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).

Effect of Different Substituents on Uracil and its 2-Hydroxy-4-oxo Enol Tautomer – A Theoretical Study

2008 ◽  
Vol 63 (10-11) ◽  
pp. 693-702
Author(s):  
Hamzeh S. M. Al-Omari
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Theoretical Study ◽  
Equilibrium Constants ◽  
Semiempirical Method ◽  
Forward Direction ◽  
Heat Of Formation ◽  
Geometrical Parameters ◽  
Homo And Lumo ◽  
Enol Tautomer

The uracil/2-hydroxy-4-oxo uracil tautomeric system was studied by employing the MNDO semiempirical method for the calculations. The uracil structure was found to be energetically favourable as indicated by the calculated heat of formation, the Gibbs free energy, the HOMO and LUMO energies, and charges. The substitution by F, OH, NH2, CH3, and BH2 at the carbon-6 position was found to affect the geometrical parameters of the substituted molecules. All of the substituents were found to shift the equilibrium in forward direction compared to the unsubstituted tautomeric pair as indicated by the calculated values for the equilibrium constants.

scholarly journals A Theoretical Study of Substituted Cyclobutanones and Their Enols

2004 ◽  
Vol 59 (11) ◽  
pp. 838-844
Author(s):  
Mohammad I. Sway ◽  
Iyad D. Al-Shawabkeh ◽  
Salim M. Khalil
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Theoretical Study ◽  
Theoretical Calculations ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Electron Densities ◽  
Complete Optimization ◽  
Electron Withdrawing Substituents

MINDO-Forces calculations have been performed with complete optimization of the geometry on cyclobutanone and its enol counterpart, perfluorination of cyclobutanones and enol counterparts, and X-cycolobutanones and their X-enols, where X is NO2, CF3, CN, OH, NH2 and F. It was found that ketone is more stable than its enol counterpart. Perfluorination destabilizes ketone on the expense of enol. These results agree with experimental and theoretical calculations. Electron releasing substituents (NH2, OH, F) stabilize cyclobutanone, while electron withdrawing substituents (CF3, NO2) destabilize it. CN substituents have almost no effect on the stabilization of this keto-enol system. Geometrical parameters, heats of formation, electron densities and Gibbs free energy are reported

A Theoretical Study of Substituted Stepwise Fluorinated Cyclopropanone Keto-Enol System

2003 ◽  
Vol 58 (12) ◽  
pp. 749-755
Author(s):  
Abdullah El-Alali ◽  
Ali A. Marashdeh ◽  
Salim M. Khalil
Keyword(s):  
Theoretical Study ◽  
Dipole Moments ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Free Energies ◽  
Isodesmic Reactions ◽  
Orbital Energies ◽  
Substantial Concentration ◽  
Homo Lumo ◽  
Complete Optimization

MINDO-Forces calculations have been performed with complete optimization of the geometries on stepwise fluorinated cyclopropanones and their enols. Increase in the number of fluorine atoms causes destabilization of cyclopropanone. Perfluorinated enol was found to be present in substantial concentration, as was mentioned in previous work. This is supported by calculations of Gibbs free energies and isodesmic reactions. Geometrical parameters, heats of formation, electron densities, dipole moments and orbital energies (HOMO-LUMO) are reported.

A Theoretical Study of Fulvene Radical Anions

1991 ◽  
Vol 46 (3) ◽  
pp. 247-255 ◽  
Author(s):  
Salim M. Khalil ◽  
Hayfa M. Jarjis
Keyword(s):  
Theoretical Study ◽  
Dipole Moments ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Radical Anions ◽  
Optimization Of Geometry ◽  
Stabilization Effect ◽  
Complete Optimization ◽  
Spin Densities

AbstractMINDO-Forces calculations have been performed, with complete optimization of geometry on fulvene and X-fulvene radical anions, where X is OH, NH2, CH3, NO,2 CN, F, dimethyl and cyclopropyl. A twisted structure with angle 5° was found for fulvene anion. All substituents are stabilizing. The stabilization effect is more pronounced in the case of NO2, and very weak in the case of CH3. It was found that the substituents CH3 and CN show amphielectronic behaviour. Geometrical parameters, heats of formation, dipole moments, electron and spin densities are reported

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>

A Theoretical Study of Monosubstituted Fulvenes

1990 ◽  
Vol 45 (6) ◽  
pp. 799-806 ◽  
Author(s):  
Hayfa M. Jarjis ◽  
Salim M. Khalil
Keyword(s):  
Dipole Moment ◽  
Double Bond ◽  
Theoretical Study ◽  
Heats Of Formation ◽  
Exocyclic Double Bond ◽  
Geometrical Parameters ◽  
Electron Densities ◽  
Orbital Energies ◽  
Optimization Of Geometry ◽  
Complete Optimization

AbstractMINDO-forces calculations have been done after complete optimization of geometry on X-monosubstituted fulvenes, where X is OH, NH2 , CH3, NO2, CN, F, dimethyl and cyclopropyl. It was found that all the substituents are stabilizing. The electron releasing substituents increase the dipole moment at the exocyclic double bond while the electron withdrawing ones increase the dipole moment at the endocyclic diene. Geometrical parameters, heats of formation, orbital energies and electron densities are reported.

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.

A Theoretical Study of Fulvene Radical Cations

1988 ◽  
Vol 43 (5) ◽  
pp. 485-493
Author(s):  
Salim M. Khalil
Keyword(s):  
Radical Cation ◽  
Theoretical Study ◽  
Dipole Moments ◽  
Radical Cations ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Electron Densities ◽  
Optimization Of Geometry ◽  
Complete Optimization

MINDO-Forces calculations have been performed, after complete optimization of geometry, on fulvene molecule, fulvene and X-fulvene radical cations, where X is OH, NH2, CH3, NO2, CN and F. A twisted structure with angle 5° was found for fulvene radical cation. The substituents OH, NH2, CH3, CN and F are stabilizing. NO2 is slightly stabilizing. Geometrical parameters, heats of formation, dipole moments and electron densities are reported.

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