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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for mathias at 2019-10-15 13:28:19 +0200
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@article{Keesee1989,
author = {Keesee, R. G.},
title = {Nucleation and particle formation in the upper atmosphere},
journal = {Journal of Geophysical Research: Atmospheres},
volume = {94},
number = {D12},
pages = {14683--14692},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/JD094iD12p14683},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/JD094iD12p14683},
year = {1989}}
@article{Gilligan2000,
title={Reactions of protonated water clusters with chlorine nitrate revisited},
author={Gilligan, JJ and Moody, DJ and Castleman, AW},
journal={Zeitschrift f{\"u}r Physikalische Chemie},
volume={214},
number={10},
pages={1383--1391},
year={2000},
publisher={De Gruyter Oldenbourg}}
@article{Sennikov2005,
title={Complexes and clusters of water relevant to atmospheric chemistry: H2O complexes with oxidants},
author={Sennikov, Petr G and Ignatov, Stanislav K and Schrems, Otto},
journal={ChemPhysChem},
volume={6},
number={3},
pages={392--412},
year={2005},
publisher={Wiley Online Library}}
@article{Cabellos2016,
author = {Vargas-Caamal, Alba and Cabellos, Jose Luis and Ortiz-Chi, Filiberto and Rzepa, Henry S. and Restrepo, Albeiro and Merino, Gabriel},
title = {How Many Water Molecules Does it Take to Dissociate HCl?},
journal = {Chemistry A European Journal},
volume = {22},
number = {8},
pages = {2812--2818},
year = {2016}}
@article{Orabi2013,
title={Polarizable interaction model for liquid, supercritical, and aqueous ammonia},
author={Orabi, Esam A and Lamoureux, Guillaume},
journal={Journal of chemical theory and computation},
volume={9},
number={4},
pages={2035--2051},
year={2013},
publisher={ACS Publications}}
@article{Bommer2016,
title={Crystallographic and computational analysis of the barrel part of the PsbO protein of photosystem II: Carboxylate--water clusters as putative proton transfer relays and structural switches},
author={Bommer, Martin and Bondar, Ana-Nicoleta and Zouni, Athina and Dobbek, Holger and Dau, Holger},
journal={Biochemistry},
volume={55},
number={33},
pages={4626--4635},
year={2016},
publisher={ACS Publications}}
@article{Galashev2010,
title={Molecular-dynamic modeling of ultradisperse water in the earth atmosphere},
author={Galashev, Alexander E},
journal={High Temperature},
volume={48},
number={4},
pages={518--526},
year={2010},
publisher={Springer}}
@article{Kulmala2004,
title={Formation and growth rates of ultrafine atmospheric particles: A review of observations},
author={M. Kulmala and H. Vehkamäki and T. Petäjä and M. Dal Maso and A. Lauri and V.-M. Kerminen and W. Birmili and P.H. McMurry},
journal={Journal of Aerosol Science},
volume={35},
number={2},
pages={143--176},
year={2004},
publisher={lsevier Limited}}
@article{Perkins1984,
title={First mass spectrometric measurements of atmospheric ions at ground level},
author={Perkins, Mark D and Eisele, Fred L},
journal={Journal of Geophysical Research: Atmospheres},
volume={89},
number={D6},
pages={9649--9657},
year={1984},
publisher={Wiley Online Library}}
@article{Arnold1997,
title={Atmospheric measurements of aerosol precursor gases in the upper troposphere and lower stratosphere},
author={Arnold, F and Wohlfrom, KH and Schneider, J and Klemm, M and Stilp, T and Grimm, F},
journal={Journal of Aerosol Science},
volume={1001},
number={28},
pages={S65--S66},
year={1997}}
@article{Stockman1992,
title={Microwave and tunable far-infrared laser spectroscopy of the ammonia--water dimer},
author={Stockman, Paul A and Bumgarner, Roger E and Suzuki, Sakae and Blake, Geoffrey A},
journal={The Journal of chemical physics},
volume={96},
number={4},
pages={2496--2510},
year={1992},
publisher={American Institute of Physics}}
@article{Herbine1985,
title={Rotational spectra and structure of the ammonia--water complex},
author={Herbine, P and Dyke, TR},
journal={The Journal of chemical physics},
volume={83},
number={8},
