THERMODYNAMICS – INTERACTION STUDIES – SOLIDS, LIQUIDS AND GASES Edited by Juan Carlos Moreno-Piraján Thermodynamics – Interaction Studies – Solids, Liquids and Gases Edited by Juan Carlos Moreno-Piraján Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. 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. 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Used under license from Shutterstock.com First published September, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org Thermodynamics – Interaction Studies – Solids, Liquids and Gases, Edited by Juan Carlos Moreno-Piraján p. cm. ISBN 978-953-307-563-1 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Chapter 1 Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design 1 Agnieszka K. Bronowska Chapter 2 Atmospheric Thermodynamics 49 Francesco Cairo Chapter 3 Thermodynamic Aspects of Precipitation Efficiency 73 Xinyong Shen and Xiaofan Li Chapter 4 Comparison of the Thermodynamic Parameters Estimation for the Adsorption Process of the Metals from Liquid Phase on Activated Carbons 95 Svetlana Lyubchik, Andrey Lyubchik, Olena Lygina, Sergiy Lyubchik and Isabel Fonseca Chapter 5 Thermodynamics of Nanoparticle Formation in Laser Ablation 123 Toshio Takiya, Min Han and Minoru Yaga Chapter 6 Thermodynamics of the Oceanic General Circulation – Is the Abyssal Circulation a Heat Engine or a Mechanical Pump? 147 Shinya Shimokawa and Hisashi Ozawa Chapter 7 Thermodynamic of the Interactions Between Gas-Solidand Solid-Liquid on Carbonaceous Materials 163 Vanessa García-Cuello, Diana Vargas-Delgadillo, Yesid Murillo-Acevedo, Melina Yara Cantillo-Castrillon, Paola Rodríguez-Estupiñán, Liliana Giraldo and Juan Carlos Moreno-Piraján Chapter 8 Thermodynamics of Interfaces 201 Omid Moradi VI Contents Chapter 9 Exergy, the Potential Work 251 Mofid Gorji-Bandpy Chapter 10 Dimensionless Parametric Analysis of Spark Ignited Free-Piston Linear Alternator 271 Jinlong Mao, Zhengxing Zuo and Huihua Feng Chapter 11 Time Resolved Thermodynamics Associated with Diatomic Ligand Dissociation from Globins 301 Jaroslava Miksovska and Luisana Astudillo Chapter 12 Some Applications of Thermodynamics for Ecological Systems 319 Eugene A. Silow, Andrey V. Mokry and Sven E. Jørgensen Chapter 13 Statistical Thermodynamics of Material Transport in Non-Isothermal Mixtures 343 Semen Semenov and Martin Schimpf Chapter 14 Thermodynamics of Surface Growth with Application to Bone Remodeling 369 Jean-François Ganghoffer Chapter 15 Thermodynamic Aspects of CVD Crystallization of Refractory Metals and Their Alloys 403 Yu. V. Lakhotkin Chapter 16 Effect of Stagnation Temperature on Supersonic Flow Parameters with Application for Air in Nozzles 421 Toufik Zebbiche Chapter 17 Statistical Mechanics That Takes into Account Angular Momentum Conservation Law - Theory and Application 445 Illia Dubrovskyi Chapter 18 The Role and the Status of Thermodynamics in Quantum Chemistry Calculations 469 Llored Jean-Pierre Chapter 19 Thermodynamics of ABO 3 -Type Perovskite Surfaces 491 Eugene Heifets, Eugene A. Kotomin, Yuri A. Mastrikov, Sergej Piskunov and Joachim Maier Chapter 20 Advances in Interfacial Adsorption Thermodynamics: Metastable-Equilibrium Adsorption (MEA) Theory 519 Gang Pan, Guangzhi He and Meiyi Zhang Contents VII Chapter 21 Towards the Authentic Ab Intio Thermodynamics 543 In Gee Kim Chapter 22 Thermodynamics of the Phase Equilibriums of Some Organic Compounds 595 Raisa Varushchenko and Anna Druzhinina Chapter 23 Thermodynamics and Thermokinetics to Model Phase Transitions of Polymers over Extended Temperature and Pressure Ranges Under Various Hydrostatic Fluids 641 Séverine A.E. Boyer, Jean-Pierre E. Grolier, Hirohisa Yoshida, Jean-Marc Haudin and Jean-Loup Chenot Chapter 24 Thermodynamics and Reaction Rates 673 Miloslav Pekař Chapter 25 The Thermodynamics in Planck's Law 695 Constantinos Ragazas Chapter 26 Statistical Thermodynamics 717 Anatol Malijevský Chapter 27 Thermodynamics Approach in the Adsorption of Heavy