STOICHIOMETRY AND RESEARCH – THE IMPORTANCE OF QUANTITY IN BIOMEDICINE Edited by Alessio Innocenti Stoichiometry and Research – The Importance of Quantity in Biomedicine Edited by Alessio Innocenti 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 Bojan Rafaj Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 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@intechweb.org Stoichiometry and Research – The Importance of Quantity in Biomedicine, Edited by Alessio Innocenti p. cm. ISBN 978-953-51-0198-7 Contents Preface IX Part 1 The Importance of Stoichiometry in Host-Guest Chemistry 1 Stoichiometric Ratio in Calixarene Complexes 3 Chapter 1 Flor de María Ramírez and Irma García-Sosa Water-Soluble Calix[4]arene Derivatives: Chapter 2 Binding Stoichiometry and Spectroscopic Evaluation of the Host-Guest Recognition Mechanism 27 Satish Balasaheb Nimse, Keum-Soo Song and Taisun Kim The Determination of the Stoichiometry of Cyclodextrin Chapter 3 Inclusion Complexes by Spectral Methods: Possibilities and Limitations 47 Cristina Tablet, Iulia Matei and Mihaela Hillebrand Part 2 Stoichiometry of Metal Complexes 77 Coordination Chemistry of Palladium(II) Ternary Chapter 4 Complexes with Relevant Biomolecules 79 Ahmed A. El-Sherif Heavy Metal Ion Chapter 5 Extraction Using Organic Solvents: An Application of the Equilibrium Slope Method 121 Tjoon Tow Teng, Yusri Yusup and Ling Wei Low Part 3 Stoichiometry in Lipids and Polymers Architecture 133 Lipid Composition in Miscible and Immiscible Phases 135 Chapter 6 Walter F. Schmidt, Michael A. Crawford, Swati Mookherji and Alva D. Mitchell VI Contents Stoichiometry of Polymer Complexes 147 Chapter 7 A.Z. El-Sonbati, M.A. Diab and A.A. El-Bindary Dermatological Application of PAMAM – Chapter 8 Vitamin Bioconjugates and Host-Guest Complexes – Vitamin C Case Study 195 Stanisław Wołowiec, Marek Laskowski, Barbara Laskowska, Agnieszka Magoń, Bogdan Mysliwiec and Marek Pyda Part 4 The Role of Stoichiometry in the Determination of Protein Interactions 211 Stoichiometry of Signalling Complexes in Immune Cells: Chapter 9 Regulation by the Numbers 213 Elad Noy, Barak Reicher and Mira Barda-Saad Determination of the Binding Chapter 10 Site-Size of the Protein-DNA Complex by Use of the Electrophoretic Mobility Shift Assay 235 Cheng-Yang Huang Stoichiometry of Protein Interactions Chapter 11 in Bacteriophage Tail Assembly 243 Fumio Arisaka Part 5 Experimental Techniques for the Evaluation of Stoichiometry 259 Methodology for Bioprocess Analysis: Chapter 12 Mass Balances, Yields and Stoichiometries 261 Farges Bérangère, Poughon Laurent, Pons Agnès and Dussap Claude-Gilles Distribution Diagrams Chapter 13 and Graphical Methods to Determine or to Use the Stoichiometric Coefficients of Acid-Base and Complexation Reactions 287 Alberto Rojas-Hernández, Norma Rodríguez-Laguna, María Teresa Ramírez-Silva and Rosario Moya-Hernández Limiting Reactants in Chemical Analysis: Chapter 14 Influences of Metals and Ligands on Calibration Curves and Formation Constants for Selected Iron-Ligand Chelates 311 Mark T. Stauffer, William E. Weller, Kimberly R. Kubas and Kelly A. Casoni Contents VII Part 6 Biomedicine and Environment: The Future is Now? 335 Recent New Characterizations Chapter 15 on the Giant Extracellular Hemoglobin of Glossoscolex paulistus and Some Other Giant Hemoglobins from Different Worms 337 Marcel Tabak, Francisco A.O. Carvalho, José W.P. Carvalho, Jose F.R. Bachega and Patrícia S. Santiago Biological Stoichiometry: Chapter 16 The Elements at the Heart of Biological Interactions 357 Mehdi Cherif Preface Science seeks to understand and explain our world, be that its physical composition (geology), chemical composition (chemistry), the way its composite matter interacts (physics), or the organisms that inhabit it (biology). We can only get an idea of what life is all about by piecing together information from each discipline to give us the big picture. We don’t have to look very far to realize that it is difficult, if not impossible, to separate biology from chemistry. After all, our body is a bag of chemicals. The proteins that form our hair, nails and muscle fibers are chemicals; the minerals that are the basis of our own bones and teeth are chemicals; even the food and