Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Determination of the Gibbs energy of diamond using a solid state cell

he chemical potential of carbon in diamond, relative to its value in graphite, has been directly determined using a solid state electrochemical cell incorporating single crystal CaF2 as the solid electrolyte. The cell can be represented as Pt, C(graphite) + CaC2 + CaF2double vertical barCaF2double vertical barCaF2 + CaC2 + C(diamond), Pt The reversible emf of this cell is directly related by the Nernst equation to the Gibbs free energy change for the conversion of diamond to graphite. The difference in the chemical potential of carbon in the two crystal structures varies linearly with temperature in the range 940 to 1260 K ?C(diamond) ? ?C(graphite) = 1100 + 4.64T (±50) J mol?1 On the average, the values given by the equation are 320 J mol?1 less positive than the currently accepted ones based on calorimetric studies. The difference is primarily in the enthalpy term.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Chemical potential of germanium in its solid solutions with Cu, Ag and Au

Thin foils of copper, silver and gold were equilibrated with tetragonal GeO2 under controlled View the MathML source gas streams at 1000 K. The equilibrium concentration of germanium in the foils was determined by the X-ray fluorescence technique. The standard free energy of formation of tetragonal GeO2 was measured by a solid oxide galvanic cell. The chemical potential of germanium calculated from the experimental data and the free energies of formation of carbon monoxide and carbon dioxide was found to decrease in the sequence Ag + Ge > Au + Ge > Cu + Ge. The more negative value for the chemical potential of germanium in solid copper, compared to that in solid gold, cannot be explained in terms of the strain energy factor, electro-negativity differences or the vaporization energies of the solvent, and suggests that the d band and its hybridization with s electrons are an important factor in determining the absolute values for the chemical potential in dilute solutions. However, the variation of the chemical potential with solute concentration can be correlated to the concentration of s and p electrons in the outer shell.

Gibbs free energies of formation of indium (III) oxide and sulphate

Emf measurements on the galvanic cell Pt, Ta, In + In,O, / Tho,-Y,03 / Cu + C+O, Pt were used to obtain the standard free energy of formation of 1%03fr om 600 to 900°C. Differential thermal analysis was used to detect the decomposition of In2(S0,), under controlled SO2 + O2 + Ar mixtures in thqtemperature range 640-8wC. X-ray diffraction analysis indicated that the decomposition product was 1%03 without an oxywlphate intermediate. The following equations were obtained for the variation of the standard free-energy change(Jlmole) with temperature:

Gibbs’ free energies of formation of Cu2Ln2O5 (Ln = Tb, Dy, Er, Yb) compounds

The standard Gibbs' free energies of formation of compounds of type Cu2L%05 (Ln = Tb,Dy,Er,Yb) were measured using the solid state cell in the temperature range of 970 to 1323 K For formation of Cu2L?O5 compounds from their binary component oxides according to the reaction 2 CUO (s) + L%03 (s) -, Cu,,L%05 (s),the Gibbs' free energy changes can be represented by the following equations:AGO = 13 080 - 13.70 'I" (+80) J mol-' (Ln = Tb)AGq = 11 480 - 13.51 T (260) J mol-I (Ln = Dy)AGO = 10 750 - 13.99 T (260) J mol-I (Ln = Er)AGO = 9 920 - 13.90 T (260) J mol-' (Ln = Yb) Since formation of the compounds is endothermic, the compounds become thermodynamically unstable with respect to their component oxides below 955 K for Cu2Tb205, 850 K for Cu2Dy205, 768 K for Cu2Er205 and 714 K for Cu2Yb2OS When the oxygen partial pressure over Cu2L%05 is lowered, they decompose according to the scheme, 2 CU,L%O, (s) -r 2 L%03 (s) +2 cu20 (s) + 02(g)The equilibrium chemical potentials of oxygen corresponding to the dissociation reactions are computed from the emf data and auxiliary information on Cu20 and CuO. The computed decomposition temperatures at an oxygen partial pressure of 5.0 x ld Pa are compared with those obtained directly from combined thermogravimetric (TGA) and differential thermal analyses (DTA).The free energy, enthalpy and entropy of formation of Cu2Ln205 compounds show systematic variation with the ionic radius of the trivalent lanthanide ion. The trends obtained in this study are compared with information available in the literature. The staZbility of Cu2Ln205 compounds increases with the decrease in ionic radii of the ~ n ion~. +

Phase equilibria in the system NiO-CaO-SiO2 and Gibbs energy of formation of CaNiSi2O6

