2979 lines
120 KiB
Plaintext
2979 lines
120 KiB
Plaintext
\begin{thebibliography}{100}
|
||
|
||
\bibitem{Cotton1964}
|
||
{\sc F~A Cotton, NF~Curtis, CB~Harris, BFG Johnson, SJ~Lippard, JT~Mague,
|
||
WR~Robinson, and JS~Wood}.
|
||
\newblock {\bf Mononuclear and polynuclear chemistry of rhenium (III): its
|
||
pronounced homophilicity}.
|
||
\newblock {\em Science}, {\bf 145}(3638):1305--1307, 1964.
|
||
|
||
\bibitem{Haberland2013}
|
||
{\sc Hellmut Haberland}.
|
||
\newblock {\em Clusters of atoms and molecules: theory, experiment, and
|
||
clusters of atoms}, ~{\bf 52}.
|
||
\newblock Springer Science \& Business Media, 2013.
|
||
|
||
\bibitem{Schmid1988}
|
||
{\sc G{\"u}nter Schmid}.
|
||
\newblock {\bf Metal clusters and cluster metals}.
|
||
\newblock {\em Polyhedron}, {\bf 7}(22-23):2321--2329, 1988.
|
||
|
||
\bibitem{Hakkinen2002}
|
||
{\sc Hannu H{\"a}kkinen, Michael Moseler, and Uzi Landman}.
|
||
\newblock {\bf Bonding in Cu, Ag, and Au clusters: relativistic effects,
|
||
trends, and surprises}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 89}(3):033401, 2002.
|
||
|
||
\bibitem{Dahl1963}
|
||
{\sc L.~F. Dahl and R.~E. Rundle}.
|
||
\newblock {\bf The crystal structure of dimanganese decacarbonyl
|
||
Mn$_2$(CO)$_{10}$}.
|
||
\newblock {\em Acta Crystallogr.}, {\bf 16}(5):419--426, 1963.
|
||
|
||
\bibitem{Fucugauchi1994}
|
||
{\sc L~Fucugauchi, S~Millan, A~Mondragon, and M~Solache-Rios}.
|
||
\newblock {\bf Chemical effects of (n, $\gamma$) nuclear reaction on
|
||
(Mo$_6$Cl$_8$)Cl$_4$}.
|
||
\newblock {\em J. Radioanal. Nucl. Chem.}, {\bf 178}(2):437--442, 1994.
|
||
|
||
\bibitem{Sutton2016}
|
||
{\sc Paul~W. Sutton and Lawrence~F. Dahl}.
|
||
\newblock \href{https://doi.org/10.1021/ja00978a016}{{\bf The Molecular
|
||
structure of Co$_3$(CO)$_9$CCH$_3$. A tricyclic organocobalt complex
|
||
containing a metal-coordinated triply bridging aliphatic carbon atom}}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 89}(2):261--268, 1967.
|
||
\newblock PMID: 22175962.
|
||
|
||
\bibitem{Schnepf2002}
|
||
{\sc Andreas Schnepf and Hansgeorg Schnöckel}.
|
||
\newblock {\bf Metalloid aluminum and gallium clusters: element modifications
|
||
on the molecular scale?}
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 41}(19):3532--3554, 2002.
|
||
|
||
\bibitem{Fassler2004}
|
||
{\sc Thomas~F. F{\"a}ssler and Stephan~D. Hoffmann}.
|
||
\newblock
|
||
\href{https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.200460427}{{\bf
|
||
Endohedral zintl ions: intermetalloid clusters}}.
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 43}(46):6242--6247, 2004.
|
||
|
||
\bibitem{Stegmaier2011}
|
||
{\sc Saskia Stegmaier and Thomas~F Fässler}.
|
||
\newblock {\bf A Bronze Matryoshka: The Discrete Intermetalloid Cluster
|
||
[Sn@Cu$_{12}$@Sn$_{20}$]$_{12}^-$ in the Ternary Phases
|
||
A$_{12}$Cu$_{12}$Sn$_{21}$ (A= Na, K)}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 133}(49):19758--19768, 2011.
|
||
|
||
\bibitem{Farges1981}
|
||
{\sc J~Farges, MF~De~Feraudy, B~Raoult, and G~Torchet}.
|
||
\newblock {\bf Structure and temperature of rare gas clusters in a supersonic
|
||
expansion}.
|
||
\newblock {\em Surf. Sci.}, {\bf 106}(1-3):95--100, 1981.
|
||
|
||
\bibitem{Kroto1991c60}
|
||
{\sc Harry~W Kroto, AW~Allaf, and SP~Balm}.
|
||
\newblock {\bf C$_{60}$: Buckminsterfullerene}.
|
||
\newblock {\em Chem. Rev.}, {\bf 91}(6):1213--1235, 1991.
|
||
|
||
\bibitem{Blase2008}
|
||
{\sc X~Blase, A~San~Miguel, A~Perez, et~al.}
|
||
\newblock {\bf Cluster assembled silicon networks}.
|
||
\newblock In {\em Nanosilicon}, pages 79--113. Elsevier, 2008.
|
||
|
||
\bibitem{Siedschlag2004}
|
||
{\sc Christian Siedschlag and Jan-Michael Rost}.
|
||
\newblock {\bf Small rare-gas clusters in soft x-ray pulses}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 93}(4):043402, 2004.
|
||
|
||
\bibitem{Rapacioli2005stacked}
|
||
{\sc M~Rapacioli, Florent Calvo, Fernand Spiegelman, C~Joblin, and DJ~Wales}.
|
||
\newblock {\bf Stacked clusters of polycyclic aromatic hydrocarbon molecules}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 109}(11):2487--2497, 2005.
|
||
|
||
\bibitem{Zhen2018}
|
||
{\sc Junfeng Zhen, Tao Chen, and Alexander~GGM Tielens}.
|
||
\newblock {\bf Laboratory photochemistry of pyrene clusters: An efficient way
|
||
to form large PAHs}.
|
||
\newblock {\em Astrophys. J.}, {\bf 863}(2):128, 2018.
|
||
|
||
\bibitem{Dyson2000}
|
||
{\sc Paul~J Dyson and J~Scott McIndoe}.
|
||
\newblock {\em Transition metal carbonyl cluster chemistry}, ~{\bf 2}.
|
||
\newblock CRC Press, 2000.
|
||
|
||
\bibitem{Colton1965}
|
||
{\sc R~Colton and R.~L. Martin}.
|
||
\newblock {\bf Magnetic evidence for trinuclear clusters in rhenium (IV)
|
||
chloride}.
|
||
\newblock {\em Nature}, {\bf 205}(4968):239--240, 1965.
|
||
|
||
\bibitem{Yoon2020}
|
||
{\sc Jiho Yoon, Edouard Lesne, Kornelia Sklarek, John Sheckelton, Chris Pasco,
|
||
Stuart S.~P. Parkin, Tyrel~M. McQueen, and Mazhar~N. Ali}.
|
||
\newblock {\bf {Anomalous thickness-dependent electrical conductivity in van
|
||
der Waals layered transition metal halide, Nb$_3$Cl$_8$}}.
|
||
\newblock {\em J. Phys. Condens. Matter}, {\bf {32}}({30}), {JUL 15} {2020}.
|
||
|
||
\bibitem{Berden1996}
|
||
{\sc Giel Berden, W~Leo Meerts, Michael Schmitt, and Karl Kleinermanns}.
|
||
\newblock {\bf High resolution UV spectroscopy of phenol and the hydrogen
|
||
bonded phenol-water cluster}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 104}(3):972--982, 1996.
|
||
|
||
\bibitem{Buck2000}
|
||
{\sc Udo Buck and Friedrich Huisken}.
|
||
\newblock {\bf Infrared spectroscopy of size-selected water and methanol
|
||
clusters}.
|
||
\newblock {\em Chem. Rev.}, {\bf 100}(11):3863--3890, 2000.
|
||
|
||
\bibitem{Harris1984}
|
||
{\sc IA~Harris, RS~Kidwell, and JA~Northby}.
|
||
\newblock {\bf Structure of charged argon clusters formed in a free jet
|
||
expansion}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 53}(25):2390, 1984.
|
||
|
||
\bibitem{Ayuela1993}
|
||
{\sc A~Ayuela, JM~L{\'o}pez, JA~Alonso, and V~Luana}.
|
||
\newblock {\bf Theoretical study of NaCl clusters}.
|
||
\newblock {\em Z. Phys. D}, {\bf 26}(1):213--215, 1993.
|
||
|
||
\bibitem{Calvo2018}
|
||
{\sc Florent Calvo}.
|
||
\newblock {\bf Melting and structural transitions}.
|
||
\newblock {\em Frontiers of Nanoscience}, {\bf 12}:295--331, 2018.
|
||
|
||
\bibitem{Alonso2000}
|
||
{\sc JA~Alonso}.
|
||
\newblock {\bf Electronic and atomic structure, and magnetism of
|
||
transition-metal clusters}.
|
||
\newblock {\em Chem. Rev.}, {\bf 100}(2):637--678, 2000.
|
||
|
||
\bibitem{Margenau2013}
|
||
{\sc Henry Margenau and Neil~R Kestner}.
|
||
\newblock {\em Theory of Intermolecular Forces: International Series of
|
||
Monographs in Natural Philosophy}, ~{\bf 18}.
|
||
\newblock Elsevier, 2013.
|
||
|
||
\bibitem{Kimura1991}
|
||
{\sc Keisaku Kimura}.
|
||
\newblock {\bf Magnetic properties of iron: from clusters to bulk}.
|
||
\newblock {\em Physics Letters A}, {\bf 158}(1-2):85--88, 1991.
|
||
|
||
\bibitem{Jortner1992}
|
||
{\sc Joshua Jortner}.
|
||
\newblock {\bf Cluster size effects}.
|
||
\newblock {\em Z. Phys. D}, {\bf 24}(3):247--275, 1992.
|
||
|
||
\bibitem{Boulon2014}
|
||
{\sc Julien Boulon, Isabelle Braud, S{\'e}bastien Zamith, Pierre Labastie, and
|
||
Jean-Marc L’Hermite}.
|
||
\newblock {\bf Experimental nanocalorimetry of protonated and deprotonated
|
||
water clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 140}(16):164305, 2014.
|
||
|
||
\bibitem{Schmidt2012}
|
||
{\sc M~Schmidt and B~von Issendorff}.
|
||
\newblock {\bf Gas-phase calorimetry of protonated water clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 136}(16):164307, 2012.
|
||
|
||
\bibitem{Hock2009}
|
||
{\sc C~Hock, M~Schmidt, R~Kuhnen, C~Bartels, L~Ma, H~Haberland, and B~v
|
||
Issendorff}.
|
||
\newblock {\bf Calorimetric observation of the melting of free water
|
||
nanoparticles at cryogenic temperatures}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 103}(7):073401, 2009.
|
||
|
||
\bibitem{Faraday1857}
|
||
{\sc Michael Faraday}.
|
||
\newblock {\bf The Bakerian Lecture.—Experimental relations of gold (and
|
||
other metals) to light}.
|
||
\newblock {\em Philosophical Transactions of the Royal Society of London}, {\bf
|
||
147}:145--181, 1857.
|
||
|
||
\bibitem{Kulmala2000}
|
||
{\sc Markku Kulmala, Liisa Pirjola, and Jyrki~M M{\"a}kel{\"a}}.
|
||
\newblock {\bf Stable sulphate clusters as a source of new atmospheric
|
||
particles}.
|
||
\newblock {\em Nature}, {\bf 404}(6773):66--69, 2000.
|
||
|
||
\bibitem{Wang2008}
|
||
{\sc Hui Wang, Ned~S Wingreen, and Ranjan Mukhopadhyay}.
|
||
\newblock {\bf Self-organized periodicity of protein clusters in growing
|
||
bacteria}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 101}(21):218101, 2008.
|
||
|
||
\bibitem{Depalma2014}
|
||
{\sc Joseph~W DePalma, Douglas~J Doren, and Murray~V Johnston}.
|
||
\newblock {\bf Formation and growth of molecular clusters containing sulfuric
|
||
acid, water, ammonia, and dimethylamine}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 118}(29):5464--5473, 2014.
|
||
|
||
\bibitem{Katakuse1985}
|
||
{\sc I~Katakuse, T~Ichihara, Y~Fujita, T~Matsuo, T~Sakurai, and H~Matsuda}.
|
||
\newblock {\bf Mass distributions of copper, silver and gold clusters and
|
||
electronic shell structure}.
|
||
\newblock {\em Int. J. Mass Spectrom. Ion Processes}, {\bf 67}(2):229--236,
|
||
1985.
|
||
|
||
\bibitem{Posthumus2009}
|
||
{\sc Jan Posthumus}.
|
||
\newblock {\em Molecules and clusters in intense laser fields}.
|
||
\newblock Cambridge University Press, 2009.
|
||
|
||
\bibitem{Castleman2009}
|
||
{\sc AW~Castleman~Jr and SN~Khanna}.
|
||
\newblock {\bf Clusters, superatoms, and building blocks of new materials}.
|
||
\newblock {\em J. Phys. Chem. C}, {\bf 113}(7):2664--2675, 2009.
|
||
|
||
\bibitem{Henglein1989}
|
||
{\sc Arnim Henglein}.
|
||
\newblock {\bf Non-metallic silver clusters in aqueous solution: stabilization
|
||
and chemical reactions}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 154}(5):473--476, 1989.
|
||
|
||
\bibitem{Korobeishchikov2005}
|
||
{\sc NG~Korobeishchikov, AE~Zarvin, V~Zh Madirbaev, and RG~Sharafutdinov}.
|
||
\newblock {\bf Condensation of argon, monosilane and their mixtures in a pulse
|
||
free jet}.
|
||
\newblock {\em Plasma Chem. Plasma Process.}, {\bf 25}(4):319--349, 2005.
|
||
|
||
\bibitem{Xu2020}
|
||
{\sc Qiaofei Xu, Baijie Xu, Hui Kong, Peipei He, Jiawei Wang, Thirumurthy
|
||
Kannan, Pengtao Ma, Jingping Wang, and Jingyang Niu}.
|
||
\newblock {\bf {Synthesis and Characterization of a Crown-Shaped 36-Molybdate
|
||
Cluster and Application in Catalyzing Knoevenagel Condensation}}.
|
||
\newblock {\em {Inorg. Chem.}}, {\bf {59}}({15}):{10665--10672}, {AUG 3}
|
||
{2020}.
|
||
|
||
\bibitem{Tian2018}
|
||
{\sc Tian Xiao-Lin, Zhao Yu-Hong, Tian Jin-Zhong, and Hou Hua}.
|
||
\newblock {\bf {Effects of interatomic potential on precipitation sequences of
|
||
medium Al concentration in Ni75AlxV25-x alloys}}.
|
||
\newblock {\em {Acta Phys. Sin.}}, {\bf {67}}({23}), {DEC 5} {2018}.
|
||
|
||
\bibitem{Deng2018}
|
||
{\sc Y.~H. Deng, D.~D. Wen, Y.~Li, J.~Liu, and P.~Peng}.
|
||
\newblock {\bf {Local atomic structures of amorphous Pd$_{80}$Si$_{20}$ alloys
|
||
and their configuration heredity in the rapid solidification}}.
|
||
\newblock {\em {Philos. Mag.}}, {\bf {98}}({31, A}):{2861--2877}, {NOV 2}
|
||
{2018}.
|
||
|
||
\bibitem{Rapacioli2019}
|
||
{\sc Mathias Rapacioli, Fernand Spiegelman, and Nathalie Tarrat}.
|
||
\newblock {\bf {Evidencing the relationship between isomer spectra and melting:
|
||
the 20-and 55-atom silver and gold cluster cases}}.
|
||
\newblock {\em {Phys. Chem. Chem. Phys.}}, {\bf {21}}({45}):{24857--24866},
|
||
{DEC 7} {2019}.
|
||
|
||
\bibitem{Castleman1978}
|
||
{\sc A.~W CASTLEMAN and P.~M. HOLLAND}.
|
||
\newblock {\bf Molecular-properties of small clusters and their relationship to
|
||
understanding nucleation phenomena}.
|
||
\newblock In {\em Abstracts of papers of the american chemical society}, ~{\bf
|
||
175}, pages 74--74. Am. Chem. Soc. 1155 16TH ST, NW, WASHINGTON, DC 20036,
|
||
1978.
|
||
|
||
\bibitem{Castleman1978the}
|
||
{\sc AW~Castleman~Jr, Paul~M Holland, and Robert~G Keesee}.
|
||
\newblock {\bf The properties of ion clusters and their relationship to
|
||
heteromolecular nucleation}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 68}(4):1760--1767, 1978.
|
||
|
||
\bibitem{Zhong2000}
|
||
{\sc Q~Zhong and AWa Castleman}.
|
||
\newblock {\bf An ultrafast glimpse of cluster solvation effects on reaction
|
||
dynamics}.
|
||
\newblock {\em Chem. Rev.}, {\bf 100}(11):4039--4058, 2000.
|
||
|
||
\bibitem{Pinkard2018}
|
||
{\sc Andrew Pinkard, Anouck~M Champsaur, and Xavier Roy}.
|
||
\newblock {\bf Molecular clusters: nanoscale building blocks for solid-state
|
||
materials}.
|
||
\newblock {\em Acc. Chem. Res.}, {\bf 51}(4):919--929, 2018.
|
||
|
||
\bibitem{Asuka2013}
|
||
{\sc Asuka Fujii and Kenta Mizuse}.
|
||
\newblock \href{https://doi.org/10.1080/0144235X.2012.760836}{{\bf Infrared
|
||
spectroscopic studies on hydrogen-bonded water networks in gas phase
|
||
clusters}}.
|
||
\newblock {\em Int. Rev. Phys. Chem.}, {\bf 32}(2):266--307, 2013.
|
||
|
||
\bibitem{Luo2016}
|
||
{\sc Zhixun Luo, A.~W. Castleman, and Shiv~N. Khanna}.
|
||
\newblock \href{https://doi.org/10.1021/acs.chemrev.6b00230}{{\bf Reactivity of
|
||
metal clusters}}.
|
||
\newblock {\em Chem. Rev.}, {\bf 116}(23):14456--14492, 2016.
|
||
\newblock PMID: 27960263.
|
||
|
||
\bibitem{Wang2016}
|
||
{\sc Lai-Sheng Wang}.
|
||
\newblock \href{https://doi.org/10.1080/0144235X.2016.1147816}{{\bf
|
||
Photoelectron spectroscopy of size-selected boron clusters: from planar
|
||
structures to borophenes and borospherenes}}.
|
||
\newblock {\em Int. Rev. Phys. Chem.}, {\bf 35}(1):69--142, 2016.
|
||
|
||
\bibitem{Jiang2019}
|
||
{\sc Shuai Jiang, Xiaoli Zhang, Xiucheng Zheng, and Xiangtao Kong}.
|
||
\newblock {\bf Structures, energetics, and infrared spectra of the cationic
|
||
monomethylamine clusters}.
|
||
\newblock {\em Chemical Physics}, {\bf 523}:7--11, 2019.
|
||
|
||
\bibitem{Meot1984}
|
||
{\sc Michael Meot-Ner}.
|
||
\newblock {\bf The ionic hydrogen bond and ion solvation. 2. Solvation of onium
|
||
ions by one to seven H2O molecules. Relations between monomolecular,
|
||
specific, and bulk hydration}.
|
||
\newblock {\em J. Am. Chem. Soc}, {\bf 106}(5):1265--1272, 1984.
|
||
|
||
\bibitem{Castleman1994}
|
||
{\sc A.~W. Castleman and S.~Wei}.
|
||
\newblock \href{https://doi.org/10.1146/annurev.pc.45.100194.003345}{{\bf
|
||
Cluster Reactions}}.
|
||
\newblock {\em Annual Review of Physical Chemistry}, {\bf 45}(1):685--719,
|
||
1994.
|
||
|
||
\bibitem{Castleman1996}
|
||
{\sc A.~W. Castleman and K.~H. Bowen}.
|
||
\newblock \href{https://doi.org/10.1021/jp961030k}{{\bf Clusters: Structure,
|
||
energetics, and dynamics of intermediate states of matter}}.
|
||
\newblock {\em J. Phys. Chem.}, {\bf 100}(31):12911--12944, 1996.
|
||
|
||
\bibitem{Farrar1988}
|
||
{\sc James~M Farrar, William~Hundley Saunders, et~al.}
|
||
\newblock {\em Techniques for the study of ion-molecule reactions}.
|
||
\newblock John Wiley \& Sons, 1988.
|
||
|
||
\bibitem{Mayer2002}
|
||
{\sc Paul~M Mayer}.
|
||
\newblock {\bf Ion rearrangement at the beginning of cluster formation:
|
||
isomerization pathways and dissociation kinetics for the ionized
|
||
dimethylamine dimer}.
|
||
\newblock {\em International J. Mass Spectrom.}, {\bf 218}(1):1--10, 2002.
|
||
|
||
\bibitem{Wales1997}
|
||
{\sc David~J Wales and Jonathan~PK Doye}.
|
||
\newblock {\bf Global optimization by basin-hopping and the lowest energy
|
||
structures of Lennard-Jones clusters containing up to 110 atoms}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 101}(28):5111--5116, 1997.
|
||
|
||
\bibitem{Wales1998}
|
||
{\sc David~J Wales and Matthew~P Hodges}.
|
||
\newblock {\bf Global minima of water clusters (H$_2$O)$_n$, n $\leqslant$ 21,
|
||
described by an empirical potential}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 286}(1-2):65--72, 1998.
|
||
|
||
\bibitem{Wales1999}
|
||
{\sc David~J Wales and Harold~A Scheraga}.
|
||
\newblock {\bf Global optimization of clusters, crystals, and biomolecules}.
