Tetrahedral Oxyanions Research Articles

Tuning of the Anion Affinity and Selectivity of Tripyrromethane‐Based Receptors by Simple Structural Modification

AbstractTripyrromethane‐based tripodal compounds 1–3 were synthesized as anion receptors. It was revealed by 1H NMR spectroscopic analyses carried out in CDCl3 that tripyrromethane 1 with an ester group was capable of recognizing F−, Cl−, Br−, and H2PO4− with relatively high selectivity for F−. By contrast, receptor 2 having an additional hydrogen bond donor of an amide group binds F− and H2PO4− with much improved affinity relative to receptor 1. On the other hand, receptor 3 bearing formyl groups on its two pyrrole subunits showed markedly enhanced selectivity for F− presumably due to the increased acidity of the pyrrolic NHs and the resulting strengthened intermolecular hydrogen bonds. In addition, tripodal receptors 1–3 were found to bind H2PO4−, a tetrahedral oxyanion, more efficiently than 2‐dimensional macrocyclic calix[4]pyrrole 4.

Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations.

Combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the catalytic mechanism of human T-cell leukemia virus type 1 (HTLV-1) protease, a retroviral aspartic protease that is a potential therapeutic target for curing HTLV-1-associated diseases. To elucidate the proteolytic cleavage mechanism, we determined the two-dimensional free energy surfaces of the HTLV-1 protease-catalyzed reactions through various possible pathways. The free energy simulations suggest that the catalytic reactions of the HTLV-1 protease occur in the following sequential steps: (1) a proton is transferred from the lytic water to Asp32', followed by the nucleophilic addition of the resulting hydroxyl to the carbonyl carbon of the scissile bond, forming a tetrahedral oxyanion intermediate, and (2) a proton is transferred from Asp32 to the peptide nitrogen of the scissile bond, leading to the spontaneous breakage of the scissile bond. The rate-limiting step of this catalytic process is the proton transfer from Asp32 to the peptide nitrogen of the scissile bond, with a free energy of activation of 21.1 kcal/mol. This free energy barrier is close to the experimentally determined free energy of activation (16.3 kcal/mol) calculated from the measured catalytic rate constant (kcat). This mechanistic study provides detailed dynamic and structural information that will facilitate the design of mechanism-based inhibitors for the treatment of HTLV-1-associated diseases.

Cleft Receptor for the Recognition and Extraction of Tetrahedral Oxyanions

We report the design and synthesis of a new cleft-shaped bis-urea receptor for the recognition of tetrahedral oxyanions from a foldameric N,N′-dimethyl-N,N′-diphenylurea scaffold. The receptor forms 3:1 host–guest complexes with sulfate, phosphate, and arsenate anions in the solid state by readily binding them through hydrogen bonding. 1H NMR analysis of binding events in a competitive medium (DMSO-d6/H2O, 90:10) revealed that the receptor has a strong and selective affinity for arsenate (Ka(3:1) = 2.41 (±0.79) × 108 M–3) in comparison with phosphate and no affinity for sulfate. The receptor extracts the three oxyanions from water into chlorinated organic solvents when the tetra-n-butyl ammonium ion is used as a cationic support. The receptor also crystallizes out the arsenate anion from water with faster kinetics in acetonitrile solution with a similar cationic support.

Anchoring H-Bond Donating/Accepting Pyrrolic Derivatives on Preorganized Scaffolds: Conformationally Switchable Bipedal/Tripodal and Locked Molecular Cage Ionophores for Potentiometric Sensing of Phosphate and Fluoride.

