Standard Molal Research Articles

Thermodynamic characteristics and mineral dissolution model of the H2O-CO2-CaCO3-Albite-SiO2 system in sedimentary basins

Diagenesis controls the formation, evolution, and distribution of deep-buried sandstone reservoirs in sedimentary basins. The essence of diagenesis is the transformation of substances between different phases (solid, gas and liquid phases) and the migration of materials transported by formation water. Fluids transport in deep-buried formations in sedimentary basins is generally slow, which lead the reaction system is in a near-equilibrium-to-equilibrium state. In this context, thermodynamics can be employed to calculate the solubility and characterize the occurrences of various minerals in different states, which can help reveal the genetic mechanism of secondary pores in the deep-buried rocks of sedimentary basins. In this study, we investigate the types and contents of particles in the aqueous solutions in the H2O-CO2-CaCO3-Albite-SiO2 system under different temperature and pressure conditions. Specifically, the Gibbs free energy of formation of minerals and gases are calculated based on the constant-pressure specific heat model; the apparent standard molal Gibbs free energy of different ions in fluids are computed using the HKF model; the equilibrium constants of different reactions are calculated according to the Gibbs function; the contents of different types of particles are computed based on the charge balance principle in the aqueous solution. The results show that the contents of various particles in the aqueous solution are mainly controlled by temperature and CO2 partial pressure, while they are rarely impacted by the total pressure. Different ions are demonstrated to have different responses to temperature changes. Specifically, types of Ca- and C-containing particles in the aqueous solution are closely related to temperature, while those of Al- and Si-rich particles are rarely changed as temperature varies. The CO2-rich fluid migration environment that results from hydrocarbon generation can be regarded as an open system for the dissolution of calcite, while it is a closed-to-semi-closed system for the dissolution of quartz and feldspar. The content of secondary pores is demonstrated to be determined by the solubility of various particles in the aqueous solution as well as the rate and duration of fluid migration, while the distribution patterns and ranges of secondary pores are controlled by responses of various particles in the solution to temperature and pressure changes.

CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Thermodynamic calculations are an essential tool for many areas of geochemistry. Thermodynamics provides a framework for the quantitative description and prediction of the solubilities and relative stabilities of different minerals, metal transport in hydrothermal fluids, and geobiochemical reactions that drive microbial metabolism and contribute to the compositional variation of proteins. Accessible and up-to-date software and databases are important for the development and reproducible application of thermodynamic models. CHNOSZ is a free package for R that has been frequently updated since its first release in 2008. The package provides an integrated set of functions to calculate the standard molal thermodynamic properties and chemical affinities of reactions. It uses the graphical capabilities of R to produce high-quality chemical activity diagrams for aqueous species and predominance diagrams including Eh-pH (Pourbaix) and logfO2-T diagrams. The extensive database utilizes the well-known revised Helgeson-Kirkham-Flowers (HKF) equations for aqueous species. Recent additions to the database include the Berman equations for minerals, the Deep Earth Water model, which extends the applicability of the HKF equations to higher pressures, and the Akinfiev-Diamond model for aqueous nonelectrolytes. The package comes with many types of documentation, including technical help pages with short code examples, longer code demos, and in-depth vignettes combining code, text and graphics, giving users a wide array of starting points for their own research. This paper provides a concise overview of the package and illustrates the new features using examples selected from the literature. Although the package does not provide a complete chemical speciation model, numerous examples from the package demonstrate the ease of reproducing selected published calculations and sometimes identifying issues with existing datasets and models.

SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92

The computer-enabled thermodynamic database associated with SUPCRT92 (Johnson et al., 1992) enables the calculation of the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions for a wide range of temperatures and pressures. However, new data on the thermodynamic properties of both aqueous species and minerals have become available since the database’s initial release in 1992 and its subsequent updates. In light of these developments, we have expanded SUPCRT92’s thermodynamic dataset and have modified the accompanying computer code for thermodynamic calculations by using newly available properties. The modifications in our new version include: (1) updating the standard state thermodynamic properties for mineral end-members with properties from Holland and Powell (2011) to improve the study of metamorphic petrology and economic geology; (2) adding As-acid, As-metal aqueous species, and As-bearing minerals to improve the study of environmental geology; (3) updating properties for Al-bearing species, SiO2°(aq) and HSiO3-, boehmite, gibbsite, and dawsonite for modeling geological carbon sequestration. The new thermodynamic dataset and the modified SUPCRT92 program were implemented in a software package called SUPCRTBL, which is available online at www.indiana.edu/~hydrogeo/supcrtbl.html.