|
||
\newblock {\em Science}, {\bf 285}(5432):1368--1372, 1999.
|
||
|
||
\bibitem{James2005}
|
||
{\sc Tim James, David~J Wales, and Javier Hern{\'a}ndez-Rojas}.
|
||
\newblock {\bf Global minima for water clusters (H$_2$O)$_n$, n$\leqslant$ 21,
|
||
described by a five-site empirical potential}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 415}(4-6):302--307, 2005.
|
||
|
||
\bibitem{Korchagina2017}
|
||
{\sc Kseniia Korchagina, Aude Simon, Mathias Rapacioli, Fernand Spiegelman,
|
||
Jean-Marc L’Hermite, Isabelle Braud, S{\'e}bastien Zamith, and
|
||
J{\'e}r{\^o}me Cuny}.
|
||
\newblock {\bf Theoretical investigation of the solid--liquid phase transition
|
||
in protonated water clusters}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(40):27288--27298, 2017.
|
||
|
||
\bibitem{Hada2003}
|
||
{\sc Yasuhiro Hada}.
|
||
\newblock {\bf A molecular dynamics simulation of cluster dissociation process
|
||
under cluster ion implantation}.
|
||
\newblock {\em Phys. Rev. B Condens. Matter}, {\bf 340}:1036--1040, 2003.
|
||
|
||
\bibitem{Chakraborty2020}
|
||
{\sc Debdutta Chakraborty, Hans Lischka, and William~L Hase}.
|
||
\newblock {\bf Dynamics of Pyrene-Dimer Association and Ensuing Pyrene-Dimer
|
||
Dissociation}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 124}(43):8907--8917, 2020.
|
||
|
||
\bibitem{Zamith2020threshold}
|
||
{\sc S{\'e}bastien Zamith, Jean-Marc L’hermite, L{\'e}o Dontot, Linjie Zheng,
|
||
Mathias Rapacioli, Fernand Spiegelman, and Christine Joblin}.
|
||
\newblock {\bf Threshold collision induced dissociation of pyrene cluster
|
||
cations}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 153}(5):054311, 2020.
|
||
|
||
\bibitem{Zheng2021}
|
||
{\sc Linjie Zheng, S{\'e}bastien Zamith, and Mathias Rapacioli}.
|
||
\newblock {\bf Dynamical simulation of collision-induced dissociation of pyrene
|
||
dimer cation}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 140}(2):1--14, 2021.
|
||
|
||
\bibitem{Tibshirani2005}
|
||
{\sc Robert Tibshirani and Guenther Walther}.
|
||
\newblock {\bf Cluster validation by prediction strength}.
|
||
\newblock {\em J. Comput. Graph. Stat.}, {\bf 14}(3):511--528, 2005.
|
||
|
||
\bibitem{Woutersen1997}
|
||
{\sc AS~Woutersen, U~Emmerichs, and HJ~Bakker}.
|
||
\newblock {\bf Femtosecond mid-IR pump-probe spectroscopy of liquid water:
|
||
Evidence for a two-component structure}.
|
||
\newblock {\em Science}, {\bf 278}(5338):658--660, 1997.
|
||
|
||
\bibitem{Ruan2004}
|
||
{\sc Chong-Yu Ruan, Vladimir~A Lobastov, Franco Vigliotti, Songye Chen, and
|
||
Ahmed~H Zewail}.
|
||
\newblock {\bf Ultrafast electron crystallography of interfacial water}.
|
||
\newblock {\em Science}, {\bf 304}(5667):80--84, 2004.
|
||
|
||
\bibitem{Brubach2005}
|
||
{\sc J-B Brubach, Al~Mermet, A~Filabozzi, A~Gerschel, and P~Roy}.
|
||
\newblock {\bf Signatures of the hydrogen bonding in the infrared bands of
|
||
water}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 122}(18):184509, 2005.
|
||
|
||
\bibitem{Bergmann2007}
|
||
{\sc Uwe Bergmann, Dennis Nordlund, Ph~Wernet, Michael Odelius, Lars~GM
|
||
Pettersson, and Anders Nilsson}.
|
||
\newblock {\bf Isotope effects in liquid water probed by x-ray Raman
|
||
spectroscopy}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 76}(2):024202, 2007.
|
||
|
||
\bibitem{Pokapanich2009}
|
||
{\sc Wandared Pokapanich, Henrik Bergersen, Ioana~L Bradeanu, Ricardo~RT
|
||
Marinho, Andreas Lindblad, Sebastien Legendre, Aldana Rosso, Svante Svensson,
|
||
Maxim Tchaplyguine, Nikolai~V Kryzhevoi, et~al.}
|
||
\newblock {\bf Auger electron spectroscopy as a probe of the solution of
|
||
aqueous ions}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 131}(21):7264--7271, 2009.
|
||
|
||
\bibitem{Sun2010}
|
||
{\sc Qiang Sun}.
|
||
\newblock {\bf The single donator-single acceptor hydrogen bonding structure in
|
||
water probed by Raman spectroscopy}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 132}(5):054507, 2010.
|
||
|
||
\bibitem{Harada2017}
|
||
{\sc Y~Harada, J~Miyawaki, H~Niwa, K~Yamazoe, Lars~GM Pettersson, and Anders
|
||
Nilsson}.
|
||
\newblock {\bf Probing the OH stretch in different local environments in liquid
|
||
water}.
|
||
\newblock {\em J. Phys. Chem. Lett.}, {\bf 8}(22):5487--5491, 2017.
|
||
|
||
\bibitem{Yamazoe2019}
|
||
{\sc Kosuke Yamazoe, Jun Miyawaki, Hideharu Niwa, Anders Nilsson, and Yoshihisa
|
||
Harada}.
|
||
\newblock {\bf Measurements of ultrafast dissociation in resonant inelastic
|
||
x-ray scattering of water}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 150}(20):204201, 2019.
|
||
|
||
\bibitem{Silvestrelli1999}
|
||
{\sc Pier~Luigi Silvestrelli and Michele Parrinello}.
|
||
\newblock {\bf Structural, electronic, and bonding properties of liquid water
|
||
from first principles}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 111}(8):3572--3580, 1999.
|
||
|
||
\bibitem{Laage2006}
|
||
{\sc Damien Laage and James~T Hynes}.
|
||
\newblock {\bf A molecular jump mechanism of water reorientation}.
|
||
\newblock {\em Science}, {\bf 311}(5762):832--835, 2006.
|
||
|
||
\bibitem{Bryantsev2009}
|
||
{\sc Vyacheslav~S Bryantsev, Mamadou~S Diallo, Adri~CT Van~Duin, and William~A
|
||
Goddard~III}.
|
||
\newblock {\bf Evaluation of B3LYP, X3LYP, and M06-class density functionals
|
||
for predicting the binding energies of neutral, protonated, and deprotonated
|
||
water clusters}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 5}(4):1016--1026, 2009.
|
||
|
||
\bibitem{Silvestrelli2017}
|
||
{\sc Pier~Luigi Silvestrelli}.
|
||
\newblock {\bf Hydrogen bonding characterization in water and small molecules}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 146}(24):244315, 2017.
|
||
|
||
\bibitem{Bernal1933}
|
||
{\sc John~D Bernal and Ralph~H Fowler}.
|
||
\newblock {\bf A theory of water and ionic solution, with particular reference
|
||
to hydrogen and hydroxyl ions}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 1}(8):515--548, 1933.
|
||
|
||
\bibitem{Shields2010}
|
||
{\sc Robert~M. Shields, Berhane Temelso, Kaye~A. Archer, Thomas~E. Morrell, and
|
||
George~C. Shields}.
|
||
\newblock {\bf Accurate predictions of water cluster formation,
|
||
(H$_2$O)$_{n=2-10}$, journal = {J. Phys. Chem. A}, volume = {114}, number =
|
||
{43}, pages = {11725-11737}, year = {2010}}.
|
||
|
||
\bibitem{Gregory1996}
|
||
{\sc Jonathon~K Gregory and David~C Clary}.
|
||
\newblock {\bf Structure of water clusters. The contribution of many-body
|
||
forces, monomer relaxation, and vibrational zero-point energy}.
|
||
\newblock {\em J. Phys. Chem.}, {\bf 100}(46):18014--18022, 1996.
|
||
|
||
\bibitem{Kunst1980}
|
||
{\sc Marinus Kunst and John~M Warman}.
|
||
\newblock {\bf Proton mobility in ice}.
|
||
\newblock {\em Nature}, {\bf 288}(5790):465--467, 1980.
|
||
|
||
\bibitem{Torrent2011}
|
||
{\sc Miquel Torrent-Sucarrat and Josep~M Anglada}.
|
||
\newblock {\bf Anharmonicity and the Eigen-Zundel dilemma in the IR spectrum of
|
||
the protonated 21 water cluster}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 7}(2):467--472, 2011.
|
||
|
||
\bibitem{Wang2010}
|
||
{\sc Xue-Bin Wang, Karol Kowalski, Lai-Sheng Wang, and Sotiris~S Xantheas}.
|
||
\newblock {\bf Stepwise hydration of the cyanide anion: A temperatur-controlled
|
||
photoelectron spectroscopy and ab initio computational study of
|
||
CN-(H$_2$O)$_n$, n = 2-5}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 132}(12):124306, 2010.
|
||
|
||
\bibitem{Bigg1975}
|
||
{\sc E.~K. Bigg}.
|
||
\newblock {\bf Stratospheric particles}.
|
||
\newblock {\em J. Atmos. Sci.}, {\bf 32}(5):910--917, 1975.
|
||
|
||
\bibitem{Vaida2000}
|
||
{\sc Veronica Vaida and Jill~E Headrick}.
|
||
\newblock {\bf Physicochemical properties of hydrated complexes in the Earth's
|
||
atmosphere}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 104}(23):5401--5412, 2000.
|
||
|
||
\bibitem{Aloisio2000}
|
||
{\sc Simone Aloisio and Joseph~S Francisco}.
|
||
\newblock {\bf Radical-water complexes in earth's atmosphere}.
|
||
\newblock {\em Acc. Chem. Res.}, {\bf 33}(12):825--830, 2000.
|
||
|
||
\bibitem{Ramanathan2001}
|
||
{\sc VCPJ Ramanathan, PJ~Crutzen, JT~Kiehl, and Daniel Rosenfeld}.
|
||
\newblock {\bf Aerosols, climate, and the hydrological cycle}.
|
||
\newblock {\em science}, {\bf 294}(5549):2119--2124, 2001.
|
||
|
||
\bibitem{Mccurdy2002}
|
||
{\sc Patrick~R McCurdy, Wayne~P Hess, and Sotiris~S Xantheas}.
|
||
\newblock {\bf Nitric acid- water complexes: Theoretical calculations and
|
||
comparison to experiment}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 106}(33):7628--7635, 2002.
|
||
|
||
\bibitem{Hartt2008}
|
||
{\sc Gregory~M Hartt, George~C Shields, and Karl~N Kirschner}.
|
||
\newblock {\bf Hydration of OCS with one to four water molecules in atmospheric
|
||
and laboratory conditions}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 112}(19):4490--4495, 2008.
|
||
|
||
\bibitem{Vaida2011}
|
||
{\sc Veronica Vaida}.
|
||
\newblock {\bf Perspective: Water cluster mediated atmospheric chemistry}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 135}(2):020901, 2011.
|
||
|
||
\bibitem{Kjaergaard2003}
|
||
{\sc Henrik~G Kjaergaard, Timothy~W Robinson, Daryl~L Howard, John~S Daniel,
|
||
Jill~E Headrick, and Veronica Vaida}.
|
||
\newblock {\bf Complexes of importance to the absorption of solar radiation}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 107}(49):10680--10686, 2003.
|
||
|
||
\bibitem{Vaida2003}
|
||
{\sc Veronica Vaida, Henrik~G Kjaergaard, and Karl~J Feierabend}.
|
||
\newblock {\bf Hydrated complexes: Relevance to atmospheric chemistry and
|
||
climate}.
|
||
\newblock {\em Int. Rev. Phys. Chem.}, {\bf 22}(1):203--219, 2003.
|
||
|
||
\bibitem{Klan2001}
|
||
{\sc Petr Kl{\'a}n, David Del~Favero, Alena Ansorgov{\'a}, Jana
|
||
Kl{\'a}nov{\'a}, and Ivan Holoubek}.
|
||
\newblock {\bf Photodegradation of halobenzenes in water ice}.
|
||
\newblock {\em Environ. Sci. Pollut. Res.}, {\bf 8}(3):195--200, 2001.
|
||
|
||
\bibitem{Amiaud2007}
|
||
{\sc L~Amiaud, F~Dulieu, J-H Fillion, A~Momeni, and JL~Lemaire}.
|
||
\newblock {\bf Interaction of atomic and molecular deuterium with a nonporous
|
||
amorphous water ice surface between 8 and 30 K}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 127}(14):144709, 2007.
|
||
|
||
\bibitem{Kahan2010}
|
||
{\sc TF~Kahan, R~Zhao, and DJ~Donaldson}.
|
||
\newblock {\bf Hydroxyl radical reactivity at the air-ice interface}.
|
||
\newblock {\em Atmos. Chem. Phys.}, {\bf 10}(2):843--854, 2010.
|
||
|
||
\bibitem{Minissale2019}
|
||
{\sc M~Minissale, T~Nguyen, and F~Dulieu}.
|
||
\newblock {\bf Experimental study of the penetration of oxygen and deuterium
|
||
atoms into porous water ice}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 622}:A148, 2019.
|
||
|
||
\bibitem{Perez2012}
|
||
{\sc Crist\'{o}bal P\'{e}rez, Matt~T. Muckle, Daniel~P. Zaleski, Nathan~A.
|
||
Seifert, Berhane Temelso, George~C. Shields, Zbigniew Kisiel, and Brooks~H.
|
||
Pate}.
|
||
\newblock \href{http://www.sciencemag.org/content/336/6083/897.abstract}{{\bf
|
||
Structures of cage, prism, and book isomers of water hexamer from broadband
|
||
rotational spectroscopy}}.
|
||
\newblock {\em Science}, {\bf 336}(6083):897--901, 2012.
|
||
|
||
\bibitem{Huneycutt2003}
|
||
{\sc Alex~J Huneycutt, Ross~J Stickland, Fredrik Hellberg, and Richard~J
|
||
Saykally}.
|
||
\newblock {\bf Infrared cavity ringdown spectroscopy of acid--water clusters:
|
||
HCl--H$_2$O, DCl--D$_2$O, and DCl--(D$_2$O)$_2$}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 118}(3):1221--1229, 2003.
|
||
|
||
\bibitem{Caleman2007}
|
||
{\sc Carl Caleman and David van~der Spoel}.
|
||
\newblock {\bf Evaporation from water clusters containing singly charged ions}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 9}(37):5105--5111, 2007.
|
||
|
||
\bibitem{Rozenberg2009}
|
||
{\sc M~Rozenberg and A~Loewenschuss}.
|
||
\newblock {\bf Matrix isolation infrared spectrum of the sulfuric acid-
|
||
monohydrate complex: new assignments and resolution of the “missing
|
||
h-bonded $\nu$ (oh) band” issue}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 113}(17):4963--4971, 2009.
|
||
|
||
\bibitem{Korchagina2016}
|
||
{\sc Kseniia~A. Korchagina, Aude Simon, Mathias Rapacioli, Fernand Spiegelman,
|
||
and Jérôme Cuny}.
|
||
\newblock {\bf Structural characterization of sulfur-containing water clusters
|
||
using a density-functional based tight-binding approach}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 120}(45):9089--9100, 2016.
|
||
|
||
\bibitem{Braud2019}
|
||
{\sc Isabelle Braud, S{\'e}bastien Zamith, J{\'e}r{\^o}me Cuny, Linjie Zheng,
|
||
and Jean-Marc L’Hermite}.
|
||
\newblock {\bf Size-dependent proton localization in hydrated uracil clusters:
|
||
A joint experimental and theoretical study}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 150}(1):014303, 2019.
|
||
|
||
\bibitem{Ryding2011}
|
||
{\sc Mauritz~Johan Ryding, Alexey~S Zatula, Patrik~Urban Andersson, and Einar
|
||
Uggerud}.
|
||
\newblock {\bf Isotope exchange in reactions between D 2 O and size-selected
|
||
ionic water clusters containing pyridine, H+(pyridine) m (H 2 O) n}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 13}(4):1356--1367, 2011.
|
||
|
||
\bibitem{Koop1996}
|
||
{\sc Thomas Koop and Kenneth~S Carslaw}.
|
||
\newblock {\bf Melting of H2SO4{\textperiodcentered} 4H2O particles upon
|
||
cooling: Implications for polar stratospheric clouds}.
|
||
\newblock {\em Science}, {\bf 272}(5268):1638--1641, 1996.
|
||
|
||
\bibitem{Carslaw1997}
|
||
{\sc Kenneth~S Carslaw, Thomas Peter, and Simon~L Clegg}.
|
||
\newblock {\bf Modeling the composition of liquid stratospheric aerosols}.
|
||
\newblock {\em Rev. Geophys.}, {\bf 35}(2):125--154, 1997.
|
||
|
||
\bibitem{Arnold1977}
|
||
{\sc F~Arnold, D~Krankowsky, and KH~Marien}.
|
||
\newblock {\bf First mass spectrometric measurements of positive ions in the
|
||
stratosphere}.
|
||
\newblock {\em Nature}, {\bf 267}(5606):30--32, 1977.
|
||
|
||
\bibitem{Arnold1982}
|
||
{\sc F~Arnold, AA~Viggiano, and H~Schlager}.
|
||
\newblock {\bf Implications for trace gases and aerosols of large negative ion
|
||
clusters in the stratosphere}.
|
||
\newblock {\em Nature}, {\bf 297}(5865):371--376, 1982.
|
||
|
||
\bibitem{Payzant1973}
|
||
{\sc JD~Payzant, AJ~Cunningham, and P~Kebarle}.
|
||
\newblock {\bf Gas phase solvation of the ammonium ion by NH$_3$ and H$_2$O and
|
||
stabilities of mixed clusters nh$_4^+$(nh$_3$)$_n$(H$_2$O)$_w$}.
|
||
\newblock {\em Can. J. Chem.}, {\bf 51}(19):3242--3249, 1973.
|
||
|
||
\bibitem{Kulmala1995}
|
||
{\sc M~Kulmala, H~Vehkam{\"a}ki, T~Vesala, JC~Barrett, and CF~Clement}.
|
||
\newblock {\bf Aerosol formation in diffusive boundary layer: Binary
|
||
homogeneous nucleation of ammonia and water vapours}.
|
||
\newblock {\em J. Aerosol Sci.}, {\bf 26}(4):547--558, 1995.
|
||
|
||
\bibitem{Kirkby2011}
|
||
{\sc Jasper Kirkby, Joachim Curtius, Jo{\~a}o Almeida, Eimear Dunne, Jonathan
|
||
Duplissy, Sebastian Ehrhart, Alessandro Franchin, St{\'e}phanie Gagn{\'e},
|
||
Luisa Ickes, Andreas K{\"u}rten, et~al.}
|
||
\newblock {\bf Role of sulphuric acid, ammonia and galactic cosmic rays in
|
||
atmospheric aerosol nucleation}.
|
||
\newblock {\em Nature}, {\bf 476}(7361):429--433, 2011.
|
||
|
||
\bibitem{Dunne2016}
|
||
{\sc Eimear~M Dunne, Hamish Gordon, Andreas K{\"u}rten, Jo{\~a}o Almeida,
|
||
Jonathan Duplissy, Christina Williamson, Ismael~K Ortega, Kirsty~J Pringle,
|
||
Alexey Adamov, Urs Baltensperger, et~al.}
|
||
\newblock {\bf Global atmospheric particle formation from CERN CLOUD
|
||
measurements}.
|
||
\newblock {\em Science}, {\bf 354}(6316):1119--1124, 2016.
|
||
|
||
\bibitem{Leger1984}
|
||
{\sc A.~{L\'{e}ger} and J.~L. {Puget}}.
|
||
\newblock {\bf {Identification of the 'unidentified' IR emission features of
|
||
interstellar dust?}}
|
||
\newblock {\em Astron. Astrophys.}, {\bf 137}:L5--L8, 1984.
|
||
|
||
\bibitem{Allamandola1985}
|
||
{\sc L~J Allamandola, A~G G~M Tielens, and JRz Barker}.
|
||
\newblock {\bf Polycyclic aromatic hydrocarbons and the unidentified infrared
|
||
emission bands-Auto exhaust along the Milky Way}.
|
||
\newblock {\em Astrophys. J.}, {\bf 290}:L25--L28, 1985.
|
||
|
||
\bibitem{Puget1989}
|
||
{\sc JL~Puget and A~L{\'e}ger}.
|
||
\newblock {\bf A new component of the interstellar matter: Small grains and
|
||
large aromatic molecules}.
|
||
\newblock {\em Annu. Rev. Astron. Astrophys.}, {\bf 27}(1):161--198, 1989.
|
||
|
||
\bibitem{Tielens2008}
|
||
{\sc Alexander G G~M Tielens}.
|
||
\newblock {\bf Interstellar polycyclic aromatic hydrocarbon molecules}.
|
||
\newblock {\em Annu. Rev. Astron. Astrophys.}, {\bf 46}:289--337, 2008.
|
||
|
||
\bibitem{Tielens2005}
|
||
{\sc Alexander G G~M Tielens}.
|
||
\newblock {\em The physics and chemistry of the interstellar medium}.
|
||
\newblock Cambridge University Press, 2005.
|
||
|
||
\bibitem{Rapacioli2006}
|
||
{\sc M~Rapacioli, F~Calvo, C~Joblin, P~Parneix, D~Toublanc, and F~Spiegelman}.
