Extensive Hydrogen-bonding Network Research Articles

A facile and efficient method to improve the proton conductivity of open-framework metal phosphates under aqueous condition

Herein, the K+ ions were doped into the inorganic layer of two 2D layer metal phosphates (C2H10N2)[Mn2(PO4)2].2H2O (1) and (C2H10N2)[Mn2(HPO4)3](H2O) (2), respectively, via ion exchange method. The resultant compounds maintained the original structures of 1 and 2, but significantly improved their proton conductivity, for example, the proton conductivity of 1 increased from 1.14 × 10−5 S.cm−1 to 3.39 × 10−2 S.cm−1 at 99% RH and 293 K after doped 0.55 K+ ions; the proton conductivity of 2 is 0.70 × 10−2 S.cm−1 at 99% RH and 293 K after doped 0.32 K+ ions, and is 4.3 times that of the orginal sample. Such a substantial increase in proton conductivity could be attributable to that the K+ ions in aqueous solutions create stronger electrostatic fields to accommodate water, and thus make a more dense and extensive hydrogen-bonding network to enhance the transport of protons.

Crystal and molecular structure of [Ni{2-H2NC(=O)C5H4N}2(H2O)2][Ni{2,6-(O2C)2C5H3N}2]·4.67H2O; DFT studies on hydrogen bonding energies in the crystal.

[Ni{2-H2NC(=O)C5H4N}2(H2O)2][Ni{2,6-(O2C)2C5H3N}2]·4.67H2O, a new complex salt containing a bis(2,6-dicarboxypyridine)nickel(II) anion and a bis(2-amidopyridine)diaquanickel(II) cation, was synthesized and characterized. The crystal is stabilized by an extensive network of hydrogen bonds. Alternate layers of anions and cations/water molecules parallel to (010) can be distinguished. Computational studies of the network packing of the title compound by high-level DFT-D/B3LYP calculations indicate stabilization of the networks with conventional and non-conventional intermolecular O-H...O, N-H...O and C-H...O hydrogen bonds along with π-stacking contacts. Due to the presence of water molecules and the importance of forming hydrogen bonds with the involvement of water clusters to the stability of the crystal packing, the importance and role of these water clusters, and the quantitative stability resulting from the formation of hydrogen bonds and possibly other noncovalent bonds such as π-stacking are examined. The binding energies obtained by DFT-D calculations for these contacts indicate that hydrogen bonds, especially O-H...O and N-H...O, control the construction of the crystalline packing. Additionally, the results of Bader's theory of AIM for these interactions agree reasonably well with the calculated energies.

Switching a HO···π Interaction to a Nonconventional OH···π Hydrogen Bond: A Completed Crystallographic Puzzle.

In this article, we present crystallographic and spectroscopic evidence of a tunable system wherein a HO···π interaction switches incrementally to a nonconventional OH···π hydrogen bonding (HB) interaction. More specifically, we report the synthesis of substituted forms of model system 1 to study the effects of aryl ring electronic density on the qualitative characteristics of OH···π hydrogen bonds therein. The OH stretch in experimental infrared data, in agreement with density-functional theory (DFT) calculations, shows continuous red-shifts as the adjacent ring becomes more electron rich. For example, the OH stretch of an amino-substituted analogue is red-shifted by roughly 50 cm-1 compared to the same stretch in the CF3 analogue, indicating a significantly stronger HB interaction in the former. Moreover, DFT calculations (ωB97XD/6-311+G**) predict that increasing electronic density on the adjacent top ring reduces the aryl π-OH σ* energy gap with a concomitant enhancement of the OH n-π* energy gap. Consequently, a dominant π-σ* interaction in the amino substituted analogue locks the system in the in-form while a favorable n-π* interaction reverses the orientation of the oxygen-bound hydrogen in its protonated form. Additionally, the 1H NMR data of various analogues reveal that stronger OH···π interactions in systems with electron-rich aromatic rings slow exchange of the alcoholic proton, thereby revealing coupling with the geminal proton. Finally, X-ray crystallographic analyses of a spectrum of analogues clearly visualize the three distinct stages of "switch"-starting with exclusive HO···π, to partitioned HO···π/OH···π, and finally to achieving exclusive OH···π forms. Furthermore, the crystal structure of the amino analogue reveals an interesting feature in which an extended HB network, involving two conventional (NH···O) and two nonconventional (OH···π) HBs, dimerizes and anchors the molecule in the unit cell.

