2019-10-15 13:28:39 +02:00
%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for mathias at 2019-10-15 13:28:19 +0200
%% Saved with string encoding Unicode (UTF-8)
@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}}
2019-09-26 19:57:18 +02:00
@article { Rasmussen2010 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
@article { Coates2018 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
@article { Imhoff2007 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
@article { Abdoul2000 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
@article { Champeaux2010 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
2019-09-27 18:55:30 +02:00
@article { Korchagina2017 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
@article { Delaunay2014 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
2019-09-27 18:55:30 +02:00
@article { Bacchus2009 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Kossoski2015 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Maclot2011 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@inproceedings { Domaracka2012 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Markush2016 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Castrovilli2017 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@incollection { Hayes1990 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Coates2017 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Neustetter2017 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Nelson1994 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
2019-09-27 18:55:30 +02:00
@article { Molina2015 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-26 19:57:18 +02:00
2019-09-27 18:55:30 +02:00
@article { Molina2016 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Sadr2014 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Bakker2008 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Simon2017 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Elstner2014 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Kruger2005 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Elstner1998 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Rapacioli2009 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Simon2012 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Simon2013 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { demonnanoCode ,
2019-10-15 13:28:39 +02:00
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).}}
2019-09-27 18:55:30 +02:00
@article { Braud2019 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Sugita1999 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Earl2005 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Nose1984 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Hoover1985 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Pedersen2014 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Weigend2005 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Weigend2006 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { GaussianCode ,
2019-10-15 13:28:39 +02:00
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.}}
2019-09-27 18:55:30 +02:00
@article { Warshel1976 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Kukk2015 ,
2019-10-15 13:28:39 +02:00
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}}
2019-09-27 18:55:30 +02:00
@article { Magnera1991 ,
2019-10-15 13:28:39 +02:00
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}}
2019-11-14 17:03:29 +01:00
@article { kapil2019pi ,
title={i-PI 2.0: A universal force engine for advanced molecular simulations},
author={Kapil, Venkat and Rossi, Mariana and Marsalek, Ondrej and Petraglia, Riccardo and Litman, Yair and Spura, Thomas and Cheng, Bingqing and Cuzzocrea, Alice and Mei{\ss}ner, Robert H and Wilkins, David M and others},
journal={Computer Physics Communications},
volume={236},
pages={214--223},
year={2019},
publisher={Elsevier}
}