pages={3768--3774},
year={1985},
publisher={American Institute of Physics}}
@article{Hvelplund2010,
title={Stability and Structure of Protonated Clusters of Ammonia and Water, H+ (NH3) m (H2O) n},
author={Hvelplund, Preben and Kurten, Theo and St{\o}chkel, Kristian and Ryding, Mauritz Johan and Nielsen, Steen Br{\o}ndsted and Uggerud, Einar},
journal={The Journal of Physical Chemistry A},
volume={114},
number={27},
pages={7301--7310},
year={2010},
publisher={ACS Publications}}
@article{Douady2009,
title={Effect of an ionic impurity on the caloric curves of water clusters},
author={Douady, Julie and Calvo, Florent and Spiegelman, Fernand},
journal={The European Physical Journal D},
volume={52},
number={1-3},
pages={47--50},
year={2009},
publisher={Springer}}
@article{Douady2008,
title={Structure, stability, and infrared spectroscopy of (H 2 O) n NH 4+ clusters: A theoretical study at zero and finite temperature},
author={Douady, Julie and Calvo, Florent and Spiegelman, Fernand},
journal={The Journal of chemical physics},
volume={129},
number={15},
pages={154305},
year={2008},
publisher={American Institute of Physics}}
@article{Morrell2010,
title={Atmospheric implications for formation of clusters of ammonium and 1- 10 water molecules},
author={Morrell, Thomas E and Shields, George C},
journal={The Journal of Physical Chemistry A},
volume={114},
number={12},
pages={4266--4271},
year={2010},
publisher={ACS Publications}}
@article{Bacelo2002,
title={Theoretical study of microscopic solvation of ammonia in water clusters: NH3 (H2O) n, n= 3, 4},
author={Bacelo, Daniel E},
journal={The Journal of Physical Chemistry A},
volume={106},
number={46},
pages={11190--11196},
year={2002},
publisher={ACS Publications}}
@article{Wang1998,
author = {Wang, Yih-Sheng and Chang, Hai-Chou and Jiang, Jyh-Chiang and Lin, Sheng H. and Lee, Yuan T. and Chang, Huan-Cheng},
title = {Structures and Isomeric Transitions of NH4+(H2O)3-6: From Single to Double Rings},
journal = {Journal of the American Chemical Society},
volume = {120},
number = {34},
pages = {8777-8788},
year = {1998}}
@article{Hulthe1997,
title={Water clusters studied by electrospray mass spectrometry},
author={Hulthe, Gustaf and Stenhagen, Gunnar and Wennerstr{\"o}m, Olof and Ottosson, Carl-Henrik},
journal={Journal of Chromatography A},
volume={777},
number={1},
pages={155--165},
year={1997},
publisher={Elsevier}}
@article{Hvelplund2010,
title={Stability and Structure of Protonated Clusters of Ammonia and Water, H+ (NH3) m (H2O) n},
author={Hvelplund, Preben and Kurten, Theo and St{\o}chkel, Kristian and Ryding, Mauritz Johan and Nielsen, Steen Br{\o}ndsted and Uggerud, Einar},
journal={The Journal of Physical Chemistry A},
volume={114},
number={27},
pages={7301--7310},
year={2010},
publisher={ACS Publications}}
@article{Herbine1985,
title={Rotational spectra and structure of the ammonia--water complex},
author={Herbine, P and Dyke, TR},
journal={The Journal of chemical physics},
volume={83},
number={8},
pages={3768--3774},
year={1985},
publisher={American Institute of Physics}}
@article{Chang1998,
title={Studying protonated ion hydration by infrared spectroscopy of size-selected NH4+ (H2O) n clusters in a free jet expansion},
author={Chang, Hai-Chou and Wang, Yih-Sheng and Lee, Yuan T and Chang, Huan-Cheng},
journal={International journal of mass spectrometry},
volume={179},
pages={91--102},
year={1998},
publisher={Elsevier}}
@article{Jiang1999,
title={Ab initio Studies of NH4+ (H2O) 1-5 and the Influence of Hydrogen-Bonding Nonadditivity on Geometries and Vibrations},
author={Jiang, JC and Chang, H-C and Lee, YT and Lin, SH},
journal={The Journal of Physical Chemistry A},
volume={103},
number={16},
pages={3123--3135},
year={1999},
publisher={ACS Publications}}
@article{Galashev2013,
title={A computer study of ammonium adsorption on water clusters},
author={Galashev, AE},
journal={Russian Journal of Physical Chemistry B},
volume={7},
number={4},
pages={502--508},
year={2013},
publisher={Springer}}
@article{Sadlej1999,