Developing the Pressure-Temperature-Magnetic Field Phase Diagram of Multiferroic [(CH3)2NH2]Mn(HCOO)3.

We combined Raman scattering and magnetic susceptibility to explore the properties of [(CH3)2NH2]Mn(HCOO)3 under compression. Analysis of the formate bending mode reveals a broad two-phase region surrounding the 4.2 GPa critical pressure that becomes increasingly sluggish below the order-disorder transition due to the extensive hydrogen-bonding network. Although the paraelectric and ferroelectric phases have different space groups at ambient-pressure conditions, they both drive toward P1 symmetry under compression. This is a direct consequence of how the order-disorder transition changes under pressure. We bring these findings together with prior magnetization work to create a pressure-temperature-magnetic field phase diagram, unveiling entanglement, competition, and a progression of symmetry-breaking effects that underlie functionality in this molecule-based multiferroic. That the high-pressure P1 phase is a subgroup of the ferroelectric Cc suggests the possibility of enhanced electric polarization as well as opportunity for strain control.

Growth, structural, optical and thermal studies of semi-organic nonlinear optical potassium hydrogen oxalate single crystal

Single crystals of semi-organic nonlinear optical material potassium hydrogen oxalate are grown from the aqueous solutions of potassium hydroxide and oxalic acid in 1:1 stoichiometric ratio by slow evaporation solution growth method at room temperature. The grown crystals are subjected to various characterization techniques to explore their structural explication, thermal, linear and nonlinear optical perspectives for optoelectronic device applications. The monoclinic structure with non-centrosymmetric space group P21/c of the titular compound has been confirmed by single-crystal X-ray diffraction. The crystal packing is ruled by extensive networks of hydrogen bonds revealed by the detailed study of the refinement of the crystal structure. Optical transparency of the crystal in the entire visible region has been confirmed by ultraviolet–visible-near infrared (UV–Vis-NIR) analysis. The robust thermal stability of the grown crystal is ensured by thermogravimetric–differential thermal analysis. The presence of expected functional groups in the grown crystal has been confirmed by Fourier transform infrared spectroscopic studies. Second-harmonic generation efficiency has been calculated by Kurtz powder method.

Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4.

Thymine:guanine base pairs are major promutagenic mismatches occurring in DNA metabolism. If left unrepaired, these mispairs can cause C to T transition mutations. In humans, T:G mismatches are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (hMBD4) and thymine-DNA glycosylase. Unlike lesion-specific DNA glycosylases, T:G-mismatch-specific DNA glycosylases specifically recognize both bases of the mismatch and remove the thymine but only from mispairs with guanine. Despite the advances in biochemical and structural characterizations of hMBD4, the catalytic mechanism of hMBD4 remains elusive. Herein, we report two structures of hMBD4 processing T:G-mismatched DNA. A high-resolution crystal structure of Asp560Asn hMBD4-T:G complex suggests that hMBD4-mediated glycosidic bond cleavage occurs via a general base catalysis mechanism assisted by Asp560. A structure of wild-type hMBD4 encountering T:G-containing DNA shows the generation of an apurinic/apyrimidinic (AP) site bearing the C1'-(S)-OH. The inversion of the stereochemistry at the C1' of the AP-site indicates that a nucleophilic water molecule approaches from the back of the thymine substrate, suggesting a bimolecular displacement mechanism (SN2) for hMBD4-catalyzed thymine excision. The AP-site is stabilized by an extensive hydrogen bond network in the MBD4 catalytic site, highlighting the role of MBD4 in protecting the genotoxic AP-site.

Crystal structure of (R,S)-2-hy-droxy-4-(methyl-sulfan-yl)butanoic acid.

