scholarly journals Temperature-dependent estimation of Gibbs energies using an updated group contribution method

2018 ◽  
Author(s):  
Bin Du ◽  
Zhen Zhang ◽  
Sharon Gruber ◽  
James T. Yurkovich ◽  
Bernhard O. Palsson ◽  
...  
Keyword(s):  
Metal Ion ◽  
Equilibrium Constants ◽  
Binding Constants ◽  
Entropy Change ◽  
Group Contribution ◽  
Mass Action ◽  
Enthalpies Of Formation ◽  
Standard Entropy ◽  
Group Contribution Method ◽  
Reaction Equilibrium

AbstractReaction equilibrium constants determine the mass action ratios necessary to drive flux through metabolic pathways. Group contribution methods offer a way to estimate reaction equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group contribution method with: 1) additional curated thermodynamic data used in fitting; and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermo-dynamic data, including reaction equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropies change of formation of compounds, and proton and metal ion binding constants. We further estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated necessary parameters, including standard entropy change of formation (ΔfS∘) and standard entropy change of reaction (ΔrS∘), using a model based on molecular properties. The median absolute errors in estimating ΔfS∘ and ΔrS∘ were 0.010 kJ/K/mol and 0.018 kJ/K/mol, respectively. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal ion concentrations. These results support the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions.

scholarly journals Spectroscopic investigation of the interaction of bovine serum albumin with a novel cardiac agent V-09

2008 ◽  
Vol 22 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Changyun Chen ◽  
Meihua Ma ◽  
Junqi Zhang ◽  
Lichen Wang ◽  
Bingren Xiang
Keyword(s):  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Bovine Serum ◽  
Average Distance ◽  
Cardiac Activity ◽  
Binding Constants ◽  
Entropy Change ◽  
Standard Entropy ◽  
Förster Energy Transfer ◽  
Standard Enthalpy Change

This study employs fluorescence spectroscopy to characterize the binding properties of a newly synthesized cardiac agent, V-09, on bovine serum albumin (BSA). This compound shows the highest cardiac activity in the whole series. The binding constantsKat 25°C and 37°C are obtained, the values are 7.12×104l mol–1, 4.66×104l mol–1, respectively. The standard enthalpy change (ΔH0) and the standard entropy change (ΔS0) are calculated to be –27.13 KJ mol–1and 1.854 J mol–1K–1, which indicated that hydrophobic forces play major role in the interaction between V-09 and BSA. The binding average distance between V-09 and BSA (2.57 nm) is obtained on the basis of the theory of Főrster energy transfer.

scholarly journals Temperature effect on ion exchange equilibrium between CMX membrane and electrolytes solutions

2015 ◽  
Vol 5 (4) ◽  
pp. 535-541 ◽  
Author(s):  
Akrem Chaabouni ◽  
Fatma Guesmi ◽  
Islem Louati ◽  
Chiraz Hannachi ◽  
Béchir Hamrouni
Keyword(s):  
Ion Exchange ◽  
Binary Systems ◽  
Equilibrium Constants ◽  
Exchange Process ◽  
Standard Free Energy ◽  
Entropy Change ◽  
Enthalpy Change ◽  
Exchange Equilibrium ◽  
Standard Entropy ◽  
Ion Exchange Process

Ion exchange equilibrium for three systems involving monovalent and divalent ions has been investigated over various temperatures (283, 298 and 313 K) using CMX cationic exchange membrane. All experiments were carried out at 0.1 mol/L. Ion exchange isotherms for the binary systems (Na+/K+), (Na+/Ca2+) and (K+/Ca2+) were established at temperatures ranging from 283 to 313 K. The obtained affinity order is: K+>Ca2+>Na+. Selectivity coefficients KK+2Na+, K2Na+Ca2+ and KCa2+2K+ were determined and found to increase with rise in temperature. Thermodynamic equilibrium constants Ki°j were calculated. Wilson and Debye–Hückel equations have been used to calculate activity coefficients in the membrane and solution, respectively. Standard free energy ΔGT°, standard enthalpy change ΔHT° and standard entropy change ΔST° were calculated. The values of ΔHT° were found to be 51.98 kJ/mol, 64.59 kJ/mol and 29.57 kJ/mol, respectively, for (Na+/K+), (Na+/Ca2+) and (K+/Ca2+) binary systems, which indicate that the ion exchange process between the CMX membrane and the studied binary systems is an endothermic process. ΔST° is found to be positive, which means that the increased randomness appeared on the membrane-solution interface during the ion exchange reaction. In addition, the standard free enthalpy change ΔGT° value for all systems is negative, which is an indication that the ion exchange equilibrium is spontaneous in standard conditions.