title={Structure and Energetics of the Weakly Bound NH3⊙⊙⊙ H2O Complex},
author={Sadlej, J and Moszynski, R and Dobrowolski, J Cz and Mazurek, AP},
journal={The Journal of Physical Chemistry A},
volume={103},
number={42},
pages={8528--8536},
year={1999},
publisher={ACS Publications}}
@article{Skurski1998,
title={Theoretical study of the dipole-bound anion (H 2 O… NH 3)-},
author={Skurski, Piotr and Gutowski, Maciej},
journal={The Journal of chemical physics},
volume={108},
number={15},
pages={6303--6311},
year={1998},
publisher={American Institute of Physics}}
@article{Lee1996,
title={Ionization of Bases in Water: Structure and Stability of the NH4+⊙⊙⊙ OH-Ionic Forms in Ammonia- Water Clusters},
author={Lee, Chengteh and Fitzgerald, George and Planas, Marc and Novoa, Juan J},
journal={The Journal of Physical Chemistry},
volume={100},
number={18},
pages={7398--7404},
year={1996},
publisher={ACS Publications}}
@article{Donaldson1999,
title={Adsorption of atmospheric gases at the air- water interface. I. NH3},
author={Donaldson, DJ},
journal={The Journal of Physical Chemistry A},
volume={103},
number={1},
pages={62--70},
year={1999},
publisher={ACS Publications}}
@article{Elstner1998,
title={Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties},
author={Elstner, Marcus and Porezag, Dirk and Jungnickel, G and Elsner, J and Haugk, M and Frauenheim, Th and Suhai, Sandor and Seifert, Gotthard},
journal={Physical Review B},
volume={58},
number={11},
pages={7260--7268},
year={1998},
publisher={APS}}
@article{Elstner2014,
title={Density functional tight binding},
author={Elstner, Marcus and Seifert, Gotthard},
journal={Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
volume={372},
number={2011},
pages={20120483},
year={2014},
publisher={The Royal Society Publishing}}
@article{Winget2003,
title={Towards a next generationneglect of diatomic differential overlap based semiempirical molecular orbital technique},
author={Winget, Paul and Selcuki, Cenk and Horn, Anselm HC and Martin, Bodo and Clark, Timothy},
journal={Theoretical Chemistry Accounts},
volume={110},
number={4},
pages={254--266},
year={2003},
publisher={Springer}
}
@article{Gaus2011dftb3,
title={DFTB3: extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB)},
author={Gaus, Michael and Cui, Qiang and Elstner, Marcus},
journal={Journal of chemical theory and computation},
volume={7},
number={4},
pages={931--948},
year={2011},
publisher={ACS Publications}}
@article{Gaus2013para,
title={Parametrization and benchmark of DFTB3 for organic molecules},
author={Gaus, Michael and Goez, Albrecht and Elstner, Marcus},
journal={Journal of Chemical Theory and Computation},
volume={9},
number={1},
pages={338--354},
year={2013},
publisher={ACS Publications}}
@article{Elstner2001,
author = {Elstner,Marcus and Hobza,Pavel and Frauenheim,Thomas and Suhai,Sándor and Kaxiras,Efthimios },
title = {Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment},
journal = {The Journal of Chemical Physics},
volume = {114},
number = {12},
pages = {5149-5155},
year = {2001}}
@article{Zhechkov2005,
title={An efficient a posteriori treatment for dispersion interaction in density-functional-based tight binding},
author={Zhechkov, Lyuben and Heine, Thomas and Patchkovskii, Serguei and Seifert, Gotthard and Duarte, Helio A},
journal={Journal of Chemical Theory and Computation},
volume={1},
number={5},
pages={841--847},
year={2005},
publisher={ACS Publications}}
@article{Thompson2003,
title={Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP},
author={Thompson, Jason D and Cramer, Christopher J and Truhlar, Donald G},
journal={Journal of computational chemistry},
volume={24},
number={11},
pages={1291--1304},
year={2003},
publisher={Wiley Online Library}}
@article{Winget2002,
title={Charge Model 3: A class IV charge model based on hybrid density functional theory with variable exchange},
author={Winget, Paul and Thompson, Jason D and Xidos, James D and Cramer, Christopher J and Truhlar, Donald G},
journal={The Journal of Physical Chemistry A},
volume={106},
number={44},
