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Density Functional Theory Based Ab Initio Molecular Dynamics Using the Car-Parrinello Approach

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Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1

Part of the book series: Lecture Notes in Physics ((LNP,volume 703))

Abstract

Ab initio Molecular Dynamics (MD) on the contrary to empirical force field Molecular Dynamics simulations employs an electronic structure calculation at each time-step of the dynamics to determine the forces on the nuclei. This allows for the simulation of materials in a broad range of situations, including during chemical reactions, while chemical bonds are broken or formed. The last few years, use of ab initio MD has spread very rapidly to many fields and is now used by many groups. At the same time many new developments have been pursued including, e.g., the calculation of electronic properties. Ab initio MD is also an integrated part of a new range of techniques to bridge length and time scales: QM/MM, transition path sampling, metadynamics etc. many of whose are discussed in this book.

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References

  1. D. Frenkel and B. Smit (2001) Understanding Molecular Simulation. Academic Press, London

    Google Scholar 

  2. R. Car and M. Parrinello (1985) Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett. 55, p. 2471

    Article  ADS  Google Scholar 

  3. A. Curioni, M. Sprik, W. Andreoni, H. Schiffer, J. Hutter, and M. Parrinello (1997) Density functional theory-based molecular dynamics simulation of acidcatalyzed chemical reactions in liquid trioxane. J. Am. Chem. Soc. 119, p. 7218

    Article  Google Scholar 

  4. E. J. Meijer and M. Sprik (1998) A Density Functional Study of the Addition of Water to SO3 in the Gas Phase and in Aqueous Solution. J. Phys. Chem. A 102, p. 2893

    Article  Google Scholar 

  5. E. J. Meijer and M. Sprik (1998) Ab Initio Molecular Dynamics Study of the Addition Reaction of Water to Formaldehyde in Sulfuric Acid Solution. J. Am. Soc. Chem. 120, p. 6345

    Article  Google Scholar 

  6. M. Sprik (2000) Computation of the pK of liquid water using coordination constraints. Chem. Phys. 258, p. 139

    Article  ADS  Google Scholar 

  7. K. Doclo and U. Rothlisberger (2000) Conformational Equilibria of Peroxynitrous Acid in Water: A First-Principles Molecular Dynamics Study. J. Phys. Chem. A 104, p. 6464

    Article  Google Scholar 

  8. P. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello (2001) Autoionization in Liquid Water. Science 291, p. 2121

    Article  ADS  Google Scholar 

  9. B. Ensing, E. J. Meijer, P. E. Blochl, and E. J. Baerends (2001) Solvation effects on the SN2 Reaction between CH3Cl and Cl- in Water. J. Phys. Chem. A. 105, p. 3300

    Article  Google Scholar 

  10. N. L. Doltsinis and M. Sprik (2003) Theoretical pKa estimates for solvated P(OH)5 from coordination constrained Car-Parrinello dynamics. Phys. Chem. Chem. Phys. 5, p. 2612

    Article  Google Scholar 

  11. J. Blumberger, L. Bernasconi, I. Tavernelli, R. Vuilleumier, and M. Sprik (2004) Electronic structure and solvation of copper and silver ions: A theoretical picture of a model aqueous redox reaction. J. Am. Chem. Soc. 126, p. 3928

    Article  Google Scholar 

  12. J. Blumberger and M. Sprik (2004) Free energy of oxidation of metal aqua Ions by an enforced change of Coordination. J. Phys. Chem. B. 108, p. 6529

    Article  Google Scholar 

  13. P. R. L. Markwick, N. L. Doltsinis, and D. Marx (2005) Targeted Car-Parrinello molecular dynamics: Elucidating double proton transfer in formic acid dimer. J. Chem. Phys. 122, 054112

    Article  ADS  Google Scholar 

  14. Y. Tateyama, J. Blumberger, M. Sprik, and I. Tavernelli (2005) Density functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes. J. Chem. Phys. 122, p. 234505

    Article  ADS  Google Scholar 

  15. F. Zipoli, M. Bernasconi, and A. Laio (2005) Ab initio simulations of Lewisacid- catalyzed hydrosilylation of alkynes. Chem. Phys. Chem. 6, p. 1772

    Google Scholar 

  16. A. D. Vita, G. Galli, A. Canning, and R. Car (1996) A microscopic model for surface-induced diamond-to-graphite transitions. Nature 379, p. 523

    Article  ADS  Google Scholar 

  17. C. Cavazzoni, G. L. Chiarotti, S. Scandolo, E. Tosatti, M. Bernasconi, and M. Parrinello (1999) Superionic and metallic states of water and ammonia at giant planet conditions. Science 283, p. 44

    Article  ADS  Google Scholar 

  18. R. Rousseau, M. Boero, M. Bernasconi, M. Parrinello, and K. Terakura (2000) Ab initio Simulation of Phase Transitions and Dissociation of H2S at High Pressure. Phys. Rev. Lett. 85, p. 1254

    Article  ADS  Google Scholar 

  19. D. D. Klug, R. Rousseau, K. Uehara, M. Bernasconi, Y. L. Page, and J. S. Tse (2001) Ab initio molecular dynamics study of the pressure-induced phase transformations in cristobalite. Phys. Rev. B 63, p. 104106

    Article  ADS  Google Scholar 

  20. C. J. Wu, J. N. Glosli, G. Galli, and F. H. Ree (2002) Liquid-liquid phase transition in elemental carbon: A first-principles investigation. Phys. Rev. Lett. 89, p. 135701

    Article  ADS  Google Scholar 

  21. L. M. Ghiringhelli and E. J. Meijer (2005) Phosphorus: First principle simulation of a liquid–liquid phase transition. J. Chem. Phys. 122, p. 184510

    Article  ADS  Google Scholar 

  22. F. Zipoli, M. Bernasconi, and R. Martoňák (2004) Constant pressure reactive molecular dynamics simulations of phase transitions under pressure: The graphite to diamond conversion revisited. Eur. Phys. J. B 39, p. 41

    Article  ADS  Google Scholar 

  23. M. McGrath, J. Siepmann, I.-F. W. Kuo, C. J. Mundy, J. VandeVondele, M. Sprik, J. Hutter, F. Mohamed, M. Krack, and M. Parrinello (2005) Toward a Monte Carlo program for simulating vapor-liquid phase equilibria from first principles. Comp. Phys. Comm. 169, p. 289

    Article  ADS  Google Scholar 

  24. R. Martoňák, A. Laio, M. Bernasconi, C. Ceriani, P. Raiteri, F. Zipoli, and M. Parrinello (2005) Simulation of structural phase transitions by metadynamics. Zeitschrift für Kristallographie 220, p. 489

    Article  Google Scholar 

  25. T. Ikeda, M. Sprik, K. Terakura, and M. Parrinello (1998) Pressure effects on Hydrogen Bonding in the Disordered Phase of Solid Hbr. Phys. Rev. Lett. 81, p. 4416

    Article  ADS  Google Scholar 

  26. T. Ikeda, M. Sprik, K. Terakura, and M. Parrinello (2000) Hydrogen elimination and solid-state reaction in hydrogen-bonded systems under pressure: The case of Hbr. J. Phys. Chem. B 104, p. 11801

    Article  Google Scholar 

  27. M. Benoit, A. H. Romero, and D. Marx (2002) Reassigning Hydrogen-Bond Centering in Dense Ice. Phys. Rev. Lett. 89, p. 145501

    Article  ADS  Google Scholar 

  28. A. Pasquarello and R. Resta (2003) Dynamical monopoles and dipoles in a condensed molecular system: The case of liquid water. Phys. Rev. B 68, p. 174302

    Article  ADS  Google Scholar 

  29. M. Sharma, R. Resta, and R. Car (2005) Intermolecular Dynamical Charge Fluctuations in Water: A Signature of the H-Bond Network. Phys. Rev. Lett. 95, p. 187401

