Aqueous solutions: State of the art in ab initio molecular dynamics

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 372, Issue 2011, 2014, Pages

  Hassanali, Ali A ^a   Cuny, Jérôme ^a,b   Verdolino, Vincenzo ^a   Parrinello, Michele ^a  

^a UNIVERSITY OF LUGANO   (Switzerland)

^b Université Paul Sabatier   (France)

Author keywords

Ab initio; Aqueous systems; Molecular dynamics

Indexed keywords

ALGORITHMS; ELECTRONIC STRUCTURE; IONS; QUANTUM ELECTRONICS; SOLUTIONS;

AB INITIO; AB INITIO MOLECULAR DYNAMICS; AQUEOUS SYSTEM; CAR-PARRINELLO MOLECULAR DYNAMICS; COMPUTATIONAL RESOURCES; DYNAMICAL PROPERTIES; NUCLEAR QUANTUM EFFECTS; THEORETICAL DEVELOPMENT;

MOLECULAR DYNAMICS;

EID: 84894275963     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2012.0482     Document Type: Review

References (244)

1. Cohen SM. 2012 Aristotle's metaphysics. Stanford, CA: The Metaphysics Research Lab, Center for the Study of Language and Information.
2. Jacobi J. (ed.) 1979 Paracelsus: selected writings. Princeton, NJ: Princeton University Press.
3. Ball P. 2008 Water as an active constituent in cell biology. Chem. Rev. 108, 74. (doi:10.1021/cr068037a)
4. Geissler PL, Dellago C, Chandler D, Hutter J, Parrinello M. 2001 Autoionization in liquid water. Science 291, 2121. (doi:10.1126/science.1056991)
5. MarxD2007 Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. Chem. Phys. Chem. 8, 209-210. (doi:10.1002/cphc.200790002)
6. Hassanali A, Prakash MK, Eshet H, Parrinello M. 2011 On the recombination of hydronium and hydroxide ions in water. Proc. Natl Acad. Sci. USA 108, 20 410-20 415. (doi:10.1073/pnas.1112486108)
7. Fayer MD. 2012 Dynamics of water interacting with interfaces, molecules, and ions. Acc. Chem. Res. 45, 3-14. (doi:10.1021/ar2000088)
8. Knight C, Voth GA. 2012 The curious case of the hydrated proton. Acc. Chem. Res. 45, 101-109. (doi:10.1021/ar200140h)
9. Agmon N. 2012 Liquid water: from symmetry distortions to diffusive motion. Acc. Chem. Res. 45, 63-73. (doi:10.1021/ar200076s)
10. Shultz MJ, Vu TH, Meyer B, Bisson P. 2012 Water: a responsive small molecule. Acc. Chem. Res. 45, 15-22. (doi:10.1021/ar200064z)
11. Laage D, Stirnemann G, Sterpone F, Hynes JT. 2012 Water jump reorientation: from theoretical prediction to experimental observation. Acc. Chem. Res. 45, 53-62. (doi:10.1021/ ar200075u)
12. Rahman A. 1964 Correlations in the motion of atoms in liquid argon. Phys. Rev. 136, A405-A411. (doi:10.1103/PhysRev.136.A405)
13. Stillinger FH, Rahman A. 1972 Molecular dynamics study of temperature effects on water structure and kinetics. J. Chem. Phys. 57, 1281-1292. (doi:10.1063/1.1678388)
14. Allen MP, Tildesley DJ. 1987 Computer simulation of liquids. Oxford, UK: Oxford University Press.
15. Stillinger FH, Rahman A. 1974 Improved simulation of liquid water by molecular dynamics. J. Chem. Phys. 60, 1545-1557. (doi:10.1063/1.1681229)
16. Rahman A, Stillinger FH. 1973 Hydrogen-bond patterns in liquid water. J. Am. Chem. Soc. 95, 7943-7948. (doi:10.1021/ja00805a003)
17. Laage D, Hynes JT. 2006 A molecular jump mechanism of water reorientation. Science 311, 832-835. (doi:10.1126/science.1122154)
18. Lawrence CP, Skinner JL. 2003 Vibrational spectroscopy of HOD in liquid D2O. III. Spectral diffusion, and hydrogen-bonding and rotational dynamics. J. Chem. Phys. 118, 264-272. (doi:10.1063/1.1525802)
19. Fecko CJ, Loparo JJ, Roberts ST, Tokmakoff A. 2005 Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D2O. J. Chem. Phys. 122, 054506. (doi:10.1063/1.1839179)
20. Berendsen HJC, Grigera JR, Straatsma TP. 1987 The missing term in effective pair potentials. J. Phys. Chem. 91, 6269-6271. (doi:10.1021/ j100308a038)
21. McCammon JA, Gelin BR, Karplus M. 1977 Dynamics of folded proteins. Nature 267, 585-590. (doi:10.1038/267585a0)
22. Vashishta P, Kalia RK, Li W, Nakanos A, Omeltchenko A, Tsuruta K, Wang J, Ebbsj I. 1996 Million atom molecular dynamics simulations ofmaterials on parallel computers. Curr. Opin. Solid State Mater. Sci. 1, 853-863. (doi:10.1016/S1359-0286(96)80113-6)
23. Rudd RE, Broughton JQ. 2005 Concurrent coupling of length scales in solid state systems. New York, NY:Wiley-VCH Verlag GmbH & Co. KGaA.
24. Jungwirth P, Tobias DJ. 2006 Specific ion effects at the air/water interface. Chem. Rev. 106, 1259-1281. (doi:10.1021/cr0403741)
25. Scheraga HA, Khalili M, Liwo A. 2007 Protein-folding dynamics: overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 58, 57-83. (doi:10.1146/annurev. physchem.58.032806.104614)
26. Dykstra CE. 1993 Electrostatic interaction potentials in molecular force fields. Chem. Rev. 93, 2339-2353. (doi:10.1021/cr00023a001)
27. Halgren TA, Damm W. 2001 Polarizable force fields. Curr. Opin. Struct. Biol. 11, 236-242. (doi:10.1016/S0959-440X(00)00196-2)
28. Agmon N. 1995 The Grotthuss mechanism. Chem. Phys. Lett. 244, 456-462. (doi:10.1016/0009-2614(95)00905-J)
29. Marx D, Hutter J. 2000 Ab initio molecular dynamics: theory and implementation. In Modern methods and algorithms of quantum chemistry, vol. 3 (ed. J Grotendorst), pp. 329-447. NIC Series. Jülich, Germany: Johen von Neumann Institute for Computing.