|
||
\newblock {\bf Formation and destruction of polycyclic aromatic hydrocarbon
|
||
clusters in the interstellar medium}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 460}(2):519--531, 2006.
|
||
|
||
\bibitem{Montillaud2014}
|
||
{\sc Julien Montillaud and Christine Joblin}.
|
||
\newblock {\bf Absolute evaporation rates of non-rotating neutral polycyclic
|
||
aromatic hydrocarbon clusters}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 567}:A45, 2014.
|
||
|
||
\bibitem{Rapacioli2009}
|
||
{\sc Mathias Rapacioli and Fernand Spiegelman}.
|
||
\newblock {\bf Modelling singly ionized coronene clusters}.
|
||
\newblock {\em The European Physical Journal D}, {\bf 52}(1):55--58, 2009.
|
||
|
||
\bibitem{Joblin2017}
|
||
{\sc Christine Joblin, L{\'e}o Dontot, GA~Garcia, Fernand Spiegelman, Mathias
|
||
Rapacioli, Laurent Nahon, Pascal Parneix, T~Pino, and P~Br{\'e}chignac}.
|
||
\newblock {\bf Size effect in the ionization energy of PAH clusters}.
|
||
\newblock {\em J. Phys. Chem. Lett.}, {\bf 8}(15):3697--3702, 2017.
|
||
|
||
\bibitem{Finlayson1986}
|
||
{\sc Barbara~J Finlayson-Pitts and James~N Pitts~Jr}.
|
||
\newblock {\bf Atmospheric chemistry. Fundamentals and experimental
|
||
techniques}.
|
||
\newblock 1986.
|
||
|
||
\bibitem{Callen2008}
|
||
{\sc MS~Call{\'e}n, MT~De~la Cruz, JM~L{\'o}pez, R~Murillo, MV~Navarro, and
|
||
AM~Mastral}.
|
||
\newblock {\bf Some inferences on the mechanism of atmospheric gas/particle
|
||
partitioning of polycyclic aromatic hydrocarbons (PAH) at Zaragoza (Spain)}.
|
||
\newblock {\em Chemosphere}, {\bf 73}(8):1357--1365, 2008.
|
||
|
||
\bibitem{Eaves2015}
|
||
{\sc NA~Eaves, SB~Dworkin, and MJ~Thomson}.
|
||
\newblock {\bf The importance of reversibility in modeling soot nucleation and
|
||
condensation processes}.
|
||
\newblock {\em Proc. Combust. Inst.}, {\bf 35}(2):1787--1794, 2015.
|
||
|
||
\bibitem{Violi2007}
|
||
{\sc Angela Violi and Sergei Izvekov}.
|
||
\newblock {\bf Soot primary particle formation from multiscale coarse-grained
|
||
molecular dynamics simulation}.
|
||
\newblock {\em Proc. Combust. Inst.}, {\bf 31}(1):529--537, 2007.
|
||
|
||
\bibitem{Scholz2013}
|
||
{\sc Reinhard Scholz, Regina Luschtinetz, Gotthard Seifert, Till
|
||
J{\"a}geler-Hoheisel, Christian K{\"o}rner, Karl Leo, and Mathias Rapacioli}.
|
||
\newblock {\bf Quantifying charge transfer energies at donor--acceptor
|
||
interfaces in small-molecule solar cells with constrained DFTB and
|
||
spectroscopic methods}.
|
||
\newblock {\em J. Condens. Matter Phys.}, {\bf 25}(47):473201, 2013.
|
||
|
||
\bibitem{Darghouth2015}
|
||
{\sc Ala Aldin~MHM Darghouth, Mark~E Casida, Walid Taouali, Kamel Alimi,
|
||
Mathias~P Ljungberg, Peter Koval, Daniel S{\'a}nchez-Portal, and Dietrich
|
||
Foerster}.
|
||
\newblock {\bf Assessment of density-functional tight-binding ionization
|
||
potentials and electron affinities of molecules of interest for organic solar
|
||
cells against first-principles GW calculations}.
|
||
\newblock {\em Computation}, {\bf 3}(4):616--656, 2015.
|
||
|
||
\bibitem{Holm2010}
|
||
{\sc Anne I~S Holm, Henning Zettergren, Henrik~AB Johansson, Fabian Seitz,
|
||
Stefan Rosen, Henning~T Schmidt, A~{\L}awicki, Jimmy Rangama, Patrick
|
||
Rousseau, Micha{\"e}l Capron, et~al.}
|
||
\newblock {\bf Ions colliding with cold polycyclic aromatic hydrocarbon
|
||
clusters}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 105}(21):213401, 2010.
|
||
|
||
\bibitem{Simon2017formation}
|
||
{\sc Aude Simon, J~A Noble, Guillaume Rouaut, Audrey Moudens, C~Aupetit,
|
||
Christophe Iftner, and Jo{\"e}lle Mascetti}.
|
||
\newblock {\bf Formation of coronene: water complexes: FTIR study in argon
|
||
matrices and theoretical characterisation}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(12):8516--8529, 2017.
|
||
|
||
\bibitem{Chen2018}
|
||
{\sc Tao Chen}.
|
||
\newblock {\bf Formation of covalently bonded polycyclic aromatic hydrocarbons
|
||
in the interstellar medium}.
|
||
\newblock {\em Astrophys. J.}, {\bf 866}(2):113, 2018.
|
||
|
||
\bibitem{Schmidt2006}
|
||
{\sc Martin Schmidt, Albert Masson, and Catherine Br{\'e}chignac}.
|
||
\newblock {\bf Coronene cluster experiments: Stability and thermodynamics}.
|
||
\newblock {\em International J. Mass Spectrom.}, {\bf 252}(2):173--179, 2006.
|
||
|
||
\bibitem{Gatchell2015}
|
||
{\sc Michael Gatchell, Mark~H Stockett, Nathalie de~Ruette, Tao Chen, Linda
|
||
Giacomozzi, Rodrigo~F Nascimento, Michael Wolf, Emma~K Anderson, Rudy
|
||
Delaunay, Violaine Vizcaino, et~al.}
|
||
\newblock {\bf Failure of hydrogenation in protecting polycyclic aromatic
|
||
hydrocarbons from fragmentation}.
|
||
\newblock {\em Phys. Rev. A}, {\bf 92}(5):050702, 2015.
|
||
|
||
\bibitem{Gatchell2017}
|
||
{\sc Michael Gatchell, Rudy Delaunay, Giovanna D'Angelo, Arkadiusz Mika,
|
||
Kostiantyn Kulyk, Alicja Domaracka, Patrick Rousseau, Henning Zettergren,
|
||
Bernd~A Huber, and Henrik Cederquist}.
|
||
\newblock {\bf Ion-induced molecular growth in clusters of small hydrocarbon
|
||
chains}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(30):19665--19672, 2017.
|
||
|
||
\bibitem{Zamith2019thermal}
|
||
{\sc S{\'e}bastien Zamith, Ming-Chao Ji, Jean-Marc l’Hermite, Christine
|
||
Joblin, L{\'e}o Dontot, Mathias Rapacioli, and Fernand Spiegelman}.
|
||
\newblock {\bf Thermal evaporation of pyrene clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 151}(19):194303, 2019.
|
||
|
||
\bibitem{Dawson1982}
|
||
{\sc PH~Dawson}.
|
||
\newblock {\bf The collision-induced dissociation of protonated water clusters
|
||
studied using a triple quadrupole}.
|
||
\newblock {\em Int. J. Mass Spectrom.}, {\bf 43}(2-3):195--209, 1982.
|
||
|
||
\bibitem{Graul1989}
|
||
{\sc Susan~T Graul and Robert~R Squires}.
|
||
\newblock {\bf Energy-Resolved Collision-Induced Dissociation of Proton-Bound
|
||
Cluster Ions as a Structural Probe: The Acetonitrile-Water System}.
|
||
\newblock {\em Int. J. Mass Spectrom. Ion Process}, {\bf 94}(1-2):41--61, 1989.
|
||
|
||
\bibitem{Wei1991}
|
||
{\sc S~Wei, WB~Tzeng, RG~Keesee, and AW~Castleman~Jr}.
|
||
\newblock {\bf Metastable Unimolecular and Collision-Induced Dissociation of
|
||
Hydrogen-Bonded Clusters: Evidence for Intracluster Molecular Rearrangement
|
||
and the Structure of Solvated Protonated Complexes}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 113}(6):1960--1969, 1991.
|
||
|
||
\bibitem{Liu2006}
|
||
{\sc B.~Liu, S.~Brondsted Nielsen, P.~Hvelplund, H.~Zettergren, H.~Cederquist,
|
||
B.~Manil, and B.~A. Huber}.
|
||
\newblock {\bf {Collision-Induced Dissociation of Hydrated Adenosine
|
||
Monophosphate Nucleotide Ions: Protection of the Ion in Water Nanoclusters}}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf {97}}({13}):{133401}, {SEP 29} {2006}.
|
||
|
||
\bibitem{Goebbert2006}
|
||
{\sc Daniel~J Goebbert, Hao Chen, and Paul~G Wenthold}.
|
||
\newblock {\bf Collision-induced dissociation studies of protonated
|
||
ether-(H$_2$O)$_n$ (n= 1--3) clusters}.
|
||
\newblock {\em J. Mass Spectrom.}, {\bf 41}(2):242--247, 2006.
|
||
|
||
\bibitem{Coates2018}
|
||
{\sc Rebecca~A Coates and PB~Armentrout}.
|
||
\newblock {\bf Binding energies of hydrated cobalt (ii) by collision-induced
|
||
dissociation and theoretical studies: evidence for a new critical size}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 20}(2):802--818, 2018.
|
||
|
||
\bibitem{Nelson1994}
|
||
{\sc Chad~C Nelson and James~A McCloskey}.
|
||
\newblock {\bf Collision-induced dissociation of uracil and its derivatives}.
|
||
\newblock {\em J. Am. Soc. Mass Spectrom.}, {\bf 5}(5):339--349, 1994.
|
||
|
||
\bibitem{Molina2015}
|
||
{\sc Estefan{\'\i}a~Rossich Molina, Daniel Ortiz, Jean-Yves Salpin, and
|
||
Riccardo Spezia}.
|
||
\newblock {\bf Elucidating collision induced dissociation products and reaction
|
||
mechanisms of protonated uracil by coupling chemical dynamics simulations
|
||
with tandem mass spectrometry experiments}.
|
||
\newblock {\em J. Mass Spectrom.}, {\bf 50}(12):1340--1351, 2015.
|
||
|
||
\bibitem{Carl2007}
|
||
{\sc Damon~R. Carl, Robert~M. Moision, and P.~B. Armentrout}.
|
||
\newblock {\bf {Binding energies for the inner hydration shells of Ca$^{2+}$:
|
||
An experimental and theoretical investigation of Ca$^{2+}$(H$_2$O)$_x$
|
||
complexes (x=5-9)}}.
|
||
\newblock {\em Int. J. Mass Spectrom.}, {\bf {265}}({2-3}):{308--325}, {SEP 1}
|
||
{2007}.
|
||
|
||
\bibitem{Nguyen2011}
|
||
{\sc Viet~Hung Nguyen, Carlos Afonso, and Jean-Claude Tabet}.
|
||
\newblock {\bf {Concomitant EDD and EID of DNA evidenced by MSn and double
|
||
resonance experiments}}.
|
||
\newblock {\em {Int. J. Mass Spectrom.}}, {\bf {301}}({1-3, SI}):{224--233},
|
||
{MAR 30} {2011}.
|
||
|
||
\bibitem{Shuck2014}
|
||
{\sc Sarah~C. Shuck, Kristie~L. Rose, and Lawrence~J. Marnett}.
|
||
\newblock \href{https://dx.doi.org/10.1021/tx400384e}{{\bf Mass spectrometric
|
||
methods for the analysis of nucleoside–protein cross-links: application to
|
||
oxopropenyl-deoxyadenosine}}.
|
||
\newblock {\em Chem. Res. Toxicol.}, {\bf 27}(1):136--146, 2014.
|
||
|
||
\bibitem{Castrovilli2017}
|
||
{\sc MC~Castrovilli, P~Markush, P~Bolognesi, P~Rousseau, S~Maclot, A~Cartoni,
|
||
R~Delaunay, A~Domaracka, J~Ko{\v{c}}i{\v{s}}ek, BA~Huber, and L~Avaldi}.
|
||
\newblock {\bf Fragmentation of pure and hydrated clusters of 5br-uracil by low
|
||
energy carbon ions: observation of hydrated fragments}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(30):19807--19814, 2017.
|
||
|
||
\bibitem{Bera2018}
|
||
{\sc Anupam Bera, Bruno Concina, Baptiste Schindler, Gina~Predelus Renois,
|
||
Gabriel Karras, Isabelle Compagnon, Atanu Bhattacharya, and Franck
|
||
L{\'e}pine}.
|
||
\newblock {\bf Collision induced dissociation of positive ions of
|
||
dimethylnitramine, a model system for nitramine energetic molecules}.
|
||
\newblock {\em Int. J. Mass Spectrom.}, {\bf 431}:15--21, 2018.
|
||
|
||
\bibitem{Klippenstein1992}
|
||
{\sc Stephen~J Klippenstein}.
|
||
\newblock {\bf Variational optimizations in the
|
||
rice--ramsperger--kassel--marcus theory calculations for unimolecular
|
||
dissociations with no reverse barrier}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 96}(1):367--371, 1992.
|
||
|
||
\bibitem{Baer1996}
|
||
{\sc Tomas Baer and William~L Hase}.
|
||
\newblock {\em Unimolecular Reaction Dynamics: Theory and Experiments}, ~{\bf
|
||
31}.
|
||
\newblock Oxford University Press on Demand, 1996.
|
||
|
||
\bibitem{Metropolis1949}
|
||
{\sc Nicholas Metropolis and Stanislaw Ulam}.
|
||
\newblock {\bf The Monte Carlo method}.
|
||
\newblock {\em J. Am. Stat. Assoc.}, {\bf 44}(247):335--341, 1949.
|
||
|
||
\bibitem{Voter2007}
|
||
{\sc Arthur~F Voter}.
|
||
\newblock {\bf Introduction to the kinetic Monte Carlo method}.
|
||
\newblock In {\em Radiation Effects in Solids}, pages 1--23. Springer, 2007.
|
||
|
||
\bibitem{Brown2009}
|
||
{\sc Theodore~Lawrence Brown}.
|
||
\newblock {\em Chemistry: the central science}.
|
||
\newblock Pearson Education, 2009.
|
||
|
||
\bibitem{MCTDH}
|
||
{\sc M.H. Beck, A.~Jäckle, G.A. Worth, and H.-D. Meyer}.
|
||
\newblock
|
||
\href{https://www.sciencedirect.com/science/article/pii/S0370157399000472}{{\bf
|
||
The multiconfiguration time-dependent hartree (MCTDH) method: a highly
|
||
efficient algorithm for propagating wavepackets}}.
|
||
\newblock {\em Phys. Rep.}, {\bf 324}(1):1--105, 2000.
|
||
|
||
\bibitem{Griffiths2018}
|
||
{\sc David~J Griffiths and Darrell~F Schroeter}.
|
||
\newblock {\em Introduction to quantum mechanics}.
|
||
\newblock Cambridge University Press, 2018.
|
||
|
||
\bibitem{Born1927}
|
||
{\sc Max Born and Robert Oppenheimer}.
|
||
\newblock {\bf Zur quantentheorie der molekeln}.
|
||
\newblock {\em Ann. Phys.}, {\bf 389}(20):457--484, 1927.
|
||
|
||
\bibitem{Epstein1966}
|
||
{\sc Saul~T Epstein}.
|
||
\newblock {\bf Ground-state energy of a molecule in the adiabatic
|
||
approximation}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 44}(2):836--837, 1966.
|
||
|
||
\bibitem{Butler1998}
|
||
{\sc Laurie~J Butler}.
|
||
\newblock {\bf Chemical reaction dynamics beyond the Born-Oppenheimer
|
||
approximation}.
|
||
\newblock {\em Ann. Rev. Phys. Chem.}, {\bf 49}(1):125--171, 1998.
|
||
|
||
\bibitem{Puzzarini2010}
|
||
{\sc Cristina Puzzarini, John~F Stanton, and Juergen Gauss}.
|
||
\newblock {\bf Quantum-chemical calculation of spectroscopic parameters for
|
||
rotational spectroscopy}.
|
||
\newblock {\em Int. Rev. Phys. Chem.}, {\bf 29}(2):273--367, 2010.
|
||
|
||
\bibitem{Helgaker1999}
|
||
{\sc Trygve Helgaker, Micha{\l} Jaszu{\'n}ski, and Kenneth Ruud}.
|
||
\newblock {\bf Ab initio methods for the calculation of NMR shielding and
|
||
indirect spin- spin coupling constants}.
|
||
\newblock {\em Chem. Rev.}, {\bf 99}(1):293--352, 1999.
|
||
|
||
\bibitem{Pedone2010}
|
||
{\sc Alfonso Pedone, Malgorzata Biczysko, and Vincenzo Barone}.
|
||
\newblock {\bf Environmental effects in computational spectroscopy: Accuracy
|
||
and interpretation}.
|
||
\newblock {\em ChemPhysChem}, {\bf 11}(9):1812--1832, 2010.
|
||
|
||
\bibitem{Fleming1986}
|
||
{\sc Graham Fleming}.
|
||
\newblock {\bf Chemical applications of ultrafast spectroscopy}.
|
||
\newblock 1986.
|
||
|
||
\bibitem{Laane1999}
|
||
{\sc Jaan Laane, Hiroaki Takahashi, and Andre Bandrauk}.
|
||
\newblock {\em Structure and Dynamics of Electronic Excited States}.
|
||
\newblock Springer Science \& Business Media, 1999.
|
||
|
||
\bibitem{Helgaker2012}
|
||
{\sc Trygve Helgaker, Sonia Coriani, Poul J{\o}rgensen, Kasper Kristensen,
|
||
Jeppe Olsen, and Kenneth Ruud}.
|
||
\newblock {\bf Recent advances in wave function-based methods of
|
||
molecular-property calculations}.
|
||
\newblock {\em Chem. Rev.}, {\bf 112}(1):543--631, 2012.
|
||
|
||
\bibitem{Jensen2017}
|
||
{\sc Frank Jensen}.
|
||
\newblock {\em Introduction to computational chemistry}.
|
||
\newblock John wiley \& sons, 2017.
|
||
|
||
\bibitem{dftb1}
|
||
{\sc Dirk Porezag, Th~Frauenheim, Th~K{\"o}hler, Gotthard Seifert, and
|
||
R~Kaschner}.
|
||
\newblock {\bf Construction of tight-binding-like potentials on the basis of
|
||
density-functional theory: application to carbon}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 51}(19):12947--12958, 1995.
|
||
|
||
\bibitem{dftb2}
|
||
{\sc G~Seifert, D~Porezag, and Th~Frauenheim}.
|
||
\newblock {\bf Calculations of molecules, clusters, and solids with a
|
||
simplified LCAO-DFT-LDA scheme}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 58}(2):185--192, 1996.
|
||
|
||
\bibitem{Elstner1998}
|
||
{\sc Marcus Elstner, Dirk Porezag, G~Jungnickel, J~Elsner, M~Haugk,
|
||
Th~Frauenheim, Sandor Suhai, and Gotthard Seifert}.
|
||
\newblock {\bf Self-consistent-charge density-functional tight-binding method
|
||
for simulations of complex materials properties}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 58}(11):7260, 1998.
|
||
|
||
\bibitem{Elstner2014}
|
||
{\sc Marcus Elstner and Gotthard Seifert}.
|
||
\newblock {\bf Density functional tight binding}.
|
||
\newblock {\em Philos. Trans. R. Soc. A-Math. Phys. Eng. Sci.}, {\bf
|
||
372}(2011):20120483, 2014.
|
||
|
||
\bibitem{Singh1986}
|
||
{\sc U~Chandra Singh and Peter~A Kollman}.
|
||
\newblock {\bf A combined ab initio quantum mechanical and molecular mechanical
|
||
method for carrying out simulations on complex molecular systems:
|
||
Applications to the CH$_3$Cl + Cl$^-$ exchange reaction and gas phase
|
||
protonation of polyethers}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 7}(6):718--730, 1986.
|
||
|
||
\bibitem{Gao1996}
|
||
{\sc Jiali Gao}.
|
||
\newblock {\bf Methods and applications of combined quantum mechanical and
|
||
molecular mechanical potentials}.
|
||
\newblock {\em Rev. Comput. Chem.}, {\bf 7}:119--186, 1996.
|
||
|
||
\bibitem{Mordasini1998}
|
||
{\sc Tiziana~Z Mordasini and Walter Thiel}.
|
||
\newblock {\bf Combined quantum mechanical and molecular mechanical
|
||
approaches}.
|
||
\newblock {\em Chimia}, {\bf 52}(6):288--291, 1998.
|
||
|
||
\bibitem{Hartree1928}
|
||
{\sc D~R Hartree}.
|
||
\newblock {\bf The waves mechanics of an atom with non-coulombic central field:
|
||
parts I, II, III}.
|
||
\newblock In {\em Proc. Cambridge Phil. Soc}, ~{\bf 24}, pages 89--132, 1928.
|
||
|
||
\bibitem{Hartree1947}
|
||
{\sc D~R Hartree}.
|
||
\newblock {\bf The calculation of atomic structures}.
|
||
\newblock {\em Rep. Prog. Phys.}, {\bf 11}:113--143, 1947.
|
||
|
||
\bibitem{Slater1968}
|
||
{\sc John~Clarke Slater}.
|
||
\newblock {\bf Quantum theory of matter}.
|
||
\newblock 1968.
|
||
|
||
\bibitem{Mcweeny1992}
|
||
{\sc Roy McWeeny}.
|
||
\newblock {\em Methods of molecular quantum mechanics}.
|
||
\newblock Academic press, 1992.
|
||
|
||
\bibitem{Szabo1996}
|
||
{\sc A~Szabo and N~S Ostlund}.
|
||
\newblock {\bf Introduction to advanced electronic structure theory}.
|
||
\newblock {\em Modern Quantum Chemistry}, 1996.
|
||
|
||
\bibitem{Kohanoff2006}
|
||
{\sc Jorge Kohanoff}.
|
||
\newblock {\em Electronic structure calculations for solids and molecules:
|
||
theory and computational methods}.
|
||
\newblock Cambridge University Press, 2006.
|
||
|
||
\bibitem{Helgaker2014}
|
||
{\sc Trygve Helgaker, Poul Jorgensen, and Jeppe Olsen}.
|
||
\newblock {\em Molecular electronic-structure theory}.
|
||
\newblock John Wiley \& Sons, 2014.
|
||
|
||
\bibitem{Roothaan1951}
|
||
{\sc Clemens Carel~Johannes Roothaan}.
|
||
\newblock {\bf New developments in molecular orbital theory}.
|
||
\newblock {\em Rev. Mod. Phys.}, {\bf 23}(2):69--89, 1951.
|
||
|
||
\bibitem{Blinder2018}
|
||
{\sc Seymour~Michael Blinder and James~E House}.
|
||
\newblock {\em Mathematical Physics in Theoretical Chemistry}.
|
||
\newblock Elsevier, 2018.
|
||
|
||
\bibitem{koch1999}
|
||
{\sc R~Koch and T~Clark}.
|
||
\newblock {\em The chemist’s electronic book of orbitals}.
|
||
\newblock Springer, 1999.
|
||
|
||
\bibitem{Moskowitz1965}
|
||
{\sc JW~Moskowitz and MC~Harrison}.
|
||
\newblock {\bf Gaussian Wavefunctions for the 10-Electron Systems. III. OH$^-$,
|
||
H$_2$O, H$_3$O$^+$}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 43}(10):3550--3555, 1965.
|
||
|
||
\bibitem{Lowdin1995}
|
||
{\sc Per-Olov L{\"o}wdin}.
|
||
\newblock {\bf The historical development of the electron correlation problem}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 55}(2):77--102, 1995.
|
||
|
||
\bibitem{Cramer2003}
|
||
{\sc Christopher~J Cramer and FM~Bickelhaupt}.
|
||
\newblock {\bf Essentials of computational chemistry}.