    Article  ADS  Google Scholar 

  30. M. McGrath, J. Siepmann, I.-F. W. Kuo, C. J. Mundy, J. VandeVondele, J. Hutter, F. Mohamed, and M. Krack (2005) First Principles: Application to Liquid Water at Ambient Conditions. Chem. Phys. Chem. 6, p. 1894

    Google Scholar 

  31. K. Laasonen, M. Sprik, M. Parrinello, and R. Car (1993) Ab initio liquid water. J. Chem. Phys. 99, p. 9080

    Article  ADS  Google Scholar 

  32. J. C. Grossman, E. Schwegler, E. W. Draeger, F. Gygi, and G. Galli (2004) Towards an assessment of the accuracy of density functional theory for first principles simulations of water. J. Chem. Phys. 120, p. 300

    Article  ADS  Google Scholar 

  33. E. Schwegler, J. C. Grossman, F. Gygi, and G. Galli (2004) Towards an assessment of the accuracy of density functional theory for first principles simulations of water. II. J. Chem. Phys. 121, p. 5400

    Article  ADS  Google Scholar 

  34. I. Bakó, J. Hutter, and G. P´link´s (2002) Car-Parrinello molecular dynamics simulation of the hydrated calcium ion. J. Chem. Phys. 117, p. 9838

    Article  ADS  Google Scholar 

  35. M. Cavalleri, M. Odelius, A. Nilsson, and L. G. M. Pettersson (2004) X-ray absorption spectra of water within a plane-wave Car-Parrinello molecular dynamics framework. J. Chem. Phys. 121, p. 10065

    Article  ADS  Google Scholar 

  36. M. Allesch, E. Schwegler, F. Gygi, and G. Galli (2004) A first principles simulation of rigid water. J. Chem. Phys. 120, p. 5192

    Article  ADS  Google Scholar 

  37. P. H.-L. Sit and N. Marzari (2005) Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics. J. Chem. Phys. 122, p. 204510

    Article  ADS  Google Scholar 

  38. I.-F. W. Kuo, C. J. Mundy, M. J. McGrath, J. I. Siepmann, J. VandeVondele, M. Sprik, J. Hutter, B. Chen, M. L. Klein, F. Mohamed, M. Krack, and M. Parrinello (2004) Liquid water from first principles, investigation of different sampling approaches. J. Phys. Chem. B 108, p. 12990

    Article  Google Scholar 

  39. J. VandeVondele, F. Mohamed, M. Krack, J. Hutter, M. Sprik, and M. Parrinello (2005) The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J. Chem. Phys. 122, 014515

    Article  ADS  Google Scholar 

  40. D. Marx, J. Hutter, and M. Parrinello (1995) Density functional study of small aqueous Be2+ clusters. Chem. Phys. Lett. 241, p. 457

    Article  ADS  Google Scholar 

  41. M. E. Tuckerman, K. Laasonen, M. Sprik, and M. Parrinello (1995) Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water. J. Phys. Chem. 99, p. 5749

    Article  Google Scholar 

  42. D. Marx, M. Sprik, and M. Parrinello (1997) Ab initio molecular dynamics of ion solvation. The case of Be2+ in water. Chem. Phys. Lett. 273, p. 360

    Article  ADS  Google Scholar 

  43. D. Marx, M. Tuckerman, J. Hutter, and M. Parrinello (1999) The nature of the hydrated excess proton in water. Nature 397, p. 601

    Article  ADS  Google Scholar 

  44. M. Tuckerman, K. Laasonen, M. Sprik, and M. Parrinello (1995) Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J. Chem. Phys. 103, p. 150

    Article  ADS  Google Scholar 

  45. L. M. Ramaniah, M. Bernasconi, and M. Parrinello (1999) Ab initio molecular dynamics simulation of K+ solvation in water. J. Chem. Phys. 111, p. 1587

    Article  ADS  Google Scholar 

  46. C. J. Mundy, J. Hutter, and M. Parrinello (2000) Microsolvation and chemical reactivity of sodium and water clusters. J. Am. Chem. Soc. 122, p. 4837

    Article  Google Scholar 

  47. R. Vuilleumier and M. Sprik (2001) Electronic properties of hard and soft ions in solution: Aqueous Na+ and Ag+ compared. J. Chem. Phys. 115, p. 3454

    Article  ADS  Google Scholar 

  48. Z.-P. Liu, P. Hu, and A. Alavi (2001) Mechanism for the high reactivity of CO oxidation on a ruthenium-oxide. J. Chem. Phys. 114, p. 5956

    Article  ADS  Google Scholar 

  49. T. S. van Erp and E. J. Meijer (2003) Ab initio molecular dynamics study of aqueous solvation of ethanol and ethylene. J. Chem. Phys. 118, p. 8831

    Article  ADS  Google Scholar 

  50. J. M. Heuft and E. J. Meijer (2003) Density functional theory based molecular dynamics study of aqueous chloride solvation. J. Chem. Phys. 119, p. 11788

    Article  ADS  Google Scholar 

  51. M. E. Tuckerman, D. Marx, and M. Parrinello (2002) The nature and transport mechanism of hydrated hydroxide ions in aqueous solution. Nature 417, p. 925

    Article  ADS  Google Scholar 

  52. B. Kirchner, J. Stubbs, and D. Marx (2002) Fast Anomalous diffusion of Small Hydrophobic Species in Water. Phys. Rev. Lett. 89, p. 215901

    Article  ADS  Google Scholar 

  53. B. Kirchner and J. Hutter (2002) The structure of a DMSO/Water mixture from Car-Parrinello simulations. Chem. Phys. Lett. 364, p. 497

    Article  ADS  Google Scholar 

  54. T. Ikeda, M. Hirata, and T. Kimura (2005) Hydration of Y3+ ion: A Car-Parrinello molecular dynamics study. J. Chem. Phys. 122, 024510

    Article  ADS  Google Scholar 

  55. S. Izvekov and G. A. Voth (2005) Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited. J. Chem. Phys. 123, 044505

    Article  ADS  Google Scholar 

  56. M. Boero, M. Parrinello, K. Terakura, T. Ikeshoji, and C. C. Liew (2003) First-Principles Molecular-Dynamics Simulations of a Hydrated Electron in Normal and Supercritical Water. Phys. Rev. Lett. 90, p. 226403

    Article  ADS  Google Scholar 

  57. C. Nicolas, R. Spezia, A. Boutin, and R. Vuilleumier (2003) Molecular Dynamics simulations of a silver atom in water: dipolar excitonic state evidence. Phys. Rev. Lett. 91, p. 208304

    Article  ADS  Google Scholar 

  58. M.-P. Gaigeot and M. Sprik (2004) Ab initio molecular dynamics study of uracil in aqueous solution. J. Phys. Chem. B 108, p. 7458

    Article  Google Scholar 

  59. L. Bernasconi, M. Sprik, and J. Hutter (2004) Hartree-Fock exchange in time dependent density functional theory: Application to charge transfer excitations in solvated molecular systems. Chem. Phys. Lett. 394, p. 141

    Article  ADS  Google Scholar 

  60. F. C. Lightstone, E. Schwegler, M. Allesch, F. Gygi, and G. Galli (2005) A first-principles molecular dynamics study of calcium in water. Chem. Phys. Chem 6, p. 1745

    Google Scholar 

  61. J. M. Heuft and E. J. Meijer (2005) Density functional theory based molecular dynamics study of aqueous fluoride solvation. J. Chem. Phys. 122, 094501

    Article  ADS  Google Scholar 

  62. J. M. Heuft and E. J. Meijer (2005) Density functional theory based molecular dynamics study of aqueous iodide solvation. J. Chem. Phys. 123, 094506

    Article  ADS  Google Scholar 

  63. J. VandeVondele and M. Sprik (2005) A molecular dynamics study of the hydroxyl radical in solution applying self-interaction corrected density functional methods. Phys. Chem. Chem. Phys. 7, p. 1363

    Article  Google Scholar 

  64. P. Hunt and M. Sprik (2005) On the position of the highest molecular orbital in aqueous solutions of simple ions. Chem. Phys. Chem. 6, p. 1805

