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Articles

Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems

ORCID Icon, , , , & ORCID Icon
Pages 249-268 | Received 08 Jun 2018, Accepted 28 Nov 2018, Published online: 12 Dec 2018

References

  • Haberland H, Langosch H. Mass spectroscopic study of some novel water clusters: (h2o)n+; n > 3. Z Phys D. 1986;2(3):243–247.
  • Liu K, Cruzan JD, Saykally RJ. Water clusters. Science. 1996;271(5251):929–933.
  • Paul JB, Collier CP, Saykally RJ, et al. Direct measurement of water cluster concentrations by infrared cavity ringdown laser absorption spectroscopy. J Phys Chem A. 1997;101(29):5211–5214.
  • Paul JB, Provencal RA, Chapo C, et al. Infrared cavity ringdown spectroscopy of the water cluster bending vibrations. J Phys Chem A. 1999;103(16):2972–2974.
  • Buck U, Huisken F. Infrared spectroscopy of size-selected water and methanol clusters. Chem Rev. 2000;100(11):3863–3890.
  • Keutsch FN, Brown MG, Petersen PB, et al. Terahertz vibration–rotation–tunneling spectroscopy of water clusters in the translational band region of liquid water. J Chem Phys. 2001;114(9):3994–4004.
  • Keutsch FN, Brown MG, Petersen PB, et al. Terahertz vibration–rotation–tunneling spectroscopy of water clusters in the translational band region of liquid water. J Chem Phys. 2001;114(9):3994–4004.
  • Gregory JK, Clary DC, Liu K, et al. The water dipole moment in water clusters. Science. 1997;275(5301):814–817.
  • Keutsch FN, Saykally RJ. Water clusters: untangling the mysteries of the liquid, one molecule at a time. Proc Natl Acad Sci USA. 2001;98(19):10533–10540.
  • Wolke CT, Fournier JA, Dzugan LC, et al. Spectroscopic snapshots of the proton-transfer mechanism in water. Science. 2016;354(6316):1131–1135.
  • Temelso B, Klein KL, Mabey JW, et al. Exploring the rich potential energy surface of (h2o)11 and its physical implications. J Chem Theory Comput. 2018;14(2):1141–1153.
  • Liu K, Brown MG, Carter C, et al. Characterization of a cage form of the water hexamer. Nature. 1996;381(6582):501–503.
  • Liu K, Brown MG, Saykally RJ. Terahertz laser vibration-rotation tunneling spectroscopy and dipole moment of a cage form of the water hexamer. J Phys Chem A. 1997;101(48):8995–9010.
  • Steinbach C, Andersson P, Melzer M, et al. Detection of the book isomer from the oh-stretch spectroscopy of size selected water hexamers. Phys Chem Chem Phys. 2004;6(13):3320–3324.
  • Saykally RJ, Wales DJ. Pinning down the water hexamer. Science. 2012;336(6083):814–815.
  • Pérez C, Muckle MT, Zaleski DP, et al. Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy. Science. 2012;336(6083):897–901.
  • Wang Y, Babin V, Bowman JM, et al. The water hexamer: cage, prism or both. full dimensional quantum simulations say both. J Am Chem Soc. 2012;134(27):11116–11119.
  • Brown SE, Götz AW, Cheng X, et al. Monitoring water clusters ‘melt’ through vibrational spectroscopy. J Am Chem Soc. 2017;139(20):7082–7088.
  • Cisneros GA, Wikfeldt KT, Ojamäe L, et al. Modeling molecular interactions in water: from pairwise to many-body potential energy functions. Chem Rev. 2016;116(13):7501–7528.
  • Chadi DJ. (110) surface atomic structures of covalent and ionic semiconductors. Phys Rev B. 1979;19:2074–2082.
  • Harrison WA. Electronic structure and the properties of solids. San Francisco, CA: W. H. Freeman and Company; 1980.
  • Ziman JM, editor. The physics of metals. Cambridge: Cambridge University Press; 2011.
  • Desjonquères MC, Spanjaard D. Concepts in surface physics. (Berlin: Springer Verlag; 1993. Springer Series in Surface Sciences; Vol 30).
  • Noguera C. Clean oxide surfaces: a theoretical review. Chem Phys Sol Surf. 2001;9:35–86.
  • Hückel EH. Quantentheoretische beitráge zum benzolproblem. Z Phys. 1931;70:204–286.
  • Wolfsberg M, Helmholz L. The spectra and electronic structure of the tetrahedral ions mno4−, cro4−, and clo4−. J Chem Phys. 1952;20:837–843.
  • Hoffman R. An extended hückel theory i. hydrocarbons. J Chem Phys. 1963;39:1397–1412.
  • Hoffman R. Extended hückel theory iii. Compounds of boron and nitrogen. J Chem Phys. 1964;40:2474–2477.