30. Tuckerman ME. 2002 Ab initio molecular dynamics: basic concepts, current trends and novel applications. J. Phys. Condens. Matter 14, R1297. (doi:10.1088/0953-8984/14/50/202)
31. Kirchner B, diDio PJ, Hutter J. 2012 Real-world predictions from ab initio molecular dynamics simulations. Top. Curr. Chem., 307, 109-153. (doi:10.1007/128-2011-195)
32. Car R, Parrinello M. 1985 Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55, 2471-2474. (doi:10.1103/ PhysRevLett.55.2471)
33. Ramirez R, Lopez-Ciudad T, Padma Kumar P, Marx D. 2004 Quantum corrections to classical time-correlation functions: hydrogen bonding and anharmonic floppy modes. J. Chem. Phys. 121, 3973-3983. (doi:10.1063/1.1774986)
34. Zhang C, Donadio D, Galli G. 2010 First-principle analysis of the IR stretching band of liquid water. J. Phys. Chem. Lett. 1, 1398-1402. (doi:10.1021/jz100232z)
35. Putrino A, Parrinello M. 2002 Anharmonic Raman spectra in high-pressure ice from ab initio simulations. Phys. Rev. Lett. 88, 176401. (doi:10.1103/PhysRevLett.88.176401)
36. Sebastiani D, Parrinello M. 2001Anew ab-initio approach forNMRchemical shifts in periodic systems. J. Phys. Chem. A 105, 1951-1958. (doi:10.1021/jp002807j)
37. Born M, Oppenheimer R. 1927 Zur quantentheorie der molekeln. Ann. Phys. 389, 457-484. (doi:10.1002/andp.19273892002)
38. Hohenberg P, Kohn W. 1964 Inhomogeneous electron gas. Phys. Rev. 136, B864-B871. (doi:10.1103/PhysRev.136.B864)
39. KohnW, Sham LJ. 1965 Self-consistent equations including exchange and correlation effects. Phys. Rev. 140, A1133-A1138. (doi:10.1103/PhysRev.140. A1133)
40. Parr RG, YangW. 1989 Density functional theory of atoms and molecules. NewYork, NY: Oxford University Press.
41. Martin RM. 2004 Electronic structure basic theory and practical methods. Cambridge, UK: Cambridge University Press.
42. Marx D, Hutter J. 2009 Ab initio molecular dynamics: basic theory and advanced methods, vol. 1. Cambridge, UK: Cambridge University Press.
43. Feynman RP. 1939 Forces in molecules. Phys. Rev. 56, 340-343. (doi:10.1103/PhysRev.56.340)
44. Giannozzi P et al. 2009 Quantum espresso: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21, 395502. (doi:10.1088/0953-8984/21/39/395502)
45. Kresse G, Hafner J. 1993 Ab initio molecular dynamics for liquid metals. Phys. Rev. B 47, 558-561. (doi:10.1103/PhysRevB.47.558)
46. Segall MD, Lindan PJD, Probert MJ, Pickard CJ, Hasnip PJ, Clark SJ, Payne MC. 2002 Firstprinciples simulation: ideas, illustrations and the CASTEP code. J. Phys. Condens. Matter 14, 2717-2744. (doi:10.1088/0953-8984/14/11/301)
47. Kühne TD, Krack M, Parrinello M. 2009 Static and dynamical properties of liquid water from first principles by a novel Car-Parrinello-like approach. J. Chem. Theory Comput. 5, 235-241. (doi:10.1021/ct800417q)
48. Feynman RP, Hibbs AR. 1965 Quantum mechanics and path integrals. NewYork, NY:McGraw-Hill.
49. Feynman RP. 1972 Statistical mechanics. Reading, MA: Benjamin.
50. Zinn-Justin J. 2005 Path integrals in quantum mechanics. Oxford, UK: Oxford University Press.
51. Ceriotti M, Bussi G, Parrinello M. 2009 Nuclear quantum effects in solids using a colorednoise thermostat. Phys. Rev. Lett. 103, 030603. (doi:10.1103/PhysRevLett.103.030603)
52. Ceriotti M, Manolopoulos DE, Parrinello M. 2011 Accelerating the convergence of path integral dynamics with a generalized Langevin equation. J. Chem. Phys. 134, 084104. (doi:10.1063/1.3556661)
53. Errington JR, Debenedetti PG. 2001 Relationship between structural order and the anomalies of liquid water. Nature 409, 318-321. (doi:10.1038/35053024)
54. Angell CA. 2008 Insights into phases of liquid water from study of its unusual glass-forming properties. Science 319, 582-587. (doi:10.1126/science. 1131939)
55. Meot-Ner (Mautner) M. 2005 The ionic hydrogen bond. Chem. Rev. 105, 213-284. (doi:10.1021/cr9411785)
56. Kemsley J. 2010 Hydrogen bond reformulation. Chem. Eng. News 88, 32-33. (doi:10.1021/ cen-v088n047.p032)
57. Eisenberg D, Kauzmann W. 1969 The structure and properties of water. Oxford, UK: Oxford University Press.
58. Laasonen K, Sprik M, Parrinello M, Car R. 1993 'Ab initio' liquid water. J. Chem. Phys. 99, 9080-9089. (doi:10.1063/1.465574)
59. Soper AK, Phillips MG. 1986 A new determination of the structure of water at 25°C. Chem. Phys. 107, 47-60. (doi:10.1016/0301-0104(86)85058-3)
60. Perdew JP. 1986 Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33, 8822-8824. (doi:10.1103/PhysRevB.33.8822)
61. Becke AD. 1988 Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A38, 3098-3100. (doi:10.1103/PhysRevA. 38.3098)
62. Laasonen K, Car R, Lee C, Vanderbilt D. 1991 Implementation of ultrasoft pseudopotentials in ab initio molecular dynamics. Phys. Rev. B 43, 6796. (doi:10.1103/PhysRevB.43.6796)
63. Laasonen K, Pasquarello A, Car R, Lee C, Vanderbilt D. 1993 Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials. Phys. Rev. B 47, 10 142. (doi:10.1103/ PhysRevB.47.10142)
64. Grossman JC, Schwegler E, Draeger EW, Gygi F, Galli G. 2004 Towards an assessment of the accuracy of density functional theory for first principles simulations of water. J. Chem. Phys. 120, 300-311. (doi:10.1063/1.1630560)
65. Silvestrelli PL, Parrinello M. 1999 Water molecule dipole in the gas and in the liquid phase. Phys. Rev. Lett. 82, 3308-3311. (doi:10.1103/PhysRevLett. 82.3308)
