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.

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.

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.

Thermodynamic properties of liquid mixtures: Selection of the pure liquid parameter

1974 ◽  
Vol 27 (3) ◽  
pp. 647 ◽  
Author(s):  
DV Fenby ◽  
NF Pasco
Keyword(s):  
Equation Of State ◽  
Thermodynamic Properties ◽  
Equations Of State ◽  
Liquid Mixtures ◽  
Pure Liquid ◽  
Excess Thermodynamic Properties ◽  
Pure Fluids ◽  
Liquid Parameter ◽  
Selection Of

There has recently been a revival of interest in theories of liquid mixtures based on analytic equations of state for pure fluids. We have shown that the method used to determine the parameters of the pure-liquid equation of state has a significant effect on the excess thermodynamic properties obtained from such theories.

Aromatic fluorocarbon mixtures. VI. Vapour pressures of carbon tetrachloride + hexafluorobenzene

1974 ◽  
Vol 27 (10) ◽  
pp. 2159 ◽  
Author(s):  
NF Pasco ◽  
DV Fenby
Keyword(s):  
Carbon Tetrachloride ◽  
Thermodynamic Properties ◽  
Equations Of State ◽  
Liquid Mixture ◽  
Excess Enthalpies ◽  
Molar Excess ◽  
Mixture Theories

Measurements are reported of the vapour pressures of the system carbon tetrachloride + hexafluorobenzene at 278.68 K. The molar excess Gibbs functions GE/M, obtained from these measurements have been combined with previously reported molar excess enthalpies to give GE/M at 298 K. Thermodynamic properties of CCl4+C6F6 at 298 K are compared with the predictions of liquid mixture theories based on analytic equations of state.

Study of dynamic and thermodynamic properties of zinc-blend and wurtzite cadmium sulfide (CdS) using density functional theory

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Teshome Gerbaba Edossa ◽  
Menberu Mengasha Woldemariam
Keyword(s):  
Density Functional Theory ◽  
Thermodynamic Properties ◽  
Density Functional ◽  
Chemical Potential ◽  
Phonon Dispersion ◽  
Dynamic Properties ◽  
Dielectric Constants ◽  
High Symmetry ◽  
Functional Theory ◽  
Zinc Blend

Abstract The dynamic and thermodynamic properties of wurtzite (wz) and zinc-blend (zb) CdS are investigated within the density functional theory using different approximation methods such as LDA, PBE, and DFT+U. Hellmann–Feynman approach is implemented for the relaxation of atomic position for both phases. To guarantee the accuracy of calculation, the convergence test of total energy with respect to energy cutoff and k-point sampling is performed. The dynamic properties such as phonon dispersion, phonon density of state, frequency along with high symmetry points, static and dynamic polarizability, and dielectric constants are calculated. The obtained values are compared with previous theoretical results. DFT + U approximation gives a good result that is consistent with the available theory. Moreover, the vibrational energy, vibrational free energy, entropy, electron chemical potential, and constant-volume specific heat are obtained within LDA, PBE, and DFT + U approximations.

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