Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

CONSPECTUS: The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen center dot center dot center dot halogen interactions (X center dot center dot center dot X) and halogen center dot center dot center dot heteroatom interactions (X center dot center dot center dot B). Many X center dot center dot center dot X and almost all X center dot center dot center dot B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms halogen and hydrogen are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X center dot center dot center dot X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen center dot center dot center dot halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be used in the design of ternary cocrystals. Structural modularity in which an entire crystal structure is defined as a combination of modules is rationalized on the basis of the intermediate strength of a halogen bond. The specific directionality of the halogen bond makes it a good tool to achieve orthogonality in molecular crystals. Mechanical properties can be tuned systematically by varying these orthogonally oriented halogen center dot center dot center dot halogen interactions. In a further development, halogen bonds are shown to play a systematic role in organization of LSAMs (long range synthon aufbau module), which are bigger structural units containing multiple synthons. With a formal definition in place, this may be the right time to look at differences between halogen bonds and hydrogen bonds and exploit them in more subtle ways in crystal engineering.

Obtaining Synthon Modularity in Ternary Cocrystals with Hydrogen Bonds and Halogen Bonds

Design of ternary cocrystals based on synthon modularity is described. The strategy is based on the idea of extending synthon modularity in binary cocrystals of 4-hydroxybenzamide:dicarboxylic acids and 4-bromobenzamide:dicarboxylic acids. If a system contains an amide group along with other functional groups, one of which is a carboxylic acid group, the amide associates preferentially with the carboxylic acid group to form an acidamide heterosynthon. If the amide and the acid groups are in different molecules, a higher multicomponent molecular crystal is obtained. This is a stable pattern that can be used to increase the number of components from two to three in a multicomponent system. Accordingly, noncovalent interactions are controlled in the design of ternary cocrystals in a more predictable manner. If a single component crystal with the amideamide dimer is considered, modularity is retained even after formation of a binary cocrystal with acidamide dimers. Similarly, when third component halogen atom containing molecules are introduced into these binary cocrystals, modularity is still retained. Here, we use acidamide and Br/I center dot center dot center dot O2N supramolecular synthons to obtain modularity in nine ternary cocrystals. The acidamide heterosynthon is robust to all the nine cocrystals. Heterosynthons may assist ternary cocrystal formation when there is a high solubility difference between the coformers. For a successful crystal engineering strategy for ternary cocrystals, one must consider the synthon itself and factors like shape and size of the component molecules, as well as the solubilities of the compounds.

Fluorine prefers hydrogen bonds over halogen bonds! Insights from crystal structures of some halofluorobenzenes

Crystal structures of a series of isomers of chlorofluorobenzene, bromofluorobenzene and iodofluorobenzene, all of which are liquids under ambient conditions, are determined by a technique of in situ cryocrystallography. These simple dihalo substituted benzenes provide clear insights into subtle interplay of packing interactions preferred by fluorine and heavier halogens for example, C-H center dot center dot center dot X hydrogen bonds vs. X center dot center dot center dot X halogen bonds (X=F, Cl, Br, I). The interaction patterns noted here are purely characteristic of halogens, having not been influenced by other stronger interactions. Variability of principal supramolecular synthons among the isomers highlights the importance of molecular shape and relative position of interacting atoms while preserving the basic intermolecular bonds. Mutually exclusive occurrence of homo (I center dot center dot center dot I) and hetero (I center dot center dot center dot F) halogen bonds in polymorphs of 4-iodofluorobenzene questions the robustness and reliability of these interactions.

Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and ``Atoms in Molecules'' analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O-H center dot center dot center dot O, O-H center dot center dot center dot pi, and C-H center dot center dot center dot pi. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact. (C) 2014 AIP Publishing LLC.

Calcium Permeable AMPA Receptor-Dependent Long Lasting Plasticity of Intrinsic Excitability in Fast Spiking Interneurons of the Dentate Gyrus Decreases Inhibition in the Granule Cell Layer

The local fast-spiking interneurons (FSINs) are considered to be crucial for the generation, maintenance, and modulation of neuronal network oscillations especially in the gamma frequency band. Gamma frequency oscillations have been associated with different aspects of behavior. But the prolonged effects of gamma frequency synaptic activity on the FSINs remain elusive. Using whole cell current clamp patch recordings, we observed a sustained decrease of intrinsic excitability in the FSINs of the dentate gyrus (DG) following repetitive stimulations of the mossy fibers at 30 Hz (gamma bursts). Surprisingly, the granule cells (GCs) did not express intrinsic plastic changes upon similar synaptic excitation of their apical dendritic inputs. Interestingly, pairing the gamma bursts with membrane hyperpolarization accentuated the plasticity in FSINs following the induction protocol, while the plasticity attenuated following gamma bursts paired with membrane depolarization. Paired pulse ratio measurement of the synaptic responses did not show significant changes during the experiments. However, the induction protocols were accompanied with postsynaptic calcium rise in FSINs. Interestingly, the maximum and the minimum increase occurred during gamma bursts with membrane hyperpolarization and depolarization respectively. Including a selective blocker of calcium-permeable AMPA receptors (CP-AMPARs) in the bath; significantly attenuated the calcium rise and blocked the membrane potential dependence of the calcium rise in the FSINs, suggesting their involvement in the observed phenomenon. Chelation of intracellular calcium, blocking HCN channel conductance or blocking CP-AMPARs during the experiment forbade the long lasting expression of the plasticity. Simultaneous dual patch recordings from FSINs and synaptically connected putative GCs confirmed the decreased inhibition in the GCs accompanying the decreased intrinsic excitability in the FSINs. Experimentally constrained network simulations using NEURON predicted increased spiking in the GC owing to decreased input resistance in the FSIN. We hypothesize that the selective plasticity in the FSINs induced by local network activity may serve to increase information throughput into the downstream hippocampal subfields besides providing neuroprotection to the FSINs. (c) 2014 Wiley Periodicals, Inc.

