The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

New reagents 41. Reduction of sulphonyl chlorides and sulphoxideswith aluminum iodide

Aluminium iodide reduces sulphonyl chlorides to disulphides and sulphoxides to sulphides under mild conditions in acetonitrile.

Hydrothermal phase equilibria in Ln2O3-H2O-CO2 systems for Tm, Yb and Lu

Phase diagrams for Tm2O3-H2O-CO2. Yb2O3-H2O-CO2 and Lu2O3-H2O-CO2 systems at 650 and 1300 bars have been investigated in the temperature range of 100–800°C. The phase diagrams are far more complex than those for the lighter lanthanides. The stable phases are Ln(OH)3, Ln2(CO3)3.3H2O (tengerite phase), orthorhombic-LnOHCO3, hexagonal-Ln2O2CO3. LnOOH and cubic-Ln2O3. Ln(OH)3 is stable only at very low partial pressures of CO2. Additional phases stabilised are Ln2O(OH)2CO3and Ln6(OH)4(CO3)7 which are absent in lighter lanthanide systems. Other phases, isolated in the presence of minor alkali impurities, are Ln6O2(OH)8(CO3)3. Ln4(OH)6(CO3)3 and Ln12O7(OH)10,(CO3)6. The chemical equilibria prevailing in these hydrothermal systems may be best explained on the basis of the four-fold classification of lanthanides.

Immunologic studies on nucleic acids and their components. I. An analysis of the specificity of anti-deoxyadenylate antibodies by a membrane-binding technique

Anti-deoxyadenylate antibodies were produced in rabbits by injecting a conjugate of deoxyadenosine 5′-phosphate with bovine serum albumin. The antisera, as analyzed by double diffusion in agar and the quantitative precipitin reaction, showed hapten-specific antibodies. The specific interaction between [3H]deoxyadenylate and antiserum was studied by a sensitive nitrocellulose membrane-binding assay. The specificity of the antibodies was analyzed by measuring the effectiveness of other nucleotides or derivatives to inhibit the hapten-antibody binding. The requirements for recognition by the antibody sites were studied by using a series of naturally occurring nucleic acid components as well as some synthetic derivatives as inhibitors. The antibodies were found to show a high degree of specificity for the whole nucleotide, the base, sugar and phosphate playing almost equally important roles. There was cross reactivity with other mononucleotides, although of a low order. The antibodies were able to react with DNA and tRNA.

R3Mn1.5CuV0.5O9 (R = Y, Ho, Er, Tm, Yb and Lu) and Lu3Mn3-3xCu2xVxO9: New noncentro symmetric oxides related to YMnO3

We report formation of new noncentrosymmetric oxides of the formula, R3Mn1.5CuV0.5O9 for R = Y, Ho, Er, Tm, Yb and Lu, possessing the hexagonal RMnO3 (space group P6(3)cm) structure. These oxides could be regarded as the x = 0.5 members of a general series R3Mn3-3xCu2xVxO9. Investigation of the Lu-Mn-Cu-V-O system reveals the existence of isostructural solid solution series, Lu3Mn3-3xCu2xVxO9 for 0 < x <= 0.75. Magnetic and dielectric properties of the oxides are consistent with a random distribution of Mn3+, Cu2+ and V5+ atoms that preserve the noncentrosymmetric RMnO3 structure. (c) 2006 Elsevier Ltd. All rights reserved.

Localized modes due to impurities in caesium iodide

The nature of the localized modes due to single substitutional impurities in a caesium iodide lattice is investigated using the models of Elliott, Dawber and Maradudin. The infra-red absorption due to U centres and their relation to the lattice spacing is also discussed.

Phase relations in the systems Cu–O–R2O3(R = Tm, Lu) and Gibbs energies of formation of Cu2R2O5 compounds

The phase relations in the systems Cu–O–R2O3(R = Tm, Lu) have been determined at 1273 K by X-ray diffraction, optical microscopy and electron probe microanalysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only ternary compounds of the type Cu2R2O5 were found to be stable. The standard Gibbs energies of formation of the compounds have been measured using solid-state galvanic cells of the type, Pt|Cu2O + Cu2R2O5+ R2O3‖(Y2O3)ZrO2‖CuO + Cu2O‖Pt in the temperature range 950–1325 K. The standard Gibbs energy changes associated with the formation of Cu2R2O5 compounds from their binary component oxides are: 2CuO(s)+ Tm2O3(s)→Cu2Tm2O5(s), ΔG°=(10400 – 14.0 T/K)± 100 J mol–1, 2CuO(s)+ Lu2O3(s)→Cu2Lu2O5(s), ΔG°=(10210 – 14.4 T/K)± 100 J mol–1 Since the formation is endothermic, the compounds become thermodynamically unstable with respect to component oxides at low temperatures, Cu2Tm2O5 below 743 K and Cu2Lu2O5 below 709 K. When the chemical potential of oxygen over the Cu2R2O5 compounds is lowered, they decompose according to the reaction, 2Cu2R2O5(s)→2R2O3(s)+ 2Cu2O(s)+ O2(g) The equilibrium oxygen potential corresponding to this reaction is obtained from the emf. Oxygen potential diagrams for the Cu–O–R2O3 systems at 1273 K are presented.

Synthesis and catalytic properties of cobalt- and molybdenum-containing mesoporous MCM-41 molecular sieves

Mesoporous MCM-41 type silicas containing molybdenum and cobalt have been prepared with pore sizes in the range 30-38 Angstrom and 54-59 Angstrom. Catalytic properties of these materials have been examined with respect to the oxidation of cyclooctene and aniline.

