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Supramolecular Organization of Functional Organic Materials in the Bulk and at Organic/Organic Interfaces: A Modeling and Computer Simulation Approach

  • Luca Muccioli
  • Gabriele D’Avino
  • Roberto Berardi
  • Silvia Orlandi
  • Antonio Pizzirusso
  • Matteo Ricci
  • Otello Maria Roscioni
  • Claudio ZannoniEmail author
Chapter
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 352)

Abstract

The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational “engine” (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions. Recent literature dealing with the simulation of organic semiconductors is critically reviewed in order of increasing complexity of the system studied, from low molecular weight molecules to semiflexible polymers, including the challenging problem of determining the morphology of heterojunctions between two different materials.

Keywords

Atomistic Coarse-graining Organic semiconductors Molecular dynamics Monte Carlo Molecular mechanics Force field Gay–Berne Liquid crystals Timescales Polymers 

Abbreviations

1D

One-dimensional

2D

Two-dimensional

3D

Three-dimensional

Alq3

Tris(8-hydroxyquinolinato) aluminum

BI

Boltzmann inversion (method)

CF

Correlation function

CG

Coarse-grained

CPU

Central processing unit

DPD

Dissipative particle dynamics

FF

Force field

GB

Gay–Berne (potential)

GPU

Graphics processing unit

KMC

Kinetic Monte Carlo (method)

LC

Liquid crystal

LJ

Lennard–Jones (potential)

MC

Monte Carlo (method)

MD

Molecular dynamics

ODF

Orientational distribution function

OLED

Organic light emitting diode

MEH-PPV

Poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylene vinylene

P3HT

Poly(3-hexylthiophene-2,5-diyl)

PBTTT

Poly[2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene]

PCBM

[6,6]-Phenyl C61 butyric acid methyl ester

PPV

Poly[phenylene vinylene]

QM

Quantum mechanics

RDF

Radial distribution function

RM

Reverse mapping

SCP

Semi conducting polymers

T6

α-Sexithiophene

UA

United atom (force field)

