pinecone/core-2020-05-10-deduplication huggingface dataset:
Selective Response of Mesoporous Silicon to Adsorbants with Nitro Groups

We demonstrate that the electronic structure of mesoporous silicon is
affected by adsorption of nitro-based explosive molecules in a
compound-selective manner. This selective response is demonstrated by probing
the adsorption of two nitro-based molecular explosives (trinitrotoluene and
cyclotrimethylenetrinitramine) and a nonexplosive nitro-based arematic molecule
(nitrotoluene) on mesoporous silicon using soft X-ray spec- troscopy. The Si
atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as
evident from the large shifts in emission energy present in the Si L2,3 X-ray
emission spectroscopy (XES) measurements. Furthermore, we find that the energy
gap of mesoporous silicon changes depending on the adsorbant, as estimated from
the Si L2,3 XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab
initio molecular dynamics calculations of model compounds suggest that these
changes are due to spontaneous breaking of the nitro groups upon contacting
surface Si atoms. This compound-selective change in electronic structure may
provide a powerful tool for the detection and identification of trace
quantities of airborne explosive molecules.Comment: 27 pages, 9 figure
Coordination Polymers Based on [Cp*FeACHTUNGTRENUNG(h5-P5)]:\ud
MAS NMR Studies

Slow diffusion reactions of the pentaphosphaferrocene ['CP AST'FE'('eta POT. 5-'P IND. 5')] ('CP AST'='eta POT. 5'- 'C IND. 5''ME IND. 5'. (1)) with 'CU'X (X='CL', 'BR', I) in different stoichiometric ratios and solvent mixtures result in the formation of one- and two-dimensional polymeric compounds 2-6 with molecular formula '[{'CU'('mü'-X)}-{'CP AST''FE'('mü IND.3','eta POT. 5':'eta POT. 1':'eta POT. 1'-'P IND. 5')}] IND. n' (X='CL' (2a), I (2'c)), '[{'CU'('mü'-I)}-{'CP AST''FE'('mü IND.3','eta POT. 5':'eta POT. 1':'eta POT. 1'-'P IND. 5')}] IND. n'(3), '[{'CU'('mü'-X)}-{'CP AST''FE'('mü IND.4','eta POT. 5':'eta POT. 1':'eta POT. 1'-'P IND. 5')}] IND. n' (X='CL' (4a), 'BR' (4b), I (4c), 'BR' (4'b), I (4'c)), '[{'CU IND.3''('mü'-I) IND. 2'('mü IND. 3'-I)}- {'CP AST''FE'('mü IND. 5','eta POT. 5':'eta POT. 1':'eta POT. 1':'eta POT. 1''P IND. 5')}] IND n' (5) and '[{'CU IND. 4''('mü'-X) IND. 4'(C'H IND. 3'CN)}- {'CP AST''FE'('mü IND. 7','eta POT. 5':'eta POT. 2':'eta POT. 1':'eta POT 1':'eta POT. 1'-'P IND. 5')}] IND n'(X='CL' (6a), 'BR' (6b)), respectively. The polymeric compounds have been characterised by single-crystal X-ray diffraction analyses and, for selected examples, by magic angle spinning (MAS) NMR spectroscopy. The solidstate structures demonstrate the versatile coordination modes of the cyclo-'P IND. 5' ligand of 1, extending from two to five coordinating phosphorus atoms in either 'sigma' or 'sigma'-and-'pi' fashion. In compounds 2a, 2'c and 3, two phosphorus atoms of 1 coordinate to copper atoms in a 1,2 coordination mode (2a, 2'c) and an unprecedented 1,3 coordination mode (3) to form one-dimensional polymers. Compounds 4a-c, 4'b, 4'c and 5 represent two-dimensional coordination polymers. In compounds 4, three phosphorus atoms coordinate to copper atoms in a 1,2,4 coordination mode, whereas in 5 the cyclo-'P IND. 5' ligand binds in an unprecedented 1,2,3,4 coordination mode. The crystal structures of 6a,b display a tilted tube, in which all P atoms of the cyclo-'P IND. 5' ligand are coordinated to copper atoms in 'sigma'- and 'pi'-bonding modes.Deutsche Forschungsgemeinschaft (projects Sche 384/26- 1 and Ec168/10, “Supramolecular Aggregations
Influence of the nucleobase and anchimeric assistance of the carboxyl Acid groups in the hydrolysis of amino Acid nucleoside phosphoramidates

