Triple Hydrogen Research Articles

Simultaneous analysis of (17) O/(16) O, (18) O/(16) O and (2) H/(1) H of gypsum hydration water by cavity ring-down laser spectroscopy.

RationaleThe recent development of cavity ring‐down laser spectroscopy (CRDS) instruments capable of measuring 17O‐excess in water has created new opportunities for studying the hydrologic cycle. Here we apply this new method to studying the triple oxygen (17O/16O, 18O/16O) and hydrogen (2H/1H) isotope ratios of gypsum hydration water (GHW), which can provide information about the conditions under which the mineral formed and subsequent post‐depositional interaction with other fluids.MethodsWe developed a semi‐automated procedure for extracting GHW by slowly heating the sample to 400°C in vacuo and cryogenically trapping the evolved water. The isotopic composition (δ17O, δ18O and δ2H values) of the GHW is subsequently measured by CRDS. The extraction apparatus allows the dehydration of five samples and one standard simultaneously, thereby increasing the long‐term precision and sample throughput compared with previous methods. The apparatus is also useful for distilling brines prior to isotopic analysis. A direct comparison is made between results of 17O‐excess in GHW obtained by CRDS and fluorination followed by isotope ratio mass spectrometry (IRMS) of O2.ResultsThe long‐term analytical precision of our method of extraction and isotopic analysis of GHW by CRDS is ±0.07‰ for δ17O values, ±0.13‰ for δ18O values and ±0.49‰ for δ2H values (all ±1SD), and ±1.1‰ and ±8 per meg for the deuterium‐excess and 17O‐excess, respectively. Accurate measurement of the 17O‐excess values of GHW, of both synthetic and natural samples, requires the use of a micro‐combustion module (MCM). This accessory removes contaminants (VOCs, H2S, etc.) from the water vapour stream that interfere with the wavelengths used for spectroscopic measurement of water isotopologues. CRDS/MCM and IRMS methods yield similar isotopic results for the analysis of both synthetic and natural gypsum samples within analytical error of the two methods.ConclusionsWe demonstrate that precise and simultaneous isotopic measurements of δ17O, δ18O and δ2H values, and the derived deuterium‐excess and 17O‐excess, can be obtained from GHW and brines using a new extraction apparatus and subsequent measurement by CRDS. This method provides new opportunities for the application of water isotope tracers in hydrologic and paleoclimatologic research. © 2015 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Kinase hinge binding scaffolds and their hydrogen bond patterns

Protein kinases constitute a major class of intracellular signaling molecules, and describe some of the most prominent drug targets. Kinase inhibitors commonly employ small chemical scaffolds that form hydrogen bonds with the kinase hinge residues connecting the N- and C-terminal lobes of the catalytic domain. In general the satisfied hydrogen bonds are required for potent inhibition, therefore constituting a conserved feature in the majority of inhibitor-kinase interactions. From systematically analyzing the kinase scaffolds extracted from Pfizer crystal structure database (CSDb) we recognize that large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds. Depending on specific substitution patterns, scaffolds may demonstrate versatile binding capacities to interact with kinase hinge. Afforded by thousands of ligand–protein binary complexes, the hinge hydrogen bond patterns were analyzed with a focus on their three-dimensional configurations. Most of the compounds engage H6 NH for hinge recognition. Dual hydrogen bonds are commonly observed with additional recruitment of H4 CO upstream and/or H6 CO downstream. Triple hydrogen bonds accounts for small number of binary complexes. An unusual hydrogen bond with a non-canonical H5 conformation is observed, requiring a peptide bond flip by a glycine residue at the H6 position. Additional hydrogen bonds to kinase hinge do not necessarily correlate with an increase in potency; conversely they appear to compromise kinase selectivity. Such learnings could enhance the prospect of successful therapy design.