pages={10707--10717},
year={2002},
publisher={ACS Publications}}
@article{Giambiagi1975,
title={Sur la d{\'e}finition dun indice de liaison (TEV) pour des bases non orthogonales. Propri{\'e}t{\'e}s et applications},
author={Giambiagi, Mario and Giambiagi, Myriam and Grempel, Daniel Rub{\'e}n and Heymann, Carlos Daniel},
journal={Journal de Chimie Physique},
volume={72},
pages={15--22},
year={1975},
publisher={EDP Sciences}}
@article{Mayer1983,
title={Charge, bond order and valence in the AB initio SCF theory},
author={Mayer, I},
journal={Chemical Physics Letters},
volume={97},
number={3},
pages={270--274},
year={1983},
publisher={Elsevier}}
@article{Odutola1980,
title={Partially deuterated water dimers: Microwave spectra and structure},
author={Odutola, JA and Dyke, TR},
journal={The Journal of Chemical Physics},
volume={72},
number={9},
pages={5062--5070},
year={1980},
publisher={American Institute of Physics}}
@article{Sugita2000,
title={Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape},
author={Sugita, Yuji and Okamoto, Yuko},
journal={Chemical Physics Letters},
volume={329},
number={3-4},
pages={261--270},
year={2000},
publisher={Elsevier}}
@article{Oliveira2015,
title={Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons},
author={Oliveira, Luiz Fernando L and Cuny, J{\'e}r{\^o}me and Morini{\`e}re, Maxime and Dontot, L{\'e}o and Simon, Aude and Spiegelman, Fernand and Rapacioli, Mathias},
journal={Physical Chemistry Chemical Physics},
volume={17},
number={26},
pages={17079--17089},
year={2015},
publisher={Royal Society of Chemistry}}
@article{Korchagina2016,
title={Structural characterization of sulfur-containing water clusters using a density-functional based tight-binding approach},
author={Korchagina, Kseniia A and Simon, Aude and Rapacioli, Mathias and Spiegelman, Fernand and Cuny, Jerome},
journal={The Journal of Physical Chemistry A},
volume={120},
number={45},
pages={9089--9100},
year={2016},
publisher={ACS Publications}}
@article{Boys2002,
title={The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors},
author={Boys, SF and Bernardi, F},
journal={Molecular Physics},
volume={100},
number={1},
pages={65--73},
year={2002},
publisher={Taylor \& Francis}}
@article{Lee2004,
title={Insights into the Structures, Energetics, and Vibrations of Monovalent Cation-(Water) 1-6 Clusters},
author={Lee, Han Myoung and Tarakeshwar, P and Park, Jungwon and Ko{\l}aski, Maciej Roman and Yoon, Yeo Jin and Yi, Hai-Bo and Kim, Woo Youn and Kim, Kwang S},
journal={The Journal of Physical Chemistry A},
volume={108},
number={15},
pages={2949--2958},
year={2004},
publisher={ACS Publications}}
@article{Pickard2005,
title={Comparison of model chemistry and density functional theory thermochemical predictions with experiment for formation of ionic clusters of the ammonium cation complexed with water and ammonia; atmospheric implications},
author={Pickard IV, Frank C and Dunn, Meghan E and Shields, George C},
journal={The Journal of Physical Chemistry A},
volume={109},
number={22},
pages={4905--4910},
year={2005},
publisher={ACS Publications}}
@article{Kazimirski2003,
title={Search for low energy structures of water clusters (H2O) n, n= 20- 22, 48, 123, and 293},
author={Kazimirski, Jan K and Buch, Victoria},
journal={The Journal of Physical Chemistry A},
volume={107},
number={46},
pages={9762--9775},
year={2003},
publisher={ACS Publications}}
@article{Bandow2006,
title={Larger water clusters with edges and corners on their way to ice: Structural trends elucidated with an improved parallel evolutionary algorithm},
author={Bandow, Bernhard and Hartke, Bernd},
journal={The Journal of Physical Chemistry A},
volume={110},
number={17},
pages={5809--5822},
year={2006},
publisher={ACS Publications}}
@article{bzar,
Author = {Iftner, Christophe and Simon, Aude and Korchagina, Kseniia and Rapacioli, Mathias and Spiegelman, Fernand},
Date = {2014},
Date-Added = {2019-10-15 11:28:17 +0000},
Date-Modified = {2019-10-15 11:28:17 +0000},
Journal = {The Journal of Chemical Physics},