Nucleoside phosphoramidates (NPs) are a class of nucleotide analogues that has been developed as potential antiviral/antitumor prodrugs. Recently, we have shown that some amino acid nucleoside phosphoramidates (aaNPs) can act as substrates for viral polymerases like HIV-1 RT. Herein, we report the synthesis and hydrolysis of a series of new aaNPs, containing either natural or modified nucleobases to define the basis for their differential reactivity. Aqueous stability, kinetics, and hydrolysis pathways were studied by NMR spectroscopy at different solution pD values (5-7) and temperatures. It was observed that the kinetics and mechanism (PN and/or PO bond cleavage) of the hydrolysis reaction largely depend on the nature of the nucleobase and amino acid moieties. Aspartyl NPs were found to be more reactive than Gly or β-Ala NPs. For aspartyl NPs, the order of reactivity of the nucleobase was 1-deazaadenine>7-deazaadenine>adenine>thymine≥3-deazaadenine. Notably, neutral aqueous solutions of Asp-1-deaza-dAMP degraded spontaneously even at 4 °C through exclusive PO bond hydrolysis (a 50-fold reactivity difference for Asp-1-deaza-dAMP vs. Asp-3-deaza-dAMP at pD 5 and 70 °C). Conformational studies by NMR spectroscopy and molecular modeling suggest the involvement of the protonated N3 atom in adenine and 1- and 7-deazaadenine in the intramolecular catalysis of the hydrolysis reaction through the rare syn conformation.status: publishe
Solution structure and conformational dynamics of deoxyxylonucleic acids (dXNA): An orthogonal nucleic acid candidate

Orthogonal nucleic acids are chemically modified nucleic acid polymers that are unable to transfer information with natural nucleic acids and thus can be used in synthetic biology to store and transfer genetic information independently. Recently, it was proposed that xylose-DNA (dXNA) can be considered to be a potential candidate for an orthogonal system. Herein, we present the structure in solution and conformational analysis of two self-complementary, fully modified dXNA oligonucleotides, as determined by CD and NMR spectroscopy. These studies are the initial experimental proof of the structural orthogonality of dXNAs. In aqueous solution, dXNA duplexes predominantly form a linear ladderlike (type-1) structure. This is the first example of a furanose nucleic acid that adopts a ladderlike structure. In the presence of salt, an equilibrium exists between two types of duplex form. The corresponding nucleoside triphosphates (dXNTPs) were synthesized and evaluated for their ability to be incorporated into a growing DNA chain by using several natural and mutant DNA polymerases. Despite the structural orthogonality of dXNA, DNA polymerase β mutant is able to incorporate the dXNTPs, showing DNA-dependent dXNA polymerase activity.status: publishe
Metal-Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

This is the peer reviewed version of the following article: Kiy, M. M., Jacobi, Z. E., & Liu, J. (2012). Metal-Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications. Chemistry - A European Journal, 18(4), 1202–1208, which has been published in final form at http://dx.doi.org/10.1002/chem.201102515 This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, nonspecific folding induced by mono- or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled HgII binding DNA and monitored metal-induced folding in the presence of various cations. While nonspecific electrostatically mediated folding can be very significant, at each tested salt condition, HgII induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signal the formation of double-stranded DNA showed a lower dependency on ionic strength.University of Waterloo ||
Canadian Foundation for Innovation
Ontario ministry of Research and Innovation ||
Natural Sciences and Engineering Research Council |
Fabrication of Mesoporous Metal Chalcogenide Nanoflake-Silica Thin Films and Spongy Mesoporous CdS and CdSe

Cataloged from PDF version of article.Mesoporous silica metal oxide (ZnO and CdO) thin films have been used as metal ion precursors to produce the first examples of mesoporous silica metal sulfide (meso-SiO2@ZnS, meso-SiO2@CdS) or silica metal selenide (meso-SiO2@ZnSe, meso-SiO2@CdSe) thin films, in which the pore walls are made up of silica and metal sulfide or metal selenide nanoflakes, respectively. A gentle chemical etching with a dilute HF solution of the meso-SiO2@CdS (or meso-SiO2@CdSe) produces mesoporous cadmium sulfide (meso-CdS) (or cadmium selenide, meso-CdSe). Surface modified meso-CdS displays bright blue photoluminescence upon excitation with a UV light. The mesoporous silica metal oxides are formed as metal oxide nanoislands over the silica walls through a self-assembly process of a mixture of metal nitrate salt-two surfactants-silica source followed by calcination step. The reactions, between the H2S (or H2Se) gas and solid precursors, have been carried out at room temperature and monitored using spectroscopy and microscopy techniques. It has been found that these reactions are: 1) taking place through the diffusion of sulfur or selenium species from the top metal oxide layer to the silica metal oxide interface and 2) slow and can be stopped at any stage to obtain mesoporous silica metal oxide metal sulfide or silica metal oxide metal selenide intermediate thin films
The Importance of Stereochemically Active Lone Pairs For Influencing Pb II  and As III  Protein Binding

