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Molecular Dynamics Simulations of Vibrational Spectra of Hydrogen-Bonded Systems

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Frontiers of Quantum Chemistry

Abstract

In this chapter, we present current studies on molecular dynamics (MD) simulations of hydrogen-bonded systems with emphasis on vibrational spectra analysis. One of the most informative experimental data are spectroscopic data (infrared and Raman spectroscopy), which give information important in diverse fields, e.g. protein folding, drug design, sensors, nanotechnology, separations, etc. Spectroscopic data are very sensitive on inter- and intramolecular interactions. The processes of melting, boiling, unfolding and strand separation involve disruption of molecular interactions, that engage attractive or repulsive forces between molecules. In this chapter, we focus on calculations of IR spectra of hydrogen-bonded complexes based on linear response theory, in which the spectral density is the Fourier transform of the autocorrelation function of the dipole moment operator involved in the IR transitions. Recently, Born–Oppenheimer molecular dynamics (BOMD), Car–Parrinello molecular dynamics (CPMD), path integral molecular dynamics (PIMD), hybrid molecular dynamics (QM/MM) and other methods which use trajectories from molecular dynamics have been employed to simulate IR spectra of hydrogen-bonded systems. Each of these methods has some advantages and disadvantages which will be discussed in this chapter presenting also recent applications of these methods.

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References

  1. D. Hadži, H.W. Thompson, International Union of Pure and Applied Chemistry, Hydrogen Bonding: Papers Presented at the Symposium on Hydrogen Bonding Held at Ljubljana, 29 July–3 Aug 1957 (Pergamon Press, London, 1959), pp. xii, 571

    Google Scholar 

  2. G.C. Pimentel, A.L. McClellan, The Hydrogen Bond, ed. by W.H. Freeman (trade distributor) (Reinhold Pub. Corp., New York, San Francisco, 1960), p. 475

    Google Scholar 

  3. P. Schuster, G. Zundel, C. Sandorfy, The Hydrogen Bond: Recent Developments in Theory and Experiments (North-Holland Pub. Co. distributor, American Elsevier Pub. Co., Amsterdam, New York, 1976)

    Google Scholar 

  4. S. Scheiner, Hydrogen Bonding: A Theoretical Perspective (Oxford University Press, New York; Oxford, 1997), pp. xix, 375