  • Hoffmann R. Extended hückel theory-v: Cumulenes, polyenes, polyacetylenes and cn. Tetrahedron. 1966;22:521–538.
  • Hoffmann R. Extended hückel theory-v: cumulenes, polyenes, polyacetylenes and cn. Tetrahedron. 1966;22:521–538.
  • Porezag D, Frauenheim T, K”ohler T, et al. Construction of tight-binding-like potentials on the basis of density functional theory – application to carbon. Phys Rev B. 1995;51:12947–12957.
  • Seifert G, Porezag D, Frauenheim T. Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme. Int J Quantum Chem. 1996;58:185–192.
  • Elstner M, Porezag D, Jungnickel G, et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B. 1998;58(11):7260–7268.
  • Simon A, Rapacioli M, Mascetti J, et al. Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons. Phys Chem Chem Phys. 2012;14(19):6771–6786.
  • Choi TH, Liang R, Maupin CM, et al. Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions. J Phys Chem B. 2013;117(17):5165–5179.
  • Yang Yu H, York D, et al. Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A. 2007;111(42):10861–10873.
  • Gaus M, Cui Q, Elstner M. Dftb3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput. 2011;7(4):931–948.
  • Domínguez A, Niehaus TA, Frauenheim T. Accurate hydrogen bond energies within the density functional tight binding method. J Phys Chem A. 2015;119(14):3535–3544.
  • Livshits E, Baer R. A well-tempered density functional theory of electrons in molecules. Phys Chem Chem Phys. 2007;9:2932–2941.
  • Baer R, Neuhauser D. Density functional theory with correct long-range asymptotic behavior. Phys Rev Lett. 2005;94:043002.
  • Niehaus TA, Della Sala F. Range separated functionals in the density functional based tight-binding method: formalism. Phys Stat Sol B. 2012;249(2):237–244.
  • Lutsker V, Aradi B, Niehaus TA. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method. J Chem Phys. 2015;143(18).184107
  • Vuong VQ, Kuriappan JA, Kubillus M, et al. Parametrization and benchmark of long-range corrected DFTB2 for organic molecules. J Chem Theory Comput. 2018;14(1):115–125.
  • Kranz JJ, Elstner M, Aradi B, et al. Time-dependent extension of the long-range corrected density functional based tight-binding method. J Chem Theory Comput. 2017;13(4):1737–1747.
  • Nishizawa H, Nishimura Y, Kobayashi M, et al. Three pillars for achieving quantum mechanical molecular dynamics simulations of Huge systems: divide-and-conquer, density-functional tight-binding, and massively parallel computation. J Comput Chem. 2016;37(21):1983–1992.
  • Nakai H, Sakti AW, Nishimura Y. Divide-and-conquer-type density-functional tight-binding molecular dynamics simulations of proton diffusion in a Bulk water system. J Phys Chem B. 2016;120(1):217–221.
  • Sakti AW, Nishimura Y, Nakai H. divide-and-conquer-type density-functional tight-binding simulations of hydroxide ion diffusion in bulk water. J Phys Chem B. 2017;121(6):1362–1371.
  • Nishimoto Y, Fedorov DG, Irle S. Density-functional tight-binding combined with the fragment molecular orbital method. J Chem Theory Comput. 2014;10(11):4801–4812.
  • Nishimoto Y, Nakata H, Fedorov DG, et al. Large-scale quantum-mechanical molecular dynamics simulations using density-functional tight-binding combined with the fragment molecular orbital method. J Phys Chem Lett. 2015;6(24):5034–5039.
  • Scemama A, Renon N, Rapacioli M. A sparse self-consistent field algorithm and its parallel implementation: application to density-functional-based tight binding. J Chem Theory Comput. 2014;10(6):2344–2354.
  • Grimme S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem. 2006;27:1787–1799.
  • Elstner M, Hobza P, Frauenheim T, et al. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment. J Chem Phys. 2001;114:5149–5155.
  • Zhechkov L, Heine T, Patchovskii S, et al. An efficient a posteriori treatment for dispersion interaction in density-functional-based tight binding. J Chem Theory Comput. 2005;1:841–847.
  • Rapacioli M, Spiegelman F, Talbi D, et al. Correction for dispersion and coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters. J Chem Phys. 2009;130:244304–10.
  • Goursot Y, Mineva T, Kevorkyants R, et al. Interaction between n-alkane chains: applicability of the empirically corrected density functional theory for van der waals complexes. J Chem Theory Comput. 2007;3:755–763.
  • Li J, Zhu T, Cramer C, et al. New class iv charge model for extracting accurate partial charges from wave functions. J Phys chem A. 1998;102:1820–1831.
  • Kalinowski JA, Lesyng B, Thompson JD, et al. Class iv charge model for the self-consistent charge density-functional tight-binding method. J Phys Chem A. 2004;108:2545–2549.
  • Joalland B, Rapacioli M, Simon A, et al. Molecular dynamics simulations of anharmonic infrared spectra of [sipah]+ π-complexes. J Phys Chem A. 2010;114:5846–5854.
