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Problems in molecular dynamics of condensed phases

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Abstract

A review of the recent theoretical and computational activity at the Chemistry Department of the University of Firenze in the field of molecular simulations of condensed phases is reported. The topics considered include quantitative methods for accurate free energy calculations, molecular dynamics of liquids and ionic solutions, chemical reactions in solutions, phase transformations and polymerization reactions at high pressures.

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References

  1. Frenkel D, Smit B (2002) Understanding molecular simulation. Academic, San Diego

    Google Scholar 

  2. Car R, Parrinello M (1985). Phys Rev Lett 55:2471

    CAS  Google Scholar 

  3. Gervasio FL, Chelli R Marchi M, Procacci P, Schettino V (2001). J Phys Chem B 105:7835

    CAS  Google Scholar 

  4. Chelli R, Gervasio FL, Procacci P, Schettino V (2002). J Am Chem Soc 124:6133

    CAS  Google Scholar 

  5. Laio A, Parrinello M (2002). Proc Natl Acad Sci USA 99:12562

    CAS  Google Scholar 

  6. Wang F, Landau DP (2001). Phys Rev Lett 86:2050

    CAS  Google Scholar 

  7. Darve E, Pohorille A (2001). J Chem Phys 115:9169

    CAS  Google Scholar 

  8. Hooft RWW, van Eijck BP, Kroon J (1992). J Chem Phys 97:6690

    CAS  Google Scholar 

  9. Mezei M (1987). J Comput Phys 68:237

    Google Scholar 

  10. Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M (2005). J Phys Chem B 109:6714

    CAS  Google Scholar 

  11. Wang F, Landau DP (2001). Phys Rev E 64:056101

    CAS  Google Scholar 

  12. Lee HK, Okabe Y, Landau DP (2006). Comp Phys Comm 175:36

    CAS  Google Scholar 

  13. Henin J, Chipot C (2004). J Chem Phys 121:2904

    CAS  Google Scholar 

  14. Marsili S, Barducci A, Chelli R, Procacci P, Schettino V (2006). J Phys Chem B 110:14011

    CAS  Google Scholar 

  15. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, Zhang W, Yang R, Cieplak P, Luo R, Lee T et al (2003). J Comput Chem 24:1999

    CAS  Google Scholar 

  16. Torrie GM, Valleau JP (1974). Chem Phys Lett 28:578

    CAS  Google Scholar 

  17. Jarzynski C (1997). Phys Rev Lett 78:2690

    CAS  Google Scholar 

  18. Crooks GE (1998). J Stat Phys 90:1481

    Google Scholar 

  19. Crooks GE (1999). Phys Rev E 60:2721

    CAS  Google Scholar 

  20. Collin D, Ritort F, Jarzynski C, Smith SB, Tinoco I, Bustamante C, (2005). Nature 437:231

    CAS  Google Scholar 

  21. Park S, Schulten K (2004). J Chem Phys 120:5946

    CAS  Google Scholar 

  22. Procacci P, Marsili S, Barducci A, Signorini GF, Chelli R (2006). J Chem Phys 125:164101

    Google Scholar 

  23. Hoover WG, (1985). Phys Rev A 31:1695

    Google Scholar 

  24. Tuckerman ME, Berne BJ, Martyna GJ, Klein ML (1993). J Chem Phys 99:2796

    Google Scholar 

  25. Gervasio FL, Chelli R, Procacci P, Schettino V (2002). PROTEINS 48:117

    CAS  Google Scholar 

  26. Chelli R, Gervasio FL, Procacci P, Schettino V (2004). PROTEINS 55:139

    CAS  Google Scholar 

  27. Pan K, Baldwin M, Nguyen J, Gasset M, Serban A, Groth D, Mehlhorn I, Huang Z, Fletterick RJ, Cohen FE et al (1993). Proc Natl Acad Sci USA 90:10962

    CAS  Google Scholar 

  28. Wille H, Michelitsch MD, Génebaut V, Supattapone S, A, Cohen FE, Agard DA, Prusiner SB (2002). Proc Natl Acad Sci USA 99:3563