    Google Scholar 

  5. G.A. Jeffrey, An Introduction to Hydrogen Bonding (Oxford University Press, New York, Oxford, 1997), pp. vii, 303

    Google Scholar 

  6. D. Hadži, Theoretical Treatments of Hydrogen Bonding (Wiley, Chichester, 1997), pp. xiii, 318

    Google Scholar 

  7. S. Grabowski, Springer Link (Online service), Hydrogen Bonding New Insights (Springer, Dordrecht, 2006)

    Book  Google Scholar 

  8. Y. Maréchal, Molecular Interactions, vol. 1, ed. by H. Ratajczak, W.J. Orville-Thomas (Willey, Chichester, 1980)

    Google Scholar 

  9. C. Sandorfy, Top. Curr. Chem. 120, 41 (1984)

    Article  CAS  Google Scholar 

  10. O. Henri-Rousseau, P. Blaise, Adv. Chem. Phys. 103, 1 (1998)

    CAS  Google Scholar 

  11. M.J. Wójcik, Adv. Chem. Phys. 160, 311–346 (2016)

    Google Scholar 

  12. J.A. Pople, Nobel lecture (1998)

    Google Scholar 

  13. S. Bratož, D. Hadži 27(5), 991 (1957)

    Google Scholar 

  14. Y. Maréchal, 48(8), 3697 (1968)

    Google Scholar 

  15. A. Witkowski, M. Wojcik, Chem. Phys. 1(1), 9 (1973)

    Article  CAS  Google Scholar 

  16. M.J. Wojcik, Int. J. Quantum Chem. 10(5), 747 (1976)

    Article  CAS  Google Scholar 

  17. M.J. Wojcik, J. Mol. Struct. 47, 303 (1978)

    Article  CAS  Google Scholar 

  18. H.T. Flakus, Theochem. J. Mol. Struc. 104(3), 281 (1993)

    Article  CAS  Google Scholar 

  19. H. Ratajczak, A.M. Yaremko, Chem. Phys. Lett. 314(1–2), 122 (1999)

    Article  CAS  Google Scholar 

  20. O. Henri-Rousseau, D. Chamma, Chem. Phys. 229(1), 37 (1998)

    Article  CAS  Google Scholar 

  21. A.M. Yaremko, H. Ratajczak, J. Baran, A.J. Barnes, E. Mozdor, B. Silvi, Chem. Phys. 306(1–3), 57 (2004)

    Article  CAS  Google Scholar 

  22. Y. Ozaki, D.H. Pliura, P.R. Carey, A.C. Storer, Biochemistry 21(13), 3102 (1982)

    Article  CAS  Google Scholar 

  23. Y. Wu, K. Murayama, Y. Ozaki, J. Phys. Chem. B 105(26), 6251 (2001)

    Article  CAS  Google Scholar 

  24. Y. Ozaki, K. Aoyagi, K. Iriyama, H. Ogoshi, T. Kitagawa. J. Phys. Chem. 93(9), 3842 (1989)

    Article  CAS  Google Scholar 

  25. P. Blaise, M.J. Wojcik, O. Henri-Rousseau, J. Chem. Phys. 122 (6), (2005)

    Google Scholar 

  26. C. Sandorfy, J. Mol. Struct. 790(1–3), 50 (2006)

    Article  CAS  Google Scholar 

  27. M. Boczar, L. Boda, M.J. Wojcik, J. Chem. Phys. 124 (8), (2006)

    Google Scholar 

  28. M.J. Wojcik, M. Boczar, L. Boda, J. Chem. Phys. 127 (8), (2007)

    Google Scholar 

  29. M.J. Wojcik, J. Kwiendacz, M. Boczar, L. Boda, Y. Ozaki, Chem. Phys. 372(1–3), 72 (2010)

    Article  CAS  Google Scholar 

  30. M.J. Wójcik, V. Buch, J.P. Devlin, J. Chem. Phys. 99, 2332 (1993)

    Article  Google Scholar 

  31. M. Boczar, Ł. Boda, M.J. Wójcik, J. Chem. Phys. 125, 084709 (2006)

    Article  CAS  Google Scholar 

  32. M. Boczar, Ł. Boda, M.J. Wójcik, J. Chem. Phys. 127, 084307 (2007)

    Article  CAS  Google Scholar 

  33. M. Boczar, J. Kwiendacz, M.J. Wójcik, J. Chem. Phys. 128, 164506 (2008)

    Article  CAS  Google Scholar 

  34. M.J. Wójcik, H. Nakamura, S. Iwata, W. Tatara, J. Chem. Phys. 112, 6322 (2000)

    Article  Google Scholar 

  35. M.J. Wójcik, Ł. Boda, M. Boczar, J. Chem. Phys. 130, 164306 (2009)

    Article  CAS  Google Scholar 

  36. R. Ramı́rez, T. López-Ciudad, P.P. Kumar, D. Marx, J. Chem. Phys. 121, 3973–3983 (2004)

    Google Scholar 

  37. M. Thomas, M. Brehm, O. Hollóczki, Z. Kelemen, L. Nyulászi, T. Pasinszki, B. Kirchner, J. Chem. Phys. 141, 024510 (2014)

    Article  CAS  Google Scholar 

  38. B. Kuhn, P. Mohr, M. Stahl, J. Med. Chem. 53(6), 2601–2611 (2010)

    Article  CAS  Google Scholar 

  39. T. Anh Pham, P. Huang, E. Schwegler, G. Galli, J. Phys. Chem. A 116(37), 925 (2012)

    Google Scholar 

  40. N. Sieffert, M. Bühl, M.-P. Gaigeot, C.A. Morrison, J. Chem. Theory Comput. 9(1), 106 (2013)

    Article  CAS  Google Scholar 

  41. E. Pluhařová, M. Ončák, R. Seidel, C. Schroeder, W. Schroeder, B. Winter, S.E. Bradforth, P. Jungwirth, P. Slavíček, J. Phys. Chem. B 116(44), 13254 (2012)