    Google Scholar 

  65. J. A. Morrone and M. E. Tuckerman (2002) Ab initio molecular dynamics study of proton mobility in liquid methanol. J. Chem. Phys. 117, p. 4403

    Article  ADS  Google Scholar 

  66. J.-W. Handgraaf, E. J. Meijer, and M.-P. Gaigeot (2004) Density-functional theory-based molecular simulation study of liquid methanol. J. Chem. Phys. 121, p. 10111

    Article  ADS  Google Scholar 

  67. J. VandeVondele, R. Lynden-Bell, E. J. Meijer, and M. Sprik (2006) Density functional theory study of tetrathiafulvalene and thianthrene in acetonitrile: structure, dynamics and redox properties. J. Phys. Chem. B 110, p. 3614

    Article  Google Scholar 

  68. A. Pasquarello, K. Laasonen, R. Car, C. Lee, and D. Vanderbilt (1992) Ab initio molecular dynamics for d-electron systems: Liquid copper at 1500 K. Phys. Rev. Lett. 69, p. 1982

    Article  ADS  Google Scholar 

  69. J. Sarnthein, A. Pasquarello, and R. Car (1995) Structural and Electronic Properties of Liquid and Amorphous SiO2: An Ab Initio Molecular Dynamics Study. Phys. Rev. Lett. 74, p. 4682

    Article  ADS  Google Scholar 

  70. P. Silvestrelli, A. Alavi, and M. Parrinello (1997) Electronic conductivity calculation in ab-initio simulations of metals. Application to liquid sodium. Phys. Rev. B 55, p. 15515

    Article  ADS  Google Scholar 

  71. M. Pohlmann, M. Benoit, and W. Kob (2004) First-principles molecular dynamics simulations of a hydrous silica melt: Structural properties and hydrogen diffusion mechanism. Phys. Rev. B 70, p. 184209

    Article  ADS  Google Scholar 

  72. M. Popolo, R. M. Lynden-Bell, and J. Kohanoff (2005) Ab Initio simulation of a room temperature ionic liquid. J. Phys. Chem. B 109, p. 5895

    Article  Google Scholar 

  73. F. Haase, J. Sauer, and J. Hutter (1997) Ab Initio Molecular Dynamics Simulation of Methanol Adsorbed in Chabazite. Chem. Phys. Lett. 266, p. 397

    Article  ADS  Google Scholar 

  74. A. Alavi, P. Hu, T. Deutsch, P. L. Silvestrelli, and J. Hutter (1998) CO Oxidation on Pt(111): An Ab Initio Density Functional Theory Study. Phys. Rev. Lett. 80, p. 3650

    Article  ADS  Google Scholar 

  75. A. Y. Lozovoi, A. Alavi, and M. Finnis (2000) Surface stoichiometry and the initial oxidation of NiAl(110). Phys. Rev. Lett. 85, p. 610

    Article  ADS  Google Scholar 

  76. P. Hu and A. Alavi (2001) Insight into electron-mediated reaction mechanisms: Catalytic CO oxidation on a ruthenium surface. J. Chem. Phys. 114, p. 8113

    Article  ADS  Google Scholar 

  77. E. S. Boek and M. Sprik (2003) Ab initio molecular dynamics study of the hydration of a sodium smectite clay. J. Phys. Chem. B 107, p. 3251

    Article  Google Scholar 

  78. X. Wu, A. Selloni, and S. K. Nayak (2004) First principles study of CO oxidation on TiO2 (110): The role of surface oxygen vacancies. J. Chem. Phys. 120, p. 4512

    Article  ADS  Google Scholar 

  79. M. W. Finnis, A. Lozovoi, and A. Alavi (2005) Ab initio calculations on the oxidation of NiAl, Annual Reviews of Materials Research 35, pp. 167–207

    Article  ADS  Google Scholar 

  80. M. Benoit, D. Marx, and M. Parrinello (1998) Tunnelling and zero-point motion in high-pressure ic. Nature 392, p. 258

    Article  ADS  Google Scholar 

  81. M. Benoit, D. Marx, and M. Parrinello (1999) The role of quantum effects and ionic defects in high-density ice. Solid State Ionics 125, p. 23

    Article  Google Scholar 

  82. A. Alavi, R. Lynden-Bell, and R. Brown (1999) Displacement and distortion of the ammonium ion in reorientational transition states of ammonium chloride and ammonium fluoride. J. Chem. Phys. 110, p. 5861

    Article  ADS  Google Scholar 

  83. A. Alavi, R. Lynden-Bell, and R. Brown (2000) Pathway for reorientation in ammonium fluoride. Chem. Phys. Lett. 320, p. 487

    Article  ADS  Google Scholar 

  84. S. Ispas, M. Benoit, P. Jund, and R. Jullien (2001) Structural and electronic properties of the sodium tetrasilicate glass Na2Si4O9 from classical and ab initio molecular dynamics simulations. Phys. Rev. B 64, p. 214206

    Article  ADS  Google Scholar 

  85. S. Ispas, M. Benoit, P. Jund, and R. Jullien (2002) Structural properties of glassy and liquid sodium tetrasilicate: comparison between ab initio and classical molecular dynamics simulations. Journal of Non-Crystalline Solids 307, p. 946

    Article  ADS  Google Scholar 

  86. J. Sarnthein, A. Pasquarello, and R. Car (1995) Model of vitreous SiO2 generated by an ab initio molecular-dynamics quench from the melt. Phys. Rev. B 52, p. 12690

    Article  ADS  Google Scholar 

  87. A. Pasquarello and R. Car (1997) Dynamical Charge Tensors and Infrared Spectrum of Amorphous SiO2. Phys. Rev. Lett. 79, p. 1766

    Article  ADS  Google Scholar 

  88. P. Carloni and U. Rothlisberger (2001) Simulations of Enzymatic Systems: Perspectives from Car-Parrinello Molecular Dynamics Simulations. In Theoretical Biochemistry – Processes and Properties of Biological Systems, ed. L. Eriksson Elsevier Science, pp. 215–251

    Google Scholar 

  89. P. Carloni, U. Rothlisberger, and M. Parrinello (2002) The Role and Perspective of Ab-initio Molecular Dynamics in the Study of Biological Systems. Acc. Chem. Res. 35, p. 455

    Article  Google Scholar 

  90. M. Sulpizi, G. Folkers, U. Rothlisberger, P. Carloni, and L. Scapozza (2002) Applications of Density Functional Theory-Based Methods in Medicinal Chemistry. Quant. Struct.-Act. Rel. 21, p. 173

    Article  Google Scholar 

  91. U. Röhrig, L. Guidoni, and U. Rothlisberger (2002) Early Steps of the Intramolecular Signal Transduction in Rhodopsin Explored by Molecular Dynamics Simulations. Biochemistry 41, p. 10799

    Article  Google Scholar 

  92. M. Colombo, L. Guidoni, A. Laio, A. Magistrato, P. Maurer, S. Piana, U. Röhrig, K. Spiegel, M. Sulpizi, J. VandeVondele, M. Zumstein, and U. Rothlisberger (2002) Hybrid QM/MM Car-Parrinello Simulations of Catalytic and Enzymatic Reactions. CHIMIA 56, p. 13

    Article  Google Scholar 

  93. A. Magistrato, W. DeGrado, U. Rothlisberger, and M. Klein (2003) Structural and Dynamical Characterization of Dizinc DF1, a Biomimetic Compound of Diiron Proteins via ab initio and Hybrid (QM/MM) Molecular Dynamics. J. Phys. Chem. B 107, p. 4182

    Article  Google Scholar 

  94. K. Spiegel, U. Rothlisberger, and P. Carloni (2004) Cisplatin Binding to DNA Oligomers from Hybrid Car-Parrinello Molecular Dynamics Simulations. J. Phys. Chem. B 108, p. 2699