66. Silvestrelli PL, Parrinello M. 1999 Structural, electronic, and bonding properties of liquid water from first principles. J. Chem. Phys. 111, 3572-3580. (doi:10.1063/1.479638)
67. Sharma M, Resta R, Car R. 2007 Dipolar correlations and the dielectric permittivity of water. Phys. Rev. Lett. 98, 247401. (doi:10.1103/PhysRevLett.98. 247401)
68. SprikM, Hutter J, Parrinello M. 1996 Ab initio molecular dynamics simulation of liquid water: comparison of three gradient-corrected density functionals. J. Chem. Phys. 105, 1142-1152. (doi:10.1063/1.471957)
69. Todorova T, Seitsonen AP, Hutter J, Kuo I-FW, Mundy CJ. 2006 Molecular dynamics simulation of liquid water: hybrid density functionals. J. Phys. Chem. B 110, 3685-3691. (doi:10.1021/jp055127v)
70. Guidon M, Schiffmann F, Hutter J, VandeVondele J. 2008 Ab-initio molecular dynamics using hybrid density functionals. J. Chem. Phys. 128, 214104. (doi:10.1063/1.2931945)
71. Fernandez-Serra MV, Artacho E. 2004 Network equilibration and first-principles liquid water. J. Chem. Phys. 121, 11 136-11 144. (doi:10.1063/1.1813431)
72. Sit PH-L, Marzari N. 2005 Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics. J. Chem. Phys. 122, 204510. (doi:10.1063/1.1908913)
73. VandeVondele J, Mohamed F, Krack M, Hutter J, Sprik M, Parrinello M. 2005 The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J. Chem. Phys. 122, 014515. (doi:10.1063/1.1828433)
74. Lee H-S, Tuckerman ME. 2006 Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit. J. Chem. Phys. 125, 154507. (doi:10.1063/1.2354158)
75. Kuo I-FW et al. 2004 Liquid water from first principles: investigation of different sampling approaches. J. Phys. Chem. B 108, 12 990-12 998. (doi:10.1021/jp047788i)
76. Zhang C, Donadio D, Gygi F, Galli G. 2011 First principles simulations of the infrared spectrum of liquid water using hybrid density functionals. J. Chem. Theory Comput. 7, 1443-1449. (doi:10.1021/ct2000952)
77. Lin I-C, Seitsonen AP, Coutinho-Neto MD, Tavernelli I, Rothlisberger U. 2009 Importance of van der Waals interactions in liquid water. J. Phys. Chem. B 113, 1127-1131. (doi:10.1021/ jp806376e)
78. Santra B, Michaelides A, Scheffler M. 2009 Coupled cluster benchmarks of water monomers and dimers extracted from density-functional theory liquid water: the importance of monomer deformations. J. Chem. Phys. 131, 124509. (doi:10.1063/1.3236840)
79. Jonchiere R, Seitsonen AP, Ferlat G, Saitta AM, Vuilleumier R. 2011 Van der Waals effects in ab initio water at ambient and supercritical conditions. J. Chem. Phys. 135, 154503. (doi:10.1063/1.3651474)
80. Zhang C, Wu J, Galli G, Gygi F. 2011 Structural and vibrational properties of liquid water from van der Waals density functionals. J. Chem. Theory Comput. 7, 3054-3061. (doi:10.1021/ ct200329e)
81. Møgelhøj A et al. 2011 Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like. J. Phys. Chem. B 115, 14 149-14 160. (doi:10.1021/jp2040345)
82. Chen B, Ivanov I, Klein ML, Parrinello M. 2003 Hydrogen bonding in water. Phys. Rev. Lett. 91, 215503. (doi:10.1103/PhysRevLett.91.215503)
83. Morrone JA, Car R. 2008 Nuclear quantum effects in water. Phys. Rev. Lett. 101, 017801. (doi:10.1103/PhysRevLett.101.017801)
84. De Raedt B, Sprik M, Klein ML. 1984 Computer simulation of muonium in water. J. Chem. Phys. 80, 5719-5724. (doi:10.1063/1.446641)
85. Paesani F, Zhang W, Case DA, Cheatham III TE, Voth GA. 2006 An accurate and simple quantum model for liquid water. J. Chem. Phys. 125, 184507. (doi:10.1063/1.2386157)
86. Habershon S, Markland TE, Manolopoulos DE. 2009 Competing quantum effects in the dynamics of a flexible water model. J. Chem. Phys. 131, 024501. (doi:10.1063/1.3167790)
87. de Grotthuss CJT. 1806 Mémoire sur la décomposition de l'eau et des corps quelle tient en dissolution à laide the l'electricité galvanique. Ann. Chim. (Paris) LVIII, 5474.
88. Danneel HZ. 1905 Notiz über Ionengeschwindigkeiten. Electrochem 11, 249. (doi:10.1002/ bbpc.19050111603)
89. EigenM, deMaeyer L. 1958 Self-dissociation and protonic charge transport in water and ice. Proc. R. Soc. Lond. A 247, 505-533. (doi:10.1098/rspa.1958. 0208)
90. Tuckerman M, Laasonen K, Sprik M, Parrinello M. 1995 Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water. J. Phys. Chem. 99, 5749-5752. (doi:10.1021/j100016a003)
91. Tuckerman M, Laasonen K, Sprik M, Parrinello M. 1995 Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J. Chem. Phys. 103, 150-161. (doi:10.1063/1.469654)
92. Eigen M. 1964 Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Part I: elementary processes. Angew. Chem. Int. Edn Engl. 3, 1-19. (doi:10.1002/anie.196400011)
93. Zundel G, MetzgerH. 1968 Energiebnder der tunnelnden berschu-protonen in flssigen suren. eine IR-spektroskopische untersuchung der natur der gruppierungen H5O+2 . Z. Phys. Chem. 58, 225-245. (doi:10.1524/zpch.1968.58.5-6. 225)
94. Markovitch O, Chen H, Izvekov S, Paesani F, Voth GA, Agmon N. 2008 Special pair dance and partner selection: elementary steps in proton transport in liquid water. J. Phys. Chem. B 112, 9456-9466. (doi:10.1021/jp804018y)
95. Zundel G. 2007 Hydrogen bonds with large proton polarizability and proton transfer processes in electrochemistry and biology. Adv. Chem. Phys. 11, 1-217.
