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%% This BibTeX bibliography file was created using BibDesk.
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@article{bzar,
|
||||
Author = {Iftner, Christophe and Simon, Aude and Korchagina, Kseniia and Rapacioli, Mathias and Spiegelman, Fernand},
|
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Date = {2014},
|
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Date-Added = {2019-10-15 11:28:17 +0000},
|
||||
Date-Modified = {2019-10-15 11:28:17 +0000},
|
||||
Journal = {The Journal of Chemical Physics},
|
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Keywords = {density functional theory; SCF calculations; binding energy; molecular configurations; argon; ionisation potential; tight-binding calculations; molecular clusters; organic compounds},
|
||||
Number = {3},
|
||||
Pages = {-},
|
||||
Title = {A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C6H6)+/0Arn clusters},
|
||||
Type = {doi:http://dx.doi.org/10.1063/1.4861431},
|
||||
Url = {http://scitation.aip.org/content/aip/journal/jcp/140/3/10.1063/1.4861431},
|
||||
Volume = {140},
|
||||
Year = {2014},
|
||||
Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/140/3/10.1063/1.4861431}}
|
||||
|
||||
@article{dftb2,
|
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Author = {Seifert, G and Porezag, D and Frauenheim, Th},
|
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Date-Added = {2019-10-15 11:27:56 +0000},
|
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Date-Modified = {2019-10-15 11:27:56 +0000},
|
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Journal = {Int. J. Quantum Chem.},
|
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Number = {2},
|
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Pages = {185--192},
|
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Publisher = {Wiley Online Library},
|
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Year = {1996}}
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@article{dftb1,
|
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Author = {Porezag, Dirk and Frauenheim, Th and K{\"o}hler, Th and Seifert, Gotthard and Kaschner, R},
|
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Date-Added = {2019-10-15 11:27:56 +0000},
|
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Date-Modified = {2019-10-15 11:27:56 +0000},
|
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Journal = {Phys. Rev. B},
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Number = {19},
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Pages = {12947--12958},
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Publisher = {APS},
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Title = {Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon},
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Volume = {51},
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Year = {1995}}
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@article{Rasmussen2010,
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title={Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines},
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author={Rasmussen, Andrew M and Lind, Maria C and Kim, Sunghwan and Schaefer III, Henry F},
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journal={Journal of chemical theory and computation},
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volume={6},
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number={3},
|
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pages={930--939},
|
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year={2010},
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publisher={ACS Publications}
|
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}
|
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Author = {Rasmussen, Andrew M and Lind, Maria C and Kim, Sunghwan and Schaefer III, Henry F},
|
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Journal = {Journal of chemical theory and computation},
|
||||
Number = {3},
|
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Pages = {930--939},
|
||||
Publisher = {ACS Publications},
|
||||
Title = {Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines},
|
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Volume = {6},
|
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Year = {2010}}
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|
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@article{Coates2018,
|
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title={Binding energies of hydrated cobalt (II) by collision-induced dissociation and theoretical studies: evidence for a new critical size},
|
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author={Coates, Rebecca A and Armentrout, PB},
|
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journal={Physical Chemistry Chemical Physics},
|
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volume={20},
|
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number={2},
|
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pages={802--818},
|
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year={2018},
|
||||
publisher={Royal Society of Chemistry}
|
||||
}
|
||||
Author = {Coates, Rebecca A and Armentrout, PB},
|
||||
Journal = {Physical Chemistry Chemical Physics},
|
||||
Number = {2},
|
||||
Pages = {802--818},
|
||||
Publisher = {Royal Society of Chemistry},
|
||||
Title = {Binding energies of hydrated cobalt (II) by collision-induced dissociation and theoretical studies: evidence for a new critical size},
|
||||
Volume = {20},
|
||||
Year = {2018}}
|
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|
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@article{Imhoff2007,
|
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title={Ionizing fragmentation of uracil and 5-bromouracil by electron impact in gas phase and hyperthermal Ar+ ion irradiation in condensed phase},
|
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author={Imhoff, Marjorie and Deng, Zongwu and Huels, Michael A},
|
||||
journal={International Journal of Mass Spectrometry},
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volume={262},
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number={1-2},
|
||||
pages={154--160},
|
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year={2007},
|
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publisher={Elsevier}
|
||||
}
|
||||
Author = {Imhoff, Marjorie and Deng, Zongwu and Huels, Michael A},
|
||||
Journal = {International Journal of Mass Spectrometry},
|
||||
Number = {1-2},
|
||||
Pages = {154--160},
|
||||
Publisher = {Elsevier},
|
||||
Title = {Ionizing fragmentation of uracil and 5-bromouracil by electron impact in gas phase and hyperthermal Ar+ ion irradiation in condensed phase},
|
||||
Volume = {262},
|
||||
Year = {2007}}
|
||||
|
||||
@article{Abdoul2000,
|
||||
title={Dissociative electron attachment to gas-phase 5-bromouracil},
|
||||
author={Abdoul-Carime, H and Huels, MA and Br{\"u}ning, F and Illenberger, E and Sanche, L},
|
||||
journal={The journal of chemical physics},
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volume={113},
|
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number={7},
|
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pages={2517--2521},
|
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year={2000},
|
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publisher={AIP}
|
||||
}
|
||||
Author = {Abdoul-Carime, H and Huels, MA and Br{\"u}ning, F and Illenberger, E and Sanche, L},
|
||||
Journal = {The journal of chemical physics},
|
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Number = {7},
|
||||
Pages = {2517--2521},
|
||||
Publisher = {AIP},
|
||||
Title = {Dissociative electron attachment to gas-phase 5-bromouracil},
|
||||
Volume = {113},
|
||||
Year = {2000}}
|
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|
||||
@article{Champeaux2010,
|
||||
title={Dehalogenation of 5-halo-uracil molecules induced by 100 keV proton collisions},
|
||||
author={Champeaux, Jean-Philippe and {\c{C}}ar{\c{c}}abal, Pierre and Rabier, Julien and Cafarelli, Pierre and Sence, Martine and Moretto-Capelle, Patrick},
|
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journal={Physical Chemistry Chemical Physics},
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volume={12},
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number={20},
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pages={5454--5461},
|
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year={2010},
|
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publisher={Royal Society of Chemistry}
|
||||
}
|
||||
Author = {Champeaux, Jean-Philippe and {\c{C}}ar{\c{c}}abal, Pierre and Rabier, Julien and Cafarelli, Pierre and Sence, Martine and Moretto-Capelle, Patrick},
|
||||
Journal = {Physical Chemistry Chemical Physics},
|
||||
Number = {20},
|
||||
Pages = {5454--5461},
|
||||
Publisher = {Royal Society of Chemistry},
|
||||
Title = {Dehalogenation of 5-halo-uracil molecules induced by 100 keV proton collisions},
|
||||
Volume = {12},
|
||||
Year = {2010}}
|
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|
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@article{Korchagina2017,
|
||||
title={Molecular dynamics study of the collision-induced reaction of h with co on small water clusters},
|
||||
author={Korchagina, Kseniia A and Spiegelman, Fernand and Cuny, Jerome},
|
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journal={The Journal of Physical Chemistry A},
|
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volume={121},
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number={49},
|
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pages={9485--9494},
|
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year={2017},
|
||||
publisher={ACS Publications}
|
||||
}
|
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|
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|
||||
Author = {Korchagina, Kseniia A and Spiegelman, Fernand and Cuny, Jerome},
|
||||
Journal = {The Journal of Physical Chemistry A},
|
||||
Number = {49},
|
||||
Pages = {9485--9494},
|
||||
Publisher = {ACS Publications},
|
||||
Title = {Molecular dynamics study of the collision-induced reaction of h with co on small water clusters},
|
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Volume = {121},
|
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Year = {2017}}
|
||||
|
||||
@article{Delaunay2014,
|
||||
title={Prompt and delayed fragmentation of bromouracil cations ionized by multiply charged ions},
|
||||
author={Delaunay, Rudy and Champeaux, Jean-Philippe and Maclot, Sylvain and Capron, Michael and Domaracka, Alicja and M{\'e}ry, Alain and Manil, Bruno and Adoui, Lamri and Rousseau, Patrick and Moretto-Capelle, Patrick and others},
|