The ionophore properties of a myriad of conformationally switchable bipedal/tripodal receptors and locked molecular cages were evaluated here for the first time to fabricate potentiometric sensors for the determination of environmentally important phosphate and fluoride. Owing to the competent ionophore properties such as high binding selectivity and affinity, the developed ion-selective electrodes displayed response preference for phosphate and fluoride with a selectivity pattern that differs distinctly from traditional Hofmeister series. Binding constants of the ionophore-anion complexes are determined to underscore how modifications in the preorganization and H-bond donating/accepting ability of a given series of ionophores can be exploited to improve the performance for potentiometric sensing. While conformationally switchable bipedal/tripodal ionophores prefer tetrahedral oxyanions, locked molecular cages shift their preference to spherical halides gradually. Nernstian potential responses with good reversibility to target anions can be observed when shifting the optimized membrane electrodes in aqueous solutions within the concentration range of 10-6.5-10-2.0 M. Moreover, potentiometric determination of phosphate and fluoride in mineral water, soil, and tap water samples was achieved in a low μM concentration range with high accuracy, confirming their promising utility in real world applications.

Bromate incorporation in calcite and aragonite

The presence of bromine as a trace-element in calcium carbonate speleothems constitutes a useful proxy of past volcanic activity, thus helping to provide input parameters for climate model simulations and risk assessment. However, the chemical nature of bromine-containing impurities in the calcium carbonate phases forming speleothems is not understood, which limits interpretation of experimental measurements on speleothems. We present here a computer simulation study, based on quantum mechanical calculations, of the incorporation of bromine as BrO3− oxyanions in CaCO3 polymorphs calcite and aragonite. We discuss how the relative distributions of bromate oxyanions and charge-compensating alkali-metal cations are determined by the interplay between an impurity binding effect (which is stronger for aragonite than for calcite, and changes in the order Li < Na < K) and a configurational entropic effect that tends to disassociate the impurities. For concentrations above parts-per-million, bromate impurities can be expected to be paired, in nearest-neighbour configurations, with the compensating cations. Bromate substitution, compensated by sodium or potassium cations, is predicted to be metastable with respect to phase separation of the impurities as solid NaBrO3 or KBrO3 phases, respectively, but the solubility limits of BrO3− in calcite and aragonite are still higher than those calculated for tetrahedral oxyanions (SO4)2− and (MoO4)2− that are used as alternative volcanic records in speleothems.

Sulfate and Molybdate Incorporation at the Calcite-Water Interface: Insights from Ab Initio Molecular Dynamics.

Sulfur and molybdenum trace impurities in speleothems (stalagmites and stalactites) can provide long and continuous records of volcanic activity, which are important for past climatic and environmental reconstructions. However, the chemistry governing the incorporation of the trace element-bearing species into the calcium carbonate phases forming speleothems is not well understood. Our previous work has shown that substitution of tetrahedral oxyanions [XO4]2– (X = S and Mo) replacing [CO3]2– in CaCO3 bulk phases (except perhaps for vaterite) is thermodynamically unfavorable with respect to the formation of competing phases, due to the larger size and different shape of the [XO4]2– tetrahedral anions in comparison with the flat [CO3]2– anions, which implied that most of the incorporation would happen at the surface rather than at the bulk of the mineral. Here, we present an ab initio molecular dynamics study, exploring the incorporation of these impurities at the mineral–water interface. We show that the oxyanion substitution at the aqueous calcite (10.4) surface is clearly favored over bulk incorporation, due to the lower structural strain on the calcium carbonate solid. Incorporation at surface step sites is even more favorable for both oxyanions, thanks to the additional interface space afforded by the surface line defect to accommodate the tetrahedral anion. Differences between sulfate and molybdate substitutions can be mostly explained by the size of the anions. The molybdate oxyanion is more difficult to incorporate in the calcite bulk than the smaller sulfate oxyanion. However, when molybdate is substituted at the surface, the elastic cost is avoided because the oxyanion protrudes out of the surface and gains stability via the interaction with water at the interface, which in balance results in more favorable surface substitution for molybdate than for sulfate. The detailed molecular-level insights provided by our calculations will be useful to understand the chemical basis of S- and Mo-based speleothem records.

Structure-based virtual screening suggests inhibitors of 3-Chymotrypsin-Like Protease of SARS-CoV-2 from Vernonia amygdalina and Occinum gratissimum.