A Remarkably Complex Supramolecular Hydrogen-Bonded Decameric Capsule Formed from an Enantiopure C₂-Symmetric Monomer by Solvent-Responsive Aggregation.

The formation of an unprecedented decameric capsule in carbon disulfide, held together by the combination of double and triple hydrogen bonds between isocytosine units embedded in an enantiomerically pure bicyclic framework is reported. The aggregation occurs via symmetry breaking of the enantiopure intrinsically C2-symmetric monomer brought about by solvent, induced tautomerization of the hydrogen-bonding unit. We show that the topology of the aggregate is responsive to the solvent in which the assembly takes place. In this study we demonstrate that in carbon disulfide the chiral decameric cavity aggregate consisting of three forms of the same monomer, differing in their hydrogen bonding to each other is selectively formed, representing a tube-like structure capped with two C2-symmetric monomers. The large cylindrical cavity produced selectively accommodates one partially solvated C60 molecule, and molecular dynamic simulations revealed the special role of the solvent in the inclusion mechanism. The strategy described herein represents the first step toward the creation of a new class of hydrogen-bonded tubular objects from only one small symmetric building block by solvent-responsive aggregation.

A hyperbranched supramolecular polymer constructed by orthogonal triple hydrogen bonding and host-guest interactions.

A hyperbranched supramolecular polymer has been constructed through orthogonal self-crosslinking by two classical binding interactions: triple hydrogen bonding interaction between a three-arm melamine derivative and DB24C8-containing bisimide and host-guest interaction between DB24C8 crown ether and ditopic dibenzyl ammonium moieties.

Bodipy-C60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer.

Supramolecular triplet photosensitizers based on hydrogen bonding-mediated molecular assemblies were prepared. Three thymine-containing visible light-harvesting Bodipy derivatives (B-1, B-2 and B-3, which show absorption at 505 nm, 630 nm and 593 nm, respectively) were used as H-bonding modules, and 1,6-diaminopyridine-appended C60 was used as the complementary hydrogen bonding module (C-1), in which the C60 part acts as a spin converter for triplet formation. Visible light-harvesting antennae with methylated thymine were prepared as references (B-1-Me, B-2-Me and B-3-Me), which are unable to form strong H-bonds with C-1. Triple H-bonds are formed between each Bodipy antenna (B-1, B-2 and B-3) and the C60 module (C-1). The photophysical properties of the H-bonding assemblies and the reference non-hydrogen bond-forming mixtures were studied using steady state UV/vis absorption spectroscopy, fluorescence emission spectroscopy, electrochemical characterization, and nanosecond transient absorption spectroscopy. Singlet energy transfer from the Bodipy antenna to the C60 module was confirmed by fluorescence quenching studies. The intersystem crossing of the latter produced the triplet excited state. The nanosecond transient absorption spectroscopy showed that the triplet state is either localized on the C60 module (for assembly B-1·C-1), or on the styryl-Bodipy antenna (for assemblies B-2·C-1 and B-3·C-1). Intra-assembly forward-backward (ping-pong) singlet/triplet energy transfer was proposed. In contrast to the H-bonding assemblies, slow triplet energy transfer was observed for the non-hydrogen bonding mixtures. As a proof of concept, these supramolecular assemblies were used as triplet photosensitizers for triplet-triplet annihilation upconversion.

On the mechanism of improvement of field emission properties of carbon-coated field emitters

To clarify the origin of the superior field emission characteristics of carbon-coated emitters, the authors investigated the field enhancement and the work function of model systems calculated by numerical simulations. They propose that the field enhancement is due to the triple junctions, which are distributed on the surface of the carbon film consisting of sp3 (diamond-like) insulating and sp2 (graphite-like) conducting nanometer-sized grains. The electric field around the triple junction is one order of magnitude higher than at other places. Based on ab initio density functional theory calculations, the authors found that (1) the work functions of diamond and graphite dramatically decrease down to 3–3.6 eV upon hydrogen termination, and (2) the effective work functions of these models decrease to 2–2.5 eV by applying an external electric field of 2.57 × 107 V/cm. They also estimated the field emission current from the potential distribution and the local density of states under the external electric field applied. As a result, the authors found that hydrogen termination significantly increases the field emission current. The results suggest that the triple junction and hydrogen termination are promising candidates as the mechanism of improving the emission of the carbon-coated emitters.

