scholarly journals Thermodynamic Hydricity of Small Borane Clusters and Polyhedral closo-Boranes

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2920 ◽  
Author(s):  
Igor E. Golub ◽  
Oleg A. Filippov ◽  
Vasilisa A. Kulikova ◽  
Natalia V. Belkova ◽  
Lina M. Epstein ◽  
...  
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Solvent Effect ◽  
Coordination Number ◽  
Gibbs Free Energy ◽  
Boron Atom ◽  
Hydride Transfer ◽  
Dft Method ◽  
Lithium Salts

Thermodynamic hydricity (HDAMeCN) determined as Gibbs free energy (ΔG°[H]−) of the H− detachment reaction in acetonitrile (MeCN) was assessed for 144 small borane clusters (up to 5 boron atoms), polyhedral closo-boranes dianions [BnHn]2−, and their lithium salts Li2[BnHn] (n = 5–17) by DFT method [M06/6-311++G(d,p)] taking into account non-specific solvent effect (SMD model). Thermodynamic hydricity values of diborane B2H6 (HDAMeCN = 82.1 kcal/mol) and its dianion [B2H6]2− (HDAMeCN = 40.9 kcal/mol for Li2[B2H6]) can be selected as border points for the range of borane clusters’ reactivity. Borane clusters with HDAMeCN below 41 kcal/mol are strong hydride donors capable of reducing CO2 (HDAMeCN = 44 kcal/mol for HCO2−), whereas those with HDAMeCN over 82 kcal/mol, predominately neutral boranes, are weak hydride donors and less prone to hydride transfer than to proton transfer (e.g., B2H6, B4H10, B5H11, etc.). The HDAMeCN values of closo-boranes are found to directly depend on the coordination number of the boron atom from which hydride detachment and stabilization of quasi-borinium cation takes place. In general, the larger the coordination number (CN) of a boron atom, the lower the value of HDAMeCN.

Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Conformational Sampling ◽  
Atomic Charges ◽  
Loop Region ◽  
Energy Cycle ◽  
Dynamics Simulations ◽  
Aspartate Residue

Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br>

scholarly journals pKa Calculations of Asp26 in Thioredoxin with Alchemical Free Energy Simulations and Hirshfeld-I Atomic Charges

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Atomic Charges ◽  
Energy Cycle ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Aspartate Residue ◽  
Experimental Reference

Thioredoxin is a protein that has been used as model system by various computational methods to predict the pK<sub>a</sub> of aspartate residue Asp26 which is 3.5 units higher than the solvent exposed Asp20. Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between the two aspartic acid residues is calculated with the Amber99sb force field in alchemical transformation. The varying polarization of Asp20/26 in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 positions and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of polarization of both aspartate residues in the free energy cycle by the HI atomic charges improve the results from the nonpolarizable force field and reproduces the experimental reference delta pK<sub>a</sub> value.

Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Conformational Sampling ◽  
Atomic Charges ◽  
Loop Region ◽  
Energy Cycle ◽  
Dynamics Simulations ◽  
Aspartate Residue

Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br>

Theoretical Study of the Effect of Different α-Substituents on the Acetaldimine-Vinylamine Tautomeric System

2004 ◽  
Vol 59 (6) ◽  
pp. 382-388
Author(s):  
Hamzeh S. M. Al-Omari
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Gibbs Free Energy ◽  
Theoretical Study ◽  
Semiempirical Method ◽  
Heats Of Formation ◽  
Geometrical Parameters

The Acetaldimine-Vinylamine tautomeric system has been studied by employing the MNDO semiempirical method. The imine structure was found to be energetically favorable, as indicated by the calculated heats of formation, Gibbs free energy, LUMO and HOMO, and charges. The substitution of F, Cl, CN, CH3, CF3, NO2 and BH2 at the α-position was found to affect the geometrical parameters. F and Cl substituents are found to favor the imine formation, while CF3, NO2, CN2 and BH2 favor the amine formation. The proton transfer in this tautomeric system is found to be easier (ΔH = 5.224 kcal/mol) than that in the keto-enol tautomeric system (ΔH = 11.1 kcal/mol).

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.

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