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journal={The European Physical Journal D},
|
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volume={68},
|
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number={6},
|
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pages={162},
|
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year={2014},
|
||||
publisher={Springer}
|
||||
}
|
||||
Author = {Delaunay, Rudy and Champeaux, Jean-Philippe and Maclot, Sylvain and Capron, Michael and Domaracka, Alicja and M{\'e}ry, Alain and Manil, Bruno and Adoui, Lamri and Rousseau, Patrick and Moretto-Capelle, Patrick and others},
|
||||
Journal = {The European Physical Journal D},
|
||||
Number = {6},
|
||||
Pages = {162},
|
||||
Publisher = {Springer},
|
||||
Title = {Prompt and delayed fragmentation of bromouracil cations ionized by multiply charged ions},
|
||||
Volume = {68},
|
||||
Year = {2014}}
|
||||
|
||||
@article{Bacchus2009,
|
||||
title={Ab initio molecular treatment of charge-transfer processes induced by collision of carbon ions with 5-halouracil molecules},
|
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author={Bacchus-Montabonel, MC and Tergiman, YS and Talbi, Dahbia},
|
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journal={Physical Review A},
|
||||
volume={79},
|
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number={1},
|
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pages={012710},
|
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year={2009},
|
||||
publisher={APS}
|
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}
|
||||
Author = {Bacchus-Montabonel, MC and Tergiman, YS and Talbi, Dahbia},
|
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Journal = {Physical Review A},
|
||||
Number = {1},
|
||||
Pages = {012710},
|
||||
Publisher = {APS},
|
||||
Title = {Ab initio molecular treatment of charge-transfer processes induced by collision of carbon ions with 5-halouracil molecules},
|
||||
Volume = {79},
|
||||
Year = {2009}}
|
||||
|
||||
@article{Kossoski2015,
|
||||
title={Negative ion states of 5-bromouracil and 5-iodouracil},
|
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author={Kossoski, Fabris and Varella, MT do N},
|
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journal={Physical Chemistry Chemical Physics},
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volume={17},
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number={26},
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pages={17271--17278},
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year={2015},
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publisher={Royal Society of Chemistry}
|
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}
|
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Author = {Kossoski, Fabris and Varella, MT do N},
|
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Journal = {Physical Chemistry Chemical Physics},
|
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Number = {26},
|
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Pages = {17271--17278},
|
||||
Publisher = {Royal Society of Chemistry},
|
||||
Title = {Negative ion states of 5-bromouracil and 5-iodouracil},
|
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Volume = {17},
|
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Year = {2015}}
|
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|
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@article{Maclot2011,
|
||||
title={Ion-Induced Fragmentation of Amino Acids: Effect of the Environment},
|
||||
author={Maclot, Sylvain and Capron, Michael and Maisonny, R{\'e}mi and {\L}awicki, Arkadiusz and M{\'e}ry, Alain and Rangama, Jimmy and Chesnel, Jean-Yves and Bari, Sadia and Hoekstra, Ronnie and Schlath{\"o}lter, Thomas and others},
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journal={ChemPhysChem},
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volume={12},
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number={5},
|
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pages={930--936},
|
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year={2011},
|
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publisher={Wiley Online Library}
|
||||
}
|
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Author = {Maclot, Sylvain and Capron, Michael and Maisonny, R{\'e}mi and {\L}awicki, Arkadiusz and M{\'e}ry, Alain and Rangama, Jimmy and Chesnel, Jean-Yves and Bari, Sadia and Hoekstra, Ronnie and Schlath{\"o}lter, Thomas and others},
|
||||
Journal = {ChemPhysChem},
|
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Number = {5},
|
||||
Pages = {930--936},
|
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Publisher = {Wiley Online Library},
|
||||
Title = {Ion-Induced Fragmentation of Amino Acids: Effect of the Environment},
|
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Volume = {12},
|
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Year = {2011}}
|
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|
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@inproceedings{Domaracka2012,
|
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title={Ion interaction with biomolecular systems and the effect of the environment},
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author={Domaracka, Alicja and Capron, Michael and Maclot, Sylvain and Chesnel, Jean-Yves and M{\'e}ry, Alain and Poully, Jean-Christophe and Rangama, Jimmy and Adoui, Lamri and Rousseau, Patrick and Huber, Bernd A},
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year={2012},
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}
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Author = {Domaracka, Alicja and Capron, Michael and Maclot, Sylvain and Chesnel, Jean-Yves and M{\'e}ry, Alain and Poully, Jean-Christophe and Rangama, Jimmy and Adoui, Lamri and Rousseau, Patrick and Huber, Bernd A},
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Booktitle = {Journal of Physics: Conference Series},
|
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Number = {1},
|
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Organization = {IOP Publishing},
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Pages = {012005},
|
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Title = {Ion interaction with biomolecular systems and the effect of the environment},
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Volume = {373},
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Year = {2012}}
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@article{Markush2016,
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title={The role of the environment in the ion induced fragmentation of uracil},
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author={Markush, Pal and Bolognesi, Paola and Cartoni, Antonella and Rousseau, Patrick and Maclot, Sylvain and Delaunay, Rudy and Domaracka, Alicja and Kocisek, Jaroslav and Castrovilli, Mattea C and Huber, Bernd A and others},
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pages={16721--16729},
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year={2016},
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publisher={Royal Society of Chemistry}
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}
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Author = {Markush, Pal and Bolognesi, Paola and Cartoni, Antonella and Rousseau, Patrick and Maclot, Sylvain and Delaunay, Rudy and Domaracka, Alicja and Kocisek, Jaroslav and Castrovilli, Mattea C and Huber, Bernd A and others},
|
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Journal = {Physical Chemistry Chemical Physics},
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Number = {25},
|
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Pages = {16721--16729},
|
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Publisher = {Royal Society of Chemistry},
|
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Title = {The role of the environment in the ion induced fragmentation of uracil},
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Volume = {18},
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Year = {2016}}
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@article{Castrovilli2017,
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title={Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments},
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author={Castrovilli, MC and Markush, P and Bolognesi, P and Rousseau, P and Maclot, S and Cartoni, A and Delaunay, R and Domaracka, A and Ko{\v{c}}i{\v{s}}ek, J and Huber, BA and others},
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publisher={Royal Society of Chemistry}
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}
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Author = {Castrovilli, MC and Markush, P and Bolognesi, P and Rousseau, P and Maclot, S and Cartoni, A and Delaunay, R and Domaracka, A and Ko{\v{c}}i{\v{s}}ek, J and Huber, BA and others},
|
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Journal = {Physical Chemistry Chemical Physics},
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Number = {30},
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Pages = {19807--19814},
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Publisher = {Royal Society of Chemistry},
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Title = {Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments},
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Volume = {19},
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Year = {2017}}
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@incollection{Hayes1990,
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title={[10] Collision-induced dissociation},
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author={Hayes, Roger N and Gross, Michael L},
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year={1990},
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Author = {Hayes, Roger N and Gross, Michael L},
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Booktitle = {Methods in enzymology},
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Pages = {237--263},
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Publisher = {Elsevier},
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Year = {1990}}
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@article{Coates2017,
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title={Thermochemical Investigations of Hydrated Nickel Dication Complexes by Threshold Collision-Induced Dissociation and Theory},
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author={Coates, Rebecca A and Armentrout, PB},
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journal={The Journal of Physical Chemistry A},
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volume={121},
