Halogen Bond Induced Structural and Photophysical Properties Modification in Organic-Inorganic Hybrid Manganese Halides.

The role of halogen bonding in organic-inorganic hybrid (OIH) halides was seldom investigated despite its potential to enhance the stability of the compound. In this context, we have synthesized (2-methylbenzimidazolium)MnCl3(H2O)·H2O (compound 1) crystallizing in a monoclinic space group P21/c with a 1D infinite chain of edge shared Mn octahedra. In contrast, the chloro-substituted derivative (5-chloro-2-methylbenzimidazolium)2MnCl4 (compound 2) exhibits 0D Mn tetrahedra with a triclinic P1̅ structure. This structural modification from 1D Mn octahedra to 0D Mn tetrahedra involves a unique type-II halogen bonding between organic chlorine (C-Cl) and inorganic chloride (Cl-Mn) ions. Compound 1 exhibits red emission, whereas compound 2 demonstrates dual-band emission, resulting from energy transfer from the organic amine to Mn centers. To rationalize this interesting modulation in structure and photophysical properties, the role of halogen bonding is explored in terms of quantitative electron density analysis and intermolecular interaction energies.

Quantitative insights into noncovalent interactions involving halogen and tetrel bonds in 2,4,6-trimethylpyrylium tetrafluoroborate.

The crystal and molecular structure of an organic salt, in which a 2,4,6-trimethylpyrylium cation forms a salt with a tetrafluoroborate anion, namely, 2,4,6-trimethylpyrylium tetrafluoroborate, C8H11O+·BF4-, has been experimentally realized. The compound crystallizes in the orthorhombic centrosymmetric space group Pnma. The crystal packing is stabilized via a subtle interplay of [F3-B-F]-...O+-C fluorine/oxygen-centred halogen/chalcogen bonds and Cδ+...Fδ- tetrel-bonded contacts. Although the O centre has a formal charge of +1, the estimation of the partial negative charges on O is in accordance with electronegativity considerations. Hirshfeld surface analysis, which also includes an analysis of the three-dimensional deformation density, along with molecular electrostatic potential (MESP) calculations, provides quantitative insights into the nature of the intermolecular interactions. The topological analysis of the electron-density distribution has been performed using AIMAll and TOPOND, and unequivocally establishes the bonding character associated with the different noncovalent interactions. In addition, NBO analysis and polarizability calculations using PolaBer render deeper physical insights into the electronic characteristics of these noncovalent interactions.

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals.

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

An Experimental Adult Zebrafish Model for Shigella Pathogenesis, Transmission, and Vaccine Efficacy Studies.

Shigellosis has been a menace to society for ages. The absence of an effective vaccine against Shigella, improper sanitation, and unhygienic use of food and water allow the disease to flourish. Shigella can also be transmitted via natural water bodies. In the absence of a good animal model, the actual nature of pathogenesis and transmission remains unclear. Zebrafish larvae have previously been described as a model for Shigella pathogenesis. However, larval fish lack a mature intestinal microbiota and immune system. Here, the adult zebrafish was assessed as a potential model for Shigella pathogenesis. Their well-developed innate and adaptive immune responses mimic the mammalian immune system. Shigella showed a clear dose-, time-, and temperature-dependent colonization of the adult zebrafish gut. Efficacy of a three-dose immunization regime was tested using bath immunization with heat-killed trivalent Shigella immunogen. The present study demonstrates the efficacy of an adult zebrafish model for pathogenesis, transmission, and vaccine efficacy studies. IMPORTANCE Shigellosis is a diarrheal disease that is prevalent in developing countries and especially dangerous in young children. Currently, animal models for shigellosis are unable to model some aspects of the infectious cycle. Here, we describe a new shigellosis model in adult zebrafish, an increasingly common model organism for studying bacterial pathogens. The zebrafish model can be used to study Shigella colonization, transmission, and immune responses, as well as test vaccine efficacy.

X-ray Electron Density Study of the Chemical Bonding Origin of Glass Formation in Metal-Organic Frameworks.