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 42}(4):381--381, 2003.
|
||
|
||
\bibitem{Head1994}
|
||
{\sc Martin Head-Gordon, Rudolph~J Rico, Manabu Oumi, and Timothy~J Lee}.
|
||
\newblock {\bf A doubles correction to electronic excited states from
|
||
configuration interaction in the space of single substitutions}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 219}(1-2):21--29, 1994.
|
||
|
||
\bibitem{Maurice1999}
|
||
{\sc David Maurice and Martin Head-Gordon}.
|
||
\newblock {\bf Analytical second derivatives for excited electronic states
|
||
using the single excitation configuration interaction method: theory and
|
||
application to benzo [a] pyrene and chalcone}.
|
||
\newblock {\em Mol. Phys.}, {\bf 96}(10):1533--1541, 1999.
|
||
|
||
\bibitem{Moller1934}
|
||
{\sc Chr M{\o}ller and Milton~S Plesset}.
|
||
\newblock {\bf Note on an approximation treatment for many-electron systems}.
|
||
\newblock {\em Phys. Rev.}, {\bf 46}(7):618, 1934.
|
||
|
||
\bibitem{Pople1976}
|
||
{\sc John~A Pople, J~Stephen Binkley, and Rolf Seeger}.
|
||
\newblock {\bf Theoretical models incorporating electron correlation}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 10}(S10):1--19, 1976.
|
||
|
||
\bibitem{Krishnan1978}
|
||
{\sc R~Krishnan and John~A Pople}.
|
||
\newblock {\bf Approximate fourth-order perturbation theory of the electron
|
||
correlation energy}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 14}(1):91--100, 1978.
|
||
|
||
\bibitem{Vcivzek1966}
|
||
{\sc Ji{\v{r}}{\'\i} {\v{C}}{\'\i}{\v{z}}ek}.
|
||
\newblock {\bf On the correlation problem in atomic and molecular systems.
|
||
Calculation of wavefunction components in Ursell-type expansion using
|
||
quantum-field theoretical methods}.
|
||
\newblock {\em J. Chem. Phys}, {\bf 45}(11):4256--4266, 1966.
|
||
|
||
\bibitem{Purvis1982}
|
||
{\sc George~D Purvis~III and Rodney~J Bartlett}.
|
||
\newblock {\bf A full coupled-cluster singles and doubles model: The inclusion
|
||
of disconnected triples}.
|
||
\newblock {\em J. Chem. Phys}, {\bf 76}(4):1910--1918, 1982.
|
||
|
||
\bibitem{Raghavachari1989}
|
||
{\sc Krishnan Raghavachari, Gary~W Trucks, John~A Pople, and Martin
|
||
Head-Gordon}.
|
||
\newblock {\bf A fifth-order perturbation comparison of electron correlation
|
||
theories}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 157}(6):479--483, 1989.
|
||
|
||
\bibitem{Van2001}
|
||
{\sc Troy Van~Voorhis and Martin Head-Gordon}.
|
||
\newblock {\bf Two-body coupled cluster expansions}.
|
||
\newblock {\em J. Chem. Phys}, {\bf 115}(11):5033--5040, 2001.
|
||
|
||
\bibitem{Curtiss1991}
|
||
{\sc Larry~A Curtiss, Krishnan Raghavachari, Gary~W Trucks, and John~A Pople}.
|
||
\newblock {\bf Gaussian-2 theory for molecular energies of first-and second-row
|
||
compounds}.
|
||
\newblock {\em J. Chem. Phys}, {\bf 94}(11):7221--7230, 1991.
|
||
|
||
\bibitem{Curtiss1998}
|
||
{\sc Larry~A Curtiss, Krishnan Raghavachari, Paul~C Redfern, Vitaly Rassolov,
|
||
and John~A Pople}.
|
||
\newblock {\bf Gaussian-3 (G3) theory for molecules containing first and
|
||
second-row atoms}.
|
||
\newblock {\em J. Chem. Phys}, {\bf 109}(18):7764--7776, 1998.
|
||
|
||
\bibitem{Ohlinger2009}
|
||
{\sc William~S Ohlinger, Philip~E Klunzinger, Bernard~J Deppmeier, and Warren~J
|
||
Hehre}.
|
||
\newblock {\bf Efficient calculation of heats of formation}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 113}(10):2165--2175, 2009.
|
||
|
||
\bibitem{Magnasco2009}
|
||
{\sc Roy McWeeny}.
|
||
\newblock {\em Post-Hartree-Fock Methods}, chapter~8, pages 133--139.
|
||
\newblock John Wiley \& Sons,Ltd.
|
||
|
||
\bibitem{Dacosta2011}
|
||
{\sc Herbert DaCosta and Maohong Fan}.
|
||
\newblock {\em Rate constant calculation for thermal reactions}.
|
||
\newblock Wiley Online Library, 2011.
|
||
|
||
\bibitem{Kohn1965}
|
||
{\sc Walter Kohn and Lu~Jeu Sham}.
|
||
\newblock {\bf Self-consistent equations including exchange and correlation
|
||
effects}.
|
||
\newblock {\em Physical review}, {\bf 140}(4A):A1133, 1965.
|
||
|
||
\bibitem{kohn1999nobel}
|
||
{\sc Walter Kohn}.
|
||
\newblock {\bf Nobel Lecture: Electronic structure of matter—wave functions
|
||
and density functionals}.
|
||
\newblock {\em Rev. Mod. Phys.}, {\bf 71}(5):1253, 1999.
|
||
|
||
\bibitem{Hohenberg1964}
|
||
{\sc Pierre Hohenberg and Walter Kohn}.
|
||
\newblock {\bf Inhomogeneous electron gas}.
|
||
\newblock {\em Physical Review}, {\bf 136}(3B):B864, 1964.
|
||
|
||
\bibitem{Levy1979}
|
||
{\sc Mel Levy}.
|
||
\newblock {\bf Universal variational functionals of electron densities,
|
||
first-order density matrices, and natural spin-orbitals and solution of the
|
||
v-representability problem}.
|
||
\newblock {\em Proc. Natl. Acad. Sci.}, {\bf 76}(12):6062--6065, 1979.
|
||
|
||
\bibitem{Thomas1927}
|
||
{\sc Llewellyn~H Thomas}.
|
||
\newblock {\bf The calculation of atomic fields}.
|
||
\newblock {\em Proc. Camb. Philos. Soc.}, {\bf 23}(5):542--548, 1927.
|
||
|
||
\bibitem{Fermi1928}
|
||
{\sc Enrico Fermi}.
|
||
\newblock {\bf Eine statistische methode zur bestimmung einiger eigenschaften
|
||
des atoms und ihre anwendung auf die theorie des periodischen systems der
|
||
elemente}.
|
||
\newblock {\em Zeitschrift f{\"u}r Physik}, {\bf 48}(1-2):73--79, 1928.
|
||
|
||
\bibitem{Herman1969}
|
||
{\sc Frank Herman, John~P Van~Dyke, and Irene~B Ortenburger}.
|
||
\newblock {\bf Improved statistical exchange approximation for inhomogeneous
|
||
many-electron systems}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 22}(16):807--811, 1969.
|
||
|
||
\bibitem{Perdew1996}
|
||
{\sc John~P Perdew and Kieron Burke}.
|
||
\newblock {\bf Comparison shopping for a gradient-corrected density
|
||
functional}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 57}(3):309--319, 1996.
|
||
|
||
\bibitem{Becke1993}
|
||
{\sc Axel~D Becke}.
|
||
\newblock {\bf Density functional thermochemistry. III. The role of exact
|
||
exchange}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 98}(492):5648--5652, 1993.
|
||
|
||
\bibitem{Becke1988}
|
||
{\sc Axel~D Becke}.
|
||
\newblock {\bf Density-functional exchange-energy approximation with correct
|
||
asymptotic behavior}.
|
||
\newblock {\em Phys. Rev. A}, {\bf 38}(6):3098, 1988.
|
||
|
||
\bibitem{Lee1988}
|
||
{\sc Chengteh Lee, Weitao Yang, and Robert~G Parr}.
|
||
\newblock {\bf Development of the Colle-Salvetti correlation-energy formula
|
||
into a functional of the electron density}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 37}(2):785--789, 1988.
|
||
|
||
\bibitem{Stephens1994}
|
||
{\sc Philip~J Stephens, Frank~J Devlin, Cary~F Chabalowski, and Michael~J
|
||
Frisch}.
|
||
\newblock {\bf Ab initio calculation of vibrational absorption and circular
|
||
dichroism spectra using density functional force fields}.
|
||
\newblock {\em J. Phys. Chem.}, {\bf 98}(45):11623--11627, 1994.
|
||
|
||
\bibitem{Adamo1999}
|
||
{\sc Carlo Adamo and Vincenzo Barone}.
|
||
\newblock {\bf Toward reliable density functional methods without adjustable
|
||
parameters: The PBE0 model}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 110}(13):6158--6170, 1999.
|
||
|
||
\bibitem{Henderson2009}
|
||
{\sc Thomas~M Henderson, Artur~F Izmaylov, Giovanni Scalmani, and Gustavo~E
|
||
Scuseria}.
|
||
\newblock {\bf Can short-range hybrids describe long-range-dependent
|
||
properties?}
|
||
\newblock {\em J. Chem. Phys.}, {\bf 131}(4):044108, 2009.
|
||
|
||
\bibitem{Krukau2006}
|
||
{\sc Aliaksandr~V Krukau, Oleg~A Vydrov, Artur~F Izmaylov, and Gustavo~E
|
||
Scuseria}.
|
||
\newblock {\bf Influence of the exchange screening parameter on the performance
|
||
of screened hybrid functionals}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 125}(22):224106, 2006.
|
||
|
||
\bibitem{Zhao2008}
|
||
{\sc Yan Zhao and Donald~G Truhlar}.
|
||
\newblock {\bf The M06 suite of density functionals for main group
|
||
thermochemistry, thermochemical kinetics, noncovalent interactions, excited
|
||
states, and transition elements: two new functionals and systematic testing
|
||
of four M06-class functionals and 12 other functionals}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 120}(1-3):215--241, 2008.
|
||
|
||
\bibitem{Li2018}
|
||
{\sc Chen Li, Xiao Zheng, Neil~Qiang Su, and Weitao Yang}.
|
||
\newblock {\bf Localized orbital scaling correction for systematic elimination
|
||
of delocalization error in density functional approximations}.
|
||
\newblock {\em Natl. Sci. Rev.}, {\bf 5}(2):203--215, 2018.
|
||
|
||
\bibitem{Foulkes1989}
|
||
{\sc W~Matthew~C Foulkes and Roger Haydock}.
|
||
\newblock {\bf Tight-binding models and density-functional theory}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 39}(17):12520, 1989.
|
||
|
||
\bibitem{Porezag1995}
|
||
{\sc Dirk Porezag, Th~Frauenheim, Th~K{\"o}hler, Gotthard Seifert, and
|
||
R~Kaschner}.
|
||
\newblock {\bf Construction of tight-binding-like potentials on the basis of
|
||
density-functional theory: Application to carbon}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 51}(19):12947, 1995.
|
||
|
||
\bibitem{Seifert1996}
|
||
{\sc G~Seifert, D~Porezag, and Th~Frauenheim}.
|
||
\newblock {\bf Calculations of molecules, clusters, and solids with a
|
||
simplified LCAO-DFT-LDA scheme}.
|
||
\newblock {\em Int. J. Quantum Chem.}, {\bf 58}(2):185--192, 1996.
|
||
|
||
\bibitem{Elstne2007}
|
||
{\sc Marcus Elstner, T~Frauenheim, J~McKelvey, and G~Seifert}.
|
||
\newblock {\bf Density functional tight binding: Contributions from the
|
||
american chemical society symposium}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 111}(26):5607--5608, 2007.
|
||
|
||
\bibitem{Oliveira2009}
|
||
{\sc Augusto~F Oliveira, Gotthard Seifert, Thomas Heine, and H{\'e}lio~A
|
||
Duarte}.
|
||
\newblock {\bf Density-functional based tight-binding: an approximate DFT
|
||
method}.
|
||
\newblock {\em J. Braz. Chem. Soc., volume={20}, number={7},
|
||
pages={1193--1205}, year={2009}, publisher={SciELO Brasil}}.
|
||
|
||
\bibitem{Gaus2011}
|
||
{\sc Michael Gaus, Qiang Cui, and Marcus Elstner}.
|
||
\newblock {\bf DFTB3: extension of the self-consistent-charge
|
||
density-functional tight-binding method (SCC-DFTB)}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 7}(4):931--948, 2011.
|
||
|
||
\bibitem{Mulliken1955}
|
||
{\sc Robert~S Mulliken}.
|
||
\newblock {\bf Electronic population analysis on LCAO--MO molecular wave
|
||
functions. I}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 23}(10):1833--1840, 1955.
|
||
|
||
\bibitem{Bader1985}
|
||
{\sc Richard F.~W. Bader}.
|
||
\newblock {\bf Atoms in molecules}.
|
||
\newblock {\em Acc. Chem. Res.}, {\bf 18}(1):9--15, 1985.
|
||
|
||
\bibitem{Bader1990}
|
||
{\sc Richard F~W Bader}.
|
||
\newblock {\em Atoms in molecules: a quantum theory}.
|
||
\newblock Oxford: Clarendon press, 1990.
|
||
|
||
\bibitem{Glendening1998}
|
||
{\sc Eric~D Glendening and Frank Weinhold}.
|
||
\newblock {\bf Natural resonance theory: II. Natural bond order and valency}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 19}(6):610--627, 1998.
|
||
|
||
\bibitem{Glendening2012}
|
||
{\sc Eric~D Glendening, Clark~R Landis, and Frank Weinhold}.
|
||
\newblock {\bf Natural bond orbital methods}.
|
||
\newblock {\em Wiley Interdiscip. Rev. Comput. Mol. Sci.}, {\bf 2}(1):1--42,
|
||
2012.
|
||
|
||
\bibitem{Singh1984}
|
||
{\sc U~Chandra Singh and Peter~A Kollman}.
|
||
\newblock {\bf An approach to computing electrostatic charges for molecules}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 5}(2):129--145, 1984.
|
||
|
||
\bibitem{Besler1990}
|
||
{\sc Brent~H Besler, Kenneth~M Merz~Jr, and Peter~A Kollman}.
|
||
\newblock {\bf Atomic charges derived from semiempirical methods}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 11}(4):431--439, 1990.
|
||
|
||
\bibitem{Li1998}
|
||
{\sc Jiabo Li, Tianhai Zhu, Christopher~J Cramer, and Donald~G Truhlar}.
|
||
\newblock {\bf New class IV charge model for extracting accurate partial
|
||
charges from wave functions}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 102}(10):1820--1831, 1998.
|
||
|
||
\bibitem{Kalinowski2004}
|
||
{\sc Jaroslaw~A Kalinowski, Bogdan Lesyng, Jason~D Thompson, Christopher~J
|
||
Cramer, and Donald~G Truhlar}.
|
||
\newblock {\bf Class IV charge model for the self-consistent charge
|
||
density-functional tight-binding method}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 108}(13):2545--2549, 2004.
|
||
|
||
\bibitem{Kelly2005}
|
||
{\sc Casey~P Kelly, Christopher~J Cramer, and Donald~G Truhlar}.
|
||
\newblock {\bf Accurate partial atomic charges for high-energy molecules using
|
||
class IV charge models with the MIDI! basis set}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 113}(3):133--151, 2005.
|
||
|
||
\bibitem{Rapacioli2009corr}
|
||
{\sc Mathias Rapacioli, Fernand Spiegelman, Dahbia Talbi, Tzonka Mineva, Annick
|
||
Goursot, Thomas Heine, and Gotthard Seifert}.
|
||
\newblock {\bf Correction for dispersion and Coulombic interactions in
|
||
molecular clusters with density functional derived methods: Application to
|
||
polycyclic aromatic hydrocarbon clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 130}(24):244304, 2009.
|
||
|
||
\bibitem{Mayer1983}
|
||
{\sc Istvan Mayer}.
|
||
\newblock {\bf Charge, bond order and valence in the AB initio SCF theory}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 97}(3):270--274, 1983.
|
||
|
||
\bibitem{Cances1997}
|
||
{\sc E~Cances, Benedetta Mennucci, and J~Tomasi}.
|
||
\newblock {\bf A new integral equation formalism for the polarizable continuum
|
||
model: Theoretical background and applications to isotropic and anisotropic
|
||
dielectrics}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 107}(8):3032--3041, 1997.
|
||
|
||
\bibitem{Lu2012}
|
||
{\sc Tian Lu and Feiwu Chen}.
|
||
\newblock {\bf Multiwfn: a multifunctional wavefunction analyzer}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 33}(5):580--592, 2012.
|
||
|
||
\bibitem{Lewis1995}
|
||
{\sc James~P Lewis and Otto~F Sankey}.
|
||
\newblock {\bf Geometry and energetics of DNA basepairs and triplets from first
|
||
principles quantum molecular relaxations}.
|
||
\newblock {\em Biophys. J.}, {\bf 69}(3):1068--1076, 1995.
|
||
|
||
\bibitem{Gianturco1999}
|
||
{\sc FA~Gianturco, F~Paesani, MF~Laranjeira, V~Vassilenko, and MA~Cunha}.
|
||
\newblock {\bf Intermolecular forces from density functional theory. III. A
|
||
multiproperty analysis for the Ar($^1$S)-CO($^1\Sigma$) interaction}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 110}(16):7832--7845, 1999.
|
||
|
||
\bibitem{Elstner2001}
|
||
{\sc Marcus Elstner, Pavel Hobza, Thomas Frauenheim, S{\'a}ndor Suhai, and
|
||
Efthimios Kaxiras}.
|
||
\newblock {\bf Hydrogen bonding and stacking interactions of nucleic acid base
|
||
pairs: A density-functional-theory based treatment}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 114}(12):5149--5155, 2001.
|
||
|
||
\bibitem{Wu2002}
|
||
{\sc Qin Wu and Weitao Yang}.
|
||
\newblock {\bf Empirical correction to density functional theory for van der
|
||
Waals interactions}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 116}(2):515--524, 2002.
|
||
|
||
\bibitem{Grimme2004}
|
||
{\sc Stefan Grimme}.
|
||
\newblock {\bf Accurate description of van der Waals complexes by density
|
||
functional theory including empirical corrections}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 25}(12):1463--1473, 2004.
|
||
|
||
\bibitem{Zimmerli2004}
|
||
{\sc Urs Zimmerli, Michele Parrinello, and Petros Koumoutsakos}.
|
||
\newblock {\bf Dispersion corrections to density functionals for water aromatic
|
||
interactions}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 120}(6):2693--2699, 2004.
|
||
|
||
\bibitem{Neumann2005}
|
||
{\sc Marcus~A Neumann and Marc-Antoine Perrin}.
|
||
\newblock {\bf Energy ranking of molecular crystals using density functional
|
||
theory calculations and an empirical van der Waals correction}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 109}(32):15531--15541, 2005.
|
||
|
||
\bibitem{Goursot2007}
|
||
{\sc Annick Goursot, Tzonka Mineva, Ruslan Kevorkyants, and Dahbia Talbi}.