Decomposition temperatures of Cu2Ln2O5 (Ln = Tb, Dy, Ho, Er, Tm, Yb, and Lu) compounds

The equilibrium decomposition temperatures of Cu2Ln2O5 (Ln = Tb, Dy, Ho, Er, Tm, Yb, and Lu) compounds have been measured using a combined DTA-TGA apparatus under a flowing Ar + O2 gas mixture, in which the partial pressure of oxygen was controlled at 5.0 × 103 Pa. The Cu2Ln2O5 compounds yield Ln2O3 and Cu2O on decomposition. The decomposition temperature increases monotonically with the atomic number of the lanthanide element. This suggests that the stability of the Cu2Ln2O5 compounds with respect to the component binary oxides increases with decreasing radius of the Ln3+ ion.

A LOWER INITIAL ABUNDANCE OF SHORT-LIVED Ca-41 IN THE EARLY SOLAR SYSTEM AND ITS IMPLICATIONS FOR SOLAR SYSTEM FORMATION

The short-lived radionuclide Ca-41 plays an important role in constraining the immediate astrophysical environment and the formation timescale of the nascent solar system due to its extremely short half-life (0.1 Myr). Nearly 20 years ago, the initial ratio of Ca-41/Ca-40 in the solar system was determined to be (1.41 +/- 0.14) x 10(-8), primarily based on two Ca-Al-rich Inclusions (CAIs) from the CV chondrite Efremovka. With an advanced analytical technique for isotopic measurements, we reanalyzed the potassium isotopic compositions of the two Efremovka CAIs and inferred the initial ratios of Ca-41/Ca-40 to be (2.6 +/- 0.9) x 10(-9) and (1.4 +/- 0.6) x 10(-9) (2 sigma), a factor of 7-10 lower than the previously inferred value. Considering possible thermal processing that led to lower Al-26/Al-27 ratios in the two CAIs, we propose that the true solar system initial value of Ca-41/Ca-40 should have been similar to 4.2 x 10(-9). Synchronicity could have existed between Al-26 and Ca-41, indicating a uniform distribution of the two radionuclides at the time of CAI formation. The new initial Ca-41 abundance is 4-16 times lower than the calculated value for steady-state galactic nucleosynthesis. Therefore, Ca-41 could have originated as part of molecular cloud materials with a free decay time of 0.2-0.4 Myr. Alternative possibilities, such as a last-minute input from a stellar source and early solar system irradiation, could not be definitively ruled out. This underscores the need for more data from diverse CAIs to determine the true astrophysical origin of Ca-41.

Thermodynamics of TmRhO3, Phase Equilibria, and Chemical Potentials in the System Tm-Rh-O

Phase equilibria in the system Tm-Rh-O at 1200 K is established by isothermal equilibration of selected compositions and phase identification after quenching to room temperature. Six intermetallic phases (Tm3Rh, Tm7Rh3, Tm5Rh3, Tm3Rh2, TmRh, TmRh2 +/-delta) and a ternary oxide TmRhO3 are identified. Based on experimentally determined phase relations, a solid-state electrochemical cell is devised to measure the standard free energy of formation of orthorhombic perovskite TmRhO3 from cubic Tm2O3 and beta-Rh2O3 in the temperature range from (900 to 1300) K. The results can be summarized as: Delta G(f,ox)(o) +/- 104/J.mol(-1) = -46474 + 3.925(T/K). Invoking the Neumann-Kopp rule, the standard enthalpy of formation of TmRhO3 from its constituent elements at 298.15 K is estimated as -1193.89 (+/- 2.86) kJ.mol(-1). The standard entropy of TmRhO3 at 298.15 K is evaluated as 103.8 (+/- 1.6) J.mol(-1).K-1. The oxygen potential-composition diagram and three-dimensional chemical potential diagram at 1200 K and temperature-composition diagrams at constant partial pressures of oxygen are computed from thermodynamic data. The compound TmRhO3 decomposes at 1688 (+/- 2) K in pure oxygen and at 1583 (+/- 2) K in air at standard pressure.

Constraints on Be-10 and Ca-41 distribution in the early solar system from Al-26 and Be-10 studies of Efremovka CAIs

Three refractory coarse grained CAIs from the Efremovka CV3 chondrite, one (E65) previously shown to have formed with live Ca-41, were studied by ion microprobe for their Al-26-Mg-26 and Be-10-B-10 systematic in order to better understand the origin of Be-10. The high precision Al-Mg data and the inferred Al-26/Al-27 values attest that the precursors of the three CAIs evolved in the solar nebula over a period of few hundred thousand years before last melting-crystallization events. The initial Be-10/Be-9 ratios and delta B-10 values defined by the Be-10 isochrons for the three Efremovka CAIs are similar within errors. The CAI Be-10 abundance in published data underscores the large range for initial Be-10/Be-9 ratios. This is contrary to the relatively small range of Al-26/Al-27 variations in CAIs around the canonical ratio. Two models that could explain the origin of this large Be-10/Be-9 range are assessed from the collateral variations predicted for the initial delta B-10 values: (i) closed system decay of Be-10 from a ``canonical'' Be-10/Be-9 ratio and (ii) formation of CAIs from a mixture of solid precursors and nebula gas irradiated during up to a few hundred thousand years. The second scenario is shown to be the most consistent with the data. This shows that the major fraction of Be-10 in CAIs was produced by irradiation of refractory grains, while contributions of galactic cosmic rays trapping and early solar wind irradiation are less dominant. The case for Be-10 production by solar cosmic rays irradiation of solid refractory precursors poses a conundrum for Ca-41 because the latter is easily produced by irradiation and should be more abundant than what is observed in CAIs. Be-10 production by irradiation from solar energetic particles requires high Ca-41 abundance in early solar system, however, this is not observed in CAIs. (C) 2013 Elsevier B.V. All rights reserved.