Antiviral culinary plants are potential bioresources for preventive nutraceuticals and/or antiviral drugs in COVID-19. Structure-based virtual screening was undertaken to screen 173 compounds previously reported from Vernonia amygdalina and Occinum gratissimum for direct interaction with the active site of the 3-Chymotrypsin-Like Protease (3CLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on docking scores and comparison with reference inhibitors, a hit-list of 10 top phytocompounds was defined, which also had strong interactions with the catalytic centre of 3CLpro from three related strains of coronavirus (SARS-CoV, MERS-CoV, HKU4). Among these, six compounds (neoandrographolide, vernolide, isorhamnetin, chicoric acid, luteolin, and myricetin) exhibited the highest binding tendencies to the equilibrated conformers of SARS-CoV-2 3CLpro in an in-depth docking analysis to 5 different representative conformations from the cluster analysis of the molecular dynamics simulation (MDS) trajectories of the protein. In silico drug-likeness analyses revealed two drug-like terpenoids viz: neoandrographolide and vernolide as promising inhibitors of SARS-CoV-2 3CLpro. These structures were accommodated within the substrate-binding pocket; and interacted with the catalytic dyad (Cys145 and His41), the oxyanion loop (residues 138–145), and the S1/S2 sub-sites of the enzyme active site through the formation of an array of hydrogen bonds and hydrophobic interactions. Molecular dynamics simulation and binding free energy calculation revealed that the terpenoid-enzyme complexes exhibit strong interactions and structural stability. Therefore, these compounds may stabilize the conformation of the flexible oxyanion loop; and thereby interfere with the tetrahedral oxyanion intermediate formation during the proteolytic activity of the enzyme.

A Hexapodal Capsule for the Recognition of Anions.

We herein describe the preparation, characterization, and recognition characteristics of novel hexapodal capsule 1 composed of two benzenes joined by six hydrogen bonding (HB) groups to encircle space. This barrel-shaped host was obtained by reversible imine condensation of hexakis-aldehyde 2 and hexakis-amine 3 in the presence of oxyanions or halides acting as templates. Fascinatingly, capsule 1 includes 18 HB donating (Csp2-H and N-H) and 12 HB accepting groups (C═O and C═N) surrounding a binding pocket (78 Å3). In this regard, the complexation of fluoride, chloride, carbonate, sulfate, and hydrogen phosphate was probed by NMR spectroscopy (DMSO) and X-ray diffraction analysis to disclose the adaptive nature of 1 undergoing an adjustment of its conformation to complement each anionic guest. Furthermore, the rate by which encapsulated chloride was substituted by sulfate or hydrogen phosphate was slow (>7 days) while the stability of [SO4⊂1]2- was greatest in the series with Ka > 107 M-1 in highly competitive DMSO. With facile access to 1, the stage is set to probe this modular, polyvalent, and novel host to further improve the extraction of tetrahedral oxyanions from waste and the environment or control their chemistry in living systems.

Halogen bonding in the co-crystallization of potentially ditopic diiodotetrafluorobenzene: a powerful tool for constructing multicomponent supramolecular assemblies.

Halogen bonding is emerging as a significant driving force for supramolecular self-assembly and has aroused great interest during the last two decades. Among the various halogen-bonding donors, we take notice of the ability of 1,4-diiodotetrafluorobenzene (1,4-DITFB) to co-crystallize with diverse halogen-bonding acceptors in the range from neutral Lewis bases (nitrogen-containing compounds, N-oxides, chalcogenides, aromatic hydrocarbons and organometallic complexes) to anions (halide ions, thio/selenocyanate ions and tetrahedral oxyanions), leading to a great variety of supramolecular architectures such as discrete assemblies, 1D infinite chains and 2D/3D networks. Some of them act as promising functional materials (e.g. fluorescence, phosphorescence, optical waveguide, laser, non-linear optics, dielectric and magnetism) and soft materials (e.g. liquid crystal and supramolecular gel). Here we focus on the supramolecular structures of multicomponent complexes and their related physicochemical properties, highlight representative examples and show clearly the main directions that remain to be developed and improved in this area. From the point of view of crystal engineering and supramolecular chemistry, the complexes summarized here should give helpful information for further design and investigation of the elusive category of halogen-bonding supramolecular functional materials.