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number={19},
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pages={3629--3646},
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year={2017},
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publisher={ACS Publications}
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}
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Author = {Coates, Rebecca A and Armentrout, PB},
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Journal = {The Journal of Physical Chemistry A},
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Number = {19},
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Pages = {3629--3646},
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Publisher = {ACS Publications},
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Title = {Thermochemical Investigations of Hydrated Nickel Dication Complexes by Threshold Collision-Induced Dissociation and Theory},
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Volume = {121},
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Year = {2017}}
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title={Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters},
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author={Neustetter, Michael and Mahmoodi-Darian, Masoomeh and Denifl, Stephan},
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journal={Journal of The American Society for Mass Spectrometry},
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pages={866--872},
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year={2017},
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publisher={Springer}
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}
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Author = {Neustetter, Michael and Mahmoodi-Darian, Masoomeh and Denifl, Stephan},
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Journal = {Journal of The American Society for Mass Spectrometry},
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Number = {5},
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Pages = {866--872},
|
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Publisher = {Springer},
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Title = {Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters},
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Volume = {28},
|
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Year = {2017}}
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@article{Nelson1994,
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title={Collision-induced dissociation of uracil and its derivatives},
|
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author={Nelson, Chad C and McCloskey, James A},
|
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journal={Journal of the American Society for Mass Spectrometry},
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pages={339--349},
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year={1994},
|
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publisher={Springer}
|
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}
|
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Author = {Nelson, Chad C and McCloskey, James A},
|
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Journal = {Journal of the American Society for Mass Spectrometry},
|
||||
Number = {5},
|
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Pages = {339--349},
|
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Publisher = {Springer},
|
||||
Title = {Collision-induced dissociation of uracil and its derivatives},
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Volume = {5},
|
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Year = {1994}}
|
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|
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@article{Molina2015,
|
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title={Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments},
|
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author={Molina, Estefan{\'\i}a Rossich and Ortiz, Daniel and Salpin, Jean-Yves and Spezia, Riccardo},
|
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journal={Journal of mass spectrometry},
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volume={50},
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number={12},
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pages={1340--1351},
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year={2015},
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publisher={Wiley Online Library}
|
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}
|
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Author = {Molina, Estefan{\'\i}a Rossich and Ortiz, Daniel and Salpin, Jean-Yves and Spezia, Riccardo},
|
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Journal = {Journal of mass spectrometry},
|
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Number = {12},
|
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Pages = {1340--1351},
|
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Publisher = {Wiley Online Library},
|
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Title = {Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments},
|
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Volume = {50},
|
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Year = {2015}}
|
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|
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@article{Molina2016,
|
||||
title={On the gas phase fragmentation of protonated uracil: a statistical perspective},
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author={Molina, Estefan{\'\i}a Rossich and Salpin, Jean-Yves and Spezia, Riccardo and Martinez-Nunez, Emilio},
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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Title = {{Atomic hydrogen interactions with gas-phase coronene cations:
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Publisher = {The Royal Society Publishing},
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year={1991},
|
||||
publisher={Elsevier}
|
||||
}
|
||||
Author = {Magnera, Thomas F and David, Donald E and Michl, Josef},
|
||||
Journal = {Chemical physics letters},
|
||||
Number = {3-4},
|
||||
Pages = {363--370},
|
||||
Publisher = {Elsevier},
|
||||
Title = {The first twenty-eight gas-phase proton hydration energies},
|
||||
Volume = {182},
|
||||
Year = {1991}}
|
||||
|
||||
@ -43,6 +43,8 @@
|
||||
\usepackage{caption}
|
||||
\newcommand{\red}[1]{{\color{red}#1}}
|
||||
\newcommand{\blue}[1]{{\color{blue}#1}}
|
||||
\newcommand{\dftbpapers}{dftb1,dftb2,SCC-dftb,augusto09}
|
||||
|
||||
|
||||
\usetikzlibrary{calc,trees,positioning,arrows,chains,shapes.geometric,%
|
||||
decorations.pathreplacing,decorations.pathmorphing,shapes,%
|
||||
@ -91,7 +93,7 @@
|
||||
%% optional argument to \title.
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\title[An \textsf{achemso} demo]
|
||||
{A dynamics collision simulation study on proton localization of uracil protonated water clusters\footnote{A dynamics collision simulation study on proton localization of uracil protonated water clusters}}
|
||||
{A dynamics collision simulation study on proton localization of uracil protonated water clusters\footnote{A dynamics collision simulation study on proton localization of uracil protonated water clusters}{\bf MR : remove the footnote}}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% Some journals require a list of abbreviations or keywords to be
|
||||
@ -123,41 +125,43 @@
|
||||
%% if an abstract is not used by the target journal.
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\begin{abstract}
|
||||
A series of dynamics collision simulations between lowest-energy uracil protonated water clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ and Argon atom were performed with the self-consistent-charge density-functional based tight-binding (SCC-DFTB) method to make a deep exploration of the collision process. From the dynamics collision simulations, the trend of different types of fragments and location of the excess proton were observed. Our initial geometries provided a reasonably uniform distribution of Argon projectiles around each uracil protonated water clusters leading Argon atom can collide at all the possible positions of each cluster. The theoretical simulation data show that the proportion of neutral uracil molecule loss and total fragmentation cross sections are consistent with those in experiment. Additionally, we observed that up to 7 water molecules the clusters had a direct dissociation mechanism after collision \blue{whereas for 12 water molecules …...} Furthermore, the calculation results indicate the excess proton location is highly dependent on the initial isomer as stated in a previous study. \blue{By conducting path-integral MD simulation, we finally observed that nuclear quantum effect XXX.} \blue{We are the first to perform this kind of simulation,} our dynamics collision simulations for predicting the type and amount of fragments and fragmentation cross sections of collision system provide a useful tool.
|
||||
A series of dynamics collision simulations between lowest-energy uracil protonated water clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ and Argon atom were performed with the self-consistent-charge density-functional based tight-binding {\bf remove acronyles in abvstract if not necessary ) : (SCC-DFTB)} method to make a deep exploration of the collision process. From the dynamics collision simulations, the trend of different types of fragments and location of the excess proton were observed. {\bf MR : remove the following sentence, details : Our initial geometries provided a reasonably uniform distribution of Argon projectiles around each uracil protonated water clusters leading Argon atom can collide at all the possible positions of each cluster. } The theoretical simulation data show that the proportion of neutral uracil molecule loss and total fragmentation cross sections are consistent with those in experiment. Additionally, we observed that up to 7 water molecules the clusters had a direct dissociation mechanism after collision \blue{whereas for 12 water molecules …...} Furthermore, the calculation results indicate the excess proton location is highly dependent on the initial isomer as stated in a previous study. {\bf put a reference in full text} \blue{By conducting path-integral MD simulation, we finally observed that nuclear quantum effect XXX.} \blue{We are the first to perform this kind of simulation,} our dynamics collision simulations for predicting the type and amount of fragments and fragmentation cross sections of collision system provide a useful tool.
|
||||
\end{abstract}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% Start the main part of the manuscript here.