References

  1. 1.
    Maddox J (1988) Nature 335:201Google Scholar
  2. 2.
    Pizzirusso A, Savini M, Muccioli L, Zannoni C (2011) J Mater Chem 21:125Google Scholar
  3. 3.
    Pasini P, Zannoni C (2000) Advances in the computer simulations of liquid crystals. NATO ASI Series, kluwer, DordrechtGoogle Scholar
  4. 4.
    Groves C, Greenham NC (2013) Monte Carlo simulations of organic photovoltaics. Top Curr Chem. doi:10.1007/128_2013_467.Google Scholar
  5. 5.
    Walker A (2013) Monte Carlo studies of electronic processes in dye-sensitized solar cells. Top Curr Chem. doi:10.1007/128_2013_472.Google Scholar
  6. 6.
    Athanasopoulos S, Emelianova EV, Walker AB, Beljonne D (2009) Phys Rev B 80:195209Google Scholar
  7. 7.
    Car R, Parrinello M (1985) Phys Rev Lett 55:2471Google Scholar
  8. 8.
    Stone AJ (1996) The theory of intermolecular forces, international series of monographs on chemistry, vol 32. Oxford University Press, OxfordGoogle Scholar
  9. 9.
    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 117:5179Google Scholar
  10. 10.
    Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25:1157Google Scholar
  11. 11.
    Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225Google Scholar
  12. 12.
    Mackerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586Google Scholar
  13. 13.
    Marcon V, van der Vegt N, Wegner G, Raos G (2006) J Phys Chem B 110:5253Google Scholar
  14. 14.
    Sancho-García J, Karpfen A (2009) Chem Phys Lett 473:49Google Scholar
  15. 15.
    Bhatta RS, Yimer YY, Tsige M, Perry DS (2012) Comput Theor Chem 995:36Google Scholar
  16. 16.
    Cheung DL, McMahon DP, Troisi A (2009) J Phys Chem B 113:9393Google Scholar
  17. 17.
    Rigby J, Izgorodina EI (2013) Phys Chem Chem Phys 15:1632Google Scholar
  18. 18.
    Kramer C, Gedeck P, Meuwly M (2012) J Comput Chem 33:1673Google Scholar
  19. 19.
    Wang B, Truhlar DG (2012) J Chem Theory Comput 8:1989Google Scholar
  20. 20.
    Berardi R, Muccioli L, Orlandi S, Ricci M, Zannoni C (2004) Chem Phys Lett 389:373Google Scholar
  21. 21.
    Lopes P, Roux B, MacKerell AD Jr (2009) Theor Chem Acc 124:11Google Scholar
  22. 22.
    Cieplak P, Dupradeau FY, Duan Y, Wang J (2009) J Phys Condens Matter 21:333102Google Scholar
  23. 23.
    Jiang W, Hardy DJ, Phillips JC, Mackerell AD, Schulten K, Roux B (2011) J Phys Chem Lett 2:87Google Scholar
  24. 24.
    Brooks BR, Brooks CL III, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) J Comput Chem 30:1545Google Scholar
  25. 25.
    Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T (2010) J Phys Chem B 114:2549Google Scholar
  26. 26.
    Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y (2011) J Phys Chem B 115:3100Google Scholar
  27. 27.
    Vorobyov IV, Anisimov VM, Mackerell AD (2005) J Phys Chem B 109:18988Google Scholar
  28. 28.
    Lopes PEM, Lamoureux G, Roux B, Mackerell AD (2007) J Phys Chem B 111:2873Google Scholar
  29. 29.
    Yang L, Tan C, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R (2006) J Phys Chem B 110:13166Google Scholar
  30. 30.
    von Lilienfeld OA, Andrienko D (2006) J Chem Phys 124:054307Google Scholar
  31. 31.
    Scott WRP, Hünenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Krüger P, van Gunsteren WF (1999) J Phys Chem A 103:3596Google Scholar
  32. 32.
    Keasler SJ, Charan SM, Wick CD, Economou IG, Siepmann JI (2012) J Phys Chem B 116:11234Google Scholar
  33. 33.
    Papadopoulos TA, Muccioli L, Athanasopoulos S, Walker AB, Zannoni C, Beljonne D (2011) Chem Sci 2:1025Google Scholar
  34. 34.
    Olivier Y, Muccioli L, Lemaur V, Geerts YH, Zannoni C, Cornil J (2009) J Phys Chem B 113:14102Google Scholar
  35. 35.
    Sapay N, Tieleman DP (2011) J Comput Chem 32:1400Google Scholar
  36. 36.
    Palermo MF, Pizzirusso A, Muccioli L, Zannoni C (2013) J Chem Phys 138:204901Google Scholar
  37. 37.
    Theodorou DN (2007) Chem Eng Sci 62:5697Google Scholar
  38. 38.
