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Assigning Structures to Ions in Mass Spectrometry ß 2006 by Taylor & Francis Group, LLC. ß 2006 by Taylor & Francis Group, LLC. Assigning Structures to Ions in Mass Spectrometry John L. Holmes Christiane Aubry Paul M. Mayer Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business ß 2006 by Taylor & Francis Group, LLC. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2007 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number-10: 0-8493-1950-1 (Hardcover) International Standard Book Number-13: 978-0-8493-1950-1 (Hardcover) This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the conse- quences of their use. No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www. copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Holmes, John L. (John Leonard), 1931- Assigning structures to ions in mass spectrometry / John Holmes, Christiane Aubry, and Paul M. Mayer. p. cm. Includes bibliographical references and index. ISBN-13: 978-0-8493-1950-1 (alk. paper) ISBN-10: 0-8493-1950-1 (alk. paper) 1. Mass spectrometry. 2. Ions--Spectra. I. Aubry, Christiane. II. Mayer, Paul M., 1968- III. Title. QC451.H66 2007 543’.65--dc22 2006021102 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com ß 2006 by Taylor & Francis Group, LLC. To the late Fred Lossing, friend, mentor, guide, and fellow enthusiast in the thrill of the scientific chase ß 2006 by Taylor & Francis Group, LLC. ß 2006 by Taylor & Francis Group, LLC. Foreword In the past 40 or so years, great technical advances have resulted in mass spectrometry becoming the analytical method of choice in many scientific fields. This stems from the very great sensitivity of the method as well as our present ability to convert almost any organic substance into a beam of positively charged ions that can be separated and identified by their mass- to-charge ratio. In addition, the production of smaller, simpler, almost wholly software-controlled instruments has allowed this powerful analytical tech- nique to become accessible to a much wider group of scientists. The purpose of this book is to be a vade-mecum for all users of the technique for whom the structure of the ions present in the mass spectrum of an organic compound is important or of general interest. Indeed it could be argued that all practitioners should have some knowledge of the unique complexities to be found in the gas-phase ion chemistry of even simple organic compounds. Their behavior in turn provides the models for under- standing larger polyatomic systems. ß 2006 by Taylor & Francis Group, LLC. ß 2006 by Taylor & Francis Group, LLC. Acknowledgments The authors wish to thank all those who made this task easier and particularly our families for putting up with the apparently never-ending chore. John L. Holmes thanks all his former students and postdoctorate collab- orators who made his laboratory life so stimulating and exciting and espe- cially two colleagues, Hans Terlouw and Peter Burgers, with whom he spent so many happy hours teasing out the intricacies of ion chemistry. Christiane Aubry wishes to sincerely thank John Holmes, a mentor and dear friend, with whom undertaking a new project has always been a privilege and a great pleasure. She also wishes to thank Orval Mamer from the McGill University Mass Spectrometry Unit for providing access to the electronic resources of the McGill University libraries. Paul M. Mayer would like to acknowledge four terrific supervisors for their guidance, knowledge, and collegiality over the years: John Westmore, John Holmes, Tom Baer, and Leo Radom. ß 2006 by Taylor & Francis Group, LLC. Additional Credits Figures 1.1, 1.2, 1.8, 1.9, 1.10, 1.12, 1.14, 1.18, 1.19 and 1.22 are all original drawings. Figures 1.3, 1.5, 1.6 and 1.7 are from Gross, M.L. and Caprioli, R. (eds.), Encyclopedia of Mass Spectrometry, Elsevier, Amsterdam, 2003, Volume 1, Chapter 5; Holmes, J.L. pp. 434–440. Figure 1.4 is from Burgers, P.C. and Holmes, J.L., Int. J. Mass Spectrom. Ion Processes, 1984, 58, 15. Figure 1.11 is from Holmes, J.L., Org. Mass Spectrom., 1985, 20, 169. Figures 1.13 to 1.17 are from Encyclopedia of Mass Spectrometry, (as above) Chapter 3; Holmes, J.L. pp. 91–98. Figure 1.20 is from Encyclopedia of Mass Spectrometry, (as above) Volume 4, Chapter 3, Terlouw, J.K. and Holmes, J.L. pp. 287–297. Figure 1.21 is from Burgers, P.C., Holmes, J.L., Mommers, A.A. and Szulejko, J.E. Org. Mass Spectrom., 1983, 18, 596. Figure 2.1 is from Holmes, J.L., Lossing, F.P., Terlouw, J.K. and Burgers, P.C., J. Am. Chem. Soc., 1982, 104, 2931. Figures 2.2 and 2.3 are from Yalcin, T., Khouw, C., Csizmadia, I.G., Peterson, M.P. and Harrison, A.G., J. Am. Soc. Mass Spectrom., 1995, 6, 1165. Figures 2.4 to 2.7 are from Holmes, J.L., Org. Mass Spectrom., 1985, 20, 169. ß 2006 by Taylor & Francis Group, LLC. Authors John Holmes was born in London, UK, and obtained his PhD from Univer- sity College, London in 1957 when that powerful chemistry department was in the care of Professors Ingold, Hughes, Nyholm, and Craig. His PhD (gas- phase pyrolysis of alkyl iodides) was under the direction of Professor Allan Maccoll. Professor Holmes spent the postdoctoral years from 1958 to 1960 at the National Research Council of Canada in Ottawa, a laboratory that attracted physical chemists from all around the world. Two years at the University of Edinburgh followed, but the delights of Canada and its great outdoors beckoned Professor Holmes and in 1962, he returned to Canada and the University of Ottawa where he remains to this day, now as Emeritus professor. In 1964, he volunteered to look after the chemistry department’s first ever mass spectrometer, a Hitachi RMU 6D, and very quickly became fascinated by the extraordinary and then very poorly understood chemistry that must lie behind the mass spectra themselves. Professor Holmes has held visiting fellowships and professorships in Australia, Ghana, the Netherlands, and Switzerland. He is a Fellow of the Royal Society of Canada and has received many awards, including the Chemical Institute of Canada Medal. He is the author of some 300 journal publications, editor of the Encyclopaedia of Analytical Chemistry, and was North American editor of Organic Mass Spectrometry for 17 years, a chore that brought new insights into human nature. Outside of science he has always sailed as often as possible, cruising across the Atlantic in 2005. For 12 years he was an international judge for yacht racing and has contributed to the training of judges for the sport for over 20 years. Christiane Aubry obtained a BSc in chemistry from the University of Sherbrooke (Quebec, Canada) in 1989. She pursued her first graduate studies there and received an MSc in organometallic photochemistry in 1991. She joined John Holmes’s mass spectrometry group at the University of Ottawa (Ontario, Canada) in 1992 where she undertook research in gas-phase ion chemistry with special interests in the thermochemistry and characterization of small organic ions. She obtained her PhD in 1997. She accepted an industrial position at the Research and Productivity Council in New Brunswick (Canada) where she shared the responsibility of the analytical mass spectrom- etry facility. In parallel, she conducted research aimed at a better understanding of the de novo production of chlorometabolites by various fungi found in the environment. She returned to the University of Ottawa in 1999 to teach at ß 2006 by Taylor & Francis Group, LLC. the undergraduate level and re-joined Professor John Holmes’s laboratory to pursue gas-phase ion chemistry. For Dr. Aubry, working on this book has provided much needed light relief to attending to the demands of a growing family. Paul M. Mayer received a BSc in chemistry at the University of Manitoba in 1990. He spent three summers working with John Westmore in biological mass spectrometry and computational chemistry and is forever indebted to John Westmore for introducing him to the field. Dr.

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