|
||
\newblock {\bf Interaction between n-alkane chains: Applicability of the
|
||
empirically corrected density functional theory for van der Waals complexes}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 3}(3):755--763, 2007.
|
||
|
||
\bibitem{Frenkel2001}
|
||
{\sc Daan Frenkel and Berend Smit}.
|
||
\newblock {\em Understanding molecular simulation: from algorithms to
|
||
applications}, ~{\bf 1}.
|
||
\newblock Elsevier, 2001.
|
||
|
||
\bibitem{Jones1924}
|
||
{\sc John~Edward Jones}.
|
||
\newblock {\bf On the determination of molecular fields.—I. From the
|
||
variation of the viscosity of a gas with temperature}.
|
||
\newblock {\em Proc. Math. Phys. Eng. Sci.}, {\bf 106}(738):441--462, 1924.
|
||
|
||
\bibitem{Lennard1924}
|
||
{\sc John~Edward Lennard-Jones}.
|
||
\newblock {\bf On the determination of molecular fields. II. From the equation
|
||
of state of gas}.
|
||
\newblock {\em Proc. Roy. Soc. A}, {\bf 106}:463--477, 1924.
|
||
|
||
\bibitem{Morse1929}
|
||
{\sc Philip~M Morse}.
|
||
\newblock {\bf Diatomic molecules according to the wave mechanics. II.
|
||
Vibrational levels}.
|
||
\newblock {\em Physical review}, {\bf 34}(1):57--64, 1929.
|
||
|
||
\bibitem{Born1932}
|
||
{\sc Max Born and Joseph~E Mayer}.
|
||
\newblock {\bf Zur gittertheorie der ionenkristalle}.
|
||
\newblock {\em Zeitschrift f{\"u}r Physik}, {\bf 75}(1-2):1--18, 1932.
|
||
|
||
\bibitem{Stillinger1985}
|
||
{\sc Frank~H Stillinger and Thomas~A Weber}.
|
||
\newblock {\bf Computer simulation of local order in condensed phases of
|
||
silicon}.
|
||
\newblock {\em Phys. Rev. B}, {\bf 31}(8):5262--5271, 1985.
|
||
|
||
\bibitem{Kaplan2006}
|
||
{\sc Ilya~G Kaplan}.
|
||
\newblock {\em Intermolecular interactions: physical picture, computational
|
||
methods and model potentials}.
|
||
\newblock John Wiley \& Sons, 2006.
|
||
|
||
\bibitem{Bahar1997}
|
||
{\sc Ivet Bahar, Ali~Rana Atilgan, and Burak Erman}.
|
||
\newblock {\bf Direct evaluation of thermal fluctuations in proteins using a
|
||
single-parameter harmonic potential}.
|
||
\newblock {\em Fold Des.}, {\bf 2}(3):173--181, 1997.
|
||
|
||
\bibitem{Girifalco1959}
|
||
{\sc Louis~A Girifalco and Victor~G Weizer}.
|
||
\newblock {\bf Application of the Morse potential function to cubic metals}.
|
||
\newblock {\em Physical Review}, {\bf 114}(3):687--690, 1959.
|
||
|
||
\bibitem{Lennard1931}
|
||
{\sc John~Edward Lennard-Jones}.
|
||
\newblock {\bf Cohesion}.
|
||
\newblock {\em Proceedings of the Physical Society}, {\bf 43}(5):461--482,
|
||
1931.
|
||
|
||
\bibitem{Monticelli2013}
|
||
{\sc Luca Monticelli and D~Peter Tieleman}.
|
||
\newblock {\bf Force fields for classical molecular dynamics}.
|
||
\newblock In {\em Biomolecular simulations}, pages 197--213. Springer, 2013.
|
||
|
||
\bibitem{Metropolis1987}
|
||
{\sc N~Metropolis}.
|
||
\newblock {\bf The beginning of the Monte Carlo method}.
|
||
\newblock {\em Los Alamos Science}, {\bf 15}:125--130, 1987.
|
||
|
||
\bibitem{Kroese2014}
|
||
{\sc Dirk~P Kroese, Tim Brereton, Thomas Taimre, and Zdravko~I Botev}.
|
||
\newblock {\bf Why the Monte Carlo method is so important today}.
|
||
\newblock {\em Wiley Interdisciplinary Reviews: Computational Statistics}, {\bf
|
||
6}(6):386--392, 2014.
|
||
|
||
\bibitem{Rosenbluth1955}
|
||
{\sc Marshall~N Rosenbluth and Arianna~W Rosenbluth}.
|
||
\newblock {\bf Monte Carlo calculation of the average extension of molecular
|
||
chains}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 23}(2):356--359, 1955.
|
||
|
||
\bibitem{Binder1993}
|
||
{\sc Kurt Binder, Dieter Heermann, Lyle Roelofs, A~John Mallinckrodt, and Susan
|
||
McKay}.
|
||
\newblock {\bf Monte Carlo simulation in statistical physics}.
|
||
\newblock {\em Comput. Phys.}, {\bf 7}(2):156--157, 1993.
|
||
|
||
\bibitem{Baeurle2009}
|
||
{\sc Stephan~A Baeurle}.
|
||
\newblock {\bf Multiscale modeling of polymer materials using field-theoretic
|
||
methodologies: a survey about recent developments}.
|
||
\newblock {\em J. Math. Chem.}, {\bf 46}(2):363--426, 2009.
|
||
|
||
\bibitem{Alder1957}
|
||
{\sc Berni~Julian Alder and Thomas~Everett Wainwright}.
|
||
\newblock {\bf Phase transition for a hard sphere system}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 27}(5):1208--1209, 1957.
|
||
|
||
\bibitem{Gibson1960}
|
||
{\sc JB~Gibson, An~N Goland, M~Milgram, and GoHo Vineyard}.
|
||
\newblock {\bf Dynamics of radiation damage}.
|
||
\newblock {\em Physical Review}, {\bf 120}(4):1229--1253, 1960.
|
||
|
||
\bibitem{Rahman1964}
|
||
{\sc Aneesur Rahman}.
|
||
\newblock {\bf Correlations in the motion of atoms in liquid argon}.
|
||
\newblock {\em Physical review}, {\bf 136}(2A):A405--A411, 1964.
|
||
|
||
\bibitem{Allen2017}
|
||
{\sc Michael~P Allen and Dominic~J Tildesley}.
|
||
\newblock {\em Computer simulation of liquids}.
|
||
\newblock Oxford university press, 2017.
|
||
|
||
\bibitem{Cicccotti1987}
|
||
{\sc G~Cicccotti, D~Frenkel, and IR~McDonald}.
|
||
\newblock {\bf Simulations of liquids and solids--molecular dynamics and monte
|
||
carlo methods in statistical mechanics}, 1987.
|
||
|
||
\bibitem{Van1990}
|
||
{\sc Wilfred~F Van~Gunsteren and Herman~JC Berendsen}.
|
||
\newblock {\bf Computer simulation of molecular dynamics: methodology,
|
||
applications, and perspectives in chemistry}.
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 29}(9):992--1023, 1990.
|
||
|
||
\bibitem{Berne1998}
|
||
{\sc Bruce~J Berne, Giovanni Ciccotti, and David~F Coker}.
|
||
\newblock {\em Classical and Quantum Dynamics in Condensed Phase Simulations:
|
||
Proceedings of the International School of Physics}.
|
||
\newblock World Scientific, 1998.
|
||
|
||
\bibitem{Tuckerman2000}
|
||
{\sc Mark~E Tuckerman and Glenn~J Martyna}.
|
||
\newblock {\bf Understanding modern molecular dynamics: techniques and
|
||
applications}, 2000.
|
||
|
||
\bibitem{Karplus2002}
|
||
{\sc Martin Karplus and J~Andrew McCammon}.
|
||
\newblock {\bf Molecular dynamics simulations of biomolecules}.
|
||
\newblock {\em Nat. Struct. Biol.}, {\bf 9}(9):646--652, 2002.
|
||
|
||
\bibitem{Rapaport2004}
|
||
{\sc Dennis~C Rapaport}.
|
||
\newblock {\em The art of molecular dynamics simulation}.
|
||
\newblock Cambridge university press, 2004.
|
||
|
||
\bibitem{Tavan2005}
|
||
{\sc Paul Tavan, Heiko Carstens, and Gerald Mathias}.
|
||
\newblock {\bf Molecular dynamics simulations of proteins and peptides:
|
||
Problems, achievements, and perspectives}.
|
||
\newblock {\em Protein Folding Handbook}, pages 1170--1195, 2005.
|
||
|
||
\bibitem{Van2006}
|
||
{\sc Wilfred~F van Gunsteren, Dirk Bakowies, Riccardo Baron, Indira
|
||
Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan~P Geerke, Alice
|
||
Gl{\"a}ttli, Philippe~H H{\"u}nenberger, et~al.}
|
||
\newblock {\bf Biomolecular modeling: goals, problems, perspectives}.
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 45}(25):4064--4092, 2006.
|
||
|
||
\bibitem{Parrinello1980}
|
||
{\sc Michele Parrinello and Aneesur Rahman}.
|
||
\newblock {\bf Crystal structure and pair potentials: A molecular-dynamics
|
||
study}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 45}(14):1196--1199, 1980.
|
||
|
||
\bibitem{Ballone1988}
|
||
{\sc Pietro Ballone, Wanda Andreoni, Roberto Car, and Michele Parrinello}.
|
||
\newblock {\bf Equilibrium structures and finite temperature properties of
|
||
silicon microclusters from ab initio molecular-dynamics calculations}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 60}(4):271--274, 1988.
|
||
|
||
\bibitem{Gutierrez1996}
|
||
{\sc Rafael Gutierrez, Thomas Frauenheim, Thomas K{\"o}hler, and Gothard
|
||
Seifert}.
|
||
\newblock {\bf Stability of silicon carbide structures: from clusters to solid
|
||
surfaces}.
|
||
\newblock {\em J. Mater. Chem. A .}, {\bf 6}(10):1657--1663, 1996.
|
||
|
||
\bibitem{Briant1975}
|
||
{\sc CL~Briant and JJ~Burton}.
|
||
\newblock {\bf Molecular dynamics study of the structure and thermodynamic
|
||
properties of argon microclusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 63}(5):2045--2058, 1975.
|
||
|
||
\bibitem{Postma1982}
|
||
{\sc Johan~PM Postma, Herman~JC Berendsen, and Jan~R Haak}.
|
||
\newblock {\bf Thermodynamics of cavity formation in water. A molecular
|
||
dynamics study}.
|
||
\newblock In {\em Faraday Symposia of the Chemical Society}, ~{\bf 17}, pages
|
||
55--67. Royal Society of Chemistry, 1982.
|
||
|
||
\bibitem{Honeycutt1987}
|
||
{\sc J~Dana Honeycutt and Hans~C Andersen}.
|
||
\newblock {\bf Molecular dynamics study of melting and freezing of small
|
||
Lennard-Jones clusters}.
|
||
\newblock {\em Journal of Physical Chemistry}, {\bf 91}(19):4950--4963, 1987.
|
||
|
||
\bibitem{Dang1997}
|
||
{\sc Liem~X Dang and Tsun-Mei Chang}.
|
||
\newblock {\bf Molecular dynamics study of water clusters, liquid, and
|
||
liquid--vapor interface of water with many-body potentials}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 106}(19):8149--8159, 1997.
|
||
|
||
\bibitem{Coveney2016}
|
||
{\sc Peter~V Coveney and Shunzhou Wan}.
|
||
\newblock {\bf On the calculation of equilibrium thermodynamic properties from
|
||
molecular dynamics}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 18}(44):30236--30240, 2016.
|
||
|
||
\bibitem{Charati1998}
|
||
{\sc SG~Charati and SA~Stern}.
|
||
\newblock {\bf Diffusion of gases in silicone polymers: molecular dynamics
|
||
simulations}.
|
||
\newblock {\em Macromolecules}, {\bf 31}(16):5529--5535, 1998.
|
||
|
||
\bibitem{Yeh2004}
|
||
{\sc In-Chul Yeh and Gerhard Hummer}.
|
||
\newblock {\bf System-size dependence of diffusion coefficients and viscosities
|
||
from molecular dynamics simulations with periodic boundary conditions}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 108}(40):15873--15879, 2004.
|
||
|
||
\bibitem{Braga2014}
|
||
{\sc Carlos Braga, Amparo Galindo, and Erich~A M{\"u}ller}.
|
||
\newblock {\bf Nonequilibrium molecular dynamics simulation of diffusion at the
|
||
liquid-liquid interface}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 141}(15):154101, 2014.
|
||
|
||
\bibitem{Pranami2015}
|
||
{\sc Gaurav Pranami and Monica~H Lamm}.
|
||
\newblock {\bf Estimating error in diffusion coefficients derived from
|
||
molecular dynamics simulations}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 11}(10):4586--4592, 2015.
|
||
|
||
\bibitem{Mondello1997}
|
||
{\sc Maurizio Mondello and Gary~S Grest}.
|
||
\newblock {\bf Viscosity calculations of n-alkanes by equilibrium molecular
|
||
dynamics}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 106}(22):9327--9336, 1997.
|
||
|
||
\bibitem{Hess2002}
|
||
{\sc Berk Hess}.
|
||
\newblock {\bf Determining the shear viscosity of model liquids from molecular
|
||
dynamics simulations}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 116}(1):209--217, 2002.
|
||
|
||
\bibitem{Zhang2015}
|
||
{\sc Yong Zhang, Akihito Otani, and Edward~J Maginn}.
|
||
\newblock {\bf Reliable viscosity calculation from equilibrium molecular
|
||
dynamics simulations: A time decomposition method}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 11}(8):3537--3546, 2015.
|
||
|
||
\bibitem{Aragon1976}
|
||
{\sc SR~Aragon and R~Pecora}.
|
||
\newblock {\bf Fluorescence correlation spectroscopy as a probe of molecular
|
||
dynamics}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 64}(4):1791--1803, 1976.
|
||
|
||
\bibitem{Vuilleumier1999}
|
||
{\sc Rodolphe Vuilleumier and Daniel Borgis}.
|
||
\newblock {\bf Transport and spectroscopy of the hydrated proton: a molecular
|
||
dynamics study}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 111}(9):4251--4266, 1999.
|
||
|
||
\bibitem{Pavone2006}
|
||
{\sc Michele Pavone, Giuseppe Brancato, Giovanni Morelli, and Vincenzo Barone}.
|
||
\newblock {\bf Spectroscopic properties in the liquid phase: combining
|
||
high-level ab initio calculations and classical molecular dynamics}.
|
||
\newblock {\em ChemPhysChem}, {\bf 7}(1):148--156, 2006.
|
||
|
||
\bibitem{Brancato2006}
|
||
{\sc Giuseppe Brancato, Nadia Rega, and Vincenzo Barone}.
|
||
\newblock {\bf A quantum mechanical/molecular dynamics/mean field study of
|
||
acrolein in aqueous solution: analysis of H bonding and bulk effects on
|
||
spectroscopic properties}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 125}(16):164515, 2006.
|
||
|
||
\bibitem{Beck2000}
|
||
{\sc Michael~H Beck, Andreas J{\"a}ckle, Graham~A Worth, and H-D Meyer}.
|
||
\newblock {\bf The multiconfiguration time-dependent Hartree (MCTDH) method: a
|
||
highly efficient algorithm for propagating wavepackets}.
|
||
\newblock {\em Phys. Rep.}, {\bf 324}(1):1--105, 2000.
|
||
|
||
\bibitem{Wang2003}
|
||
{\sc Haobin Wang and Michael Thoss}.
|
||
\newblock {\bf Multilayer formulation of the multiconfiguration time-dependent
|
||
Hartree theory}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 119}(3):1289--1299, 2003.
|
||
|
||
\bibitem{Wei1994}
|
||
{\sc Hua Wei and Tucker Carrington~Jr}.
|
||
\newblock {\bf Discrete variable representations of complicated kinetic energy
|
||
operators}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 101}(2):1343--1360, 1994.
|
||
|
||
\bibitem{Light2000}
|
||
{\sc John~C Light and Tucker Carrington~Jr}.
|
||
\newblock {\bf Discrete-variable representations and their utilization}.
|
||
\newblock {\em Advances in Chemical Physics}, {\bf 114}:263--310, 2000.
|
||
|
||
\bibitem{Batina1991}
|
||
{\sc John~T Batina}.
|
||
\newblock {\bf Unsteady Euler algorithm with unstructured dynamic mesh for
|
||
complex-aircraft aerodynamic analysis}.
|
||
\newblock {\em AIAA J.}, {\bf 29}(3):327--333, 1991.
|
||
|
||
\bibitem{Butcher2008}
|
||
{\sc John~Charles Butcher and Nicolette Goodwin}.
|
||
\newblock {\em Numerical methods for ordinary differential equations}, ~{\bf
|
||
2}.
|
||
\newblock Wiley Online Library, 2008.
|
||
|
||
\bibitem{Gear1966}
|
||
{\sc Charles~William Gear}.
|
||
\newblock {\bf The numerical integration of ordinary differential equations of
|
||
various orders}.
|
||
\newblock Technical report, Argonne National Lab., Ill., 1966.
|
||
|
||
\bibitem{Diethelm2002}
|
||
{\sc Kai Diethelm, Neville~J Ford, and Alan~D Freed}.
|
||
\newblock {\bf A predictor-corrector approach for the numerical solution of
|
||
fractional differential equations}.
|
||
\newblock {\em Nonlinear Dyn.}, {\bf 29}(1-4):3--22, 2002.
|
||
|
||
\bibitem{Runge1895}
|
||
{\sc Carl Runge}.
|
||
\newblock {\bf {\"U}ber die numerische Aufl{\"o}sung von
|
||
Differentialgleichungen}.
|
||
\newblock {\em Math. Ann}, {\bf 46}(2):167--178, 1895.
|
||
|
||
\bibitem{Kutta1901}
|
||
{\sc Wilhelm Kutta}.
|
||
\newblock {\bf Beitrag zur naherungsweisen Integration totaler
|
||
Differentialgleichungen}.
|
||
\newblock {\em Z. Math. Phys.}, {\bf 46}:435--453, 1901.
|
||
|
||
\bibitem{Butcher1996}
|
||
{\sc John~Charles Butcher}.
|
||
\newblock {\bf A history of Runge-Kutta methods}.
|
||
\newblock {\em Appl. Numer. Math.}, {\bf 20}(3):247--260, 1996.
|
||
|
||
\bibitem{Butcher2015}
|
||
{\sc JC~Butcher}.
|
||
\newblock {\bf Runge--Kutta methods for ordinary differential equations}.
|
||
\newblock In {\em Numerical Analysis and Optimization}, pages 37--58. Springer,
|
||
2015.
|
||
|
||
\bibitem{Verlet1967}
|
||
{\sc Loup Verlet}.
|
||
\newblock {\bf Computer" experiments" on classical fluids. I. Thermodynamical
|
||
properties of Lennard-Jones molecules}.
|
||
\newblock {\em Physical review}, {\bf 159}(1):98--103, 1967.
|
||
|
||
\bibitem{Fraige2004}
|
||
{\sc FY~Fraige and PA~Langston}.
|
||
\newblock {\bf Integration schemes and damping algorithms in distinct element
|
||
models}.
|
||
\newblock {\em Advanced Powder Technology}, {\bf 15}(2):227--245, 2004.
|
||
|
||
\bibitem{Swope1982}
|
||
{\sc William~C Swope, Hans~C Andersen, Peter~H Berens, and Kent~R Wilson}.
|
||
\newblock {\bf A computer simulation method for the calculation of equilibrium
|
||
constants for the formation of physical clusters of molecules: Application to
|
||
small water clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 76}(1):637--649, 1982.
|
||
|
||
\bibitem{Ray1981}
|
||
{\sc John~R Ray and HW~Graben}.
|
||
\newblock {\bf Direct calculation of fluctuation formulae in the microcanonical
|
||
ensemble}.
|
||
\newblock {\em Mol. Phys.}, {\bf 43}(6):1293--1297, 1981.
|
||
|
||
\bibitem{Ray1999}
|
||
{\sc John~R Ray and Hongwei Zhang}.
|
||
\newblock {\bf Correct microcanonical ensemble in molecular dynamics}.
|
||
\newblock {\em Phys. Rev. E}, {\bf 59}(5):4781--4785, 1999.
|
||
|
||
\bibitem{Nose1984}
|
||
{\sc Shuichi Nos{\'e}}.
|
||
\newblock {\bf A unified formulation of the constant temperature molecular
|
||
dynamics methods}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 81}(1):511--519, 1984.
|
||
|
||
\bibitem{Nose1984M}
|
||
{\sc Sh{\=u}ichi Nos{\'e}}.
|
||
\newblock {\bf A molecular dynamics method for simulations in the canonical
|
||
ensemble}.
|
||
\newblock {\em Mol. Phys.}, {\bf 52}(2):255--268, 1984.
|
||
|
||
\bibitem{Hoover1985}
|
||
{\sc William~G Hoover}.
|
||
\newblock {\bf Canonical dynamics: Equilibrium phase-space distributions}.
|
||
\newblock {\em Phys. Rev. A}, {\bf 31}(3):1695--1697, 1985.
|
||
|
||
\bibitem{Hunenberger2005}
|
||
{\sc Philippe~H H{\"u}nenberger}.
|
||
\newblock {\bf Thermostat algorithms for molecular dynamics simulations}.
|
||
\newblock In {\em Advanced computer simulation}, pages 105--149. Springer,
|
||
2005.
|
||
|
||
\bibitem{Torrie1977}
|
||
{\sc Glenn~M Torrie and John~P Valleau}.
|
||
\newblock {\bf Nonphysical sampling distributions in Monte Carlo free-energy
|
||
estimation: Umbrella sampling}.
