MOLECULAR DYNAMICS – THEORETICAL DEVELOPMENTS AND APPLICATIONS IN NANOTECHNOLOGY AND ENERGY Edited by Lichang Wang Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Edited by Lichang Wang Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Daria Nahtigal Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published April, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy, Edited by Lichang Wang p. cm. ISBN 978-953-51-0443-8 Contents Preface IX Part 1 Molecular Dynamics Theory and Development 1 Chapter 1 Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations 3 Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano and Hirotoshi Mori Chapter 2 Advanced Molecular Dynamics Simulations on the Formation of Transition Metal Nanoparticles 25 Lichang Wang and George A. Hudson Chapter 3 Numerical Integration Techniques Based on a Geometric View and Application to Molecular Dynamics Simulations 43 Ikuo Fukuda and Séverine Queyroy Chapter 4 Application of Molecular Dynamics Simulation to Small Systems 57 Víctor M. Rosas-García and Isabel Sáenz-Tavera Chapter 5 Molecular Dynamics Simulations and Thermal Transport at the Nano-Scale 73 Konstantinos Termentzidis and Samy Merabia Part 2 Molecular Dynamics Theory Beyond Classical Treatment 105 Chapter 6 Developing a Systematic Approach for Ab Initio Path-Integral Simulations 107 Kin-Yiu Wong Chapter 7 Antisymmetrized Molecular Dynamics and Nuclear Structure 133 Gaotsiwe J. Rampho and Sofianos A. Sofianos VI Contents Chapter 8 Antisymmetrized Molecular Dynamics with Bare Nuclear Interactions: Brueckner-AMD, and Its Applications to Light Nuclei 149 Tomoaki Togashi and Kiyoshi Katō Part 3 Formation and Dynamics of Nanoparticles 171 Chapter 9 Formation and Evolution Characteristics of Nano-Clusters (For Large-Scale Systems of 10 6 Liquid Metal Atoms) 173 Rang-su Liu, Hai-rong Liu, Ze-an Tian, Li-li Zhou and Qun-yi Zhou Chapter 10 A Molecular Dynamics Study on Au 201 Yasemin Öztekin Çiftci, Kemal Çolakoğlu and Soner Özgen Chapter 11 Gelation of Magnetic Nanoparticles 215 Eldin Wee Chuan Lim Chapter 12 Inelastic Collisions and Hypervelocity Impacts at Nanoscopic Level: A Molecular Dynamics Study 229 G. Gutiérrez, S. Davis, C. Loyola, J. Peralta, F. González, Y. Navarrete and F. González-Wasaff Part 4 Dynamics of Molecules on Surfaces 253 Chapter 13 Recent Advances in Molecular Dynamics Simulations of Gas Diffusion in Metal Organic Frameworks 255 Seda Keskin Chapter 14 Molecular Dynamic Simulation of Short Order and Hydrogen Diffusion in the Disordered Metal Systems 281 Eduard Pastukhov, Nikolay Sidorov, Andrey Vostrjakov and Victor Chentsov Chapter 15 Molecular Simulation of Dissociation Phenomena of Gas Molecule on Metal Surface 307 Takashi Tokumasu Chapter 16 A Study of the Adsorption and Diffusion Behavior of a Single Polydimethylsiloxane Chain on a Silicon Surface by Molecular Dynamics Simulation 327 Dan Mu and Jian-Quan Li Part 5 Dynamics of Ionic Species 339 Chapter 17 The Roles of Classical Molecular Dynamics Simulation in Solid Oxide Fuel Cells 341 Kah Chun Lau and Brett I. Dunlap Contents VII Chapter 18 Molecular Dynamics Simulation and Conductivity Mechanism in Fast Ionic Crystals Based on Hollandite Na x Cr x Ti 8-x O 16 371 Kien Ling Khoo and Leonard A. Dissado Chapter 19 MD Simulation of the Ion Solvation in Methanol-Water Mixtures 399 Ewa Hawlicka and Marcin Rybicki Preface Molecular dynamics (MD) simulations have played increasing roles in our understanding of physical and chemical processes of complex systems and in advancing science and technology. Over the past forty years, MD simulations have made great progress from developing sophisticated theories for treating complex systems to broadening applications to a wide range of scientific and technological fields. The chapters of Molecular Dynamics are a reflection of the most recent progress in the field of MD simulations. This is the first book of Molecular Dynamics which focuses on the theoretical developments and the applications in nanotechnology and energy. This book is divided into five parts. The first part deals with the development of molecular dynamics theory. Komeiji et al. summarize, in Chapter 1, the advances made in fragment molecular orbital based molecular dynamics, which is the ab inito molecular dynamics simulations, to treat large molecular systems with solvent molecules being treated explicitly. In Chapter 2, Wang & Hudson present a new meta-molecular dynamics method, i.e. beyond the conventional MD simulations, that allows monitoring the change of electronic state of the system during the dynamical process. Fukuda & Queyroy discuss in Chapter 3 two numerical techniques, i.e. phase space time-invariant function and numerical integrator, to enhance the MD performance. In Chapter 4, Rosas-García & Sáenz-Tavera provide a summary of MD methods to perform a configurational search of clusters of less than 100 atoms. In Chapter 5, Termentzidis & Merabia describe MD simulations in the calculation of thermal transport properties of nanomaterils. The second part consists of three chapters that describe MD theory beyond a classical treatment. In Chapter 6, Wong describes a practical ab inito path-integral method, denoted as method, for macromolecules. Chapters 7 and 8, by Rampho and Togashi & Katō, respectively, deal with the asymmetric molecular dynamics simulations of nuclear structures. Part III is on nanoparticles. In Chapter 9, Liu et al. provide a detailed description of MD simulations to study liquid metal clusters consisting of up to 10 6 atoms. In Chapter 10, Çiftci & Özgen provide a MD study of Au clusters on the melting, glass formation, and crystallization processes. Lim provides a MD study of gelation of magnetic nanoparticles in Chapter 11. Chapter 12 by Gutiérrez et al. provides a MD simulation of a nanoparticle colliding inelastically with a solid surface. The fourth part is about