scholarly journals Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1121
Author(s):  
Yuliya V. Kordonskaya ◽  
Vladimir I. Timofeev ◽  
Yulia A. Dyakova ◽  
Margarita A. Marchenkova ◽  
Yury V. Pisarevsky ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Change ◽  
Energy Change ◽  
Free Energies ◽  
Dimer Formation ◽  
Dimer Model ◽  
Crystallization Solution ◽  
Favorable State ◽  
Chemical Conditions ◽  
Physical And Chemical

We use the MM/GBSA method to calculate the free energies of dimer formation by binding two monomers with different combinations of precipitant ions, both embedded in the structure of monomers and in the crystallization solution. It shows that the largest difference in free energy values corresponds to the most accurate dimer model, which considers all precipitant ions in their structure. In addition, it shows that in the absence of precipitant ions in the solution of lysozyme molecules, a monomer is a more energetically favorable state.

scholarly journals Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations

2018 ◽  
Author(s):  
Louis G. Smith ◽  
Zhen Tan ◽  
Aleksandar Spasic ◽  
Debapratim Dutta ◽  
Leslie A. Salas-Estrada ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Simulations ◽  
Umbrella Sampling ◽  
Reaction Coordinate ◽  
Free Energy Change ◽  
Energy Change ◽  
Random Coil ◽  
Free Energies ◽  
Rna Hairpins ◽  
Rna Hairpin

AbstractThis study describes a comparison between melts and simulated stabilities of the same RNAs that could be used to benchmark RNA force fields, and potentially to determine future melt-ing experiments. Using umbrella sampling molecular simulations of three 12-nucleotide RNA hairpin stem loops, for which there are experimentally determined free energies of unfold-ing, we projected unfolding onto the reaction coordinate of end to end (5′ to 3′ hydroxyl oxygen) distance. We estimate the free energy change of the transition from the native con-formation to a fully extended conformation—the stretched state—with no hydrogen bonds between non-neighboring bases. Each simulation was performed four times using the AM-BER FF99+bsc0+χOL3 force field and each window, spaced at 1 Å intervals, was sampled for 1 μs, for a total of 552 μs of simulation. We compared differences in the simulated free energy changes to analogous differences in free energies from optical melting experiments using ther-modynamic cycles where the free energy change between stretched and random coil sequences is assumed to be sequence independent. The differences between experimental and simulated ΔΔG° are on average 1.00 ± 0.66 kcal/mol, which is chemically accurate and suggests analo-gous simulations could be used predictively. We also report a novel method to identify where replica free energies diverge along the reaction coordinate, thus indicating where additional sampling would most improve convergence. We conclude by discussing methods to more economically perform such simulations.

The enol content of simple carbonyl compounds: a thermochemical approach

1979 ◽  
Vol 57 (2) ◽  
pp. 240-248 ◽  
Author(s):  
J. Peter Guthrie ◽  
Patricia A. Cullimore
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Carbonyl Compounds ◽  
Free Energy Change ◽  
Energy Change ◽  
Free Energies ◽  
Enol Ethers ◽  
Free Energy Of Formation ◽  
Hydrolysis Of ◽  
Energy Of Formation

From the heats of hydrolysis of enol ethers, the heats of formation of the enol ethers, and thence the free energies of formation of the enol ethers in aqueous solution can be calculated. For this calculation it was necessary to determine the free energies of transfer from the gas phase to aqueous solution. By methods previously published it was possible to estimate the free energy change for the hypothetical hydrolysis reaction leading from the enol ether to the enol, which in turn made possible calculation of the free energy of formation of the enol. Finally the free energy change for enolization in aqueous solution could be calculated using the known free energy of formation of the corresponding keto tautomer. In this way the following were determined: carbonyl compound, pKenol = −log ([enol]/[keto]): acetaldehyde, 5.3; propionaldehyde, 3.9; isobutyraldehyde, 2.8; acetone, 7.2; 2-butanone, 8.3; 3-pentanone, 7.8; cyclopentanone, 7.2; cyclohexanone, 5.7; acetophenone, 6.7.

Modeling of Electrical Resistivity Evolution Using Free Energy Analysis for NiTi Shape Memory Alloy Wires

2011 ◽  
Vol 311-313 ◽  
pp. 2282-2285
Author(s):  
Jian Jun Zhang
Keyword(s):  
Electrical Resistivity ◽  
Free Energy ◽  
Shape Memory Alloy ◽  
Shape Memory ◽  
Free Energy Change ◽  
Energy Change ◽  
Niti Shape Memory Alloy ◽  
Scanning Calorimetry ◽  
Proposed Model ◽  
Free Energy Analysis

This paper presents a transformation kinetics model of NiTi shape memory alloy (SMA) wires based on electrical resistivity (ER) derivative study under the assumption that the derivative of electrical resistivity with respect to temperature is in linear relationship with the derivative of free energy change with respect to temperature. Free energy change and electrical resistivity properties of SMA are analyzed based on differential scanning calorimetry (DSC) experiments during phase transformation. The simulated evolution of electrical resistivity during thermomechanical transformation is presented using the proposed model.