    CAS  Google Scholar 

  29. Govaerts C, Wille H, Prusiner SB, Cohen FE (2004). Proc Natl Acad Sci USA 101:8342

    CAS  Google Scholar 

  30. DeMarco ML, Daggett V (2004). Proc Natl Acad Sci USA 101:2293

    CAS  Google Scholar 

  31. Prusiner SB (1996). Trends BioChem Sci 21:482

    CAS  Google Scholar 

  32. Riesner D (2003). Br Med Bull 66:21

    CAS  Google Scholar 

  33. Gsponer J, Ferrara P, Caflisch A (2001). J Mol Graph Model 20:169

    CAS  Google Scholar 

  34. El Bastawissy E, Knaggs MH, Gilbert IH (2001). J Mol Graph Model 20:145

    CAS  Google Scholar 

  35. Gu W, Wang T, Zhu J, Shi Y, Liu H (2003). BioPhys Chem 104:79

    CAS  Google Scholar 

  36. Alonso DO, DeArmond SJ, Cohen FE, Daggett V (2001). Proc Natl Acad Sci USA 98:2985

    CAS  Google Scholar 

  37. Sekijima M, Motono C, Yamasaki S, Kaneko K, Akiyama Y (2003). BioPhys J 85:1176

    Article  CAS  Google Scholar 

  38. Langella E, Improta R, Barone V (2004). BioPhys J 87:3623

    CAS  Google Scholar 

  39. Langella E, Improta R, Crescenzi O, Barone V (2006). PROTEINS 64:167

    CAS  Google Scholar 

  40. Barducci A, Chelli R, Procacci P, Schettino V (2005). BioPhys J 88:1334

    CAS  Google Scholar 

  41. Barducci A, Chelli R, Procacci P, Schettino V, Gervasio FL, Parrinello M (2006). J Am Chem Soc 128:2705

    CAS  Google Scholar 

  42. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995). J Am Chem Soc 117:5179

    CAS  Google Scholar 

  43. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983). J Chem Phys 79:926

    CAS  Google Scholar 

  44. Pavone M, Brancato G, Morelli G, Barone V (2006). Chem Phys Chem 7:148

    CAS  Google Scholar 

  45. Brancato G, Di Nola A, Barone V, Amadei A (2005). J Chem Phys 122:154109

    Google Scholar 

  46. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995). J Chem Phys 103:8577