A fluorescent hyperbranched supramolecular polymer based on triple hydrogen bonding interactions

A fluorescent hyperbranched supramolecular polymer was constructed through triple hydrogen bonding interactions between a three-arm monomer (PTDA) which possesses one melamine moiety in each arm and a perylene bisimide derivative (PBI 1) in dichloromethane.

Effects of water molecules on rearrangements of formamide on the kaolinite basal (001) surface.

The effects of kaolinite mineral surfaces on the unimolecular rearrangements of formamide (FM) were investigated using periodic density functional theory in conjunction with pseudopotential plane-wave approach. Surface hydroxyl groups covering the octahedral surface of kaolinite were found to play the role of catalysts in the transformations of FM. They induce a reduction of 31 kcal/mol on the energy barrier for formation of its isomer aminohydroxymethylene (AHM), which is close to the reduction amount calculated for water-catalyzed reactions. This suggests that the kaolinite octahedral surface exerts a catalytic effect similar to that of the water molecule. As the tetrahedral surface does not contain catalytic surface hydroxyl groups, only water-assisted FM transformation was therefore studied on this surface whose energy barrier amounts to ∼17 kcal/mol. The combined effect of both water and kaolinite on FM rearrangements via triple hydrogen transfer reactions does not significantly lower the energy barriers, as compared to those of double hydrogen transfer reactions. The triple hydrogen transfer energy barriers amount to ∼20 and ∼36 kcal/mol, and the double ones are ∼21 and ∼40 kcal/mol for formation of formimic acid and AHM isomers, respectively. However, the energies of the systems in water-catalyzed channels lie below the available energies of the original reactants, and thus these channels are more favored than the water-free ones. With its multiple functions as both a supporting plate-form and a catalyst for FM reactions, kaolinite can thus be regarded as an important natural catalyst for prebiotic synthesis.

Detection of melamine by a magnetic relaxation switch assay with functionalized Fe/Fe3O4 nanoparticles

The detection for melamine has attracted much attention due to its toxicity to the kidney of animals and humans. Herein, we reported a magnetic relaxation switch (MRSw) assay for melamine with Fe/Fe3O4 nanoparticles functionalized by the dopamine conjugated with methoxypoly (ethylene glycol) carboxyl acid (mPEG-COOH) and (2,4,6-trioxo-1,3,5-triazin-1-yl) acetic acid (TTAA) (TTAA–Fe/Fe3O4 NPs). The approach of the MRSw assay for melamine is based on the aggregation of TTAA–Fe/Fe3O4 NPs induced by the special triple hydrogen bonds between melamine and TTAA, which results in the increase of the spin–spin relaxation time (T2) of surrounding water protons of nanoparticles. Due to no limitation of light scattering, the detection of melamine with the MRSw assay can be performed in a turbid medium without pre-treatment and purification. Upon addition of the different concentration of melamine to an aqueous solution of TTAA–Fe/Fe3O4 NPs ([Fe]=32μM), the change of T2 value has a good linear relationship with the concentration of melamine below 16μM. The limit of detection (LOD) for melamine is ∼2μM. Furthermore, the MRSw assay exhibits a high selectivity for melamine over cytosine, uracil and thymine with the similar structure.