Molybdenum and sulfur incorporation as oxyanion substitutional impurities in calcium carbonate minerals: A computational investigation

Marked increases in sulfur and molybdenum concentration in stalagmites have been proposed as possible evidence of volcanic activity in the past. Thus, speleothems have great potential to deliver long and continuous records of volcanic activity. However, little is known about the chemical nature of these impurities in the calcium carbonate (CaCO3) phases forming stalagmites, which hinders the rationalization of the incorporation mechanisms. While sulfur is known to incorporate as a sulfate anion in CaCO3 polymorphs, the nature and stability of molybdenum incorporation in these minerals has not been investigated before. Here, we present a computer simulation study, based on density functional theory, comparing the thermodynamics of incorporation of sulfur and molybdenum as tetrahedral oxyanions [XO4]2− (X = S, Mo) in anion sites of CaCO3 polymorphs (calcite, aragonite, vaterite, monohydrocalcite and ikaite). Among the different polymorphs, vaterite incorporates [XO4]2− ions most favourably, which reflects the relatively low density of this carbonate phase. We show that molybdate anions are very unstable (more so than sulfate anions) in the bulk of all three anhydrous carbonate phases, with respect to the formation of naturally occurring competing phases. Most of the Mo impurities found in typical calcite/aragonite stalagmites is therefore likely to concentrate at surface/interface regions such as grain boundaries. Using the calcite (10.4) surface as a model, we show that the energies of substitution are indeed much lower at the surface than at the bulk. Our results suggest that factors affecting the crystallinity of CaCO3 in stalagmites, and therefore the specific surface area, will have a significant effect on the concentration of incorporated molybdenum, which should be a key consideration when interpreting data from Mo-based speleothem archives.

Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design

HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.

(Invited) Insights into Proton Transport in Superprotonic Solid Acids

Superprotonic solid acid electrolytes, materials with chemical and physical properties intermediate between conventional acids (e.g., H3PO4) and conventional salts (e.g., Cs3PO4) have emerged as attractive candidates for fuel cell and other electrochemical applications. Key characteristics of these materials are tetrahedral oxyanion groups linked by hydrogen bonds, and a polymorphic structural transition to a disordered state at moderate temperatures. Rapid oxyanion reorientation and dynamic disorder of the hydrogen bond network facilitate high proton conductivity in the high temperature phase. Materials exhibiting a superprotonic transition include CsHSO4, Cs3H(SeO4)2, CsH2PO4, and Cs2(HSO4)(H2PO4). Here we review the present state of understanding of proton transport mechanisms and the factors governing the transition behavior as gathered from macroscale measurements of conductivity and thermal properties and from atomistic level studies using nuclear magnetic resonance spectroscopy. We focus in particular on CsH2PO4, the technologically most significant superprotonic solid acid, and its chemical modifications produced by substitution on either the alkali metal or proton site (deuterated materials). Dramatic changes in phase behavior and proton conductivity can be induced by only minor changes in chemistry, suggesting routes for tuning behavior to achieve desired outcomes.

Synthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and Acceptors.

A molecular cage, macrobicycle 2, containing amide and pyrrole groups as hydrogen-bonding donors and imine groups as hydrogen-bonding acceptors has been synthesized. Compound 2 was found to recognize tetrahedral oxyanions with high affinities, such as H2PO4-, HSO4-, SO42-, and HP2O73-, as well as the spherical halide anions, in chloroform. A single-crystal X-ray diffraction analysis revealed that compound 2 formed a 1:1 complex with H2PO4- in the solid state.

Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8.