    Huang DM, Faller R, Do K, Moule AJ (2010) J Chem Theory Comput 6:526Google Scholar
  39. 39.
    Liu DJ, Selinger RLB, Weeks JD (1996) J Chem Phys 105:4751Google Scholar
  40. 40.
    Girifalco LA (1992) J Phys Chem 96:858Google Scholar
  41. 41.
    Sazonovas A, Orlandi S, Ricci M, Zannoni C, Gorecka E (2006) Chem Phys Lett 430:297Google Scholar
  42. 42.
    Kniaz K, Girifalco LA, Fischer JE (1995) J Phys Chem 99:16804Google Scholar
  43. 43.
    Girifalco LA, Hodak M, Lee RS (2000) Phys Rev B 62:13104Google Scholar
  44. 44.
    Peter C, Kremer K (2010) Faraday Discuss 144:9Google Scholar
  45. 45.
    Peter C, Kremer K (2009) Soft Matter 5:4357Google Scholar
  46. 46.
    Karimi-Varzaneh HA, Müller-Plathe F (2012) In: Kirchner B, Vrabec J (eds) Multiscale molecular methods in applied chemistry, Topics in current chemistry, vol 307. Springer, Berlin, pp. 295–321Google Scholar
  47. 47.
    Karimi-Varzaneh HA, van der Vegt NFA, Müller-Plathe F, Carbone P (2012) Chemphyschem 13:3428Google Scholar
  48. 48.
    Müller-Plathe F (2002) Chemphyschem 3:754Google Scholar
  49. 49.
    Takada S (2012) Curr Opin Struct Biol 22:130Google Scholar
  50. 50.
    Ayton GS, Lyman E, Voth GA (2010) Faraday Discuss 144:347Google Scholar
  51. 51.
    Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) J Phys Chem B 111:7812Google Scholar
  52. 52.
    Rudzinski JF, Noid WG (2011) J Chem Phys 135:214101Google Scholar
  53. 53.
    Reith D, Pütz M, Müller-Plathe F (2003) J Comput Chem 24:1624Google Scholar
  54. 54.
    Lyubartsev AP, Laaksonen A (1995) Phys Rev E 52:3730Google Scholar
  55. 55.
    Wong-Ekkabut J, Baoukina S, Triampo W, Tang IM, Tieleman DP, Monticelli L (2008) Nat Nanotechnol 3:363Google Scholar
  56. 56.
    Rossi G, Monticelli L, Puisto SR, Vattulainen I, Ala-Nissila T (2011) Soft Matter 7:698Google Scholar
  57. 57.
    Tschöp W, Kremer K, Hahn O, Batoulis J, Bürger T (1998) Acta Polymerica 49:75Google Scholar
  58. 58.
    Marcon V, Fritz D, van der Vegt NFA (2012) Soft Matter 8:5585Google Scholar
  59. 59.
    Fritz D, Herbers CR, Kremer K, van der Vegt NFA (2009) Soft Matter 5:4556Google Scholar
  60. 60.
    Fritz D, Koschke K, Harmandaris VA, van der Vegt NFA, Kremer K (2011) Phys Chem Chem Phys 13:10412Google Scholar
  61. 61.
    Harmandaris VA, Kremer K (2009) Macromolecules 42(3):791Google Scholar
  62. 62.
    Mukherjee B, Delle Site L, Kremer K, Peter C (2012) J Phys Chem B 116:8474Google Scholar
  63. 63.
    Huang DM, Moule AJ, Faller R (2011) Fluid Phase Equilibria 302:21Google Scholar
  64. 64.
    Gay J, Berne B (1981) J Chem Phys 74:3316Google Scholar
  65. 65.
    Lennard-Jones J (1924) Proc R Soc London Ser A 106:463Google Scholar
  66. 66.
    Zannoni C (2001) J Mater Chem 11:2637Google Scholar
  67. 67.
    Emerson A, Luckhurst G, Whatling S (1994) Mol Phys 82:113Google Scholar
  68. 68.
    Orlandi S, Muccioli L, Ricci M, Berardi R, Zannoni C (2007) Chem Cent J 1:15Google Scholar
  69. 69.
    Cleaver D, Care C, Allen M, Neal M (1996) Phys Rev E 54:559Google Scholar
  70. 70.
    Berardi R, Fava C, Zannoni C (1998) Chem Phys Lett 297:8Google Scholar
  71. 71.
    Fejer SN, Chakrabarti D, Wales DJ (2011) Soft Matter 7:3553Google Scholar
  72. 72.
    Berardi R, Orlandi S, Zannoni C (1996) Chem Phys Lett 261:357Google Scholar
  73. 73.
    Wilson M (1997) J Chem Phys 107:8654Google Scholar
  74. 74.
    Berardi R, Micheletti D, Muccioli L, Ricci M, Zannoni C (2004) J Chem Phys 121:9123Google Scholar
  75. 75.
    Stimson L, Wilson M (2005) J Chem Phys 123:034908Google Scholar
  76. 76.
    Lee CK, Hua CC, Chen SA (2010) J Chem Phys 133:064902Google Scholar
  77. 77.
    Lee CK, Hua CC, Chen SA (2012) J Chem Phys 136:084901Google Scholar
  78. 78.
    Wilson M, Stimson L, Ilnytskyi J (2006) Liq Cryst 33:1167Google Scholar
  79. 79.
    Skacej G, Zannoni C (2012) PNAS 109:10193Google Scholar
  80. 80.
    Orlandi S, Muccioli L, Ricci M, Zannoni C (2009) Soft Matter 5:4484Google Scholar