Predicting Thermodynamic Behaviors of Non-Protein Amino Acids as a Function of Temperature and pH.

Why does life use α-amino acids exclusively as building blocks of proteins? To address that fundamental question from an energetic perspective, this study estimated the standard molal thermodynamic data for three non-α-amino acids (β-alanine, γ-aminobutyric acid, and ε-aminocaproic acid) and α-amino-n-butyric acid in their zwitterionic, negative, and positive ionization states based on the corresponding experimental measurements reported in the literature. Temperature dependences of their heat capacities were described based on the revised Helgeson-Kirkham-Flowers (HKF) equations of state. The obtained dataset was then used to calculate the standard molal Gibbs energies (∆G (o)) of the non-α-amino acids as a function of temperature and pH. Comparison of their ∆G (o) values with those of α-amino acids having the same molecular formula showed that the non-α-amino acids have similar ∆G (o) values to the corresponding α-amino acids in physiologically relevant conditions (neutral pH, <100 °C). In acidic and alkaline pH, the non-α-amino acids are thermodynamically more stable than the corresponding α-ones over a broad temperature range. These results suggest that the energetic cost of synthesis is not an important selection pressure to incorporate α-amino acids into biological systems.

Energetics of Amino Acid Synthesis in Alkaline Hydrothermal Environments.

Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent-ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.

Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature

Estimates of standard molal Gibbs energy (ΔGf°) and enthalpy (ΔHf°) of formation, entropy (S°), heat capacity (CP°) and volume (V°) at 25°C and 1bar of aqueous phenanthrene (P) and 1-, 2-, 3-, 4- and 9-methylphenanthrene (1-MP, 2-MP, 3-MP, 4-MP, 9-MP) were made by combining reported standard-state properties of the crystalline compounds, solubilities and enthalpies of phenanthrene and 1-MP, and relative Gibbs energies, enthalpies and entropies of aqueous MP isomers from published quantum chemical simulations. The calculated properties are consistent with greater stabilities of the β isomers (2-MP and 3-MP) relative to the α isomers (1-MP and 9-MP) at 25°C. However, the metastable equilibrium values of the abundance ratios 2-MP/1-MP (MPR) and (2-MP+3-MP)/(1-MP+9-MP) (MPI-3) decrease with temperature, becoming <1 at ∼375–455°C. The thermodynamic model is consistent with observations of reversals of these organic maturity parameters at high temperature in hydrothermal and metamorphic settings. Application of the model to data reported for the Paleoproterozoic Here’s Your Chance (HYC) Pb–Zn–Ag ore deposit (McArthur River, Northern Territory, Australia) indicates a likely effect of high-temperature equilibration on reported values of MPR and MPI-3, but this finding is contingent on the location within the deposit. If metastable equilibrium holds, a third aromatic maturity ratio, 1.5×(2-MP+3-MP)/(P+1-MP+9-MP) (MPI-1), can be used as a proxy for oxidation potential. Values of logaH2aq determined from data reported for HYC and for a sequence of deeply buried source rocks are indicative of more reducing conditions at a given temperature than those inferred from data reported for two sets of samples exposed to contact or regional metamorphism. These results are limiting-case scenarios for the modeled systems that do not account for effects of non-ideal mixing or kinetics, or external sources or transport of the organic matter. Nevertheless, quantifying the temperature dependence of equilibrium constants of organic reactions enables the utilization of organic maturity parameters as relative geothermometers at temperatures higher than the nominal limits of the oil window.

Calculation of the standard molal thermodynamic properties of crystalline peptides

To augment the relatively sparse set of thermodynamic data available for high molecular weight biopolymers, group additivity algorithms have been developed to estimate the heat capacity power function coefficients and standard molal thermodynamic properties of crystalline peptides in the multitude of biogeochemical environments in which they are found. Group contributions representing the 20 common amino acids plus 5-hydroxylysine and 4-hydroxyproline for each coefficient and property were generated using the thermodynamic properties of crystalline amino acids, polypeptides and other organic compounds. These group contributions were in turn used to compute the thermodynamic properties of naturally occurring proteins that are found in a crystalline state in cells. The coefficients and properties of the model compounds, group contributions and proteins are tabulated. In a demonstration of the uncertainty of the thermodynamic properties of the groups generated in this study, experimentally determined heat capacities and entropies of crystalline homopolypeptides and proteins taken from the literature have been compared to estimates of these quantities. Additionally, standard molal volumes for 24 amino acids have been recalculated in light of inconsistencies in an earlier analysis, and the standard molal thermodynamic properties of aqueous and crystalline methionine at 25°C and 0.1MPa have been reassessed. Calculations of this kind can be carried out to thermodynamically describe the biogeochemical interactions throughout the broad range of environmental settings in which they are known to occur.

