scholarly journals Group additivity calculation of the standard molal thermodynamic properties of aqueous amino acids, polypeptides and unfolded proteins as a function of temperature, pressure and ionization state

2005 ◽  
Vol 2 (5) ◽  
pp. 1515-1615 ◽  
Author(s):  
J. M. Dick ◽  
D. E. LaRowe ◽  
H. C. Helgeson
Keyword(s):  
Amino Acids ◽  
Thermodynamic Properties ◽  
Equations Of State ◽  
Reference Model ◽  
Accurate Determination ◽  
Group Additivity ◽  
Unfolded Proteins ◽  
Ionization State ◽  
Degree Of Ionization ◽  
Temperature And Pressure

Abstract. Thermodynamic calculation of the chemical speciation of proteins and the limits of protein metastability affords a quantitative understanding of the biogeochemical constraints on the distribution of proteins within and among different organisms and chemical environments. These calculations depend on accurate determination of the ionization states and standard molal Gibbs free energies of proteins as a function of temperature and pressure, which are not generally available. Hence, to aid predictions of the standard molal thermodynamic properties of ionized proteins as a function of temperature and pressure, calculated values are given below of the standard molal thermodynamic properties at 25°C and 1 bar and the revised Helgeson-Kirkham-Flowers equations of state parameters of the structural groups comprising amino acids, polypeptides and unfolded proteins. Group additivity and correlation algorithms were used to calculate contributions by ionized and neutral sidechain and backbone groups to the standard molal Gibbs free energy (Δ G°), enthalpy (Δ H°), entropy (S°), isobaric heat capacity (C°P), volume (V°) and isothermal compressibility (κ°T) of multiple reference model compounds. Experimental values of C°P, V° and κ°T at high temperature were taken from the recent literature, which ensures an internally consistent revision of the thermodynamic properties and equations of state parameters of the sidechain and backbone groups of proteins, as well as organic groups. As a result, Δ G°, Δ H°, S° C°P, V° and κ°T of unfolded proteins in any ionization state can be calculated up to T~-300°C and P~-5000 bars. In addition, the ionization states of unfolded proteins as a function of not only pH, but also temperature and pressure can be calculated by taking account of the degree of ionization of the sidechain and backbone groups present in the sequence. Calculations of this kind represent a first step in the prediction of chemical affinities of many biogeochemical reactions, as well as of the relative stabilities of proteins as a function of temperature, pressure, composition and intra- and extracellular chemical potentials of O2 and H2, NH3, H2PO4 and CO2.

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

2006 ◽  
Vol 3 (3) ◽  
pp. 311-336 ◽  
Author(s):  
J. M. Dick ◽  
D. E. LaRowe ◽  
H. C. Helgeson
Keyword(s):  
Thermodynamic Properties ◽  
Gibbs Energy ◽  
Chemical Potential ◽  
Equations Of State ◽  
Reference Model ◽  
Extracellular Proteins ◽  
Group Additivity ◽  
Unfolded Proteins ◽  
Ionization State ◽  
Complexation Reactions

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.

Thermodynamic Properties of Pure and Mixed Thermal Plasmas Over a Wide Range of Temperature and Pressure

2017 ◽  
Vol 140 (3) ◽  
Author(s):  
Omid Askari
Keyword(s):  
Thermodynamic Properties ◽  
Specific Heat ◽  
Fluid Dynamic ◽  
Thermal Plasmas ◽  
Statistical Thermodynamic ◽  
Reference Source ◽  
Degree Of Ionization ◽  
Wide Range ◽  
Self Consistent ◽  
Temperature And Pressure

Chemical composition and thermodynamics properties of different thermal plasmas are calculated in a wide range of temperatures (300–100,000 K) and pressures (10−6–100 atm). The calculation is performed in dissociation and ionization temperature ranges using statistical thermodynamic modeling. The thermodynamic properties considered in this study are enthalpy, entropy, Gibbs free energy, specific heat at constant pressure, specific heat ratio, speed of sound, mean molar mass, and degree of ionization. The calculations have been done for seven pure plasmas such as hydrogen, helium, carbon, nitrogen, oxygen, neon, and argon. In this study, the Debye–Huckel cutoff criterion in conjunction with the Griem’s self-consistent model is applied for terminating the electronic partition function series and to calculate the reduction of the ionization potential. The Rydberg and Ritz extrapolation laws have been used for energy levels which are not observed in tabulated data. Two different methods called complete chemical equilibrium and progressive methods are presented to find the composition of available species. The calculated pure plasma properties are then presented as functions of temperature and pressure, in terms of a new set of thermodynamically self-consistent correlations for efficient use in computational fluid dynamic (CFD) simulations. The results have been shown excellent agreement with literature. The results from pure plasmas as a reliable reference source in conjunction with an alternative method are then used to calculate the thermodynamic properties of any arbitrary plasma mixtures (mixed plasmas) having elemental atoms of H, He, C, N, O, Ne, and Ar in their chemical structure.