  81. 81.
    Bacchiocchi C, Hennebicq E, Orlandi S, Muccioli L, Beljonne D, Zannoni C (2008) J Phys Chem B 112:1752Google Scholar
  82. 82.
    Kremer K, Grest GS (1990) J Chem Phys 92:5057Google Scholar
  83. 83.
    Everaers R, Sukumaran SK, Grest GS, Svaneborg C, Sivasubramanian A, Kremer K (2004) Science 303:823Google Scholar
  84. 84.
    Hoogerbrugge P, Koelman J (1992) Europhys Lett 19:155Google Scholar
  85. 85.
    Groot RD, Madden TJ, Tildesley DJ (1999) J Chem Phys 110:9739Google Scholar
  86. 86.
    Martinez-Veracoechea FJ, Escobedo FA (2006) J Chem Phys 125:104907/1Google Scholar
  87. 87.
    Huang HK, Lin CH (2008) Phys Rev E 77:031804/1Google Scholar
  88. 88.
    Pal S, Seidel C (2006) Macromol Theor Simul 15:668Google Scholar
  89. 89.
    Espanol P (1995) Phys Rev E 52:1734Google Scholar
  90. 90.
    Espanol P, Warren P (1995) Europhys Lett 30:191Google Scholar
  91. 91.
    Groot R, Warren P (1997) J Chem Phys 107:4423Google Scholar
  92. 92.
    Chen S, Phan-Thien N, Fan XJ, Khoo B (2004) J Nonnewton Fluid Mech 118:65Google Scholar
  93. 93.
    Cheung DL, Troisi A (2009) Phys Chem Chem Phys 11:2105Google Scholar
  94. 94.
    Lintuvuori JS, Wilson MR (2009) Phys Chem Chem Phys 11:2116Google Scholar
  95. 95.
    Allen MP, Tildesley DJ (1989) Computer simulation of liquids. Oxford University Press, OxfordGoogle Scholar
  96. 96.
    Frenkel D, Smit B (2001) Understanding molecular simulations, 2nd edn. Academic, San DiegoGoogle Scholar
  97. 97.
    Voter AF, Montalenti F, Germann TC (2002) Annu Rev Mater Res 32:321Google Scholar
  98. 98.
    Theodorou DN (2010) Ind Eng Chem Res 49:3047Google Scholar
  99. 99.
    Chipot C, Pohorille A (2007) Free energy calculations: theory and applications in chemistry and biology, Springer series in chemical physics. Springer–Verlag, Berlin HeidelbergGoogle Scholar
  100. 100.
    Christ CD, Mark AE, van Gunsteren WF (2010) J Comput Chem 31:1569Google Scholar
  101. 101.
    Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) J Chem Phys 21:1087Google Scholar
  102. 102.
    Alder BJ, Wainwright TE (1959) J Chem Phys 31:459Google Scholar
  103. 103.
    Knuth D (1998) Seminumerical algorithms. Addison–WesleyGoogle Scholar
  104. 104.
    Van Kampen N (1992) Stochastic processes in physics and chemistry. North-Holland Personal Library, Elsevier Science, AmsterdamGoogle Scholar
  105. 105.
    Chatterjee A, Vlachos DG (2007) J Comp Mater Design 14:253Google Scholar
  106. 106.
    Gillespie DT (2007) Ann Rev Phys Chem 58:35Google Scholar
  107. 107.
    Kamberaj H, Low RJ, Neal MP (2005) J Chem Phys 122:224114Google Scholar
  108. 108.
    Altmann SL (2005) Rotations, quaternions, and double groups. Dover, New YorkGoogle Scholar
  109. 109.
    Berardi R, Muccioli L, Zannoni C (2008) J Chem Phys 128:024905Google Scholar
  110. 110.
    Hünenberger PH (2005) In: Holm C, Kremer K (eds) Advanced computer simulation approaches for soft matter sciences I—series: advances in polymer science, vol 173. Springer, chap. 2, pp 105–149. http://link.springer.com/chapter/10.1007/b99427
  111. 111.
    Kirkpatrick J, Marcon V, Kremer K, Nelson J, Andrienko D (2008) J Chem Phys 129:094506Google Scholar
  112. 112.
    Poelking C, Cho E, Malafeev A, Ivanov V, Kremer K, Risko C, Brédas JL, Andrienko D (2013) J Chem Phys C 117:1633Google Scholar
  113. 113.
    Cinacchi G, Colle R, Tani A (2004) J Phys Chem B 108:7969Google Scholar
  114. 114.
    Andrienko D, Marcon V, Kremer K (2006) J Chem Phys 125:124902Google Scholar
  115. 115.
    Zannoni C (1994) In: Luckhurst G, Veracini C (eds) The molecular dynamics of liquid crystals. Kluwer, Dordrecht, Chap. 2, pp 11–36Google Scholar
  116. 116.
    Pizzirusso A, Berardi R, Muccioli L, Ricci M, Zannoni C (2012) Chem Sci 3:573Google Scholar
  117. 117.
    Roscioni OM, Muccioli L, Della Valle RG, Pizzirusso A, Ricci M, Zannoni C (2013) Langmuir 23:8950Google Scholar