96. Chandra A, Tuckerman ME, Marx D. 2007 Connecting solvation shell structure to proton transport kinetics in hydrogen-bonded networks via population correlation functions. Phys. Rev. Lett. 99, 145901. (doi:10.1103/PhysRevLett.99.145901)
97. Berkelbach TC, Lee H-S, Tuckerman ME. 2009 Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: a first-principles molecular dynamics study. Phys. Rev. Lett. 103, 238302. (doi:10.1103/ PhysRevLett.103.238302)
98. Swanson JMJ, Simons J. 2009 Role of charge transfer in the structure and dynamics of the hydrated proton. J. Phys. Chem. B 113, 5149-5161. (doi:10.1021/jp810652v)
99. Knight C, Maupin CM, Izvekov S, Voth GA. 2010 Defining condensed phase reactive force fields from ab-initio molecular dynamics simulations: the case of the hydrated excess proton. J. Chem. Theory Comput. 6, 3223-3232. (doi:10.1021/ct1004438)
100. Wigner E. 1932 On the quantum correction for thermodynamic equilibrium. Phys. Rev. 40, 749-759. (doi:10.1103/PhysRev.40.749)
101. Marx D, Tuckerman ME, Hutter J, Parrinello M. 1999 The nature of the hydrated excess proton in water. Nature 397, 601-604. (doi:10.1038/17579)
102. Hayes RL, Paddison SJ, Tuckerman ME. 2011 Proton transport in triflic acid pentahydrate studied via ab initio path integral molecular dynamics. J. Phys. Chem. A 115, 6112-6124. (doi:10.1021/jp110953a)
103. von Rosenvinge T, Tuckerman ME, Klein ML. 1997 Ab initio molecular dynamics study of crystal hydrates of HCl including path integral results. Faraday Discuss. 106, 273-289. (doi:10.1039/a702374j)
104. Buch V, Dubrovskiy A, Mohamed F, Parrinello M, Sadlej J, Hammerich AD, Devlin JP. 2008 HCl hydrates as model systems for protonated water. J. Phys. Chem. A 112, 2144-2161. (doi:10.1021/jp076391m)
105. Hassanali AA, Cuny J, Ceriotti M, Pickard CJ, Parrinello M. 2012 The fuzzy quantum proton in the hydrogen chloride hydrates. J. Am. Chem. Soc. 134, 8557-8569. (doi:10.1021/ja3014727)
106. Tuckerman ME, Chandra A, Marx D. 2006 Structure and dynamics of OH-(aq). Acc. Chem. Res. 39, 151-158. (doi:10.1021/ar040207n)
107. Marx D, Chandra A, Tuckerman ME. 2010 Aqueous basic solutions: hydroxide solvation, structural diffusion, and comparison to the hydrated proton. Chem. Rev. 110, 2174-2216. (doi:10.1021/cr900233f)
108. Meot-Ner M, Speller CV. 1986 Filling of solvent shells about ions. 1. Thermochemical criteria and the effects of isomeric clusters. J. Phys. Chem. 90, 6616-6624. (doi:10.1021/j100283a006)
109. Robertson WH, Diken EG, Price EA, Shin J-W, Johnson MA. 2003 Spectroscopic determination of the OH solvation shell in the OH (H2O)n clusters. Science 299, 1367-1372. (doi:10.1126/science.1080695)
110. Aziz EF, Ottosson N, Faubel M, Hertel IV, Winter B. 2008 Interaction between liquid water and hydroxide revealed by core-hole de-excitation. Nature 455, 89-91. (doi:10.1038/ nature07252)
111. Marx D, Tuckerman ME, Parrinello M. 2002 The nature and transport mechanism of hydrated hydroxide ions in aqueous solution. Nature 417, 925-929. (doi:10.1038/ nature00797)
112. Asthagiri D, Pratt LR, Kress JD, Gomez MA. 2004 Hydration and mobility of HO-. Proc. Natl Acad. Sci. USA 101, 7229-7233. (doi:10.1073/pnas.0401696101)
113. Natzle WC, Moore CB. 1985 Recombination of hydrogen ion (H+) and hydroxide in pure liquid water. J. Phys. Chem. 89, 2605-2612. (doi:10.1021/j100258a035)
114. Bolhuis PG, Chandler D, Dellago C, Geissler PL. 2002 Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53, 291-318. (doi:10.1146/annurev.physchem.53.082301.113146)
115. Egorov AV, Komolkin AV, Chizhik VI, Yushmanov PV, Lyubartsev AP, Laaksonen A. 2003 Temperature and concentration effects on Li+-ion hydration. A molecular dynamics simulation study. J. Phys. Chem. B 107, 3234-3242. (doi:10.1021/jp026677l)
116. White JA, Schwegler E, Galli G, Gygi F. 2000 The solvation of Na+ in water: first-principles simulations. J. Chem. Phys. 113, 4668-4673. (doi:10.1063/1.1288688)
117. Ramaniah LM, BernasconiM, Parrinello M. 1999 Ab initio molecular-dynamics simulation of K+ solvation in water. J. Chem. Phys. 111, 1587-1591. (doi:10.1063/1.479418)
118. Liu Y, Lu H, Wu Y, Hu T, Li Q. 2010 Hydration and coordination of K+ solvation in water from ab initio molecular-dynamics simulations. J. Chem. Phys. 132, 124503. (doi:10.1063/1.3369624)
119. Marx D, Sprik M, Parrinello M. 1997 Ab initio molecular dynamics of ion solvation. The case of Be+2 in water. Chem. Phys. Lett. 273, 360-366. (doi:10.1016/S0009-2614(97)00618-0)
120. Lightstone FC, Schwegler E, Hood RQ, Gygi F, Galli G. 2001 A first principles molecular dynamics simulation of the hydrated magnesium ion. Chem. Phys. Lett. 343, 549-555. (doi:10.1016/S0009-2614(01)00735-7)
121. Bako I, Hutter J, Palinkas G. 2002 Car-Parrinello molecular dynamics simulation of the hydrated calcium ions. J. Chem. Phys. 117, 9838-9843. (doi:10.1063/1.1517039)
122. Naor MM, Nostrand KV, Dellago C. 2003 Car-Parrinello molecular dynamics simulation of the calcium ion in liquid water. Chem. Phys. Lett. 369, 159-164. (doi:10.1016/S0009-2614(02)01998-X)
123. Lightstone FC, Schwegler E, Allesch M, Gygi F, Galli G. 2005 A first-principles molecular dynamics study of calcium in water. Chem. Phys. Chem. 6, 1745-1749. (doi:10.1002/cphc. 200500053)
124. Ikeda T, Boero M, Terakura K. 2007 Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics. J. Chem. Phys. 127, 074503. (doi:10.1063/1.2768063)
125. Di Tommaso D, de Leeuw NH. 2010 Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations. Phys. Chem. Chem. Phys. 12, 894-901. (doi:10.1039/b915329b)