    Article  Google Scholar 

  95. L. Guidoni, K. Spiegel, M. Zumstein, and U. Rothlisberger (2004) Green Oxidation Catalysts: Computational Design of High Efficiency Models of Galactose Oxidase. Angew. Chem. 116, p. 3348

    Article  Google Scholar 

  96. F. L. Gervasio, A. Laio, M. Parrinello, and M. Boero (2005) Charge Localization in DNA Fibers. Phys. Rev. Lett. 94, p. 158103

    Article  ADS  Google Scholar 

  97. CPMD, Copyright IBM Corp 1990–2001, Copyright MPI für Festkörperforschung Stuttgart (1997–2004)

    Google Scholar 

  98. J. Hutter and M. Iannuzzi (2005) CPMD: Car-Parrinello molecular dynamics. Z. für Kristallographie 220, p. 549

    Article  Google Scholar 

  99. S. Baroni, A. D. Corso, S. de Gironcoli, P. Giannozzi, C. Cavazzoni, G. Ballabio, S. Scandolo, G. Chiarotti, P. Focher, A. Pasquarello, K. Laasonen, A. Trave, R. Car, N. Marzari, and A. Kokalj, http://www.pwscf.org/

    Google Scholar 

  100. G. Kresse and J. Furthmüller (1996) Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B 54, p. 11169

    Article  ADS  Google Scholar 

  101. M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulos (1992) Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients. Rev. Mod. Phys. 64, p. 1045

    Article  ADS  Google Scholar 

  102. S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. I. J. Probert, K. Refson, and M. C. Payne (2005) First principles methods using CASTEP. Zeitschrift für Kristallographie 220, p. 567

    Article  Google Scholar 

  103. J. N. Michel Bockstedte, A. Kley, and M. Scheffler (1997) Density-functional theory calculations for poly-atomic systems: electronic structure, static and elastic properties and ab initio molecular dynamics. Comput. Phys. Comm. 107, p. 187

    Article  MATH  ADS  Google Scholar 

  104. Nwchem, developed and distributed by Pacic Northwest National Laboratory, USA

    Google Scholar 

  105. X. Gonze (2005) A brief introduction to the ABINIT software packag. Zeitschrift für Kristallographie 220, p. 558

    Article  Google Scholar 

  106. R. Dovesi, R. Orlando, B. Civalleri, C. Roetti, V. R. Saunders, and C. M. Zicovich-Wilsonan (2005) CRYSTAL: A computational tool for the ab initio study of the electronic properties of crystals. Zeitschrift für Kristallographie 220, p. 571

    Article  Google Scholar 

  107. S. Scandolo, P. Giannozzi, C. Cavazzoni, S. de Gironcoli, A. Pasquarello, and S. Baroni (2005) First-principles codes for computational crystallography in the Quantum-ESPRESSO package. Zeitschrift für Kristallographie 220, p. 574

    Article  Google Scholar 

  108. M. E. Tuckerman, D. A. Yarne, S. O. Samuelson, A. L. Hughes, and G. J. Martyna (2000) Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers. Comp. Phys. Comm. 128, p. 333

    Article  MATH  ADS  Google Scholar 

  109. The cp2k developers group, http://cp2k.berlios.de/ (2004)

    Google Scholar 

  110. J. Vandevondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, and J. Hutter (2005) Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Comp. Phys. Comm. 167, p. 103

    Article  ADS  Google Scholar 

  111. D. Marx and J. Hutter (2000) Ab initio molecular dynamics: Theory and implementation; Modern Methods and Algorithms of Quantum Chemistry. In NIC Series, ed. J. Grotendorst Forschungszentrum Jülich 1

    Google Scholar 

  112. M. Tuckerman and G. Martyna (2000) Understanding modern molecular dynamics methods: Techniques and Applications. J. Phys. Chem. 104, p. 159

    Google Scholar 

  113. D. Sebastiani and U. Rothlisberger (2003) Advances in Density Functional Based Modelling Techniques: Recent Extensions of the Car-Parrinello Approach. In Medicinal Quantum Chemistry, eds. P. Carloni and F. Alber Wiley-VCH, Weinheim. Methods and Principles in Medicinal Chemistry, pp. 5–40

    Google Scholar 

  114. J. Hutter (2004) Large Scale Density Functional Calculations. In Multiscale Modelling and Simulation, eds. S. Attinger and P. Koumoutsakos Springer, Heidelberg. Lecture Notes in Computational Science and Engineering, p. 39

    Google Scholar 

  115. A. Messiah (2000) Quantum Mechanics, 2 volumes Bound as One. Chap. XVIII, Dover, New York

    Google Scholar 

  116. R. P. Feynman (1939) Forces in Molecules. Phys. Rev. 56, p. 340

    Article  MATH  ADS  Google Scholar 

  117. L. Verlet (1967) Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev. 159, p. 98

    Article  ADS  Google Scholar 

  118. D. M. Ceperley and B. J. Alder (1980) Ground State of the Electron Gas by a Stochastic Method. Phys. Rev. Lett. 45, p. 566

    Article  ADS  Google Scholar 

  119. C. Pierleoni, D. M. Ceperley, and M. Holzmann (2004) Coupled Electron-Ion Monte Carlo Calculations of Dense Metallic Hydrogen. Phys. Rev. Lett. 93, p. 146402

    Article  ADS  Google Scholar 

  120. R. M. Dreizler and E. K. U. Gross (1990) Density Functional Theory. Springer-Verlag, Berlin Heidelberg

    MATH  Google Scholar 

  121. R. G. Parr and Y. Weitao (1994) Density-Functional Theory of Atoms and Molecules. Oxford University Press

    Google Scholar 

  122. R. M. Martin (2004) Electronic Structure : Basic Theory and Practical Methods. Cambridge University Press

    Google Scholar 

  123. P. Hohenberg and W. Kohn (1964) Inhomogeneous Electron Gas. Phys. Rev. 136, p. B864

    Article  ADS  MathSciNet  Google Scholar 

  124. M. Levy (1979) Universal Variational Functionals of Electron Densities, First-Order Density Matrices, and Natural Spin-Orbitals and Solution of the v-Representability Problem. Proc. Nat. Acad. Science 76, p. 6062

    Article  ADS  Google Scholar 

  125. W. Kohn and L. J. Sham (1965) Self-Consistent Equations Including Exchange and Correlation effects. Phys. Rev. 140, p. A1133

    Article  ADS  MathSciNet  Google Scholar 

  126. S. H. Vosko, L. Wilk, and M. Nusair (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can. J. Phys. 58, p. 1200

    Article  ADS  Google Scholar 

  127. J. P. Perdew and Y. Wang (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys. Rev. B 45, p. 13244

    Article  ADS  Google Scholar 

  128. J. P. Perdew and A. Zunger (1981) Self-interaction correction to density functional approximations for many-electron systems. Phys. Rev. B 23, p. 5048

    Article  ADS  Google Scholar 

  129. S. Goedecker, M. Teter, and J. Hutter (1996) Seperable Dual-Space Gaussian Pseudopotentials. Phys. Rev. B 54, p. 1703

    Article  ADS  Google Scholar 

  130. J. P. Perdew, K. Burke, and M. Ernzerhof (1996) Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 77, p. 3865

    Article  ADS  Google Scholar 

  131. J. P. Perdew, J. A. Chevary, S. H. Vosko, Koblar, A. Jackson, M. R. Pederson, D. J. Singh, and C. Fiolhais (1992) Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. Phys. Rev. B 46, p. 6671

    Article  ADS  Google Scholar 

  132. J. P. Perdew (1991) in Electronic Structure of Solids ‘91, eds. P. Ziesche and H. Eschrig Akademie Verlag, Berlin, p. 11

    Google Scholar 

  133. A. D. Becke (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38, p. 3098

    Article  ADS  Google Scholar 

  134. C. Lee, W. Yang, and R. G. Parr (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, p. 785

    Article  ADS  Google Scholar 

  135. F. A. Hamprecht, A. J. Cohen, D. J. Tozer, and N. C. Handy (1998) Development and assessment of new exchange-correlation functionals. J. Chem. Phys. 109, p. 6264