|
||
\newblock {\em J. Comput. Phys.}, {\bf 23}(2):187--199, 1977.
|
||
|
||
\bibitem{Hansmann1993}
|
||
{\sc Ulrich~HE Hansmann and Yuko Okamoto}.
|
||
\newblock {\bf Prediction of peptide conformation by multicanonical algorithm:
|
||
New approach to the multiple-minima problem}.
|
||
\newblock {\em J. Comput. Chem}, {\bf 14}(11):1333--1338, 1993.
|
||
|
||
\bibitem{Marchi1999}
|
||
{\sc Massimo Marchi and Pietro Ballone}.
|
||
\newblock {\bf Adiabatic bias molecular dynamics: a method to navigate the
|
||
conformational space of complex molecular systems}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 110}(8):3697--3702, 1999.
|
||
|
||
\bibitem{Bartels2000}
|
||
{\sc Christian Bartels}.
|
||
\newblock {\bf Analyzing biased Monte Carlo and molecular dynamics
|
||
simulations}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 331}(5-6):446--454, 2000.
|
||
|
||
\bibitem{Darve2001}
|
||
{\sc Eric Darve and Andrew Pohorille}.
|
||
\newblock {\bf Calculating free energies using average force}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 115}(20):9169--9183, 2001.
|
||
|
||
\bibitem{Laio2002}
|
||
{\sc Alessandro Laio and Michele Parrinello}.
|
||
\newblock {\bf Escaping free-energy minima}.
|
||
\newblock {\em Proc. Natl. Acad. Sci.}, {\bf 99}(20):12562--12566, 2002.
|
||
|
||
\bibitem{Iannuzzi2003}
|
||
{\sc Marcella Iannuzzi, Alessandro Laio, and Michele Parrinello}.
|
||
\newblock {\bf Efficient exploration of reactive potential energy surfaces
|
||
using Car-Parrinello molecular dynamics}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 90}(23):238302, 2003.
|
||
|
||
\bibitem{Barducci2011}
|
||
{\sc Alessandro Barducci, Massimiliano Bonomi, and Michele Parrinello}.
|
||
\newblock {\bf Metadynamics}.
|
||
\newblock {\em Wiley Interdiscip. Rev. Comput. Mol. Sci.}, {\bf 1}(5):826--843,
|
||
2011.
|
||
|
||
\bibitem{Kirkpatrick1983}
|
||
{\sc Scott Kirkpatrick, C~Daniel Gelatt, and Mario~P Vecchi}.
|
||
\newblock {\bf Optimization by simulated annealing}.
|
||
\newblock {\em science}, {\bf 220}(4598):671--680, 1983.
|
||
|
||
\bibitem{Van1987}
|
||
{\sc Peter~JM Van~Laarhoven and Emile~HL Aarts}.
|
||
\newblock {\bf Simulated annealing}.
|
||
\newblock In {\em Simulated annealing: Theory and applications}, pages 7--15.
|
||
Springer, 1987.
|
||
|
||
\bibitem{Swendsen1986}
|
||
{\sc Robert~H Swendsen and Jian-Sheng Wang}.
|
||
\newblock {\bf Replica Monte Carlo simulation of spin-glasses}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 57}(21):2607, 1986.
|
||
|
||
\bibitem{Geyer1991}
|
||
{\sc Charles~J Geyer et~al.}
|
||
\newblock {\bf Computing science and statistics: Proceedings of the 23rd
|
||
Symposium on the Interface}.
|
||
\newblock {\em American Statistical Association, New York}, {\bf 156}, 1991.
|
||
|
||
\bibitem{Hukushima1996}
|
||
{\sc Koji Hukushima and Koji Nemoto}.
|
||
\newblock {\bf Exchange Monte Carlo method and application to spin glass
|
||
simulations}.
|
||
\newblock {\em J. Phys. Soc. Jpn.}, {\bf 65}(6):1604--1608, 1996.
|
||
|
||
\bibitem{Falcioni1999}
|
||
{\sc Marco Falcioni and Michael~W Deem}.
|
||
\newblock {\bf A biased Monte Carlo scheme for zeolite structure solution}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 110}(3):1754--1766, 1999.
|
||
|
||
\bibitem{Earl2005}
|
||
{\sc David~J Earl and Michael~W Deem}.
|
||
\newblock {\bf Parallel tempering: Theory, applications, and new perspectives}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 7}(23):3910--3916, 2005.
|
||
|
||
\bibitem{Sugita1999}
|
||
{\sc Yuji Sugita and Yuko Okamoto}.
|
||
\newblock {\bf Replica-exchange molecular dynamics method for protein folding}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 314}(1-2):141--151, 1999.
|
||
|
||
\bibitem{Hartke1993}
|
||
{\sc Bernd Hartke}.
|
||
\newblock {\bf Global geometry optimization of clusters using genetic
|
||
algorithms}.
|
||
\newblock {\em J. Phys. Chem.}, {\bf 97}(39):9973--9976, 1993.
|
||
|
||
\bibitem{Unger1993}
|
||
{\sc Ron Unger and John Moult}.
|
||
\newblock {\bf Genetic algorithms for protein folding simulations}.
|
||
\newblock {\em J. Mol. Biol., volume={231}, number={1}, pages={75--81},
|
||
year={1993}, publisher={Elsevier}}.
|
||
|
||
\bibitem{Sivanandam2008}
|
||
{\sc SN~Sivanandam and SN~Deepa}.
|
||
\newblock {\bf Genetic algorithms}.
|
||
\newblock In {\em Introduction to genetic algorithms}, pages 15--37. Springer,
|
||
2008.
|
||
|
||
\bibitem{Toledo2014}
|
||
{\sc Claudio Fabiano~Motta Toledo, L~Oliveira, and Paulo~Morelato
|
||
Fran{\c{c}}a}.
|
||
\newblock {\bf Global optimization using a genetic algorithm with
|
||
hierarchically structured population}.
|
||
\newblock {\em J. Comput. Appl. Math.}, {\bf 261}:341--351, 2014.
|
||
|
||
\bibitem{deMonNano2009}
|
||
{\sc T~Heine, M~Rapacioli, S~Patchkovskii, J~Frenzel, A~Koster, P~Calaminici,
|
||
HA~Duarte, S~Escalante, R~Flores-Moreno, and A~Goursot}.
|
||
\newblock {\bf deMonNano}, 2009.
|
||
|
||
\bibitem{Gaus2013para}
|
||
{\sc Michael Gaus, Albrecht Goez, and Marcus Elstner}.
|
||
\newblock {\bf Parametrization and benchmark of DFTB3 for organic molecules}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 9}(1):338--354, 2013.
|
||
|
||
\bibitem{Thompson2003}
|
||
{\sc Jason~D Thompson, Christopher~J Cramer, and Donald~G Truhlar}.
|
||
\newblock {\bf Parameterization of charge model 3 for AM1, PM3, BLYP, and
|
||
B3LYP}.
|
||
\newblock {\em J. Comput. Chem.}, {\bf 24}(11):1291--1304, 2003.
|
||
|
||
\bibitem{Zhechkov2005}
|
||
{\sc Lyuben Zhechkov, Thomas Heine, Serguei Patchkovskii, Gotthard Seifert, and
|
||
Helio~A Duarte}.
|
||
\newblock {\bf An efficient a posteriori treatment for dispersion interaction
|
||
in density-functional-based tight binding}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 1}(5):841--847, 2005.
|
||
|
||
\bibitem{Simon2012}
|
||
{\sc Aude Simon, Mathias Rapacioli, Jo{\"e}lle Mascetti, and Fernand
|
||
Spiegelman}.
|
||
\newblock {\bf Vibrational Spectroscopy and Molecular Dynamics of Water
|
||
Monomers and Dimers Adsorbed on Polycyclic Aromatic Hydrocarbons}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 14}(19):6771--6786, 2012.
|
||
|
||
\bibitem{Odutola1980}
|
||
{\sc JA~Odutola and TR~Dyke}.
|
||
\newblock {\bf Partially deuterated water dimers: Microwave spectra and
|
||
structure}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 72}(9):5062--5070, 1980.
|
||
|
||
\bibitem{Sugita2000}
|
||
{\sc Yuji Sugita and Yuko Okamoto}.
|
||
\newblock {\bf Replica-exchange multicanonical algorithm and multicanonical
|
||
replica-exchange method for simulating systems with rough energy landscape}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 329}(3-4):261--270, 2000.
|
||
|
||
\bibitem{Douady2009}
|
||
{\sc Julie Douady, Florent Calvo, and Fernand Spiegelman}.
|
||
\newblock {\bf Effect of an ionic impurity on the caloric curves of water
|
||
clusters}.
|
||
\newblock {\em Eur. Phys. J. D}, {\bf 52}(1-3):47--50, 2009.
|
||
|
||
\bibitem{Wolken2000}
|
||
{\sc Jill~K Wolken and Franti{\v{s}}ek Ture{\v{c}}ek}.
|
||
\newblock {\bf Proton affinity of uracil. A computational study of protonation
|
||
sites}.
|
||
\newblock {\em J. Am. Soc. Mass Spectrom.}, {\bf 11}(12):1065--1071, 2000.
|
||
|
||
\bibitem{Pedersen2014}
|
||
{\sc Sara~{\O}vad Pedersen, Camilla~Skinnerup Byskov, Frantisek Turecek, and
|
||
Steen~Br{\o}ndsted Nielsen}.
|
||
\newblock {\bf Structures of protonated thymine and uracil and their
|
||
monohydrated gas-phase ions from ultraviolet action spectroscopy and theory}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 118}(24):4256--4265, 2014.
|
||
|
||
\bibitem{Weigend2005}
|
||
{\sc Florian Weigend and Reinhart Ahlrichs}.
|
||
\newblock {\bf Balanced basis sets of split valence, triple zeta valence and
|
||
quadruple zeta valence quality for H to Rn: design and assessment of
|
||
accuracy}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 7}(18):3297--3305, 2005.
|
||
|
||
\bibitem{Weigend2006}
|
||
{\sc Florian Weigend}.
|
||
\newblock {\bf Accurate Coulomb-fitting basis sets for H to Rn}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 8}(9):1057--1065, 2006.
|
||
|
||
\bibitem{GaussianCode}
|
||
{\sc 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, and
|
||
{\it et. al.}}
|
||
|
||
\bibitem{Boys2002}
|
||
{\sc SF~Boys and F~Bernardi}.
|
||
\newblock {\bf The calculation of small molecular interactions by the
|
||
differences of separate total energies. Some procedures with reduced errors}.
|
||
\newblock {\em Mol. Phys.}, {\bf 100}(1):65--73, 2002.
|
||
|
||
\bibitem{Keesee1989}
|
||
{\sc R.~G. Keesee}.
|
||
\newblock
|
||
\href{https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/JD094iD12p14683}{{\bf
|
||
Nucleation and particle formation in the upper atmosphere}}.
|
||
\newblock {\em J. Geophys. Res. Atmos.}, {\bf 94}(D12):14683--14692, 1989.
|
||
|
||
\bibitem{Gilligan2000}
|
||
{\sc J~J Gilligan, DJ~Moody, and A~W Castleman}.
|
||
\newblock {\bf Reactions of protonated water clusters with chlorine nitrate
|
||
revisited}.
|
||
\newblock {\em Z. Phys. Chem.}, {\bf 214}(10):1383--1391, 2000.
|
||
|
||
\bibitem{Sennikov2005}
|
||
{\sc Petr~G Sennikov, Stanislav~K Ignatov, and Otto Schrems}.
|
||
\newblock {\bf Complexes and clusters of water relevant to atmospheric
|
||
chemistry: H2O complexes with oxidants}.
|
||
\newblock {\em ChemPhysChem}, {\bf 6}(3):392--412, 2005.
|
||
|
||
\bibitem{Cabellos2016}
|
||
{\sc Alba Vargas-Caamal, Jose~Luis Cabellos, Filiberto Ortiz-Chi, Henry~S.
|
||
Rzepa, Albeiro Restrepo, and Gabriel Merino}.
|
||
\newblock {\bf How Many Water Molecules Does it Take to Dissociate HCl?}
|
||
\newblock {\em Chem. Eur. J.}, {\bf 22}(8):2812--2818, 2016.
|
||
|
||
\bibitem{Orabi2013}
|
||
{\sc Esam~A Orabi and Guillaume Lamoureux}.
|
||
\newblock {\bf Polarizable interaction model for liquid, supercritical, and
|
||
aqueous ammonia}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 9}(4):2035--2051, 2013.
|
||
|
||
\bibitem{Bommer2016}
|
||
{\sc Martin Bommer, Ana-Nicoleta Bondar, Athina Zouni, Holger Dobbek, and
|
||
Holger Dau}.
|
||
\newblock {\bf 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}.
|
||
\newblock {\em Biochemistry}, {\bf 55}(33):4626--4635, 2016.
|
||
|
||
\bibitem{Rodgers2003}
|
||
{\sc SD~Rodgers and SB~Charnley}.
|
||
\newblock {\bf Chemical evolution in protostellar envelopes: Cocoon chemistry}.
|
||
\newblock {\em Astrophys. J.}, {\bf 585}(1):355, 2003.
|
||
|
||
\bibitem{Van2004}
|
||
{\sc Ewine~F Van~Dishoeck}.
|
||
\newblock {\bf ISO spectroscopy of gas and dust: from molecular clouds to
|
||
protoplanetary disks}.
|
||
\newblock {\em Annu. Rev. Astrophys. J.}, {\bf 42}, 2004.
|
||
|
||
\bibitem{Gibb2004}
|
||
{\sc EL~Gibb, DCB Whittet, ACA Boogert, and AGGM Tielens}.
|
||
\newblock {\bf Interstellar ice: the infrared space observatory legacy}.
|
||
\newblock {\em Astrophys. J., Suppl. Ser.}, {\bf 151}(1):35, 2004.
|
||
|
||
\bibitem{Parise2005}
|
||
{\sc B~Parise, C~Ceccarelli, and S~Maret}.
|
||
\newblock {\bf Theoretical HDO emission from low-mass protostellar envelopes}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 441}(1):171--179, 2005.
|
||
|
||
\bibitem{Boogert2015}
|
||
{\sc AC~Adwin Boogert, Perry~A Gerakines, and Douglas~CB Whittet}.
|
||
\newblock {\bf Observations of the icy universe}.
|
||
\newblock {\em Annu. Rev. Astron. Astrophys.}, {\bf 53}, 2015.
|
||
|
||
\bibitem{Dulieu2010}
|
||
{\sc F~Dulieu, L~Amiaud, E~Congiu, J-H Fillion, E~Matar, A~Momeni,
|
||
V~Pirronello, and JL~Lemaire}.
|
||
\newblock {\bf Experimental evidence for water formation on interstellar dust
|
||
grains by hydrogen and oxygen atoms}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 512}:A30, 2010.
|
||
|
||
\bibitem{Michoulier2018}
|
||
{\sc Eric Michoulier, Nadia~Ben Amor, Mathias Rapacioli, Jennifer~A Noble,
|
||
Jo{\"e}lle Mascetti, C{\'e}line Toubin, and Aude Simon}.
|
||
\newblock {\bf Theoretical determination of adsorption and ionisation energies
|
||
of polycyclic aromatic hydrocarbons on water ice}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 20}(17):11941--11953, 2018.
|
||
|
||
\bibitem{Kulmala2004}
|
||
{\sc M.~Kulmala, H.~Vehkamäki, T.~Petäjä, M.~Dal Maso, A.~Lauri, V.-M.
|
||
Kerminen, W.~Birmili, and P.H. McMurry}.
|
||
\newblock {\bf Formation and growth rates of ultrafine atmospheric particles: A
|
||
review of observations}.
|
||
\newblock {\em J. Aerosol Sci.}, {\bf 35}(2):143--176, 2004.
|
||
|
||
\bibitem{Ziereis1986}
|
||
{\sc H~Ziereis and F~Arnold}.
|
||
\newblock {\bf Gaseous ammonia and ammonium ions in the free troposphere}.
|
||
\newblock {\em Nature}, {\bf 321}(6069):503--505, 1986.
|
||
|
||
\bibitem{Perkins1984}
|
||
{\sc Mark~D Perkins and Fred~L Eisele}.
|
||
\newblock {\bf First mass spectrometric measurements of atmospheric ions at
|
||
ground level}.
|
||
\newblock {\em J. Geophys. Res. Atmos.}, {\bf 89}(D6):9649--9657, 1984.
|
||
|
||
\bibitem{Arnold1997}
|
||
{\sc F~Arnold, KH~Wohlfrom, J~Schneider, M~Klemm, T~Stilp, and F~Grimm}.
|
||
\newblock {\bf Atmospheric measurements of aerosol precursor gases in the upper
|
||
troposphere and lower stratosphere}.
|
||
\newblock {\em J. Aerosol Sci.}, {\bf 1001}(28):S65--S66, 1997.
|
||
|
||
\bibitem{Herbine1985}
|
||
{\sc P~Herbine and TR~Dyke}.
|
||
\newblock {\bf Rotational spectra and structure of the ammonia--water complex}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 83}(8):3768--3774, 1985.
|
||
|
||
\bibitem{Stockman1992}
|
||
{\sc Paul~A Stockman, Roger~E Bumgarner, Sakae Suzuki, and Geoffrey~A Blake}.
|
||
\newblock {\bf Microwave and tunable far-infrared laser spectroscopy of the
|
||
ammonia-water dimer}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 96}(4):2496--2510, 1992.
|
||
|
||
\bibitem{Hulthe1997}
|
||
{\sc Gustaf Hulthe, Gunnar Stenhagen, Olof Wennerstr{\"o}m, and Carl-Henrik
|
||
Ottosson}.
|
||
\newblock {\bf Water clusters studied by electrospray mass spectrometry}.
|
||
\newblock {\em J. Chromatogr. A}, {\bf 777}(1):155--165, 1997.
|
||
|
||
\bibitem{Wang1998}
|
||
{\sc Yih-Sheng Wang, Hai-Chou Chang, Jyh-Chiang Jiang, Sheng~H. Lin, Yuan~T.
|
||
Lee, and Huan-Cheng Chang}.
|
||
\newblock {\bf Structures and isomeric transitions of NH$_4^+$(H$_2$O)$_{3-6}$:
|
||
from single to double rings}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 120}(34):8777--8788, 1998.
|
||
|
||
\bibitem{Chang1998}
|
||
{\sc Hai-Chou Chang, Yih-Sheng Wang, Yuan~T Lee, and Huan-Cheng Chang}.
|
||
\newblock {\bf Studying protonated ion hydration by infrared spectroscopy of
|
||
size-selected NH$_4^+$(H$_2$O)$_n$ clusters in a free jet expansion}.
|
||
\newblock {\em Int. J. Mass Spectrom.}, {\bf 179}:91--102, 1998.
|
||
|
||
\bibitem{Jiang1999}
|
||
{\sc J~C Jiang, H-C Chang, YT~Lee, and SH~Lin}.
|
||
\newblock {\bf Ab initio studies of NH$_4^+$(H$_2$O)$_{1-5}$ and the influence
|
||
of hydrogen-bonding nonadditivity on geometries and vibrations}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 103}(16):3123--3135, 1999.
|
||
|
||
\bibitem{Hvelplund2010}
|
||
{\sc Preben Hvelplund, Theo Kurten, Kristian St{\o}chkel, Mauritz~Johan Ryding,
|
||
Steen~Br{\o}ndsted Nielsen, and Einar Uggerud}.
|
||
\newblock {\bf Stability and structure of protonated clusters of ammonia and
|
||
water, H$^+$(NH$_3$)$_m$(H$_2$O)$_n$}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 114}(27):7301--7310, 2010.
|
||
|
||
\bibitem{Douady2008}
|
||
{\sc Julie Douady, Florent Calvo, and Fernand Spiegelman}.
|
||
\newblock {\bf Structure, stability, and infrared spectroscopy of
|
||
(H$_2$O)$_n$NH$_4^+$ clusters: A theoretical study at zero and finite
|
||
temperature}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 129}(15):154305, 2008.
|
||
|
||
\bibitem{Morrell2010}
|
||
{\sc Thomas~E Morrell and George~C Shields}.
|
||
\newblock {\bf Atmospheric implications for formation of clusters of ammonium
|
||
and 1-10 water molecules}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 114}(12):4266--4271, 2010.
|
||
|
||
\bibitem{Bacelo2002}
|
||
{\sc Daniel~E Bacelo}.
|
||
\newblock {\bf Theoretical study of microscopic solvation of ammonia in water
|
||
clusters: NH$_3$(H$_2$O)$_n$, $n=$ 3, 4}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 106}(46):11190--11196, 2002.
|
||
|
||
\bibitem{Galashev2013}
|
||
{\sc AE~Galashev}.
|
||
\newblock {\bf A computer study of ammonium adsorption on water clusters}.
|
||
\newblock {\em Russ. J. Phys. Chem. B}, {\bf 7}(4):502--508, 2013.
|
||
|
||
\bibitem{Lee1996}
|
||
{\sc Chengteh Lee, George Fitzgerald, Marc Planas, and Juan~J Novoa}.
|
||
\newblock {\bf Ionization of bases in water: Structure and stability of the
|
||
NH$_4^+$ $\cdots$ OH$^-$ ionic forms in ammonia-water clusters}.
|
||
\newblock {\em J. Phys. Chem.}, {\bf 100}(18):7398--7404, 1996.
|
||
|
||
\bibitem{Skurski1998}
|
||
{\sc Piotr Skurski and Maciej Gutowski}.
|
||
\newblock {\bf Theoretical study of the dipole-bound anion (H$_2$O $\ldots$
|
||
NH$_3$)$^-$}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 108}(15):6303--6311, 1998.
|
||
|
||
\bibitem{Donaldson1999}
|
||
{\sc DJ~Donaldson}.
