The solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying LennardJones 6-12 and 10-12 perturbations to the hydrogen-bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 progr
Free energy calculations involving NH4+ in water
✍ Scribed by Stéphane Boudon; Georges Wipff
- Publisher
- John Wiley and Sons
- Year
- 1991
- Tongue
- English
- Weight
- 845 KB
- Volume
- 12
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
The analysis of the hydration of NH4+ and the estimation of relative or absolute free energies of hydration by means of Monte Carlo computer simulations using different 1-6-12 potential fcnctions is reported. Two electrostatic representations of NH,+ (used respectively by W. L. Jorgensen and P. A. Kollman) in conjunction with two common water models (TIP3P and TIP4P) are considered. A change in relative hydration free energies of 1.7 kcal/mol is found when the NH4+ models are mutated into each other in either TIP3P or TIP4P. The NH4+ -+ Na+ mutation in both solvent models leads to similar but overestimated relative hydration energies of about -28.7 kcal/mol. Similarly, the NH4+ annihilation significantly overestimates the absolute free energy of hydration. H TIP3P 0 H -0.400 -0.896 +0.474
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