The Formulation of Chemical Potentials and Free Energy Changes in Biochemical Reactions

2021 ◽  
Author(s):  
William Cannon ◽  
Lionel Raff
Keyword(s):  
Free Energy ◽  
Free Energies ◽  
Biochemical Reactions ◽  
Chemical Potentials

In 1994, an IUBMB-IUPAC joint committee recommended a revised formulation for standard chemical potentials and reaction free energies motivated by the fact that, in biochemistry, the reactants and products often...

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

Molecular orientation of liquid aliphatic hydrocarbons on the surface and at the interface with water

1989 ◽  
Vol 54 (12) ◽  
pp. 3171-3186 ◽  
Author(s):  
Jan Kloubek
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Molecular Orientation ◽  
Phase Changes ◽  
Aliphatic Hydrocarbons ◽  
Water Molecules ◽  
Free Energies ◽  
Dispersion Component ◽  
System Water ◽  
Orientation Of Molecules

The validity of the Fowkes theory for the interaction of dispersion forces at interfaces was inspected for the system water-aliphatic hydrocarbons with 5 to 16 C atoms. The obtained results lead to the conclusion that the hydrocarbon molecules cannot lie in a parallel position or be randomly arranged on the surface but that orientation of molecules increases there the ration of CH3 to CH2 groups with respect to that in the bulk. This ratio is changed at the interface with water so that the surface free energy of the hydrocarbon, γH, rises to a higher value, γ’H, which is effective in the interaction with water molecules. Not only the orientation of molecules depends on the adjoining phase and on the temperature but also the density of hydrocarbons on the surface of the liquid phase changes. It is lower than in the bulk and at the interface with water. Moreover, the volume occupied by the CH3 group increases on the surface more than that of the CH2 group. The dispersion component of the surface free energy of water, γdW = 19.09 mJ/m2, the non-dispersion component, γnW = 53.66 mJ/m2, and the surface free energies of the CH2 and CH3 groups, γ(CH2) = 32.94 mJ/m2 and γ(CH3) = 15.87 mJ/m2, were determined at 20 °C. The dependence of these values on the temperature in the range 15-40 °C was also evaluated.

Chemical equilibrium and chemical kinetics

2018 ◽  
Author(s):  
Dennis Sherwood ◽  
Paul Dalby
Keyword(s):  
Free Energy ◽  
Equilibrium Constant ◽  
Gibbs Free Energy ◽  
Chemical Kinetics ◽  
Chemical Equilibrium ◽  
First Principles ◽  
Effect Of Temperature ◽  
Total System ◽  
Free Energies

Building on the previous chapter, this chapter examines gas phase chemical equilibrium, and the equilibrium constant. This chapter takes a rigorous, yet very clear, ‘first principles’ approach, expressing the total Gibbs free energy of a reaction mixture at any time as the sum of the instantaneous Gibbs free energies of each component, as expressed in terms of the extent-of-reaction. The equilibrium reaction mixture is then defined as the point at which the total system Gibbs free energy is a minimum, from which concepts such as the equilibrium constant emerge. The chapter also explores the temperature dependence of equilibrium, this being one example of Le Chatelier’s principle. Finally, the chapter links thermodynamics to chemical kinetics by showing how the equilibrium constant is the ratio of the forward and backward rate constants. We also introduce the Arrhenius equation, closing with a discussion of the overall effect of temperature on chemical equilibrium.

scholarly journals Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Germano Heinzelmann ◽  
Michael K. Gilson
Keyword(s):  
Free Energy ◽  
Early Stage ◽  
Binding Free Energy ◽  
Low Cost ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Drug Candidates ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