    Article  ADS  Google Scholar 

  136. A. D. Boese and N. C. Handy (2001) A new parametrization of exchange correlation generalized gradient approximation functionals. J. Chem. Phys. 114, p. 5497

    Article  ADS  Google Scholar 

  137. A. D. Boese, N. L. Doltsinis, N. C. Handy, and M. Sprik (2000) New generalized gradient approximation functionals. J. Chem. Phys. 112, p. 1670

    Article  ADS  Google Scholar 

  138. A. D. Corso, A. Pasquarello, A. Baldereschi, and R. Car (1996) Generalizedgradient approximations to density-functional theory: A comparative study for atoms and solids. Phys. Rev. B 53, p. 1180

    Article  ADS  Google Scholar 

  139. M. Sprik, J. Hutter, and M. Parrinello (1996) Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient-corrected density functionals. J. Chem. Phys. 105, p. 1142

    Article  ADS  Google Scholar 

  140. A. Becke (1996) Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exact-exchange mixing. J. Chem. Phys. 104, p. 1040

    Article  ADS  Google Scholar 

  141. M. d’Avezac, M. Calandra, and F. Mauri (2005) Density functional theory description of hole-trapping in SiO2 : A self-interaction-corrected approach. Phys. Rev. B 71, p. 205210

    Article  ADS  Google Scholar 

  142. I. Ciofini, C. Adamo, and H. Chermette (2005) Effect of self-interaction error in the evaluation of the bond length alternation in trans-polyacetylene using density-functional theory. J. Chem. Phys. 123, p. 121102

    Article  ADS  Google Scholar 

  143. W. Pollard and R. Friesner (1993) Efficient Fock matrix diagonalization by a Krylov-space method. J. Chem. Phys. 99, p. 6742

    Article  ADS  Google Scholar 

  144. J. Cullum and R. A. Willoughby (1985) Lanczos algorithms for large symmetric eigenvalue computations, 1 : Theory of Progress in Scientific Computing. Birkhauser, Boston, 3 edn

    Google Scholar 

  145. A. Alavi, J. Kohanoff, M. Parrinello, and D. Frenkel (1994) Ab Initio Molecular Dynamics with Excited Electrons. Phys. Rev. Lett. 73, p. 2599

    Article  ADS  Google Scholar 

  146. D. G. Anderson (1965) Iterative Procedures for Nonlinear Integral Equations. J. Assoc. Comput. Mach. 12, p. 547

    MATH  MathSciNet  Google Scholar 

  147. M. P. Teter, M. C. Payne, and D. C. Allen (1989) Solution of Schrödinger’s equation for large systems. Phys. Rev. B 40, p. 12255

    Article  ADS  Google Scholar 

  148. P. Pulay (1980) Convergence acceleration of iterative sequences the case of scf iteration. Chem. Phys. Lett. 73, p. 393

    Article  ADS  Google Scholar 

  149. C. Csaszar and P. Pulay (1984) Geometry optimization by direct inversion in the iterative subspace. J. Mol. Struc. 114, p. 31

    Article  ADS  Google Scholar 

  150. J. Hutter, H. P. Luthi, and M. Parrinello (1994) Electronic Structure Optimisation in Plane-Wave-Based Density Functional Calculations by Direct Inversion in the Iterative Subspace. Comput. Mat. Sci. 2, p. 244

    Article  Google Scholar 

  151. R. Spezia, C. Nicolas, F.-X. Coudert, P. Archirel, R. Vuilleumier, and A. Boutin (2004) Reactivity of an excess electron with monovalent cations in bulk water by mixed quantum classical molecular dynamics simulations. Mol. Sim. 30, p. 749

    Article  MATH  Google Scholar 

  152. R. W. Hockney (1970) The potential calculation and some applications. Methods Comput. Phys. 9, p. 136

    Google Scholar 

  153. G. J. Martyna and M. E. Tuckerman (1999) A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters. J. Chem. Phys. 110, p. 2810

    Article  ADS  Google Scholar 

  154. A. Filippetti, D. Vanderbilt, W. Zhong, Y. Cai, and G. B. Bachelet (1995) Chemical hardness, linear response, and pseudopotential transferability. Phys. Rev. B 52, p. 11793

    Article  ADS  Google Scholar 

  155. D. R. Hamann, M. Schlüter, and C. Chiang (1979) Norm-Conserving Pseudopotentials. Phys. Rev. Lett. 43, p. 1494

    Article  ADS  Google Scholar 

  156. G. B. Bachelet, D. R. Hamann, and M. Schlüter (1982) Pseudopotentials that work: From H to Pu. Phys. Rev. B 26, p. 4199

    Article  ADS  Google Scholar 

  157. N. Troullier and J. L. Martins (1991) Efficient pseudopotentials for plane-wave calculations. Phys. Rev. B 43, p. 1993

    Article  ADS  Google Scholar 

  158. L. Kleinman and D. M. Bylander (1982) Efficacious Form for Model Pseudopotentials. Phys. Rev. Lett. 48, p. 1425

    Article  ADS  Google Scholar 

  159. P. E. Blöchl (1990) Generalized separable potentials for electronic-structure calculations. Phys. Rev. B 41, p. 5414

    Article  ADS  Google Scholar 

  160. C. Hartwigsen, S. Goedecker, and J. Hutter (1998) Relativistic separable dualspace Gaussian pseudopotentials from H to Rn. Phys. Rev. B 58, p. 3641

    Article  ADS  Google Scholar 

  161. O. A. von Lilienfeld, I. Tavernelli, U. Rothlisberger, and D. Sebastiani (2005) Variational optimization of effective atom centered potentials for molecular properties. J. Chem. Phys. 122, 014113

    Article  ADS  Google Scholar 

  162. O. A. von Lilienfeld, I. Tavernelli, U. Rothlisberger, and D. Sebastiani (2004) Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory. Phys. Rev. Lett. 93, p. 153004

    Article  ADS  Google Scholar 

  163. D. Vanderbilt (1985) Optimally smooth norm-conserving pseudopotentials. Phys. Rev. B 32, p. 8412

    Article  ADS  Google Scholar 

  164. D. Vanderbilt (1990) Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B 41, p. 7892

    Article  ADS  Google Scholar 

  165. K. Laasonen, R. Car, C. Lee, and D. Vanderbilt (1991) Implementation of ultrasoft pseudopotentials in ab initio molecular dynamics. Phys. Rev. B 43, p. 6796

    Article  ADS  Google Scholar 

  166. K. Laasonen, A. Pasquarello, R. Car, C. Lee, and D. Vanderbilt (1993) Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials. Phys. Rev. B 47, p. 10142

    Article  ADS  Google Scholar 

  167. J. Hutter, M. E. Tuckerman, and M. Parrinello (1995) Integrating the Car-Parrinello equations III. J. Chem. Phys. 102, p. 859

    Article  ADS  Google Scholar 

  168. M. Iannuzzi, T. Chassaing, T. Wallman, and J. Hutter (2005) Ground and Excited State Density Functional Calculations with the Gaussian and Augmented-Plane-Wave Method. Chimia 59, p. 499

    Article  Google Scholar 

  169. S. Nosé (1984) A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys 81, p. 511

    Article  ADS  Google Scholar 

  170. W. G. Hoover (1985) Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A 31, p. 1695

    Article  ADS  Google Scholar 

  171. J. B. Abrams, M. E. Tuckerman, and G. J. Martyna, Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamic. Lect. Notes in Phys. 703, pp. 139–192

    Google Scholar 

  172. J. VandeVondele and J. Hutter (2003) An Efficient orbital transformation method for electronic structure calculations. J. Chem. Phys. 118, p. 4365

    Article  ADS  Google Scholar 

  173. M. E. Tuckerman, J. Hutter, and M. Parrinello (1994) Integrating the Car-Parrinello equations I. J. Chem. Phys. 101, p. 1302