Calculation of the Relative Chemical Stabilities of Proteins as a Function of Temperature and Redox Chemistry in a Hot Spring

Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems.

Thermodynamic properties of organic iodine compounds

A critical evaluation has been made of the thermodynamic properties reported in the literature for 43 organic iodine compounds in the solid, liquid, or ideal gas state. These compounds include aliphatic, cyclic and aromatic iodides, iodophenols, iodocarboxylic acids, and acetyl and benzoyl iodides. The evaluation has been made on the basis of carbon number systematics and group additivity relations, which also allowed to provide estimates of the thermodynamic properties of those compounds for which no experimental data were available. Standard molal thermodynamic properties at 25 °C and 1 bar and heat capacity coefficients are reported for 13 crystalline, 29 liquid, and 39 ideal gas organic iodine compounds, which can be used to calculate the corresponding properties as a function of temperature and pressure. Values derived for the standard molal Gibbs energy of formation at 25 °C and 1 bar of these crystalline, liquid, and ideal gas organic iodine compounds have subsequently been combined with either solubility measurements or gas/water partition coefficients to obtain values for the standard partial molal Gibbs energies of formation at 25 °C and 1 bar of 32 aqueous organic iodine compounds. The thermodynamic properties of organic iodine compounds calculated in the present study can be used together with those for aqueous inorganic iodine species to predict the organic/inorganic speciation of iodine in marine sediments and petroleum systems, or in the near- and far-field of nuclear waste repositories.

Enthalpy of Solution for Anhydrous VOSO4 and Estimated Enthalpy of Reaction for Formation of the Ion Pair [VOSO4]0

The molal enthalpies of solution of VOSO4·nH2O (n = 4.21, 3.90, 3.00, and 2.63) at various molalities in water, ΔsolHm, were measured by a solution−reaction isoperibol calorimeter at (298.15 ± 0.01) K. The standard molal enthalpies of solution of VOSO4·nH2O(s), ΔsolHm0(n), were determined according to Archer’s method. The standard molal enthalpies of solution for anhydrous VOSO4(s), ΔsolHm0 = (−49.19 ± 0.65) kJ·mol−1, were obtained using extrapolation, and relative apparent molal enthalpies, φL, of aqueous VOSO4 were calculated. In terms of the Bjerrum theory for ion association and the values of φL, the enthalpy of reaction for the formation of the ion pair [VOSO4]0, ΔasHm0 = (3.42 ± 0.04) kJ·mol−1, was estimated using a semiempirical method.

Biomolecules in hydrothermal systems: Calculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures

Calculation of the thermodynamic properties of biomolecules at high temperatures and pressures is fundamental to understanding the biogeochemistry of hydrothermal systems. Ample evidence indicates that hyperthermophilic microbes interact chemically with their mineralogical environment in these systems. Nevertheless, little is known about the thermodynamic properties of the biomolecules involved in such processes. Recent advances in theoretical biogeochemistry make it possible to calculate these properties using the limited experimental data available in the literature, together with correlation and group additivity algorithms, reference model compounds, and the revised HKF equations of state. This approach permits calculation of the standard molal thermodynamic properties of the 120 common protonated and deprotonated nucleotides and their constituent nucleic-acid bases and nucleosides as a function of temperature and pressure. The requisite equations of state parameters can be calculated from experimental standard molal heat capacities, volumes, and compressibilities reported in the literature for nucleic-acid bases and nucleosides. Because no calorimetric or densimetric data are available for the nucleotides, experimental heats of reaction taken from the literature were used together with correlation and group additivity algorithms to generate provisional values of the corresponding equations of state parameters for the nucleotides. The thermodynamic properties and revised HKF equations of state parameters generated in the present study can be used to carry out comprehensive mass transfer and Gibbs energy calculations to describe and quantify the chemical interaction of minerals and microbes in hydrothermal systems.

Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins

Abstract. Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential constraints on the interactions of microbes with their environment.