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,
Author = {Seifert, G and Porezag, D and Frauenheim, Th},
Date-Added = {2019-10-15 11:27:56 +0000},
Date-Modified = {2019-10-15 11:27:56 +0000},
Journal = {Int. J. Quantum Chem.},
Number = {2},
Pages = {185--192},
Publisher = {Wiley Online Library},
Title = {Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme},
Volume = {58},
Year = {1996}}
@article{dftb1,
Author = {Porezag, Dirk and Frauenheim, Th and K{\"o}hler, Th and Seifert, Gotthard and Kaschner, R},
Date-Added = {2019-10-15 11:27:56 +0000},
Date-Modified = {2019-10-15 11:27:56 +0000},
Journal = {Phys. Rev. B},
Number = {19},
Pages = {12947--12958},
Publisher = {APS},
Title = {Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon},
Volume = {51},
Year = {1995}}
@article{Rasmussen2010,
Author = {Rasmussen, Andrew M and Lind, Maria C and Kim, Sunghwan and Schaefer III, Henry F},
Journal = {Journal of chemical theory and computation},
Number = {3},
Pages = {930--939},
Publisher = {ACS Publications},
Title = {Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines},
Volume = {6},
Year = {2010}}
@article{Coates2018,
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}}
@article{Imhoff2007,
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,
Author = {Abdoul-Carime, H and Huels, MA and Br{\"u}ning, F and Illenberger, E and Sanche, L},
Journal = {The journal of chemical physics},
Number = {7},
Pages = {2517--2521},
Publisher = {AIP},
Title = {Dissociative electron attachment to gas-phase 5-bromouracil},
Volume = {113},
Year = {2000}}
@article{Champeaux2010,
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}}
@article{Korchagina2017,
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},
Volume = {121},
Year = {2017}}
@article{Delaunay2014,
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,
Author = {Bacchus-Montabonel, MC and Tergiman, YS and Talbi, Dahbia},
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,
Author = {Kossoski, Fabris and Varella, MT do N},
Journal = {Physical Chemistry Chemical Physics},
Number = {26},
Pages = {17271--17278},
Publisher = {Royal Society of Chemistry},
Title = {Negative ion states of 5-bromouracil and 5-iodouracil},
Volume = {17},
Year = {2015}}
@article{Maclot2011,
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},
Number = {5},
Pages = {930--936},
Publisher = {Wiley Online Library},
Title = {Ion-Induced Fragmentation of Amino Acids: Effect of the Environment},
Volume = {12},
Year = {2011}}
@inproceedings{Domaracka2012,
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},
Booktitle = {Journal of Physics: Conference Series},
Number = {1},
Organization = {IOP Publishing},
Pages = {012005},
Title = {Ion interaction with biomolecular systems and the effect of the environment},
Volume = {373},
Year = {2012}}
@article{Markush2016,
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},
Journal = {Physical Chemistry Chemical Physics},
Number = {25},
Pages = {16721--16729},
Publisher = {Royal Society of Chemistry},
Title = {The role of the environment in the ion induced fragmentation of uracil},
Volume = {18},
Year = {2016}}
@article{Castrovilli2017,
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},
Journal = {Physical Chemistry Chemical Physics},
Number = {30},
Pages = {19807--19814},
Publisher = {Royal Society of Chemistry},
Title = {Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments},
Volume = {19},
Year = {2017}}
@incollection{Hayes1990,
Author = {Hayes, Roger N and Gross, Michael L},
Booktitle = {Methods in enzymology},
Pages = {237--263},
Publisher = {Elsevier},
Title = {[10] Collision-induced dissociation},
Volume = {193},
Year = {1990}}
@article{Coates2017,
Author = {Coates, Rebecca A and Armentrout, PB},
Journal = {The Journal of Physical Chemistry A},
Number = {19},
Pages = {3629--3646},
Publisher = {ACS Publications},
Title = {Thermochemical Investigations of Hydrated Nickel Dication Complexes by Threshold Collision-Induced Dissociation and Theory},
Volume = {121},
Year = {2017}}
@article{Neustetter2017,
