Incorporating excluded solvent volume and physical dipoles for computing solvation free energy
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| 024 | 7 | 0 | |a 10.1007/s00894-015-2731-0 |2 doi |
| 035 | |a (NATIONALLICENCE)springer-10.1007/s00894-015-2731-0 | ||
| 100 | 1 | |a Yang |D Pei-Kun |u Department of Biomedical Engineering, College of Medicine, I-SHOU University, 82445, Kaohsiung, Taiwan, Republic of China |4 aut | |
| 245 | 1 | 0 | |a Incorporating excluded solvent volume and physical dipoles for computing solvation free energy |h [Elektronische Daten] |c [Pei-Kun Yang] |
| 520 | 3 | |a The solvation free energy described using the Born equation depends on the solute charge, solute radius, and solvent dielectric constant. However, the dielectric polarization derived from Gauss's law used in the Born equation differs from that obtained from molecular dynamics simulations. Therefore, the adjustment of Born radii is insufficient for fitting the solvation free energy to various solute conformations. In order to mimic the dielectric polarization surrounding a solute in molecular dynamics simulations, the water molecule in the first coordination shell is modeled as a physical dipole in a van der Waals sphere, and the intermediate water is treated as a bulk solvent. The electric dipole of the first-shell water is modeled as positive and negative surface charge layers with fixed charge magnitudes, but with variable separation distance as derived from the distributions of hydrogen and oxygen atoms of water dictated by their orientational distribution functions. An equation that describes the solvation free energy of ions using this solvent scheme with a TIP3P water model is derived, and the values of the solvation free energies of ions estimated from this derived equation are found to be similar to those obtained from the experimental data. | |
| 540 | |a Springer-Verlag Berlin Heidelberg, 2015 | ||
| 690 | 7 | |a Born equation |2 nationallicence | |
| 690 | 7 | |a First coordination shell |2 nationallicence | |
| 690 | 7 | |a Molecular dynamic simulations |2 nationallicence | |
| 690 | 7 | |a TIP3P water model |2 nationallicence | |
| 773 | 0 | |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/7(2015-07-01), 1-19 |x 1610-2940 |q 21:7<1 |1 2015 |2 21 |o 894 | |
| 856 | 4 | 0 | |u https://doi.org/10.1007/s00894-015-2731-0 |q text/html |z Onlinezugriff via DOI |
| 898 | |a BK010053 |b XK010053 |c XK010000 | ||
| 900 | 7 | |a Metadata rights reserved |b Springer special CC-BY-NC licence |2 nationallicence | |
| 908 | |D 1 |a research-article |2 jats | ||
| 949 | |B NATIONALLICENCE |F NATIONALLICENCE |b NL-springer | ||
| 950 | |B NATIONALLICENCE |P 856 |E 40 |u https://doi.org/10.1007/s00894-015-2731-0 |q text/html |z Onlinezugriff via DOI | ||
| 950 | |B NATIONALLICENCE |P 100 |E 1- |a Yang |D Pei-Kun |u Department of Biomedical Engineering, College of Medicine, I-SHOU University, 82445, Kaohsiung, Taiwan, Republic of China |4 aut | ||
| 950 | |B NATIONALLICENCE |P 773 |E 0- |t Journal of Molecular Modeling |d Springer Berlin Heidelberg |g 21/7(2015-07-01), 1-19 |x 1610-2940 |q 21:7<1 |1 2015 |2 21 |o 894 | ||