The energetics of metabolism in hydrothermal systems: Calculation of the standard molal thermodynamic properties of magnesium-complexed adenosine nucleotides and NAD and NADP at elevated temperatures and pressures

Calculation of the thermodynamic properties of biomolecules at high temperatures and pressures is fundamental to understanding the energetics of metabolism in hydrothermal systems. Perhaps the most direct interaction between hyperthermophilic microbes and their aquatic and mineralogic habitat involves conversion of environmentally available redox potential into biochemically useful energy. Although chemical thermodynamics can be used to quantify this process, little is known about the thermodynamic properties of the biomolecules involved, especially at high temperatures. However, recent advances in theoretical biogeochemistry make it possible to calculate these properties using the limited experimental data available in the literature, together with group additivity and correlation algorithms, reference model compounds and reactions, and the revised-HKF equations of state. This approach permits calculation of the standard molal thermodynamic properties and equations of state parameters for magnesium-complexed adenosine nucleotides, nicotinamide adenine dinucleotides (NADs), and nicotinamide adenine dinucleotide phosphates (NADPs) as a function of pressure and temperature. The thermodynamic properties and revised-HKF equations of state parameters generated in the present study can be used to carry out comprehensive mass transfer and Gibbs energy calculations to quantify the energetics of microbial energy production in hydrothermal systems.

Carbohydrates in thermophile metabolism: calculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures

Experimental thermodynamic data for aqueous organic compounds can be combined with the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate parameters that can be used to estimate standard molal properties as functions of temperature and pressure. In this study, we regressed thermodynamic data for aqueous carbohydrates at temperatures up to 393 K reported in the literature to permit the calculation of the apparent standard molal Gibbs free energies and enthalpies of formation (ΔGo and ΔHo, respectively) and the standard molal entropies (S2o), heat capacities (CP,2o), and volumes (V2o) to 423 K and several hundred MPa of aqueous C5 aldoses (ribose, arabinose, xylose, lyxose) and C5 ketoses (ribulose, xylulose) as well as C6 aldoses (glucose, mannose, galactose) and C6 ketoses (fructose, sorbose). Values of ΔGo for these 11 aqueous carbohydrates are given as a function of temperature at the saturated water vapor pressure (PSAT) and at 50 MPa. Values of ΔGo for aqueous glucose are then combined with those of other aqueous organic and inorganic compounds to calculate values of the standard molal Gibbs free energies of 13 fermentation and respiration reactions (ΔGro) known or likely to be carried out by thermophilic microorganisms. Finally, values of the overall Gibbs free energies of these reactions (ΔGr) are calculated at the temperature, pressure, and chemical composition that obtain in the hydrothermal fluids of Vulcano Island, southern Italy, a site that is widely known for its tremendous diversity of organisms able to live at high temperatures. At likely activities of aqueous glucose, it is shown that thermophiles in the hot springs of Vulcano at 373 K and ∼0.1 MPa can gain between 400 and 3000 kJ per mole of glucose fermented or respired.

Geological constraints on the thermodynamic properties of the stilbite—stellerite solid solution in low-grade metabasalts

Standard state thermodynamic data for stilbite (Ca2NaAl5Si13O36∗16H2O) and stellerite (Ca2Al4Si14O36∗14H2O), together with mixing properties of the stilbite -stellerite solid solution (stilbite SS) are derived through assessment of geological observations of stilbite SS compositions in metabasalts, experimental phase equilibria, and calorimetric observations. Measured compositions of stilbite SS in Tertiary metabasalts in Iceland and Icelandic geothermal systems change systematically towards the stellerite endmember with increasing stratigraphic depth and temperature. Standard molal volumes, heat capacities, and entropies for the endmembers of the solid solution are derived through critical review of published crystallographic and calorimetric data for natural stilbite SS. Standard molal Gibbs energies of formation at 298.15 K and 1 bar for stilbite (−4,946,475cal mol−1) and stellerite (−4,762,036 cal mol−1) and the mixing properties of the solid solution are retrieved from observed phase- and compositional-relations in metabasalts at Berufjördur, Iceland, measured temperatures of zeolite mineral distribution in active geothermal systems, and published observations of reversed phase equilibria. Mixing in stilbite SS can be described with an athermal solid solution model. Thermodynamic data resulting from our analysis provide close correlation between compositions of stilbite SS in Icelandic geothermal systems predicted from compositions of geothermal solutions and observed compositions of these minerals in low-grade metabasalts of Iceland, as well as the observed temperature of the stilbite SS to laumontite (leonhardite) transition in Icelandic geothermal systems. Stilbite SS composition in metabasalts is a sensitive function of temperature, fluid composition, coexisting minerals (especially silica polymorphs) and geothermal gradient.

