Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field
Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonl...
| Main Authors: | , , |
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| Format: | Journal Article |
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Springer
2018
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| Online Access: | http://purl.org/au-research/grants/arc/LP140100993 http://hdl.handle.net/20.500.11937/69715 |
| _version_ | 1848762115364487168 |
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| author | Stachura, S. Malajczuk, C. Mancera, Ricardo |
| author_facet | Stachura, S. Malajczuk, C. Mancera, Ricardo |
| author_sort | Stachura, S. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields. |
| first_indexed | 2025-11-14T10:42:26Z |
| format | Journal Article |
| id | curtin-20.500.11937-69715 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T10:42:26Z |
| publishDate | 2018 |
| publisher | Springer |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-697152023-02-02T03:24:11Z Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field Stachura, S. Malajczuk, C. Mancera, Ricardo Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields. 2018 Journal Article http://hdl.handle.net/20.500.11937/69715 10.1007/s00894-018-3720-x http://purl.org/au-research/grants/arc/LP140100993 Springer restricted |
| spellingShingle | Stachura, S. Malajczuk, C. Mancera, Ricardo Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title | Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title_full | Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title_fullStr | Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title_full_unstemmed | Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title_short | Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field |
| title_sort | molecular dynamics simulations of a dmso/water mixture using the amber force field |
| url | http://purl.org/au-research/grants/arc/LP140100993 http://hdl.handle.net/20.500.11937/69715 |