    CAS  Google Scholar 

  47. Liemann S, Glockshuber R (1999). BioChemistry 38:3258

    CAS  Google Scholar 

  48. Bussi G, Laio A, Parrinello M (2006). Phys Rev Lett 96:090601

    Google Scholar 

  49. Chelli R, Procacci P, Cardini G, Della Valle RG, Califano S (1999). Phys Chem Chem Phys 1:871

    CAS  Google Scholar 

  50. Chelli R, Procacci P, Cardini G, Califano S (1999). Phys Chem Chem Phys 1:879

    CAS  Google Scholar 

  51. Chelli R, Ciabatti S, Cardini G, Righini R, Procacci P (1999). J Chem Phys 111:4218

    CAS  Google Scholar 

  52. Chelli R, Gervasio FL, Gellini C, Procacci P, Cardini G, Schettino V (2000). J Phys Chem A 104:5351

    CAS  Google Scholar 

  53. Chelli R, Cardini G, Procacci P, Righini R, Califano S, Albrecht A (2000). J Chem Phys 113:6851

    CAS  Google Scholar 

  54. Ricci M, Bartolini P, Chelli R, Cardini G, Califano S, Righini R (2001). Phys Chem Chem Phys 3:2795

    CAS  Google Scholar 

  55. Chelli R, Cardini G, Ricci M, Bartolini P, Righini R, Califano S (2001). Phys Chem Chem Phys 3:2803

    CAS  Google Scholar 

  56. Chelli R, Cardini G, Procacci P, Righini R, Califano S (2002). J Chem Phys 116:6205

    CAS  Google Scholar 

  57. Chelli R, Cardini G, Procacci P, Righini R, Califano S (2003). J Chem Phys 119:357

    CAS  Google Scholar 

  58. Račko D, Chelli R, Cardini G, Bartoš J, Califano S (2005). Eur Phys J D 32:289

    Google Scholar 

  59. Chelli R, Righini R, Califano S (2005). J Phys Chem B 109:17006

    CAS  Google Scholar 

  60. Magro A, Frezzato D, Polimeno A, Moro GJ, Chelli R, Righini R (2005). J Chem Phys 123:124511

    Google Scholar 

  61. Pagliai M, Cardini G, Righini R, Schettino V (2003). J Chem Phys 119:6655

    CAS  Google Scholar 

  62. Chelli R, Gervasio FL, Gellini C, Procacci P, Cardini G, Schettino V (2000). J Phys Chem A 104:11220

    CAS  Google Scholar 

  63. Brandt W, Dupasquier A (1983) Positron solid state physics. North-Holland, Amsterdam

    Google Scholar 

  64. Bartos J, Sausa O, Bandzuch P, Zrubcova J, Kristiak J (2002). J Non-Cryst Solids 307:417

    Google Scholar 

  65. Götze W (1991) Liquids: freezing and glass transition. North-Holland, Amsterdam

    Google Scholar 

  66. Pagliai M, Cardini G, Righini R, Schettino V (2003). J Chem Phys 119:6655

    CAS  Google Scholar 

  67. Almenningen A, Bastiansen O, Motzfeldt T (1969). Acta Chem Scand 23:2848

    CAS  Google Scholar 

  68. Jedlovszky P, Turi L (1997). J Phys Chem B 101:5429

    CAS  Google Scholar 

  69. Gaffney KJ, Davis PH, Piletic IR, Levinger NE, Fayer MD (2002). J Phys Chem A 106:12012

    CAS  Google Scholar 

  70. Chelli R, Schettino V, Procacci P (2005). J Chem Phys 122:234107

    Google Scholar 

  71. Chelli R, Procacci P (2002). J Chem Phys 117:9175

    CAS  Google Scholar 

  72. Gresh N (1997). J Phys Chem A 101:8680

    CAS  Google Scholar 

  73. Chelli R, Pagliai M, Procacci P, Cardini G, Schettino V (2005). J Chem Phys 122:074504

    Google Scholar 

  74. Mortier WJ, Ghosh SK, Shankar S (1986). J Am Chem Soc 108:4315

    CAS  Google Scholar 

  75. Pagliai M, Cardini G, Schettino V (2005). J Phys Chem B 109:7475

    CAS  Google Scholar 

  76. Faralli C, Pagliai M, Cardini G, Schettino V (2006). J Phys Chem B 110:14923

    CAS  Google Scholar 

  77. Faralli C, Pagliai M, Cardini G, Schettino V (2006) Phys Chem Chem Phys (submitted)

  78. Faralli C, Pagliai M, Cardini G, Schettino V (2006) (in preparation)

  79. Hutter J, Alavi A, Deutch T, Bernasconi M, Goedecker S, Marx D, Tuckerman M, Parrinello M, (1995–1999) CPMD. MPI für Festkörperforschung and IBM Zurich Research Laboratory, Stuttgart

  80. Becke AD (1988). Phys Rev A 38:3098

    CAS  Google Scholar 

  81. Lee C, Yang W, Parr RG (1988). Phys Rev B 37:785

    CAS  Google Scholar 

  82. Troullier N, Martins JL (1991). Phys Rev B 43:1993

    CAS  Google Scholar 

  83. Vuilleumier R, Sprik M (2001). J Chem Phys 115(8):3454

    CAS  Google Scholar 

  84. Goedecker S, Teter M, Hutter J (1996). Phys Rev B 54:1703

    CAS  Google Scholar 

  85. Hartwigsen C, Goedecker S, Hutter (1998). J, Phys Rev B 58:3641

    CAS  Google Scholar 

  86. Krack M (2005). Theor Chem Acc 114:145

    CAS  Google Scholar 

  87. Marzari N, Vanderbilt D (1997). Phys Rev B 56:12848

    Google Scholar 

  88. Silvestrelli P, Marzari N, Vanderbilt D, Parrinello M (1998). Solid State Commun 107:7

    CAS  Google Scholar 

  89. Silvestrelli PL (1999). Phys Rev B 59:9703

    CAS  Google Scholar 

  90. Bader WRF (1991). Chem Rev 91:893

    CAS  Google Scholar 

  91. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Jr, Stratmann RE et al (1998) Gaussian 98, Revision A.11. Gaussian Inc., Pittsburg PA

