Home Page and Syllabus for Chem 454

Instrumental Analysis – Spring 2021

Frank Cheng, Renfrew 003, 885-6387, ifcheng@uidaho.edu

Office Hours 2:00-4:00 MW, You are welcome to stop by and ask questions anytime.

Cheng Group Web Site                             Link To Chem 454 Labs

What is Analytical Chemistry? “their measurements are used to assure the safety and quality of food, pharmaceuticals, and water; to assure compliance with environmental and other regulations; to support the legal process; to help physicians diagnose diseases; and to provide measurements and documentation essential to trade and commerce.”

Historical Example of Analytical Chemistry: The Touchstone, James Burke Connections Ep 2. 1:00 – 5:00, The Lydians

Analytical Chemists make measurements that directly affect people’s lives, judicial outcomes and well-being.

Ethics of Clinical Chemistry “The work performed by the clinical chemist may deeply affect the decisions of the doctor and the well-being of the patient. Yet in contrast to the doctor and to the nurse the clinical chemist usually has no personal relationship with the patient.” Link 2, 3. Careers in Clinical Chemistry.

Ethics of Forensic SciencesBook, DOJ - NIST

Recommended Texts - Recent Editions of:

Principles of Instrumental Analysis, Douglas Skoog et. al, Contemporary Instrumental Analysis Rubinson and Rubinson, Quantitative Chemical Analysis, DC Harris, Analytical Chemistry 2.1

See Also: LibreText Analytical Sciences Digital Library & Analytical Sciences Digital Library

1. Introduction and Review of Statistics and Error Analysis

1.1 Basic Nomenclature * Technique vs. Method * Qualitative v. Quantitative * Accuracy v. Precision * Analyte v. Sample * Interferent

1.2 Chem 253 v. Chem 454 * ‘Wet’ Techniques & Methods

            Analyte Concentrations, typical 1-10%

                        Accuracy +/- 0.1% or 1 ppt

                        Precision 1%

            Instrumental Techniques & Methods

            Analyte Concentrations, typical 1ppt to 1ppm or less

                        Accuracy +/- 10%

                        Precision 10%

1.3 About Horwitz’s Trumpet (link 2, 3)

1.4 Standard Deviation. z-score.

1.5 Student’s t-Test

1.6 Method of Standard Addition - Journal of Chemical Education 1980, 57, 703, Search for least squares tutorial from Yahoo

1.7 Grubbs Test for Outlier (Calculator)

1.8 Detection limit (calculator), LOD, other definitions in Clinical Chemistry, Univ. of Tartu, Signal to Noise Demo (1:29 to 1:50)

1.9 Sensitivity * Background and Noise * Linear Range * Dynamic Range

1.10 Method of Least Squares * Correlation Coefficient * Calibration Curve * Standard Addition * What’s the difference between calibration curve and standard addition? * When should you a calibration curve vs. standard addition? * Matrix Effects

 

Spurious Correlations.

Video: An Analytical Chemist Gone Bad. Another One.

Flawed FBI assumptions about bullets (1, 2, 3, 4, 5)

Molecular and Atomic Spectroscopy at ASDL

2. Spectrophotometry Spectrometer vs. Spectrophotometer (Link 2)

2.1 Electronic Transitions * Electromagnetic Spectrum * Spectroscopy * Spectrophotometer * Jablonski Diagram (link 2, 3)

2.2 Atomic Spectra NIST Database vs. Spectrum of Benzene Vapor vs. Benzene in Hexane – Why the difference?

2.3 Beer's Law

2.4 Stray Radiation & Example

2.5 Noise Libretext * Noise & Hear the Noise, 60 Hz * 1/f Flicker Noise or pink noise and its appearance in nature*Light Chopper and 1/f noise

Shot Noise J. Chem. Ed., 2014,91,1455-1457 * 1/f and Shot Noise Power Spectrum (see Fig 1.), Youtube, What is the difference between thermal and shot noise?

Environmental Noise, 60 Hz

2.6 Noise Filters * Faraday Cage - Wikipedia, A demonstration from Youtube

2.7 Luminescence * Fluorescence and Structure * Excitation vs. Emission Spectra * Chemiluminescence – Luminol detection of iron in blood at crime scenes (Link 2)

3. Components of Optical Instruments.

6.1 Sources: Blackbody Emission, D2 Lamp*W Lamp (2)*D2, W Emission Spectra*Xe Arc Lamp*Hg vapor Lamp

6.2 Wavelength Isolation: Double Slit Experiment*Echelle & Echellette (Link 2) Gratings*Interference Filter*Monochromator (1, 2)

6.3 Transducers: Photomultiplier Tube (1,2)*Photodiode Array*Charged Coupled Device*Single Beam Spectrophotometer*Dual Beam Spectrophotometer*Diode Array Spectrophotometer a (description)*CCD Array Spectrophotometer * CCD vs. PDA * PDA Advantages * Libretext on Photon Detectors

Science Magazine Review of Miniaturized Spectrophotometers.