Adsorption of Liquids and Swelling of Wood. Part VI. Saturated Amounts and Some Thermodynamic Values of Adsorption

Holzforschung ◽  
2002 ◽  
Vol 56 (1) ◽  
pp. 91-97
Author(s):  
Kei Morisato ◽  
Yutaka Ishimaru ◽  
Hiroyuki Urakami
Keyword(s):  
Free Energy ◽  
Standard Free Energy ◽  
Molecular Size ◽  
Free Energy Change ◽  
Energy Change ◽  
Multilayer Adsorption ◽  
Monolayer Adsorption ◽  
Wood Part ◽  
Cohesive Interaction

Summary To understand the swelling phenomenon of wood in liquids,the saturated amount of adsorption of liquids onto wood and the standard free energy changes of the adsorption were determined. The saturated amount of adsorption obtained by regression for several liquids decreased with increasing molecular size of the solvents. The mechanism of wood swelling is discussed systematically taking all the liquids examined in previous experiments into account. Since methanol molecules require more energy for release from cohesive interactions within bulk liquids in the adsorption onto pre-swollen wood,the values of free energy change of adsorption for methanol were lower than the values for acetone,although the relative swelling with methanol was higher. These results suggest that although the cohesive interaction within the bulk liquids reduces adsorptivity,the phenomenon of wood swelling is influenced not only by monolayer adsorption but also by multilayer adsorption. Therefore,the cohesive interaction within the bulk liquids reduces adsorptivity but enhances the condensation which strongly influences the swelling of wood.

scholarly journals REMOVAL OF CU (II) FROM DYE EFFLUENT USING NATURAL AND PHOSPHATE-MODIFIED NIGERIAN KAOLINITE CLAY

2019 ◽  
Vol 7 (8) ◽  
pp. 402-414
Author(s):  
S. C. Olu ◽  
P. E. Dim ◽  
J. O. Okafor
Keyword(s):  
Free Energy ◽  
Metal Ion ◽  
Fourier Transforms ◽  
Lattice Structure ◽  
Enthalpy Change ◽  
Free Energy Change ◽  
Energy Change ◽  
Order Model ◽  
Acid Modification ◽  
Kaolinite Clay

This study indicates kaolinite clay as an effective adsorbent for the uptake of Cu (II) from wastewater. The adsorption process was studied with variation of time, temperature and adsorbent dosage at the effluent pH of 6. X-ray diffraction (XRD), Fourier transforms infrared spectroscopy (FTIR), Brunauer Emmett and Teller (BET) and Scanning electron microscopy (SEM) were used to characterize the adsorbents. XRD spectra showed that modification with KH2PO4 did not significantly change the crystal spacing on the lattice structure of the clay mineral; however, there were shifts in the intensity of the peaks for the modified kaolinite clay. The FTIR spectra showed that certain functional groups are responsible for binding the metal ions from solution. SEM indicated an increase in the porosity of the modified adsorbent as compared with the unmodified kaolinite, which enhances metal ion adsorption on modified kaolinite clay. The BET indicate that acid modification increased the surface area and total pore volume of the kaolinite clay. The kinetic study revealed that the pseudo-first-order model fitted poorly to the equilibrium data, however, the pseudo-second-order model had a good fit for all reaction time at different initial concentrations. The mechanism of the sorption process was evaluated using thermodynamic properties such as enthalpy change (ΔH), Gibbs free energy change (ΔG), and entropy change (ΔS), which were evaluated using Van’t Hoff equations. The negative values of free energy change (ΔG), suggests spontaneity and feasibility of the process. The positive values of enthalpy change (ΔH) indicate endothermic nature of the process.

scholarly journals Kinetic and Thermodynamic Studies of Lysozyme Adsorption on Cibacron Blue F3GA Dye-Ligand Immobilized on Aminated Nanofiber Membrane

Membranes ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 963
Author(s):  
Ai Hsin ◽  
Su-Chun How ◽  
Steven S.-S. Wang ◽  
Chien Wei Ooi ◽  
Chen-Yaw Chiu ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Change ◽  
Energy Change ◽  
Nanofiber Membrane ◽  
Cibacron Blue ◽  
Pseudo Second Order ◽  
Nanofiber Membranes ◽  
Lysozyme Adsorption ◽  
Cibacron Blue F3ga ◽  
Pan Nanofiber

The polyacrylonitrile (PAN) nanofiber membrane was prepared by the electrospinning technique. The nitrile group on the PAN nanofiber surface was oxidized to carboxyl group by alkaline hydrolysis. The carboxylic group on the membrane surface was then converted to dye affinity membrane through reaction with ethylenediamine (EDA) and Cibacron Blue F3GA, sequentially. The adsorption characteristics of lysozyme onto the dye ligand affinity nanofiber membrane (namely P-EDA-Dye) were investigated under various conditions (e.g., adsorption pH, EDA coupling concentration, lysozyme concentration, ionic strength, and temperature). Optimum experimental parameters were determined to be pH 7.5, a coupling concentration of EDA 40 μmol/mL, and an immobilization density of dye 267.19 mg/g membrane. To understand the mechanism of adsorption and possible rate controlling steps, a pseudo first-order, a pseudo second-order, and the Elovich models were first used to describe the experimental kinetic data. Equilibrium isotherms for the adsorption of lysozyme onto P-EDA-Dye nanofiber membrane were determined experimentally in this work. Our kinetic analysis on the adsorption of lysozyme onto P-EDA-Dye nanofiber membranes revealed that the pseudo second-order rate equation was favorable. The experimental data were satisfactorily fitted by the Langmuir isotherm model, and the thermodynamic parameters including the free energy change, enthalpy change, and entropy change of adsorption were also determined accordingly. Our results indicated that the free energy change had a negative value, suggesting that the adsorption process occurred spontaneously. Moreover, after five cycles of reuse, P-EDA-Dye nanofiber membranes still showed promising efficiency of lysozyme adsorption.

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