Section A: Foundations

Profile – A Scenario
1.1 – 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 – Further Reading
1.8 – Additional Exercises
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
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 – Further Reading
3.7 – Additional Exercises
Profile – Alessandro Volta
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
Diodes
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 – Further Reading
4.9 – Additional Exercises
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 – Further Reading
5.8 – Additional Exercises

Section B: Spectroscopy & Spectrometry

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 – Further Reading
6.12 – Additional Exercises
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 – Further Reading
7.10 – Additional Exercises
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 – Further Reading
8.7 – Additional Exercises
Profile – Using fluorescence to determine concentrations of DNA and RNA
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 – Further Reading
9.6 – Additional Exercises
Profile – A modern day gold rush.
10.1 – Principles of X-ray Fluorescence (XRF)
Profile – W. C. Röntgen
XRF Transitions: Terminology
Photoelectric Absorption
Compare and Contrast – Optical Absorption vs.Photoelectric Absorption
Absorption of X-rays
10.2 – X-ray Sources
Radioisotopes
X-ray tubes
Synchrotron Radiation
Profile –Lost Inscriptions
10.3 – X-ray Optics
Profile – XRF Analysis of a 15th Painting
Reflection Optics
Diffraction Optics
Profile – Lost Painting by Vincent van Gogh
10.4 – Wavelength Dispersive Spectrometers
Sequential and Simultaneous
WDXRF Detectors
10.5 – Energy Dispersive Spectrometers
EDXRF Detectors
10.6 – Direct Comparison: WDXRF & EDXRF
Compare and Contrast – AAS, AES & XRF
10.7 – Sample Introduction
10.8 – Total Reflection XRF (TXRF)
Profile – Christiaan Huygens
Profile – Max Von Laue
10.9 – X-ray Induced Photoelectron Spectroscopy & Auger Electron Spectroscopy
Compare and Contrast – XRF, XPS & AES
XPS
AES
Profile – Pierre Victor Auger
XPS & AES Instrumentation
10.10 – Single Crystal X-ray Diffractometry
Scatter
X-ray Diffraction
Bragg’s Law
Profile – Henry and Lawrence Bragg
The Lattice
Obtaining A Crystal Structure
The Diffractometer
10.11 – Further Reading
10.12 – Additional Exercises
Advanced Exercises
11.1 – 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
11.2 – Time Domain vs. Frequency Domain Spectroscopy: The Fourier Transformation
Activity – Creating a Beat Pattern
Activity – Performing a Fourier Transform
11.3 – FTIR & Wavelength Discrimination
The Michelson Interferometer
Resolution
Activity – Exploring Resolution
11.4 – Sources
The Nernst Glower
The Globar
Coiled Wire Sources
Solid State Sources
11.5 – Detectors
Thermal Detectors
Pyroelectric Detectors
Profile – PZT Ceramics
Photoconductive Detectors
Profile – MCT Detectors
Quantum Well Detectors
11.6 – Spectral Output
Transmittance vs. Absorbance
Quantitative Measurements and Deviations from Beer’s Law
11.7 – Developments; Two Dimensional Infrared Spectroscopy
11.8 – Sample Introduction
Optical Materials
Gasses
Solution IR Spectroscopy
Neat Liquids
Solids
ATR
Compare and Contrast – UV-vis versus FTIR in Quantitative & Qualitative Analysis
11.9 – Useful Data
11.10 – Further Reading
11.11 – Additional Exercises
Profile – Raman Applications in Art and Medicine
12.1 – 7Introduction
Rayleigh Scattering
12.2 – Theory of Raman Scattering
Selection Rules
Case Study – Vibrations in the linear molecule CO2
Case Study – Raman spectroscopy of a tetrahedral molecule; CCl4
12.3 – 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
12.4 – 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
12.5 – Further Reading
12.6 – Additional Exercises
13.1 – Basic Principles & Comparisons to an Optical Spectrophotometer
Profile – Puffer MS
13.2 – 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
13.3 – Mass Analyzers
Sector & Double-focusing
Profile – Eugen Goldstein
Quadrupole
Profile – R. Graham Cooks
Time-of-flight
FT Ion Cyclotron Resonance
13.4 – Detectors
Activity – Selected Ion Game
13.5 – Additional Techniques
Tandem Techniques
Isotope Ratio Mass Spectrometry
Accelerator Mass Spectrometry
Profile – 10Be as a Geological Clock
Profile – Human Scent Fingerprinting
13.6 – Further Reading
13.7 – Additional Exercises
Advanced Exercises
14.1 – Introduction
Profile – NMR versus HIV
Spectral Analysis – A Quick Review
14.2 – NMR Spectroscopy is all about the Nucleus
Nuclear Quantum Numbers
A Nucleus in a Magnetic Field
Tesla vs. MHz
14.3 – The NMR Signal
Compare and Contrast – Population distribution for common spectroscopic methods
Profile – Felix Bloch
14.4 – 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”
14.5 – Chemical Shift and Resolution
Profile – Richard R. Ernst
The Chemical Shift (ppm)
Chemical Shift Reference
Resolution
14.6 – The Instrument
Shimming
Loading
14.7 – Signal Processing
Increasing the signal to noise ratio
Profile – Angela Gronenborn
14.8 – Magnetic Resonance Imaging
Profile – MRI and Brain Concussion
14.9 – Further Reading
Texts
On Line Resources
Some interesting laboratory experiments
14.10 – Additional Exercises