4. IR/FT-IR

7.1 General Theory (Libretext) * Wavenumbers       

7.2 IR Source: Globar * Sample holders * IR Regions, NIR, Database of Common Organics from NIST, Applied Spectroscopy,

7.3 Example of Analyses Using IR * Wood * Wheat from UI Ag Extension * MTBE in Gasoline. ASTM * Explosives *Ethanol in Gasoline

7.4 Detectors – Ewing’s Analytical Instrumentation Handbook *Heat Detectors-DTGS, TGS*Photon Detectors-PbS, InSb, HgCdTe*Video

7.5 FT-IR - Wikipedia*History and Theory*Libretext*Hardware*Interferometer Amination

7.6 Apodization – Math from Wikipedia, “Ringing” also Wolfram Research, From Columbia U (see figure 10)

Signal Averaging – Chemometrics In Analytical Chemistry.

5. Raman

8.1 Introduction – Renishaw*Wikipedia*Washington University*Venkata Raman Bio

8.2 Rayleigh Scattering, Stokes Lines

8.3 Lasers (link 2, 3, 4) types

8.4 Why FT-Raman has not overtaken dispersive Raman. Link 1, 2, 3

8.5 Example of MTBE analysis with Raman * Forensic analysis of inks using a Raman microscope (Link 2). Of cocaine on fingernails.

6. Atomic Spectroscopy

9.1 Libretext*Atomic Absorption *RSC start on page 2

9.2 Components: Slot Burner*Flame Temperature and Fuel Mixtures*Flame Structure*Nebulizers*Pneumatic*Ultrasonic

9.3 Hollow Cathode Lamps*Labtraining.com*

9.4 Line Broadening: Pressure*Doppler effect and broadening in AAS

9.5 Ionization Suppression*Interferences from Molecular Species*Background Correction*Continuum Source Correction (Link 2, 3, 4)*Zeeman Effect*Smith-Heiftje

9.6 Electrothermal*Graphite Furnace AAS*Schematic (Link 2, 3 see Figures 6.10-12)

9.7 Atomic Emission*ASDL*ICP-MS (Link 3)

9.8 Relative LOD for Flame AAS, AES, GFAAS, and ICP

9.9 Applications*Horiba*Analysis of carbon filters*Be in blood*Cholesterol via colloidal Au*Forensics (Link 1, 2, 3)

7. Introduction to Separations

10.1 Introduction Wikipedia - Library for Science* Michael Tswett * Martin and Synge work on LC and the 1952 Nobel Prize

10.2 Basic Terms: Column Chromatography * Stationary Phase, s.p. * Mobile Phase, m.p. * Partition Coefficient, K * Retention Time, tr * Dead Time, tm * Capacity Factor, k’* Relative Retention Factor (selectivity), α

10.3 Band Broadening * Plate Height, H = σ2/L * Longitudinal Diffusion, B/u * Mass Transfer Effects, Cu * Within the Stationary Phase, Cs * Within the Mobile Phase, Cm * Multiple Paths for Solute Flow, Eddy Diffusion A, German animation * The van Deemter Equation, H = A + B/u + Cu * Efficiency of Separation

10.4 Resolution, Rs (Link 2) * Plates, N = L/H * N and Rs * Rs α L1/2

8. Gas Chromatography

11.1 GC Block Diagram

11.2 Basics: Injection Port * Split Injections * Carrier Gas * Column *Makeup Gas * Detectors

11.3 Columns: Packed vs. Capillary Columns (link 2, 3) * Van Deemter Equation Considerations * Effect of A – Single Path for Capillary Columns * B/u effects – Largest in the gas phase, fast u desirable * Cu effects – Thin s.p. * Types of GC stationary phases (Link 1) * Polar vs. Nonpolar * Temperature Programming * Example of a effects on a chromatogram, another link

11.4 Carrier Gases * Almost Always He * N2 and H2 are possible

11.5 Sample Injection (see page 3) Also Link 2. * Split Injections * Splitess * Solid Phase Microextraction (SPME)

11.6 Detectors for Gas Chromatography * Make-up Gas * Thermal Conductivity Detector (TCD) Link 2 * Flame Ionization Detector (FID) Link 2 * NPD * FPD * Electron Capture Detector (ECD) Link 2, Link 3 * Photoionization Detector (PID) Link 2 * FT-IR * Mass Spectrometers

11.7 Quantitative Analysis * Calibration Curve * Standard Addition * Method of Internal Standard (from Cal State – Fresno) *