    Article  ADS  Google Scholar 

  174. M. E. Tuckerman, J. Hutter, and M. Parrinello (1994) Integrating the Car-Parrinello equations II. J. Chem. Phys. 101, p. 1316

    Article  ADS  Google Scholar 

  175. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen (1977) Numerical integration of the Cartesian equation of motion of a system with constraints: molecular dynamics of N-alkanes. J. of Computational Physics 23, p. 327

    Article  ADS  Google Scholar 

  176. H. C. Andersen (1983) Rattle: A velocity version of the shake algorithm for molecular dynamics calculations. J. Comp. Phys. 52, p. 24

    Article  MATH  ADS  Google Scholar 

  177. G. J. Martyna, M. L. Klein, and M. Tuckerman (1992) Nosé-Hoover chains: The canonical ensemble via continuous dynamics. J. Chem. Phys. 97, p. 2635

    Article  ADS  Google Scholar 

  178. G. Pastore, E. Smargiassi, and F. Buda (1991) Theory of ab initio molecular dynamics calculations. Phys. Rev. A 44, p. 6334

    Article  ADS  Google Scholar 

  179. F. A. Bornemann and C. Schutte (1998) A mathematical investigation of the Car-Parrinello method. Numer. Math. 78, p. 359

    Article  MATH  MathSciNet  Google Scholar 

  180. F. A. Bornemann and C. Schutte (1999) Adaptive accuracy control for Car-Parrinello simulations. Numer. Math. 83, p. 179

    Article  MATH  MathSciNet  Google Scholar 

  181. P. Tangney and S. Scandolo (2002) How well do Car-Parrinello simulations reproduce the Born-Oppenheimer surface? Theory and examples. J. Chem. Phys. 116, p. 14

    Article  ADS  Google Scholar 

  182. O. G. Jepps, G. Ayton, and D. J. Evans (2000) Microscopic expressions for the thermodynamic temperature. Phys. Rev. E 62, p. 4757

    Article  ADS  Google Scholar 

  183. P. Tangney (2006) On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter. J. Chem. Phys. 124, 044111

    Article  ADS  Google Scholar 

  184. M. Sprik (1991) Hydrogen bonding and the static dielectric constant in liquid water. J. Chem. Phys. 95, p. 6762

    Article  ADS  Google Scholar 

  185. M. Sprik and M. L. Klein (1988) A polarizable model for water using distributed charge sites. J. Chem. Phys. 89, p. 7556

    Article  ADS  Google Scholar 

  186. M. Marchi, D. Borgis, N. Levy, and P. Ballone (2001) A dielectric continuum molecular dynamics method. J. Chem. Phys. 114, p. 4377

    Article  ADS  Google Scholar 

  187. R. Vuilleumier and D. Borgis (2000) Wavefunction quantisation of the proton motion in a H5O+ 2 dimer solvated in liquid water. Journal of Molecular Structure 552, p. 117

    Article  ADS  Google Scholar 

  188. R. Resta (1998) Quantum-Mechanical Position Operator in Extended Systems. Phys. Rev. Lett. 80, p. 1800

    Article  ADS  Google Scholar 

  189. R. Resta and S. Sorella (1999) Electron Localization in the Insulating State. Phys. Rev. Lett. 82, p. 370

    Article  ADS  Google Scholar 

  190. R. Resta (1994) Macroscopic polarization in crystalline dielectrics: the geometric phase approach. Rev. Mod. Phys. 66, pp. 899–915

    Article  ADS  Google Scholar 

  191. D. Vanderbilt and R. D. King-Smith (1993) Electric polarization as a bulk quantity and its relation to surface charge. Phys. Rev. B 48, p. 4442

    Article  ADS  Google Scholar 

  192. R. D. King-Smith and D. Vanderbilt (1993) Theory of polarization of crystalline solids. Phys. Rev. B 47, p. 1651

    Article  ADS  Google Scholar 

  193. P. L. Silvestrelli, M. Bernasconi, and M. Parrinello (1997) Ab initio infrared spectrum of liquid water. Chem. Phys. Lett. 277, p. 478

    Article  ADS  Google Scholar 

  194. M.-P. Gaigeot and M. Sprik (2003) Ab initio molecular dynamics computation of the infrared spectrum of aqueous uracil. J. Phys. Chem. B 107, p. 10344

    Article  Google Scholar 

  195. M. Gaigeot, R. Vuilleumier, M. Sprik, and D. Borgis (2005) Infrared spectroscopy of N-methyl-acetamide revisited by ab initio molecular dynamics simulations. J. Chem. Theory Comput. 1, p. 772

    Article  Google Scholar 

  196. A. Putrino, D. Sebastiani, and M. Parrinello (2000) Generalized variational density functional perturbation theory. J. Chem. Phys. 113, p. 7102

    Article  ADS  Google Scholar 

  197. A. Putrino and M. Parrinello (2002) Anharmonic Raman Spectra in High-Pressure Ice from Ab Initio Simulations. Phys. Rev. Lett. 88, p. 176401

    Article  ADS  Google Scholar 

  198. I. Souza, J. Íñiguez, and D. Vanderbilt (2002) First-Principles Approach to Insulators in Finite Electric Fields. Phys. Rev. Lett. 89, p. 117602

    Article  ADS  Google Scholar 

  199. P. Umari and A. Pasquarello (2002) Ab initio Molecular Dynamics in a Finite Homogeneous Electric Field. Phys. Rev. Lett. 89, p. 157602

    Article  ADS  Google Scholar 

  200. V. Dubois, P. Umari, and A. Pasquarello (2004) Dielectric susceptibility of dipolar molecular liquids by ab initio molecular dynamics: application to liquid HCl. Chem. Phys. Lett. 390, p. 193

    Article  ADS  Google Scholar 

  201. R. Ramrez, T. Lopez-Ciudad, P. Kumar, and D. Marx (2004) Quantum corrections to classical time-correlation functions: Hydrogen bonding and anharmonic floppy modes. J. Chem. Phys. 121, p. 3973

    Article  ADS  Google Scholar 

  202. R. Iftimie and M. E. Tuckerman (2005) Decomposing total IR spectra of aqueous systems into solute and solvent contributions: A computational approach using maximally localized Wannier orbitals. J. Chem. Phys. 122, p. 214508

    Article  ADS  Google Scholar 

  203. J. E. Bertie and Z. Lan (1996) Infrared Intensities of Liquids XX: The Intensity of the OH Stretching Band of Liquid Water Revisited, and the Best Current Values of the Optical Constants of H2O(l) at 25°C. App. Spec. 50, p. 1047

    Article  ADS  Google Scholar 

  204. X. Gonze (1995) Adiabatic density-functional perturbation theory. Phys. Rev. A 52, p. 1096

    Article  ADS  Google Scholar 

  205. X. Gonze (1995) Perturbation expansion of variational principles at arbitrary order. Phys. Rev. A 52, p. 1086

    Article  ADS  Google Scholar 

  206. D. Sebastiani and M. Parrinello (2002) Ab-initio study of NMR chemical shifts of water under normal and supercritical conditions. Chem. Phys. Chem. 3, p. 675

    Google Scholar 

  207. J. Schmidt and D. Sebastiani (2005) Anomalous temperature dependence of nuclear quadrupole interactions in strongly hydrogen-bonded systems from first principles. J. Chem. Phys. 123, 074501

    Article  ADS  Google Scholar 

  208. M. Benoit and D. Marx (2005) The Shapes of Protons in Hydrogen Bonds Depend on the Bond Length. Chem. Phys. Chem. 6, p. 1738

    Google Scholar 

  209. M. Profeta, M. Benoit, F. Mauri, and C. J. Pickard (2004) First-Principles Calculation of the NMR Parameters in Ca Oxide and Ca Aluminosilicates: the Partially Covalent Nature of the Ca-O Bond, a Challenge for Density Functional Theory. J. Am. Chem. Soc. 126, p. 12628

    Article  Google Scholar 

  210. I. Frank, J. Hutter, D. Marx, and M. Parrinello (1998) Molecular dynamics in low-spin excited states. J. Chem. Phys. 108, p. 4060