Author = {Neustetter, Michael and Mahmoodi-Darian, Masoomeh and Denifl, Stephan},
Journal = {Journal of The American Society for Mass Spectrometry},
Number = {5},
Pages = {866--872},
Publisher = {Springer},
Title = {Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters},
Volume = {28},
Year = {2017}}
@article{Nelson1994,
Author = {Nelson, Chad C and McCloskey, James A},
Journal = {Journal of the American Society for Mass Spectrometry},
Number = {5},
Pages = {339--349},
Publisher = {Springer},
Title = {Collision-induced dissociation of uracil and its derivatives},
Volume = {5},
Year = {1994}}
@article{Molina2015,
Author = {Molina, Estefan{\'\i}a Rossich and Ortiz, Daniel and Salpin, Jean-Yves and Spezia, Riccardo},
Journal = {Journal of mass spectrometry},
Number = {12},
Pages = {1340--1351},
Publisher = {Wiley Online Library},
Title = {Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments},
Volume = {50},
Year = {2015}}
@article{Molina2016,
Author = {Molina, Estefan{\'\i}a Rossich and Salpin, Jean-Yves and Spezia, Riccardo and Martinez-Nunez, Emilio},
Journal = {Physical Chemistry Chemical Physics},
Number = {22},
Pages = {14980--14990},
Publisher = {Royal Society of Chemistry},
Title = {On the gas phase fragmentation of protonated uracil: a statistical perspective},
Volume = {18},
Year = {2016}}
@article{Sadr2014,
Author = {Sadr-Arani, Leila and Mignon, Pierre and Chermette, Henry and Douki, Thierry},
Journal = {Chemical Physics Letters},
Pages = {108--114},
Publisher = {Elsevier},
Title = {Theoretical and experimental study of the fragmentation of protonated uracil},
Volume = {605},
Year = {2014}}
@article{Bakker2008,
Author = {Bakker, Joost M and Sinha, Rajeev K and Besson, Thierry and Brugnara, Maurizio and Tosi, Paolo and Salpin, Jean-Yves and Ma{\^\i}tre, Philippe},
Journal = {The Journal of Physical Chemistry A},
Number = {48},
Pages = {12393--12400},
Publisher = {ACS Publications},
Title = {Tautomerism of uracil probed via infrared spectroscopy of singly hydrated protonated uracil},
Volume = {112},
Year = {2008}}
@article{Simon2017,
Author = {Simon, Aude and Rapacioli, Mathias and Rouaut, Guillaume and Trinquier, Georges and Gad{\'e}a, FX},
Journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
Number = {2092},
Pages = {20160195},
Publisher = {The Royal Society Publishing},
Title = {Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies},
Volume = {375},
Year = {2017}}
@article{Elstner2014,
Author = {Elstner, Marcus and Seifert, Gotthard},
Journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
Number = {2011},
Pages = {20120483},
Publisher = {The Royal Society Publishing},
Title = {Density functional tight binding},
Volume = {372},
Year = {2014}}
@article{Kruger2005,
Author = {Kr{\"u}ger, Thomas and Elstner, Marcus and Schiffels, Peter and Frauenheim, Thomas},
Journal = {The Journal of chemical physics},
Number = {11},
Pages = {114110},
Publisher = {AIP},
Title = {Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data},
Volume = {122},
Year = {2005}}
@article{Elstner1998,
Author = {Elstner, Marcus and Porezag, Dirk and Jungnickel, G and Elsner, J and Haugk, M and Frauenheim, Th and Suhai, Sandor and Seifert, Gotthard},
Journal = {Physical Review B},
Number = {11},
Pages = {7260--7268},
Publisher = {APS},
Title = {Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties},
Volume = {58},
Year = {1998}}
@article{Rapacioli2009,
Author = {Rapacioli, Mathias and Spiegelman, Fernand and Talbi, Dahbia and Mineva, Tzonka and Goursot, Annick and Heine, Thomas and Seifert, Gotthard},
Journal = {The Journal of chemical physics},
Number = {24},
Pages = {244304},
Publisher = {AIP},
Title = {Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters},
Volume = {130},
Year = {2009}}
@article{Simon2012,
Author = {Simon, Aude and Rapacioli, Mathias and Mascetti, Jo{\"e}lle and Spiegelman, Fernand},
Journal = {Physical Chemistry Chemical Physics},
Number = {19},
Pages = {6771--6786},
Publisher = {Royal Society of Chemistry},
Title = {Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons},