  118. 118.
    Marconi UMB, Puglisi A, Rondoni L, Vulpiani A (2008) Phys Rep 461:111Google Scholar
  119. 119.
    Muccioli L, D’Avino G, Zannoni C (2011) Adv Mat 23:4532Google Scholar
  120. 120.
    De Leener C, Hennebicq E, Sancho-Garcia JC, Beljonne D (2009) J Phys Chem B 113:1311Google Scholar
  121. 121.
    D’Avino G, Mothy S, Muccioli L, Zannoni C, Wang L, Cornil J, Beljonne D, Castet F (2013) J Phys Chem C 117:12981Google Scholar
  122. 122.
    Cantrell R, Clancy P (2008) Surf Sci 602:3499Google Scholar
  123. 123.
    Cantrell RA, James C, Clancy P (2011) Langmuir 27:9944Google Scholar
  124. 124.
    O’Neill M, Kelly SM (2011) Adv Mater 23:566Google Scholar
  125. 125.
    Bardwell DA, Adjiman CS, Arnautova YA, Bartashevich E, Boerrigter SXM, Braun DE, Cruz-Cabeza AJ, Day GM, Della Valle RG, Desiraju GR, van Eijck BP, Facelli JC, Ferraro MB, Grillo D, Habgood M, Hofmann DWM, Hofmann F, Jose KVJ, Karamertzanis PG, Kazantsev AV, Kendrick J, Kuleshova LN, Leusen FJJ, Maleev AV, Misquitta AJ, Mohamed S, Needs RJ, Neumann MA, Nikylov D, Orendt AM, Pal R, Pantelides CC, Pickard CJ, Price LS, Price SL, Scheraga HA, van de Streek J, Thakur TS, Tiwari S, Venuti E, Zhitkov IK (2011) Acta Crystallogr B 67:535Google Scholar
  126. 126.
    Anwar J, Zahn D (2011) Angew Chem Int Ed 50:1996Google Scholar
  127. 127.
    Martinelli NG, Savini M, Muccioli L, Olivier Y, Castet F, Zannoni C, Beljonne D, Cornil J (2009) Adv Funct Mater 19:3254Google Scholar
  128. 128.
    Troisi A, Orlandi G (2006) J Phys Chem A 110:4065Google Scholar
  129. 129.
    Motta SD, Donato ED, Negri F, Orlandi G, Fazzi D, Castiglioni C (2009) JACS 131:6591Google Scholar
  130. 130.
    Wang L, Li Q, Shuai Z, Chen L, Shi Q (2010) Phys Chem Chem Phys 12:3309Google Scholar
  131. 131.
    Troisi A (2007) Adv Mater 19:2000Google Scholar
  132. 132.
    Martinelli NG, Ide J, Sanchez-Carrera RS, Coropceanu V, Bredas JL, Ducasse L, Castet F, Cornil J, Beljonne D (2010) J Phys Chem C 114:20678Google Scholar
  133. 133.
    Martinelli NG, Olivier Y, Athanasopoulos S, Delgado MCR, Pigg KR, da Silva Filho DA, Sanchez-Carrera RS, Venuti E, Valle RGD, Bredas JL, Beljonne D, Cornil J (2009) Chemphyschem 10:2265Google Scholar
  134. 134.
    Motta SD, Siracusa M, Negri F (2011) J Phys Chem C 115:20754Google Scholar
  135. 135.
    Schrader M, Fitzner R, Hein M, Elschner C, Baumeier B, Leo K, Riede M, Bäuerle P, Andrienko D (2012) J Am Chem Soc 134:6052Google Scholar
  136. 136.
    Vehoff T, Chung YS, Johnston K, Troisi A, Yoon DY, Andrienko D (2010) J Phys Chem C 114:10592Google Scholar
  137. 137.
    Vehoff T, Baumeier B, Troisi A, Andrienko D (2010) J Am Chem Soc 132:11702Google Scholar
  138. 138.
    Chang J, Sandler SI (2006) J Chem Phys 125:054705Google Scholar
  139. 139.
    Cheung DL, Troisi A (2010) J Phys Chem C 114:20479Google Scholar
  140. 140.
    Frigerio F, Casalegno M, Carbonera C, Nicolini T, Meille SV, Raos G (2012) J Mater Chem 22:5434Google Scholar
  141. 141.
    May F, Al-Helwi M, Baumeier B, Kowalsky W, Fuchs E, Lennartz C, Andrienko D (2012) J Am Chem Soc 134:13818Google Scholar
  142. 142.
    Kwiatkowski JJ, Nelson J, Li H, Bredas JL, Wenzel W, Lennartz C (2008) Phys Chem Chem Phys 10:1852Google Scholar
  143. 143.
    Nagata Y, Lennartz C (2008) J Chem Phys 129:034709Google Scholar
  144. 144.
    Lukyanov A, Lennartz C, Andrienko D (2009) Phys Status Solidi A 206:2737Google Scholar
  145. 145.
    Schrader M, Körner C, Elschner C, Andrienko D (2012) J Mater Chem 22:22258Google Scholar
  146. 146.
    Tiberio G, Muccioli L, Berardi R, Zannoni C (2009) Chem Phys Chem 10:125Google Scholar
  147. 147.
    Tant J, Geerts YH, Lehmann M, De Cupere V, Zucchi G, Laursen BW, Bjornholm T, Lemaur V, Marcq V, Burquel A, Hennebicq E, Gardebien F, Viville P, Beljonne D, Lazzaroni R, Cornil J (2005) J Phys Chem B 109:20315Google Scholar
  148. 148.
