Sample Preparation Techniques in Analytical Chemistry

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1 Sample Preparation Techniques in Analytical Chemistry

2 CHEMICAL ANALYSIS A SERIES OF MONOGRAPHS ON ANALYTICAL CHEMISTRY AND ITS APPLICATIONS Editor J. D. WINEFORDNER VOLUME 162 A complete list of the titles in this series appears at the end of this volume.

3 Sample Preparation Techniques in Analytical Chemistry Edited by SOMENATH MITRA Department of Chemistry and Environmental Science New Jersey Institute of Technology A JOHN WILEY & SONS, INC., PUBLICATION

4 Copyright by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, , fax , or on the web at Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) , fax (201) , permreq@wiley.com. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best e orts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services please contact our Customer Care Department within the U.S. at , outside the U.S. at or fax Wiley also publishes its books in a variety of electronic formats. Some content that appears in print, however, may not be available in electronic format. Library of Congress Cataloging-in-Publication Data: Sample preparation techniques in analytical chemistry / edited by Somenath Mitra. p. cm. (Chemical analysis ; v. 162) Includes index. ISBN (cloth : acid-free paper) 1. Sampling. 2. Chemistry, Analytic Methodology. I. Mitra, S. (Somenath), 1959 II. Series. QD75.4.S24S dc Printed in the United States of America

5 To the hands in the laboratory and the heads seeking information

6 CONTENTS CONTRIBUTORS PREFACE CHAPTER 1 xvii xix SAMPLE PREPARATION: AN ANALYTICAL PERSPECTIVE 1 Somenath Mitra and Roman Brukh 1.1. The Measurement Process Qualitative and Quantitative Analysis Methods of Quantitation Errors in Quantitative Analysis: Accuracy and Precision Accuracy Precision Statistical Aspects of Sample Preparation Method Performance and Method Validation Sensitivity Detection Limit Range of Quantitation Other Important Parameters Method Validation Preservation of Samples Volatilization Choice of Proper Containers Absorption of Gases from the Atmosphere Chemical Changes Preservation of Unstable Solids 20 vii

7 viii contents 1.5. Postextraction Procedures Concentration of Sample Extracts Sample Cleanup Quality Assurance and Quality Control during Sample Preparation Determination of Accuracy and Precision Statistical Control Matrix Control Contamination Control 32 References 35 SECTION A CHAPTER 2 EXTRACTION AND ENRICHMENT IN SAMPLE PREPARATION PRINCIPLES OF EXTRACTION AND THE EXTRACTION OF SEMIVOLATILE ORGANICS FROM LIQUIDS 37 Martha J. M. Wells 2.1. Principles of Extraction Volatilization Hydrophobicity Acid Base Equilibria Distribution of Hydrophobic Ionogenic Organic Compounds Liquid Liquid Extraction Recovery Methodology Procedures Recent Advances in Techniques Liquid Solid Extraction Sorption Solid-Phase Extraction Sorbents in SPE Sorbent Selection Recovery Methodology 108

8 contents ix Procedures Recent Advances in SPE Solid-Phase Microextraction Sorbents Sorbent Selection Methodology Recent Advances in Techniques Stir Bar Sorptive Extraction Sorbent and Analyte Recovery Methodology Recent Advances in Techniques Method Comparison 130 References 131 CHAPTER 3 EXTRACTION OF SEMIVOLATILE ORGANIC COMPOUNDS FROM SOLID MATRICES 139 Dawen Kou and Somenath Mitra 3.1. Introduction Extraction Mechanism Preextraction Procedures Postextraction Procedures Soxhlet and Automated Soxhlet Soxhlet Extraction Automated Soxhlet Extraction Comparison between Soxtec and Soxhlet Ultrasonic Extraction Selected Applications and Comparison with Soxhlet Supercritical Fluid Extraction Theoretical Considerations Instrumentation Operational Procedures Advantages/Disadvantages and Applications of SFE Accelerated Solvent Extraction 155

9 x contents Theoretical Considerations Instrumentation Operational Procedures Process Parameters Advantages and Applications of ASE Microwave-Assisted Extraction Theoretical Considerations Instrumentation Procedures and Advantages/ Disadvantages Process Parameters Applications of MAE Comparison of the Various Extraction Techniques 173 References 178 CHAPTER 4 EXTRACTION OF VOLATILE ORGANIC COMPOUNDS FROM SOLIDS AND LIQUIDS 183 Gregory C. Slack, Nicholas H. Snow, and Dawen Kou 4.1. Volatile Organics and Their Analysis Static Headspace Extraction Sample Preparation for Static Headspace Extraction Optimizing Static Headspace Extraction E ciency and Quantitation Quantitative Techniques in Static Headspace Extraction Dynamic Headspace Extraction or Purge and Trap Instrumentation Operational Procedures in Purge and Trap Interfacing Purge and Trap with GC Solid-Phase Microextraction 200