Volume = {14},
Year = {2012}}
@article{Simon2013,
Author = {Simon, Aude and Spiegelman, Fernand},
Journal = {Computational and Theoretical Chemistry},
Pages = {54--61},
Publisher = {Elsevier},
Title = {Conformational dynamics and finite-temperature infrared spectra of the water octamer adsorbed on coronene},
Volume = {1021},
Year = {2013}}
@article{demonnanoCode,
Author = {Heine, T.; Rapacioli, M.; Patchkovskii, S.; Frenzel, J.; Koster, A.; Calaminici, P.; Duarte, H.; Escalante, S.; Flores-Moreno, R.; Goursot, A.; et al.},
Publisher = {deMonNano. http://demon-nano.ups-tlse.fr/ (accessed 24 October 2016).}}
@article{Braud2019,
Author = {Braud, Isabelle and Zamith, S{\'e}bastien and Cuny, J{\'e}r{\^o}me and Zheng, Linjie and L'Hermite, Jean-Marc},
Journal = {The Journal of chemical physics},
Number = {1},
Pages = {014303},
Publisher = {AIP Publishing},
Title = {Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study},
Volume = {150},
Year = {2019}}
@article{Sugita1999,
Author = {Sugita, Yuji and Okamoto, Yuko},
Journal = {Chemical physics letters},
Number = {1-2},
Pages = {141--151},
Publisher = {Elsevier},
Title = {Replica-exchange molecular dynamics method for protein folding},
Volume = {314},
Year = {1999}}
@article{Earl2005,
Author = {Earl, David J and Deem, Michael W},
Journal = {Physical Chemistry Chemical Physics},
Number = {23},
Pages = {3910--3916},
Publisher = {Royal Society of Chemistry},
Title = {Parallel tempering: Theory, applications, and new perspectives},
Volume = {7},
Year = {2005}}
@article{Nose1984,
Author = {Nos{\'e}, Shuichi},
Journal = {The Journal of chemical physics},
Number = {1},
Pages = {511--519},
Publisher = {AIP},
Title = {A unified formulation of the constant temperature molecular dynamics methods},
Volume = {81},
Year = {1984}}
@article{Hoover1985,
Author = {Hoover, William G},
Journal = {Physical review A},
Number = {3},
Pages = {1695--1697},
Publisher = {APS},
Title = {Canonical dynamics: Equilibrium phase-space distributions},
Volume = {31},
Year = {1985}}
@article{Pedersen2014,
Author = {Pedersen, Sara {\O}vad and Byskov, Camilla Skinnerup and Turecek, Frantisek and Nielsen, Steen Br{\o}ndsted},
Journal = {The Journal of Physical Chemistry A},
Number = {24},
Pages = {4256--4265},
Publisher = {ACS Publications},
Title = {Structures of protonated thymine and uracil and their monohydrated gas-phase ions from ultraviolet action spectroscopy and theory},
Volume = {118},
Year = {2014}}
@article{Weigend2005,
Author = {Weigend, Florian and Ahlrichs, Reinhart},
Journal = {Physical Chemistry Chemical Physics},
Number = {18},
Pages = {3297--3305},
Publisher = {The Royal Society of Chemistry},
Title = {Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy},
Volume = {7},
Year = {2005}}
@article{Weigend2006,
Author = {Weigend, Florian},
Journal = {Physical chemistry chemical physics},
Number = {9},
Pages = {1057--1065},
Publisher = {Royal Society of Chemistry},
Title = {Accurate Coulomb-fitting basis sets for H to Rn},
Volume = {8},
Year = {2006}}
@article{GaussianCode,
Author = {M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson et al.},
Publisher = {G AUSSIAN 09, Revision D.01, Gaussian, Inc., Wallingford, CT, 2009.}}
@article{Warshel1976,
Author = {Warshel, Arieh and Levitt, Michael},
Journal = {Journal of molecular biology},
Number = {2},
Pages = {227--249},
Publisher = {Elsevier},
Title = {Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme},
Volume = {103},
Year = {1976}}
@article{Kukk2015,
Author = {Kukk, Edwin and Ha, DT and Wang, Y and Piekarski, Dariusz Grzegorz and Diaz-Tendero, Sergio and Kooser, Kuno and It{\"a}l{\"a}, Eero and Levola, Helena and Alcam{\'\i}, Manuel and Rachlew, Elisabeth and others},
Journal = {Physical Review A},
Number = {4},
Pages = {043417},
Publisher = {APS},
Title = {Internal energy dependence in X-ray-induced molecular fragmentation: an experimental and theoretical study of thiophene},
Volume = {91},
Year = {2015}}
@article{Magnera1991,
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}}