    Marcon V, Breiby DW, Pisula W, Dahl J, Kirkpatrick J, Patwardhan S, Grozema F, Andrienko D (2009) J Am Chem Soc 131:11426Google Scholar
  149. 149.
    Lemaur V, Bouzakraoui S, Olivier Y, Brocorens P, Burhin C, El Beghdadi J, Martin-Hoyas A, Jonas AM, Serban DA, Vlad A, Boucher N, Leroy J, Sferrazza M, Mouthuy PO, Melinte S, Sergeev S, Geerts Y, Lazzaroni R, Cornil J, Nysten B (2010) J Phys Chem C 114:4617Google Scholar
  150. 150.
    May F, Marcon V, Hansen MR, Grozema F, Andrienko D (2011) J Mater Chem 21:9538Google Scholar
  151. 151.
    Marcon V, Vehoff T, Kirkpatrick J, Jeong C, Yoon DY, Kremer K, Andrienko D (2008) J Chem Phys 129:094505Google Scholar
  152. 152.
    Feng X, Marcon V, Pisula W, Hansen MR, Kirkpatrick J, Grozema F, Andrienko D, Kremer K, Müllen K (2009) Nat Mater 8:1476Google Scholar
  153. 153.
    Idé J, Mereau R, Ducasse L, Castet F, Olivier Y, Martinelli N, Cornil J, Beljonne D (2011) J Phys Chem B 115:5593Google Scholar
  154. 154.
    Lamarra M, Muccioli L, Orlandi S, Zannoni C (2012) Phys Chem Chem Phys 14:5368Google Scholar
  155. 155.
    Doi M, Edwards S (1988) The theory of polymer dynamics. Oxford science publications. Oxford University PressGoogle Scholar
  156. 156.
    McMahon DP, Troisi A (2010) Chemphyschem 11:2067Google Scholar
  157. 157.
    Topham PD, Parnell AJ, Hiorns RC (2011) J Polym Sci Part B Polym Phys 49:1131Google Scholar
  158. 158.
    Yassar A, Miozzo L, Gironda R, Horowitz G (2013) Prog Polym Sci 38:791Google Scholar
  159. 159.
    Bates FS, Hillmyer MA, Lodge TP, Bates CM, Delaney KT, Fredrickson GH (2012) Science 336:434Google Scholar
  160. 160.
    Ramanathan M, Darling SB (2011) Prog Polym Sci 36:793Google Scholar
  161. 161.
    Micheletti D, Muccioli L, Berardi R, Ricci M, Zannoni C (2005) J Chem Phys 123:224705Google Scholar
  162. 162.
    Yung KL, He L, Xu Y, Shen YW (2005) Polymer 46:11881Google Scholar
  163. 163.
    Berardi R, Lintuvuori JS, Wilson MR, Zannoni C (2011) J Chem Phys 135:134119Google Scholar
  164. 164.
    Makke A, Lame O, Perez M, Barrat JL (2012) Macromolecules 45:8445Google Scholar
  165. 165.
    Arosio P, Moreno M, Famulari A, Raos G, Catellani M, Meille SV (2009) Chem Mater 21:78Google Scholar
  166. 166.
    Moreno M, Casalegno M, Raos G, Meille SV, Po R (2010) J Phys Chem B 114:1591Google Scholar
  167. 167.
    Niedzialek D, Lemaur V, Dudenko D, Shu J, Hansen MR, Andreasen JW, Pisula W, Müllen K, Cornil J, Beljonne D (2013) Adv Mater 25:1939Google Scholar
  168. 168.
    DuBay KH, Hall ML, Hughes TF, Wu C, Reichman DR, Friesner RA (2012) J Chem Theory Comput 8:4556Google Scholar
  169. 169.
    Arbe A, Alvarez F, Colmenero J (2012) Soft Matter 8:8257Google Scholar
  170. 170.
    Rivnay J, Mannsfeld SCB, Miller CE, Salleo A, Toney MF (2012) Chem Rev 112:5488Google Scholar
  171. 171.
    Brocorens P, Van Vooren A, Chabinyc ML, Toney MF, Shkunov M, Heeney M, McCulloch I, Cornil J, Lazzaroni R (2009) Adv Mat 21:1193Google Scholar
  172. 172.
    Cho E, Risko C, Kim D, Gysel R, Cates Miller N, Breiby DW, McGehee MD, Toney MF, Kline RJ, Bredas JL (2012) J Am Chem Soc 134:6177Google Scholar
  173. 173.
    Ren XK, Wu YC, Wang SJ, Jiang SD, Zheng JF, Yang S, Chen EQ, Wang CL, Hsu CS (2013) Macromolecules 46:155Google Scholar
  174. 174.
    Fonner JM, Schmidt CE, Ren P (2010) Polymer 51:4985Google Scholar
  175. 175.
    Granadino-Roldan J, Vukmirovic N, Fernandez-Gomez M, Wang LW (2011) Phys Chem Chem Phys 13:14501Google Scholar
  176. 176.
    Curcó D, Alemán C (2007) J Comput Chem 28:1743Google Scholar
  177. 177.
    Kilina S, Batista ER, Yang P, Tretiak S, Saxena A, Martin RL, Smith DL (2008) ACS Nano 2:1381Google Scholar
  178. 178.
    Jakobsson M, Linares M, Stafstrom S (2012) J Chem Phys 137:114901Google Scholar
  179. 179.
    Do K, Huang DM, Faller R, Moule AJ (2010) Phys Chem Chem Phys 12:14735Google Scholar
  180. 180.
    Vehoff T, Baumeier B, Andrienko D (2010) J Chem Phys 133:134901Google Scholar