A group contribution method for the estimation of equilibrium constants for biochemical reactions

1988 ◽  
Vol 2 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Michael L. Mavrovouniotis ◽  
Patrick Bayol ◽  
Tu-Kien Michael Lam ◽  
George Stephanopoulos ◽  
Gregory Stephanopoulos
Keyword(s):  
Equilibrium Constants ◽  
Group Contribution ◽  
Group Contribution Method ◽  
Biochemical Reactions

scholarly journals Interaction of thiacloprid with bovine hemoglobin using spectroscopic and molecular modeling methods

2010 ◽  
Vol 24 (5) ◽  
pp. 559-566
Author(s):  
Chang-Yun Chen ◽  
Bo Zhao ◽  
Zheng-Wu Wang
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Modeling ◽  
Protein Secondary Structure ◽  
Binding Constants ◽  
Entropy Change ◽  
Binding Mode ◽  
Cd Spectroscopy ◽  
Bovine Hemoglobin ◽  
Standard Entropy ◽  
Α Helix

The interaction of thiacloprid (TL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using fluorescence spectroscopy, circular dichroism spectroscopy (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of TL. It is observed that there was a prominent interaction between TL and BHb. The binding constantsKAat 288, 298 and 308 K obtained are 8.04, 5.26 and 3.08×104l · mol–1, respectively. The standard enthalpy change (ΔH°) and the standard entropy change (ΔS°) are calculated to be –34.54 KJ · mol–1and –25.77 J · mol–1 · K–1, which indicated that hydrogen bonding forces play major role in the interaction between TL and BHb. The alternations of protein secondary structure in the presence of TL were determined by CD spectroscopy. The results revealed that the content of α-helix was decreased from 51.85% in free BHb to 48.14% in TL–BHb complex. Molecular modeling study and our experimental results both showed that the binding mode of TL–BHb complex could be attributed to hydrogen bonding and hydrophobic interaction.

EVIDENCE FOR SELF-ASSOCIATION OF PROTHROMBIN FRAGMENT 1 IN THE ABSENCE OF CALCIUM IONS: IMPLICATIONS FOR THE INTERPRETATION OF COOPERATIVITY OF CALCIUM BINDING

1987 ◽  
Author(s):  
Craig M Jackson ◽  
George M Brenckle ◽  
Philip J Hogg ◽  
Donald J Winzor
Keyword(s):  
Calcium Binding ◽  
Metal Ion ◽  
Equilibrium Constants ◽  
Binding Constants ◽  
Sedimentation Equilibrium ◽  
Equilibrium Studies ◽  
Prothrombin Fragment ◽  
Preferential Binding ◽  
Exclusion Chromatography ◽  
Self Association

The necessity to consider the binding of metal ion by prothrombin and its fragment 1 in terms of two entirely different mechanistic models has been removed. Cooperativity of Ca+T binding to prothrombin and prothrombin fragment 1 may reflect isomerization and/or self association of the protein. Sedimentation equilibrium studies have demonstrated that both prothrombin and its fragment 1 reversibly dimerize in the absence of Ca++.Based on this pre-existing equilibrium, a model for preferential binding of Ca++ to the dimer has been found capable of accounting quantitatively for the interaction of Ca2+ with fragment 1. This phenomenon is described by the relationship r ={pkA[A][S] (1 + kA[S])p-1 + qkc X [A]2[S](1 + kc [S])q-1}/[A] in which X (1,000 M-1) denotes the association constant for the pre-existing monomer-dimer equilibrium, and p, kA (10, 100 M-1) and q, kc (20, 2,000 M-1) are the respective stoichiometries and intrinsic binding constants for the interactions of Ca++ with monomeric and dimeric fragment 1, A. There is also evidence from exclusion chromatography and sedimentation velocity experiments that different isomeric states of prothrombin and its fragment 1 exist. It is therefore proposed that a model based on co-existence of isomeric and dimeric protein states will enable quantitative differences in the Ca++-mediated responses of fragment 1 and prothrombin to be rationalized solely in terms of differences in the relative magnitudes of equilibrium constants for the same interactions in the two systems.

Experimental Investigation of Thermodynamics, Kinetics, and Equilibrium of Nickel Ion Removal from Wastewater Using Zinc Oxide Nanoparticles as the Adsorbent

2020 ◽  
Vol 38 (7A) ◽  
pp. 1047-1061
Author(s):  
Shurooq T. Remedhan
Keyword(s):  
Zinc Oxide ◽  
Aqueous Solutions ◽  
Zno Nanoparticles ◽  
Metal Ion ◽  
Entropy Change ◽  
Ion Concentration ◽  
Standard Entropy ◽  
Nickel Ion ◽  
X Ray ◽  
Operation Conditions

In the present study commercial zinc oxide (ZnO) nanoparticles in the size of 30 nm were utilized as an adsorbent for the removal of Ni (II) ion from synthetic waste aqueous solution. Adsorption capacity of ZnO for removing Ni (II) ions from aqueous solutions was measured at different pH, adsorbent dose, contact time, temperature and metal ion concentration. Moreover,  adsorption isotherms, kinetics and thermodynamics were studied to understand  the  nature  and  mechanism  of  adsorption. ZnO nanoparticles were characterized by X-Ray diffract analysis(XRD),Fourier Transform Infrared Spectroscopy(FT-IR), scanning electron microscopy (SEM),energy dispersive X-ray spectroscopy(EDS) and Brunauer-Emmett-Teller (BET). The maximum amount of Ni (II) removal were found to be (98.71%) from its aqueous solutions by ZnO nanoparticles which was achieved at the evaluated optimum conditions. The experimental kinetic data were examined using the pseudo-second-order rate model with a high regression coefficient. The adsorption isotherm was well described to the equilibrium data by Langmuir isotherm model (R2=0.990). In addition, the calculated thermodynamic parameters, the standard Gibbs free energy ΔGo, the change in standard enthalpy ∆Ho and the standard entropy change ∆So showed that the adsorption of Ni (II) onto ZnO nanoparticles was feasible, endothermic and spontaneous respectively. The experimental results suggest that ZnO nanoparticles can be used as a potential adsorbent for the efficient removal of heavy metals from aqueous solutions than any other adsorbent because an economical and low- consumption energy due to its ambient operation conditions.

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