    Article  CAS  Google Scholar 

  42. W. Lin, F. Paesani, J. Phys. Chem. A 119(19), 4450 (2015)

    Article  CAS  Google Scholar 

  43. T.R. Cundari, M.T. Benson, M.L. Lutz, S.O. Sommerer, Reviews in Computational Chemistry, vol. 8, ed. by K.B. Lipkowitz, D.B. Boyd 131 (VCH, New York, 1996), p. 145

    Google Scholar 

  44. D. Marx, Classical and quantum dynamics in condensed phase simulations, Chap. 15, ed. by B.J. Berne, G. Ciccotti, D.F. Coker (World Scientific, Singapore, 1998)

    Google Scholar 

  45. M.E. Tuckerman, A. Hughes, Classical and quantum dynamics in condensed phase simulations, Chap. 14, ed. by B.J. Berne, G. Ciccotti, D.F. Coker (World Scientific, Singapore, 1998), p. 311

    Google Scholar 

  46. I. Sumner, S.S. Iyengar, J. Phys. Chem. A 111, 10313 (2007)

    Article  CAS  Google Scholar 

  47. X. Li, S.S. Iyengar, J. Phys. Chem. A 115, 6269 (2011)

    Article  CAS  Google Scholar 

  48. J. VandeVondele, P. Tröster, P. Tavan, G. Mathias. J. Phys. Chem. A 116(10), 2466 (2012)

    Article  CAS  Google Scholar 

  49. E. Pluhařová, M.D. Baer, C.J. Mundy, B. Schmidt, P. Jungwirth, J. Phys. Chem. Lett. 5(13), 2235 (2014)

    Article  CAS  Google Scholar 

  50. M. Born, R. Oppenheimer, Ann. Phys. 84, 457–484 (1927)

    Article  CAS  Google Scholar 

  51. D. Marx, J. Hutter, Ab Initio Molecular Dynamics (Cambridge University Press, Cambridge, 2009), pp. 45–46

    Book  Google Scholar 

  52. M. Krack, M. Parrinello, Forschungszentrum Jülich. NIC Series 25, 29 (2004)

    Google Scholar 

  53. Y. Zhao, H. Li, X.C. Zeng, J. Am. Chem. Soc. 135(41), 15549 (2013)

    Article  CAS  Google Scholar 

  54. A. Mondal, S. Balasubramanian, J. Phys. Chem. B 119(5), 1994 (2015)

    Article  CAS  Google Scholar 

  55. R. Car, M. Parrinello, Phys. Rev. Lett. 55(22), 2471–2474 (1985)

    Article  CAS  Google Scholar 

  56. I.-F.W. Kuo, C.J. Mundy, M.J. McGrath, J.I. Siepmann, J. Chem. Theory Comput. 2, 1274–1281 (2006)

    Article  CAS  Google Scholar 

  57. D. Marx, M. Parrinello, Zeitschrift für Physik B Condensed Matter 95(2), 143 (1994)

    Article  CAS  Google Scholar 

  58. D. Marx, M. Parrinello, J. Chem. Phys. 104, 4077 (1996)

    Article  CAS  Google Scholar 

  59. J. Gao, K.-Y. Wong, D.T. Major, J. Comput. Chem. 29, 514 (2008)

    Article  CAS  Google Scholar 