  181. 181.
    Shaytan AK, Schillinger EK, Khalatur PG, Mena-Osteritz E, Hentschel J, Börner HG, Bäuerle P, Khokhlov AR (2011) ACS Nano 5:6894Google Scholar
  182. 182.
    Melis C, Colombo L, Mattoni A (2011) J Chem Phys C 115:576Google Scholar
  183. 183.
    Dag S, Wang LW (2010) J Phys Chem B 114:5997Google Scholar
  184. 184.
    Buono A, Son NH, Raos G, Gila L, Cominetti A, Catellani M, Meille SV (2010) Macromolecules 43:6772Google Scholar
  185. 185.
    Alexiadis O, Mavrantzas VG (2013) Macromolecules 46:2450Google Scholar
  186. 186.
    McMahon DP, Cheung DL, Goris L, na Javier D, Salleo A, Troisi A (2011) J Chem Phys C 115:19386Google Scholar
  187. 187.
    Lee CK, Hua CC, Chen SA (2008) J Phys Chem B 112:11479Google Scholar
  188. 188.
    Lee CK, Hua CC, Chen SA (2011) Macromolecules 44:320Google Scholar
  189. 189.
    Chiu M, Kee TW, Huang DM (2012) Aust J Chem 65:463Google Scholar
  190. 190.
    Lukyanov A, Malafeev A, Ivanov V, Chen HL, Kremer K, Andrienko D (2010) J Mater Chem 20:10475Google Scholar
  191. 191.
    Lee CK, Pao CW, Chu CW (2011) Energy Environ Sci 4:4124Google Scholar
  192. 192.
    Lee CK, Pao CW (2012) J Chem Phys C 116:12455Google Scholar
  193. 193.
    Beljonne D, Cornil J, Muccioli L, Zannoni C, Brédas JL, Castet F (2011) Chem Mater 23:591Google Scholar
  194. 194.
    Tsige M, Grest GS (2005) J Phys Condens Matter 17:S4119Google Scholar
  195. 195.
    Yimer YY, Dhinojwala A, Tsige M (2012) J Chem Phys 137:044703Google Scholar
  196. 196.
    Marsh HS, Jayaraman A (2013) J Polym Sci Part B Polym Phys 51:64Google Scholar
  197. 197.
    Verlaak S, Beljonne D, Cheyns D, Rolin C, Linares M, Castet F, Cornil J, Heremans P (2009) Adv Funct Mater 19:3809Google Scholar
  198. 198.
    Meredig B, Salleo A, Gee R (2009) ACS Nano 3:2881Google Scholar
  199. 199.
    Poschlad A, Meded V, Maul R, Wenzel W (2012) Nanoscale Res Lett 7:1Google Scholar
  200. 200.
    Liu T, Cheung DL, Troisi A (2011) Phys Chem Chem Phys 13:21461Google Scholar
  201. 201.
    McMahon DP, Cheung DL, Troisi A (2011) J Phys Chem Lett 2:2737Google Scholar
  202. 202.
    Marcon V, Raos G (2006) J Am Chem Soc 128:1408Google Scholar
  203. 203.
    Yost SR, Wang LP, Van Voorhis T (2011) J Chem Phys C 115:14431Google Scholar
  204. 204.
    Reddy SY, Kuppa VK (2012) J Chem Phys C 116:14873Google Scholar
  205. 205.
    Reddy SY, Kuppa VK (2012) Synth Met 162:2117Google Scholar
  206. 206.
    Mou W, Ohmura S, Hattori S, Nomura K, Shimojo F, Nakano A (2012) J Chem Phys 136:184705Google Scholar
  207. 207.
    Hattori S, Mou W, Rajak P, Shimojo F, Nakano A (2013) Appl Phys Lett 102:093302Google Scholar
  208. 208.
    Fu YT, Risko C, Brédas JL (2013) Adv Mater 25:878Google Scholar
  209. 209.
    Clancy P (2011) Chem Mater 23:522Google Scholar
  210. 210.
    Verlaak S, Rolin C, Heremans P (2007) J Phys Chem B 111:139Google Scholar
  211. 211.
    Liu H, Lin Z, Zhigilei LV, Reinke P (2008) J Chem Phys C 112:4687Google Scholar
  212. 212.
    Cantrell RA, Clancy P (2012) J Chem Theory Comput 8:1048Google Scholar
  213. 213.
    Goose JE, First EL, Clancy P (2010) Phys Rev B 81:205310Google Scholar
  214. 214.
    Goose JE, Clancy P (2007) J Chem Phys C 111:15653Google Scholar
  215. 215.
    Goose JE, Killampalli A, Clancy P, Engstrom JR (2009) J Phys Chem C 113:6068Google Scholar
  216. 216.
    Tuckerman M, Berne BJ, Martyna GJ (1992) J Chem Phys 97:1990Google Scholar
  217. 217.
    Ryckaert J, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327Google Scholar
  218. 218.
    Harvey M, Frabritiis GD (2009) J Chem Theory Comput 5:2371Google Scholar
  219. 219.
    Case D, Darden T, Cheatham T III, Simmerling C, Wang J, Duke R, Luo R, Walker R, Zhang W, Merz K, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz A, Kolossvry I, Wong K, Paesani F, Vanicek J, Wolf R, Liu J, Wu X, Brozell S, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe D, Mathews D, Seetin M, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman P. Amber 12. http://ambermd.org. University of California, San Francisco
