Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.     

Fragmentation of Na(NH3) n + cluster ions

Photoionization and -fragmentation of Na(NH₃)_n clusters by 170 fs and 8 ns laser pulses are studied with photon energies of 2.98 eV to 3.46 eV. In the reflectron timeof- flight mass spectra a strong metastable loss of NH₃ is observed independent of the laser pulse length. From the fragmentation rate constants the internal energy of the cluster ions prior to the fragmentation process is determined by an RRK approach.     

Not all G-quadruplexes exhibit ion-channel-like properties: NMR study of ammonium ion (non)movement within the d(G(3)T(4)G(4))(2) quadruplex

A solution-state NMR study on 15NH4(+) ion movement within d(G(3)T(4)G(4))(2), a dimeric G-quadruplex consisting of three G-quartets and two T(4) loops, rather unexpectedly demonstrated the absence of 15NH4(+) ion movement between the binding sites U and L along the central axis of the G-quadruplex. Distinct temperature dependences of autocorrelation signals for U and L binding sites have been observed in 15N-1H NzExHSQC spectra which correlate with the local stiffness of the G-quadruplex. The volumes of the cross-peaks, which are the result of 15NH4(+) ion movement, have been interpreted in terms of rate constants, T(1) relaxation, and proton exchange. 15NH4(+) ion movements from the binding sites U and L into the bulk solution are characterized by lifetimes of 139 ms and 1.7 s at 298 K, respectively. The 12 times faster movement from the binding site U demonstrates that 15NH4(+) ion movement is controlled by the structure of T4 loop residues, which through diagonal- vs edge-type orientations impose distinct steric restraints for cations to leave or enter the G-quadruplex. Arrhenius-type analysis has afforded an activation energy of 66 kJ mol(-)1 for the UB process, while it could not be determined for the LB process due to slow rates at temperatures below 298 K. We further the use of the 15NH4(+) ion as an NMR probe to gain insight into the occupancy of binding sites by cations and kinetics of ion movement which are intrinsically correlated with the structural details, dynamic fluctuations, and local flexibility of the DNA structure.     

The sodium ions inside a lipophilic G-quadruplex channel as probed by solid-state (23)Na NMR

We report solid-state 23Na NMR and X-ray crystallographic results for a self-assembled G-quadruplex channel formed by a guanine nucleoside, 5'-tert-butyl-dimethylsilyl-2',3'-O-isopropylidene guanosine (G 1). The study provides an unambiguous 23Na NMR identification for the Na+ ions inside a lipophilic G-quadruplex channel. The crystalline nature of the sample yields a remarkably high resolution in the 23Na multiple-quantum magic-angle spinning (MQMAS) spectrum, making it possible to extract very accurate 23Na NMR parameters for each of the three crystallographically distinct Na sites. The observation of a single Na+ ion from a 9-kDa system demonstrates the potential of solid-state 23Na NMR as a complementary technique to X-ray for detecting Na+ ions in biological structures.     

Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

A comparative study of the competitive cation exchange between the alkali metal ions K⁺, Rb⁺, and Cs⁺ and the Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂ was performed in aqueous solution by a combined use of the ²³Na and ¹H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G‐quadruplex and, in particular, major differences in the behavior of Cs⁺ as compared to the other ions were found. Accordingly, Cs⁺ competes with Na⁺ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K⁺ and Rb⁺ are also able to replace sodium ions located inside the quadruplex. Furthermore, the ¹H NMR results relative to the CsCl titration evidence a close approach of Cs⁺ ions to the phosphate groups in the narrow groove of [d(G₄T₄G₄)]₂. Based on a three‐site exchange model, the ²³Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs⁺ versus Na⁺ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G‐quadruplex formed by 5′‐guanosinemonophosphate and for the surface of double‐helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA. Copyright © 2009 John Wiley & Sons, Ltd.     

