Solvation free energy of light alkanes in polar and amphiphilic environments
Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids, which can be useful for interpreting the result...
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| Format: | Article |
| Language: | English |
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Department of Physics, Mahendra Morang Adarsh Multiple Campus, Tribhuvan University
2018-11-01
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| Series: | Bibechana |
| Subjects: | |
| Online Access: | https://www.nepjol.info/index.php/BIBECHANA/article/view/21136 |
| _version_ | 1797194073469091840 |
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| author | Sunil Pokharel Shyam Prakash Khanal N P Adhikari |
| author_facet | Sunil Pokharel Shyam Prakash Khanal N P Adhikari |
| author_sort | Sunil Pokharel |
| collection | DOAJ |
| description |
Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids, which can be useful for interpreting the results of certain biophysical experiments. In this work, we have estimated the solvation free energy for light alkane (methane, ethane, propane and n-butane) dissolved in water and methanol respectively over a broad range of temperatures, from 275 K to 375 K, using molecular dynamics simulations. The alkane (methane, ethane, propane and n-butane), and methanol molecules are described by the OPLS-AA (Optimized Potentials for Liquid Simulations-All Atom) potential, while water is modeled by TIP3P (Transferable Intermolecular Potential with 3-Points) model. We have used the free energy perturbation method (Bennett Acceptance Ratio (BAR) method) for the calculation of free energy of solvation. The estimated values of solvation free energy of alkane in the corresponding solvents agree well with the available experimental data.
BIBECHANA 16 (2019) 91-104
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| first_indexed | 2024-04-24T05:50:29Z |
| format | Article |
| id | doaj.art-bc2accac68294262827b4bf163f5c848 |
| institution | Directory Open Access Journal |
| issn | 2091-0762 2382-5340 |
| language | English |
| last_indexed | 2024-04-24T05:50:29Z |
| publishDate | 2018-11-01 |
| publisher | Department of Physics, Mahendra Morang Adarsh Multiple Campus, Tribhuvan University |
| record_format | Article |
| series | Bibechana |
| spelling | doaj.art-bc2accac68294262827b4bf163f5c8482024-04-23T13:05:18ZengDepartment of Physics, Mahendra Morang Adarsh Multiple Campus, Tribhuvan UniversityBibechana2091-07622382-53402018-11-011610.3126/bibechana.v16i0.2113616369Solvation free energy of light alkanes in polar and amphiphilic environmentsSunil Pokharel0Shyam Prakash Khanal1N P Adhikari2Central Department of Physics, Tribhuvan University, KirtipurCentral Department of Physics, Tribhuvan University, KirtipurCentral Department of Physics, Tribhuvan University, Kirtipur Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids, which can be useful for interpreting the results of certain biophysical experiments. In this work, we have estimated the solvation free energy for light alkane (methane, ethane, propane and n-butane) dissolved in water and methanol respectively over a broad range of temperatures, from 275 K to 375 K, using molecular dynamics simulations. The alkane (methane, ethane, propane and n-butane), and methanol molecules are described by the OPLS-AA (Optimized Potentials for Liquid Simulations-All Atom) potential, while water is modeled by TIP3P (Transferable Intermolecular Potential with 3-Points) model. We have used the free energy perturbation method (Bennett Acceptance Ratio (BAR) method) for the calculation of free energy of solvation. The estimated values of solvation free energy of alkane in the corresponding solvents agree well with the available experimental data. BIBECHANA 16 (2019) 91-104 https://www.nepjol.info/index.php/BIBECHANA/article/view/21136AlkaneFree EnergyMolecular dynamicsBAR |
| spellingShingle | Sunil Pokharel Shyam Prakash Khanal N P Adhikari Solvation free energy of light alkanes in polar and amphiphilic environments Bibechana Alkane Free Energy Molecular dynamics BAR |
| title | Solvation free energy of light alkanes in polar and amphiphilic environments |
| title_full | Solvation free energy of light alkanes in polar and amphiphilic environments |
| title_fullStr | Solvation free energy of light alkanes in polar and amphiphilic environments |
| title_full_unstemmed | Solvation free energy of light alkanes in polar and amphiphilic environments |
| title_short | Solvation free energy of light alkanes in polar and amphiphilic environments |
| title_sort | solvation free energy of light alkanes in polar and amphiphilic environments |
| topic | Alkane Free Energy Molecular dynamics BAR |
| url | https://www.nepjol.info/index.php/BIBECHANA/article/view/21136 |
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