Glass-forming metal-organic frameworks (MOFs) have novel applications, but the origin of their peculiar melting behavior is unclear. Here, we report synchrotron X-ray diffraction electron densities of two zeolitic imidazolate frameworks (ZIFs), the glass-forming Zn-ZIF-zni and the isostructural thermally decomposing Co-ZIF-zni. Electron density analysis shows that the Zn-N bonds are more ionic than the Co-N bonds, which have distinct covalent features. Variable-temperature Raman spectra reveal the onset of significant imidazolate bond weakening in Co-ZIF-zni above 673 K. Melting can be controlled by tuning the metal-ligand and imidazole bonding strength as shown from thermal analysis of nine solid-solution Cox Zn1-x -ZIF-zni (x=0.3 to 0.003) MOFs, and a mere 4 % Co-doping into Zn-ZIF-zni results in thermal decomposition instead of melting. The present findings demonstrate the key role of the metal-ligand bonds and imidazolate bonds in controlling the delicate balance between melting and decomposition processes in this class of ZIF compounds.

Sensitivity of the glass transition and melting in a metal-organic framework to ligand chemistry.

The effect of substituting linkers with electron-donating moieties for part of the conventional ones on the melting and glass transition behaviours of ZIF-62 was investigated by calorimetry and X-ray diffraction. Specifically, substituting 5,6-dimethylbenzimidazole for benzimidazole in ZIF-62 increases both Tm and Tg. The structural origin of this effect was explained.

Experimental Insights into the Electronic Nature, Spectral Features, and Role of Entropy in Short CH3···CH3 Hydrophobic Interactions.

Hydrophobic interactions are often explored in solution-state aggregation of molecules. However, an experimental electron density description about these interactions is still lacking. Here, we report a systematic study on the electronic nature of methyl···methyl hydrophobic interactions in a series of multicomponent crystals of biologically active molecules. Charge density models based on high-resolution X-ray diffraction allow the visualization of subtle details of electron density features in the interaction region. Our study classifies these interactions as atypical group···group interactions in contrast to σ-hole interactions, which are stabilized by the minimized electrostatic repulsion and maximized dispersion forces. For the first time, we quantified the solid-state entropic contribution from the torsional mode of the methyl groups in stabilizing these interactions by thermal motion analysis based on neutron diffraction as well as variable-temperature crystallography. The carbon atoms in methyl···methyl interactions show a unique upfield chemical shift in the 13C solid-state NMR signal.

Studies on formulation of a combination heat killed immunogen from diarrheagenic Escherichia coli and Vibrio cholerae in RITARD model.

Multiple diarrheagenic enteric bacterial infections cause global morbidity and mortality. A combination vaccine is needed to combat different diarrhea-causing organisms. In our present work, we formulated a combination of antigens from three different diarrheagenic Escherichia coli strains and three different Vibrio cholerae strains. We demonstrated that our newly formulated combination immunogen was able to raise species-specific immunogenicity. This formulation also gave protection against different diarrheagenic E. coli strains in the removable intestinal tie-adult rabbit diarrhea model. However, protective efficacy was not found against the V. cholerae El Tor Ogawa Haitian variant, but challenged with V. cholerae El Tor Inaba or O139 showed protection in rabbits. This is the first report of a single formulated nonliving heat-killed combination immunogen from different diarrheagenic E. coli and V. cholerae that could bestow protection against different bacteria in an animal model.

Dissemination of newly emerged polymyxin B sensitive Vibrio cholerae O1 containing Haitian-like genetic traits in different parts of India.