The toxicity of heavy metals, which is associated with the high affinity of the metals for thiolate rich proteins, constitutes a problem worldwide. However, despite this tremendous toxicity concern, the binding mode of As III  and Pb II  to proteins is poorly understood. To clarify the requirements for toxic metal binding to metalloregulatory sensor proteins such as As III  in ArsR/ArsD and Pb II  in PbrR or replacing Zn II  in δ‐aminolevulinc acid dehydratase (ALAD), we have employed computational and experimental methods examining the binding of these heavy metals to designed peptide models. The computational results show that the mode of coordination of As III  and Pb II  is greatly influenced by the steric bulk within the second coordination environment of the metal. The proposed basis of this selectivity is the large size of the ion and, most important, the influence of the stereochemically active lone pair in hemidirected complexes of the metal ion as being crucial. The experimental data show that switching a bulky leucine layer above the metal binding site by a smaller alanine residue enhances the Pb II  binding affinity by a factor of five, thus supporting experimentally the hypothesis of lone pair steric hindrance. These complementary approaches demonstrate the potential importance of a stereochemically active lone pair as a metal recognition mode in proteins and, specifically, how the second coordination sphere environment affects the affinity and selectivity of protein targets by certain toxic ions.     Experimental and computational  methods have been employed to study the influence of the lone pair of As III  and Pb II  for the binding of these ions in proteins using designed peptide models. The results show that the mode of coordination of As III  and Pb II  is greatly influenced by the steric bulk within the second coordination environment of the metals (see figure)
A new, highly conductive, lithium salt/nonionic surfactant, lyotropic liquid-crystalline mesophase and its application

The phase behavior and ionic conductivity of a new class of hydrated-salt/surfactant lyotropic liquid-crystalline (LLC) mesophase is investigated. The LLC samples were prepared by adding each ingredients such as salt, surfactant, and water in the required amounts and the resulting mixture was then homogenized by constant shaking in a shaking water bath at 60-110 8C for 24 h. A large region in the phase diagram belongs to a hexagonal LLC mesophase. At a moderate water/salt mole ratio, the salt/surfactant mole ratio can be varied between 2 and 8 to form stable LLC mesophases. The ionic conductivity shows a nearly Arrhenius-type relation with temperature. However, deviations increase as the temperature is lowered. The switching time, robustness, and the stability of the system suggest that the LLC gel electrolyte is a promising candidate for the electrochromic devices and optical displays
Controlled Synthesis of Carbon-Encapsulated Copper Nanostructures by Using Smectite Clays as Nanotemplates

Rhomboidal and spherical metallic-copper nanostructures were encapsulated within well-formed graphitic shells by using a simple chemical method that involved the catalytic decomposition of acetylene over a copper catalyst that was supported on different smectite clays surfaces by ion-exchange. These metallic-copper nanostructures could be separated from the inorganic support and remained stable for months. The choice of the clay support influenced both the shape and the size of the synthesized Cu nanostructures. The synthesized materials and the supported catalysts from which they were produced were studied in detail by TEM and SEM, powder X-ray diffraction, thermal analysis, as well as by Raman and X-ray photoelectron spectroscopy.
Directed Remote Aromatic Metalations: Mechanisms and Driving Forces

Directed remote aromatic metalations are useful synthetic transformations allowing for rapid regioselective access to elaborate highly substituted carbocyclic aromatic and heteroaromatic systems. This review unravels the tangle of data reported on directed remote aromatic metalations. Through a careful analysis of critically selected examples, advanced rationalizations of remote metalation regioselectivities are presented. These extend beyond the complex-induced proximity effect (CIPE). Mechanisms, driving forces, and parameters influencing remote metalations are discussed. An understanding of these metalation mechanisms enables more accurate predictability of justification of regiochemical outcomes of these useful synthetic transformations.Griffith Sciences, Griffith Institute for Drug DiscoveryFull Tex
Ensemble-averaged QM/MM kinetic isotope effects for the SN2 reaction of cyanide anions with chloroethane in DMSO solution