  60. D.T. Major, M. Garcia-Viloca, J. Gao, J. Chem. Theory Comput. 2(2), 236 (2006)

    Article  CAS  Google Scholar 

  61. A. Warshel, M. Levitt, J. Mol. Biol. 103(2), 227–249 (1976)

    Article  CAS  Google Scholar 

  62. G. Jindal, A. Warshel, J. Phys. Chem. B 120(37), 9913 (2016)

    Article  CAS  Google Scholar 

  63. S. Dapprich, I. Komáromi, K.S. Byun, K. Morokuma, M.J. Frisch, J. Mol. Struct. (Theochem) 462, 1 (1999)

    Article  Google Scholar 

  64. T. Vreven, K. Morokuma, Ö. Farkas, H.B. Schlegel, M.J. Frisch, J. Comp. Chem. 24, 760 (2003)

    Article  CAS  Google Scholar 

  65. T. Vreven, K. Morokuma, Annual Reports Comp. Chem. 2, 35–51 (2006)

    Article  CAS  Google Scholar 

  66. Jernej Stare Aneta Jezierska Gabriela Ambrožič Iztok J. Košir Jurka Kidrič Aleksander Koll Janez Mavri Dušan Hadži. J. Am. Chem. Soc. 126(13), pp. 4437–4443 (2004)

    Google Scholar 

  67. G.G. Balintkurti, R.N. Dixon, C.C. Marston, Int. Rev. Phys. Chem. 11(2), 317–344 (1992)

    Article  CAS  Google Scholar 

  68. G. Pirc, J. Mavri, J. Stare, P Vib. Spectrosc. 58, 153–162 (2012)

    Article  CAS  Google Scholar 

  69. G.H. Wannier, Phys. Rev. A 52(3), 7 (1937)

    Article  Google Scholar 

  70. M. Brela, A. Michalak, P.P. Power, T. Ziegler, Inorg. Chem. 53(4), 2325 (2014)

    Article  CAS  Google Scholar 

  71. S. Yamamoto, Y. Morisawa, H. Sato, H. Hoshina, Y. Ozaki, J. Phys. Chem. B 117, 2180–2187 (2013)

    Article  CAS  Google Scholar 

  72. P. Durlak, Z. Latajka, S. Berski, J. Chem. Phys. 131(2), (2009)

    Google Scholar 

  73. P. Dopieralski, Z. Latajka, I. Olovsson, Acta Cryst. B 66, 222–228 (2010)

    Article  CAS  Google Scholar 

  74. P. Dopieralski, Z. Latajka, I. Olovsson, Chem. Phys. Lett. 476, 223–226 (2009)

    Article  CAS  Google Scholar 

  75. W.D. Price, R.A. Jockusch, E.R. Williams, J. Am. Chem. Soc. 119(49), 11988–11989 (1997)

    Article  CAS  Google Scholar 

  76. A. Jezierska, J.J. Panek, J. Chem. Theory Comput. 4(3), 375–384 (2008)

    Article  CAS  Google Scholar 

  77. P. Durlak, Z. Latajka, Chem. Phys. Lett. 477(4–6), 249–254 (2009)

    Article  CAS  Google Scholar 

  78. M. Wojcik, B Acad. Pol. Sci. Chim. 22(2), 71–73 (1974)

    CAS  Google Scholar 

  79. J.J. Panek, A. Jezierska-Mazzarello, P. Lipkowski, A. Martyniak, A. Filarowski, J. Chem. Inf. Model. 54, 86–95 (2014)

