Preface

Chapter 1. The Analyst's Toolbox
Profile - A Scenario
1.2 - Introduction
1.2 - Ultraviolet - visible Spectroscopy
1.3 - Infrared Spectroscopy
Compare and Contrast - UV-vis vs. FTIR in Quantitative Analysis
1.4 - Nuclear Magnetic Resonance Spectrometry
1.5 - Mass Spectrometry
Profile - Putting it All Together
1.6 - Chromatography
Profile - Establishing a Forensic Protocol
1.7 - Additional Exercises

Chapter 2. Quantum Mechanics and Spectroscopy
Profile- The Brain Initiative and everyday spectroscopy
2.1- Introduction
2.2- The interaction between electromagnetic radiation and matter - absorption and emission of light
Profile - Erwin Schrödinger
2.3- Molecular vibrations lead to quantized energy levels
Profile - London's Millennium Bridge
Profile- Mass Dampers
2.4- Molecular rotation leads to quantized energy levels
2.5- Transitions between vibrational and rotational states -the role of thermal energy and nonradiative decay
Prelude - The Boltzmann Distribution
2.6- Transitions between electronic, vibrational, and rotational states - putting it all together
The Jablonski diagram
Fluorescence and Phosphorescence
2.7 Energy levels of a proton in a magnetic field - Nuclear Magnetic Resonance (NMR) Spectroscopy
2.8- Additional Exercises

Chapter 3. An Introduction to Optics
Profile: The diffraction grating is a key component for many optical instruments
3.1 - An Introduction to the Properties of Light
Wavelength, Energy, and Frequency
Coherence
Polarization
Interference
Diffraction
Scattering
Profile- The photoelectric effect shows the particle nature of light
3.2- Controlling optical beams
Mirrors and Reflection
Lenses and Refraction
Collecting and Collimating Light
Focusing a Collimated Laser Beam
Polarizers
3.3- Wavelength Selection
Introduction to Prism and Grating Monochromators
The Diffraction Grating
Putting it all together- Details on the Grating Monochromator
Profile- Optics that operate by diffraction- the Fresnel Zone Plate
The Michelson Interferometer
Optical Filters & Power Reduction
3.4 - Common Optical Materials
3.5- Beyond Linear Optics
Profile- Innovation and discovery in optics - metamaterials hold promise for the perfect lens, invisibility cloaks, and more
3.6 - Additional Exercises

Chapter 4. An Introduction to Instrumental Electronics
4.1 - Introduction
Circuit Symbols
4.2 - DC Circuits
Current, Voltage, and Multimeter Basics
Series Circuit Elements and the Voltage Divider
Parallel Circuit Elements and the Current Divider
The Multimeter
Voltage and Current Loading Error
Profile - Electronics for a Very Simple Light Sensing Instrument: Voltage Divider Photoresistor circuit
4.3- Capacitors and RC Circuits
4.4- AC Circuits
Ohm's law for AC circuits
Low-pass, High-pass, Band-pass, and Band Stop Filters
Activity- RC Filter Spreadsheet Tool
4.5 - Operational Amplifiers
Inverting and Non-inverting op amps
Summing op amp
Current to Voltage Amplifier
The Voltage Follower
Op Amp Comparator
Cascading op amps
A Cascaded Op Amp Example- Instrumentation Op Amp
Profile- Electronics for an Automatic Titrator: Cascaded Op Amps and the Differentiating Op Amp
4.6 - Quick Survey of Components
Potentiometers
Diode
Transistors
Profile- Electronics for a Simple Absorption Spectrophotometer: Op Amp Circuit as Current to Voltage Amplifier
Profile- What if you need a constant voltage under varying loads? A basic schematic of a potentiostat
4.7 - Analog and Digital Signals
4.8 - Additional Exercises

Chapter 5. Signals and Noise: An Introduction to Signal Processing
Profile- Spectroscopy of single molecules?
5.1 - Introduction to Signals
5.2 - Sources and Characteristics of Noise
5.3 - Signal to Noise Ratio and Ensemble Averaging
5.4- Processing Signals with Hardware and Software
Analog Filters
Boxcar averaging with hardware
Modulating Signals and the Lock-In Amplifier
Digital Filters
Rolling average, Boxcar average, Savitzky-Golay Filter, and Fourier Filtering
5.5 - Sampling Rates, the Nyquist Frequency, and Aliasing
5.6- Analog to Digital Conversion
5.7 - Additional Exercises