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section{Introduction }
|
||||
{\bf nice you learned latex ! please try to use as much as possible section to make section and subsection instead of textbf}
|
||||
|
||||
The nucleobases in DNA and RNA play a very important role in the encoding and expression of genetic information in living systems while water represents the natural medium of many reactions in living organisms. Therefore, it is a significant point to study the interaction between nucleobase molecules and aqueous environment.
|
||||
The radiation effect on RNA and DNA molecules is still a medical challenge in modern times. The radiation can cause damages on these molecules. Radiation damages are proficiently applied in radiotherapy for cancer treatment. The major drawback in radiotherapy is the unselective damage in both healthy and tumor cells, which has a big side effect. This makes it particularly important to explore the radiation fragments. RNA nucleobase, uracil C$_4$H$_4$N$_2$O$_2$ (U), has attracted scientist’s attention a lot. Protonated uracil UH$^+$ can be generated by radiation damages. Through the study of hydration effects on cytosine, uracil, and thymine pyrimidines by including one and two water molecules explicitly, Schaefer III \textit{et al.} found that a water molecule is more likely to interact with a charged species than with a neutral one.\cite{Rasmussen2010} However, the study about protonated necleobases in aqueous environment is not so much.
|
||||
The radiation effect on RNA and DNA molecules is still a medical challenge in modern times. {\bf MR : remove sentence : The radiation can cause damages on these molecules.} Radiation damages {\bf on these molecules} are proficiently applied in radiotherapy for cancer treatment. The major drawback in radiotherapy is the unselective damage in both healthy and tumor cells, which has a big side effect. This makes it particularly important to explore the radiation fragments. RNA nucleobase, uracil C$_4$H$_4$N$_2$O$_2$ (U), has attracted scientist’s attention a lot. Protonated uracil UH$^+$ can be generated by radiation damages. Through the study of hydration effects on cytosine, uracil, and thymine pyrimidines by including one and {\bf or ? } two water molecules explicitly, Schaefer III \textit{et al.} {\bf III is in his name ? } found that a water molecule is more likely to interact with a charged species than with a neutral one.\cite{Rasmussen2010} However, the study about protonated necleobases in aqueous environment is not so much.
|
||||
JC MUCH BLABLA
|
||||
JC Add a sentence to say hydration of molecules can help to do something in real life
|
||||
|
||||
Studying hydration of molecules and biomolecules is of paramount important to get insights into their behavior in aqueous medium, in particular their structure, stability and dynamics. To do so, gas phase investigations of molecules play an important role in understanding the intrinsic properties of molecules, which is free from the effects of solvents or other factors. It allows to study the evolution of this behavior as the function of the hydration degree of the molecule and also probe the influence of the protonated state.
|
||||
Studying hydration of molecules and biomolecules is of paramount important {\bf importance } to get insights into their behavior in aqueous medium, in particular their structure, stability and dynamics. To do so, gas phase investigations of molecules play an important role in understanding the intrinsic properties of molecules, which is free from the effects of solvents or other factors. It allows to study the evolution of this behavior as the function of the hydration degree of the molecule and also probe the influence of the protonated state.
|
||||
Collision experiments in the gas phase is a useful tool that can be applied to provide structural information about molecular species.\cite{Coates2018} For instance, considering U molecule, which has attracted scientist’s attention a lot due to its important role in the encoding and expression of genetic information in living systems, various collision experiments have been conducted. Fragmentation of halogen substituted uracil molecules in the gas phase through collisions experiments have been performed.\cite{Imhoff2007,Abdoul2000,Champeaux2010,Delaunay2014} The theoretical calculations about the charge-transfer processes induced by collision have been also reported.\cite{Bacchus2009, Kossoski2015} Nevertheless, the gas phase study needs to be extended towards more realistic biomolecular systems, to reveal how the intrinsic molecular properties are affected by the surrounding medium when the biomolecules are in a natural environment.\cite{Maclot2011, Domaracka2012, Markush2016, Castrovilli2017}
|
||||
(JC, make this part smaller)
|
||||
|
||||
It is reported that many collision experiments have been made via threshold collision-induced dissociation (TCID) for the hermodynamic information, electron ionization and fragmentation, binding energies and other properties of biomolecules.\cite{Hayes1990, Coates2017, Neustetter2017, Coates2018} Fragmentation of isolated protonated uracil has been studied through collision-induced dissociation (CID) with tandem mass sepctrometry, \cite{Nelson1994, Molina2015, Molina2016, Sadr2014} however, there are few studies concerning the surrounding aqueous environment effect on such collision process in experiment. Some theory studies have been performed about this but those studies have been limited to small water clusters. \cite{Bakker2008} Recently, Zamith’s group in collaboration with our group reported the CID experiment on uracil protonated water clusters (H$_2$O)$_{n=1-15}$UH$^+$ and theoretical study to determine the lowest-energy structures. \cite{Braud2019} In Zamith’s experiment, the collisions only lead to intermolecular bond breaking rather than intramolecular bond breaking in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters. The collisions were performed with with(H$_2$O)$_{n=1-15}$UH$^+$ clusters and M= H$_2$O, D$_2$O, Ne, and Ar. They found no matter which M was used, the results were the same. They only showed the results with Ne. The branching ratios of different charged fragments were determined through mass spectra of the collision products. Fragmentation cross section of (H$_2$O)$_{n=1-15}$UH$^+$ clusters were obtained at a collision energy 7.2 eV as a function of the total number molecules in the clusters. The proportion of neutral uracil molecules loss were detected as a function of the number n of water molecules in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters at 7.2 eV of mass collision energy. From the proportion results of neutral uracil molecules loss, it shows where the excess proton lies after collision. An obvious growth of neutral uracil molecules loss was observed from n = 5-6. Those experiment were complemented by theoretical calculations that aim at finding the lowest-energy (H$_2$O)$_{n=1-7}$UH$^+$ clusters. From the structures of lowest-energy isomers, it clearly shows that (i) for small clusters (when n = 1-2), the excess proton is on the uracil; (ii) for n = 3-4, the excess proton is still on the uracil but it has a tendency to be displaced towards adjacent water molecules; (iii) when n is larger than 4, the excess proton is completely transferred to the water clusters. These results are in full agreement with the CID measurements.