PURPOSE: Two natural epidemic biotypes of Vibrio cholerae O1, classical and El Tor, exhibit different patterns of sensitivity against the antimicrobial peptide polymyxin B. This difference in sensitivity has been one of the major markers in biotype classification system for several decades. A recent report regarding the emergence of polymyxin B-sensitive El Tor V. cholerae O1 in Kolkata has motivated us to track the spread of the strains containing this important trait, along with Haitian-like genetic content, in different parts of India. METHODOLOGY: We have collected 260 clinical V. cholerae O1 strains from 12 states in India and screened them for polymyxin B susceptibility. Genetic characterization was also performed to study the tcpA, ctxB and rtxA genotypes by allele-specific polymerase chain reaction (PCR) and nucleotide sequencing. RESULTS: Interestingly, 88.85 % of the isolates were found to be sensitive to polymyxin B. All of the states, with the exception of Assam, had polymyxin B-sensitive V. cholerae strains and complete replacement with this strain was found in eight of the states. However, from 2016 onwards, all the strains tested showed sensitivity to polymyxin B. Allele-specific PCR and sequencing confirmed that all strains possessed Haitian-like genetic traits. CONCLUSION: Polymyxin B-sensitive strains have begun to spread throughout India and may lead to the revision of the biotype classification. The dissemination of these new variant strains needs to be carefully monitored in different endemic populations through active holistic surveillance to understand their clinical and epidemiological consequences.

Isolation and Characterization of Novel Broad Host Range Bacteriophages of Vibrio cholerae O1 from Bengal.

OBJECTIVES: We have isolated a total of five newer cholera phages which are novel broad host range to incorporate with the existing phage typing schemes for an extended typing scheme. MATERIALS AND METHODS: These newly isolated phages were well characterized including the electron micrograph. A total of 300 Vibrio cholerae strains were isolated from the different endemic region in India were included in phage typing study. RESULTS: These phages were found different from the existing phages. Electron microscopic results showed that the phages belonged to myophage and podophage group. Characterization of the phages based on pH, temperature, and organic solvent sensitivity showed differences among the phages used in this study. All the strains of Vibrio O1 were typeable (100%) with the five set of cholera phages. Of these, 40% strains were clustered under Type-1. CONCLUSION: The newer Vibrio phages are novel and broad host range and will be useful to incorporate with the existing phage typing system for more precisely discriminate the strains of Vibrio cholerae.

Exploring the rare S-H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid.

Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S-H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S-H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. The para-substituted mercaptobenzoic acid depicts a type I S...S interaction.

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction.

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. Calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. The study described is the first practical application of In-House Time-Resolved diffraction, made possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.

A heuristic approach to evaluate peri interactions versus intermolecular interactions in an overcrowded naphthalene.

Octachloronaphthalene (OCN), a serious environmental pollutant, has been investigated by charge density analysis to unravel several unexplored factors responsible for steric overcrowding. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge-density studies. A new facet in the fundamental understanding of peri interactions is revealed by NCI (non-covalent interaction) analysis. The potential role of these interactions in deforming the molecular geometry and subsequent effect on aromaticity are substantiated from NICS (Nuclear Independent Chemical Shift) and QTAIM (Quantum Theory of Atoms in Molecules) calculations. The eye-catching dissimilarity in the out-of-plane twisting of OCN renders the molecule in an asymmetric geometry in the crystalline phase compared with symmetric geometry in the optimized solvated phase. This is uniquely characterized by their molecular electrostatic potential (MESP), respectively, and is explained in terms of conflict between two opposing forces - peri interactions, and symbiotic intermolecular Cl⋯Cl and Cl⋯π contacts.

Acetazolamide polymorphism: a case of hybridization induced polymorphism?

The unusual phenomenon of the formation of the kinetic form as against the thermodynamic form upon slow cooling of boiling aqueous solution in the case of diuretic drug acetazolamide is rationalized in terms of "hybridization induced polymorphism" based on extensive experimental and theoretical investigations.

Trends in the genomic epidemiology of Vibrio cholerae O1 isolated worldwide since 1961.