Chapter 6. Molecular Ultraviolet and Visible Spectroscopy
Profile - James Clerk Maxwell
6.1 - Introduction
6.2 - Electronic Excitation and Molecular Structure
Structure and "Color"
Heteroatoms
DPK - A Case Study
Solvent Polarity
Transition Metal Coordination Compounds
Vibronic Transitions
Sidebar - The Spectroscopic Series
6.3 - Quantitative Measurements
Selection Rules
Beer's Law
Sidebar - Derivation of Beer's Law
Deviations from Beer's Law
Bandwidth Resolution
Activity - Explore the effects on the relationship of A vs. c
6.4 - Instrumentation Designs
Fixed Wavelength Spectrometers
Profile - HACH DR3900
Scanning Spectrometers
Compare and Constrast - Single & Dual Beam Spectrometers
Array Spectrophotometers
6.5 - Monochromators
6.6 - Sources
Deuterium Arc/Tungsten Halogen Bulb
Xenon Arc Lamps
Light Emitting Diodes
Profile - The Jaz® by Ocean Optics
6.7 - Detectors
The PMT
Photovoltaic Cells
Charge Coupled Device
6.8 - Noise
Stray Light
Detector Noise
Profile - Walter Hermann Schottky
Source Noise
6.9 - Kinetic UV-vis Techniques
Stop Flow UV-vis
Flash Photolysis
Profile - Building a functional monochromator
6.10 - Useful Data
6.11 - Additional Exercises

Chapter 7. Atomic Absorption Spectroscopy
7.1- Introduction
Profile - The Birth of Atomic Absorption Spectroscopy (AAS)
7.2 - Molecular vs. Atomic Absorption
Analytical Specificity
7.3 - Spectral Bandwidth
Lifetime Broadening
Profile - Review of Term Symbols
Magnetic Field Broadening
Profile - Lightning over Salty Waters
Pressure Broadening
Note - IUPAC nomenclature for pressure broadening.
Doppler Broadening
7.4 -AAS Sources
The Hollow-Cathode Lamp
Profile - Nutritional Contents of Breast Milk
Electrodeless Discharge Lamps
Activity - Soil Analysis
7.5 - Sample Introduction
Flame - AAS
The Flame
The Flame Height
Electrothermal-AAS/GFAAS
Flame vs Electrothermal AAS
Profile- AAS Analysis of Oil
Hydride - AAS
Cold Vapor-AAS
Compare and Contrast - Detection Limit Ranges
7.6 - Measuring Atomic Absorption
Background Correction
Zeeman Background Correction
Smith-Hieftje background correction
Spectral Interference
Profile-Demystifying the Zeeman Effect
7.7 - Sample Preparation
Acid Digestion
7.8 - Performing an AAS analysis
7.9 - Additional Exercises

Chapter 8. Luminescence Spectroscopy
8.1 - Introduction
8.2 - Theory
Principles of Fluorescence and Phosphorescence
Profile - Is your $100 bill real? Find out with time-resolved fluorescence
Relating fluorescence and molecular structure
Profile - Fluorescence quenching helps with aerodynamics
8.3 -The Fluorescence Spectrometer
Excitation sources
Wavelength discrimination and instrument resolution
Detectors
Putting it all together- Walking through the luminescence system
Excitation spectra
Sample introduction
Profile- Fluorescence pushes the limits of detection- single molecule detection and femtomolar concentrations
8.4- Challenges with Fluorescence Spectroscopy
Detector response correction
Source intensity correction
Stray light contamination
Challenges with high absorbance
Photobleaching
8.5 -Additional Fluorescence based techniques
Chemiluminescence
Fluorescence polarization
Resonance energy transfer spectroscopy
Multiphoton excitation
8.6 - Additional Exercises
Profile - Using fluorescence to determine concentrations of DNA and RNA

Chapter 9. Atomic Emission Spectroscopy
9.1 - Introduction
Profile - Get The Lead Out
9.2 - The Atomizer and the Excitation Source
Profile - Columbia
Inductively Coupled Plasma Torch
Direct Current Plasma Source
Profile - The Plasma Torch
Microwave Induced Plasma Source
Profile - Atmospheric MP-AES
Profile - LIBS in Space
Laser Ablation
Profile- Visualizing a Plasma
9.3 - Sample Introduction
Applications
Sources AAS vs. AES
Sample preparation and interferences
Zeeman Background Correction
9.4 - Measuring Atomic Emission
Compare and Contrast FAAS, GFAAS & ICP-AES
9.5- Additional Exercises