The title compound, a major animal feed supplement, abbreviated as HMTBA and alternatively called dl-me-thio-nine hy-droxy analogue, C5H10O3S, (I), was isolated in pure anhydrous monomeric form. The melting point is 302.5 K and the compound crystallizes in the monoclinic space group P21/c, with two conformationally non-equivalent mol-ecules [(I A ) and (I B )] in the asymmetric unit. The crystal structure is formed by alternating polar and non-polar layers running along the bc plane and features an extensive hydrogen-bonding network within the polar layers. The Hirshfeld surface analysis revealed a significant contribution of non-polar H⋯H and H⋯S inter-actions to the packing forces for both mol-ecules.

Molecular Basis for Hormone Recognition and Activation of Corticotropin-Releasing Factor Receptors.

Corticotropin-releasing factor (CRF) and the three related peptides urocortins 1-3 (UCN1-UCN3) are endocrine hormones that control the stress responses by activating CRF1R and CRF2R, two members of class B G-protein-coupled receptors (GPCRs). Here, we present two cryoelectron microscopy (cryo-EM) structures of UCN1-bound CRF1R and CRF2R with the stimulatory G protein. In both structures, UCN1 adopts a single straight helix with its N terminus dipped into the receptor transmembrane bundle. Although the peptide-binding residues in CRF1R and CRF2R are different from other members of class B GPCRs, the residues involved in receptor activation and G protein coupling are conserved. In addition, both structures reveal bound cholesterol molecules to the receptor transmembrane helices. Our structures define the basis of ligand-binding specificity in the CRF receptor-hormone system, establish a common mechanism of class B GPCR activation and G protein coupling, and provide a paradigm for studying membrane protein-lipid interactions for class B GPCRs.

Simple Transformation of Covalent Organic Frameworks to Highly Proton-Conductive Electrolytes.

We report the rational design and implementation of a new class of gel guest-assisted, ionic covalent organic framework (COF) membranes that exhibit superior H+ conduction. The as-synthesized COFs are postmodified via a lithiation (or sodiation) treatment. The hydrophilic Li or Na ions in the COFs form a dense and extensive hydrogen-bonding network of H2O molecules with mobile H+ at the periphery, thereby transforming COFs into H+ conductors. Then, the ionic COFs are assembled into a flexible H+ conductor membrane via a gelation process, where the organic gel provides both mechanical strength and additional H+ carriers for fast H+ conduction. The final COF-based membrane exhibits an excellent H+ conductivity of 1.3 × 10-1 S cm-1 at 313 K and 98% relative humidity, which are the highest values of the COF-based H+ conductors reported until now and are even comparable with those of the typical commercial Nafion membrane. We anticipate that the two-in-one strategy would open up a porous COF-driven new molecular framework and membrane architectural design/opportunity for development of next-generation ionic conductors.

Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study

The replica exchange molecular dynamics (REMD) simulation is demonstrated to readily predict the conformations of the macrocyclic drug lorlatinib, as validated by solution NMR studies. In aqueous solution, lorlatinib adopts a conformer identical to its target bound structure. This conformer is stabilized by an extensive hydrogen bond network to the solvents. In chloroform, lorlatinib populates two conformers with the second one being less polar, which may contribute to lorlatinib’s ability to cross cell membranes.

A computational method for design of connected catalytic networks in proteins.

Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding side‐chain functional groups which maximize transition‐state stabilization, and then searching for sites in protein scaffolds where the specified side‐chain–transition‐state interactions can be realized. A limitation of this approach is that the interactions between the side chains themselves are not constrained. An extensive connected hydrogen bond network involving the catalytic residues was observed in a designed retroaldolase following directed evolution. Such connected networks could increase catalytic activity by preorganizing active site residues in catalytically competent orientations, and enabling concerted interactions between side chains during catalysis, for example, proton shuffling. We developed a method for designing active sites in which the catalytic side chains, in addition to making interactions with the transition state, are also involved in extensive hydrogen bond networks. Because of the added constraint of hydrogen‐bond connectivity between the catalytic side chains, to find solutions, a wider range of interactions between these side chains and the transition state must be considered. Our new method starts from a ChemDraw‐like two‐dimensional representation of the transition state with hydrogen‐bond donors, acceptors, and covalent interaction sites indicated, and all placements of side‐chain functional groups that make the indicated interactions with the transition state, and are fully connected in a single hydrogen‐bond network are systematically enumerated. The RosettaMatch method can then be used to identify realizations of these fully‐connected active sites in protein scaffolds. The method generates many fully‐connected active site solutions for a set of model reactions that are promising starting points for the design of fully‐preorganized enzyme catalysts.