126. Kapitán J, Dračínský M, Kaminský J, Benda L, Bouř P. 2010 Theoretical modeling of magnesium ion imprints in the Raman scattering of water. J. Phys. Chem. B 114, 3574-3582. (doi:10.1021/jp9110508)
127. Adeagbo WA, Doltsinis NL, Burchard M, Maresch WV, Fockenberg T. 2012 Ca2+ solvation as a function of p, T, and pH from ab initio simulation. J. Chem. Phys. 137, 124502. (doi:10.1063/1.4754129)
128. Laasonen K, Klein ML. 1994 Ab initio molecular dynamics study of hydrochloric acid in water. J. Am. Chem. Soc. 116, 11 620-11 621. (doi:10.1021/ja00104a073)
129. Laasonen K. 1996 Ab initio molecular dynamics study of dilute hydrofluoric acid. Mol. Phys. 88, 135-142. (doi:10.1080/00268979609482405)
130. Petit L, Vuilleumier R, Maldivi P, Adamo C. 2008 Ab initio molecular dynamics study of a highly concentrated LiCl aqueous solution. J. Chem. Theory Comput. 4, 1040-1048. (doi:10.1021/ct800007v)
131. Todorova T, Hünenberger PH, Hutter J. 2008 Car-Parrinello molecular dynamics simulations of CaCl2 aqueous solutions. J. Chem. Theory Comput. 4, 779-789. (doi:10.1021/ct700302m)
132. Raugei S, Klein ML. 2001 Dynamics of water molecules in the Br-solvation shell: an ab initio molecular dynamics study. J. Am. Chem. Soc. 123, 9484-9485. (doi:10.1021/ja011030k)
133. Raugei S, Klein ML. 2002 An ab initio study of water molecules in the bromide ion solvation shell. J. Chem. Phys. 116, 196-202. (doi:10.1063/1. 1421366)
134. Kropman MF, Bakker HJ. 2001 Dynamics of water molecules in aqueous solvation shells. Science 291, 2118-2120. (doi:10.1126/science.1058190)
135. Izvekov S, Philpott MR. 2000 Ab initio molecular dynamics simulation of LiBr association in water. J. Chem. Phys. 113, 10 676-10 684. (doi:10.1063/1.1311965)
136. Schmidt DA, Scipioni R, Boero M. 2009 Water solvation properties: an experimental and theoretical investigation of salt solutions at finite dilution. J. Phys. Chem. A 113, 7725-7729. (doi:10.1021/jp9016932)
137. Chen B, Ivanov I, Park JM, Parrinello M, Klein ML. 2002 Solvation structure and mobility mechanism of OH-: a Car-Parrinello molecular dynamics investigation of alkaline solutions. J. Phys. Chem. B 106, 12 006-12 016. (doi:10.1021/jp026504w)
138. Pasquarello A et al. 2001 First solvation shell of the Cu(ii) aqua ion: evidence for fivefold coordination. Science 291, 856-859. (doi:10.1126/science. 291.5505.856)
139. Swaddle TW, Rosenqvist J, Yu P, Bylaska E, Phillips BL, CaseyWH. 2005 Kinetic evidence for five-coordination in AlOH(aq)2+ ion. Science 308, 1450-1453. (doi:10.1126/science.1110231)
140. Akitt JW, Elders JM. 1985 Aluminium-27 nuclear magnetic resonance studies of the hydrolysis of aluminium(iii). Part 7. Spectroscopic evidence for the cation [AlOH]+2 from line-broadening studies at high dilution. J. Chem. Soc. Faraday Trans. 1 81, 1923-1930. (doi:10.1039/f19858101923)
141. Kloprogge JT, Seykens D, Geus JW, Jansen BH. 1993 The effects of concentration and hydrolysis on the oligomerization and polymerization of Al(iii) as evident from the 27Al NMR chemical shifts and linewidths. J. Non-Cryst. Solids 160, 144-151. (doi:10.1016/ 0022-3093(93)90294-8)
142. Faust BC, Labiosa WB, Dai KH, MacFall JS, Browne BA, Ribeiro AA, Richter DD. 1995 Speciation of aqueous mononuclear Al(iii)-hydroxo and other Al(iii) complexes at concentrations of geochemical relevance by aluminum-27 nuclear magnetic resonance spectroscopy. Geochim. Cosmochim. Acta 59, 2651-2661. (doi:10.1016/0016-7037(95)00162-S)
143. Vuilleumier R, Sprik M. 2001 Electronic properties of hard and soft ions in solution: aqueous Na+ and Ag+ compared. J. Chem. Phys. 115, 3454-3468. (doi:10.1063/1.1388901)
144. Blumberger J, Bernasconi L, Tavernelli I, Vuilleumier R, Sprik M. 2004 Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction. J. Am. Chem. Soc. 126, 3928-3938. (doi:10.1021/ja0390754)
145. Blumberger J, Sprik M. 2004 Free energy of oxidation of metal aqua ions by an enforced change of coordination. J. Phys. Chem. B 108, 6529-6535. (doi:10.1021/jp036610d)
146. Ensing B, Buda F, Blochl PE, Baerends EJ. 2002 A Car-Parrinello study of the formation of oxidizing intermediates from Fenton's reagent in aqueous solution. Phys. Chem. Chem. Phys. 4, 3619-3627. (doi:10.1039/b201864k)
147. Amira S, Spangberg D, Zelin V, Probst C, Hermansson K. 2005 Car-Parrinello molecular dynamics simulation of Fe3+(aq). J. Phys. Chem. B 109, 14 235-14 242. (doi:10.1021/jp050186u)
148. Sit PH-L, Cococcioni M, Marzari N. 2007 Car-Parrinello molecular dynamics in the DFT+u formalism: structure and energetics of solvated ferrous and ferric ions. J. Electroanal. Chem. 607, 107-112. (doi:10.1016/j.jelechem.2007.01.008)
149. Yazyev O, Helm L. 2006-03-01 Hyperfine interactions in aqueous solution of Cr3+: an ab initio molecular dynamics study. Theor. Chem. Acc. 115, 190-195. (doi:10.1007/s00214-005-0052-6)
150. Spezia R, Duvail M, Vitorge P, Cartailler T, Tortajada J, Chillemi G, D'Angelo P, Gaigeot M-P. 2006 A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co2+. J. Phys. Chem. A 110, 13 081-13 088. (doi:10.1021/jp064688z)
151. Beret EC, Martinez JM, Pappalardo RR, Marcos ES, Doltsinis NL, Marx D. 2008 Explaining asymmetric solvation of Pt(ii) versus Pd(ii) in aqueous solution revealed by ab initio molecular dynamics simulations. J. Chem. Theory Comp. 4, 2108-2121. (doi:10.1021/ ct800010q)
152. Beret EC, Pappalardo RR, Doltsinis NL, Marx D, Marcos ES. 2008 Aqueous PdII and PtII: anionic hydration revealed by Car-Parrinello simulations. Chem. Phys. Chem. 9, 237-240. (doi:10.1002/cphc.200700435)
153. Tavernelli I, Vuilleumier R, Sprik M. 2002 Ab initio molecular dynamics for molecules with variable numbers of electrons. Phys. Rev. Lett. 88, 213002. (doi:10.1103/PhysRevLett. 88.213002)