  • Rapacioli M, Simon A, Dontot L, et al. Extensions of DFTB to investigate molecular complexes and clusters. Phys Stat Sol B. 2012;249(2):245–258.
  • Michoulier E, BenAmor N, Rapacioli M, et al. Theoretical determination of adsorption and ionisation energies of polycyclic aromatic hydrocarbons on water ice. Phys Chem Chem Phys. 2018;20:11941–11953.
  • Rapacioli M, Spiegelman F. Modelling singly ionized coronene clusters. Eur Phys J D. 2009;52:55–58.
  • Hourahine B, Aradi B, Frauenheim T. Dftb+ and lanthanides. J Phys: Conf Series. 2010;242(1):012005.
  • Rapacioli M, Spiegelman F, Scemama A, et al. Modeling charge resonance in cationic molecular clusters: combining dft-tight binding with configuration interaction. J Chem Theo Comp. 2011;7:44–55.
  • Wu Q, Van Voorhis T. Constrained density functional theory and its application in long-range electron transfer. J Chem Theory Comput. 2006;2:765–774.
  • Wu Q, Kaduk B, Van Voorhis T. Constrained density functional theory based configuration interaction improves the prediction of reaction barrier heights. J Chem Phys. 2009;130:034109–7.
  • Iftner C, Simon A, Korchagina K, et al. A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: application to (c6h6)+/0arn clusters. J Chem Phys. 2014;140(3):034301–00.
  • Spirko V, Engkvist O, Soldan P, et al. Structure and vibrational dynamics of the benzene dimer. J Chem Phys. 1999;111:572–582.
  • Gaigeot MP, Sprik M. Ab initio molecular dynamics computation of the infrared spectrum of aqueous uracil. J Phys Chem B. 2003;107:10344–10358.
  • Simon A, Rapacioli M, Lanza M, et al. Molecular dynamics simulations on [fepah]+ π-complexes of astrophysical interest: anharmonic infrared spectroscopy. Phys Chem Chem Phys. 2011;13:3359–3374.
  • Van-Oanh NT, Parneix P, Bréchignac P. Vibrational dynamics of the neutral naphthalene molecule from a tight-binding approach. J Phys Chem A. 2002;106:10144–10151.
  • Habershon S, Manolopoulos DE, Markland TE, et al. Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. Annu Rev Phys Chem. 2013;64(1):387–413.
  • Calvo F, Falvo C, Parneix P. Atomistic modeling of vibrational action spectra in polyatomic molecules: nuclear quantum effects. J Phys Chem A. 2014;118(29):5427–5436.
  • Wales DJ, Miller MA, Walsh TR. Archetypal energy landscapes. Nature. 1998;394:758–760.
  • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314(1-2):141–151.
  • Sugita Y, Okamoto Y. Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape. Chem Phys Lett. 2000;329(3-4):261–270.
  • Bussi G. A simple asynchronous replica-exchange implementation. Il Nuovo Cimento C. 2008;32:61–65.
  • Gallicchio E, Levy RM, Parashar M. Asynchronous replica exchange for molecular simulations. J Comput Chem. 2008;29(5):788–794.
  • Gallicchio E, Xia J, Flynn WF, et al. Asynchronous replica exchange software for grid and heterogeneous computing. Comput Phys Commun. 2015;196:236–246.
  • Labastie P, Whetten RL. statistical thermodynamics of the cluster solid-liquid transition. Phys Rev Lett. 1990;65(13):1567–1570.
  • Heine T, Rapacioli M, Patchkovskii S, et al. demonnano: http://demon-nano.ups-tlse.fr/; 2009.
  • Rocher-Casterline BE, Chang LC, Mollner AK, et al. Communication: determination of the bond dissociation energy (D0) of the Water Dimer, (H2O)2, by Velocity Map Imaging. J Chem Phys. 2011;134(21):1–4. 211101.
  • Shostak SL, Ebenstein WL, Muenter JS. The dipole moment of water. i. dipole moments and hyperfine properties of H2O and HDO in the ground and excited vibrational states. J Chem Phys. 1991;94(9):5875–5882.
  • Simon A, Spiegelman F. Water clusters adsorbed on polycyclic aromatic hydrocarbons: energetics and conformational dynamics. J Chem Phys. 2013;138(19):194309.
  • Temelso B, Archer KA, Shields GC. Benchmark structures and binding energies of small water clusters with anharmonicity corrections. J Phys ChemA. 2011;115(43):12034–12046.
  • Simon A, Spiegelman F. Conformational dynamics and finite-temperature infrared spectra of the water octamer adsorbed on coronene. Comput Theor Chem. 2013;1021(SI):54–61.
  • Oliveira LFL, Cuny J, Moriniere M, et al. Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons. Phys Chem Chem Phys. 2015;17(26):17079–17089.