    Article  ADS  Google Scholar 

  211. E. K. U. Gross and W. Kohn (1990) Time-dependent density functional theory. Adv. Quant. Chem. 21, p. 255

    Article  Google Scholar 

  212. E. K. U. Gross, J. F. Dobson, and M. Petersilka (1996) Density-functional theory of time-dependent phenomena. In Topics in Current Chemistry, Springer Berlin Heidelberg, pp. 81–172

    Google Scholar 

  213. K. Burke and E. K. U. Gros (1998) A guided tour of time-dependent density functional theory. In Density Functionals: Theory and Applications, ed. D. Joubert, Springer Berlin Heidelberg, pp. 116–146

    Google Scholar 

  214. N. T. Maitra, K. Burke, E. K. U. G. H. Appel, and R. van Leeuwen (2002) Ten topical questions in time-dependent density functional theory. In Reviews in Modern Quantum Chemistry: A Celebration of the Contributions of R.G. Parr, ed. K. D. Sen, World Scientific, pp. 1186–1225

    Google Scholar 

  215. M. A. L. Marques and E. K. U. Gross (2004) Time-Dependent Density-Functional Theory. Annu. Rev. Phys. Chem. 55, p. 427

    Article  ADS  Google Scholar 

  216. E. Runge and E. K. U. Gross (1984) Density functional theory for time dependent systems. Phys. Rev. Lett. 52, p. 997

    Article  ADS  Google Scholar 

  217. K. Burke, J. Werschnik, and E. K. U. Gross (2005) Time-dependent density functional theory: Past, present, and future. J. Chem. Phys. 123, 062206

    Article  ADS  Google Scholar 

  218. M. Petersilka, E. K. U. Gross, and K. Burke (2000) Excitation energies from time-dependent density-functional theory using exact and approximate potentials. Int. J. Quant. Chem. 80, p. 534

    Article  Google Scholar 

  219. T. Grabo, M. Petersilka, and E. K. U. Gross (2000) Molecular excitation energies from time-dependent density-functional theory. Journal of Molecular Structure (Theochem) 501, p. 353

    Article  Google Scholar 

  220. H. Appel, E. K. U. Gross, and K. Burke (2003) Excitations in Time-Dependent Density-Functional Theory. Phys. Rev. Lett. 90, 043005

    Article  ADS  Google Scholar 

  221. N. L. Doltsinis and M. Sprik (2000) Electronic excitation spectra from time dependent density functional response theory using plane wave methods. Chem. Phys. Lett. 330, p. 563

    Article  ADS  Google Scholar 

  222. J. Hutter (2003) Excited state nuclear forces from the Tamm-Dancoff approximation to time-dependent density functional theory within the plane wave basis set framework. J. Chem. Phys. 118, p. 3928

    Article  ADS  Google Scholar 

  223. L. Bernasconi, M. Sprik, and J. Hutter (2003) Time dependent density functional theory study of charge-transfer and intramolecular electronic excitations in acetone–water systems. J. Chem. Phys. 119, p. 12417

    Article  ADS  Google Scholar 

  224. L. Bernasconi, J. Blumberger, M. Sprik, and R. Vuilleumier (2004) Density functional calculation of the electronic absorption spectrum of Cu+ and Ag+ aqua ions. J. Chem. Phys. 121, p. 11885

    Article  ADS  Google Scholar 

  225. M. Sulpizi, P. Carloni, J. Hutter, and U. Röthlisberger (2003) A hybrid TDDFT/MM investigation of the optical properties of aminocoumarins in water and acetonitrile solution. Phys. Chem. Chem. Phys. 5, p. 4798

    Article  Google Scholar 

  226. M. Sulpizi, U. F. Röhrig, J. Hutter, and U. Rothlisberger (2005) Optical properties of molecules in solution via hybrid TDDFT/MM simulations. Int. J. Quant. Chem. 101, p. 671

    Article  Google Scholar 

  227. L. Bernasconi and M. Sprik (2005) Time-dependent density functional theory description of on-site electron repulsion and ligand field effects in the optical spectrum of hexa-aquoruthenium(II) in solution. J. Phys. Chem. B 109, p. 12222

    Article  Google Scholar 

  228. W. Kohn, Y. Meir, and D. E. Makarov (1998) van der Waals Energies in Density Functional Theory. Phys. Rev. Lett. 80, p. 4153

    Article  ADS  Google Scholar 

  229. M. Lein, J. F. Dobson, and E. K. U. Gross (1999) Towards the description of van der Waals interactions within density-functional theory. J. Comput. Chem. 20, p. 12

    Article  Google Scholar 

  230. M. Odelius, D. Laikov, and J. Hutter (2003) Excited state geometries within time-dependent and restricted open-shell density functional theories. J. Mol. Struc. (Theochem) 630, p. 163

    Article  Google Scholar 

  231. N. L. Doltsinis and D. S. Kosov (2005) Plane wave/pseudopotential implementation of excited state gradients in density functional linear response theory: A new route via implicit dierentiation. J. Chem. Phys. 122, p. 144101

    Article  ADS  Google Scholar 

  232. H. Langer and N. L. Doltsinis (2003) Excited state tautomerism of the DNA base guanine: A restricted open-shell Kohn-Sham study. J. Chem. Phys. 118, p. 5400

    Article  ADS  Google Scholar 

  233. N. L. Doltsinis and D. Marx (2002) Nonadiabatic Car-Parrinello molecular dynamics. Phys. Rev. Lett. 88, p. 166402

    Article  ADS  Google Scholar 

  234. N. L. Doltsinis (2004) Excited state proton transfer and internal conversion in o-hydroxybenzaldehyde: New insights from nonadiabatic ab initio molecular dynamics. Mol. Phys. 102, p. 499

    Article  ADS  Google Scholar 

  235. J. M. Foster and S. F. Boys (1960) Canonical Configurational Interaction Procedure. Rev. Mod. Phys. 32, p. 300

    Article  ADS  MathSciNet  Google Scholar 

  236. C. Edmiston and K. Ruedenberg (1963) Localized Atomic and Molecular Orbitals. Rev. Mod. Phys. 35, p. 457

    Article  MATH  ADS  Google Scholar 

  237. W. von Niessen (1972) Density Localization of Atomic and Molecular Orbitals. I. J. Chem. Phys. 56, p. 4290

    Article  ADS  Google Scholar 

  238. N. Marzari and D. Vanderbilt (1997) Maximally localized generalized Wannier functions for composite energy bands. Phys. Rev. B 56, p. 12847

    Article  ADS  Google Scholar 

  239. P. L. Silvestrelli (1999) Maximally localized Wannier functions for simulations with supercells of general symmetry. Phys. Rev. B 59, p. 9703

    Article  ADS  Google Scholar 

  240. G. Berghold, C. J. Mundy, A. H. Romero, J. Hutter, and M. Parrinello (2000) General and Efficient Algorithms for Obtaining Maximally-Localized Wannier Functions. Phys. Rev. B 61, p. 10040

    Article  ADS  Google Scholar 

  241. I. Souza, N. Marzari, and D. Vanderbilt (2002) Maximally localized Wannier functions for entangled energy bands. Phys. Rev. B 65, 035109

    Article  ADS  Google Scholar 

  242. P. L. Silvestrelli and M. Parrinello (1999) Water Molecule Dipole in the Gas and in the Liquid Phase. Phys. Rev. Lett. 82, p. 3308

    Article  ADS  Google Scholar 

  243. M. Boero, K. Terakura, T. Ikeshoji, C. C. Liew, and M. Parrinello (2000) Hydrogen Bonding and Dipole Moment of Water at Supercritical Conditions: A First-Principles Molecular Dynamics Study. Phys. Rev. Lett. 85, p. 3245

    Article  ADS  Google Scholar 

  244. B. Kirchner and J. Hutter (2004) Solvent effects on electronic properties from Wannier functions in a dimethyl sulfoxide/water mixture. J. Chem. Phys. 121, p. 5133