Metals 737 Mohammed A. Al-Anber Chapter 28 Thermodynamics as a Tool for the Optimization of Drug Binding 765 Ruth Matesanz, Benet Pera and J. Fernando Díaz Chapter 29 On the Chlorination Thermodynamics 785 Brocchi E. A. and Navarro R. C. S. Chapter 30 Thermodynamics of Reactions Among Al 2 O 3 , CaO, SiO 2 and Fe 2 O 3 During Roasting Processes 825 Zhongping Zhu, Tao Jiang, Guanghui Li, Yufeng Guo and Yongbin Yang Chapter 31 Thermodynamic Perturbation Theory of Simple Liquids 839 Jean-Louis Bretonnet Chapter 32 Probing Solution Thermodynamics by Microcalorimetry 871 Gregory M. K. Poon Chapter 33 Thermodynamics of Metal Hydrides: Tailoring Reaction Enthalpies of Hydrogen Storage Materials 891 Martin Dornheim Preface Thermodynamics is one of the most exciting branches of physical chemistry which has greatly contributed to the modern science. Since its inception, great minds have built their theories of thermodynamics. One should name those of Sadi Carnot, Clapeyron Claussius, Maxwell, Boltzman, Bernoulli, Leibniz etc. Josiah Willard Gibbs had perhaps the greatest scientific influence on the development of thermodynamics. His attention was for some time focused on the study of the Watt steam engine. Analysing the balance of the machine, Gibbs began to develop a method for calculating the variables involved in the processes of chemical equilibrium. He deduced the phase rule which determines the degrees of freedom of a physicochemical system based on the number of system components and the number of phases. He also identified a new state function of thermodynamic system, the so-called free energy or Gibbs energy (G), which allows spontaneity and ensures a specific physicochemical process (such as a chemical reaction or a change of state) experienced by a system without interfering with the environment around it. The essential feature of thermodynamics and the difference between it and other branches of science is that it incorporates the concept of heat or thermal energy as an important part in the energy systems. The nature of heat was not always clear. Today we know that the random motion of molecules is the essence of heat. Some aspects of thermodynamics are so general and deep that they even deal with philosophical issues. These issues also deserve a deeper consideration, before tackling the technical details. The reason is a simple one - before one does anything, one must understand what they want. In the past, historians considered thermodynamics as a science that is isolated, but in recent years scientists have incorporated more friendly approach to it and have demonstrated a wide range of applications of thermodynamics. These four volumes of applied thermodynamics, gathered in an orderly manner, present a series of contributions by the finest scientists in the world and a wide range of applications of thermodynamics in various fields. These fields include the environmental science, mathematics, biology, fluid and the materials science. These four volumes of thermodynamics can be used in post-graduate courses for students and as reference books, since they are written in a language pleasing to the reader. X Preface They can also serve as a reference material for researchers to whom the thermodynamics is one of the area of interest. Juan Carlos Moreno-Piraján Department of Chemistry University of the Andes Colombia [...]... Axilrod-Teller theory, which predicts a dramatic (i.e much stronger than for pairwise interactions) decrease of three-atom interactions with distance (Axilrod and Teller, 1943) Indeed, detailed calculations of single-atom liquids (Sadus, 1998) and solids 6 Thermodynamics – Interaction Studies – Solids, Liquids and Gases (Donchev, 2006) indicate that multi-body effects amount to only 5% of the total... Poornima and Dean, 1995a) Those water molecules may be regarded as part of the protein structure Ligand-protein interactions are often mediated by water molecules buried in the binding site and forming multiple hydrogen