Phase relations in the pseudoternary system NiO-CaO-SiO2 at 1373 K are established. The coexisting phases are identified by X-ray diffraction and energy-dispersive X-ray analysis of equilibrated samples. There is only one quaternary oxide CaNiSi2O6 with clinopyroxene structure. The Gibbs energy of formation of CaNiSi2O6 is measured using a solid state galvanic cell incorporating stabilized zirconia as the solid electrolyte in the temperature range of 1000 to 1400 K:Pt, Ni + SiO2 + CaSiO3 + CaNiSi2O6 \ (Y2O3)ZrO2 \ Ni + NiO, Pt From the electromotive force (emf) of the cell, the Gibbs energy of formation of CaNiSi2O6 from NiO, SiO2, and CaSiO3 is obtained. To derive the Gibbs energy of formation of the quaternary oxide from component binary oxides, the free energy of formation of CaSiO, is determined separately using a solid state cell based on single crystal CaF2 as the electrolyte: Pt, O-2, CaO + CaF2 \ CaF2 \ CaSiO3 + SiO2 + CaF2, O-2, Pt The results can be expressed by the following equations: NiO (r.s) + CaO (r.s) + 2SiO(2) (qz) --> CaNiSi2O6 (pyr) Delta G degrees = -115,700 + 10.63T (+/-100) J mol(-1) CaO (r.s) + SiO2 (qz) --> CaSiO3 (wol) Delta G degrees = -90,030 -0.61T (+/-60) J mol(-1).

System Ho-Rh-O: Phase Equilibria, Chemical Potentials and Gibbs Energy of Formation of HoRhO3

The thermodynamic properties of the HoRhO3 were determined in the temperature range from 900 to 1300 K by using a solid-state electrochemical cell incorporating calcia-stabilized zirconia as the electrolyte. The standard Gibbs free energy of formation of orthorhombic perovskite HoRhO3, from Ho2O3 with C-rare earth structure and Rh2O3 with orthorhombic structure, can be expressed by the equation; Delta G(f)degrees((ox)) (+/- 78)/(J/mol) = -50535 + 3.85(T/K) Using the thermodynamic data of HoRhO3 and auxiliary data for binary oxides from the literature, the phase relations in the Ho-Rh-O system were computed at 1273 K. Thermodynamic data for intermetallic phases in the binary Ho-Rh were estimated from experimental enthalpy of formation for three compositions from the literature and Miedema's model, consistent with the phase diagram. The oxygen potential-composition diagram and three-dimensional chemical potential diagram at 1273 K, and temperature-composition diagrams at constant oxygen partial pressures were computed for the system Ho-Rh-O. The decomposition temperature of HoRhO3 is 1717(+/- 2) K in pure O-2 and 1610(+/- 2) K in air at a total pressure p(o) = 0.1 MPa.

Electrochemical Determination of Gibbs Energy of Formation of LaCrO3 Using a Composition-Graded Bielectrolyte

Presented are new measurements of the standard Gibbs free energy of formation of rhombohedral LaCrO3 from component oxides La2O3 and Cr2O3 in the temperature range from 875 to 1175K, using a bielectrolyte solid-state cell incorporating single crystal CaF2 and composition-graded solid electrolyte (LaF3)(y)(CaF2)(1-y) (y=0-0.32). The results can be represented analytically as Delta G(f(ox))(o) (+/- 2270)/Jmol(-1)=-72329+4.932 (T/K). The measurements were undertaken to resolve serious discrepancies in the data reported in the literature. A critical analysis of previous electrochemical measurements indicates several deficiencies that have been rectified in this study. The enthalpy of formation obtained in this study is consistent with calorimetric data. The standard enthalpy of formation of orthorhombic LaCrO3 from elements at 298.15K computed from the results of this study is Delta H-f(298.15)(o)/kJmol(-1)=-1536.2 (+/- 7). The standard entropy of orthorhombic LaCrO3 at 298.15K is estimated as 99.0 (+/- 4.5)J(molK)(-1).

Phase formation and stability of alloy phases in free nanoparticles: some insights

This paper explores phase formation and phase stability in free nanoparticles of binary alloys. A procedure for estimating the size and composition dependent free energies incorporating the contributions from the interfaces has been presented. Both single phase solid solution and two phase morphology containing interphase interfaces have been considered. A free energy scenario has been evaluated for two binary alloy systems Ag-Ni and Ag-Cu to predict the microstructure of the alloy nanoparticles at different size ranges as a function of composition. Both Ag-Cu and Ag-Ni systems exhibit wide bulk immiscibility. Ag-Ni nanoparticles were synthesized using the wet chemical synthesis technique whereas Ag-Cu nanoparticles were synthesized using laser ablation of a Ag-Cu target immersed in distilled water. Microstructural and compositional characterization of Ag-Ni and Ag-Cu nanoparticles on a single nanoparticle level was conducted using transmission electron microscopy. Nanoparticle microstructures observed from the microscopic investigation have been correlated with thermodynamic calculation results. It is shown that the observed two phase microstructure consisting of Ag-Ni solid solution in partial decomposed state coexisting with pure Ag phases in the case of Ag-Ni nanoparticles can be only be rationalized by invoking the tendency for phase separation of an initial solid solution with increase in nanoparticle size. Smaller sized Ag-Ni nanoparticles prefer a single phase solid solution microstructure. Due to an increase in particle size during the synthesis process the initial solid solution decomposes into an ultrafine scale phase separated microstructure. We have shown that it is necessary to invoke critical point phenomenon and wetting transition in systems showing a critical point that leads to phase separated Ag-Ni nanoparticles providing a catalytic substrate for the nucleation of equilibrium Ag over it. In the case of the Ag-Cu system, we report the experimental observation of a core shell structure at small sizes. This can be rationalized in terms of a metastable solid solution. It is argued that the nucleation barrier can prevent the formation of biphasic morphology with an internal interface. In such a situation, demixing of the solid solution can bring the system to a lower energy configuration. This has lead to the observed core-shell morphology in the Ag-Cu system during room temperature synthesis.