10 contents xi SPME Method Development for Volatile Organics Choosing an SPME Fiber Coating Optimizing Extraction Conditions Optimizing SPME GC Injection Liquid Liquid Extraction with Large- Volume Injection Large-Volume GC Injection Techniques Liquid Liquid Extraction for Large-Volume Injection Membrane Extraction Membranes and Membrane Modules Membrane Introduction Mass Spectrometry Membrane Extraction with Gas Chromatography Optimization of Membrane Extraction Conclusions 223 References 223 CHAPTER 5 PREPARATION OF SAMPLES FOR METALS ANALYSIS 227 Barbara B. Kebbekus 5.1. Introduction Wet Digestion Methods Acid Digestion Wet Ashing Microwave Digestion Comparison of Digestion Methods Pressure Ashing Wet Ashing for Soil Samples Dry Ashing Organic Extraction of Metals Extraction with Supercritical Fluids Ultrasonic Sample Preparation 245

11 xii contents 5.4. Solid-Phase Extraction for Preconcentration Sample Preparation for Water Samples Precipitation Methods Preparation of Sample Slurries for Direct AAS Analysis Hydride Generation Methods Colorimetric Methods Metal Speciation Types of Speciation Speciation for Soils and Sediments Sequential Schemes for Metals in Soil or Sediment Speciation for Metals in Plant Materials Speciation of Specific Elements Contamination during Metal Analysis Safe Handling of Acids 264 References 264 SECTION B CHAPTER 6 SAMPLE PREPARATION FOR NUCLEIC ACID ANALYSIS SAMPLE PREPARATION IN DNA ANALYSIS 271 Satish Parimoo and Bhama Parimoo 6.1. DNA and Its Structure Physical and Chemical Properties of DNA Isolation of DNA Isolation of DNA from Bacteria Phenol Extraction and Precipitation of DNA Removal of Contaminants from DNA Isolation of Plasmid DNA Plasmid DNA Preparation Purification of Plasmid DNA Genomic DNA Isolation from Yeast 287

12 contents xiii 6.5. DNA from Mammalian Tissues Blood Tissues and Tissue Culture Cells DNA from Plant Tissue Isolation of Very High Molecular Weight DNA DNA Amplification by Polymerase Chain Reaction Starting a PCR Reaction Isolation of DNA from Small Real- World Samples for PCR Assessment of Quality and Quantitation of DNA Precautions for Preparing DNA Assessment of Concentration and Quality Storage of DNA 299 References 299 CHAPTER 7 SAMPLE PREPARATION IN RNA ANALYSIS 301 Bhama Parimoo and Satish Parimoo 7.1. RNA: Structure and Properties Types and Location of Various RNAs RNA Isolation: Basic Considerations Methods of Extraction and Isolation of RNA Phenol Extraction and RNA Recovery: Basic Principles Examples of RNA Isolation Using Phenol Extraction Guanidinium Salt Method Examples of RNA Isolation Using Guanidinium Salts Isolation of RNA from Nuclear and Cytoplasmic Cellular Fractions 317

13 xiv contents 7.6. Removal of DNA Contamination from RNA Fractionation of RNA Using Chromatography Methods Fractionation of Small RNA by HPLC mrna Isolation by A nity Chromatography Isolation of RNA from Small Numbers of Cells In Vitro Synthesis of RNA Assessment of Quality and Quantitation of RNA Storage of RNA 328 References 329 CHAPTER 8 TECHNIQUES FOR THE EXTRACTION, ISOLATION, AND PURIFICATION OF NUCLEIC ACIDS 331 Mahesh Karwa and Somenath Mitra 8.1. Introduction Methods of Cell Lysis Mechanical Methods of Cell Lysis Nonmechanical Methods of Cell Lysis Isolation of Nucleic Acids Solvent Extraction and Precipitation Membrane Filtration Chromatographic Methods for the Purification of Nucleic Acids Size-Exclusion Chromatography Anion-Exchange Chromatography Solid-Phase Extraction A nity Purification Automated High-Throughput DNA Purification Systems Electrophoretic Separation of Nucleic Acids 360

14 contents xv Gel Electrophoresis for Nucleic Acids Purification Techniques for the Isolation of DNA from Gels Capillary Electrophoresis for Sequencing and Sizing Microfabricated Devices for Nucleic Acids Analysis Sample Preparation on Microchips 370 References 373 SECTION C SAMPLE PREPARATION IN MICROSCOPY AND SPECTROSCOPY CHAPTER 9 SAMPLE PREPARATION FOR MICROSCOPIC AND SPECTROSCOPIC CHARACTERIZATION OF SOLID SURFACES AND FILMS 377 Sharmila M. Mukhopadhyay 9.1. Introduction Microscopy of Solids Spectroscopic Techniques for Solids Sample Preparation for Microscopic Evaluation Sectioning and Polishing Chemical and Thermal Etching Sample Coating Techniques Specimen Thinning for TEM Analysis Ion Milling Reactive Ion Techniques Chemical Polishing and Electropolishing Tripod Polishing Ultramicrotomy Special Techniques and Variations Summary: Sample Preparation for Microscopy 400