Calculation of the standard molal thermodynamic properties as a function of temperature and pressure of some geochemically important organic sulfur compounds

The standard molal thermodynamic properties and heat capacity power function coefficients of more than 100 organic sulfur compounds in the crystalline, liquid, and/or gas state have been calculated by combining regressions of experimental data reported in the literature together with carbon number systematics and group additivity algorithms. The compounds for which these calculations have been made include carbon disulfide, branched thiols, cyclic thiols, aromatic thiols, n-alkyl sulfides, branched sulfides, cyclic sulfides (including long-chain n-alkylthiolanes and n-alkylthianes), aromatic sulfides, n-alkyl disulfides, alkylthiophenes, methylated benzothiophenes and dibenzothiophenes, and thianthrene. In addition, the corresponding properties and coefficients for 12 sulfur-containing groups in the crystalline, liquid, and/or gas states have been retrieved, which can be used to estimate the standard molal thermodynamic properties and heat capacity power function coefficients of sulfur-rich kerogens or other high molecular weight organic sulfur compounds of geochemical interest.

Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria.

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.

Partial dehydration of laumontite: thermodynamic constraints and petrogenetic implications

AbstractLaumontite is a common zeolite mineral indicative of low-grade metamorphism of lavas and volcaniclastic sediments. Stoichiometric laumontite (CaAl2Si4O12·4.5H2O) dehydrates in air at 298.15 K, 1 bar to leonhardite (CaAl2Si4O12·3.5H2O) via loss of water from the W1 crystallographic site. Consideration of reported X-ray diffraction and calorimetric data indicates that the standard molal volume and entropy for dehydration of laumontite to leonhardite + liquid water are ∼13 cc/mol and ∼8 cal/molK, respectively, at 298.15 K, 1 bar. Equilibrium between laumontite and leonhardite occurs at 70 to 80% relative humidity at 298.15 K, 1 bar, corresponding to a standard molal Gibbs energy and enthalpy of reaction of ∼170±40 and ∼2630±100 cal/mol, respectively. Calculated univariant equilibrium for this reaction is nearly linear from 46±3°C at 1 bar to 235±3°C at 5000 bar. Comparison of geological observations with these results suggests that laumontite forms as ‘leonhardite’ during metamorphism and diagenesis. Consideration of ‘leonhardite’, instead of laumontite, in low-grade metamorphic phase relations facilitates prediction of the relative stabilities of zeolites in natural and geologic systems, where calculated entropies of reaction incorrectly predict that assemblages bearing fully hydrated laumontite are stable at lower temperatures than the zeolites heulandite and stilbite.

Thermodynamics of the cell { Li- Amalgam | LiX (m)| AgX | Ag }(X = Cl,Br) and medium effects upon LiX in (acetonitrile + water), (1,4-dioxane + water), and (methanol + water) solvent mixtures with related solvation parameters

The electromotive forces E of the amalgam cells {LixHg1−x| LiCl(m)| AgCl | Ag} and {LixHg1−x| LiBr(m)| AgBr | Ag} have been measured as a function of the mole fraction x of Li metal in amalgams and of the molalities m of LiCl as well as LiBr at T= 298.15 K. For LiCl, the solvents investigated have been (acetonitrile + water), (1,4-dioxane + water), and (methanol + water) mixtures containing up to mass fraction 0.8 of the organic component, but only (acetonitrile + water) mixtures for LiBr. The standard molal electromotive forces Emohave been determined and, for all the solvent systems explored, they appear to vary linearly with the mole fraction y of the organic component involved, according to the following equations: Emo(LiCl)/V = 2.4169 − 0.2961yA;Emo(LiCl)/V = 2.4175 − 0.5951yD;Emo(LiCl)/V = 2.4163 − 0.1749yM;Emo(LiBr)/V = 2.2672 − 0.2092yA, where A denotes acetonitrile, D is 1,4-dioxane, and M is methanol. The relevant mean molal activity coefficients as functions of the LiCl and LiBr molalities have also been determined. The primary medium effects upon LiCl and LiBr, analysed in terms of the Feakins–French theory, lead to primary hydration numbers of ≈5 for LiCl and ≈4 for LiBr. These are somewhat lower than those obtained by other methods, but their difference is expected considering the known primary hydration numbers of the anions Cl−and Br−.

Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures II. Unfolded proteins

Equations of state for completely unfolded proteins have been generated from group additivity algorithms and the revised Helgeson–Kirkham–Flowers (HKF) equations of state to compute the standard molal thermodynamic properties of these molecules at elevated temperatures and pressures. The requisite equations of state parameters were computed from those of groups retrieved by regression of experimental calorimetric and densimetric data reported in the literature. This approach permits calculation of the standard molal thermodynamic properties as a function of temperature and pressure for any completely unfolded protein for which the amino acid sequence is known. Calculations of this kind have been carried out for 11 thermophilic proteins. The thermodynamic properties reported below can be combined with those for protein unfolding to compute the corresponding properties of completely folded (i.e. native) proteins.