  • Choi TH. Simulation of the (h2o)8 cluster with the SCC-DFTB electronic structure method. Chem Phys Lett. 2012;543:45–49.
  • Simon A, Iftner C, Mascetti J, et al. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential. J Phys Chem A. 2015;119(11):2449–2467.
  • Yu H, Cui Q. The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding. J Chem Phys. 2007;127(23):234504.
  • Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B. 2011;115(20):6790–6805.
  • Korchagina K, Simon A, Rapacioli M, et al. Theoretical investigation of the solid-liquid phase transition in protonated water clusters. Phys Chem Chem Phys. 2017;19(40):27288–27298.
  • Korchagina KA, Simon A, Rapacioli M, et al. Structural characterization of sulfur-containing water clusters using a density-functional based tight-binding approach. J Phys Chem A. 2016;120(45):9089–9100.
  • Korchagina KA, Spiegelman F, Cuny J. Molecular dynamics study of the collision-induced reaction of h with co on small water clusters. J Phys Chem A. 2017;121(49):9485–9494.
  • Boulon J, Braud I, Zamith S, et al. Experimental nanocalorimetry of protonated and deprotonated water clusters. J Chem Phys. 2014;140(16):16435.
  • Jortner J. Cluster size effects. Z Phys D - Atoms Molec Clusters. 1992;24(3):247–275.
  • Labastie P, Calvo F. Thermodynamics and solid-liquid transition, nanomaterials and nanochemistry. New York: Springer; 2007.
  • Hansen K, Andersson PU, Uggerud E. Activation energies for evaporation from protonated and deprotonated water clusters from mass spectra. J Chem Phys. 2009;131(12):124303.
  • Lee SW, Freivogel P, Schindler T, et al. Freeze-dried biomolecules: Ft-icr studies of the specific solvation of functional groups and clathrate formation observed by the slow evaporation of water from hydrated peptides and model compounds in the gas phases. J Am Chem Soc. 1998;120(45):11758–11765.
  • Shin JW, Hammer NI, Diken EG, et al. Infrared signature of structures associated with the H+(H2O)n (n = 6 to 27) clusters. Science. 2004;304(5674):1137–1140.
  • Wu CC, Lin CK, Chang HC, et al. Protonated clathrate cages enclosing neutral water molecules: H+(H2O)21 and H+(H2O)28. J Chem Phys. 2005;122(7):074315.
  • Hodges MP, Wales DJ. Global minima of protonated water clusters. Chem Phys Lett. 2000;324(4):279–288.
  • Iyengar SS, Petersen MK, Day TJF, et al.The properties of ion-water clusters i. the protonated 21-water cluster. J Chem Phys. 2005;123(8):084309.
  • Miyazaki M, Fujii A, Ebata T, et al. Infrared spectroscopic evidence for protonated water clusters forming nanoscale cages. Science. 2004;304(5674):1134–1137.
  • Singh NJ, Park M, Min SK, et al. Magic and antimagic protonated water clusters: exotic structures with unusual dynamic effects. Angew Chem Int Ed. 2006;45(23):3795–3800.
  • Pedulla JM, Jordan KD. Melting Behavior of the (H2O)6 and (H2O)8 Clusters. Chem Phys. 1998;239(September):593–601.
  • Douady J, Calvo F, Spiegelman F. Effect of an ionic impurity on the caloric curves of water clusters. Eur Phys J D. 2009;52:47–50.
  • Yu F, Turco RP, Kärcher B, et al. On the mechanisms controlling the formation and properties of volatile particles in aircraft wakes. Geophys Res Lett. 1998;25(20):3839–3842.
  • Shaw GE. Production of condensation nuclei in clean air by nucleation of H2SO4. Atmos Environ. 1989;23(12):2841–2846.
  • Kulmala M, Pirjola L, Makela JM. Stable sulphate clusters as a source of new atmospheric particles. Nature. 2000;404(6773):66–69.
  • Yu F, Turco RP. From molecular clusters to nanoparticles: role of ambient ionization in tropospheric aerosol formation. J Geophys Res D. 2001;106(D5):4797–4814.
  • Metzger A, Verheggen B, Dommen J, et al. Evidence for the role of organics in aerosol particle formation under atmospheric conditions. Proc Natl Acad Sci USA. 2010;107(15):6646–6651.
  • Schobesberger S, Junninen H, Bianchi F, et al. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules. Proc Natl Acad Sci USA. 2013;110(43):17223–17228.
  • K”urten A, Jokinen T, Simon M, et al. Neutral molecular cluster formation of sulfuric acid–dimethylamine observed in real time under atmospheric conditions. Proc Natl Acad Sci USA. 2014;111(42):15019–15024.
  • Dunne EM, Gordon H, Kürten A, et al. Global atmospheric particle formation from cern cloud measurements. Science. 2016;354(6316):1119–1124.