Structure and Dynamics of Cinnamycin-Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids.

Cinnamycin is a lantibiotic peptide, which selectively binds to and permeabilizes membranes containing phosphatidylethanolamine (PE) lipids. As PE is a major component of many bacterial cell membranes, cinnamycin has considerable potential for destroying these. In this study, molecular dynamics simulations are used to elucidate the structure of a lipid–cinnamycin complex and the origin of selective lipid binding. The simulations reveal that cinnamycin selectively binds to PE by forming an extensive hydrogen-bonding network involving all three hydrogen atoms of the primary ammonium group of the PE head group. The substitution of a single hydrogen atom with a methyl group on the ammonium nitrogen destabilizes this hydrogen-bonding network. In addition to binding the primary ammonium group, cinnamycin also interacts with the phosphate group of the lipid through a previously uncharacterized phosphate-binding site formed by the backbone Phe10-Abu11-Phe12-Val13 moieties (Abu = 1-α-aminobutyric acid). In addition, hydroxylation of Asp15 at Cβ plays a role in selective binding of PE due to its tight interaction with the charged amine of the lipid head group. The simulations reveal that the position and orientation of the peptide in the membrane depend on the type of lipid to which it binds, suggesting a reason for why cinnamycin selectively permeabilizes PE-containing membranes.

Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins.

Membrane proteins that function as transporters or receptors must communicate with both sides of the lipid bilayer in which they sit. This long distance communication enables transporters to move protons or other ions and small molecules across the bilayer and receptors to transmit an external signal to the cell. Hydrogen bonds, hydrogen-bond networks, and lipid-protein interactions are essential for the motions and functioning of the membrane protein and, consequently, of outmost interest to structural biology and numerical simulations. We present here Bridge, an algorithm tailored for efficient analyses of hydrogen-bond networks in membrane transporter and receptor proteins. For channelrhodopsin, a membrane protein whose functioning involves proton-transfer reactions, Bridge identifies extensive networks of protein-water hydrogen bonds and an unanticipated network that can bridge transiently two proton donors across a distance of ∼20 Å. Graphs of the protein hydrogen bonds reveal rapid propagation of structural changes within hydrogen-bond networks of mutant transporters and identify protein groups potentially important for the proton transfer activity. The algorithm is made available as a plugin for PyMol.

Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate

The epimerase MoeE5 from Streptomyces viridosporus converts UDP-glucuronic acid (UDP-GlcA) to UDP-galacturonic acid (UDP-GalA) to provide the first sugar in synthesizing moenomycin, a potent inhibitor against bacterial peptidoglycan glycosyltransferases. The enzyme belongs to the UDP-hexose 4-epimerase family, and uses NAD+ as its cofactor. Here we present the complex crystal structures of MoeE5/NAD+/UDP-GlcA and MoeE5/NAD+/UDP-glucose, determined at 1.48 Å and 1.66 Å resolution. The cofactor NAD+ is bound to the N-terminal Rossmann-fold domain and the substrate is bound to the smaller C-terminal domain. In both crystals the C4 atom of the sugar moiety of the substrate is in close proximity to the C4 atom of the nicotinamide of NAD+, and the O4 atom of the sugar is also hydrogen bonded to the side chain of Tyr154, suggesting a productive binding mode. As the first complex structure of this protein family with a bound UDP-GlcA in the active site, it shows an extensive hydrogen-bond network between the enzyme and the substrate. We further built a model with the product UDP-GalA, and found that the unique Arg192 of MoeE5 might play an important role in the catalytic pathway. Consequently, MoeE5 is likely a specific epimerase for UDP-GlcA to UDP-GalA conversion, rather than a promiscuous enzyme as some other family members.