Solubility in the system Na2Cr2O7 + 2NH4Cl ⇆ (NH4)2Cr2O7 + 2NaCl-H2O

The solubility in the water-salt quaternary reciprocal system Na₂Cr₂O₇ + 2NH₄Cl ⇆ (NH₄)₂Cr₂O₇ + 2NaCl-H₂O has been investigated for the first time at 25, 50, and 75°C. Using a formal analytical model, the boundaries of the phase fields have been determined, and the univariant lines and invariant points have been calculated. The experimental data have been used to calculate the temperature and concentration parameters of the circular isohydric process of potassium dichromate preparation with the participation of ammonium salts as intermediates.     

(NH4)2SiF6 evaporation in the presence of SiO2

The kinetics and mechanism of the solid-phase reaction between (NH₄)₂SiF₆ and silica at molar ratios of (0.5–5): 1 were studied. SiO₂ is bound with (NH₄)₂SiF₆ to form volatile NH₄SiOF₃, which abruptly enhances the ammonium hexafluorosilicate evaporation. The activation energy and rate constants of evaporation were calculated for an (NH₄)₂SiF₆ + SiO₂ (2: 1) mixture in the range 220–300°C. The reaction with crystalline SiO₂ has a higher yield than with an amorphous “white soot.” The role of the SiO₂ surface in the formation of the volatile products is discussed. The phase and chemical composition of the sublimates was studied.     

Na2Mn(NH2)4: Ein neuer Schichtenstrukturtyp

Na₂Mn(NH₂)₄: A New Type of Layered Structure The structure of Na₂Mn(NH₂)₄ was solved by X-ray single crystal data including H-positions: P2₁/c, Z = 4, a = 6.331(1) Å, b = 14.542(3) Å, c = 7.212(1) Å, β = 116.29(1)°, Z(F ≥ 3σ = (F)) = 1343, Z(parameters) = 96, R/R_W = 0.023/0.029. The compound crystallizes in a new type of structure. Within layered blocks the amide ions are arranged with the motif of a hexagonal closest packing of spheres. Within these blocks alternating layers contain sodium in all octahedral sites and manganese in an ordered way in a quarter of tetrahedral sites.     

Thermal decomposition of (NH4)2MoO2S2, (NH4)2MoS4, (NH4)2WO2S2 and (NH4)2WS4

The thermal decomposition of (NH₄)₂MoO₂S₂,(NH₄)₂MoS₄, (NH₄)₂WO₂S₂ and (NH₄)₂WS₄ has been studied by DTA and TGA methods. All compounds decompose in two steps. The tetrathio compounds decompose as represented by the equations, (NH₄)₂MeS₄ → 2NH₃ + H₂O + MeS₃ MeS₃ → MeS₂ + S (Me  Mo, W). The thermal decomposition of the dithio salts is very complex. It is presumed that mixtures of oxysulphides and sulphides are formed as intermediate compounds. The final product of decomposition of the dithio-molybdate is very close to MoS₂, the final product of the decomposition of the dithio-tungstate yielding a mixture of WS₂ and WO₂ of the average composition WO_0·5S_1·75. The formal energies of activation which qualitatively describe the thermal properties of the compounds and heats of decomposition for the first reaction step were calculated from the thermal decomposition curves.     

First characterization of the ammine-ammonium complex [(NH4(NH3)4)2(mu-NH3)2]2+ in the crystal structure of [NH4(NH3)4][B(C6H5)4].NH3 and the [NH4(NH3)4]+ complex in [NH4(NH3)4][Ca(NH3)7]As3S6.2NH3 and [NH4(NH3)4][Ba(NH3)8]As3S6.NH3

