Difference between revisions of "Hauptseminar Multiscale Simulations SS 2016/Ab initio molecular dynamics: Proton transport in water"
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== Contents == | == Contents == | ||
| + | |||
| + | In this topic, the mechanism of proton transfer in water will be discussed. Basics of ab initio molecular dynamics, and the mechanism of proton transfer in water will be presented. | ||
| + | The mechanism in water will be compared to the one in phosphoric acid. Furthermore, influences of applied methods, solvation environment, and quantum nuclear effects should be discussed briefly. | ||
== Literature == | == Literature == | ||
| Line 14: | Line 17: | ||
=== AIMD === | === AIMD === | ||
| − | * Kirchner, B; di Dio, P.J.; Hutter, J; Top Curr Chem. 307, 109-53. (2012) | + | * Kirchner, B; di Dio, P.J.; Hutter, J; Top Curr Chem. 307, 109-53. (2012) [http://dx.doi.org/10.1007/128_2011_195 doi:10.1007/128_2011_195] |
| − | * Hutter, J. et al.; Wiley Interdisciplinary Reviews: Computational Molecular Science 4, 15-25 (2014) | + | * Hutter, J. et al.; Wiley Interdisciplinary Reviews: Computational Molecular Science 4, 15-25 (2014) [http://dx.doi.org/10.1002/wcms.1159 doi:10.1002/wcms.1159] |
* Marx, D and Hutter, J; Ab-initio Molecular Dynamics: Theory and Implementation In: Modern Methods and Algorithms of Quantum Chemistry, ed. by J. Grotendorst. Forschungszentrum Jülich, chap. 13, pp. 301-449.; [https://juser.fz-juelich.de/record/44687/files/NIC-Band-1.pdf link] | * Marx, D and Hutter, J; Ab-initio Molecular Dynamics: Theory and Implementation In: Modern Methods and Algorithms of Quantum Chemistry, ed. by J. Grotendorst. Forschungszentrum Jülich, chap. 13, pp. 301-449.; [https://juser.fz-juelich.de/record/44687/files/NIC-Band-1.pdf link] | ||
=== Proton-transfer in water === | === Proton-transfer in water === | ||
| − | * Agmon, N; Chemical Physics Letters 244, 456–462 (1995) | + | * Agmon, N; Chemical Physics Letters 244, 456–462 (1995) [http://dx.doi.org/10.1016/0009-2614(95)00905-J doi:10.1016/0009-2614(95)00905-J] |
| − | * Tuckerman, M; Laasonen, K; Sprik, M; Parrinello, M; J. Chem. Phys. 103, 150 (1995) | + | * Tuckerman, M; Laasonen, K; Sprik, M; Parrinello, M; J. Chem. Phys. 103, 150 (1995) [http://dx.doi.org/10.1063/1.469654 doi:10.1063/1.469654] |
| − | * Tuckerman, ME; Marx, D; Parrinello, M; Nature 417, 925-929 (2002) | + | * Tuckerman, ME; Marx, D; Parrinello, M; Nature 417, 925-929 (2002) [http://dx.doi.org/10.1038/nature00797 doi:10.1038/nature00797] |
| − | * Marx, D; Tuckerman, ME; Hutter, J; Parrinello; M; Nature 397, 601-604 (1999) | + | * Asthagiri, D; Pratt, LR; Kress, JD; Gomez, MA; Proc. Nat. Acad. Sci 101, 7229–7233 (2004) [http://dx.doi.org/10.1073/pnas.0401696101 doi: 10.1073/pnas.0401696101] |
| + | * Marx, D; Tuckerman, ME; Hutter, J; Parrinello; M; Nature 397, 601-604 (1999) [http://dx.doi.org/10.1038/17579 doi:10.1038/17579] | ||
* Marx, D; Chem. Phys. Chem. 7, 1848-1870 (2006); [http://dx.doi.org/10.1002/cphc.200600128 doi:10.1002/cphc.200600128] | * Marx, D; Chem. Phys. Chem. 7, 1848-1870 (2006); [http://dx.doi.org/10.1002/cphc.200600128 doi:10.1002/cphc.200600128] | ||
| − | * Hassanali, A; Prakash, MK; Eshet, H; Parrinello, M, Proc. Nat. Acad. Sci. 108, 20410-20415 (2014) | + | * Hassanali, A; Prakash, MK; Eshet, H; Parrinello, M, Proc. Nat. Acad. Sci. 108, 20410-20415 (2014) [http://dx.doi.org/10.1073/pnas.1112486108 doi:10.1073/pnas.1112486108] |
* Kale, S; Herzfeld, J; Angew. Chem. Int. Ed. 51, 11029–11032 (2012) [http://dx.doi.org/10.1002/anie.201203568 doi:10.1002/anie.201203568] | * Kale, S; Herzfeld, J; Angew. Chem. Int. Ed. 51, 11029–11032 (2012) [http://dx.doi.org/10.1002/anie.201203568 doi:10.1002/anie.201203568] | ||