    Article  CAS  Google Scholar 

  80. K. Mackeprang, Z.-H. Xu, Z. Maroun, M. Meuwly, H.G. Kjaergaard, Phys. Chem. Chem. Phys. 18, 24654 (2016)

    Article  CAS  Google Scholar 

  81. P. Durlak, S. Berski, Z. Latajka, Chem. Phys. Lett. 644, 5–13 (2015)

    Article  CAS  Google Scholar 

  82. M. Boczar, M.J. Wójcik, K. Szczeponek, D. Jamróz, S. Ikeda, Int. J. Quantum Chem. 90, 689 (2002)

    Article  CAS  Google Scholar 

  83. M. Boczar, M.J. Wójcik, K. Szczeponek, D. Jamróz, A. Zięba, B. Kawałek, Chem. Phys. 286, 63 (2003)

    Article  CAS  Google Scholar 

  84. M. Boczar, Ł. Boda, M.J. Wójcik, J. Chem. Phys. 124, 084306 (2006)

    Article  CAS  Google Scholar 

  85. Mavri, J.; Pirc, G.; Stare, J., J Chem Phys 2010, 132 (22)

    Google Scholar 

  86. M.J. Wojcik, J. Kwiendacz, M. Boczar, Chem. Phys. Lett. 501(4–6), 623–627 (2011)

    Google Scholar 

  87. J. Mavri, A. Jezierska, J.J. Panek, A. Koll, J. Chem. Phys. 126(20), (2007)

    Google Scholar 

  88. J. Stare, J. Panek, J. Eckert, J. Grdadolnik, J. Mavri, D. Hadzi, J. Phys. Chem. A 112(7), 1576–1586 (2008)

    Article  CAS  Google Scholar 

  89. M.J. Wojcik, M. Boczar, L. Boda, J. Chem. Phys. 125(8), (2006)

    Google Scholar 

  90. M.J. Wojcik, M. Boczar, R. Kurczab, Vib. Spectrosc. 52(1), 39–47 (2010)

    Article  CAS  Google Scholar 

  91. M.J. Wojcik, M. Boczar, J. Kwiendacz, J. Chem. Phys. 128(16), (2008)

    Google Scholar 

  92. A.N. Manin, A.P. Voronin, A.V. Shishkina, M.V. Vener, A.V. Churakov, G.L. Perlovich, J. Phys. Chem. B 119, 10466–10477 (2015)

    Article  CAS  Google Scholar 

  93. V.V. Zhurov, A.A. Pinkerton, J. Phys. Chem. A 119(52), 13092–13100 (2015)

    Article  CAS  Google Scholar 

  94. M. Brela, J. Stare, G. Pirc, M. Sollner Dolenc, M. Boczar, M.J. Wójcik, J. Mavri, J. Phys. Chem. B 116, 4510–4518 (2012)

    Article  CAS  Google Scholar 

  95. M.Z. Brela, M.J. Wójcik, M. Boczar, Ł. Witek, M. Yasuda, Y. Ozaki, J. Phys. Chem. B 119(25), 7922–7930 (2015)

    Article  CAS  Google Scholar 

  96. M.J. Wójcik, M. Gług, M. Boczar, Ł. Boda, Chem. Phys. Lett. 612, 162–166 (2014)

    Article  CAS  Google Scholar 

  97. J. Stare, J. Panek, J. Eckert, J. Grdadolnik, J. Mavri, D. Hadzi, J. Phys. Chem. A 112, 1576–1586 (2008)

    Article  CAS  Google Scholar 

  98. P. Dopieralski, Z. Latajka, I. Olovsson, J. Chem. Theory Comput. 6, 1455–1461 (2010)

    Article  CAS  Google Scholar 

  99. M.Z. Brela, M.J. Wójcik, Ł.J. Witek, M. Boczar, E. Wrona, R. Hashim, Y. Ozaki, J. Phys. Chem. B 120(16), 3854–3862 (2016)

    Article  CAS  Google Scholar 

  100. M. Gług, M. Boczar, Ł. Boda, M.J. Wójcik, Chem. Phys. 459(28), 102–111 (2015)

    Article  CAS  Google Scholar 

  101. M.E. Brown, W.M. Calvin, Science 287, 107 (2000)

    Article  CAS  Google Scholar 

  102. M.J. Iedema, M.J. Dresser, D.L. Doering, J.B. Rowland, W.P. Hess, A.A. Tsekouras, J.P. Cowin, J. Phys. Chem. B 102, 9203 (1998)

