Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The potentials of mean force (PMFs) re determined for systems forming cationic and anionic homocomplexes composed of acetic acid, phenol, isopropylamine, n-butylamine, imidazole, and 4(5)-methylimidazole, and their conjugated bases or acids, respectively, in three solvents with different polarity and hydrogen-bonding propensity: acetonitrile (AN), dimethyl sulfoxide (DMSO), and water (H 2 O). For each pair and each solvent a series of umbrella-sampling molecular dynamics simulations with the AMBER force field, explicit solvent, and counterions added to maintain a zero net charge of a system re carried out and the PMF was calculated by using the ighted Histogram Analysis Method (WHAM). Subsequently, homoconjugation-equilibrium constants re calculated by numerical integration of the respective PMF profiles. In all cases but imidazole stable homocomplexes re found to form in solution, which was manifested as the presence of contact minima corresponding to hydrogen-bonded species in the PMF curves. The calculated homoconjugation constants re found to be greater for complexes with the OHO bridge (acetic acid and phenol) than with the NHN bridge and they re found to decrease with increasing polarity and hydrogen-bonding propensity of the solvent (i.e., in the series AN > DMSO > H 2 O), both facts being in agreement with the available experimental data. It was also found that interactions with counterions are manifested as the broadening of the contact minimum or appearance of additional minima in the PMF profiles of the acetic acid-acetate, phenol/ phenolate system in acetonitrile, and the 4(5)-methylimidazole/4(5)-methylimidzole cation conjugated base system in dimethyl sulfoxide.
['Joanna Makowska', 'Mariusz Makowski', 'Adam Liwo', 'Lech Chmurzyński']
I am writing a research paper on a idea Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force.
[{"from": "human", "value": "I am writing a research paper on a idea Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force."}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The potentials of mean force (PMFs) re determined for systems forming cationic and anionic homocomplexes composed of acetic acid, phenol, isopropylamine, n-butylamine, imidazole, and 4(5)-methylimidazole, and their conjugated bases or acids, respectively, in three solvents with different polarity and hydrogen-bonding propensity: acetonitrile (AN), dimethyl sulfoxide (DMSO), and water (H 2 O). For each pair and each solvent a series of umbrella-sampling molecular dynamics simulations with the AMBER force field, explicit solvent, and counterions added to maintain a zero net charge of a system re carried out and the PMF was calculated by using the ighted Histogram Analysis Method (WHAM). Subsequently, homoconjugation-equilibrium constants re calculated by numerical integration of the respective PMF profiles. In all cases but imidazole stable homocomplexes re found to form in solution, which was manifested as the presence of contact minima corresponding to hydrogen-bonded species in the PMF curves. The calculated homoconjugation constants re found to be greater for complexes with the OHO bridge (acetic acid and phenol) than with the NHN bridge and they re found to decrease with increasing polarity and hydrogen-bonding propensity of the solvent (i.e., in the series AN > DMSO > H 2 O), both facts being in agreement with the available experimental data. It was also found that interactions with counterions are manifested as the broadening of the contact minimum or appearance of additional minima in the PMF profiles of the acetic acid-acetate, phenol/ phenolate system in acetonitrile, and the 4(5)-methylimidazole/4(5)-methylimidzole cation conjugated base system in dimethyl sulfoxide."}]