Micronutrients such as metal ions are indispensable for the growth and survival of microorganisms in assorted environmental niches. However, change in cellular concentration of metal ions is pernicious for an organism; thus metal ion homeostasis is crucial for their survival and growth. An eminent mechanism for maintaining metal ion homeostasis in microorganisms is ATP-binding cassette (ABC) transporters, which transport metal ions in their ionic/complex forms across the cell membrane. For the uptake, metals are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains (TMDs) for their transport. In this work, a high-throughput data mining analysis has been performed to identify open reading frames (ORFs) encoding metal-specific ABC transporters in a thermophilic bacterium Thermus thermophilus HB8. In total, 22 ORFs resulting in eight ABC transport systems were identified, which are potentially involved in the uptake of metal ions. This study suggests that three out of eight metal-specific ABC import systems are specific to iron ions. Among the remaining five, two are particular to divalent metal ions such as Mg2+ and Zn2+/Mn2+, another two are for tetrahedral oxyanions such as MoO42- and WO42- and the remaining one imports cyanocobalamin (vitamin B12). Besides these, the results of this study demonstrate the existence of a mechanism where TMD and NBD components are shared among different ABC transport systems hinting that multiple substrates can be imported via a single transporter. This study thus provides the first ever preliminary glimpse into the entire repertoire of metal uptake ABC transporters in a thermophilic organism.

Crystal structures of NiSO4\xb79H2O and NiSO4\xb78H2O: magnetic properties, stability with respect to morenosite (NiSO4\xb77H2O), the solid-solution series (MgxNi1\u2212x)SO4\xb79H2O

Since being discovered initially in mixed-cation systems, a method of forming end-member NiSO4·9H2O and NiSO4·8H2O has been found. We have obtained powder diffraction data from protonated analogues (with X-rays) and deuterated analogues (using neutrons) of these compounds over a range of temperatures, allowing us to determine their crystal structures—including all H-atoms—and to characterise the transitions on warming from 220 to 278 K; glass → 9-hydrate → 8-hydrate + ice → 7-hydrate + ice → partial melt (7-hydrate + liquid). NiSO4·8D2O is triclinic, space-group Pbar {1}, Z = 2, with unit cell parameters at 150 K, a = 6.12463(8) Å, b = 6.8401(1) Å, c = 12.5339(2) Å, α = 92.846(1)°, β = 97.822(1)°, γ = 96.627(1)° and V = 515.58(1) Å3. The structure consists of two symmetry-inequivalent Ni(D2O)6 octahedra on sites of bar {1} symmetry. These are directly joined by a water–water H-bond to form chains of octahedra parallel with the c-axis at x = 0. Two interstitial water molecules serve both to bridge the Ni(D2O)6 octahedral chains in the b–c plane and also to connect with the SO42− tetrahedral oxyanion. These tetrahedra are linked by the two interstitial water molecules in a reticular motif to form sheets perpendicular to c. NiSO4·9D2O is monoclinic, space-group P21/c, Z = 4, with unit-cell parameters at 150 K, a = 6.69739(6) Å, b = 11.8628(1) Å, c = 14.5667(1) Å, β = 94.9739(8)° and V = 1152.96(1) Å3. The structure is isotypic with the Mg analogue described elsewhere (Fortes et al., Acta Cryst B 73:47‒64, 2017b). It shares the motif of H-bonded octahedral chains with NiSO4·8D2O, although in the enneahydrate these run parallel with the b-axis at x = 0. Three interstitial water molecules bridge the Ni(D2O)6 octahedra to the SO42− tetrahedral oxyanion. The tetrahedra sit at x ≈ 0.5 and are linked by two of the three interstitial water molecules in a pentagonal motif to form ribbons parallel with b. A solid-solution series exists between Mg and Ni enneahydrate end-members where we observe preferential partitioning of Ni2+ into the octahedral sites on the 2c Wyckoff positions rather than the 2a sites. The solution is slightly non-ideal, as indicated by the small positive excess volume of mixing. Measurements of the DC magnetisation of quenched NiSO4 solutions reveal anomalies in the molar susceptibility on warming through the region from 221 to 225 K, probably due to devitrification of the (assumed) glassy specimen into a mixture of NiSO4·9H2O + ice Ih. Further temperature-dependent measurements on repeated warming and cooling provide no evidence of magnetic ordering and indicate a weak ferromagnetic coupling between neighbouring Ni2+ ions, likely via super-exchange through the H-bond between neighbouring Ni(H2O)6 octahedra.