|
||||
It is reported that many collision experiments have been made via threshold collision-induced dissociation (TCID) for the {\bf t}hermodynamic information, electron ionization and fragmentation, binding energies and other properties of biomolecules.\cite{Hayes1990, Coates2017, Neustetter2017, Coates2018} Fragmentation of isolated protonated uracil has been studied through collision-induced dissociation (CID) with tandem mass sepctrometry {\bf spectrometry}, \cite{Nelson1994, Molina2015, Molina2016, Sadr2014} however, there are few studies concerning the surrounding aqueous environment effect on such collision process in experiment. Some theory studies have been performed about this but those studies have been limited to small water clusters. \cite{Bakker2008} Recently, Zamith’s group in collaboration with our group reported the CID experiment on uracil protonated water clusters (H$_2$O)$_{n=1-15}$UH$^+$ and theoretical study to determine the lowest-energy structures. \cite{Braud2019} In Zamith’s experiment, the collisions only lead to intermolecular bond breaking rather than intramolecular bond breaking in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters. The collisions were performed with {\bf with} (H$_2$O)$_{n=1-15}$UH$^+$ clusters and {\bf an impacting atom or molecule } M= H$_2$O, D$_2$O, Ne, and Ar. They found no matter which M was used, the results were the same {\bf similar}. They only showed the results with Ne. The branching ratios of different charged fragments were determined through mass spectra of the collision products. Fragmentation cross section of (H$_2$O)$_{n=1-15}$UH$^+$ clusters were obtained at a collision energy {\bf of} 7.2 eV {\bf remove : as a function of the total number molecules in the clusters. The proportion of neutral uracil molecules loss were detected as a function of the number n of water molecules in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters at 7.2 eV of mass collision energy. From the proportion results of neutral uracil molecules loss, it shows where the excess proton lies after collision. } {\bf replace by : as well as the proportion of neutral versus protonated uracil} An obvious growth of neutral uracil molecules loss was observed from n = 5-6. Those experiment were complemented by theoretical calculations that aim at finding the lowest-energy (H$_2$O)$_{n=1-7}$UH$^+$ clusters. From the structures of lowest-energy isomers, it clearly shows that (i) for small clusters (when n = 1-2), the excess proton is on the uracil; (ii) for n = 3-4, the excess proton is still on the uracil but it has a tendency to be displaced towards adjacent water molecules; (iii) when n is larger than 4, the excess proton is completely transferred to the water clusters. {\bf replace These results are in full agreement with the CID measurements. by These results suggest that the location of the proton after the collision recorded in the CID experiment is strongly correlated to its position in the theoretically determined most stable parent isomer}.
|
||||
|
||||
However, although the location of the excess proton in lowest-energy isomers is clear, there are still some issues that need to be settled: (i) What’s the main path of the fragmentation mechanisms? (ii) What are the fragments after the collision? (iii) How does the proportion of the fragments change according to the time? (iv) If the proportion of neutral uracil molecules loss only determined by the lowest-energy isomers? With interests in these questions, it pursues us to do an explicit dynamics exploration for these uracil protonated water clusters.
|
||||
|
||||
Some studies have already been done about the dynamics collision simulation.\cite{Tomsic2013, Korchagina2017, Simon2017, Rapacioli2018} In the present work, we made the dynamics simulation to investigate the collision of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters and Ar. Based on the dynamics collision simulations, we analyzed the fragmentation cross section of mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters according to the total number molecules in the clusters. The branching ratios of different charged fragments were explored of the collision products. The proportion of neutral uracil molecules loss in the mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were also investigated. From all the above investigations, the two fragmentation mechanisms after collision, the mixed cluster has an immediately direct dissociation and the mixed cluster has a longer life before completed dissociation, which one is dominant is clear.
|
||||
\blue{All simulations are performed in the microcanonical ensemble within the Born–Oppenheimer??}
|
||||
However, although the location of the excess proton in lowest-energy isomers is clear, there are still some issues that need to be settled: (i) What’s the main path of the fragmentation mechanisms? (ii) What are the fragments after the collision? (iii) How does the proportion of the fragments change according to the time? (iv) If {\bf Is} the proportion of neutral uracil molecules loss only determined by the lowest-energy isomers? With interests in these questions, it pursues us to do an explicit dynamics exploration for these uracil protonated water clusters.
|
||||
|
||||
Some studies have already been done about the dynamics collision simulation.\cite{Tomsic2013, Korchagina2017, Simon2017, Rapacioli2018} {\bf precise the link because as written we think that collisions have already been simulated for your system}. In the present work, we made the dynamics simulation to investigate the collision of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters and Ar. {\bf remove : Based on the dynamics collision simulations,} {\bf We} we analyzed {\bf (i)} the fragmentation cross section {\bf remove : of mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters} according to the total number molecules in the clusters {\bf (i)} the branching ratios of different charged fragments {\bf remove : were explored of the collision products} and {\bf (iii)} the proportion of neutral uracil molecules loss {bf remove : in the mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were also investigated}. From all the above investigations {\bf not sure I understand, does above refer only to this work or the previously cited papers ?} , the two fragmentation mechanisms after collision, the mixed cluster has an immediately direct dissociation and the mixed cluster has a longer life before completed dissociation, which one is dominant is clear.
|
||||
\blue{All simulations are performed in the microcanonical ensemble within the Born–Oppenheimer??}
|
||||
{\bf I woudl put it in the method section or at the begining of this paragraph ``we made the dynamics simulation `` on the BO surface}
|
||||
|
||||
\section{Computational Methods} \label{Comput_meth}
|
||||
\textbf{Exploration of the PES}
|
||||
{\bf Rque general : their was plenty of ab initio calculation to benchmark the proton transfer etc .. it would be good to mention them and may be to put some data, may be some of them in the manuscirpt and others in the supplementary files}
|
||||
DFTB is approximated from DFT scheme whose efficiency relies on the use of parameterized integrals with a much lower computational cost. {\bf \cite{Elstner2014,Elstner1998,dftb1,dftb2}} The DFTB approach has been particularly well studied and it has already proven its efficiency to describe chemical processes. \cite{Kruger2005} In this work, we used the second-order version of DFTB, Self Consistent Charge DFTB, with the mio-set for the Slater-Koster tables of integrals. \cite{Elstner1998} To improve the intermolecular interaction, the class IV/charge model 3 (CM3) charges instead of the original Mulliken charges as well as the empirical terms were used to describe dispersion interactions. \cite{Rapacioli2009} For the parameterization of CM3 charges, the bond parameter D$_{OH}$ = 0.129 proposed by Simon and co-workers was applied, \blue{DNH = 0.120 tested by ourselves, (part of this work has been published[]){\bf mettre une ref}} while all other bond parameter values were set to be 0.000, which corresponds to a Mulliken evaluation of the charges.\cite{Simon2012, Simon2013} {\bf In a QM/MM scheme, the Argon atom is treated as a polarizable MM particule interacting with the Uracil-water cluster treated at the DFTB level. Details about this model can be found in the original paper \cite{bzar}. } All the SCC-DFTB calculations in the present work were carried out with the deMonNano code. \cite{demonnanoCode}
|
||||
|
||||
DFTB is approximated from DFT scheme whose efficiency relies on the use of parameterized integrals with a much lower computational cost. \cite{Elstner2014} The DFTB approach has been particularly well studied and it has already proven its efficiency to describe chemical processes. \cite{Kruger2005} In this work, we used the second-order version of DFTB, Self Consistent Charge DFTB, with the mio-set for the Slater-Koster tables of integrals. \cite{Elstner1998} To improve the intermolecular interaction, the class IV/charge model 3 (CM3) charges instead of the original Mulliken charges as well as the empirical terms were used to describe dispersion interactions. \cite{Rapacioli2009} For the parameterization of CM3 charges, the bond parameter D$_{OH}$ = 0.129 proposed by Simon and co-workers was applied, \blue{DNH = 0.120 tested by ourselves, (part of this work has been published[])} while all other bond parameter values were set to be 0.000, which corresponds to a Mulliken evaluation of the charges.\cite{Simon2012, Simon2013} All the SCC-DFTB calculations in the present work were carried out with the deMonNano code. \cite{demonnanoCode}