  220. 220.
    Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) In: Proceedings of the 2006 ACM/IEEE conference on Supercomputing, SC’06. ACM, New YorkGoogle Scholar
  221. 221.
    Smith Y (2002) Mol Sim 28:385Google Scholar
  222. 222.
    Limbach H, Arnold A, Mann B, Holm C (2006) Comput Phys Comm 174:704Google Scholar
  223. 223.
    Berendsen HJC, van der Spoel D, van Drunen R (1995) Comput Phys Commun 91:43Google Scholar
  224. 224.
    Morozov I, Kazennov A, Bystryi R, Norman G, Pisarev V, Stegailov V (2011) Comput Phys Commun 182:1974Google Scholar
  225. 225.
    Plimpton S (1995) J Comput Phys 117:1Google Scholar
  226. 226.
    Accelrys Software Inc. (2013) Material studio, release 6.1. Accelrys Software Inc., San DiegoGoogle Scholar
  227. 227.
    Phillips J, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R, Kale L, Schulten K (2005) J Comput Chem 26:1781Google Scholar
  228. 228.
    Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, Pande VS (2013) J Chem Theory Comput 9:461Google Scholar
  229. 229.
    Matthey T, Cickovski T, Hampton SS, Ko A, Ma Q, Nyerges M, Raeder T, Slabach T, Izaguirre JA (2004) ACM Trans Math Softw 30:237Google Scholar
  230. 230.
    Rühle V, Junghans C, Lukyanov A, Kremer K, Andrienko D (2009) J Chem Theory Comput 5:3211Google Scholar
  231. 231.
    Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) J Chem Theory Comput 4:435Google Scholar
  232. 232.
    Vmd – visual molecular dynamics. www.ks.uiuc.edu/Research/vmd
  233. 233.
    Humphrey W, Dalke A, Schulten K (1996) J Mol Graphics 14:33Google Scholar
  234. 234.
    Eargle J, Wright D, Luthey-Schulten Z (2006) Bioinformatics 22:504Google Scholar
  235. 235.
    Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org
  236. 236.
    Mercury-crystal structure visualisation, exploration and analysis made easy. http://www.ccdc.cam.ac.uk/products/mercury/
  237. 237.
    GDIS, a program for the display and manipulation of isolated molecules and periodic systems. http://gdis.sourceforge.net/
  238. 238.
    Avogadro: an open-source molecular builder and visualization tool. http://avogadro.openmolecules.net
  239. 239.
    Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) J Chem Inf 4:17Google Scholar
  240. 240.
    OVITO – the open visualization tool. http://www.ovito.org
  241. 241.
    Stukowski A (2010) Model Simul Mater Sci Eng 18:015012Google Scholar
  242. 242.
    Schrödinger LLC (2013) The PyMOL molecular graphics system, version 1.5.0.4. http://pymol.org/
  243. 243.
    Varetto U Molekel molecular visualization. http://molekel.cscs.ch. Swiss National Supercomputing Centre, Lugano
  244. 244.
    Sayle R, Milner-White EJ (1995) Trends Biochem Sci 20:374Google Scholar
  245. 245.
  246. 246.
    Favre-Nicolin V, Cerny R (2007) Z Kristallogr 222:105Google Scholar
  247. 247.
    QMGA: Qt-based molecular graphics application. www.qmga.sourceforge.net
  248. 248.
    Gabriel AT, Meyer T, Germano G (2008) J Chem Theory Comput 4:468Google Scholar
  249. 249.
    UCSF Chimera package. http://www.cgl.ucsf.edu/chimera
  250. 250.
    Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E, Ferrin T (2004) J Comput Chem 25:1605Google Scholar
  251. 251.
    BALLView – the BALL website. www.ballview.org/
  252. 252.
    Moll A, Hildebrandt A, Lenhof H, Kohlbacher O (2006) Bioinformatics 22:365Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Luca Muccioli
    • 1
  • Gabriele D’Avino
    • 1
  • Roberto Berardi
    • 1
  • Silvia Orlandi
    • 1
  • Antonio Pizzirusso
    • 1
  • Matteo Ricci
    • 1
  • Otello Maria Roscioni
    • 1
  • Claudio Zannoni
    • 1
    Email author
  1. 1.Department of Industrial Chemistry “Toso Montanari”University of BolognaBolognaItaly

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