scholarly journals Pressure effect of the mechanical, electronics and thermodynamic properties of Mg–B compounds A first-principles investigations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
GuoWei Zhang ◽  
Chao Xu ◽  
MingJie Wang ◽  
Ying Dong ◽  
FengEr Sun ◽  
...  
Keyword(s):  
Thermodynamic Properties ◽  
First Principles ◽  
Boron Content ◽  
Structural Parameters ◽  
Debye Model ◽  
Total Density ◽  
First Principle ◽  
Volume Deformation ◽  
Temperature And Pressure ◽  
Total Density Of States

AbstractFirst principle calculations were performed to investigate the structural, mechanical, electronic properties, and thermodynamic properties of three binary Mg–B compounds under pressure, by using the first principle method. The results implied that the structural parameters and the mechanical properties of the Mg–B compounds without pressure are well matched with the obtainable theoretically simulated values and experimental data. The obtained pressure–volume and energy–volume revealed that the three Mg–B compounds were mechanically stable, and the volume variation decreases with an increase in the boron content. The shear and volume deformation resistance indicated that the elastic constant Cij and bulk modulus B increased when the pressure increased up to 40 GPa, and that MgB7 had the strongest capacity to resist shear and volume deformation at zero pressure, which indicated the highest hardness. Meanwhile, MgB4 exhibited a ductility transformation behaviour at 30 GPa, and MgB2 and MgB7 displayed a brittle nature under all the considered pressure conditions. The anisotropy of the three Mg–B compounds under pressure were arranged as follows: MgB4 > MgB2 > MgB7. Moreover, the total density of states varied slightly and decreased with an increase in the pressure. The Debye temperature ΘD of the Mg–B compounds gradually increased with an increase in the pressure and the boron content. The temperature and pressure dependence of the heat capacity and the thermal expansion coefficient α were both obtained on the basis of Debye model under increased pressure from 0 to 40 GPa and increased temperatures. This paper brings a convenient understanding of the magnesium–boron alloys.

scholarly journals THERMODYNAMIC PROPERTIES OF SOLUTIONS OF AMINO ACIDS AND RELATED SUBSTANCES

1942 ◽  
Vol 144 (3) ◽  
pp. 737-745
Author(s):  
Paul K. Smith ◽  
Alice T. Gorham ◽  
Elizabeth R.B. Smith
Keyword(s):  
Amino Acids ◽  
Thermodynamic Properties ◽  
Related Substances

FIRST-PRINCIPLES HIGH-PRESSURE ELASTIC AND THERMODYNAMIC PROPERTIES OF TANTALUM

2011 ◽  
Vol 25 (10) ◽  
pp. 1393-1407 ◽  
Author(s):  
JING-HE WU ◽  
XIAN-LIN ZHAO ◽  
YOU-LIN SONG ◽  
GUO-DONG WU
Keyword(s):  
Thermodynamic Properties ◽  
Elastic Constants ◽  
First Principles ◽  
Equations Of State ◽  
Debye Model ◽  
Thermal Expansivity ◽  
Orbital Method ◽  
Full Potential ◽  
Body Centered Cubic ◽  
Theoretical Results

The all-electron full-potential linearized muffin-tin orbital method, by means of quasi-harmonic Debye model, is applied to investigate the elastic constant and thermodynamic properties of body-centered-cubic tantalum (bcc Ta). The calculated elastic constants of bcc Ta at 0 K is consistent with the previous experimental and theoretical results. Our calculations give the correct trends for the pressure dependence of elastic constants. By using the convenient quasi-harmonic Debye model, we refined the thermal equations of state. The thermal expansivity and some other thermal properties agree well with the previous experimental and theoretical results.

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