|
||||
|
||||
All the energy minima for (H$_2$O)$_{n=3-7}$UH$^+$, have already been obtained in the previous study.\cite{Braud2019} In this present work, we calculated the lowest-energy isomers of (H$_2$O)$_{12}$UH$^+$ cluster. To obtain them, the same two-step theoretical method with the one used for the calculation of lowest energy isomers of clusters (H$_2$O)$_{n=1-7}$UH$^+$ was applied.\cite{Braud2019} Firstly, the potential energy surface (PES) of (H$_2$O)$_{12}$UH$^+$ was roughly explored using the parallel temperature molecular dynamics (PTMD) simulations in combination with SCC-DFTB description of the energies and gradients.\cite{Sugita1999, Earl2005} In the PTMD algorithm, 40 replicas with temperatures going linearly from 50 to 350 K were carried out. All the trajectories were 4 ns long, and the integration time step was 0.5 fs. A Nosé-Hoover chain of five thermostats with frequencies of 800 cm$^{-1}$ was used to obtain an exploration in the canonical emsemble. \cite{Nose1984, Hoover1985} To avoid any spurious influence of the initial geometry on the PES exploration, three distinct PTMD simulations were carried out. In the three series, a distinct initial proton location was set: on the uracil in two cases and on the water cluster in another one. In the former cases, the u178 and u138 UH$^+$ isomers were used as initial geometries which was named by Pedersen \cite{Pedersen2014}. 600 geometries per temperature were linearly selected along each PTMD simulation for subsequent geometry optimization leading to 72000 structures optimized at SCC-DFTB level. These structures were sorted in ascending energy order. Secondly, 29 isomers were selected from the 72000 optimized structures at SCC-DFTB level and were optimized at a high accurate MP2/Def2TZVP level, which is a tight criteria for geometry convergence and an ultrafine grid for the numerical integration. \cite{Weigend2005, Weigend2006} From the MP2/Def2TZVP calculation, the lowest energy isomers of cluster (H$_2$O)$_{12}$UH$^+$ were obtained. All MP2 calculations were carried out with the Gaussian 09 package.\cite{GaussianCode}
|
||||
All the energy minima for (H$_2$O)$_{n=3-7}$UH$^+$, have already been obtained in the previous study.\cite{Braud2019} In this present work, we calculated the lowest-energy isomers of (H$_2$O)$_{12}$UH$^+$ cluster. To obtain them, the same two-step theoretical method with the one used for the calculation of lowest energy isomers of clusters (H$_2$O)$_{n=1-7}$UH$^+$ was applied.\cite{Braud2019} Firstly, the potential energy surface (PES) of (H$_2$O)$_{12}$UH$^+$ was roughly explored using the parallel temperature molecular dynamics{\bf move here refs to PTMD} (PTMD) simulations in combination with SCC-DFTB description of the energies and gradients.\cite{Sugita1999, Earl2005} In the PTMD algorithm, 40 replicas with temperatures going linearly from 50 to 350 K were carried out. All the trajectories were 4 ns long, and the integration time step was 0.5 fs. A Nos{\bf \'e} é-Hoover chain of five thermostats with frequencies of 800 cm$^{-1}$ was used to obtain an exploration in the canonical emsemble. \cite{Nose1984, Hoover1985} To avoid any spurious influence of the initial geometry on the PES exploration, three distinct PTMD simulations were carried out. In the three series, a distinct initial proton location was set: on the uracil in two cases and on the water cluster in another one. In the former cases, the u178 and u138 UH$^+$ isomers were used as initial geometries which was named by Pedersen \cite{Pedersen2014} {\bf -> we also used two isomers from Pedersen, reported in this work as u178 and u138 UH$^+$}. 600 geometries per temperature were linearly selected along each PTMD simulation for subsequent geometry optimization leading to 72000 structures optimized at SCC-DFTB level. These structures were sorted in ascending energy order. Secondly, 29 isomers were selected from the 72000 optimized structures at SCC-DFTB level and were optimized at a high accurate MP2/Def2TZVP level, which is a tight criteria for geometry convergence {\bf I don't understand what is the tight criteria ? the convergencey threshold ? } and an ultrafine grid for the numerical integration. \cite{Weigend2005, Weigend2006} From the MP2/Def2TZVP calculation, the lowest energy isomers of cluster (H$_2$O)$_{12}$UH$^+$ were obtained. All MP2 calculations were carried out with the Gaussian 09 package.\cite{GaussianCode}
|
||||
|
||||
\textbf{Dynamics Collision Simulations}
|
||||
|
||||
QM/MM method was used to describe the collision process of uracil protonated water cluster (QM) and Argon atom (MM) in the developed deMonNano code.\cite{Warshel1976} In the dynamics collision calculation, a Fermi distribution (Fermi temperature 2000 K) was applied to determine the molecular orbital occupations. It can avoid the oscillation problems during the search for a self-consistent solution, often appearing when DFTB energy for dissociated or close to dissociation system was calculated, which allows to recover the continuity in energy and gradients in the case of level crossing. \cite{Kukk2015} In the dynamics collision simulation, at the time of 200 fs, the Argon atom was given a velocity (0.0589 Å·fs$^{-1}$) corresponding to the 7.2 eV center of mass collision energy used in the experiment. \cite{Braud2019}. A series of dynamics collision simulation models were generated according to the distance between collision position and the center of size of the cluster. 600 dynamics collision simulations were performed every 0.5 Å from the center of size of each obtained lowest-energy cluster (H$_2$O)$_{n=3-7, 12}$UH$^+$ at molecular dynamics (MD) bath temperature 25 K. In case missing any collision, we set the biggest distance between collision position and the center of size of the cluster to be (R + 1) Å rather than the cluster radius R. So totally 600(2R + 3) simulations were calculated. Owing to cluster was set to rotate regularly during the generation of the models, the Ar atom can collide at almost all the possible positions of the cluster. The total simulation time was divided into 600(2R + 3) segments of 15 ps duration for each (H$_2$O)$_{n=3-7, 12}$UH$^+$. After the dynamics collision computation ends of every segment, the geometry of the system was analyzed to detect the possible fragments. A dissociation was defined to arise when the smallest distance between the atoms of two fragments is larger than a given critical distance 5.0 Å.
|
||||
{\bf QM/MM method was used to describe the collision process of uracil protonated water cluster (QM) and Argon atom (MM) in the developed deMonNano code.\cite{Warshel1976} Wrong reference, I prefere to put this in the PES exploration section see above} In the dynamics collision calculation, a Fermi distribution (Fermi temperature 2000 K) was applied to determine the molecular orbital occupations. It can avoid the oscillation problems during the search for a self-consistent solution, often appearing when DFTB energy for dissociated or close to dissociation system was calculated, which allows to recover the continuity in energy and gradients in the case of level crossing. \cite{Kukk2015} {\bf
|
||||
A bit of reordering : First describe in the right order what is a collsiion : 1=thermalistion 2=send the Argon 3=collect the results (fragments) Second, say what and how it is repeated : change in the impact parameter, 600 dynamics} In the dynamics collision simulation, at the time of 200 fs, the Argon atom was given a velocity (0.0589 Å·fs$^{-1}$) corresponding to the 7.2 eV center of mass collision energy used in the experiment. \cite{Braud2019}. A series of dynamics collision simulation models were generated according to the distance between collision position and the center of size of the cluster. 600 dynamics collision simulations were performed every 0.5 Å from the center of size of each obtained lowest-energy cluster (H$_2$O)$_{n=3-7, 12}$UH$^+$ at molecular dynamics (MD) bath temperature 25 K. {\bf in the following I think you speak about the distance which is actually the impact parameter ... } In case missing any collision, we set the biggest distance between collision position and the center of size of the cluster to be (R + 1) Å rather than the cluster radius R. So totally 600(2R + 3) {\bf it is not clear where this 2R+3 comes from} simulations were calculated. Owing to cluster was set to rotate regularly during the generation of the models, the Ar atom can collide at almost all the possible positions of the cluster. {\bf Rotateds regularly implies a motion which is not the case here. The target was randomly rotated to to allow for all possible collision point on the cluster} The total simulation time was divided into 600(2R + 3) segments of 15 ps duration for each {\bf remove (H$_2$O)$_{n=3-7, 12}$UH$^+$ replace by parent cluster}. After the dynamics collision computation ends of every segment, the geometry of the system was analyzed to detect the possible fragments. A dissociation was defined to arise when the smallest distance between the atoms of two fragments is larger than a given critical distance {\bf , typically} 5.0 Å.