154. Bühl M, Parrinello M. 2001 Medium effects on 51v NMR chemical shifts: a density functional study. Chem. Eur. J. 7, 4487-4494. (doi:10.1002/1521-3765(20011015)7:20<4487:: AID-CHEM4487>3.0.CO;2-G)
155. Bühl M. 2005 Molecular dynamics of a vanadate-dipeptide complex in aqueous solutions. Inorg. Chem. 44, 6277-6283. (doi:10.1021/ic050694i)
156. Sadoc A, Messaoudi S, Furet E, Gautier R, Le Fur E, le Pollès L, Pivan J-Y. 2007 Structure and stability of VO+2 in aqueous solution: a Car-Parrinello and static ab initio study. Inorg. Chem. 46, 4835-4843. (doi:10.1021/ic0614519)
157. BühlM. 2002 Structure, dynamics, and magnetic shieldings of permanganate ion in aqueous solution. A density functional study. J. Phys. Chem. A 106, 10 505-10 509. (doi:10.1021/ jp026441h)
158. Bühl M, Mauschick FT. 2002 Thermal and solvent effects on 57Fe NMR chemical shifts. Phys. Chem. Chem. Phys. 4, 5508-5514. (doi:10.1039/B202894H)
159. Bühl M, Mauschick FT, Terstegen F, Wrackmeyer B. 2002 Remarkably large geometry dependence of 57Fe NMR chemical shifts. Angew. Chem. Int. Ed. 41, 2312-2315. (doi:10.1002/ 1521-3773(20020703)41:13<2312::AID-ANIE2312>3.0. CO;2-P)
160. BühlM, Grigoleit S, Kabrede H, Mauschick FT. 2006 Simulation of 59Co NMR chemical shifts in aqueous solution. Chem. Eur. J. 12, 477-488. (doi:10.1002/chem.200500285)
161. Vilà-Nadal L, Wilson EF, Miras HN, Rodríguez-Fortea A, Cronin L, Poblet JM. 2011 Combined theoretical and mass spectrometry study of the formation-fragmentation of small polyoxomolybdates. Inorg. Chem. 50, 7811-7819. (doi:10.1021/ic200969h)
162. BühlM, Kabrede H. 2006 Mechanism of water exchange in aqueous uranyl(vi) ion. a density functional molecular dynamics study. Inorg. Chem. 45, 3834-3836. (doi:10.1021/ic060156l)
163. Bühl M, Golubnychiy V. 2007 Binding of pertechnetate to uranyl(vi) in aqueous solution. A density functional theory molecular dynamics study. Inorg. Chem. 46, 8129-8131. (doi:10.1021/ic701431u)
164. Bühl M, Sieffert N, Golubnychiy V, Wipff G. 2008 Density functional theory study of uranium(vi) aquo chloro complexes in aqueous solution. J. Phys. Chem. A 112, 2428-2436. (doi:10.1021/jp710093w)
165. BühlM, Schreckenbach G. 2010 Oxygen exchange in uranyl hydroxide via two 'nonclassical' ions. Inorg. Chem. 49, 3821-3827. (doi:10.1021/ic902508z)
166. Bühl M, Grenthe I. 2011 Binding modes of oxalate in UO2(oxalate) in aqueous solution studied with first-principles molecular dynamics simulations. Implications for the chelate effect. Dalton Trans. 40, 11 192-11 199. (doi:10.1039/c1dt10796h)
167. Wrackmeyer B, Tok OL, Herberhold M. 2001 57Fe NMR of ferrocenes by 1h 57Fe inept techniques. Organometallics 20, 5774-5776. (doi:10.1021/om010756m)
168. De Angelis F, Tarantelli F, Alunni S. 2006 Ab initio molecular dynamics simulations of elimination reactions in water solution: exploring the borderline region between the E1cb and E2 reaction mechanisms. J. Phys. Chem. B 110, 11 014-11 019. (doi:10.1021/jp061321l)
169. Ensing B, Meijer EJ, Blöchl PE, Baerends EJ. 2001 Solvation effects on the SN2 reaction between CH3Cl and Cl- in water. J. Phys. Chem. A 105, 3300-3310. (doi:10.1021/jp003468x)
170. Ensing B, Buda F, Baerends EJ. 2003 Fenton-like chemistry in water: oxidation catalysis by Fe(iii) and H2O2. J. Phys. Chem. A 107, 5722-5731. (doi:10.1021/jp0267149)
171. Ensing B, Buda F, Gribnau MCM, Baerends EJ. 2004 Methane-to-methanol oxidation by the hydrated iron(iv) oxo species in aqueous solution: a combined DFT and Car-Parrinello molecular dynamics study. J. Am. Chem. Soc. 126, 4355-4365. (doi:10.1021/ja038865a)
172. Louwerse MJ, Vassilev P, Baerends EJ. 2008 Oxidation of methanol by FeO2+ in water: DFT calculations in the gas phase and ab initio MD simulations in water solution. J. Phys. Chem. A 112, 1000-1012. (doi:10.1021/jp075914n)
173. Sulpizi M, Sprik M. 2008 Acidity constants from vertical energy gaps: density functional theory based molecular dynamics implementation. Phys. Chem. Chem. Phys. 10, 5238-5249. (doi:10.1039/b802376j)
174. DoltsinisNL, SprikM. 2003 Theoretical pKa estimates for solvated p(OH)5 from coordination constrained Car-Parrinello molecular dynamics. Phys. Chem. Chem. Phys. 5, 2612-2618. (doi:10.1039/b301994b)
175. Ivanov I, Chen B, Raugei S, Klein ML. 2006 Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation. J. Phys. Chem. B 110, 6365-6371. (doi:10.1021/jp056750i)
176. Cheng J, Sulpizi M, Sprik M. 2009 Redox potentials and pka for benzoquinone from density functional theory based molecular dynamics. J. Chem. Phys. 131, 154504. (doi:10.1063/1.3250438)
177. Davies JE, Doltsinis NL, Kirby AJ, Roussev CD, Sprik M. 2002 Estimating pKa values for pentaoxyphosphoranes. J. Am. Chem. Soc. 124, 6594-6599. (doi:10.1021/ja025779m)
178. Chen Y-L, Doltsinis NL, Hider RC, Barlow DJ. 2012 Prediction of absolute hydroxyl pka values for 3-hydroxypyridin-4-ones. J. Phys. Chem. Lett. 3, 2980-2985. (doi:10.1021/ jz301061m)
179. Chang T-M, Dang LX. 2006 Recent advances in molecular simulations of ion solvation at liquid interfaces. Chem. Rev. 106, 1305-1322. (doi:10.1021/ cr0403640)
180. Mundy CJ, Kuo I-FW. 2006 First-principles approaches to the structure and reactivity of atmospherically relevant aqueous interfaces. Chem. Rev. 106, 1282-1304. (doi:10.1021/ cr040375t)
181. Zaera F. 2012 Probing liquid/solid interfaces at the molecular level. Chem. Rev. 112, 2920-2986. (doi:10.1021/cr2002068)
182. Pal SK, Zewail AH. 2004 Dynamics of water in biological recognition. Chem. Rev. 104, 2099-2124. (doi:10.1021/cr020689l)
183. Bagchi B. 2005 Water dynamics in the hydration layer around proteins and micelles. Chem. Rev. 105, 3197-3219. (doi:10.1021/cr020661+)