Chapter 10. Infrared Spectroscopy
10.1 -Chemical Structure and Molecular Vibrations
Profile - The Future of FTIR
Wavenumbers
Group Frequencies
Normal Modes
Vibrational Categories
Profile - Olive Oil
The Selection Rules and Molecular Symmetry
Vibronic Coupling
10.2 - Time Domain vs. Frequency Domain Spectroscopy: The Fourier Transformation
Activity: Creating a Beat Pattern
Activity: Performing a Fourier Transform
10.3 -FTIR & Wavelength Discrimination
The Michelson Interferometer
Resolution
Activity: Exploring Resolution
10.4 -Sources
The Nernst Glower
The Globar
Coiled Wire Sources
Solid State Sources
10.5 -Detectors
Thermal Detectors
Pyroelectric Detectors
Profile- PZT Ceramics
Photoconductive Detectors
Profile- MCT Detectors
Quantum Well Detectors
10.6 -Spectral Output
Transmittance vs. Absorbance
Quantitative Measurements and Deviations from Beer's Law
10.7- Developments; Two Dimensional Infrared Spectroscopy
10.8 - Sample Introduction
Optical Materials
Gasses
Solution IR Spectroscopy
Neat Liquids
Solids
ATR
Compare and Contrast: UV-vis versus FTIR in Quantitative & Qualitative Analysis
10.9 - Useful Data
10.10- Additional Exercises

Chapter 11. Raman Spectroscopy
Profile - Raman Applications in Art and Medicine
11.1 -Introduction
Rayleigh Scattering
11.2 - Theory of Raman Scattering
Selection Rules
Case Study - Vibrations in the linear molecule CO2
Case Study- Raman spectroscopy of a tetrahedral molecule; CCl4
11.3 -The Raman Spectrometer
Instrument Basics
Radiant Source
Wavelength Discrimination and Raman
Spectrometer Resolution
Filters
Detectors
Compare and Contrast - A side-by-side evaluation of FTIR and Raman spectroscopy.
Handheld Raman Analyzers
Profile - Drug detection using commercial handheld Raman spectrometers
Fiber optic probes
11.4- Additional Raman based techniques
Raman Imaging
Polarized Raman Spectroscopy
Fourier Transform Raman Spectroscopy (FT-Raman)
Surface enhanced Raman Spectroscopy (SERS)
Profile - Using Raman spectroscopy to identify compounds from a distance
11.5 - Additional Exercises

Chapter 12. Mass Spectrometry
12.1 - Basic Principles & Comparisons to an Optical Spectrophotometer
Profile - Puffer MS
12.2 - Ion sources
Electron Ionization
Profile - J. J. Thomson
Chemical Ionization
Electrospray Ionization
Profile - John Fenn
Matrix Assisted Laser Desorption Ionization
Secondary Ion
Thermal Ionization
Inductively Coupled Plasma
Compare & Contrast - Elemental Methods
Profile - TOF-MS in Space
12.3 - Mass Analyzers
Sector & Double-focusing
Profile - Eugen Goldstein Quadrupole
Profile - R. Graham Cooks
Time-of-flight
FT Ion Cyclotron Resonance
12.4 - Detectors
Activity - Selected Ion Game
12.5 - Additional Techniques
Tandem Techniques
Isotope Ratio Mass Spectrometry
Accelerator Mass Spectrometry
Profile - 10Be as a Geological Clock
Profile - Human Scent Fingerprinting
12.6 - Additional Exercises
Advanced Exercises

Chapter 13. An Introduction to Nuclear Magnetic Resonance Spectroscopy
13.1 - Introduction
Profile - NMR versus HIV
Spectral Analysis - A Quick Review
13.2 - NMR Spectroscopy is all about the Nucleus
Nuclear Quantum Numbers
A Nucleus in a Magnetic Field
Tesla vs. MHz
13.3 - The NMR Signal
Compare and Contrast - Population distribution for common spectroscopic methods
Profile - Felix Bloch
13.4 - The RF Pulse: Inducing nuclear magnetic resonance
FT-NMR: Time Domain vs. Frequency Domain Spectroscopy & The Fourier Transformation
Free Induction Decay (FID): The FT-NMR "Beat Pattern"
13.5 - Chemical Shift and Resolution
Profile - Richard R. Ernst
The Chemical Shift (ppm)
Chemical Shift Reference
Resolution
13.6 - The Instrument
Shimming
Loading
13.7 - Signal Processing
Increasing the signal to noise ratio
Profile - Angela Gronenborn
13.8 - Magnetic Resonance Imaging
Profile - MRI and Brain Concussion
Texts
On Line Resources
Some interesting laboratory experiments
13.9 - Additional Exercises