bonds with both binding partners (Poornima and Dean, 1995a-c) In other cases, those bound water molecules are released to 10 Thermodynamics – Interaction Studies – Solids, Liquids and Gases. .. stable-isotope labelling and isotope-edited NMR in the investigation of ligand-protein interactions Recent development of techniques allowed for 18 Thermodynamics – Interaction Studies – Solids, Liquids and Gases the study of ligand-induced conformational changes, investigating positions and dynamic behaviour of bound water molecules, and for quantification of conformational entropy The steady-state heteronuclear... unbound (apo) protein and a ligand-protein complex (holo), or two ligand-protein complexes with different ligands In the framework of FEP, the difference in the free energy difference for two states is obtained from the Zwanzig equation (10) 24 Thermodynamics – Interaction Studies – Solids, Liquids and Gases  E  EA  G A  B  GB  G A  k BT ln exp   B k BT      (10) A where A and B represent... molecular design, the 2 Thermodynamics – Interaction Studies – Solids, Liquids and Gases bottlenecks of methods employed in such process, and the directions for future development The information content provided by thermodynamic parameters is vast It plays a prominent role in the elucidation of the molecular mechanism of the binding phenomenon, and – through the link to structural data – enables the establishment... be, in some cases, caused by structural tightening through the presence of additional interactions; inter-atomic distances become shorter and interaction becomes 12 Thermodynamics – Interaction Studies – Solids, Liquids and Gases enthalpically more favorable Evidence for such a mechanism has been reported for many ligand-protein complexes; biotin-streptavidin being one of the most extensively studied... Interaction Studies – Solids, Liquids and Gases G  H  T S (1) where G is free binding energy, H is enthalpy, S entropy, and T is the temperature The enthalpic contribution to the free energy reflects the specificity and strength of the interactions between both partners These include ionic, halogen, and hydrogen bonds, electrostatic (Coulomb) and van der Waals interactions, and polarisation of... free rotation of a bond vector (here – N-H) in a cone The semi-angle  is displayed Smaller S 2 parameters correspond to more flexible bond vectors S 2  0 means unrestricted rotation of the bond vector 20 Thermodynamics – Interaction Studies – Solids, Liquids and Gases There were attempts to relate order parameters to structural characteristics of proteins and ligand-protein complexes It was observed... halogen bond increases with the size of halogen atom 8 Thermodynamics – Interaction Studies – Solids, Liquids and Gases Halogen atoms can interact with the oxygen and with the carbon atoms of C=O groups, as well The former attributes to the halogen bond formation, the latter is a hallmark of socalled orthogonal multipolar interactions These interactions are formed by two dipolar functional groups,... charge-dipole interactions, which are the interactions between ionised amino acid side chains and the dipole of the ligand moiety or water molecule The dipole moments of the polar side chains of amino acid also affect their interaction with ligands 2.2.2 Van der Waals interactions Van der Waals interactions are very important for the structure and interactions of biological molecules There are both attractive and . THERMODYNAMICS – INTERACTION STUDIES – SOLIDS, LIQUIDS AND GASES Edited by Juan Carlos Moreno-Piraján Thermodynamics – Interaction Studies – Solids, Liquids and Gases. enthalpic, and an entropic, terms: Thermodynamics – Interaction Studies – Solids, Liquids and Gases 4 GHTS     (1) where G  is free binding energy, H  is enthalpy, S  entropy, and. parameters in molecular design, the Thermodynamics – Interaction Studies – Solids, Liquids and Gases 2 bottlenecks of methods employed in such process, and the directions for future development.