Influences of Hydration Force and Elastic Strain Energy on the Stability of Solid Film in a Very Thin Solid-on-Liquid Structure

Since hydration forces become very strong at short range and are particularly important for determining the magnitude of the adhesion between two surfaces or interaction energy, the influences of the hydration force and elastic strain energy due to hydration-induced layering of liquid molecules close to a solid film surface on the stability of a solid film in a solid-on-liquid (SOL) nanostructure are studied in this paper. The liquid of this thin SOL structure is a kind of water solution. Since the surface forces play an important role in the structure, the total free energy change of SOL structures consists of the changes in the bulk elastic energy within the solid film, the surface energy at the solid-liquid interface and the solid-air interface, and highly nonlinear volumetric component associated with interfacial forces. The critical wavelength of one-dimensional undulation, the critical thickness of the solid film, and the critical thickness of the liquid layer are studied, and the stability regions of the solid film have been determined. Emphasis is placed on calculation of critical values, which are the basis of analyzing the stability of the very thin solid film.

On the Dynamics of the Adenylate Energy System: Homeorhesis vs Homeostasis

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.

A novel approach to isoscaling: The role of the order parameter m = N-f-Z(f)/A(f)

Isoscaling is derived within a recently proposed modified Fisher model where the free energy near the critical point is described by the Landau O(m(6)) theory. In this model m = N-f-Z(f)/A(f) is the order parameter, a consequence of (one of) the symmetries of the nuclear Hamiltonian. Within this framework we show that isoscaling depends mainly on this order parameter through the 'external (conjugate) field' H. The external field is just given by the difference in chemical potentials of the neutrons and protons of the two sources. To distinguish from previously employed isoscaling relationships, this approach is dubbed: m-scaling. We discuss the relationship between this framework and the standard isoscaling formalism and point out some substantial differences in interpretation of experimental results which might result. These should be investigated further both theoretically and experimentally. (C) 2010 Elsevier B.V. All rights reserved.

Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements.

The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded (U), intermediate (I), and sulfate-bound folded (F) states of RNase P protein, using an efficient and accurate nuclear magnetic resonance-monitored titration approach that utilizes internal reference compounds and a parametric fitting method. The three histidines in the sulfate-bound folded protein have pKa values depressed by 0.21 ± 0.01, 0.49 ± 0.01, and 1.00 ± 0.01 units, respectively, relative to that of the model compound N-acetyl-l-histidine methylamide. In the unliganded and unfolded protein, the pKa values are depressed relative to that of the model compound by 0.73 ± 0.02, 0.45 ± 0.02, and 0.68 ± 0.02 units, respectively. Above pH 5.5, H22 displays a separate resonance, which we have assigned to I, whose apparent pKa value is depressed by 1.03 ± 0.25 units, which is ∼0.5 units more than in either U or F. The depressed pKa values we observe are consistent with repulsive interactions between protonated histidine side chains and the net positive charge of the protein. However, the pKa differences between F and U are small for all three histidines, and they have little ionic strength dependence in F. Taken together, these observations suggest that unfavorable electrostatics alone do not account for the fact that RNase P protein is intrinsically unfolded in the absence of ligand. Multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

A simple model of atomic interactions in noble metals based explicitly on electronic structure

A total energy tight-binding model with a basis of just one s state per atom is introduced. It is argued that this simplest of all tight-binding models provides a surprisingly good description of the structural stability and elastic constants of noble metals. By assuming inverse power scaling laws for the hopping integrals and the repulsive pair potential, it is shown that the density matrix in a perfect primitive crystal is independent of volume, and structural energy differences and equations of state are then derived analytically. The model is most likely to be of use when one wishes to consider explicitly and self-consistently the electronic and atomic structures of a generic metallic system, with the minium of computation expense. The relationship to the free-electron jellium model is described. The applicability of the model to other metals is also considered briefly.