OH radical in water from ab initio molecular dynamics simulation employing hybrid functionals

This work presents for the first time ab initio molecular dynamics simulations for the OH⋆-(H2O)n cluster with n = 0–5 and the OH radical in the bulk phase, using B3LYP as a functional. Furthermore, for OH⋆-w31, simulations with PBE0 and HSE03 are also investigated. In all systems, the OH radical is a stronger hydrogen bond donor than acceptor; a stronger hydrogen bond donor than water and a weaker hydrogen bond acceptor than water. Radial distribution functions (RDFs) reveal that for all systems, neither a hemibond between radical and water nor hydrogen abstraction is present. Comparisons with past simulations indicate that BLYP leads to artifacts, such as overstructuring of water in OH⋆-w31 and the hemibonded structure. In order to have strong hydrogen bonds with an extensive hydrogen bond network, at least four water molecules are necessary. RDFs as well as continuous dimer existence autocorrelation functions show that the OH radical is not disrupting the hydrogen bond network of water. In the bulk phase, the acceptor interaction is a very low probable interaction, whereas in the gas phase, it has a higher probability. The orientation of the water molecule around the OH radical is in the bulk liquid phase much less and in the gas phase enhanced, especially for the OH radical acting as a hydrogen bond donor toward one water molecule. PBE0 results for OH⋆-w31 in a strong hydrogen bond donor interaction compared to HSE03 and B3LYP, which has the weakest interaction. HSE03 leads to strong O–H interactions in OH⋆-w31, followed by PBE0 and B3LYP.

Ecological toxicity reduction of dinotefuran to honeybee: New perspective from an enantiomeric level

In last decade, there has been a concerted effort to reduce the potential threats of honeybees' population due to exposure to neonicotinoid pesticides. A new perspective was put forward to reduce the potential ecological toxicity of neonicotinoid dinotefuran to honeybee in terms of an enantiomeric level in the study. Toxicity of dinotefuran was enantioselective, and S-dinotefuran was 41.1- to 128.4-fold more toxic than R-dinotefuran to honeybee Apis mellifera (Apis mellifera Linnaeus), whereas R-dinotefuran exhibited comparative insecticidal activities (1.7–2.4 times) to typical sucking pests Aphis gossypii and Apolygus lucorum compared to racemic mixtures. Our data suggested that use of R-dinotefuran could have a good efficacy in controlling target pests while minimizing hazard to honeybees. The mechanism for chiral specific toxicity to honeybee was further characterized by electrophysiological studies and molecular docking. S-dinotefuran appears to be more toxic by binding to α8 subunit of nAChR of Apis mellifera. The α8 also have a more stable, functional binding cavity to S-dinotefuran with a higher binding score of 7.15, primarily due to an extensive hydrogen bond network. Therefore, new chiral products with a high proportion of or an enantiomeric pure R-dinotefuran are recommended to achieve effective pests control reducing hazard to honeybee populations.

Crystal Structure of a Highly Thermostable α-Carbonic Anhydrase from Persephonella marina EX-H1.

Bacterial α-type carbonic anhydrase (α-CA) is a zinc metalloenzyme that catalyzes the reversible and extremely rapid interconversion of carbon dioxide to bicarbonate. In this study, we report the first crystal structure of a hyperthermostable α-CA from Persephonella marina EX-H1 (pmCA) in the absence and presence of competitive inhibitor, acetazolamide. The structure reveals a compactly folded pmCA homodimer in which each monomer consists of a 10-stranded β-sheet in the center. The catalytic zinc ion is coordinated by three highly conserved histidine residues with an exchangeable fourth ligand (a water molecule, a bicarbonate anion, or the sulfonamide group of acetazolamide). Together with an intramolecular disulfide bond, extensive interfacial networks of hydrogen bonds, ionic and hydrophobic interactions stabilize the dimeric structure and are likely responsible for the high thermal stability. We also identified novel binding sites for calcium ions at the crystallographic interface, which serve as molecular glue linking negatively charged and otherwise repulsive surfaces. Furthermore, this large negatively charged patch appears to further increase the thermostability at alkaline pH range via favorable charge-charge interactions between pmCA and solvent molecules. These findings may assist development of novel α-CAs with improved thermal and/or alkaline stability for applications such as CO2 capture and sequestration.