Poly(alkylene itaconate)s - an interesting class of polyesters with periodically located exo-chain double bonds susceptible to Michael addition

Itaconic acid is a bio-sourced dicarboxylic acid that carries a double bond; although several reports have dealt with the radical-initiated chain polymerization of dialkyl itaconates, only a few studies have utilized it as a di-acid monomer to prepare polyesters. In this study, we demonstrate that dibutyl itaconate can be melt-condensed with aliphatic diols to generate unsaturated polyesters; importantly, we show that the double bonds remain unaffected during the melt polymerization. A particularly useful attribute of these polyesters is that the exo-chain double bonds are conjugated to the ester carbonyl and, therefore, can serve as excellent Michael acceptors. A variety of organic thiols, such as alkane thiols, MPEG thiol, thioglycerol, derivatized cysteine etc., were shown to quantitatively Michael-add to the exo-chain double bonds and generate interesting functionalized polyesters. Similarly, organic amines, such as N-methyl-benzylamine, diallyl amine and proline, also add across the double bond; thus, these poly(alkylene itaconate)s could serve as potentially bio-benign polyesters that could be quantitatively transformed into a variety of interesting and potentially useful functionalized polymers.

Three centered hydrogen bonds of the type C=O...H(N)...X-C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies

The existence of three centered C=O...H(N)...X-C hydrogen bonds (H-bonds) involving organic fluorine and other halogens in diphenyloxamide derivatives has been explored by NMR spectroscopy and quantum theoretical studies. The three centered H-bond with the participation of a rotating CF3 group and the F...H-N intramolecular hydrogen bonds, a rare observation of its kind in organofluorine compounds, has been detected. It is also unambiguously established by a number of one and two dimensional NMR experiments, such as temperature perturbation, solvent titration, N-15-H-1 HSQC, and F-19-H-1 HOESY, and is also confirmed by theoretical calculations, such as quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and non-covalent interaction (NCI).

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Unusually Short Chalcogen Bonds Involving Organoselenium: Insights into the Se-N Bond Cleavage Mechanism of the Antioxidant Ebselen and Analogues

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se center dot center dot center dot O chalcogen bonds that lead to conserved supramolecular recognition units. Se center dot center dot center dot O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se center dot center dot center dot O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se center dot center dot center dot O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se center dot center dot center dot O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se center dot center dot center dot O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS).

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H center dot center dot center dot F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)J(FH), and (1h)J(FN), provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and N-15-H-1 HSQC experiments. The H-1 DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

Inter molecular azide-diisocyanate coupling: new insights for energetic solid propellants

Hydroxyl terminated azide binders can undergo a spurious reaction with diisocyanates to form tetrazoline-5-one via an inter molecular 1,3-dipolar cycloaddition reaction apart from urethane/allophanate groups which has been overlooked. This has serious implications on solid propellants. The computed activation barrier using density functional theory (DFT) for urethane formation reaction is 28.4 kJ mol(-1) and that for tetrazoline-5-one formation reaction is 108.0 kJ mol(-1). DFT studies reveal that the rate limiting step of the reaction is 1,3-dipolar cycloaddition between azide and isocyanate. A dual cure was observed in the temperature ranges 42-77 degrees C and 78-146 degrees C by differential scanning calorimetry (DSC) and rheological studies, confirming multiple reactions. Tetrazoline-5-one formation was confirmed by Fourier transform infrared spectroscopy (FTIR) and solid state nuclear magnetic resonance spectroscopy (NMR).

Halogen bonds in some dihalogenated phenols: applications to crystal engineering

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I4(1)/a with a short axis of 3.7926 (9) angstrom. The structure is unique in that both type I and type II Cl.....Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl....Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P2(1)/c packing of compound (3) is different; while the structure still has O-H....O hydrogen bonds, the tetramer O-H.....O synthon seen in (1) and (2) is not seen. Rather than a type I Br....Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br....O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P2(1)/c and I4(1)/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br....Br interaction in (2) is stronger than the corresponding type II Cl....Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

Asymmetric cell division of granule neuron progenitors in the external granule layer of the mouse cerebellum

The plane of division of granule neuron progenitors (GNPs) was analysed with respect to the pial surface in P0 to P14 cerebellum and the results showed that there was a significant bias towards the plane of cell division being parallel to pial surface across this developmental window. In addition, the distribution of beta-Catenin in anaphase cells was analysed, which showed that there was a significant asymmetry in the distribution of beta-Catenin in dividing GNPs. Further, inhibition of Sonic Hedgehog (Shh) signalling had an effect on plane of cell division. Asymmetric distribution of beta-Catenin was shown to occur towards the source of a localized extracellular cue.

A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin

The structure of a new cysteine framework (-C-CC-C-C-C) ``M''-superfamily conotoxin, Mo3964, shows it to have a beta-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K+ currents in rat dorsal root ganglion neurons and increases the reversal potential of the Na(V)1.2 channels. The structure of Mo3964 (PDB ID: 2MW7) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the ``M''-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)J(NC') scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 +/- 0.18 angstrom, with 87% and 13% of the backbone dihedral (phi, psi) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.