DNA sequencing by polymer synthesis with variable ratio of deoxynucleotide triphosphate and fluorescent dideoxynucleotide triphosphate

The chemical mechanism of double stranded DNA polymer synthesis is a complex process. The nucleotides are joined together by phosphodiester bond between 5' C of deoxynucleotide triphosphate and O at 3' C of another deoxynucleotide triphosphate with the release of pyrophosphate and hydrogen ion. The synthesis reaction is performed on the template strand based on the complimentary addition of nucleotide attached by hydrogen bonds. The nucleotide adenine A pairs with thymine T and cytosine C pairs with guanine G by double and triple hydrogen bonds respectively. The deoxynucleotide triphosphate dNTP are the synthesizing molecules and fluorescent dideoxynucleotide triphosphate ddNTP are the terminator molecules in the polymer synthesis. The fluorescent ddNTP lacking O at 3' C, terminate the further addition of nucleotide and fluorescence of attached dye is captured by laser light excitation and absorption on the detector. The fluorescence detection read the nucleotide in the synthesis cycle. The DNA sequencing is the reading of nucleotide in the polymer synthesis with the dNTP and fluorescent ddNTP. We have investigated a chemical mechanism of DNA polymer synthesis with variable ratio of dNTP and ddNTP to elucidate the best design of DNA sequencing for robust, error free long read length to scan the genome. The short tandem repeat sequence STR and single nucleotide polymorphism with the reference sequence SNP are molecular markers reside in the size range of 100 to 1000 nucleotides sequence of genome. The variation in the molecular markers is analyzed for human genetic identification and diversity.

Diaminopurine-Substitution Modify DNA Elasticity and Favors L-Helices

Proteins searching DNA for recognition sites in order to carry out replication, transcription, or mitosis must navigate on this remarkably stiff polymer. Electrostatics, base stacking and hydrogen bonding all contribute to stiffness and presumably limit deformability. Therefore, recognition depends not only on sequence per se but also on the stiffness and conformational dynamics of a sequence. Single molecule experiments have demonstrated a facile, progressive transition from a B- to an L-form helix that begins at negative linking numbers of a few percent when DNA gently stretched by as little as one picoNewton is progressively uncoiled. Since the particular sequence of a DNA segment heavily influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. As a fundamental test of this, the DNA was synthesized by PCR substituting adenine with diaminopurine to establish triple hydrogen bonding for all base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally, perhaps due to reduced helix breathing and enhanced base stacking, while softened DNA by 30% torsionally. Compared to normal DNA, upon unwinding under high tension (> 1 pN) DAP-substituted DNA more readily transitioned from B to L. Furthermore, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. This model of enhanced hydrogen bonding and base stacking achieved with DAP substitution indicates that the L-form helix forms spontaneously with high frequency under physiological conditions.

Synthesis, Structure and Properties of Two Novel 2D Zinc(II) Coordination Polymers based on Fluconazole and Benzene Carboxylic Acid

E-mail: pgh1919@163.comReceived June 5, 2013, Accepted September 13, 2013Key Words : Triple hydrogen bond, Coordination polymer, Fluconazole, UV-vis spectra, FluorescenceNowadays, the design and synthesis of coordination poly-mers have aroused great interest owing to their intriguingaesthetic structures and potential applications in nonlinearoptics, gas storage, ion exchange, luminescence, magnetismand catalysis.

Synthesis, Structure and Properties of a 2D Cadmium(II) Coordination Polymer Based on Fluconazole and Isophthalate Ligands

A Cd(II) complex based on fluconazole and isophthalate ligands, {[Cd(HFlu)(IPA)(H2O)] · H2O}n (1), (HFlu=fluconazole; H2IPA=isophthalic acid) has been synthesized. Single-crystal X-ray analysis reveals that complex 1 has a 2D network structure including unusual triple hydrogen bonds between hydroxyl and triazolyl groups. The complex has also been characterized by IR, UV=Vis and fluorescence spectroscopy, elemental analysis, and thermogravimetry

DNA Insecticides: Application of the Iap-2 Gene Single-stranded Fragments from Three Different Nucleopolyhedroviruses against Second Instar Gypsy Moth Larvae