Ammelinium Sulfate Monohydrate and Ammelinium Sulfate Cyanuric Acid – Synthesis and Structural Characterization

Two ionic carbon nitride type compounds containing the ammelinium cation, ammelinium sulfate cyanuric acid (6C3N5H6O+·3SO42–·1⅔C3N3H3O3·H2O) (1) and ammelinium sulfate monohydrate (2C3N5H6O+·SO42–·H2O) (2) were synthesized through hydrolysis of melam (C6N11H9) in diluted sulfuric acid. 1 crystallizes in hexagonal space group P63 (no. 173) with lattice parameters of a = 14.642(3), c = 13.113(4), and Z = 2. The structure is comprised of protonated ammelinium ions and neutral cyanuric acid molecules, which form a layered structure, as well as sulfate ions that span through these layers. 2 crystallizes in the triclinic space group P1 with lattice parameters of a = 7.404(3), b = 9.673(4), c = 10.040(4), α = 91.098(15), β = 109.884(10), γ = 92.567(13), and Z = 2. As for 1, the ammelinium rings form layers with the sulfate ions located in between. In both structures, no extended hydrogen bond networks between the respective triazine‐based molecules are formed. Instead, single molecules or small building blocks occur isolated and interact primarily with sulfate anions. Compound 1, which was obtained phase pure, was further investigated by FTIR spectroscopy, solid‐state NMR spectroscopy and powder X‐ray diffractometry.

KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors.

Sunflower trypsin inhibitor (SFTI-1) is a 14 amino acid serine protease inhibitor. The dual antiparallel β-sheet arrangement of SFTI-1 is stabilized by an N-terminal-C-terminal backbone cyclization and a further disulfide bridge to form a final bicyclic structure. This constrained structure is further rigidified by an extensive network of internal hydrogen bonds. Thus, the structure of SFTI-1 in solution resembles the protease-bound structure, reducing the entropic penalty upon protease binding. When cleaved at the scissile bond, it is thought that the rigidifying features of SFTI-1 maintain its structure, allowing the scissile bond to be reformed. The lack of structural plasticity for SFTI-1 is proposed to favor initial protease binding and continued occupancy in the protease active site, resulting in an equilibrium between the cleaved and uncleaved inhibitor in the presence of a protease. We have determined, at 1.15 Å resolution, the X-ray crystal structures of complexes between human kallikrein-related peptidase 4 (KLK4) and SFTI-FCQR(Asn14) and between KLK4 and an acyclic form of the same inhibitor, SFTI-FCQR(Asn14)[1,14], with the latter displaying a cleaved scissile bond. Structural analysis and MD simulations together reveal the roles of the altered contact sequence, intramolecular hydrogen bonding network, and backbone cyclization in altering the state of SFTI's scissile bond ligation at the protease active site. Taken together, the data presented reveal insights into the role of dynamics in the standard-mechanism inhibition and suggest that modifications on the non-contact strand may be a useful, underexplored approach for generating further potent or selective SFTI-based inhibitors against members of the serine protease family.

Design-properties relationships of polyurethanes elastomers depending on different chain extenders structures

In this study, the effect of the structure and amount of the chain extenders on the morphological image and physico-chemical properties of some new polyurethane elastomers has been investigated. To achieve this, three series of polyurethane elastomers based on poly(tetramethylene ether) glycol, hexamethylene diisocyanate and chain extenders with different structures (triethylene glycol, 3,6-dithia-1,8-octanediol, 1,6-hexanediol) were synthesized. The chain-extenders which introduce oxygen or sulfur atoms into the polyurethane backbone chains (hard domains) change the behavior of the properties compared to the corresponding polyurethanes chain-extended with aliphatic diols. The structures of the new polyurethane elastomers were examined by FTIR, X-ray diffraction analysis and by atomic force microscopy (AFM). They were also characterized for thermal and tensile properties. The polyurethanes with sulfur into their hard segment structure were found to exhibit improved thermal stability properties and equivalent mechanical properties with polyurethanes obtained with aliphatic diols. This is due to the extensive and many fold hydrogen bond network that characterizes polyurethanes with sulfur in their hard segment structure.