A Computational Investigation into the Mechanism of the Histone Acetyltransferase, Gcn5

Post-translational modifications (PTMs) can have a profound effect on protein structure and function. One such PTM is the acetylation of histone (a protein involved in DNA binding). In this reaction, an enzyme catalyzes the transfer of the acetyl group from acetyl CoA to a free lysine on the histone. This transfer neutralizes the positively charged lysine, which ultimately allows the DNA to be exposed for transcription. In our study, we focus on the acetyltransferase, Gcn5. Details regarding the reaction mechanism used by Gcn5 remain obscured. However, current mechanistic hypotheses suggest that the reaction occurs through a tetrahedral oxyanion intermediate, which is stabilized by a hydrogen bond to a nearby residue, i.e. an oxyanion hole. We utilize molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations in order to further probe possible mechanistic schemes of this reaction.

Structure, thermal expansion and incompressibility of MgSO4·9H2O, its relationship to meridianiite (MgSO4·11H2O) and possible natural occurrences

Since being discovered initially in mixed-cation systems, a method of forming end-member MgSO4·9H2O has been found. We have obtained powder diffraction data from protonated analogues (using X-rays) and deuterated analogues (using neutrons) of this compound over a range of temperatures and pressures. From these data we have determined the crystal structure, including all hydrogen positions, the thermal expansion over the range 9–260 K at ambient pressure, the incompressibility over the range 0–1.1 GPa at 240 K and studied the transitions to other stable and metastable phases. MgSO4·9D2O is monoclinic, space group P21/c, Z = 4, with unit-cell parameters at 9 K, a = 6.72764 (6), b = 11.91154 (9), c = 14.6424 (1) Å, β = 95.2046 (7)° and V = 1168.55 (1) Å3. The structure consists of two symmetry-inequivalent Mg(D2O)6 octahedra on sites of \bar 1 symmetry. These are directly joined by a water–water hydrogen bond to form chains of octahedra parallel with the b axis at a = 0. Three interstitial water molecules bridge the Mg(D2O)6 octahedra to the SO4 2− tetrahedral oxyanion. These tetrahedra sit at a ≃ 0.5 and are linked by two of the three interstitial water molecules in a pentagonal motif to form ribbons parallel with b. The temperature dependences of the lattice parameters from 9 to 260 K have been fitted with a modified Einstein oscillator model, which was used to obtain the coefficients of the thermal expansion tensor. The volume thermal expansion coefficient, αV, is substantially larger than that of either MgSO4·7D2O (epsomite) or MgSO4·11D2O (meridianiite), being ∼ 110 × 10−6 K−1 at 240 K. Fitting to a Murnaghan integrated linear equation of state gave a zero-pressure bulk modulus for MgSO4·9D2O at 240 K, K 0 = 19.5 (3) GPa, with the first pressure derivative of the bulk modulus, K′ = 3.8 (4). The bulk modulus is virtually identical to meridianiite and only ∼ 14% smaller than that of epsomite. Above ∼ 1 GPa at 240 K the bulk modulus begins to decrease with pressure; this elastic softening may indicate a phase transition at a pressure above ∼ 2 GPa. Synthesis of MgSO4·9H2O from cation-pure aqueous solutions requires quench-freezing of small droplets, a situation that may be relevant to spraying of MgSO4-rich cryomagmas into the surface environments of icy satellites in the outer solar system. However, serendipitously, we obtained a mixture of MgSO4·9H2O, mirabilite (Na2SO4·10H2O) and ice by simply leaving a bottle of mid-winter brine from Spotted Lake (Mg/Na ratio = 3), British Columbia, in a domestic freezer for a few hours. This suggests that MgSO4·9H2O can occur naturally – albeit on a transient basis – in certain terrestrial and extraterrestrial environments.

Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii.

Enzymes of carbohydrate esterase (CE) family 14 catalyze hydrolysis of N-acetyl groups at the non-reducing end of the N-acetylglucosamine (GlcNAc) residue of chitooligosaccharides or related compounds. N,N'-diacetylchitobiose deacetylase (Dac) belongs to the CE-14 family and plays a role in the chitinolytic pathway in archaea by deacetylating N,N'-diacetylchitobiose (GlcNAc2), which is the end product of chitinase. In this study, we revealed the structural basis of reaction specificity in CE-14 deacetylases by solving a crystal structure of Dac from Pyrococcus horikoshii (Ph-Dac) in complex with a novel reaction intermediate analog. We developed 2-deoxy-2-methylphosphoramido-d-glucose (MPG) as the analog of the tetrahedral oxyanion intermediate of the monosaccharide substrate GlcNAc. The crystal structure of Ph-Dac in complex with MPG demonstrated that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue. The amino acid residues responsible for recognition of the MPG glucose moiety are spatially conserved in other CE-14 deacetylases. Molecular dynamics simulation of the structure of the Ph-Dac-GlcNAc2 complex indicated that the reducing GlcNAc residue is placed in a large intermolecular cleft and is not involved with specific interactions with the enzyme. This observation was consistent with results indicating that Ph-Dac displayed similar kinetic parameters for both GlcNAc and GlcNAc2. This study provides the structural basis of reaction-site specificity of Dac and related CE-14 enzymes.

Entrapment of Cyclic Fluoride–Water and Sulfate–Water–Sulfate Cluster Within the Self-Assembled Structure of Linear meta-Phenylenediamine Based Bis-Urea Receptors: Positional Isomeric Effect

meta-Phenylenediamine based two linear bis-urea anion receptors, L1 (meta-nitro) and L2 (para-nitro), have been synthesized which showed strong binding affinities toward halides as well as planar and tetrahedral oxyanions. In the presence of excess fluoride anion, L1 self-assembles to entrap a cyclic fluoride–water tetrameric cluster within its tetrameric pillar-like assembly of each urea arm (complex 1a). In the presence of sulfate anion, L1 self-assembles in an identical fashion to entrap the bigger tetrahedral anion (complex 1b), whereas two urea moieties of two different receptor molecules of L1 have been structurally authenticated to be sufficient to stabilize the simple Y-shaped acetate anion in complex 1c. On the other hand, receptor L2, with a bis(para-nitro urea) functional group, especially in the presence of sulfate anion, self-assembles like long straight pillars entrapping sulfate–water–sulfate cluster {SO42–-(H2O)3-SO42–} (complex 2a). Additionally, L2 forms a host–guest assembly with the ca...

Anion Binding-Induced White Light Emission using a Water-Tolerant Fluorescent Molecular Tweezer.

A novel fluorescent molecular tweezer (FMT), built on the pyridine-2,6-bis-carboxamide framework, has been developed that, in presence of a red emitter, gives rise to white light emission in response to the addition of H2 PO4- anions. The FMT incorporates two pyrene moieties as fluorescent reporter units and a strategically placed amine residue that imparts pH sensitivity to the fluorescence and offers additional electrostatic/hydrogen-bonding interactions to the anions. As a result, this FMT selectively binds monoanionic tetrahedral oxyanions such as H2 PO4- and HSO4- that contain hydrogen bond donors and acceptors, and can sense their presence in aqueous acetonitrile through changes in fluorescence. Anion binding results in excimer formation by the pyrenes and a bluish-green emission from the FMT. Both amide and amine residues of the FMT interact with these anions. The binding stoichiometry with H2 PO4- and HSO4- was found to be 1:1 and affinity of the FMT for these anions is of the order of 104 m-1 . The limit of detection for H2 PO4- was found to be 13 nm. Addition of a perylene monoimide-based red emitter gives rise to panchromatic emission perceived as white light.