We discovered that the external application of a solution containing one single-stranded DNA fragment, 18 nucleotides long, either from the BIR domain of the AcMNPV IAP-2 gene or the RING domain of the TnSNPV IAP-2 gene, induces a significantly higher mortality of gypsy moth larvae compared to a solution of distilled water. The results show the insecticidal potential of viral DNA fragments that can be used to create safe, relatively inexpensive and fast-acting insecticides to control quantity of pest insect populations. In our opinion, insecticidal effect may depend on the specific sequence of double and triple hydrogen bonds in a single-stranded DNA fragment or on a sequence of a few nitrogenous bases at specific sites of an oligonucleotide. The results suggest that small single-stranded viral DNA fragments may have practical applications as DNA insecticides.

Chain center-functionalized amphiphilic block polymers: Complementary hydrogen bond self-assembly in aqueous solution

Hydrogen bonding self-assemblies were formed in an aqueous medium from a pair of an amphiphilic ABA triblock copolymer and a hydrophobic homopolymer, both with a triple hydrogen bonding site that was complementary to each other and precisely placed at the main-chain center: (PEGMA)m–(MMA)n–ADA–(MMA)n–(PEGMA)m and (MMA)p–DAD–(MMA)p (A = hydrogen acceptor; D = hydrogen donor; PEGMA: PEG methacrylate; MMA: methyl methacrylate). The polymers were synthesized by the ruthenium-catalyzed living radial polymerization with bifunctional initiators (Br–ADA–Br and Cl–DAD–Cl) aiming at pinpoint chain center functionalization to give a symmetric segmental sequence; ADA and DAD initiators were derived from 2,6-diaminopyridine and thymine, respectively. On mixed equimolar in tetrahydrofuran (THF), both polymers spontaneously associated, and the apparently 1:1 assembly further grew into higher aggregate particles on subsequent addition of water. The aggregates in water/THF were relatively stable and uniform in size, which most likely stems from the intermolecular complementary hydrogen bond interaction at polymer chain centers. In sharp contrast, an equimolar mixture of ADA-block polymer and DAD-free poly(MMA) in water/THF resulted in larger and irregular particles, and thus short-lived to eventually collapse. These results indicate that, however structurally marginal, precise pinpoint functionalization of macromolecular chains allows stable self-assemblies via complementary hydrogen bond interaction even in aqueous media. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4498–4504

Association ofN-(Pyridin-2-yl),N′-substituted Ureas with 2-Amino-1,8-naphthyridines and Benzoates: NMR and Quantum Chemical Studies of the Substituent Effect on Complexation

Association of four N-(pyridin-2-yl),N'-R(1)-ureas (R(1) = ethyl, n-butyl, phenyl, and tert-butyl) with substituted 2-amino-1,8-naphthyridines and benzoates were studied by (1)H NMR spectroscopic titrations and quantum chemical calculations. The benzoates and 2-amino-1,8-naphthyridines were selected as representatives of double and triple hydrogen bonding counterparts, respectively. The classical substituent effect on the association was studied. A prerequisite and a crucial step for the complex formation was the breaking of the intramolecular hydrogen bond in urea derivatives. The QTAIM calculation method was employed to explain the hydrogen bonding within complexes. In the case of benzoates carrying an electron-donating substituent the experimental findings were explained by the formation of two complexes. These observations were rationalized by the electronic repulsions between atoms in a close proximity and further verified by calculations. Single-crystal X-ray diffraction was used to confirm the structure of studied ureas in the crystalline state. These results are in line with the solution studies of self-association of ureas.