  • Lehtipalo K, Rondo L, Kontkanen J, et al. The effect of acid-base clustering and ions on the growth of atmospheric nano-particles. Nat Commun. 2016;7:11594.
  • Boyer HC, Dutcher CS, et al. Atmospheric aqueous aerosol surface tensions: isotherm-based modeling and biphasic microfluidic measurements. J Phys Chem A. 2017;121(25):4733–4742.
  • Wang XB, Nicholas JB, Wang LS. Electronic instability of isolated SO42− and its solvation stabilization. J Chem Phys. 2000;113(24):10837–10840.
  • Wang XB, Yang X, Nicholas JB, et al. Bulk-like features in the photoemission spectra of hydrated doubly charged anion clusters. Science. 2001;294(5545):1322–1325.
  • Zhou J, Santambrogio G, Br”ummer M, et al. Infrared spectroscopy of hydrated sulfate dianions. J Chem Phys. 2006;125(11):111102.
  • Bush MF, Saykally RJ, Williams ER. Evidence for water rings in the hexahydrated sulfate dianion from IR spectroscopy. J Am Chem Soc. 2007;129(8):2220–2221.
  • O'Brien JT, Prell JS, Bush MF, et al. Sulfate ion patterns water at long distance. J Am Chem Soc. 2010;132(24):8248–8249.
  • O'Brien JT, Williams ER. Effects of ions on hydrogen-bonding water networks in large aqueous nanodrops. J Am Chem Soc. 2012;134(24):10228–10236.
  • Yang X, Wang XB, et al. Photodetachment of hydrated sulfate doubly charged anions: SO42−(H2O)n (n = 4-40). J Phys Chem A. 2002;106(33):7607–7616.
  • Wang XB, Sergeeva AP, Yang J, et al. Photoelectron spectroscopy of cold hydrated sulfate clusters, so42−(H2O)n (n = 4-7): temperature-dependent isomer populations. J Phys Chem A. 2009;113(19):5567–5576.
  • Pye CC, Rudolph WW. An ab initio and raman investigation of sulfate ion hydration. J Am Chem Soc. 2001;105(5):905–912.
  • Whitehead A, Barrios R, Simons J. Stabilization calculation of the energy and lifetime of metastable SO42−. J Chem Phys. 2002;116(7):2848–2851.
  • Wong RL, Williams ER. Dissociation of SO42−(H2O)n clusters, n = 3-17. J Phys Chem A. 2003;107(50):10976–10983.
  • Thaunay F, Clavaguera C, Ohanessian G. Hydration of the sulfate dianion in cold nanodroplets: SO42−(H2O)12 and SO42−(H2O)13. Phys Chem Chem Phys. 2015;17:25935–25945.
  • Lambrecht DS, Clark GNI, Head-Gordon T, et al. Exploring the rich energy landscape of sulfate-water clusters so42−(h2o)n=3−7: An electronic structure approach. J Phys Chem A. 2011;115(41):11438–11454.
  • Wan Q, Spanu L, Galli G. Solvation properties of microhydrated sulfate anion clusters: insights from ab initio calculations. J Phys Chem B. 2012;116(31):9460–9466.
  • Mardirossian N, Lambrecht DS, McCaslin L, et al. The performance of density functionals for sulfate-water clusters. J Chem Theory Comput. 2013;9(3):1368–1380.
  • Smeeton LC, Farrell JD, Oakley MT, et al. Structures and energy landscapes of hydrated sulfate clusters. J Chem Theory Comput. 2015;11(5):2377–2384.
  • Hey JC, Smeeton LC, Oakley MT, et al. Isomers and energy landscapes of perchlorate–water clusters and a comparison to pure water and sulfate–water clusters. J Phys Chem A. 2016;120(23):4008–4015.
  • Bandy AR, Ianni JC. Study of the hydrates of H2SO4 using density functional theory. J Phys Chem A. 1998;102(32):6533–6539.
  • Arstila H, Laasonen K, Laaksonen A. Ab initio study of gas-phase sulphuric acid hydrates containing 1 to 3 water molecules. J Chem Phys. 1998;108(3):1031–1039.
  • Re S, Osamura Y, Morokuma K. Coexistence of neutral and ion-pair clusters of hydrated sulfuric acid H2SO4(H2O)n (n = 1-5) a molecular orbital study. J Phys Chem A. 1999;103(18):3535–3547.
  • Ding CG, Taskila T, Laasonen K, et al. Reliable potential for small sulfuric acid-water clusters. Chem Phys. 2003;287(1–2):7–19.
  • Laasonen K, Ding CG. Partially and fully deprotonated sulfuric acid in H2SO4(H2O)n (n=6-9) clusters. Chem Phys Lett. 2004;390(4-6):307–313.
  • Miller Y, Chaban GM, et al. Ab initio vibrational calculations for H2SO4 and H2SO4.H2O: Spectroscopy and the nature of the anharmonic couplings. J Phys Chem A. 2005;109(29):6565–6574.
