomers and halogen bond (XB) donors containing C−X and C≡C bonds were evaluated using computational vibrational spectroscopy. Conventional probes into select vibrational stretching frequencies can often lead to disconnected results. To elucidate this behavior, local mode analyses were performed on the XB donors and complexes identified previously at the M06‐2X/aVDZ‐PP level of theory. Due to coupling between low and high energy C−X vibrations, the C≡C stretch is deemed a better candidate when analyzing XB complex properties or detecting XB formation. The local force constants support this conclusion, as the C≡C values correlate much better with theσ‐hole magnitude than their C−X counterparts. The intermolecular local stretching force constants were also assessed, and it was found that attractive forces other than halogen bonding play a supporting role in complex formation. 

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3. The relationship between the crystal habit and the energy framework pattern: a case study involving halogen bonding on the edge of a covalent bond

   https://doi.org/10.1039/d3ce00316g  

   Torubaev, Yury V.; Howe, Devin; Leitus, Gregory; Rosokha, Sergiy V. (June 2023, CrystEngComm)

   The relationship between solid-state supramolecular interactions and crystal habits is highlighted based on experimental and computational analysis of the crystal structure of strong halogen-bonded (HaB) associations between iodine-containing dihalogens (ICl, IBr) with 1,4-diazabicyclo[2,2,2]octane (DABCO) as well as with substituted pyridines and phenazine. The pattern of the energy frameworks and the interplay of the attractive and repulsive interactions in the solid-state associations involving these HaB donors and acceptors directly correlated with their crystal habits. This correlation suggests that analysis of the energy framework serves as a useful tool (complementary to the earlier developed methods) to rationalize and predict the crystal habit. The X-ray structural analysis also revealed that the I⋯N distances in the complexes were in the 2.24–2.54 Å range, i.e. they were much closer to the I⋯N covalent bond length than to the van der Waals separation. The computational analysis of the nature of halogen bonding in these complexes showed delocalization of their molecular orbitals' between donor and acceptors resulting in a substantial charge transfer from the nucleophiles to dihalogens and elongation of the I⋯X bond. As a result, both I⋯N and I⋯X bonds in the strongest complexes ( e.g. , ICl with DABCO or 4-dimethylaminopyridine) are characterized by the comparable Mayer bonds orders of about 0.6, along with the electron and energy densities at their bond critical points of about 0.1 a.u. and −0.02 a.u., respectively. These data as well as the density overlap regions indicator (DORI) point to the covalency of the I⋯N bonding and suggest that the interaction within the IX complexes can be described as (unsymmetrical) hypervalent 3c/4e N⋯I⋯X bonding akin to that in trihalide or halonium ions. 

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4. Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis

   https://doi.org/10.1039/c7cp06959f  

   Thirman, Jonathan; Engelage, Elric; Huber, Stefan M.; Head-Gordon, Martin (January 2018, Physical Chemistry Chemical Physics)

   The halogen bond is a class of non-covalent interaction that has attracted considerable attention recently. A widespread theory for describing them is the σ-hole concept, which predicts that the strength of the interaction is proportional to the size of the σ-hole, a region of positive electrostatic potential opposite a σ bond. Previous work shows that in the case of CX 3 I, with X equal to F, Cl, Br, and I, the σ-hole trend is exactly opposite to the trend in binding energy with common electron pair donors. Using energy decomposition analysis (EDA) applied to a potential energy scan as well as the recent adiabatic EDA technique, we show that the observed trend is a result of charge transfer. Therefore a picture of the halogen bond that excludes charge transfer cannot be complete, and permanent and induced electrostatics do not always provide the dominant stabilizing contributions to halogen bonds. Overall, three universally attractive factors, polarization, dispersion and charge transfer, together with permanent electrostatics, which is usually attractive, drive halogen bonding, against Pauli repulsion. 

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5. Intermolecular binding preferences of haloethynyl halogen-bond donors as a function of molecular electrostatic potentials in a family of N -(pyridin-2-yl)amides

   https://doi.org/10.1039/d1ob01133b  

   Abeysekera, Amila M.; Averkiev, Boris B.; Le Magueres, Pierre; Aakeröy, Christer B. (January 2021, Organic & Biomolecular Chemistry)

   null (Ed.)

   In order to explore how σ-hole potentials, as evaluated by molecular electrostatic potential (MEP) calculations, affect the ability of halogen atoms to engage in structure-directing intermolecular interactions, we synthesized four series of ethynyl halogen-substituted amide containing pyridines (activated targets); ( N -(pyridin-2-yl)benzamides (Bz-act-X), N -(pyridin-2-yl)picolinamides (2act-X), N -(pyridin-2-yl)nicotinamides (3act-X) and N -(pyridin-2-yl) isonicotinamides (4act-X), where X = Cl/Br/I. The molecules are deliberately equipped with three distinctly different halogen-bond acceptor sites, π, N(pyr), and OC, to determine binding site preferences of different halogen-bond donors. Crystallographic data for ten (out of a possible twelve) new compounds were thus analyzed and compared with data for the corresponding unactivated species. The calculated MEPs of all the halogen atoms were higher in the activated targets in comparison to the unactivated targets and were in the order of iodine ≈ chloroethynyl < bromoethynyl < iodoethynyl. This increased positive σ-hole potential led to a subsequent increase in propensity for halogen-bond formation. Two of the four chloroethynyl structures showed halogen bonding, and all three of the structurally characterized bromoethynyl species engaged in halogen bonding. The analogous unactived species showed no halogen bonds. Each chloroethynyl donor selected a π-cloud as acceptor and the bromoethynyl halogen-bond donors opted for either π or N(pyr) sites, whereas all halogen bonds involving an iodoethynyl halogen-bond donor (including both polymorphs of Bz-act-I ) engaged exclusively with a N(pyr) acceptor site. 

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