caa a22 4500 60551156X CHVBK 20210128100651.0 cr unu---uuuuu 210128e20150701xx s 000 0 eng 10.1007/s00894-015-2731-0 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2731-0 Yang Pei-Kun Department of Biomedical Engineering, College of Medicine, I-SHOU University, 82445, Kaohsiung, Taiwan, Republic of China aut Incorporating excluded solvent volume and physical dipoles for computing solvation free energy [Elektronische Daten] [Pei-Kun Yang] 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. Springer-Verlag Berlin Heidelberg, 2015 Born equation nationallicence First coordination shell nationallicence Molecular dynamic simulations nationallicence TIP3P water model nationallicence Journal of Molecular Modeling Springer Berlin Heidelberg 21/7(2015-07-01), 1-19 1610-2940 21:7<1 2015 21 894 https://doi.org/10.1007/s00894-015-2731-0 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2731-0 text/html Onlinezugriff via DOI NATIONALLICENCE 100 1- Yang Pei-Kun Department of Biomedical Engineering, College of Medicine, I-SHOU University, 82445, Kaohsiung, Taiwan, Republic of China aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/7(2015-07-01), 1-19 1610-2940 21:7<1 2015 21 894