    Article  CAS  Google Scholar 

  103. H. Wang, R.C. Bell, M.J. Iedema, A.A. Tsekouras, J.P. Cowin, Astrophys. J. 620, 1027 (2005)

    Article  CAS  Google Scholar 

  104. M.Z. Brela, M.J. Wójcik, M. Boczar, R. Hashim, Chem. Phys. Lett. 558, 88–92 (2013)

    Article  CAS  Google Scholar 

  105. Y. Ozaki, Y. Futami, Y. Ozaki, Y. Hamada, M.J. Wojcik, J. Phys. Chem. A 115(7), 1194–1198 (2011)

    Article  CAS  Google Scholar 

  106. J. Stare, J. Mavri, J. Grdadolnik, J. Zidar, Z.B. Maksic, R. Vianello, J. Phys. Chem. B 115(19), 5999–6010 (2011)

    Article  CAS  Google Scholar 

  107. D. Janezic, A. Jezierska, J. Panek, U. Borstnik, J. Mavri, J. Phys. Chem. B 111(19), 5243–5248 (2007)

    Article  CAS  Google Scholar 

  108. I-F.W. Kuo, C.J. Mundy, M.J. McGrath, J.I. Siepmann, J. Chem. Theory Comput. 2(5), 1274–1281 (2006)

    Google Scholar 

  109. M. Pagliai, F. Muniz-Miranda, G. Cardini, R. Righini, V. Schettino, J. Phys. Chem. Lett. 1, 2951–2955 (2010)

    Article  CAS  Google Scholar 

  110. S. Park, M. Odelius, K.J. Gaffney, J. Phys. Chem. B 113, 7825–7835 (2009)

    Article  CAS  Google Scholar 

  111. P. Dopieralski, C.L. Perrin, Z.J. Latajka, Chem. Theory. Comput. 7, 3505–3513 (2011)

    Article  CAS  Google Scholar 

  112. K. Laasonen, F. Csajka, M. Parrinello, Chem. Phys. Leu. 194, 172 (1992)

    Article  CAS  Google Scholar 

  113. C. Lee, D. Vanderbilt, K. Laasonen, R. Car, M. Parrinello, Phys. Rev. Lett. 69(1992) 462; Phys. Rev. B 47, 4863 (1993)

    Google Scholar 

  114. K. Laasonen, M. Parrinello, R. Car, Ch. Lee, D. Vanderbilt, Chem. Phys. Lett. 207, 208 (1993)

    Article  CAS  Google Scholar 

  115. K. Laasonen, M. Sprik, M. Parrinello, R. Car, J. Chem. Phys. 99, 9080 (1993)

    Article  CAS  Google Scholar 

  116. E.S. Fois, M. Sprik, M. Parrinello, Chem. Phys. Lett. 223, 411 (1994)

    Article  CAS  Google Scholar 

  117. K. Laasonen, M.L. Klein, J. Am. Chem. Soc. 116, 11620 (1994)

    Article  CAS  Google Scholar 

  118. M. Tuckerman, K. Laasonen, M. Sprik, M. Parrinelto, J. Phys. Condens. Matter 6 (1994) A93; J. Phys. Chem. 99, 5749 (1995); J. Chem. Phys. 103, 150 (1995)

    Google Scholar 

  119. M. Spfik, J. Hutter, M. Parrinello, J. Chem. Phys. 105, 1142 (1996)

    Article  Google Scholar 

  120. A. Eilmes, P. Kubisiak, B. Brela, J. Phys. Chem. B 120, 11026 (2016)

    Article  CAS  Google Scholar 

  121. A. Payaka, A. Tongraar, B.M. Rode, J. Phys. Chem. A 114, 10443–10453 (2010)

    Article  CAS  Google Scholar 

  122. Randall T. Cygan, Luke L. Daemen, Anastasia G. Ilgen, James L. Krumhansl, M. Tina, J. Nenoff, Phys. Chem. C 119, 28005–28019 (2015)