Section C: Separation Science

15.1 – Introduction
Profile – Mikhail S. Tswett
15.2 – 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
15.3 – 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
15.4 – 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
15.5 – Instrumentation
Overview
HPLC Components
Profile – Ultrahigh Pressure LC
Mobile Phase
Columns
Injectors
Pumps
Detectors
Profile – Major Players, the Chromatography Industry
15.6 – Further Reading
15.7 – Additional Exercises
Profile – Odorants, Pheromones, and Chemosignals
16.1 – Introduction
Profile – Gas Chromatography on Mars
16.2 – Basic GC Instrument Design
16.3 – Method Development: a case study
Case Study – Peanut Butter
Profile – The NIST 14 Gas Chromatography (GC) Library with Search Software
16.4 – Modes of Separation
Isothermal vs. Temperature gradients
The Column
16.5 – Carrier Gas and Injector
Carrier Gases
16.6 – Detectors
Ionizing Detectors
Optical Detectors
Thermal Conductivity Detectors
Electrochemical Detectors
Tandem Instrument Detection
Quantitative and Qualitative
Considerations
16.7 – New Developments and Directions in GC
Multidimensional GC Techniques
Profile – Breath and Air Quality
Miniaturization, Portability, Speed, and Throughput
16.8 – Extended Theory
Evaluation of the GC Separation
The Relationship between VN, k, and Selectivity
The General Elution Problem
16.9 – Useful Information
Table 16.3 – GC column Manufacturers
16.10 – Further Reading
16.11 – Additional Exercises
17.1 – Introduction
Profile – The Father of Electrophoresis
17.2 – Fundamental Principles
17.3 – The Basic Apparatus
Profile – DNA Markers
17.4 – Paper Electrophoresis
Activity – Demystifying Electrophoresis: Build Your Own Electrophoresis Apparatus
17.5 – Gel Electrophoresis
Polyacrylamide Gel Electrophoresis (PAGE)
SDS PAGE
Agarose Gel Electrophoresis
17.6 – Ending the Analysis: The Time Factor
17.7 – Gel Sample Detection
Visualization
Blotting
Quantitative Electrophoresis
17.8 – Enhancing Resolution
Disc Electrophoresis
Isoelectric Focusing
2D Gel Electrophoresis Techniques
Profile – 2D Success
17.9 – 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
17.10 – Useful Data
Table 17.1 – Polyacrylamide Gel Separation Ranges
Table 17.2 – Stains for Gels
17.11 – Further Reading
17.12 – Additional Exercises