15 xvi contents 9.5. Sample Preparation for Surface Spectroscopy Ion Bombardment Sample Heating In Situ Abrasion and Scraping In Situ Cleavage or Fracture Stage Sample Preparation/Treatment Options for In Situ Reaction Studies Summary: Sample Preparation for Surface Spectroscopy 409 References 410 CHAPTER 10 SURFACE ENHANCEMENT BY SAMPLE AND SUBSTRATE PREPARATION TECHNIQUES IN RAMAN AND INFRARED SPECTROSCOPY 413 Zafar Iqbal Introduction Raman E ect Fundamentals of Surface-Enhanced Raman Spectroscopy Attenuated Total Reflection Infrared Spectroscopy Fundamentals of Surface-Enhanced Infrared Spectroscopy Sample Preparation for SERS Electrochemical Techniques Vapor Deposition and Chemical Preparation Techniques Colloidal Sol Techniques Nanoparticle Arrays and Gratings Sample Preparation for SEIRA Potential Applications 433 References 436 INDEX 439

16 CONTRIBUTORS Roman Brukh, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ Zafar Iqbal, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey Mahesh Karwa, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ Barbara B. Kebbekus, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ Dawen Kou, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ Somenath Mitra, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ Sharmila M. Mukhopadhyay, Department of Mechanical and Materials Engineering, Wright State University, Dayton, OH Bhama Parimoo, Department of Pharmaceutical Chemistry, Rutgers University College of Pharmacy, Piscataway, NJ Satish Parimoo, Aderans Research Institute, Inc., 3701 Market Street, Philadelphia, PA Gregory C. Slack, Department of Chemistry, Clarkson University, Potsdam, NY Nicholas H. Snow, Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ Martha J. M. Wells, Center for the Management, Utilization and Protection of Water Resources and Department of Chemistry, Tennessee Technological University, Cookeville, TN xvii

17 PREFACE There has been unprecedented growth in measurement techniques over the last few decades. Instrumentation, such as chromatography, spectroscopy and microscopy, as well as sensors and microdevices, have undergone phenomenal developments. Despite the sophisticated arsenal of analytical tools, complete noninvasive measurements are still not possible in most cases. More often than not, one or more pretreatment steps are necessary. These are referred to as sample preparation, whose goal is enrichment, cleanup, and signal enhancement. Sample preparation is often the bottleneck in a measurement process, as they tend to be slow and labor-intensive. Despite this reality, it did not receive much attention until quite recently. However, the last two decades have seen rapid evolution and an explosive growth of this industry. This was particularly driven by the needs of the environmental and the pharmaceutical industries, which analyze large number of samples requiring significant e orts in sample preparation. Sample preparation is important in all aspects of chemical, biological, materials, and surface analysis. Notable among recent developments are faster, greener extraction methods and microextraction techniques. Specialized sample preparations, such as self-assembly of analytes on nanoparticles for surface enhancement, have also evolved. Developments in highthroughput workstations for faster preparation analysis of a large number of samples are impressive. These use 96-well plates (moving toward 384 wells) and robotics to process hundreds of samples per day, and have revolutionized research in the pharmaceutical industry. Advanced microfabrication techniques have resulted in the development of miniaturized chemical analysis systems that include microscale sample preparation on a chip. Considering all these, sample preparation has evolved to be a separate discipline within the analytical/measurement sciences. The objective of this book is to provide an overview of a variety of sample preparation techniques and to bring the diverse methods under a common banner. Knowing fully well that it is impossible to cover all aspects in a single text, this book attempts to cover some of the more important and widely used techniques. The first chapter outlines the fundamental issues relating to sample preparation and the associated quality control. The xix

18 xx preface remainder of the book is divided into three sections. In the first we describe various extraction and enrichment approaches. Fundamentals of extraction, along with specific details on the preparation of organic and metal analytes, are presented. Classical methods such as Soxhlett and liquid liquid extraction are described, along with recent developments in widely accepted methods such as SPE, SPME, stir-bar microextraction, microwave extraction, supercritical extraction, accelerated solvent extraction, purge and trap, headspace, and membrane extraction. The second section is dedicated to the preparation for nucleic acid analysis. Specific examples of DNA and RNA analyses are presented, along with the description of techniques used in these procedures. Sections on highthroughput workstations and microfabricated devices are included. The third section deals with sample preparation techniques used in microscopy, spectroscopy, and surface-enhanced Raman. The book is intended to be a reference book for scientists who use sample preparation in the chemical, biological, pharmaceutical, environmental, and material sciences. The other objective is to serve as a text for advanced undergraduate and graduate students. I am grateful to the New Jersey Institute of Technology for granting me a sabbatical leave to compile this book. My sincere thanks to my graduate students Dawen Kou, Roman Brukh, and Mahesh Karwa, who got going when the going got tough; each contributed to one or more chapters. New Jersey Institute of Technology Newark, NJ Somenath Mitra

Advanced Analytical Chemistry The University of Toledo Department of Chemistry and Biochemistry CHEM / /

Advanced Analytical Chemistry The University of Toledo Department of Chemistry and Biochemistry CHEM 4305 001/6300 001/8300 001 Instructor: Emanuela Gionfriddo Email: emanuela.gionfriddo@utoledo.edu Office