Synthesis,crystal structure and Raman spectra of [dabcoH2]CuICl3, [dabcoH2]3Cl4CuIICl4(DMSO) and Cu3Cl3(dabco)(DMSO) (dabco = 1,4-diazabicyclo [2.2.2] octane)

Dissolving elemental copper in a CCl₄–DMSO mixture in the presence of dabco (dabco = 1,4-diazabicyclo [2.2.2] octane) resulted in the formation of a compound with the composition [dabcoH₂][CuCl₃] featuring a univalent copper salt. This compound, composed of discrete dabcoH₂²⁺ cations and CuCl₃^2? anions, represents the first example of a copper(I) chloride derivative containing a doubly protonated [dabcoH₂]²⁺ unit, and a very rare example of the oxidative dissolving of copper in a CCl₄–DMSO mixture to give a Cu(I) compound. The addition of some drops of water to the initial reaction mixture led to the formation of the [dabcoH₂]₃Cl₄CuCl₄(DMSO). Three [dabcoH₂]²⁺ units and four Cl^? anions, bound via N–H…Cl hydrogen bonds, form a horseshoe-like cationic fragment. The divalent copper ion possesses a rather unusual pseudo-tetrahedral surrounding. The comproportionation reaction of CuCl₂·2H₂O and copper powder in the presence of dabco in DMSO results in the formation of the Cu₃Cl₃(dabco)(DMSO) complex. Copper and chlorine ions form unprecedented Cu₆Cl₆ cores, interconnected by neutral dabco linkers into infinite 2-D layers. All the compounds were characterized using the single-crystal X-ray diffraction technique and Raman spectroscopy.     

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP‐Binding RNA Aptamer

RNA tertiary structure motifs are stabilized by a wide variety of hydrogen‐bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pK _a values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP‐binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pK _a value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pK _a for A nucleotides in single‐stranded RNA. This is the largest pK _a shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pK _a shifts observed for amino acid side chains in proteins. Both RNA pre‐folding and ligand binding contribute to the pK _a shift.     

N1 Protonated Salt of Adenine: Solid‐State Linear Dichroic Infrared Spectral Analysis

Abstract

An illustration of the possibilities of solid‐state linear‐dichroic infrared (IR‐LD) spectral analysis of a suspension of a sample in a nematic liquid crystal for supramolecular stereostructural characterization is demonstrated comparing the IR‐LD spectral results of solid adenine (Ade) and its new N₁ protonated salt (AdeH). In addition, a detailed IR‐spectral characterization of the AdeH derivative that explains the corresponding frequencies that change as a result of the protonation process was also done.     

Inverse Vulcanization of a Natural Monoene with Sulfur as Sustainable Electrochemically Active Materials for Lithium-Sulfur Batteries

A novel soluble copolymer poly(S-MVT) was synthesized using a relatively quick one-pot solvent-free method, inverse vulcanization. Both of the two raw materials are sustainable, i.e., elemental sulfur is a by-product of the petroleum industry and 4-Methyl-5-vinylthiazole (MVT) is a natural monoene compound. The microstructure of poly(S-MVT) was characterized by FT-IR, ¹H NMR, XPS spectroscopy, XRD, DSC SEM, and TEM. Test results indicated that the copolymers possess protonated thiazole nitrogen atoms, meso/macroporous structure, and solubility in tetrahydrofuran and chloroform. Moreover, the improved electronic properties of poly(S-MVT) relative to elemental sulfur have also been investigated by density functional theory (DFT) calculations. The copolymers are utilized successfully as the cathode active material in Li-S batteries. Upon employment, the copolymer with 15% MVT content provided good cycling stability at a capacity of ∼514 mA h g⁻¹ (based on the mass of copolymer) and high Coulombic efficiencies (∼100%) over 100 cycles, as well as great rate performance.     

Crystal and molecular structure of [Au(C<Subscript>14</Subscript>H<Subscript>24</Subscript>N<Subscript>4</Subscript>)][H<Subscript>3</Subscript>O](ClO<Subscript>4</Subscript>)<Subscript>4</Subscript>

The crystal and molecular structure of doubly protonated tetraazamacrocyclic complex of gold(III) [Au(C₁₄H₂₄N₄)][H₃O](ClO₄)₄ has been determined. The crystals are monoclinic: a = 11.158(2) Å, b = 8.243(1) Å, c = 14.756(2) Å; β = 98.65(1)°, V = 1341.8(3) ų, Z = 2, ρ(calc) = 1.134 g/cm³, space group P2₁/n. The structure is built of almost flat centrosymmetrical Au(C₁₄H₂₄N₄)]³⁺ and [H₃O]⁺ cations and [ClO₄]^? anions. The gold atom is coordinated with four nitrogen atoms of the ligand forming a flat square. The coordinated ligand is protonated at its γ-carbon atoms of the two six-membered chelate rings. The Au-N bond lengths are almost identical (the mean value is 1.994 Å). The six-membered rings of the complex contain C=N diimine bonds. The [H₃O]⁺ oxonium ion has H-bonds with the oxygen atoms of perchlorate ions.     

Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions

Green fluorescent proteins (GFPs) are widely used as tools in biochemistry, cell biology, and molecular genetics due to their unusual optical spectroscopic characteristics. The spectrophotometric and fluorescence properties of GFPs are controlled by the protonation states and possibly cis-trans isomerization of the chromophore (p-hydroxybenzylideneimidazolinone). In this work, we have investigated electronic structures, liquid structures, and solvent shifts of the three possible protonated states (neutral, anionic, and zwitterionic) and their cis-trans isomerization of a model compound 4'-hydroxybenzylidene-2-methyl-imidazolin-5-one-3-acetate (HBMIA) in aqueous solutions. Our calculated results suggest that HBMIA could adopt both cis and trans conformations in a solution, and it exists in three different protonation states depending on the pH conditions. The absorption spectrum observed in neutral solution is thus assigned to the electronic excitations within the neutral form and the cis isomer of the zwitterionic form, while the absorption band at 425 nm in the basic solution is due to the excitations within the anionic form and the trans isomer of the zwitterionic form. Some technical problems related to the computation of electronic excitations within the HBMIA at the anionic state are also discussed.     

Fragmentation reactions of protonated peptides containing glutamine or glutamic acid

A variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy-resolved mass spectrometry and triple-stage mass spectrometry (MS(3)) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H-Gln-Gly-OH fragments by loss of NH(3) and loss of H(2)O in metastable ion fragmentation; under collision-induced dissociation (CID) conditions loss of H-Gly-OH + CO from the [MH - NH(3)](+) ion forms the base peak C(4)H(6)NO(+) (m/z 84). Protonated dipeptides with an alpha-linkage, H-Glu-Xxx-OH, are characterized by elimination of H(2)O and by elimination of H-Xxx-OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a gamma-linkage, H-Glu(Xxx-OH)-OH, do not show elimination of H(2)O or formation of m/z 102 but rather show elimination of NH(3), particularly in metastable ion fragmentation, and elimination of H-Xxx-OH to form m/z 130. Both the alpha- and gamma-dipeptides show formation of [H-Xxx-OH]H(+), with this reaction channel increasing in importance as the proton affinity (PA) of H-Xxx-OH increases. The characteristic loss of H(2)O and formation of m/z 102 are observed for the protonated alpha-tripeptide H-Glu-Gly-Phe-OH whereas the protonated gamma-tripeptide H-Glu(Gly-Gly-OH)-OH shows loss of NH(3) and formation of m/z 130 as observed for dipeptides with the gamma-linkage. Both tripeptides show abundant formation of the y(2)' ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H-Xxx-Glu-OH show abundant elimination of H(2)O whereas those of structure H-Xxx-Gln-OH show abundant elimination of NH(3). The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a(1) ion or the y(1)' ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH(3) from the glutamine containing dipeptide is followed by elimination of a second NH(3) while the initial loss of H(2)O from the glutamic acid dipeptide is followed by elimination of NH(3). Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H-Gly-Glu-Gly-OH]H(+) and [H-Gly-Gln-Gly-OH]H(+) fragment mainly to form b(2) and a(2) ions, the latter also shows elimination of NH(3) plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon-bonded hydrogens in the formation of protonated glycinamide.     

Chemical and morphological modification of complex manganese oxides with different sizes of structural tunnels

The methods for the synthesis of protonated forms of complex manganese oxides Mg _x Mn₄O₈·H₂O and Ba₆Mn₂₄O₄₈ (1h and 2h, respectively) in the form of whisker crystals possessing tunnel crystal structures of different sizes were optimized. The microstructural features and physicochemical properties of the synthesized materials were studied. The treatment with nitric acid leads to the formation of the Mn-O-H hydroxy groups due to the insertion of protons into the structural tunnels. The protonated forms of the 1h and 2h phases are active in ion-exchange processes in aqueous solutions, the tunnel size being the determining factor for the sorption of heavy metal cations. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1130—1135, June, 2008.