Section D: Electroanalytical Techniques

18.1 – Basic Principles: Probes and Biosensors
Profile – Handheld water quality probe
18.2 – 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
18.3 – Non-potentiometric probes
The Dissolved Oxygen
The Chloride Probe
The Total Salinity Probe
18.4 – 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
18.5 – Further Reading
18.6 – Additional Exercises
Profile – Behind Frankenstein
19.1 – Basic Principles
Profile – Parsing Method Names
19.2 – The Three-Cell Electrode Cell
19.3 – Chronoamperometry
The Experiment
Noise in CA and Related Methods
Charging Current
Mass Transport
Controlling Mass Transport
Profile – Chronoamperometric Nerve Gas Sensor
The Cottrell Equation
Profile – VX Probe
19.4 – Linear Sweep and Cyclic Voltammetry
Profile – The International Space Station Electronic Tongue
Background
The Experiment
Reversibility
Quantitative Analysis with CV – The Randles-Sevcik Equation
Qualitative Analysis with CV
Solvents, Electrolytes and the Electrochemical Window
19.5 – Square Wave Voltammetry
19.6 – Working Electrodes
Common Working Electrodes
Ultramicroelectrodes and Nanoelectrodes
Profile – Cyclic Voltammetry in a Single C ell
19.7 – Useful Data
Temperature Dependence of Reference Electrodes
Temperature Dependence of 2.3026RT/F
Solvent Drying Techniques
19.8 – Further Reading
19.9 – Additional Exercises

Section E: Additional Topics

20.1 – Introduction
Profile – Characterizing metal nanoparticles for water purification: electron microscopy in action
20.2 – Microscopy
ProfileMicroscopy and the Nobel Prize in Physics
Atomic Force Microscopy (AFM)
Profile – Controlling the shape of silver nanoparticles with pH- AFM in action
Scanning Tunneling Microscopy (STM)
Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM)
Compare and Contrast – Resolutions for different microscopy techniques
20.3 – Thermoanalytic Techniques
Profile – Thermogravimetric Analysis
Differential Thermal Analysis (DTA)
Thermogravimetric Analysis (TGA)
Profile – TG/MS
Differential scanning calorimetry (DSC)
Compare and Contrast – DTA, TGA, & DSC
Profile – A Crime Scene Analysis
20.4 – Mechanical Stress Analysis
Dynamic Mechanical Analysis
20.5 – Further reading
20.6 – Additional Exercises
21.1 – Introduction7
Profile – Adriaan “Ad” Bax
21.2 – Resonance in the Rotating Frame
21.3 – The Pulse Experiment
Relaxation of the excited state
Longitudinal Relaxation (Spin-Lattice): T1
Measuring T1: Inversion Recovery
Transverse Relaxation (Spin-Spin): T2
Measuring T2: Spin-Echo
21.4 – The Influence of Nuclear Neighbors:
J-Coupling
Dipolar Coupling and The Nuclear Overhauser Effect
Profile – Albert W. Overhauser
Profile – Jean Jeener
21.5 – Introduction to 2D NMR
COSY and TOSCY
NOESY
Profile – G. Marius Clore
Profile – Kurt Wuthrich
21.6 – Special Topics in NMR
Variable Temperature NMR
Solid State NMR
Other Spin-Active Nuclei
Phosphorus-31
Nitrogen-15
Platinum-195
Fluorine-19
21.7 – Useful Data
21.8 – Further Reading
21.9 – Additional Exercises
22.1 – Introduction
22.2 – Types of Error
Gross Error
Systematic Error
Random Error
22.3 – Precision vs. Accuracy
22.4 – 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
22.5 – Linear Regression Analysis
22.6 – LOD, LOQ, and LDR
22.7 – Further Reading
22.8 – Additional Exercises
Appendix: Table of Acronyms and Abbreviations
Index