    Article  ADS  Google Scholar 

  245. P. Hunt, M. Sprik, and R. Vuilleumier (2003) Thermal versus electronic broadening in the density of states of liquid water. Chem. Phys. Lett. 376, p. 68

    Article  ADS  Google Scholar 

  246. R. Iftimie, J. W. Thomas, and M. E. Tuckerman (2004) On-the-fly localization of electronic orbitals in Car–Parrinello molecular dynamics. J. Chem. Phys. 120, p. 2169

    Article  ADS  Google Scholar 

  247. I. Coluzza, M. Sprik, and G. Ciccotti (2003) Constrained reaction coordinate dynamics for systems with constraints. Mol. Phys. 101, p. 2885

    Article  ADS  Google Scholar 

  248. J. VandeVondele and U. Rothlisberger (2000) Efficient Multidimensional Free Energy Calculations for ab initio Molecular Dynamics Using Classical Bias Potentials. J. Chem. Phys. 113, p. 4863

    Article  ADS  Google Scholar 

  249. J. VandeVondele and U. Rothlisberger (2002) Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces. J. Phys. Chem. B 106, p. 203

    Article  Google Scholar 

  250. L. Rosso, P. Minary, Z. Zhu, and M. E. Tuckerman (2002) On the use of adiabatic molecular dynamics to calculate free energy profiles. J. Chem. Phys. 116, p. 4389

    Article  ADS  Google Scholar 

  251. A. Laio and M. Parrinello (2002) Escaping free-energy minima. Proc. Nat. Acad. Sciences 99, p. 12562

    Article  ADS  Google Scholar 

  252. P. L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello (2000) Ab initio analysis of proton transfer dynamics in (H2O)3H+. Chem. Phys. Lett. 321, p. 225

    Article  ADS  Google Scholar 

  253. R. Vuilleumier and M. Sprik (2002) Electronic control using density functional perturbation methods. Chem. Phys. Lett. 365, p. 305

    Article  ADS  Google Scholar 

  254. J. VandeVondele and U. Rothlisberger (2001) Estimating Equilibrium Properties from Non-Hamiltonian Dynamics. J. Chem. Phys. 115, p. 7859

    Article  ADS  Google Scholar 

  255. J. VandeVondele and U. Rothlisberger (2002) Accelerating Rare Reactive Events by Means of a Finite Electronic Temperature. J. Am. Chem. Soc. 124, p. 8163

    Article  Google Scholar 

  256. P. Silvestrelli, A. Alavi, M. Parrinello, and D. Frenkel (1996) Hot electrons and the approach to metallic behaviour in Kx(KCl)1-x. Euro. Phys. Lett. 33, p. 551

    Article  ADS  Google Scholar 

  257. R. Vuilleumier, M. Sprik, and A. Alavi (2000) Computation of electronic chemical potentials using free energy density functionals. Journal of Molecular Structure (THEOCHEM) 506, p. 343

    Article  Google Scholar 

  258. A. Y. Lozovoi, A. Alavi, J. Kohanoff, and R. M. Lynden-Bell (2001) Ab initio simulation of charged slabs at constant chemical potential. J. Chem. Phys. 115, p. 1661

    Article  ADS  Google Scholar 

  259. I. Tavernelli, R. Vuilleumier, and M. Sprik (2002) Ab initio molecular dymamics for molecules with variable numbers of electrons. Phys. Rev. Lett. 88, p. 213002

    Article  ADS  Google Scholar 

  260. J. Blumberger, Y. Tateyama, and M. Sprik (2005) Ab initio molecular dynamics simulation of redox reactions in solution. Comp. Pys. Comm. 169, p. 256

    Article  ADS  Google Scholar 

  261. D. Marx and M. Parrinello (1996) Ab initio path integral molecular dynamics: Basic ideas. J. Chem. Phys. 104, p. 4077

    Article  ADS  Google Scholar 

  262. M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello (1996) Efficient and general algorithms for path integral Car-Parrinello molecular dynamics. J. Chem. Phys. 104, p. 5579

    Article  ADS  Google Scholar 

  263. M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello (1997) On the Quantum Nature of the Shared Proton in Hydrogen Bonds. Science 275, p. 817

    Article  Google Scholar 

  264. S. Miura, M. Tuckerman, and M. Klein (1998) An ab initio path integral molecular dynamics study of double proton transfer in the formic acid dimer. J. Chem. Phys. 109, p. 5290

    Article  ADS  Google Scholar 

  265. M. Benoit, D. Marx, and M. Parrinello (1998) Quantum effects on phase transitions in high-pressure ice. Comp. Mat. Sci. 10, p. 88

    Article  Google Scholar 

  266. M. Diraison, G. J. Martyna, and M. E. Tuckerman (1999) Simulation studies of liquid ammonia by classical ab initio, classical, and path-integral molecular dynamics. J. Chem. Phys. 111, p. 1096

    Article  ADS  Google Scholar 

  267. D. Marx, M. E. Tuckerman, and G. J. Martyna (1999) Quantum dynamics via adiabatic ab initio centroid molecular dynamics. Comput. Phys. Commun. 118, p. 166

    Article  MATH  ADS  Google Scholar 

  268. D. Marx, M. E. Tuckerman, and M. Parrinello (2000) Solvated excess protons in water: quantum effects on the hydration structure. J. Phys.: Condens. Matter A 12, p. 153

    Article  ADS  Google Scholar 

  269. U. Roethlisberger, M. Sprik, and J. Hutter (2002) Time and length scales in ab initio molecular dynamics. In Bridging time scales: Molecular simulations for the next decade, eds. P. Niebala, M. Maraschal and G. Ciccotti, Springer Verlag, p. 413

    Google Scholar 

  270. L. Guidoni, P. Maurer, S. Piana, and U. Rothlisberger (2002) Hybrid Car-Parrinello/Molecular Mechanics Modelling of Transition Metal Complexes: Structure, Dynamics and Reactivity. Quant. Struct.-Act. Rel. 21, p. 119

    Article  Google Scholar 

  271. U. Röhrig, I. Frank, J. Hutter, A. Laio, J. VandeVondele, and U. Röthlisberger (2003) A QM/MM Car-Parrinello Molecular Dynamics Study of the Solvent effects on the Ground State and on the First Excited Singlet State of Acetone in Water. Chem. Phys. Chem. 4, p. 1177

    Google Scholar 

  272. M. Sulpizi, A. Laio, J. VandeVondele, U. Rothlisberger, A. Cattaneo, and P. Carloni (2003) Reaction Mechanism of Caspases: Insights from Mixed QM/MM Car-Parrinello Simulations. Proteins-Structure, Function and Genetics 52, p. 212

    Article  Google Scholar 

  273. Y. Liu, D. A. Yarne, and M. E. Tuckerman (2003) Ab initio molecular dynamics calculations with simple, localized, orthonormal real-space basis sets. Phys. Rev. B 68, p. 125110

    Article  ADS  Google Scholar 

  274. F. R. Krajewski and M. Parrinello (2005) Stochastic linear scaling for metals and nonmetals. Phys. Rev. B 71, p. 233105

    Article  ADS  Google Scholar 

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  1. Laboratoire de Physique Théorique de la Matière Condensée, Tour 24-25, 2ème étage, c.c. 121, Université Pierre et Marie Curie, 4 place Jussieu, F-75005, Paris, France

    R. Vuilleumier

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  1. Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi, 213/A, 41100, Modena, Italy

    Mauro Ferrario Professor

  2. Dipartimento di Fisica, INFN, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy

    Giovanni Ciccotti Professor

  3. Institut für Physik, Universität Mainz, Staudinger Weg 7, 55128, Mainz, Germany

    Kurt Binder Professor

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Vuilleumier, R. (2006). Density Functional Theory Based Ab Initio Molecular Dynamics Using the Car-Parrinello Approach. In: Ferrario, M., Ciccotti, G., Binder, K. (eds) Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Lecture Notes in Physics, vol 703. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-35273-2_7

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