|
||||
|
||||
\blue{i-PI?}
|
||||
|
||||
@ -165,25 +169,26 @@ QM/MM method was used to describe the collision process of uracil protonated wat
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section{Results and Discussion} \label{resul_disc}
|
||||
\textbf{The Distributions of the Initial Collision Models} In order to simulate the collision process of the obtained lowest-energy configuration of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters with Ar, a reasonable construction of the collision models are needed. In our dynamics collision simulations, totally 2R+3 series were performed for every (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster. And 600 models were conducted in every series. For visualization, the distribution maps of the initial positions of Ar atom with respect to each (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster configuration were made. Here we take the collision of Ar to (H$_2$O)$_4$UH$^+$ cluster as an example, Figure \ref{fig:sphere} displays the collision models of the relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration of the first series that the collision positions are at the center of size of the cluster. As shown in Figure \ref{fig:sphere}, the sphere in picture a is composed of 200 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. The sphere in picture b is composed of 400 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series and the sphere in picture c is composed of 600 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. From pictures a, b, and c in Figure \ref{fig:sphere}, it indicates the more simulations are performed, the more colliding opportunities at all the possible positions of (H$_2$O)$_4$UH$^+$ cluster Ar will have. As shown in picture d of Figure \ref{fig:sphere}, the outer layer of the sphere is the 200 relative Ar positions in the first series and the inner layer is the 200 relative Ar positions to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the last series (the distance between collision positions and the center of size of the cluster is R$_{(H_2O)_4UH^+}$ Å. The collision models of Ar and (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters are displayed in Figure SX in the SI. In experiment, the collision positions are randomly, which means that Ar can reach any position of the clusters. All the collision model pictures of Ar and (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters shows our constructions for the collision simulation models are reliable and close to the collision situation in the experiment. With these reasonable models, the explicit collision simulations were conducted. To confirm the statistical convergence is reached, we compare the proportions of neutral uracil molecules loss and the total fragmentation cross sections of (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters with those in experiment. As shown in Table S1 in SI, the data of 200 simulations, 400 simulations, and 600 simulations in every series for all (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters were almost the same, which indicates 600(2R + 3) simulations are enough.
|
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\textbf{The Distributions of the Initial Collision Models}
|
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{\bf MR : To me this part is not a result, it is a benchmark of that the collision simulations are well performed, it shoudl go at the end of the dynalics collision simulation section} In order to simulate the collision process of the obtained lowest-energy configuration of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters with Ar, a reasonable construction of the collision models are needed. In our dynamics collision simulations, totally 2R+3 series were performed for every (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster. And 600 models were conducted in every series. For visualization, the distribution maps of the initial positions of Ar atom with respect to each (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster configuration were made {\bf this discussion about the oritentation shoudl just be mentionned in the previous section when we speak about the rotation of the target and the plot go in the supplementary materials, this is technical benchmark}. Here we take the collision of Ar to (H$_2$O)$_4$UH$^+$ cluster as an example, Figure \ref{fig:sphere} displays the collision models of the relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration of the first series that the collision positions are at the center of size of the cluster. As shown in Figure \ref{fig:sphere}, the sphere in picture a is composed of 200 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. The sphere in picture b is composed of 400 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series and the sphere in picture c is composed of 600 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. From pictures a, b, and c in Figure \ref{fig:sphere}, it indicates the more simulations are performed, the more colliding opportunities at all the possible positions of (H$_2$O)$_4$UH$^+$ cluster Ar will have. As shown in picture d of Figure \ref{fig:sphere}, the outer layer of the sphere is the 200 relative Ar positions in the first series and the inner layer is the 200 relative Ar positions to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the last series (the distance between collision positions and the center of size of the cluster is R$_{(H_2O)_4UH^+}$ Å. The collision models of Ar and (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters are displayed in Figure SX in the SI. In experiment, the collision positions are randomly, which means that Ar can reach any position of the clusters. {\bf All the collision model pictures of Ar and (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters shows our constructions for the collision simulation models are reliable and close to the collision situation in the experiment. } With these reasonable models, the explicit collision simulations were conducted. To confirm the statistical convergence is reached {\bf comparing theory and experience does not proof that statistical convergence is reached,}, we compare the proportions of neutral uracil molecules loss and the total fragmentation cross sections of (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters with those in experiment. As shown in Table S1 in SI, the data of 200 simulations, 400 simulations, and 600 simulations in every series for all (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters were almost the same, which indicates 600(2R + 3) simulations are enough.
|
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\begin{figure}
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\includegraphics[width=0.4\linewidth]{figure/sphere}
|
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\centering
|
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\caption{Representation of initial Ar positions of the first series to perform collision simulations with the lowest-energy isomer of (H$_2$O)$_4$UH$^+$; For the first series, a: 200 representation of initial Ar positions; b: 400 representation of initial Ar positions; c: 600 representation of initial Ar positions; d: 200 representation of initial Ar positions of the first series and last series, separately.}
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\caption{Representation of initial Ar positions of the first series to perform collision simulations with the lowest-energy isomer of (H$_2$O)$_4$UH$^+$; For the first series, a: 200 representation of initial Ar positions; b: 400 representation of initial Ar positions; c: 600 representation of initial Ar positions; d: 200 representation of initial Ar positions of the first series and last series, separately. {\bf what about the impact parameter ? is it zero everywhere ? please precise otherwhise it is miseleading} }
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\label{fig:sphere}
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\end{figure}
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\textbf{Proportion of Neutral Uracil Molecule Loss}
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{\bf MR : to be discussed, I have the feeling that we give too much importanc to the experiment from the begeining, which might be not our best strencght, woudl it be more convincing to first discuss only our theoretical results in details, position iof the proton in table 1 as a function of the initial geometry, same for fragmentation ratio and only after compare with the experiment. In the therory part, we could say that the fragmentation ratio does not evolve a lot with the isomer but the PNUL evomves a lot, and then say we have almost zero for U-H; larger values for WHU and even larger for W-H, with some exceptions to be discussed. }
|
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Formula of calculating the proportion of neutral uracil loss:
|
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|
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In this part, the proportion of neutral uracil molecule loss of each lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster by colliding with Ar atom will be discussed. No neutral uracil loss for (H$_2$O)$_{n=1-4}$UH$^+$, the evaporation of uracil starts at n=5, and becomes significant at n=6 were observed in experiment.\cite{Braud2019} In our calculations, the proportions of neutral uracil molecule loss extracted from 600(2R + 3) dynamics collision simulations for (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were plotted in Figure \ref{fig:neutralUloss} as a function of number of water molecules n. As displayed in Figure \ref{fig:neutralUloss}, the overall trend of the proportion of neutral uracil molecule loss in theory is consistent with the one in experiment except the case n=5. The evaporation of neutral uracil molecule means the excess proton stayed in the water clusters. When n = 3-4, and 6-7 the neutral uracil loss increases with n. It indicates with the increase of the number of water molecules in the cluster, the excess proton is more likely to lie in the water cluster after collision.