184. Petersen PB, Saykally RJ. 2005 Evidence for an enhanced hydronium concentration at the liquid water surface. J. Phys. Chem. B 109, 7976-7980. (doi:10.1021/jp044479j)
185. Buch V, Milet A, Vcha R, Jungwirth P, Devlin JP. 2007Water surface is acidic. Proc. Natl Acad. Sci. USA 104, 7342-7347. (doi:10.1073/pnas.0611285104)
186. Beattie JK, Djerdjev AM, Warr GG. 2009 The surface of neat water is basic. Faraday Discuss. 141, 31-39. (doi:10.1039/b805266b)
187. Kathmann SM, Kuo I-FW, Mundy CJ. 2008 Electronic effects on the surface potential at the vapor-liquid interface of water. J. Am. Chem. Soc. 130, 16 556-16 561. (doi:10.1021/ja802851w)
188. Vcha R, Marsalek O, Willard AP, Bonthuis DJ, Netz RR, Jungwirth P. 2012 Charge transfer between water molecules as the possible origin of the observed charging at the surface of pure water. J. Phys. Chem. Lett. 3, 107-111. (doi:10.1021/jz2014852)
189. Mundy CJ, Kuo I-FW, Tuckerman ME, Lee H-S, Tobias DJ. 2009 Hydroxide anion at the air- water interface. Chem. Phys. Lett. 481, 2-8. (doi:10.1016/j.cplett.2009.09.003)
190. Kühne TD, Pascal TA, Kaxiras E, Jung Y. 2011 New insights into the structure of the vapor/water interface from large-scale first-principles simulations. J. Phys. Chem. Lett. 2, 105-113. (doi:10.1021/jz101391r)
191. Eisenthal KB. 1996 Liquid interfaces probed by second-harmonic and sum-frequency spectroscopy. Chem. Rev. 96, 1343-1360. (doi:10.1021/cr9502211)
192. Richmond GL. 2002 Molecular bonding and interactions at aqueous surfaces as probed by vibrational sum frequency spectroscopy. Chem. Rev. 102, 2693-2724. (doi:10.1021/cr0006876)
193. Tarbuck TL, Ota ST, Richmond GL. 2006 Spectroscopic studies of solvated hydrogen and hydroxide ions at aqueous surfaces. J. Am. Chem. Soc. 128, 14 519-14 527. (doi:10.1021/ ja063184b)
194. Takahashi M. 2005 ζ potential of microbubbles in aqueous solutions: electrical properties of the gas-water interface. J. Phys. Chem. B 109, 21 858-21 864. (doi:10.1021/jp0445270)
195. Iarlori S, Ceresoli D, Bernasconi M, Donadio D, Parrinello M. 2001 Dehydroxylation and silanization of the surfaces of β-cristobalite silica: an ab initio simulation. J. Phys. Chem. B 105, 8007-8013. (doi:10.1021/ jp010800b)
196. Adeagbo WA, Doltsinis NL, Klevakina K, Renner J. 2008 Transport processes at α- quartzwater interfaces: insights from first-principles molecular dynamics simulations. Chem. Phys. Chem 9, 994-1002. (doi:10.1002/cphc.200700819)
197. Leung K, Nielsen IMB, Criscenti LJ. 2009 Elucidating the bimodal acid base behavior of the water silica interface from first principles. J. Am. Chem. Soc. 131, 18 358-18 365. (doi:10.1021/ ja906190t)
198. Skelton AA, Wesolowski DJ, Cummings PT. 2011 Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics. Langmuir 27, 8700-8709. (doi:10.1021/la2005826)
199. Skelton AA, Fenter P, Kubicki JD, Wesolowski DJ, Cummings PT. 2011 Simulations of the quartz(1011)/water interface: a comparison of classical force fields, ab initio molecular dynamics, and X-ray reflectivity experiments. J. Phys. Chem. C 115, 2076-2088. (doi:10.1021/jp109446d)
200. Sulpizi M, Gaigeot M-P, Sprik M. 2012 The silica water interface: how the silanols determine the surface acidity and modulate the water properties. J. Chem. Theory Comput. 8, 1037-1047. (doi:10.1021/ct2007154)
201. Hassanali AA, Zhang H, Knight C, Shin YK, Singer SJ. 2010 The dissociated amorphous silica surface: model development and evaluation. J. Chem. Theory Comput. 6, 3456-3471. (doi:10.1021/ct100260z)
202. Tilocca A, Cormack AN. 2009 Modeling the water bioglass interface by ab initio molecular dynamics simulations. ACS Appl. Mater. Interfaces 1, 1324-1333. (doi:10.1021/am900198t)
203. Zhang C, Lindan PJD. 2003 Multilayer water adsorption on rutile TiO2(110): a first-principles study. J. Chem. Phys. 118, 4620-4630. (doi:10.1063/1.1543983)
204. Kumar N, Neogi S, Kent PRC, Bandura AV, Kubicki JD, Wesolowski DJ, Cole D, Sofo JO. 2009 Hydrogen bonds and vibrations of water on (110) rutile. J. Phys. Chem. C 113, 13 732-13 740. (doi:10.1021/jp901665e)
205. Cheng H, Selloni A. 2010 Hydroxide ions at the water/anatase TiO2(101) interface: structure and electronic states from first principles molecular dynamics. Langmuir 26, 11 518-11 525. (doi:10.1021/la100672f)
206. Cheng J, Sprik M. 2010 Acidity of the aqueous rutile TiO2(110) surface from density functional theory based molecular dynamics. J. Chem. Theory Comput. 6, 880-889. (doi:10.1021/ct100013q)
207. Liu L-M, Zhang C, Thornton G, Michaelides A. 2010 Structure and dynamics of liquid water on rutile TiO2(110). Phys. Rev. B 82, 161415. (doi:10.1103/PhysRevB.82.161415)
208. Sun C, Liu L-M, Selloni A, Lu GQ, Smith SC. 2010 Titania-water interactions: a review of theoretical studies. J. Mater. Chem. 20, 10 319-10 334. (doi:10.1039/c0jm01491e)
209. Leung K, Criscenti LJ. 2012 Predicting the acidity constant of a goethite hydroxyl group from first principles. J. Phys. Condens. Matter 24, 124105. (doi:10.1088/0953-8984/24/12/124105)
210. Hass KC, Schneider WF, Curioni A, Andreoni W. 1998 The chemistry of water on alumina surfaces: reaction dynamics from first principles. Science 282, 265-268. (doi:10.1126/science.282.5387.265)
211. Scipioni R, Donadio D, Ghiringhelli LM, Delle Site L. 2011 Proton wires via onedimensional water chains adsorbed on metallic steps. J. Chem. Theory Comput. 7, 2681-2684. (doi:10.1021/ct200326u)
212. Tsuchida E, Kanada Y, Tsukada M. 1999 Density-functional study of liquid methanol. Chem. Phys. Lett. 311, 236-240. (doi:10.1016/S0009-2614(99)00851-9)