| − | <!-- * Petersen, MK; Iyengar, SS; Day, TJF; Voth, GA; J. Phys. Chem. B 108, 14804–14806 (2004) | + | <!-- * Petersen, MK; Iyengar, SS; Day, TJF; Voth, GA; J. Phys. Chem. B 108, 14804–14806 (2004) [http://dx.doi.org/10.1021/jp046716o doi:10.1021/jp046716o] --> |
<!-- * Buch, V; Milet, A; Vácha, R; Jungwirth, P.; Devlin, JP; Proc. Nat. Acad. Sci. 104, 7342–7347 (2007) [http://dx.doi.org/10.1073/pnas.0611285104 doi:10.1073/pnas.0611285104] --> | <!-- * Buch, V; Milet, A; Vácha, R; Jungwirth, P.; Devlin, JP; Proc. Nat. Acad. Sci. 104, 7342–7347 (2007) [http://dx.doi.org/10.1073/pnas.0611285104 doi:10.1073/pnas.0611285104] --> | ||
* Baer, M; Tobias, DJ; Mundy, CJ; J. Phys. Chem. B 118, 8364-8372 (2014) [http://dx.doi.org/10.1021/jp501854h doi:10.1021/jp501854h] | * Baer, M; Tobias, DJ; Mundy, CJ; J. Phys. Chem. B 118, 8364-8372 (2014) [http://dx.doi.org/10.1021/jp501854h doi:10.1021/jp501854h] | ||
| + | * Tuckerman, ME; Chandra, A; Marx, D; Acc. Chem. Res. 39, 151 (2006) [http://dx.doi.org/10.1021/ar040207n doi:10.1021/ar040207n] | ||
=== Proton-transfer in phosphoric acid and in general === | === Proton-transfer in phosphoric acid and in general === | ||
| − | * Vilčiauskas, L.; Tuckerman, ME; Bester, G.; Paddison, SJ; Kreuer, KD, Nature Chem. 4, 461-466 (2012) | + | * Vilčiauskas, L.; Tuckerman, ME; Bester, G.; Paddison, SJ; Kreuer, KD, Nature Chem. 4, 461-466 (2012) [http://dx.doi.org/10.1038/nchem.1329 doi:10.1038/nchem.1329] |
| − | * Kreuer, KD; Chem. Mater. 8, 610–641 (1996) | + | * Kreuer, KD; Chem. Mater. 8, 610–641 (1996) [http://dx.doi.org/10.1021/cm950192a doi:10.1021/cm950192a] |
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- Topic
- Ab initio molecular dynamics: Proton transfer in water
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Contents
In this topic, the mechanism of proton transfer in water will be discussed. Basics of ab initio molecular dynamics, and the mechanism of proton transfer in water will be presented. The mechanism in water will be compared to the one in phosphoric acid. Furthermore, influences of applied methods, solvation environment, and quantum nuclear effects should be discussed briefly.
Literature
AIMD
- Kirchner, B; di Dio, P.J.; Hutter, J; Top Curr Chem. 307, 109-53. (2012) doi:10.1007/128_2011_195
- Hutter, J. et al.; Wiley Interdisciplinary Reviews: Computational Molecular Science 4, 15-25 (2014) doi:10.1002/wcms.1159
- Marx, D and Hutter, J; Ab-initio Molecular Dynamics: Theory and Implementation In: Modern Methods and Algorithms of Quantum Chemistry, ed. by J. Grotendorst. Forschungszentrum Jülich, chap. 13, pp. 301-449.; link
Proton-transfer in water
- Agmon, N; Chemical Physics Letters 244, 456–462 (1995) doi:10.1016/0009-2614(95)00905-J
- Tuckerman, M; Laasonen, K; Sprik, M; Parrinello, M; J. Chem. Phys. 103, 150 (1995) doi:10.1063/1.469654
- Tuckerman, ME; Marx, D; Parrinello, M; Nature 417, 925-929 (2002) doi:10.1038/nature00797
- Asthagiri, D; Pratt, LR; Kress, JD; Gomez, MA; Proc. Nat. Acad. Sci 101, 7229–7233 (2004) doi: 10.1073/pnas.0401696101
- Marx, D; Tuckerman, ME; Hutter, J; Parrinello; M; Nature 397, 601-604 (1999) doi:10.1038/17579
- Marx, D; Chem. Phys. Chem. 7, 1848-1870 (2006); doi:10.1002/cphc.200600128
- Hassanali, A; Prakash, MK; Eshet, H; Parrinello, M, Proc. Nat. Acad. Sci. 108, 20410-20415 (2014) doi:10.1073/pnas.1112486108
- Kale, S; Herzfeld, J; Angew. Chem. Int. Ed. 51, 11029–11032 (2012) doi:10.1002/anie.201203568
- Baer, M; Tobias, DJ; Mundy, CJ; J. Phys. Chem. B 118, 8364-8372 (2014) doi:10.1021/jp501854h
- Tuckerman, ME; Chandra, A; Marx, D; Acc. Chem. Res. 39, 151 (2006) doi:10.1021/ar040207n
Proton-transfer in phosphoric acid and in general
- Vilčiauskas, L.; Tuckerman, ME; Bester, G.; Paddison, SJ; Kreuer, KD, Nature Chem. 4, 461-466 (2012) doi:10.1038/nchem.1329
- Kreuer, KD; Chem. Mater. 8, 610–641 (1996) doi:10.1021/cm950192a