|
||
\newblock {\bf Adsorption of atmospheric gases at the air- water interface. I.
|
||
NH$_3$}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 103}(1):62--70, 1999.
|
||
|
||
\bibitem{Sadlej1999}
|
||
{\sc J~Sadlej, R~Moszynski, J~Cz Dobrowolski, and AP~Mazurek}.
|
||
\newblock {\bf Structure and energetics of the weakly bound NH$_3$ $\cdots$
|
||
H$_2$O complex}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 103}(42):8528--8536, 1999.
|
||
|
||
\bibitem{Kozack1992polar}
|
||
{\sc RE~Kozack and PC~Jordan}.
|
||
\newblock {\bf Polarizability effects in a four-charge model for water}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 96}(4):3120--3130, 1992.
|
||
|
||
\bibitem{Pei2015}
|
||
{\sc Shi-Tu Pei, Shuai Jiang, Yi-Rong Liu, Teng Huang, Kang-Ming Xu, Hui Wen,
|
||
Yu-Peng Zhu, and Wei Huang}.
|
||
\newblock {\bf Properties of ammonium ion--water clusters: analyses of
|
||
structure evolution, noncovalent interactions, and temperature and humidity
|
||
effects}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 119}(12):3035--3047, 2015.
|
||
|
||
\bibitem{Walters2018}
|
||
{\sc Wendell~W Walters, Jiajue Chai, and Meredith~G Hastings}.
|
||
\newblock {\bf Theoretical phase resolved ammonia--ammonium nitrogen
|
||
equilibrium isotope exchange fractionations: Applications for tracking
|
||
atmospheric ammonia gas-to-particle conversion}.
|
||
\newblock {\em ACS Earth Space Chem.}, {\bf 3}(1):79--89, 2018.
|
||
|
||
\bibitem{Choi2010}
|
||
{\sc Tae~Hoon Choi and Kenneth~D Jordan}.
|
||
\newblock {\bf Application of the SCC-DFTB method to H$^+$(H$_2$O)$_6$,
|
||
H$^+$(H$_2$O)$_{21}$, and H$^+$(H$_2$O)$_{22}$}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 114}(20):6932--6936, 2010.
|
||
|
||
\bibitem{Choi2013}
|
||
{\sc Tae~Hoon Choi, Ruibin Liang, C~Mark Maupin, and Gregory~A Voth}.
|
||
\newblock {\bf Application of the SCC-DFTB method to hydroxide water clusters
|
||
and aqueous hydroxide solutions}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 117}(17):5165--5179, 2013.
|
||
|
||
\bibitem{Simon2019}
|
||
{\sc Aude Simon, Mathias Rapacioli, Eric Michoulier, Linjie Zheng, Kseniia
|
||
Korchagina, and J{\'e}r{\^o}me Cuny}.
|
||
\newblock {\bf Contribution of the density-functional-based tight-binding
|
||
scheme to the description of water clusters: methods, applications and
|
||
extension to bulk systems}.
|
||
\newblock {\em Mol. Simul.}, {\bf 45}(4-5):249--268, 2019.
|
||
|
||
\bibitem{Simon2013water}
|
||
{\sc Aude Simon and Fernand Spiegelman}.
|
||
\newblock {\bf Water clusters adsorbed on polycyclic aromatic hydrocarbons:
|
||
Energetics and conformational dynamics}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 138}(19):194309, 2013.
|
||
|
||
\bibitem{Winget2003}
|
||
{\sc Paul Winget, Cenk Selcuki, Anselm~HC Horn, Bodo Martin, and Timothy
|
||
Clark}.
|
||
\newblock {\bf Towards a ‘‘next generation’’neglect of diatomic
|
||
differential overlap based semiempirical molecular orbital technique}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 110}(4):254--266, 2003.
|
||
|
||
\bibitem{Lee2004}
|
||
{\sc Han~Myoung Lee, P~Tarakeshwar, Jungwon Park, Maciej~Roman Ko{\l}aski,
|
||
Yeo~Jin Yoon, Hai-Bo Yi, Woo~Youn Kim, and Kwang~S Kim}.
|
||
\newblock {\bf Insights into the structures, energetics, and vibrations of
|
||
monovalent cation-(water) 1-6 clusters}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 108}(15):2949--2958, 2004.
|
||
|
||
\bibitem{Pickard2005}
|
||
{\sc Frank~C Pickard~IV, Meghan~E Dunn, and George~C Shields}.
|
||
\newblock {\bf 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}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 109}(22):4905--4910, 2005.
|
||
|
||
\bibitem{Kazimirski2003}
|
||
{\sc Jan~K Kazimirski and Victoria Buch}.
|
||
\newblock {\bf Search for low energy structures of water clusters (H$_2$O)$_n$,
|
||
$n$= 20- 22, 48, 123, and 293}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 107}(46):9762--9775, 2003.
|
||
|
||
\bibitem{Bandow2006}
|
||
{\sc Bernhard Bandow and Bernd Hartke}.
|
||
\newblock {\bf Larger water clusters with edges and corners on their way to
|
||
ice: Structural trends elucidated with an improved parallel evolutionary
|
||
algorithm}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 110}(17):5809--5822, 2006.
|
||
|
||
\bibitem{Kozack1992empiri}
|
||
{\sc RE~Kozack and PC~Jordan}.
|
||
\newblock {\bf Empirical models for the hydration of protons}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 96}(4):3131--3136, 1992.
|
||
|
||
\bibitem{Labastie1990}
|
||
{\sc Pierre Labastie and Robert~L Whetten}.
|
||
\newblock {\bf {Statistical Thermodynamics of the Cluster Solid-Liquid
|
||
Transition}}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 65}(13):1567--1570, 1990.
|
||
|
||
\bibitem{Maclot2011}
|
||
{\sc Sylvain Maclot, Michael Capron, R{\'e}mi Maisonny, Arkadiusz {\L}awicki,
|
||
Alain M{\'e}ry, Jimmy Rangama, Jean-Yves Chesnel, Sadia Bari, Ronnie
|
||
Hoekstra, Thomas Schlath{\"o}lter, B~Manil, L~Adoui, P~Rousseau, and
|
||
BA~Huber}.
|
||
\newblock {\bf Ion-induced fragmentation of amino acids: effect of the
|
||
environment}.
|
||
\newblock {\em ChemPhysChem}, {\bf 12}(5):930--936, 2011.
|
||
|
||
\bibitem{Domaracka2012}
|
||
{\sc Alicja Domaracka, Michael Capron, Sylvain Maclot, Jean-Yves Chesnel, Alain
|
||
M{\'e}ry, Jean-Christophe Poully, Jimmy Rangama, Lamri Adoui, Patrick
|
||
Rousseau, and Bernd~A Huber}.
|
||
\newblock {\bf Ion interaction with biomolecular systems and the effect of the
|
||
environment}.
|
||
\newblock {\em J. Phys. Conf. Ser.}, {\bf 373}:012005, 2012.
|
||
|
||
\bibitem{Markush2016}
|
||
{\sc Pal Markush, Paola Bolognesi, Antonella Cartoni, Patrick Rousseau, Sylvain
|
||
Maclot, Rudy Delaunay, Alicja Domaracka, Jaroslav Kocisek, Mattea~C
|
||
Castrovilli, Bernd~A Huber, and Lorenzo Avaldi}.
|
||
\newblock {\bf The role of the environment in the ion induced fragmentation of
|
||
Uracil}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 18}(25):16721--16729, 2016.
|
||
|
||
\bibitem{Wincel2009}
|
||
{\sc Henryk Wincel}.
|
||
\newblock {\bf Microhydration of protonated nucleic acid bases and protonated
|
||
nucleosides in the gas phase}.
|
||
\newblock {\em J. Am. Soc. Mass Spectrom.}, {\bf 20}(10):1900--1905, 2009.
|
||
|
||
\bibitem{Boudaiffa2000}
|
||
{\sc Badia Bouda{\"i}ffa, Pierre Cloutier, Darel Hunting, Michael~A Huels, and
|
||
L{\'e}on Sanche}.
|
||
\newblock {\bf Resonant formation of DNA strand breaks by low-energy (3 to 20
|
||
eV) electrons}.
|
||
\newblock {\em Science}, {\bf 287}(5458):1658--1660, 2000.
|
||
|
||
\bibitem{Smyth2011}
|
||
{\sc Maeve Smyth and Jorge Kohanoff}.
|
||
\newblock {\bf Excess electron localization in solvated DNA bases}.
|
||
\newblock {\em Phys. Rev. Lett.}, {\bf 106}(23):238108, 2011.
|
||
|
||
\bibitem{Siefermann2011}
|
||
{\sc Katrin~R Siefermann and Bernd Abel}.
|
||
\newblock {\bf The hydrated electron: a seemingly familiar chemical and
|
||
biological transient}.
|
||
\newblock {\em Angew. Chem. Int. Ed.}, {\bf 50}(23):5264--5272, 2011.
|
||
|
||
\bibitem{Alizadeh2013}
|
||
{\sc Elahe Alizadeh, Ana~G Sanz, Gustavo Garcia, and Leon Sanche}.
|
||
\newblock {\bf Radiation damage to DNA: The indirect effect of low-energy
|
||
electrons}.
|
||
\newblock {\em J. Phys. Chem. Lett.}, {\bf 4}(5):820--825, 2013.
|
||
|
||
\bibitem{Rasmussen2010}
|
||
{\sc Andrew~M Rasmussen, Maria~C Lind, Sunghwan Kim, and Henry~F Schaefer~III}.
|
||
\newblock {\bf Hydration of the lowest triplet states of the DNA/RNA
|
||
pyrimidines}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 6}(3):930--939, 2010.
|
||
|
||
\bibitem{Sadr2014}
|
||
{\sc Leila Sadr-Arani, Pierre Mignon, Henry Chermette, and Thierry Douki}.
|
||
\newblock {\bf Theoretical and experimental study of the fragmentation of
|
||
protonated uracil}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 605}:108--114, 2014.
|
||
|
||
\bibitem{Molina2016}
|
||
{\sc Estefan{\'\i}a~Rossich Molina, Jean-Yves Salpin, Riccardo Spezia, and
|
||
Emilio Martinez-Nunez}.
|
||
\newblock {\bf On the gas phase fragmentation of protonated uracil: A
|
||
statistical perspective}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 18}(22):14980--14990, 2016.
|
||
|
||
\bibitem{Bakker2008}
|
||
{\sc Joost~M Bakker, Rajeev~K Sinha, Thierry Besson, Maurizio Brugnara, Paolo
|
||
Tosi, Jean-Yves Salpin, and Philippe Ma{\^\i}tre}.
|
||
\newblock {\bf Tautomerism of uracil probed via infrared spectroscopy of singly
|
||
hydrated protonated uracil}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 112}(48):12393--12400, 2008.
|
||
|
||
\bibitem{Shishkin2000}
|
||
{\sc Oleg~V Shishkin, Leonid Gorb, and Jerzy Leszczynski}.
|
||
\newblock {\bf Modeling of the hydration shell of uracil and thymine}.
|
||
\newblock {\em Int. J. Mol. Sci.}, {\bf 1}(2):17--27, 2000.
|
||
|
||
\bibitem{Gadre2000}
|
||
{\sc Shridhar~R Gadre, K~Babu, and Alistair~P Rendell}.
|
||
\newblock {\bf Electrostatics for exploring hydration patterns of molecules. 3.
|
||
Uracil}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 104}(39):8976--8982, 2000.
|
||
|
||
\bibitem{Van2001diffu}
|
||
{\sc Tanja van Mourik, Sarah~L Price, and David~C Clary}.
|
||
\newblock {\bf Diffusion Monte Carlo simulations on uracil--water using an
|
||
anisotropic atom--atom potential model}.
|
||
\newblock {\em Faraday discussions}, {\bf 118}:95--108, 2001.
|
||
|
||
\bibitem{Gaigeot2001}
|
||
{\sc Marie-Pierre Gaigeot and Mahmoud Ghomi}.
|
||
\newblock {\bf Geometrical and Vibrational Properties of Nucleic Acid
|
||
Constituents Interacting with Explicit Water Molecules as Analyzed by Density
|
||
Functional Theory Calculations. 1. Uracil + n$_w$H$_2$O (n$_w$= 1, ..., 7)}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 105}(21):5007--5017, 2001.
|
||
|
||
\bibitem{Danilov2006}
|
||
{\sc Victor~I Danilov, Tanja van Mourik, and Valery~I Poltev}.
|
||
\newblock {\bf Modeling of the 'hydration shell' of uracil and thymine in small
|
||
water clusters by DFT and MP2 methods}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 429}(1-3):255--260, 2006.
|
||
|
||
\bibitem{Bacchus2015}
|
||
{\sc Marie-Christine Bacchus-Montabonel and Florent Calvo}.
|
||
\newblock {\bf Nanohydration of uracil: emergence of three-dimensional
|
||
structures and proton-induced charge transfer}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 17}(15):9629--9633, 2015.
|
||
|
||
\bibitem{Dalleska1993}
|
||
{\sc NF~Dalleska, Kenji Honma, and PB~Armentrout}.
|
||
\newblock {\bf Stepwise solvation enthalpies of protonated water clusters:
|
||
Collision-induced dissociation as an alternative to equilibrium studies}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 115}(25):12125--12131, 1993.
|
||
|
||
\bibitem{Zamith2012}
|
||
{\sc S{\'e}bastien Zamith, Pierre Labastie, and Jean-Marc l'Hermite}.
|
||
\newblock {\bf Fragmentation cross sections of protonated water clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 136}(21):214301, 2012.
|
||
|
||
\bibitem{Myers2007}
|
||
{\sc Richard~L Myers}.
|
||
\newblock {\em The 100 most important chemical compounds: a reference guide}.
|
||
\newblock ABC-CLIO, 2007.
|
||
|
||
\bibitem{Hansen2009}
|
||
{\sc K~Hansen, PU~Andersson, and E~Uggerud}.
|
||
\newblock {\bf Activation energies for evaporation from protonated and
|
||
deprotonated water clusters from mass spectra}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 131}(12):124303, 2009.
|
||
|
||
\bibitem{Kurinovich2002}
|
||
{\sc Mary~Ann Kurinovich, Linda~M Phillips, Seema Sharma, and Jeehiun~K Lee}.
|
||
\newblock {\bf The gas phase proton affinity of uracil: measuring multiple
|
||
basic sites and implications for the enzyme mechanism of orotidine
|
||
5'-monophosphate decarboxylase}.
|
||
\newblock {\em Chemical communications}, {\bf 21}(20):2354--2355, 2002.
|
||
|
||
\bibitem{Magnera1991}
|
||
{\sc Thomas~F Magnera, Donald~E David, and Josef Michl}.
|
||
\newblock {\bf The first twenty-eight gas-phase proton hydration energies}.
|
||
\newblock {\em Chem. Phys. Lett.}, {\bf 182}(3-4):363--370, 1991.
|
||
|
||
\bibitem{Cheng1998}
|
||
{\sc Hai-Ping Cheng}.
|
||
\newblock {\bf Water clusters: fascinating hydrogen-bonding networks, solvation
|
||
shell structures, and proton motion}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 102}(31):6201--6204, 1998.
|
||
|
||
\bibitem{Zundel1968}
|
||
{\sc G.~Zundel and H.~Metzger}.
|
||
\newblock {\bf Energieb{\"a}nder der tunnelnden {\"U}berschu{\ss}-Protonen in
|
||
fl{\"u}ssigen S{\"a}uren. Eine IR-spektroskopische Untersuchung der Natur der
|
||
Gruppierungen H$_5$O$_2^+$}.
|
||
\newblock {\em Proc. Z. Phys. Chem.}, {\bf 58}(5\_6):225--245, 1968.
|
||
|
||
\bibitem{Brechignac1989}
|
||
{\sc C~Br{\'e}chignac, Ph~Cahuzac, J~Leygnier, and J~Weiner}.
|
||
\newblock {\bf Dynamics of unimolecular dissociation of sodium cluster ions}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 90}(3):1492--1498, 1989.
|
||
|
||
\bibitem{Brechignac1994}
|
||
{\sc C~Br{\'e}chignac, H~Busch, Ph~Cahuzac, and J~Leygnier}.
|
||
\newblock {\bf Dissociation pathways and binding energies of lithium clusters
|
||
from evaporation experiments}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 101}(8):6992--7002, 1994.
|
||
|
||
\bibitem{Wong2004}
|
||
{\sc Richard~L Wong, Kolja Paech, and Evan~R Williams}.
|
||
\newblock {\bf Blackbody infrared radiative dissociation at low temperature:
|
||
Hydration of X$^{2+}$(H$_2$O)$_n$, for X= Mg, Ca}.
|
||
\newblock {\em International J. Mass Spectrom.}, {\bf 232}(1):59--66, 2004.
|
||
|
||
\bibitem{Bush2008}
|
||
{\sc Matthew~F Bush, Richard~J Saykally, and Evan~R Williams}.
|
||
\newblock {\bf Reactivity and infrared spectroscopy of gaseous hydrated
|
||
trivalent metal ions}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 130}(28):9122--9128, 2008.
|
||
|
||
\bibitem{Gatchell2014}
|
||
{\sc Michael Gatchell, Patrick Rousseau, A~Domaracka, Mark~H Stockett, Tao
|
||
Chen, Henning~T Schmidt, JY~Chesnel, A~M{\'e}ry, S~Maclot, L~Adoui, et~al.}
|
||
\newblock {\bf Ions colliding with mixed clusters of C$_{60}$ and coronene:
|
||
Fragmentation and bond formation}.
|
||
\newblock {\em Phys. Rev. A}, {\bf 90}(2):022713, 2014.
|
||
|
||
\bibitem{Boering1992}
|
||
{\sc Kristie~A Boering, Joseph Rolfe, and John~I Brauman}.
|
||
\newblock {\bf Low energy collision induced dissociation: phase-shifting
|
||
excitation control of ion kinetic energy in ion cyclotron resonance
|
||
spectrometry}.
|
||
\newblock {\em Int. J. Mass Spectrom. Ion Processes}, {\bf 117}:357--386, 1992.
|
||
|
||
\bibitem{Wells2005}
|
||
{\sc J~Mitchell Wells and Scott~A McLuckey}.
|
||
\newblock {\bf Collision-induced dissociation (CID) of peptides and proteins}.
|
||
\newblock {\em Methods Enzymol.}, {\bf 402}:148--185, 2005.
|
||
|
||
\bibitem{Ma1997}
|
||
{\sc YL~Ma, QM~Li, H~Van~den Heuvel, and M~Claeys}.
|
||
\newblock {\bf Characterization of flavone and flavonol aglycones by
|
||
collision-induced dissociation tandem mass spectrometry}.
|
||
\newblock {\em Rapid Commun. Mass}, {\bf 11}(12):1357--1364, 1997.
|
||
|
||
\bibitem{Chowdhury2009}
|
||
{\sc Saiful~M Chowdhury, Xiuxia Du, Nikola Tolic, Si~Wu, Ronald~J Moore,
|
||
M~Uljana Mayer, Richard~D Smith, and Joshua~N Adkins}.
|
||
\newblock {\bf Identification of cross-linked peptides after click-based
|
||
enrichment using sequential collision-induced dissociation and electron
|
||
transfer dissociation tandem mass spectrometry}.
|
||
\newblock {\em Anal. Chem.}, {\bf 81}(13):5524--5532, 2009.
|
||
|
||
\bibitem{Sleno2004ion}
|
||
{\sc Lekha Sleno and Dietrich~A Volmer}.
|
||
\newblock {\bf Ion activation methods for tandem mass spectrometry}.
|
||
\newblock {\em J. Mass Spectrom.}, {\bf 39}(10):1091--1112, 2004.
|
||
|
||
\bibitem{Cody1982}
|
||
{\sc RB~Cody, RC~Burnier, and BS~Freiser}.
|
||
\newblock {\bf Collision-induced dissociation with Fourier transform mass
|
||
spectrometry}.
|
||
\newblock {\em Anal. Chem.}, {\bf 54}(1):96--101, 1982.
|
||
|
||
\bibitem{Olsen2007higher}
|
||
{\sc Jesper~V Olsen, Boris Macek, Oliver Lange, Alexander Makarov, Stevan
|
||
Horning, and Matthias Mann}.
|
||
\newblock {\bf Higher-energy C-trap dissociation for peptide modification
|
||
analysis}.
|
||
\newblock {\em Nat. Methods.}, {\bf 4}(9):709--712, 2007.
|
||
|
||
\bibitem{Hart2011}
|
||
{\sc Gene Hart-Smith and Mark~J Raftery}.
|
||
\newblock {\bf Detection and characterization of low abundance glycopeptides
|
||
via higher-energy C-trap dissociation and orbitrap mass analysis}.
|
||
\newblock {\em J. Am. Soc. Mass Spectrom.}, {\bf 23}(1):124--140, 2011.
|
||
|
||
\bibitem{Gauthier1991}
|
||
{\sc JW~Gauthier, TR~Trautman, and DB~Jacobson}.
|
||
\newblock {\bf Sustained off-resonance irradiation for collision-activated
|
||
dissociation involving Fourier transform mass spectrometry.
|
||
Collision-activated dissociation technique that emulates infrared multiphoton
|
||
dissociation}.
|
||
\newblock {\em Anal. Chim. Acta}, {\bf 246}(1):211--225, 1991.
|
||
|
||
\bibitem{Laskin2005}
|
||
{\sc Julia Laskin and Jean~H Futrell}.
|
||
\newblock {\bf Activation of large lons in FT-ICR mass spectrometry}.
|
||
\newblock {\em Mass Spectrom. Rev.}, {\bf 24}(2):135--167, 2005.