    Article  CAS  Google Scholar 

  123. J.D. Watson, F.H. Crick, Nature 171, 737–738 (1953)

    Article  CAS  Google Scholar 

  124. A.L. Sobolewski, W. Domcke, Phys. Chem. Chem. Phys. 6, 2763 (2004)

    Article  CAS  Google Scholar 

  125. T. Schultz, E. Samoylova, W. Radloff, I.V. Hertel, A.L. Sobolewski, W. Domcke, Science 306, 1765 (2004)

    Article  CAS  Google Scholar 

  126. S. Perun, A.L. Sobolewski, W. Domcke, J. Phys. Chem. A 110, 9031 (2006)

    Article  CAS  Google Scholar 

  127. A.L. Sobolewski, W. Domcke, Europhys. News 37, 20 (2006)

    Article  CAS  Google Scholar 

  128. Z. Lan, L.M. Frutos, A.L. Sobolewski, W. Domcke, Proc. Natl. Acad. Sci. 105, 12707 (2008)

    Article  CAS  Google Scholar 

  129. Z. Lan, W. Domcke, Chem. Phys. 350, 125 (2008)

    Article  CAS  Google Scholar 

  130. D. Shemesh, A.L. Sobolewski, W. Domcke, J. Am. Chem. Soc. 131, 1374 (2009)

    Article  CAS  Google Scholar 

  131. A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley, New York, 1991), pp. xiv, 236

    Google Scholar 

  132. Z.D. Nagel, J.P. Klinman, Nat. Chem. Biol. 5(8), 543–550 (2009)

    Article  CAS  Google Scholar 

  133. J.P. Klinman, M.J. Knapp, K. Rickert, J. Am. Chem. Soc. 124(15), 3865–3874 (2002)

    Article  CAS  Google Scholar 

  134. A. Warshel, M.H.M. Olsson, J. Mavri, Philos. T. R. Soc. B 361(1472), 1417–1432 (2006)

    Article  CAS  Google Scholar 

  135. A. Warshel, J. Mavri, H.B. Liu, M.H.M. Olsson, J. Phys. Chem. B 112(19), 5950–5954 (2008)

    Article  CAS  Google Scholar 

  136. F.H. Westheimer, Chem. Rev. 61, 265–273 (1961)

    Article  CAS  Google Scholar 

  137. L. Melander, W.H. Saunders Jr., Reaction Rates of Isotopic Molecules (Wiley, New York, 1980)

    Google Scholar 

  138. J. Bigeleisen, M. Wolfsberg, Adv. Chem. Phys. 1, 15–76 (1958)

    CAS  Google Scholar 

  139. J.A. Smiley, P. Paneth, M.H. O’Leary, J.B. Bell, M.E. Jones, Biochemistry 30, 6216–6223 (1991)

    Article  CAS  Google Scholar 

  140. J. Mavri, R.A. Matute, Z.T. Chu, R. Vianello, J. Phys. Chem. B 120, 3488–3492 (2016)

    Article  CAS  Google Scholar 

  141. U. Palanivela, S. Lakshmipathia, J. Biomol. Struct. Dyn. (2015). doi:10.1080/07391102.2015.1085903

  142. R. Elber, J. Chem. Phys. 144, 060901 (2016)

    Article  CAS  Google Scholar 

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Acknowledgements

This work was financially supported by National Science Centre, Poland, grant 2016/21/B/ST4/02102.

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Authors and Affiliations

  1. Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland

    Mateusz Z. Brela, Marek Boczar, Łukasz Boda & Marek J. Wójcik

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  1. Mateusz Z. Brela
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Correspondence to Marek J. Wójcik .

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Editors and Affiliations

  1. Jagiellonian University, Kraków, Poland

    Marek J. Wójcik

  2. Quantum Chemistry Research Institute, Nishikyo-ku, Kyoto, Japan

    Hiroshi Nakatsuji

  3. University of California, Santa Barbara, California, USA

    Bernard Kirtman

  4. School of Science and Technology, Kwansei Gakuin University, Sanda, Japan

    Yukihiro Ozaki

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© 2018 Springer Nature Singapore Pte Ltd.

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Brela, M.Z., Boczar, M., Boda, Ł., Wójcik, M.J. (2018). Molecular Dynamics Simulations of Vibrational Spectra of Hydrogen-Bonded Systems. In: Wójcik, M., Nakatsuji, H., Kirtman, B., Ozaki, Y. (eds) Frontiers of Quantum Chemistry. Springer, Singapore. https://doi.org/10.1007/978-981-10-5651-2_15

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