drinks we consume are chemicals. Chemistry explores life at the level of atoms and molecules. It is really all about understanding how atoms interact to form larger, more complicated substances. Biology then looks at their behavior when they are combined on a larger scale (cells, tissues, organisms, populations). Chemistry is encapsulated by a handful of essential concepts that are epitomized by the world around us. Just grasping these concepts is sufficient to get to grips with many of the key chemical principles that underpin biology. Life is the result of thousands of different biochemical reactions occurring in every cell of our body. At first glance many of these reactions seem very complicated. Beneath the façade of complexity, however, lie simple principles and tools that give support to all chemical reactions. Some of them undergo the general concept of stoichiometry. The word stoichiometry may sound mysterious, but it is simply based on Greek words meaning ‘element measure’. It is a branch of chemistry that deals with the relative quantities of reactants and products in chemical reactions. At first blush one could think of stoichiometry as something confined to a general chemistry course or a student laboratory, but a deeper consideration of the term itself reveals a surprisingly wide range of applications. We are surrounded every day by tens of thousands of different chemical compounds with contrasting characteristics. Sometimes, the presence of a compound is essential for our existence, like O 2 in the air or glucose in the food. By contrast, the presence of a compound may be detrimental, like pollutants X Preface in the water of alcohol in our blood stream. This is the reason why we need ways of determining what is in our chemical environment, of knowing what is there and, more importantly, how much. Evaluating the amount of a compound we have in a system is often vital: too much of a compound may be toxic to the point of being lethal, too little may be equally harmful. The aim of this book is to provide an overview of the importance of stoichiometry in the biomedical field. It contains a collection of selected research articles and reviews all providing adequate and up-to-date information related to stoichiometry from different point of views. The first section deals with host-guest chemistry, focusing on selected calixarenes, cyclodextrins and crown ethers derivatives. In the second and third sections the book presents some issues concerning stoichiometry of metal complexes and lipids and polymers architecture. The fourth section aims to to clarify the role of stoichiometry in the determination of protein interactions, while in the fifth section some selected experimental techniques applied to specific systems are introduced. The last section of the book is an attempt at showing some interesting connections between biomedicine and the environment, introducing the concept of biological stoichiometry and presenting some data that prove how the two disciplines entwine. On this basis, the present volume would definitely be an ideal source of scientific information to advanced students, junior researchers, faculties and scientists involved in biomedicine, biochemistry and other areas involving stoichiometry evaluation. A special word of appreciation is due to Mr Bojan Rafaj, the Publishing Process Manager who oversaw and coordinated the publishing of all materials and assisted me and the authors in completing our work easily and in a timely manner. My profound thanks also to the technical editor who prepared these manuscripts for publication by InTech - Open Access Publisher. Dr. Alessio Innocenti Department of Chemistry, University of Florence, Italy . STOICHIOMETRY AND RESEARCH – THE IMPORTANCE OF QUANTITY IN BIOMEDICINE Edited by Alessio Innocenti Stoichiometry and Research – The Importance of Quantity in Biomedicine. cavity made up of aromatic Stoichiometry and Research – The Importance of Quantity in Biomedicine 4 nuclei and easily modified rims, has attracted the attention of many theoretical and experimental. Mandolini & Ungaro, 2000). Stoichiometry and Research – The Importance of Quantity in Biomedicine 8 In metal-calixarene complexes (Fig. 3, bottom right), the coordination ability of the