|
||
|
||
\bibitem{Mcquinn2009}
|
||
{\sc Keri McQuinn, Fraser Hof, and J~Scott McIndoe}.
|
||
\newblock {\bf Collision-induced dissociation of protonated nanodroplets}.
|
||
\newblock {\em Int. J. Mass Spectrom.}, {\bf 279}(1):32--36, 2009.
|
||
|
||
\bibitem{Carl2013}
|
||
{\sc Damon~R Carl and Peter~B Armentrout}.
|
||
\newblock {\bf Hreshold collision-induced dissociation of hydrated magnesium:
|
||
experimental and theoretical investigation of the binding energies for
|
||
Mg$^{2+}$(H$_2$O)$_x$ complexes (x= 2--10)}.
|
||
\newblock {\em ChemPhysChem}, {\bf 14}(4):681--697, 2013.
|
||
|
||
\bibitem{Hofstetter2013}
|
||
{\sc Theresa~E. Hofstetter and P.~B. Armentrout}.
|
||
\newblock \href{https://doi.org/10.1021/jp3044829}{{\bf Threshold
|
||
collision-induced dissociation and theoretical studies of hydrated Fe(II):
|
||
binding energies and coulombic barrier heights}}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 117}(6):1110--1123, 2013.
|
||
|
||
\bibitem{Coates2017}
|
||
{\sc Rebecca~A Coates and PB~Armentrout}.
|
||
\newblock {\bf Thermochemical investigations of hydrated nickel dication
|
||
complexes by threshold collision-induced dissociation and theory}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 121}(19):3629--3646, 2017.
|
||
|
||
\bibitem{Haag2009}
|
||
{\sc N~Haag, B~Liu, S~Br{\o}ndsted Nielsen, H~Zettergren, P~Hvelplund, B~Manil,
|
||
B~A Huber, H~A~B Johansson, H~T Schmidt, and H~Cederquist}.
|
||
\newblock {\bf Collisions with biomolecules embedded in small water clusters}.
|
||
\newblock {\em J. Phys. Conf. Ser.}, {\bf 194}(1):012053, nov 2009.
|
||
|
||
\bibitem{Li1992}
|
||
{\sc Shijian Li and Elliot~R Bernstein}.
|
||
\newblock {\bf Toluene-water clusters: Ion fragmentation and chemistry}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 97}(2):792--803, 1992.
|
||
|
||
\bibitem{Bobbert2002}
|
||
{\sc C~Bobbert, S~Sch{\"u}tte, C~Steinbach, and U~Buck}.
|
||
\newblock {\bf Fragmentation and reliable size distributions of large ammonia
|
||
and water clusters}.
|
||
\newblock {\em Eur. Phys. J. D}, {\bf 19}(2):183--192, 2002.
|
||
|
||
\bibitem{Spasov2000}
|
||
{\sc Vassil~A Spasov, Taeck-Hong Lee, and Kent~M Ervin}.
|
||
\newblock {\bf Threshold collision-induced dissociation of anionic copper
|
||
clusters and copper cluster monocarbonyls}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 112}(4):1713--1720, 2000.
|
||
|
||
\bibitem{Armentrout2008}
|
||
{\sc PB~Armentrout, Kent~M Ervin, and MT~Rodgers}.
|
||
\newblock {\bf Statistical rate theory and kinetic energy-resolved ion
|
||
chemistry: theory and applications}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 112}(41):10071--10085, 2008.
|
||
|
||
\bibitem{Rodgers1998}
|
||
{\sc MT~Rodgers and PB~Armentrout}.
|
||
\newblock {\bf Statistical modeling of competitive threshold collision-induced
|
||
dissociation}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 109}(5):1787--1800, 1998.
|
||
|
||
\bibitem{Armentrout2007}
|
||
{\sc PB~Armentrout}.
|
||
\newblock {\bf Statistical modeling of sequential collision-induced
|
||
dissociation thresholds}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 126}(23):234302, 2007.
|
||
|
||
\bibitem{Braud2017}
|
||
{\sc Isabelle Braud, S{\'e}bastien Zamith, and J-M L’Hermite}.
|
||
\newblock {\bf A gas aggregation source for the production of heterogeneous
|
||
molecular clusters}.
|
||
\newblock {\em Rev. Sci. Instrum.}, {\bf 88}(4):043102, 2017.
|
||
|
||
\bibitem{Chirot2006new}
|
||
{\sc Fabien Chirot, S{\'e}bastien Zamith, Pierre Labastie, and J-M
|
||
L’Hermite}.
|
||
\newblock {\bf New device to study unimolecular cluster nucleation}.
|
||
\newblock {\em Rev. Sci. Instrum.}, {\bf 77}(6):063108, 2006.
|
||
|
||
\bibitem{Frenzel2004}
|
||
{\sc J~Frenzel, AF~Oliveira, N~Jardillier, T~Heine, and G~Seifert}.
|
||
\newblock {\bf Semi-relativistic, self-consistent charge Slater-Koster tables
|
||
for density-functional based tight-binding (DFTB) for materials science
|
||
simulations}.
|
||
\newblock {\em Zeolites}, {\bf 2}(3):7, 2004.
|
||
|
||
\bibitem{Spiegelman2020}
|
||
{\sc Fernand Spiegelman, Nathalie Tarrat, J{\'e}r{\^o}me Cuny, Leo Dontot,
|
||
Evgeny Posenitskiy, Carles Mart{\'\i}, Aude Simon, and Mathias Rapacioli}.
|
||
\newblock {\bf Density-functional tight-binding: basic concepts and
|
||
applications to molecules and clusters}.
|
||
\newblock {\em Adv. Phys. -X}, {\bf 5}(1):1710252, 2020.
|
||
|
||
\bibitem{Simon2017}
|
||
{\sc Aude Simon, Mathias Rapacioli, Guillaume Rouaut, Georges Trinquier, and
|
||
FX~Gad{\'e}a}.
|
||
\newblock {\bf Dissociation of polycyclic aromatic hydrocarbons: molecular
|
||
dynamics studies}.
|
||
\newblock {\em Philos. Trans. R. Soc. A}, {\bf 375}(2092):20160195, 2017.
|
||
|
||
\bibitem{Rapacioli2018}
|
||
{\sc Mathias Rapacioli, Nathalie Tarrat, and Fernand Spiegelman}.
|
||
\newblock {\bf Melting of the Au$_{20}$ gold cluster: Does charge matter?}
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 122}(16):4092--4098, 2018.
|
||
|
||
\bibitem{Simon2018}
|
||
{\sc Aude Simon, Jean-Philippe Champeaux, Mathias Rapacioli, Patrick
|
||
Moretto-Capelle, X.~Gad{\'e}a, Florent, and Martine Sence}.
|
||
\newblock {\bf Dissociation of polycyclic aromatic hydrocarbons at high energy:
|
||
MD/DFTB simulations versus collision experiments}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 137}(7):106, 2018.
|
||
|
||
\bibitem{Warshel1976}
|
||
{\sc Arieh Warshel and Michael Levitt}.
|
||
\newblock {\bf Theoretical studies of enzymic reactions: dielectric,
|
||
electrostatic and steric stabilization of the carbonium ion in the reaction
|
||
of lysozyme}.
|
||
\newblock {\em J. Mol. Biol.}, {\bf 103}(2):227--249, 1976.
|
||
|
||
\bibitem{Cui2001}
|
||
{\sc Qiang Cui, Marcus Elstner, Efthimios Kaxiras, Thomas Frauenheim, and
|
||
Martin Karplus}.
|
||
\newblock {\bf A QM/MM implementation of the self-consistent charge density
|
||
functional tight binding (SCC-DFTB) method}.
|
||
\newblock {\em J. Phys. Chem. B}, {\bf 105}(2):569--585, 2001.
|
||
|
||
\bibitem{Iftner2014}
|
||
{\sc Christophe Iftner, Aude Simon, Kseniia Korchagina, Mathias Rapacioli, and
|
||
Fernand Spiegelman}.
|
||
\newblock {\bf A density functional tight binding/force field approach to the
|
||
interaction of molecules with rare gas clusters: Application to
|
||
(C$_6$H$_6$)$^{+/0}$Ar$_n$ clusters}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 140}(3):034301, 2014.
|
||
|
||
\bibitem{Kukk2015}
|
||
{\sc Edwin Kukk, DT~Ha, Y~Wang, Dariusz~Grzegorz Piekarski, Sergio
|
||
Diaz-Tendero, Kuno Kooser, Eero It{\"a}l{\"a}, Helena Levola, Manuel
|
||
Alcam{\'\i}, Elisabeth Rachlew, et~al.}
|
||
\newblock {\bf Internal energy dependence in X-ray-induced molecular
|
||
fragmentation: an experimental and theoretical study of thiophene}.
|
||
\newblock {\em Phys. Rev. A}, {\bf 91}(4):043417, 2015.
|
||
|
||
\bibitem{Rapacioli2018atomic}
|
||
{\sc Mathias Rapacioli, St{\'e}phanie Cazaux, Nolan Foley, Aude Simon, Ronnie
|
||
Hoekstra, and Thomas Schlath{\"o}lter}.
|
||
\newblock {\bf Atomic hydrogen interactions with gas-phase coronene cations:
|
||
hydrogenation versus fragmentation}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 20}(35):22427--22438, 2018.
|
||
|
||
\bibitem{Dontot2019}
|
||
{\sc L{\'e}o Dontot, Fernand Spiegelman, and Mathias Rapacioli}.
|
||
\newblock {\bf Structures and energetics of neutral and cationic pyrene
|
||
clusters}.
|
||
\newblock {\em J. Phys. Chem. A}, {\bf 123}(44):9531--9543, 2019.
|
||
|
||
\bibitem{Chung2011}
|
||
{\sc Seung-Hyun Chung and Angela Violi}.
|
||
\newblock {\bf Peri-condensed aromatics with aliphatic chains as key
|
||
intermediates for the nucleation of aromatic hydrocarbons}.
|
||
\newblock {\em Proc. Combust. Inst.}, {\bf 33}(1):693--700, 2011.
|
||
|
||
\bibitem{Saggese2015}
|
||
{\sc Chiara Saggese, Sara Ferrario, Joaquin Camacho, Alberto Cuoci, Alessio
|
||
Frassoldati, Eliseo Ranzi, Hai Wang, and Tiziano Faravelli}.
|
||
\newblock {\bf Kinetic modeling of particle size distribution of soot in a
|
||
premixed burner-stabilized stagnation ethylene flame}.
|
||
\newblock {\em Combust. Flame}, {\bf 162}(9):3356--3369, 2015.
|
||
|
||
\bibitem{Mao2017}
|
||
{\sc Qian Mao, Adri~CT Van~Duin, and KH~Luo}.
|
||
\newblock {\bf Formation of incipient soot particles from polycyclic aromatic
|
||
hydrocarbons: a ReaxFF molecular dynamics study}.
|
||
\newblock {\em Carbon}, {\bf 121}:380--388, 2017.
|
||
|
||
\bibitem{Wang2018}
|
||
{\sc Chen~S Wang, Norman~C Bartelt, Regina Ragan, and Konrad Th{\"u}rmer}.
|
||
\newblock {\bf Revealing the molecular structure of soot precursors}.
|
||
\newblock {\em Carbon}, {\bf 129}:537--542, 2018.
|
||
|
||
\bibitem{Kyrtopoulos2001}
|
||
{\sc SA~Kyrtopoulos, Panagiotis Georgiadis, H~Autrup, N~Demopoulos, P~Farmer,
|
||
A~Haugen, K~Katsouyanni, B~Lambert, S~Ovrebo, R~Sram, et~al.}
|
||
\newblock {\bf Biomarkers of genotoxicity of urban air pollution: overview and
|
||
descriptive data from a molecular epidemiology study on populations exposed
|
||
to moderate-to-low levels of polycyclic aromatic hydrocarbons: the AULIS
|
||
project}.
|
||
\newblock {\em Mutat. Res. Genet. Toxicol. Environ.}, {\bf 496}(1-2):207--228,
|
||
2001.
|
||
|
||
\bibitem{Farmer2003}
|
||
{\sc Peter~B Farmer, Rajinder Singh, Balvinder Kaur, Radim~J Sram, Blanka
|
||
Binkova, Ivan Kalina, Todor~A Popov, Seymour Garte, Emanuela Taioli, Alena
|
||
Gabelova, et~al.}
|
||
\newblock {\bf Molecular epidemiology studies of carcinogenic environmental
|
||
pollutants: effects of polycyclic aromatic hydrocarbons (PAHs) in
|
||
environmental pollution on exogenous and oxidative DNA damage}.
|
||
\newblock {\em Mutat. Res.-Rev. Mutat. Res.}, {\bf 544}(2-3):397--402, 2003.
|
||
|
||
\bibitem{Aumaitre2019}
|
||
{\sc Cyril Aumaitre and Jean-Fran{\c{c}}ois Morin}.
|
||
\newblock {\bf Polycyclic aromatic hydrocarbons as potential building blocks
|
||
for organic solar cells}.
|
||
\newblock {\em Chem. Rec.}, {\bf 19}(6):1142--1154, 2019.
|
||
|
||
\bibitem{Rapacioli2005}
|
||
{\sc M~Rapacioli, C~Joblin, and P~Boissel}.
|
||
\newblock {\bf Spectroscopy of polycyclic aromatic hydrocarbons and very small
|
||
grains in photodissociation regions}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 429}(1):193--204, 2005.
|
||
|
||
\bibitem{Berne2008}
|
||
{\sc O~Bern{\'e}, C~Joblin, M~Rapacioli, J~Thomas, J-C Cuillandre, and
|
||
Y~Deville}.
|
||
\newblock {\bf Extended red emission and the evolution of carbonaceous
|
||
nanograins in NGC 7023}.
|
||
\newblock {\em Astron. Astrophys.}, {\bf 479}(3):L41--L44, 2008.
|
||
|
||
\bibitem{Eschenbach1998}
|
||
{\sc Annette Eschenbach, Reinhard Wienberg, and Bernd Mahro}.
|
||
\newblock {\bf Fate and stability of nonextractable residues of [14C] PAH in
|
||
contaminated soils under environmental stress conditions}.
|
||
\newblock {\em Environ. Sci. Technol.}, {\bf 32}(17):2585--2590, 1998.
|
||
|
||
\bibitem{Goulart2017}
|
||
{\sc Marcelo Goulart, Martin Kuhn, Bilal Rasul, Johannes Postler, Michael
|
||
Gatchell, Henning Zettergren, Paul Scheier, and Olof Echt}.
|
||
\newblock {\bf The structure of coronene cluster ions inferred from H 2 uptake
|
||
in the gas phase}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(41):27968--27973, 2017.
|
||
|
||
\bibitem{Lei2019}
|
||
{\sc Lei Lei, Yuzhong Yao, Jie Zhang, Dale Tronrud, Wei Kong, Chengzhu Zhang,
|
||
Lan Xue, L{\'e}o Dontot, and Mathias Rapacioli}.
|
||
\newblock {\bf Electron diffraction of pyrene nanoclusters embedded in
|
||
superfluid helium droplets}.
|
||
\newblock {\em J. Phys. Chem. Lett.}, {\bf 11}(3):724--729, 2019.
|
||
|
||
\bibitem{Roser2015}
|
||
{\sc JE~Roser and A~Ricca}.
|
||
\newblock {\bf Polycyclic aromatic hydrocarbon clusters as sources of
|
||
interstellar infrared emission}.
|
||
\newblock {\em Astrophys. J.}, {\bf 801}(2):108, 2015.
|
||
|
||
\bibitem{Lemmens2019}
|
||
{\sc Alexander~K Lemmens, S{\'e}bastien Gruet, Amanda~L Steber, Jens Antony,
|
||
Stefan Grimme, Melanie Schnell, and Anouk~M Rijs}.
|
||
\newblock {\bf Far-IR and UV spectral signatures of controlled complexation and
|
||
microhydration of the polycyclic aromatic hydrocarbon acenaphthene}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 21}(7):3414--3422, 2019.
|
||
|
||
\bibitem{Delaunay2015}
|
||
{\sc Rudy Delaunay, Michael Gatchell, Patrick Rousseau, Alicja Domaracka,
|
||
Sylvain Maclot, Yang Wang, Mark~H Stockett, Tao Chen, Lamri Adoui, Manuel
|
||
Alcam{\'\i}, et~al.}
|
||
\newblock {\bf Molecular growth inside of polycyclic aromatic hydrocarbon
|
||
clusters induced by ion collisions}.
|
||
\newblock {\em J. Phys. Chem. Lett.}, {\bf 6}(9):1536--1542, 2015.
|
||
|
||
\bibitem{Piacenza2005}
|
||
{\sc Manuel Piacenza and Stefan Grimme}.
|
||
\newblock {\bf Van der Waals complexes of polar aromatic molecules: Unexpected
|
||
structures for dimers of azulene}.
|
||
\newblock {\em J. Am. Chem. Soc.}, {\bf 127}(42):14841--14848, 2005.
|
||
|
||
\bibitem{Birer2015}
|
||
{\sc {\"O}~Birer and E~Yurtsever}.
|
||
\newblock {\bf Dimer formation of perylene: An ultracold spectroscopic and
|
||
computational study}.
|
||
\newblock {\em J. Mol. Struct.}, {\bf 1097}:29--36, 2015.
|
||
|
||
\bibitem{Zhao2008truhlar}
|
||
{\sc Y.~Zh{ao} and Donald~G. Truhlar}.
|
||
\newblock \href{http://pubs.acs.org/doi/abs/10.1021/jp710918f}{{\bf A Prototype
|
||
for graphene material simulation; structures and interaction potentials of
|
||
coronene dimers}}.
|
||
\newblock {\em J. Phys. Chem. C}, {\bf 112}:4061--4067, 2008.
|
||
|
||
\bibitem{Bowal2019}
|
||
{\sc Kimberly Bowal, Jacob~W Martin, and Markus Kraft}.
|
||
\newblock {\bf Partitioning of polycyclic aromatic hydrocarbons in
|
||
heterogeneous clusters}.
|
||
\newblock {\em Carbon}, {\bf 143}:247--256, 2019.
|
||
|
||
\bibitem{Ricca2013}
|
||
{\sc Alessandra Ricca, Charles~W Bauschlicher~Jr, and Louis~J Allamandola}.
|
||
\newblock {\bf The infrared spectroscopy of neutral polycyclic aromatic
|
||
hydrocarbon clusters}.
|
||
\newblock {\em Astrophys. J.}, {\bf 776}(1):31, 2013.
|
||
|
||
\bibitem{Grafenstein2009}
|
||
{\sc J{\"u}rgen Gr{\"a}fenstein and Dieter Cremer}.
|
||
\newblock {\bf The self-interaction error and the description of non-dynamic
|
||
electron correlation in density functional theory}.
|
||
\newblock {\em Theor. Chem. Acc.}, {\bf 123}(3):171--182, 2009.
|
||
|
||
\bibitem{Dontot2016}
|
||
{\sc L{\'e}o Dontot, Nicolas Suaud, Mathias Rapacioli, and Fernand Spiegelman}.
|
||
\newblock {\bf An extended DFTB-CI model for charge-transfer excited states in
|
||
cationic molecular clusters: model studies versus ab initio calculations in
|
||
small PAH clusters}.
|
||
\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 18}(5):3545--3557, 2016.
|
||
|
||
\bibitem{Dontot2020}
|
||
{\sc L{\'e}o Dontot, Fernand Spiegelman, S{\'e}bastien Zamith, and Mathias
|
||
Rapacioli}.
|
||
\newblock {\bf Dependence upon charge of the vibrational spectra of small
|
||
Polycyclic Aromatic Hydrocarbon clusters: the example of pyrene}.
|
||
\newblock {\em Eur. Phys. J. D}, {\bf 74}(11):1--9, 2020.
|
||
|
||
\bibitem{Rapacioli2011}
|
||
{\sc Mathias Rapacioli, Fernand Spiegelman, Anthony Scemama, and Andr{\'e}
|
||
Mirtschink}.
|
||
\newblock {\bf Modeling charge resonance in cationic molecular clusters:
|
||
combining DFT-tight binding with configuration interaction}.
|
||
\newblock {\em J. Chem. Theory Comput.}, {\bf 7}(1):44--55, 2011.
|
||
|
||
\bibitem{Gatchell2016}
|
||
{\sc Michael Gatchell}.
|
||
\newblock {\em Molecular Hole Punching: Impulse Driven Reactions in Molecules
|
||
and Molecular Clusters}.
|
||
\newblock PhD thesis, Department of Physics, Stockholm University, 2016.
|
||
|
||
\bibitem{Gatchell2016knockout}
|
||
{\sc Michael Gatchell and Henning Zettergren}.
|
||
\newblock {\bf Knockout driven reactions in complex molecules and their
|
||
clusters}.
|
||
\newblock {\em J. Phys. B}, {\bf 49}(16):162001, 2016.
|
||
|
||
\bibitem{Levine1987}
|
||
{\sc Raphael~D Levine, Richard~Barry Bernstein, et~al.}
|
||
\newblock {\em Molecular reaction dynamics and chemical reactivity}.
|
||
\newblock Oxford University Press, USA, 1987.
|
||
|
||
\bibitem{Chen2014}
|
||
{\sc Tao Chen, Michael Gatchell, Mark~H Stockett, John~D Alexander, Y~Zhang,
|
||
Patrick Rousseau, A~Domaracka, S~Maclot, R~Delaunay, L~Adoui, et~al.}
|
||
\newblock {\bf Absolute fragmentation cross sections in atom-molecule
|
||
collisions: scaling laws for non-statistical fragmentation of polycyclic
|
||
aromatic hydrocarbon molecules}.
|
||
\newblock {\em J. Chem. Phys.}, {\bf 140}(22):224306, 2014.
|
||
|
||
\end{thebibliography}
|