  • Miller Y, Gerber BR. Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O: hydrogen-hopping and photodissociation processes. J Am Chem Soc. 2006;128(30):9594–9595.
  • Niehaus T, Elstner M, Frauenheim T, et al. Application of an approximate density-functional method to sulfur containing compounds. J Mol Struct THEOCHEM. 2001;541(1):185–194.
  • Gaus M, Goez A, Elstner M. Parametrization and benchmark of DFTB3 for organic molecules. J Chem Theory Comput. 2013;9(1):338–354.
  • Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. Wiley Interdiscip Rev Comput Mol Sci. 2014;4(1):49–61.
  • Weigend F, Ahlrichs R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for h to rn: design and assessment of accuracy. Phys Chem Chem Phys. 2005;7:3297–3305.
  • Weigend F. Accurate coulomb-fitting basis sets for h to rn. Phys Chem Chem Phys. 2006;8:1057–1065.
  • Lis DC, Blake GA, Herbst E. Astrochemistry: recent successes and current challenges. 1st ed. Proceedings of the International Astronomical Union Symposia and Colloquia (IAU S231). Cambridge: Cambridge University Press; 2006.
  • Tielens AGGM, Tokunaga AT, Geballe TR, et al. Interstellar solid co - polar and nonpolar interstellar ices. Astrophys J. 1991;381:181–199.
  • Crovisier J. Physics and chemistry of comets: recent results from comets hyakutake and hale-bopp answers to old questions and new enigmas. Farad Discuss. 1998;109:437–452.
  • Watanabe N, Shiraki T, Kouchi A. The dependence of h2co and ch3oh formation on the temperature and thickness of h2o-co ice during the successive hydrogenation of co. Astrophys J Lett. 2003;588(2):L121–L124.
  • Watanabe N, Nagaoka A, Hidaka H, et al. Dependence of the effective rate constants for the hydrogenation of co on the temperature and composition of the surface. Planet Space Sci. 2006;54(11):1107–1114.
  • Hidaka H, Miyauchi N, Kouchi A, et al. Structural effects of ice grain surfaces on the hydrogenation of co at low temperatures. Chem Phys Lett. 2008;456(1-3):36–40.
  • Hiraoka K, Ohashi N, Kihara Y, et al. Formation of formaldehyde and methanol from the reactions of h atoms with solid co at 10–20 k. Chem Phys Lett. 1994;229(4–5):408–414.
  • Hiraoka K, Sato T, Sato S, et al. Formation of formaldehyde by the tunneling reaction of h with solid co at 10 k revisited. Astrophys J. 2002;577:265–270.
  • Pirim C, Krim L, Laffon C, et al. Preliminary study of the influence of environment conditions on the successive hydrogenations of co. J Phys Chem A. 2010;114(9):3320–3328.
  • Watanabe N, Kouchi A. Efficient formation of formaldehyde and methanol by the addition of hydrogen atoms to co in h2o-co ice at 10 k. Astrophys J Lett. 2002;571(2):L173–L176.
  • WOON DE. Modeling gas-grain chemistry with quantum chemical cluster calculations i. heterogeneous hydrogenation of co and h2co on icy grain mantles. Astrophys J. 2002;569(1):541–548.
  • Cao Q, Berski S, Räsänen M, et al. Spectroscopic and computational characterization of the HCO⋯H2O complex. J Phys Chem A. 2013;117(21):4385–4393.
  • Woon DE. An ab initio benchmark study of the h+co→ HCO reaction. J Chem Phys. 1996;105(22):9921–9926.
  • Rimola A, Taquet V, Ugliengo P, et al. Combined quantum chemical and modeling study of co hydrogenation on water ice. Astron Astr. 2014;572:A70.
  • Peters PS, Duflot D, Faure A, et al. Theoretical investigation of the isomerization of trans-hcoh to h2co: an example of a water-catalyzed reaction. J Phys Chem A. 2011;115(32):8983–8989.
  • Guennoun Z, Aupetit C, Mascetti J. Photochemistry of coronene with water at 10 K: first tentative identification by infrared spectroscopy of oxygen containing coronene products. Phys Chem Chem Phys. 2011;13(16):7340–7347.
  • Guennoun Z, Aupetit C, Mascetti J. Photochemistry of pyrene with water at low temperature: study of atmospherical and astrochemical interest. J Phys Chem A. 2011;115(10):1844–1852.
  • Noble JA, Jouvet C, Aupetit C, et al. Efficient photochemistry of coronene:water complexes. Astron Astrophys. 2017;599:A124.
  • Simon A, Noble JA, Rouaut G, et al. Formation of coronene:water complexes: FTIR study in argon matrices and theoretical characterisation. Phys Chem Chem Phys. 2017;19:8516–8529.