The existence of solvent fluctuations leads to populations of reactant-state (RS) and transition-state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC -+EtCl→NCEt+Cl - in DMSO solution at 30°C are best obtained as the ratio 〈f RS〉/ 〈f TS〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS-AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α- 2H 2, 2° β- 2H 3, α- 11C/ 14C, leaving group 37Cl, and nucleophile 13C and 15N) for this reaction in the correct direction as measured experimentally. These thermally-averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes. Better on average! Average AM1/OPLS-AA kinetic isotope effects (KIEs) computed for NC -+EtCl in DMSO agree with experiment for isotopic substitutions in six positions, and their distributions for individual configurations provide insight into solvent fluctuation effects. A single-molecule view of chemical change should be replaced by a picture involving averages over representative collections of molecules (see figure)
Cyclic RGD peptidomimetics containing bifunctional diketopiperazine scaffolds as new potent integrin ligands

The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α vβ 3 and α vβ 5, which are involved in tumor angiogenesis. Nanomolar IC 50 values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by 1H NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8 Å]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α vβ 3 complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex. Copyright © 2012 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim
Preparation of bifunctional mesoporous silica nanoparticles by orthogonal click reactions and their application in cooperative catalysis

The synthesis of bifunctional mesoporous silica nanoparticles is described. Two chemically orthogonal functionalities are incorporated into mesoporous silica by co-condensation of tetraethoxysilane with two orthogonally functionalized triethoxyalkylsilanes. Post-functionalization is achieved by orthogonal surface chemistry. A thiol-ene reaction, Cu-catalyzed 1,3-dipolar alkyne/azide cycloaddition, and a radical nitroxide exchange reaction are used as orthogonal processes to install two functionalities at the surface that differ in reactivity. Preparation of mesoporous silica nanoparticles bearing acidic and basic sites by this approach is discussed. Particles are analyzed by solid state NMR spectroscopy, elemental analysis, infrared-spectroscopy, and scanning electron microscopy. As a first application, these particles are successfully used as cooperative catalysts in the Henry reaction.DFG (SFB 858
A Library Approach to the Development of BenzaPhos, Highly Efficient Chiral Supramolecular Ligands for Asymmetric Hydrogenation

A library of chiral supramolecular ligands named BenzaPhos, of straightforward preparation (two steps from commercial or readily available starting materials) and modular structure, was designed and synthesized. The ligands were screened in the search of new rhodium catalysts for the enantioselective hydrogenation of several benchmark and industrially relevant substrates. Once a series of hits were identified, structural modifications were introduced on three of the best ligands and a small second-generation library was created. Members of the latter showed outstanding levels of activity and enantioselectivity in the hydrogenation of challenging olefins such as enamide S4  and beta-dehydroamino ester S5 (> 99% ee: best value ever reported in both cases). A series of control experiments were undertaken in order to clarify the role of hydrogen bonding in determining the catalytic properties of the new ligands. The results of these experiments, together with those of computational studies carried out on four dihydride complexes involved in the catalytic hydrogenation of substrate S4, strongly suggest that a substrate orientation takes place in the catalytic cycle by formation of a hydrogen bond between the ligand amide oxygen and the substrate amide NH
Double activation of an N-alkylimidazole

El pdf del artículo es el manuscrito de autor.Make it a double¡ A coordinated N-methylimidazole has been transformed, by double activation, into a bridging ligand that is simultaneously an abnormal N-heterocyclic carbene (NHC) and a Fischer carbene.The authors gratefully acknowledge the Spanish Ministry of Science and Innovation (MICINN)/FEDER (project number CTQ2009-12366), the Principality of Asturias (project number IB08-104) and the Spanish National Research Council (CSIC) (project number PIE-201080I038) for financial support.Peer Reviewe
Femtogram Detection of Explosive Nitroaromatics: Fluoranthene-Based Fluorescent Chemosensors

Herein we report a novel fluoranthene-based fluorescent fluorophore 7,10-bis(4-bromophenyl)-8,9-bis4-(hexyloxy)phenyl]fluoranthene (S-3) and its remarkable properties in applications of explosive detection. The sensitivity towards the detection of nitroaromatics (NACs) was evaluated through fluorescence quenching in solution, vapor, and contact mode approaches. The contact mode approach using thin-layer silica chromatograp- hic plates exhibited a femtogram (1.15 fg cm(-2)) detection limit for trinitrotoluene (TNT) and picric acid (PA), whereas the solution-phase quenching showed PA detection at the 2-20 ppb level. Fluorescence lifetime measurements revealed that the quenching is static in nature and the quenching process is fully reversible. Binding energies between model binding sites of the S-3 and analyte compounds reveal that analyte molecules enter into the cavity created by substituted phenyl rings of fluoranthene and are stabilized by strong intermolecular interactions with alkyl chains. It is anticipated that the sensor S-3 could be a promising material for the construction of portable optical devices for the detection of onsite explosive nitroaromatics