AbstractAbsolute binding free energy calculations with explicit solvent molecular simulations can provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to find new drug candidates. However, these calculations can be complex to implement and perform. Here, we introduce the software BAT.py, a Python tool that invokes the AMBER simulation package to automate the calculation of binding free energies for a protein with a series of ligands. The software supports the attach-pull-release (APR) and double decoupling (DD) binding free energy methods, as well as the simultaneous decoupling-recoupling (SDR) method, a variant of double decoupling that avoids numerical artifacts associated with charged ligands. We report encouraging initial test applications of this software both to re-rank docked poses and to estimate overall binding free energies. We also show that it is practical to carry out these calculations cheaply by using graphical processing units in common machines that can be built for this purpose. The combination of automation and low cost positions this procedure to be applied in a relatively high-throughput mode and thus stands to enable new applications in early-stage drug discovery.

scholarly journals The bulk, surface and corner free energies of the anisotropic triangular Ising model

2020 ◽  
Vol 476 (2234) ◽  
pp. 20190713
Author(s):  
Rodney J. Baxter
Keyword(s):  
Free Energy ◽  
Ising Model ◽  
Partition Function ◽  
Temperature Series ◽  
Isotropic Case ◽  
Series Expansions ◽  
Exact Results ◽  
Free Energies ◽  
Bulk Surface ◽  
Bulk Free Energy

We consider the anisotropic Ising model on the triangular lattice with finite boundaries, and use Kaufman’s spinor method to calculate low-temperature series expansions for the partition function to high order. From these, we can obtain 108-term series expansions for the bulk, surface and corner free energies. We extrapolate these to all terms and thereby conjecture the exact results for each. Our results agree with the exactly known bulk-free energy and with Cardy and Peschel’s conformal invariance predictions for the dominant behaviour at criticality. For the isotropic case, they also agree with Vernier and Jacobsen’s conjecture for the 60 ° corners.

scholarly journals Use of scaled-particle theory in the assessment of the Ph4As+/Ph4B− assumption for single ions

1979 ◽  
Vol 57 (1) ◽  
pp. 71-76 ◽  
Author(s):  
Michael H. Abraham ◽  
Asadollah Nasehzadeh
Keyword(s):  
Free Energy ◽  
Recent Work ◽  
Scaled Particle Theory ◽  
Cavity Formation ◽  
Energy Term ◽  
Free Energies ◽  
Particle Theory ◽  
Novel Method ◽  
Energy Of Interaction ◽  
Solvent Molecules

A novel method for the assessment of the Ph4As+/Ph4B− assumption for free energies of transfer of single ions has recently been suggested by Treiner, and used by him to deduce that the assumption is not valid for transfers between water, propylene carbonate, sulpholane, dimethylsulphoxide, N-methyl-2-pyrrolidone, and perhaps also dimethylformamide. The basis of the method is the estimation of the free energy of cavity formation by scaled-particle theory, together with the hypothesis that the free energy of interaction of Ph4As+ (or Ph4B−) with solvent molecules is the same in all solvents, ΔGt0(int) = 0. It is shown in the present paper that (a) whether or not the Ph4As+/Ph4B− assumption applies to transfer to a given solvent depends on which other solvent is taken as the reference solvent in Treiner's method, (b) the calculation of the cavity free energy term by scaled-particle theory and by the theory of Sinanoglu – Reisse – Moura Ramos (SRMR) yields values so different that the method cannot be considered reliable, (c) the calculation of cavity enthalpies and entropies for Ph4As+ or Ph4B− by scaled-particle theory yields results that are chemically not reasonable, (d) the hypothesis that ΔGt0(int) = 0 conflicts with SRMR theory, and (e) the conclusions reached by Treiner are not in accord with recent work that in general supports the Ph4As+/Ph4B− assumption for solvents that are rejected by Treiner.

scholarly journals Calculating free energies of organic molecules on insulating substrates

2017 ◽  
Vol 8 ◽  
pp. 667-674
Author(s):  
Julian Gaberle ◽  
David Z Gao ◽  
Alexander L Shluger
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Computational Cost ◽  
Potential Of Mean Force ◽  
Free Energies ◽  
Energy Profiles ◽  
Integration Techniques ◽  
Ring Structures ◽  
Anchoring Groups ◽  
Insulating Substrates

The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.

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