Here we describe the international scenario of Vibrio cholerae with a comparative analysis of different aspects of typing. Representative V. cholerae strains (n=108) associated with endemic cholera regions from 29 states of India and worldwide were subjected to microbiological, molecular and phylogenetic study. All of the strains were V. cholerae serogroup O1 biotype El Tor and were typed according to both the new phage (NP) type and Basu & Mukherjee (BM) typing schemes. The predominant phage type was T-27 (NP)/T-4 (BM) (65.7%; n=71), followed by phage type T-27 (NP)/T-2 (BM) (14.8%; n=16), T-26 (NP)/T4 (BM) (12.0%; n=13), T-13 (NP)/T-4 (BM) (2.8%; n=3), T-20 (NP)/T-4 (BM) (1.9%; n=2), T-3 (NP)/T-4 (BM) (0.9%; n=1), T-23 (NP)/T-4 (BM) (0.9%; n=1) and T-24 (NP)/T-2 (BM) (0.9%; n=1). Mismatch amplification mutation assay PCR (MAMA-PCR) findings showed the dominance of ctxB El Tor genotype (77.1%; 54/70) from 1961-1991, whilst the next two epochs showed the supremacy of ctxB classical genotype. Multidrug-resistant strains showed resistance to erythromycin, streptomycin, trimethoprim/sulfamethoxazole, norfloxacin and ampicillin. The regional resistance of epidemic clones in India draws a layout of the rapid dissemination of resistance in the past 30 years and the necessity of proper treatment to protect populations at risk.

Experimental validation of 'pnicogen bonding' in nitrogen by charge density analysis.

The participation of a nitrogen atom acting as an electrophile in pnicogen bonding, a hitherto unexplored interaction has been established by experimental charge density analysis. QTAIM and NBO analyses ratify this observation.

Hydrogen and methanol exchange processes for (TMP)Rh-OCH3(CH3OH) in binary solutions of methanol and benzene.

Tetramesityl porphinato rhodium(III) methoxide ((TMP)Rh-OCH(3)) binds with methanol in benzene to form a 1:1 methanol complex ((TMP)Rh-OCH(3)(CH(3)OH)) (1). Dynamic processes are observed to occur for the rhodium(III) methoxide methanol complex (1) that involve both hydrogen and methanol exchange. Hydrogen exchange between coordinated methanol and methoxide through methanol in solution results in an interchange of the environments for the non-equivalent porphyrin faces that contain methoxide and methanol ligands. Interchange of the environments of the coordinated methanol and methoxide sites in 1 produces interchange of the inequivalent mesityl o-CH(3) groups, but methanol ligand exchange occurs on one face of the porphyrin and the mesityl o-CH(3) groups remain inequivalent. Rate constants for dynamic processes are evaluated by full line shape analysis for the (1)H NMR of the mesityl o-CH(3) and high field methyl resonances of coordinated methanol and methoxide groups in 1. The rate constant for interchange of the inequivalent porphyrin faces is associated with hydrogen exchange between 1 and methanol in solution and is observed to increase regularly with the increase in the mole fraction of methanol. The rate constant for methanol ligand exchange between 1 and the solution varies with the solution composition and fluctuates in a manner that parallels the change in the activation energy for methanol diffusion which is a consequence of solution non-ideality from hydrogen bonded clusters.

Comparison of Rh-OCH3 and Rh-CH2OH bond dissociation energetics from methanol C-H and O-H bond reactions with rhodium(II) porphyrins.

Reaction of methanol in toluene with tetramesityl rhodium(II) porphyrin ((TMP)Rh(II•)) produces a (1)H NMR-observable equilibrium with rhodium methoxide ((TMP)Rh-OCH(3)(CH(3)OH)) and rhodium hydride ((TMP)Rh-H) complexes. Equilibrium concentrations for each of these species, obtained from integration of (1)H NMR spectra, were used in determining the equilibrium constant, K(298 K) = [Rh-OCH(3)(CH(3)OH)][Rh-H]/[Rh(II•)](2)[CH(3)OH](2) = 3.0(0.3), and free energy change, ΔG(0)(298 K) = -0.65(0.5) kcal mol(-1), for the reaction. Equilibrium thermodynamic measurements in CD(2)Cl(2) give ΔG(0)(298 K) = -5.5(0.2) kcal mol(-1) for association of methanol with (TMP)Rh-OCH(3) to form the six-coordinate 18-electron complex (TMP)Rh-OCH(3)(CH(3)OH). Equilibrium measurements in conjunction with (TMP)Rh-H and CH(3)O-H bond energetics are used to evaluate the (TMP)Rh-OCH(3) bond dissociation free energy (Rh-OCH(3) BDFE(298 K) = 38 (1.3) kcal mol(-1)), which is 15 kcal mol(-1) smaller than the Rh-H BDFE and approximately equal to the Rh-CH(2)OH BDFE.