Crystallization of Supramolecular Pseudoblock Copolymers

Because of the presence of supramolecular bonds, the crystallization process of supramolecular pseudoblock copolymers (SPBCP) is more complex in comparison to conventional covalently bonded block copolymers (BCP). Thus, supramolecular binding motives included on the polymer chain-ends display additional dynamic effects as well as possible nuclei for the crystallization. In this article we systematically study nonisothermal crystallization processes in SPBCP’s consisting of a crystallizable poly(e-caprolactone) (PCL) connected via triple hydrogen bonds to either a short alkyl-modified 2,4-diaminotriazine, or bound to a large block of amorphous poly(isobutylene) (PIB). The crystallization of the PCL is studied with both groups acting as supramolecular barriers for the crystallization process, either during nucleation or during crystal growth. A strong influence of the short alkyl-modified 2,4-diaminotriazine barrier on the crystallization temperature of the PCL compared to the control sample devoid of this ...

Superstructures of Diketopyrrolopyrrole Donors and Perylenediimide Acceptors Formed by Hydrogen-Bonding and π···π Stacking

Synthetic supramolecular systems can provide insight into how complex biological systems organize as well as produce self-organized systems with functionality comparable to their biological counterparts. Herein, we study the assembly into superstructures of a system composed of diketopyrrolopyrrole (DPP) donors with chiral and achiral side chains that can form triple hydrogen bonds with perylene diimide (PDI) acceptors into superstructures. The homoaggregation of the individual components as well as the heteroaggregate formation, as a result of π···π stacking and H-bonding, were studied by variable-temperature UV/vis and CD spectroscopies and electronic structure theory calculations. It was found that, upon cooling, the achiral PDIs bind to disordered DPP stacks, which drives the formation of chiral superstructures. A new thermodynamic model was developed for this unprecedented assembly that is able to isolate the thermodynamic binding parameters (ΔH°, ΔS°) for all the different noncovalent contacts that drive the assembly. This novel assembly as well as the quantitative model described in this work may help researchers develop complex self-assembled systems with emergent properties that arise as a direct result of their supramolecular structures.

Elaboration of Hydrogen-Bonded 2D Supramolecular Assemblies on Au(111) From Solutions: Toward Naphthalene Tetracarboxylic Diimide–Melamine Nanoporous Networks

Melamine and naphthalene tetracarboxylic diimide (NTCDI) supramolecular assemblies have been elaborated by a solution-based approach on Au(111) and studied by scanning tunneling microscopy (STM). We discuss the role of π-oligomers and H-oligomers in the mechanism of the network formation. Whereas the role of the first seems negligible, thermodynamical considerations establish the key role of the H-oligomers in the network extension in relation with the solvent nature. Density functional theory (DFT) calculations on the networks support the experimental structures. We discuss the influence and advantages of the solution method on the assemblies comparatively to ultrahigh vacuum (UHV) conditions. The NTCDI–melamine network exhibits a honeycomb structure which is obtained for the first time on the Au(111) substrate. The supramolecular mixed network is remarkably robust due to the stabilization from the triple hydrogen bonds established between the neighboring NTCDI and melamine molecules.

Synthesis, characterization and photophysical properties of a melamine-mediated hydrogen-bound phthalocyanine–perylenediimide assembly

The synthesis and supramolecular organization of a phthalocyanine 3 functionalized with a melamine moiety is described. 3 self-assembles in solution to form dimeric species – driven by double hydrogen-bonding between the aromatic amine functionality that is directly attached to the phthalocyanine ring and the melamine pyridinic nitrogens. In the presence of perylenediimide 2, endowed with a complementary tritopic functionality, electron donor–acceptor assembly Pc–PDI (3)222222·2 is spontaneously formed. (3)222222·2 consists of two phthalocyanines of type 3 and a perylenediimide 2, connected via triple hydrogen bonding between the melamine and the complementary unsubstituted imido functions. Electronic interactions between 2 and 3 in (3)222222·2 give rise, upon selective photoexcitation of 2, to an intramolecular electron transfer, affording a several nanosecond lived PDI˙−/H2Pc˙+ species, while photoexcitation of 3 is only followed by an ordinary intersystem crossing.