  • Ceponkus J, Uvdal P, Nelander B. Water tetramer, pentamer, and hexamer in inert matrices. J Phys Chem A. 2012;116(20):4842–50.
  • Bouwman J, Cuppen HM, Steglich M, et al.Photochemistry of polycyclic aromatic hydrocarbons in cosmic water Ice II. Near UV/VIS spectroscopy and ionization rates. Astron Astrophys. 2011;529:A46.
  • Osberg KI. Photochemistry and astrochemistry: photochemical pathways to interstellar complex organic molecules. Chem Rev. 2016;116(17):9631–9663.
  • de Barros ALF, Mattioda AL, Ricca A, et al. Photochemistry of coronene in cosmic water ice analogs at different concentrations. Astrophys J. 2017;848(2):112.
  • Bernstein MP, Dworkin JP, Sandford SA, et al. Ultraviolet irradiation of naphthalene in h2o ice: implications for meteorites and biogenesis. Meteor Planet Sci. 2001;36(3):351–358.
  • Bernstein MP, Sandford SA, Mattioda AL, et al. Near- and mid-infrared laboratory spectra of pah cations in solid h2o. Astrophys J. 2007;664(2):1264.
  • Bernstein MP, Sandford SA, Allamandola LJ, et al. Uv irradiation of polycyclic aromatic hydrocarbons in ices: production of alcohols, quinones, and ethers. Science. 1999;283(5405):1135–1138.
  • Bouwman J, Paardekooper DM, Cuppen HM, et al. Real-time optical spectroscopy of vacuum ultraviolet irradiated pyrene:h2o interstellar ice. Astrophys J. 2009;700(1):56.
  • Bouwman J, Cuppen HM, Bakker A, et al. Photochemistry of the PAH pyrene in water ice: the case for ion-mediated solid-state astrochemistry. Astron Astrophys. 2010;511:A33.
  • Gudipati MS, Allamandola LJ. Polycyclic aromatic hydrocarbon ionization energy lowering in water ices. Astrophys J. 2004;615(2):L177–L180.
  • Woon DE, Park JY. Photoionization of benzene and small polycyclic aromatic hydrocarbons in ultraviolet-processed astrophysical ices: a computational study. Astrophys J. 2004;607(1):342–345.
  • Gudipati MS, Allamandola LJ. Unusual stability of polycyclic aromatic hydrocarbon radical cations in amorphous water ices up to 120 K: astronomical implications. Astrophys J. 2006;638(1):286–292.
  • Michoulier E, Noble JA, Simon A, et al. Adsorption of PAHS on interstellar ice viewed by classical molecular dynamics. Phys Chem Chem Phys. 2018;20:8753–8764.
  • Novakovskaya YV, Stepanov NF. Nonempirical description of the atmospherically important anionic species. i. water cluster anions. Struct Chem. 2004;15:65–70.
  • Maupin CM, Aradi B, Voth GA. The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations. J Phys Chem B. 2010;114(20):6922–6931.
  • Liang R, Swanson JMJ, Voth GA. Benchmark study of the scc-dftb approach for a biomolecular proton channel. J Chem Theory Comput. 2014;10(1):451–462.
  • Goyal P, Qian HJ, Irle S, et al. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B. 2014;118(38):11007–11027.
  • Sprik M, Hutter J, Parrinello M. Ab initio molecular dynamics simulation of liquid water: comparison of three gradient-corrected density functionals. J Chem Phys. 1996;105(3):1142–1152.
  • Silvestrelli PL, Parrinello M. Water molecule dipole in the gas and in the liquid phase. Phys Rev Lett. 1999;82:3308–3311.
  • Grossman JC, Schwegler E, Draeger EW, et al. Towards an assessment of the accuracy of density functional theory for first principles simulations of water. J Chem Phys. 2004;120(1):300–311.
  • Chen B, Ivanov I, Klein ML, et al.Hydrogen bonding in water. Phys Rev Lett. 2003;91(21):215503.
  • Ramirez R, Lopez-Ciudad T, Kumar PP, et al. Quantum corrections to classical time-correlation functions: hydrogen bonding and anharmonic floppy modes. J Chem Phys. 2004;121(9):3973–3983.
  • Kuo IFW, Mundy CJ, McGrath MJ, et al. Liquid water from first principles: investigation of different sampling approaches. J Phys Chem B. 2004;108(34):12990–12998.
  • Lee HS, Tuckerman ME. Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit. J Chem Phys. 2006;125(15):154507.
  • Zhang C, Donadio D, Galli G. First-principle analysis of the ir stretching band of liquid water. J Phys Chem Lett. 2010;1(9):1398–1402.
  • Laage D, Stirnemann G, Sterpone F, et al. Water jump reorientation: from theoretical prediction to experimental observation. Acc Chem Res. 2011;45(1):53–62.
  • Heyden M, Sun J, Forbert H, et al. Understanding the origins of dipolar couplings and correlated motion in the vibrational spectrum of water. J Phys Chem Lett. 2012;2135–2140.