Comparative studies of preferential binding of group nine metalloporphyrins (M = Co, Rh, Ir) with methoxide/methanol in competition with hydroxide/water in aqueous solution.

Aqueous solutions of iridium(III) tetra-(p-sulfonatophenyl)porphyrin [(TSPP)Ir(III)] form a hydrogen ion dependent equilibrium distribution of bisaquo ([(TSPP)Ir(III)(OD(2))(2)](3-)), monoaquo/monohydroxo ([(TSPP)Ir(III)(OD(2))(OD)](4-)) and bishydroxo ([(TSPP)Ir(III)(OD)(2)](5-)) complexes. Comparison of acid dissociation constants of group nine ([(TSPP)M(III)(OD(2))(2)](3-)) (M = Co, Rh, Ir) complexes show that the extent of proton dissociation in water increases regularly on moving down the group from cobalt to iridium consistent with increasing metal ligand bond strength. Addition of small quantities of methanol to aqueous solutions of [(TSPP)Ir(III)] results in the formation of methanol and methoxide complexes in equilibria with aquo and hydroxo complexes that are observed by (1)H NMR. Direct quantitative evaluation of competitive equilibria of [(TSPP)Ir(III)] complexes reveals a remarkable thermodynamic preference for methanol binding over that of water (DeltaG degrees (298 K) = -5.2 kcal mol(-1)) and methoxide binding over that of hydroxide (DeltaG degrees (298 K) = -6.1 kcal mol(-1)) in aqueous media. A comparison of equilibrium thermodynamic values for displacement of hydroxide by methoxide for group nine (TSPP)M(III) (M = Co, Rh, Ir) complexes in aqueous media are also reported.

Methanol as a reaction medium and reagent in substrate reactions of rhodium porphyrins.

Methanol solutions of rhodium(III) tetra(p-sulfonatophenyl) porphyrin [(TSPP)Rh(III)] have a hydrogen ion dependent equilibrium between bis-methanol, monomethoxy monomethanol, and bis-methoxy complexes. Reactions of dihydrogen (D(2)) with solutions of [(TSPP)Rh(III)] complexes in methanol produce equilibrium distributions of a rhodium hydride [(TSPP)Rh(III)-D(CD(3)OD)](-4) and rhodium(I) complex [(TSPP)Rh(I)(CD(3)OD)](-5). The rhodium hydride complex in methanol functions as a weak acid with an acid dissociation constant of 1.1(0.1) x 10(-9) at 298 K. Patterns of rhodium hydride substrate reactions in methanol are illustrated by addition with ethene, acetaldehyde, and carbon monoxide to form rhodium alkyl, alpha-hydroxyethyl, and formyl complexes, respectively. The free energy change for the addition reaction of [(TSPP)Rh(III)-D(CD(3)OD)](-4) with CO in methanol to produce a formyl complex (DeltaG(o)(298K) = -4.7(0.1) kcal mol(-1)) is remarkably close to DeltaG(o)(298K) values for analogous reactions in water and benzene. Addition reactions of the rhodium hydride ([(TSPP)Rh(III)-D(CD(3)OD)](-4)) with vinyl olefins invariably yield the anti-Markovnikov product which places the rhodium porphyrin on the less hindered terminal primary carbon center. Addition of the rhodium-methoxide unit in [(TSPP)Rh(III)-OCD(3)(CD(3)OD)](-4) with olefins to form beta-methoxyalkyl complexes places rhodium on the terminal carbon for alkene hydrocarbons and vinyl acetate, but vinyl olefins that have pi-electron withdrawing substituents have a thermodynamic preference for placing rhodium on the interior carbon where negative charge is better accommodated. Equilibrium thermodynamic values for addition of the Rh-OCD(3) unit to olefins in methanol are evaluated and compared with values for Rh-OH addition to olefins in water.