    Google Scholar 

  92. Sesé G, Guàrdia E, Padró JA (1996). J Chem Phys 105: 8826

    Google Scholar 

  93. Tanida H, Sakane H, Watanabe I (1994). J Chem Soc Dalton Trans 2321–2326

  94. Watanabe I (1995). J Mol Liq 65/66:245

    Google Scholar 

  95. Impey RW, Sprik M, Klein ML (1987). J Am Chem Soc 109:5900

    CAS  Google Scholar 

  96. Wu C-C, Wang Y-S, Chandhuri C, Jiang JC, Chang H-C (2004). Chem Phys Lett 388:457

    CAS  Google Scholar 

  97. Megyes T, Radnai T, Grósz T, Pálinkàs G (2002). J Mol Liq 101:3

    CAS  Google Scholar 

  98. Carter E, Ciccotti G, Hynes J, Kapral R (1989). Chem Phys Lett 98:472

    Google Scholar 

  99. Sprik M (1998). Faraday Discuss. 110:437

    CAS  Google Scholar 

  100. Raugei S, Cardini G, Schettino V (1998). Mol Phys 95:477

    CAS  Google Scholar 

  101. Deng L, Branchadell V, Ziegler T (1994). J Am Chem Soc 116:10645

    CAS  Google Scholar 

  102. Raugei S, Cardini G, Schettino V (1999). J Chem Phys 111:10887

    CAS  Google Scholar 

  103. Raugei S, Cardini G, Schettino V (2001). J Chem Phys 114:4089

    CAS  Google Scholar 

  104. Pagliai M, Raugei S, Cardini G, Schettino V (2001). Phys Chem Chem Phys 3:2559

    CAS  Google Scholar 

  105. Pagliai M, Raugei S, Cardini G, Schettino V (2001). Phys Chem Chem Phys 3:4870

    CAS  Google Scholar 

  106. Pagliai M, Raugei S, Cardini G, Schettino V (2002). J Chem Phys 117:2199

    CAS  Google Scholar 

  107. Mugnai M, Cardini G, Schettino V (2003). J Chem Phys 118:2767

    CAS  Google Scholar 

  108. Mugnai M, Cardini G, Schettino V (2003). J Phys Chem A 107:2540

    CAS  Google Scholar 

  109. Pagliai M, Raugei S, Cardini G, Schettino V (2003). J Chem Phys 119:9063

    CAS  Google Scholar 

  110. Mugnai M, Cardini G, Schettino V (2004). Rend Fis Acc Lincei s.9, 15:99

    Article  Google Scholar 

  111. Boese AD, Doltsinis NL, Handy NC, Sprik M (2000). J Chem Phys 112:1670

    CAS  Google Scholar 

  112. Pagliai M, Raugei S, Cardini G, Schettino V (2003). J Mol Struct THEOCHEM 630:141

    CAS  Google Scholar 

  113. Mugnai M, Cardini G, Schettino V, Nielsen CJ (2006) Phys Chem Chem Phys (Submitted)

  114. Pratesi S (2006) Master’s Thesis, Università di Firenze (in preparazione)

  115. Perdew JP, Wang Y (1992). Phys Rev B 45:13244

    Google Scholar 

  116. Perdew JP, Burke K, Ernzerhof M (1996). Phys Rev Lett 77:3865

    CAS  Google Scholar 

  117. Vanderbilt D (1990). Phys Rev B 41:7892

    Google Scholar 

  118. Laasonen K, Car R, Lee C, Vanderbilt D (1991). Phys Rev B 43:6796

    CAS  Google Scholar 

  119. Laasonen K, Pasquarello A, Lee C, Car R, Vanderbilt D (1993). Phys Rev. B 47:10142

    CAS  Google Scholar 

  120. di Pietro E, Cardini G, Schettino V (2006) (in preparation)