diffusion of gas molecules in solid, an important research area related to gas storage, gas separation, catalysis, and biomedical applications. In Chapter 13, Keskin describes MD simulations of the gas diffusion in molecular organic framework (MOF). In Chapter 14, Pastukhov et al. provide the MD results on the H 2 dynamics on various solid surfaces. In Chapter 15, Tokumasu provides a summary of MD results on H2 dissociation on Pt(111). In Chapter 16, Mu & Li discuss MD simulation of the adsorption and diffusion of polydimethylsiloxane (PDMS) on a Si(111) surface. In the last part of the book, ionic conductivity in solid oxides is discussed. Solid oxides are especially important materials in the field of energy, including the development of fuel cells and batteries. In Chapter 17, Lau & Dunlap describe the dynamics of O 2- in Y 2O3 and in Y2O3 doped crystal and amorphous ZrYO. Khoo & Dissado provide a study of the mechanism of Na + conductivity in hollandites in Chapter 18. The last chapter of this part deals with the ion solvation in methanol/water mixture. Hawlicka and Rybicki summarize the Mg 2+ , Ca 2+ , and Cl - solvation in the liquid mixture and I hope the readers can find connections between the liquid and solid ionic conductivities. With strenuous and continuing efforts, a greater impact of MD simulations will be made on understanding various processes and on advancing many scientific and technological areas in the foreseeable future. In closing I would like to thank all the authors taking primary responsibility to ensure the accuracy of the contents covered in their respective chapters. I also want to thank my publishing process manager Ms. Daria Nahtigal for her diligent work and for keeping the book publishing progress in check. Lichang Wang Department of Chemistry and Biochemistry Southern Illinois University Carbondale USA [...]... developed and made available (Fujiwara et al., 2011) 2.2.7 Periodic Boundary Condition (PBC) PBC was finally introduced to FMO-MD in the TINKER/ABINIT-MP system by Fujita et al (2011) PBC is a standard protocol for both classical and ab intio MD simulations 8 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Nonetheless, partly due to the complexity of PBC in formulation... Pt-Cl bonds fluctuation Since trans-platin has inversion symmetry, the 18 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy dipole moment of trans-platin is much smaller than that of cis-platin This means that the number of water molecules which coordinates to the platin complex is larger for cis-platin than for trans-platin Thus, the CT interaction coupled with... patterns are drawn for three solute molecules, A–C Reproduced from Komeiji et al (2010) with permission 10 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy The DF algorithm gracefully handles molecular systems consisting of small solute and solvent molecules, but not those containing large molecules such as proteins and DNA, which should be fragmented at covalent... 2008), pp 2396-2397, ISSN 0002-7863 24 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Sato, M.; Yamataka, H.; Komeiji, Y.; Mochizuki, Y & Nakano, T (2010) Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics Chemistry-A European Journal,... approximiated by simple Coulombic interactions (dimer-ES approximation, Nakano et al., 2002) This approximation is mandatory to reduce the computation cost from O(N4) to O(N2) 6 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy The total energy of the molecular system, U, is obtained by adding the electrostatic interaction energy between nuclei to E, namely,... stronger in cis-platin than in trans-platin As a result, the Pt-Cl bonds are easier to elongate for the cleavage in the hydrated cis-platin than in the hydrated trans-platin Thus, by using FMOMD simulations, we obtained new quantum chemical insight into the solvation of platin complexes Fig 12 (Left) Time evolution of natural charge on the Pt, NH3, and Cl sites in the cis- and trans-platin Solid and dotted... FMO2/HF/6-31G level CH3-N2+ was optimized in the gas phase and then hydrated in a sphere of 156 water molecules The water was optimized at 300 K for 0.5 ps with the RATTLE bond constraint The temperature of the molecular system was raised to 1000 K, 12 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy and the simulation was continued for 5 ps From the 1000 K trajectory,... zwitterion (ZW) intermediate (Fig 7) The results indicated that the reaction proceeds through a stepwise mechanism with ZW as a stable intermediate 14 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Fig 7 Two contradictory schemes of H2CO amination RT: reactant; ZW: zwitterion; PD: product The FMO-MD simulations were designed as follows RC was defined as RN-C-RN-H... Structure-THEOCHEM, Vol 898, Nos 1-3, (March 2009), pp 2-9, ISSN 0166-1280 22 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Komeiji, Y.; Mochizuki, Y & Nakano, T (2010) Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD) Chemical Physics Letters, Vol 484, Nos 4-6, (January 2010),... and the other for MD Most of the simulations presented in this article were 4 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy Fig 1 Schematics of the FMO-MD method exemplified by an ion solvation with four water molecules The atomic nuclei are represented by black circles (the large one for the ion, medium ones for Oxygens, and small ones for Hydrogens) and . MOLECULAR DYNAMICS – THEORETICAL DEVELOPMENTS AND APPLICATIONS IN NANOTECHNOLOGY AND ENERGY Edited by Lichang Wang Molecular Dynamics – Theoretical Developments and. Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy 6 The total energy of the molecular system, U, is obtained by adding the electrostatic interaction. one for FMO and the other for MD. Most of the simulations presented in this article were Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy 4