213. Handgraaf J-W, van Erp TS, Meijer EJ. 2003 Ab initio molecular dynamics study of liquid methanol. Chem. Phys. Lett. 367, 617-624. (doi:10.1016/S0009- 2614(02)01779-7)
214. Morrone JA, Tuckerman ME. 2002 Ab initio molecular dynamics study of proton mobility in liquid methanol. J. Chem. Phys. 117, 4403-4413. (doi:10.1063/1.1496457)
215. Pagliai M, Cardini G, Schettino V. 2005 Solvation dynamics of Li+ and Cl- ions in liquid methanol. J. Phys. Chem. B 109, 7475-7481. (doi:10.1021/ jp050428q)
216. Faralli C, PagliaiM, Cardini G, Schettino V. 2006 Structure and dynamics of Br- ion in liquid methanol. J. Phys. Chem. B 110, 14 923-14 928. (doi:10.1021/jp061230o)
217. Handgraaf J-W, Meijer EJ. 2007 Realistic modeling of ruthenium-catalyzed transfer hydrogenation. J. Am. Chem. Soc. 129, 3099-3103. (doi:10.1021/ ja062359e)
218. Faralli C, Pagliai M, Cardini G, Schettino V. 2007 Ab initio molecular dynamics study of Mg2+ and Ca2+ ions in liquid methanol. J. Chem. Theory Comput. 4, 156-163. (doi:10.1021/ct700209v)
219. Faralli C, Pagliai M, Cardini G, Schettino V. 2007 The solvation dynamics of Na+ and K+ ions in liquid methanol. Theor. Chem. Acc. 118, 417-423. (doi:10.1007/s00214-007-0286-6)
220. Pagliai M, Muniz-Miranda F, Cardini G, Righini R, Schettino V. 2010 Hydrogen bond dynamics of methyl acetate in methanol. J. Phys. Chem. Lett. 1, 2951-2955. (doi:10.1021/ jz1010994)
221. Martyna GJ, Deng Z, Klein ML. 1993 Quantum simulation studies of singlet and triplet bipolarons in liquid ammonia. J. Chem. Phys. 98, 555-563. (doi:10.1063/1.464650)
222. Diraison M, Martyna GJ, Tuckerman ME. 1999 Simulation studies of liquid ammonia by classical ab initio, classical, and path-integral molecular dynamics. J. Chem. Phys. 111, 1096-1103. (doi:10.1063/1.479194)
223. Daniel Boese A, Chandra A, Martin JML, Marx D. 2003 From ab initio quantum chemistry to molecular dynamics: the delicate case of hydrogen bonding in ammonia. J. Chem. Phys. 119, 5965-5980. (doi:10.1063/1.1599338)
224. Rothlisberger U, Parrinello M. 1997 Ab initio molecular dynamics simulation of liquid hydrogen fluoride. J. Chem. Phys. 106, 4658-4664. (doi:10.1063/1.473988)
225. Kim D, Klein ML. 1999 Liquid hydrogen fluoride with an excess proton: ab initio molecular dynamics study of a superacid. J. Am. Chem. Soc. 121, 11 251-11 252. (doi:10.1021/ja993098u)
226. Dubois V, Pasquarello A. 2005 Ab initio molecular dynamics of liquid hydrogen chloride. J. Chem. Phys. 122, 114512. (doi:10.1063/1.1869972)
227. Vilčiauskas L, Tuckerman ME, Bester G, Paddison SJ, Kreuer K-D. 2012 The mechanism of proton conduction in phosphoric acid. Nat. Chem. 4, 461-466. (doi:10.1038/nchem.1329)
228. Torrie GM, Valleau JP. 1977 Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23, 187-199. (doi:10.1016/0021-9991(77)90121-8)
229. Laio A, Parrinello M. 2002 Escaping free-energy minima. Proc. Natl Acad. Sci. USA 99, 12 562-12 566. (doi:10.1073/pnas.202427399)
230. Iannuzzi M, Laio A, Parrinello M. 2003 Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys. Rev. Lett. 90, 238302. (doi:10.1103/PhysRevLett.90.238302)
231. Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. 2005 Assessing the accuracy of metadynamics. J. Phys. Chem. B 109, 6714-6721. (doi:10.1021/jp045424k)
232. Laio A, Gervasio FL. 2008 Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys. 71, 126601. (doi:10.1088/0034-4885/71/12/126601)
233. Barducci A, Bonomi M, Parrinello M. 2011 Metadynamics. WIREs Comput. Mol. Sci. 1, 826-843. (doi:10.1002/wcms.31)
234. Barducci A, Bussi G, Parrinello M. 2008 Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys. Rev. Lett. 100, 020603. (doi:10.1103/PhysRevLett.100.020603)
235. Ensing B, De Vivo M, Liu Z, Moore P, Klein ML. 2005 Metadynamics as a tool for exploring free energy landscapes of chemical reactions. Acc. Chem. Res. 39, 73-81. (doi:10.1021/ar040198i)
236. Bonomi M. 2009 Plumed: a portable plugin for free-energy calculations with molecular dynamics. Comput. Phys. Commun. 180, 1961-1972. (doi:10.1016/j.cpc.2009.05.011)
237. Park JM, Laio A, Iannuzzi M, Parrinello M. 2006 Dissociation mechanism of acetic acid in water. J. Am. Chem. Soc. 128, 11 318-11 319. (doi:10.1021/ja060454h)
238. Vilà-Nadal L, Rodríguez-Fortea A, Yan L-K, Wilson EF, Cronin L, Poblet JM. 2009 Nucleation mechanisms of molecular oxides: a study of the assembly-dissassembly of [W6O19]2- by theory and mass spectrometry. Angew. Chem. Int. Edn 48, 5452-5456.
239. Vilà-Nadal L, Rodríguez-Fortea A, Poblet JM. 2009 Theoretical analysis of the possible intermediates in the formation of [W6O19]2-. Eur. J. Inorg. Chem. 2009, 5125-5133. (doi:10.1002/ejic.200900714)
240. Blumberger J, Klein ML. 2006 Revisiting the free energy profile for the nucleophilic attack of hydroxide on formamide in aqueous solution. Chem. Phys. Lett. 422, 210-217. (doi:10.1016/j.cplett.2006.02.035)
241. Blumberger J, Ensing B, Klein ML. 2006 Formamide hydrolysis in alkaline aqueous solution: insight from ab initio metadynamics calculations. Angew. Chem. Int. Edn 45, 2893-2897. (doi:10.1002/anie.200600283)
242. Gunaydin H, Houk KN. 2008 Molecular dynamics prediction of the mechanism of ester hydrolysis in water. J. Am. Chem. Soc. 130, 15 232-15 233. (doi:10.1021/ja8050525)
243. Lau JK-C, Ensing B. 2010 Hydrolysis of cisplatin-a first-principles metadynamics study. Phys. Chem. Chem. Phys. 12, 10 348-10 355. (doi:10.1039/b918301a)
244. Kulik HJ, Schwegler E, Galli G. 2012 Probing the structure of salt water under confinement with first-principles molecular dynamics and theoretical x-ray absorption spectroscopy. J. Phys. Chem. Lett. 3, 2653-2658. (doi:10.1021/jz300932p)