|
||||
In this part, the proportion of neutral uracil molecule loss of each lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster by colliding with Ar atom will be discussed. {\bf No neutral uracil loss for (H$_2$O)$_{n=1-4}$UH$^+$, -> is very small not zero} the evaporation of uracil starts at n=5, and becomes significant at n=6 were observed in experiment.\cite{Braud2019} In our calculations, the proportions of neutral uracil molecule loss extracted from 600(2R + 3) dynamics collision simulations for (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were plotted in Figure \ref{fig:neutralUloss} as a function of number of water molecules n. As displayed in Figure \ref{fig:neutralUloss}, the overall trend of the proportion of neutral uracil molecule loss in theory is consistent with the one in experiment except the case n=5 {\bf MR: This is misleading because picture 1 is presented befiore saying that we took only the values we did like. Presenting all the therory before would make an easier way of presenting things. Saying clearly that we have to options, either we take the low energy ones or we take the isomers that fit the data. I also think that these two options shoudl be on the graph.}. The evaporation of neutral uracil molecule means the excess proton stayed in the water clusters. When n = 3-4, and 6-7 the neutral uracil loss increases with n. It indicates with the increase of the number of water molecules in the cluster, the excess proton is more likely to lie in the water cluster after collision.
|
||||
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.5\linewidth]{figure/Neutral_U_loss.eps}
|
||||
\centering
|
||||
\caption{Proportion of neutral uracil loss after collision of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ with Ar from both theoretical (pink line) and experiment (green line) results.}
|
||||
\caption{Proportion of neutral uracil loss after collision of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ with Ar from both theoretical (pink line) and experiment (green line) results. {\bf May be one shoudl put two theory curves, the lowest isomers and the one that fit the experiment}}
|
||||
\label{fig:neutralUloss}
|
||||
\end{figure}
|
||||
|
||||
@ -191,7 +196,7 @@ The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:
|
||||
|
||||
\begin{table}
|
||||
\begin{center}
|
||||
\caption{Neutral uracil loos proportion and total fragmentation cross section of different isomers of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ (PNUL refers to the proportion of neutral uracil loss; TFCS refers to the total fragmentation cross section; LEP refers to the location of the excess proton; U-H refers to the excess proton is on the uracil; W-H-U refers to the excess proton is on the water cluster but adjacent to one oxygen atom of uracil; W-H refers to the excess proton is completely on the water cluster and far from uracil).}
|
||||
\caption{Neutral uracil loos proportion and total fragmentation cross section of different isomers of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ (PNUL refers to the proportion of neutral uracil loss; TFCS refers to the total fragmentation cross section; LEP refers to the location of the excess proton; U-H refers to the excess proton is on the uracil; W-H-U refers to the excess proton is on the water cluster but adjacent to one oxygen atom of uracil; W-H refers to the excess proton is completely on the water cluster and far from uracil). {\bf could you please also add here the relative energy of the secondary minima and put in color the lines corresponding to the isomers that are choosen to fit the experiment. }}
|
||||
|
||||
\label{tab:table1}
|
||||
\begin{tabular}{c|c|c|l}
|
||||
@ -255,7 +260,7 @@ From Table \ref{tab:table1}, we can see for clusters (H$_2$O)$_{n=3-4}$UH$^+$ wi
|
||||
|
||||
\textbf{Total Fragmentation Cross Section} Formula of calculating the cross section:
|
||||
|
||||
In the light of the results of 600(2R + 3) dynamics collision simulations for each lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster, the total fragmentation cross sections of the (H$_2$O)$_{n=3-7}$UH$^+$ clusters were determined and compared with those in experiment. As shown in Table \ref{tab:table1}, for different isomers of lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters, the total fragmentation cross sections are very close. So in this part, we only discuss the total fragmentation cross section of the lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster who has the closest neutral uracil loss proportion compared with the one in experiment.
|
||||
In the light of the results of 600(2R + 3) dynamics collision simulations for each lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster, the total fragmentation cross sections of the (H$_2$O)$_{n=3-7}$UH$^+$ clusters were determined and compared with those in experiment. As shown in Table \ref{tab:table1}, for different isomers of lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters, the total fragmentation cross sections are very close. So in this part, we only discuss the total fragmentation cross section of the lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster who has the closest neutral uracil loss proportion compared with the one in experiment. {\bf this is miseleading because Figs 2 and 6 does not represent the salme `theory' data, I would prefer to have on both pictures two theory curves : the lowest isomers and the one with the isomers fitting the best the data for PNUL}
|
||||
|
||||
The total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters from our simulation results of collision with Ar and the corresponding experiment results are plotted in Figure \ref{fig:crosssection} as a function of the number of water molecules n at 7.2 eV center of mass collision energy. As displayed in Figure \ref{fig:crosssection}, the curves in theory and in experiment have the same overall trend that the total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters increase according to the number of water molecules. This indicates when the size of the clusters increase, the Ar and the cluster has a higher opportunity to collide. For (H$_2$O)$_7$UH$^+$ cluster, the value in theory is slightly lower than the one of (H$_2$O)$_6$UH$^+$ cluster but the difference is only 1.3 Å$^2$, which is within the limit of error. Additionally, the absolute value of total fragmentation cross sections of (H$_2$O)$_{n=3-7}$UH$^+$ clusters in theory and experiment are close to each other. The biggest and smallest differences of the total fragmentation cross section for (H$_2$O)$_{n=3-7}$UH$^+$ clusters are 7.0 and 1.5 Å$^2$, separately between our calculation results and those in the experiment. Those results imply our simulations results are good enough.
|
||||
|
||||
@ -363,7 +368,8 @@ As displayed in Figure \ref{fig:mass_spec}, the intensity of fragments (H$_2$O)$
|
||||
\end{figure}
|
||||
|
||||
|
||||
\textbf{Time-Dependent Proportion of Each Fragment}
|
||||
\textbf{Time-Dependent Proportion of Each Fragment}
|
||||
{\bf MR : this is a pure theory part, this deals with short times convergency, to me it should reinforce the result part analysing the theoretical results before any reference to the experiment is done.}
|
||||
|
||||
In addition, the time-dependent proportion of each fragment was extracted from 600(2R + 3) dynamics collision simulations. Here we take the time-dependent proportion of each fragment from the dissociation second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ and the sixth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are showed in Figure 7. The proportions of the main fragment of clusters (H$_2$O)$_{n=3-6}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag_7_2}, it is clear that the parent cluster (H$_2$O)$_7$UH$^+$ exists from the beginning and different fragments starts to appear after collision. It can be seen when the collision is finished, the fragment proportions almost doesn’t change any more. It is worth noticing the fragment (H$_2$O)$_6$UH$^+$ increase first and then it decreases, which indicates there are water molecules dissociated from it. For fragment proportios of cluster (H$_2$O)$_{12}$UH$^+$, from Figure \ref{fig:proporEachFrag_12_6}, it shows fragments
|
||||
(H$_2$O)$_{11}$UH$^+$ and (H$_2$O)$_{10}$UH$^+$ increase at the beginning and then decrease, and finally they tend to be steady. The second and the third or more times dissociation after collision and all the main fragment proportion do not tend to a constant so fast imply that there are more chances to rearrange prior to complete dissociation.
|
||||
|
||||
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Reference in New Issue
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