Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration
The hydration of phosphate ions, an essential component of many biological molecules, is studied using all-atom molecular dynamics (MD) simulation and quantum chemical methods. MD simulations are carried out by employing a mean-field polarizable water model. A good linear correlation between the sel...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Liquids |
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| Online Access: | https://www.mdpi.com/2673-8015/3/3/18 |
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| author | Sandeep Verma Arup Kumar Pathak |
| author_facet | Sandeep Verma Arup Kumar Pathak |
| author_sort | Sandeep Verma |
| collection | DOAJ |
| description | The hydration of phosphate ions, an essential component of many biological molecules, is studied using all-atom molecular dynamics (MD) simulation and quantum chemical methods. MD simulations are carried out by employing a mean-field polarizable water model. A good linear correlation between the self-diffusion coefficient and phosphate anion concentration is ascertained from the computed mean-square displacement (MSD) profiles. The HB dynamics of the hydration of the phosphate anion is evaluated from the time-dependent autocorrelation function C<i><sub>HB</sub></i>(t) and is determined to be slightly faster for the phosphate–anion system as compared to that of the water–water system at room temperature. The coordination number (CN) of the phosphate ion is found to be 15.9 at 298 K with 0.05 M phosphate ion concentration. The average CN is also calculated to be 15.6 for the same system by employing non-equilibrium MD simulation, namely, the well-tempered meta-dynamics method. A full geometry optimization of the PO<sub>4</sub><sup>3−</sup>·16H<sub>2</sub>O cluster is investigated at the ωB97X-D/aug-cc-pVTZ level of theory, and the hydration of the phosphate anion is observed to have both singly and doubly bonded anion–water hydrogen bonds and inter-water hydrogen bonds in a range between 0.169–0.201 nm and 0.192–0.215 nm, respectively. Modified Stokes–Einstein relation is used to calculate the conductivity of the phosphate ion and is found to be in good agreement with the experimentally observed value. |
| first_indexed | 2024-03-10T22:32:21Z |
| format | Article |
| id | doaj.art-c133f55cc23f4560ac4e602392723c3a |
| institution | Directory Open Access Journal |
| issn | 2673-8015 |
| language | English |
| last_indexed | 2024-03-10T22:32:21Z |
| publishDate | 2023-06-01 |
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| series | Liquids |
| spelling | doaj.art-c133f55cc23f4560ac4e602392723c3a2023-11-19T11:38:30ZengMDPI AGLiquids2673-80152023-06-013327828710.3390/liquids3030018Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and ConcentrationSandeep Verma0Arup Kumar Pathak1Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, IndiaTheoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, IndiaThe hydration of phosphate ions, an essential component of many biological molecules, is studied using all-atom molecular dynamics (MD) simulation and quantum chemical methods. MD simulations are carried out by employing a mean-field polarizable water model. A good linear correlation between the self-diffusion coefficient and phosphate anion concentration is ascertained from the computed mean-square displacement (MSD) profiles. The HB dynamics of the hydration of the phosphate anion is evaluated from the time-dependent autocorrelation function C<i><sub>HB</sub></i>(t) and is determined to be slightly faster for the phosphate–anion system as compared to that of the water–water system at room temperature. The coordination number (CN) of the phosphate ion is found to be 15.9 at 298 K with 0.05 M phosphate ion concentration. The average CN is also calculated to be 15.6 for the same system by employing non-equilibrium MD simulation, namely, the well-tempered meta-dynamics method. A full geometry optimization of the PO<sub>4</sub><sup>3−</sup>·16H<sub>2</sub>O cluster is investigated at the ωB97X-D/aug-cc-pVTZ level of theory, and the hydration of the phosphate anion is observed to have both singly and doubly bonded anion–water hydrogen bonds and inter-water hydrogen bonds in a range between 0.169–0.201 nm and 0.192–0.215 nm, respectively. Modified Stokes–Einstein relation is used to calculate the conductivity of the phosphate ion and is found to be in good agreement with the experimentally observed value.https://www.mdpi.com/2673-8015/3/3/18hydrationmolecular dynamicselectronic structuremean square displacementshydrogen bondingsolvent-berg model |
| spellingShingle | Sandeep Verma Arup Kumar Pathak Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration Liquids hydration molecular dynamics electronic structure mean square displacements hydrogen bonding solvent-berg model |
| title | Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration |
| title_full | Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration |
| title_fullStr | Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration |
| title_full_unstemmed | Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration |
| title_short | Hydration of Phosphate Ion in Polarizable Water: Effect of Temperature and Concentration |
| title_sort | hydration of phosphate ion in polarizable water effect of temperature and concentration |
| topic | hydration molecular dynamics electronic structure mean square displacements hydrogen bonding solvent-berg model |
| url | https://www.mdpi.com/2673-8015/3/3/18 |
| work_keys_str_mv | AT sandeepverma hydrationofphosphateioninpolarizablewatereffectoftemperatureandconcentration AT arupkumarpathak hydrationofphosphateioninpolarizablewatereffectoftemperatureandconcentration |