Chapter 14. Liquid Chromatography
14.1 - Introduction
Profile- Mikhail S. Tswett
14.2 - Theory
Distribution Equilibrium
Profile - Other Applications of Partition Coefficients
Principles of Chromatography
Activity: TLC at home
The Retention Factor
Resolution and Theoretical Plates
Band Broadening
14.3 - Basic Method Development
Thermodynamics and Kinetics Factors
Isocratic vs. Gradient
Profile: The Role of Temperature
Qualitative vs. Quantitative
Profile: Analysis of Wine - Qualitative and Quantitative
14.4 - Stationary Phase Materials and Modes of Separation
Profile: LC-MS in Athletic Doping
Normal Phase
Reversed Phase
Ion Exchange
Hydrophilic Interaction Chromatography (HIC)
Affinity
Chiral Chromatography
Profile - The Chiral Medicine Cabinet
Size Exclusion
14.5 - Instrumentation
Overview
HPLC Components
Profile -Ultrahigh Pressure LC
Mobile Phase
Columns
Injectors
Pumps
Detectors
Profile- Major Players, the Chromatography Industry
14.7 - Additional Exercises

Chapter 15. Gas Chromatography
Profile - Odorants, Pheromones, and Chemosignals
15.1 - Introduction
Profile - Gas Chromatography on Mars
15.2 - Basic GC Instrument Design
15.3 - Method Development: a case study
A Case Study - Peanut Butter
Profile - The NIST 14 Gas Chromatography (GC) Library with Search Software
15.4 - Modes of Separation
Isothermal vs. Temperature gradients
The Column
15.5 - Carrier Gas and Injector
Carrier Gases
15.6 - Detectors
Ionizing Detectors
Optical Detectors
Thermal Conductivity Detectors
Electrochemical Detectors
Tandem Instrument Detection
Quantitative and Qualitative Considerations
15.7 - New Developments and Directions in GC
Multidimensional GC Techniques
Profile - Breath and Air Quality
Miniaturization, Portability, Speed, and Throughput
15.8 - Extended Theory
Evaluation of the GC Separation
The Relationship between VN, k, and Selectivity
The General Elution Problem
15.9 - Useful Information
Table 16.3 - GC column Manufacturers
15.10 - Additional Exercises

Chapter 16. Electrophoresis
16.1 - Introduction
Profile - The Father of Electrophoresis
16.2 - Fundamental Principles
16.3 - The Basic Apparatus
Profile - DNA Markers
16.4 - Paper Electrophoresis
Activity -Demystifying Electrophoresis: Build Your Own Electrophoresis Apparatus
16.5 - Gel Electrophoresis
Polyacrylamide Gel Electrophoresis (PAGE)
SDS PAGE
Agarose Gel Electrophoresis
16.6 - Ending the Analysis: The Time Factor
16.7 - Gel Sample Detection
Visualization
Blotting
Quantitative Electrophoresis
16.8 - Enhancing Resolution
Disc Electrophoresis
Isoelectric Focusing
2D Gel Electrophoresis Techniques
Profile - 2D Success
16.9 - Capillary Electrophoresis
Profile - Capillary Electrophoresis and the Human Genome Project
Introduction to Capillary Electrophoresis
The Instrument
Separation Efficiency
Electroosmotic Flow
Sample Loading and Throughput
Dynamic Coating
Detection
Recent Developments in CE
Compare and Contrast: A look back at four different separation techniques
16.10 - Useful Data
Table 16.1 - Polyacrylamide Gel Separation Ranges
Table 16.2 - Stains for Gels
16.11 - Additional Exercises

Chapter 17. Potentiometry & Probes
17.1 -Basic Principles: Probes and Biosensors
Profile- Handheld water quality probe
17.2 - Potentiometric Probes
Profile - The Standard Hydrogen Electrode
The pH Probe
Profile - Nano-scale pH probe for in-vivo use
The Nitrate Probe
Profile - Construction of a Salicylate ISE
The Oxygen Probe
17.3 - Non-potentiometric probes
The Dissolved Oxygen
The Chloride Probe
The Total Salinity Probe
17.4 - Probes for Measurements in the Human Body
The Glucose Probe - a Biosensor
Profile- The Number of Adults Treated for Diabetes Doubled in a Decade
The Alcohol Fuel Cell Probe
Profile - "Smart" Toilets
17.5 - Additional Exercises

Chapter 18: Statistical Data Analysis
18.1-Introduction
18.2 -Types of Error
Gross Error
Systematic Error
Random Error
18.3 -Precision vs. Accuracy
18.4 -Statistical Tools
Population vs. Sample
Mean
Standard Deviation and Variance
Standard Error and Error Bars.
Normal Distributions
Confidence Limits
Using Spreadsheets to Determine Confidence Limits
Propagation of Error
Data Sets
Identifying Outliers: The Q-Test
Identifying Outliers: The Grubb's Test
Analyzing Variance: The F-Test
ANOVA: A 2-Dimenstional F-Test
18.5 -Linear Regression Analysis
18.6 -LOD, LOQ, and LDR
18.7 - Additional Exercises

Index