  • Kühne TD, Khaliullin RZ. Electronic signature of the instantaneous asymmetry in the first coordination shell of liquid water. Nat Commun. 2013;4:1450.
  • Hassanali AA, Cuny J, Verdolino V, et al. Aqueous solutions: state of the art in ab initio molecular dynamics. Philos Trans R Soc London, Ser A. 2014;372(2011).
  • Gillan MJ, Alfè D, Michaelides A. Perspective: how good is dft for water?. J Chem Phys. 2016;144(13):130901.
  • Gasparotto P, Hassanali AA, Ceriotti M. Probing defects and correlations in the hydrogen-bond network of ab initio water. J Chem Theory Comput. 2016;12(4):1953–1964.
  • Miceli G, Hutter J, Pasquarello A. Liquid water through density-functional molecular dynamics: plane-wave vs atomic-orbital basis sets. J Chem Theory Comput. 2016;12(8):3456–3462.
  • Chen M, Ko HY, Remsing RC, et al. Ab initio theory and modeling of water. Proc Natl Acad Sci USA. 2017;114(41):10846–10851.
  • Sit PHL, Marzari N. Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics. J Chem phys. 2005;122(20):204510.
  • VandeVondele J, Mohamed F, Krack M, et al. The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J Chem Phys. 2005;122(1):014515.
  • Todorova T, Seitsonen AP, Hutter J, et al. Molecular dynamics simulation of liquid water: hybrid density functionals. J Phys Chem B. 2006;110(8):3685–3691.
  • Guidon M, Schiffmann F, Hutter J, et al. Ab–initio molecular dynamics using hybrid density functionals. J Chem Phys. 2008;128(21):214104. (pages 15).
  • Zhang C, Donadio D, Gygi F, et al. First principles simulations of the infrared spectrum of liquid water using hybrid density functionals. J Chem Theory Comput. 2011;7(5):1443–1449.
  • DiStasio RA, Santra B, Li Z, et al. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water. J Chem Phys. 2014;141(8):084502.
  • Ambrosio F, Miceli G, Pasquarello A. Structural, dynamical, and electronic properties of liquid water: a hybrid functional study. J Phys Chem B. 2016;120(30):7456–7470.
  • Pestana LR, Mardirossian N, Head-Gordon M, et al. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem Sci. 2017;8:3554–3565.
  • Lin IC, Seitsonen AP, Coutinho-Neto MD, et al. Importance of van der waals interactions in liquid water. J Phys Chem B. 2009;113(4):1127–1131.
  • Møgelhøj A, Kelkkanen AK, Wikfeldt KT, et al. Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like. J Phys Chem B. 2011;115(48):14149–14160.
  • Zhang C, Wu J, Galli G, et al. Structural and vibrational properties of liquid water from van der waals density functionals. J Chem Theory Comput. 2011;7(10):3054–3061.
  • Jonchiere R, Seitsonen AP, Ferlat G, et al. Van der waals effects in ab initio water at ambient and supercritical conditions. J Chem Phys. 2011;135(15).
  • Morrone JA, Car R. Nuclear quantum effects in water. Phys Rev Lett. 2008;101:017801.
  • Ceriotti M, Cuny J, Parrinello M, et al. Nuclear quantum effects and hydrogen bond fluctuations in water. Proc Natl Acad Sci USA. 2013;110(39):15591–15596.
  • Fritsch S, Potestio R, Donadio D, et al. Nuclear quantum effects in water: a multiscale study. J Chem Theory Comput. 2014;10(2):816–824.
  • Ceriotti M, Fang W, Kusalik PG, et al. Nuclear quantum effects in water and aqueous systems: experiment, theory, and current challenges. Chem Rev. 2016;116:7529–7550.
  • Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys. 1984;81(1):511.
  • Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A. 1985;31(3):1695–1697.
  • Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A. 1985;31(3):1695–1697.
  • Liu J, Zhao Y, Ren S. Molecular dynamics simulation of self-aggregation of asphaltenes at an oil/water interface: formation and destruction of the asphaltene protective film. Energy Fuels. 2015;29(2):1233–1242.
  • Laio A, Parrinello M. Escaping free-energy minima. Proc Natl Acad Sci USA. 2002;99(20):12562–12566.
  • Iannuzzi M, Laio A, Parrinello M. Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics. Phys Rev Lett. 2003;90(23):238302.
  • Laio A, Rodriguez-Fortea A, Gervasio FL, et al. Assessing the accuracy of metadynamics. J Phys Chem B. 2005;109(14):6714–6721.
  • Rapacioli M, A S, Marshall CC, et al. Cationic methylene-pyrene isomers and isomerization pathways: finite temperature theoretical studies. J Phys Chem A. 2015;119:9089–9100.
  • Cuny J, Korchagina K, Menakbi C, et al. Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study. J Mol Mod. 2017;23(3):167.

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