  121. Schettino V, Bini R (2003). Phys Chem Chem Phys 5:1951

    CAS  Google Scholar 

  122. Parrinello M (2000). Comput Sci Eng 2:22

    CAS  Google Scholar 

  123. Iannuzzi M, Laio A, Parrinello M (2003). Phys Rev Lett 90:238302

    Google Scholar 

  124. Parrinello M, Rahman A (1980). Phys Rev Lett 45:1196

    CAS  Google Scholar 

  125. Pagliai M, Iannuzzi M, Cardini G, Parrinello M, Schettino V (2006). Chem Phys Chem 7:141

    CAS  Google Scholar 

  126. Von Göttlicher S, Kieselbach B (1976). Acta Cryst. A32:185

    Google Scholar 

  127. Mair SL (1978). Acta Cryst A34:542

    Google Scholar 

  128. di Pietro E, Pagliai M, Cardini G, Schettino V (2006). J Phys Chem B 110:13539

    Google Scholar 

  129. Silvestrelli PL, Parrinello M (1999). Phys Rev Lett 82:3308

    CAS  Google Scholar 

  130. Silvestrelli PL, Parrinello M (1999). J Chem Phys 111:3572

    CAS  Google Scholar 

  131. Eremets M, Gavriliuk G, Serebryanaya NR, Trojan IA, Dzivenko DA, Boehler R, Mao K, Hemley R (2004). J Chem Phys 121:11296

    CAS  Google Scholar 

  132. Muniz F (2006) Master’s Thesis, Univeristà di Firenze (in preparazione)

  133. Gregoryanz E, Sanloup C, Bini R, Kreutz J, Jodl H, Somayazulu M, Mao K, Hemley R (2006). J Chem Phys 124:16102

    Google Scholar 

  134. Schettino V, Bini R, Ceppatelli M, Ciabini L, Citroni M (2005). Adv Chem Phys 131:105

    CAS  Google Scholar 

  135. Bernasconi M, Chiarotti GL, Focher P, Parrinello M, Tosatti E (1996). Phys Rev Lett 76:2081

    CAS  Google Scholar 

  136. Bernasconi M, Chiarotti GL, Focher P, Parrinello M, Tosatti E (1997). Phys Rev Lett 78:2008

    CAS  Google Scholar 

  137. Mugnai M, Cardini G, Schettino V (2004). J Chem Phys 120:5327

    CAS  Google Scholar 

  138. Mugnai M, Cardini G, Schettino V (2004) Phys Rev B 70:020101(1)

    Google Scholar 

  139. Mugnai M, Pagliai M, Cardini G, Schettino V (2006) (in preparation)

  140. Pignataro G (2005) Master’s Thesis, Università di Firenze

  141. Ciabini L, Gorelli FA, Santoro M, Bini R, Schettino V, Raugei S (2006) Nature Mater (in press)

  142. Chelazzi D, Ceppatelli M, Santoro M, Bini R, Schettino V (2004). Nature Mater 3:470

    CAS  Google Scholar 

  143. Citroni M, Ceppatelli M, Bini R and Schettino V (2002). Science 295:2058

    CAS  Google Scholar 

  144. Cohen M (1975). Ang Chem Int Ed Engl 14:386

    Google Scholar 

  145. Chelazzi D, Ceppatelli M, Santoro M, Bini R, Schettino V (2004). J Phys Chem B 109:21658

    Google Scholar 

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Authors and Affiliations

  1. Laboratorio di Spettroscopia Molecolare, Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, Sesto Fiorentino, Italy

    Vincenzo Schettino, Riccardo Chelli, Simone Marsili, Alessandro Barducci, Cristian Faralli, Marco Pagliai, Piero Procacci & Gianni Cardini

  2. European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, Sesto Fiorentino, Italy

    Vincenzo Schettino, Riccardo Chelli, Simone Marsili, Alessandro Barducci, Cristian Faralli, Marco Pagliai, Piero Procacci & Gianni Cardini

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  1. Vincenzo Schettino
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  2. Riccardo Chelli
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  3. Simone Marsili
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Correspondence to Vincenzo Schettino.

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Schettino, V., Chelli, R., Marsili, S. et al. Problems in molecular dynamics of condensed phases. Theor Chem Account 117, 1105–1120 (2007). https://doi.org/10.1007/s00214-006-0223-0

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