The compound [NH4(NH3)4][B(C6H5)4].NH3 (1) was prepared by the reaction of NaB(C(6)H(5))(4) with a proton-charged ion-exchange resin in liquid ammonia. [NH(4)(NH(3))(4)][Ca(NH(3))(7)]As(3)S(6).2NH(3) (2) and [NH4(NH3)4][Ba(NH3)8]As3S6.NH3 (3) were synthesized by reduction of As(4)S(4) with Ca and Ba in liquid ammonia. All ammoniates were characterized by low-temperature single-crystal X-ray structure analysis. They were found to contain the ammine-ammonium complex with the maximal possible number of coordinating ammonia molecules, the [NH4(NH3)4]+ ion. 1 contains a special dimer, the [(NH4(NH3)4)2(mu-NH3)2]2+ ion, which is formed by two[NH4(NH3)4]+ ions linked by two ammonia molecules. The H(3)N-H...N hydrogen bonds in all three compounds range from 1.82 to 2.20 A (DHA = Donor-H...Acceptor angles: 156-178 degrees). In 2 and 3, additional H(2)N-H...S bonds to the thioanions are observed, ranging between 2.49 and 3.00 A (DHA angles: 120-175 degrees). Two parallel phenyl rings of the [B(C(6)H(5))(4)](-) anion in 1 form a pi...pi hydrogen bond (C...C distance, 3.38 A; DHA angles, 82 degrees), leading to a dimeric [B(C6H5)4]2(2-) ion.     

The role of distonic ions in the formation of CH3NH 3 + and (CH3)2NH 2 + from the molecular ions of octopamine and synephrine

It is shown by mass-analyzed ion kinetic energy spectrometry that the metastably decomposing molecular ions of octopamine (p-HOC₆H₄CH(OH)CH₂NH₂) and synephrine (p-HOC₆H₄CH(OH)CH₂NHCH₃) yield only protonated methylamine and dimethylamine, respectively, as product ions. From deuterium labeling and variation of the internal energy of the molecular ions, experimental support has been obtained that these product ions are generated via the occurrence of a distonic ion-neutral complex. In the case of octopamine, this complex would consist of a nitrogen-protonated aminomethyl radical and p-hydroxylbenzaldehyde in which the former species abstracts the aldehydic or phenolic hydrogen atom from the latter to give protonated dimethylamine.     

Thermal decomposition of (NH4)2MoS4 and (NH4)2WS4heat of formation of (NH4)2MoS4

The reactions (NH₄)₂MeS₄ = 2 NH₃ + H₂S + MeS₃ (Me = Mo, W) were investigated by measuring the decomposition vapour pressures. Thermochemical data were obtained from these measurements: ΔH = 52 kcal/mole and ΔS = 105 cal/deg.mole for the decomposition of the tetrathiomolybdate. Similarly, ΔH = 69 kcal/mole and ΔS = 106 cal/deg.mole were obtained for the decomposition of the tetrathiotungstate. The normal heat of formation of (NH₄)₂MoS₄ was found to be ΔH = ?140 kcal/mole. The kinetics of thermal decomposition of the above reactions were also measured.     

Vibrational analysis of Ag3(PO2NH)3, Na3(PO2NH)3 x H2O, Na3(PO2NH)3 x 4H2O,

FT IR and FT Raman spectra of Ag3(PO2NH), (Compound 1), Na3(PO2NH)3 x H2O (Compound II), Na3(PO2NH)3 x 4H2O (Compound III), [C(NH2)3]3(PO2NH)3 x H2O (Compound IV) and (NH4)4(PO2NH)4 x 4H2O (Compound V) are recorded and analyzed on the basis of the anions, cations and water molecules present in each of them. The PO2NH- anion ring in compound I is distorted due to the influence of Ag+ cation. Wide variation in the hydrogen bond lengths in compound III is indicated by the splitting of the v2 and v3 modes of vibration of water molecules. The NH4 ion in compound V occupies lower site symmetry and exhibits hindered rotation in the lattice. The correlations between the symmetric and asymmetric stretching vibrations of P-N-P bridge and the P-N-P bond angle have also been discussed.     

Dynamics of the NH4+ ion in ABX3 perovskites

The Raman and ir spectra of NH₄MnF₃, NH₄ZnF₃ and NH₄MnCl₃ have been measured in order to study the internal vibration modes of NH₄⁺ in different surrounding conditions. The internal force constants have been determined and compared to their values in ammonium halides and in the free ion, Their trends have been discussed in terms of the hydrogen bonding and volume effects. The intraionic polarizability parameters have also been obtained and compared to those of CH₄.