11.8 GC troubleshooting guide for HP-GC's (now Agilent) * Capillary columns from Sigma-Aldrich * Chromtech

11.9 GC in Forensics * Controlled Substances Forensic Drug Identification by GC-IR * An example of explosives detection from the FBI * GC/MS screening for amphetamines from the DOJ * Los Alamos National Lab Forensics Science Center * Purge and Trap * Clinical Chemistry Application

9. Liquid Chromatography

12.1 AJP Martin and RLM Synge’s Original Paper on Liquid Chromatography, Synge’s Biography

12.2 HPLC Components * Liquid Mobile Phase * Pump * Injection Valve * Separation Column * Detector

12.3 Band Broadening in LC * Van Deemter Considerations, H = A + B/u + Cu * B/U effects – diffusion is 100x less in liquids when compared to gases * Cu effects largest in LC * Minimizing Cu effects requires smaller packing particles – Surface area/ Volume – High pressures * Effect of particle size on separation efficiency, see Figure 2, Link 2

12.4 HPLC Pumps * Pressures to 6000 psi + * Pulse free – prevents solute remixing * Control  Flow Rates 0.1 to 10 mL/min * Reciprocating Pumps * Single Piston * Dual Piston * Syringe Pump * Pulse Dampers * Coils * Diaphragms

12. 5 Sampling Valves, page 2

12.6 Pre-Column Filters + Analytical HPLC Columns (images) * Silica * Modified Silica, C-18, C-8, others * Reversed (polar m.p.-nonpolar s.p.) vs. Normal Phase (nonpolar m.p. – polar s.p.)  Separations * Partition (modified silica)  vs. Adsorption (unmodified silica) Chromatography * Column Care, Link 2

12. 7 Mobile Phases * Polar vs. non polar * Most Separations handled by C-18 s.p. and H2O/MeOH or H2O/CH3CN m.p. * Isocratic (constant composition) vs. Gradient (variable composition) elutions * Column Heaters, improvement of Cu characteristics

12. 8 Detectors * Refractive Index (RI), page 2 * UV-vis Absorbance * Fixed Wavelength * Diode Array (2 pages) * Fluorescence  * Conductivity (read all three pages) * FT-IR * Evaporative Light Scattering Detector (2 pages) * Electrochemical Detectors * Mass Spectrometry * HPLC-MS interface

12.9 UPLC Link 1

12.10 User’s Guide From University of Kentucky  * HPLC troubleshooting guides Link 1, 2, 3, 4, 5, 6, A Google Search * An HPLC Simulator * GC and LC in Clinical Chemistry *

Interesting Analytes: Cocaine In Municipal Waters, Other Drugs of Abuse in Wastewaters, Hormones, 

10. Capillary Electrophoresis (CE)

13.1 Electrophoresis vs. CE * Basic Block Diagram

13.2 Van Deemter Equation Considerations (H = A + B/u + Cu) * A = 0, as only one path is possible * Cu = 0, as there is no s.p. in CE * Theoretical Plates: HPLC – 2,000 to 10,000, CE – 50,000 to 500,000

13.3 Theory of Electrophoresis * Electrophoretic mobility * Electro-osmosis * tr trends cations < neutrals < anions * flow velocity profiles, CE vs. HPLC

Theoretical Plates

13.4 Sample Injections * Pressure Injection * Electro-kinetic

13.5 Microfluidic Chips, See this video

13.6 Detectors see Table 1 page 298A * Challenges * Narrow capillary/channels (20-75 μm) * UV-vis Absorbance * Fluorescence * Tagging agents (an example from Beckman) * CE-LIF

CE-arrays * Electrochemical * Mass Spec

13.7 Electrospray – 2002 Nobel Prize for John B. Fenn of Virginia Commonwealth University

13.8 Modified CE separations * Surfactant Modified, Anions < Neutrals < Cations * Micellar Electrokinetic Chromatography (1)

A Comparison of LC vs. MEC-CE

13.9 Analytical Chemistry Articles * 1989 Analytical Chemistry A-page article by AG Ewing * "How capillary electrophoresis sequenced the human genome.", N. J. Dovichi and J. Z. Zhang, Angew. Chem. Int. Ed., 39 4463 (2000). * Analytical Chemistry “How Analytical Chemists Saved the Human Genome Project…or at least gave it a helping hand” * A CE-LIF array from DOE’s Joint Genome Institute. * “Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips” AT Wooley, RA Mathies, Proc. Natl Acad Sci. 91, 1994 11348-11352 * Coupled with PCR Amplification * RA Mathies Group at UC Berkeley * N. Dovichi at Notre Dame * Sanger DNA Sequencing - Capillary Electrophoresis Animation

11. Mass Spectrometry

14.1 Wikipedia * Basic Block Diagram

Sample Inlet à Ion Source* à Mass Analyzer* à Ion Transducer* à Signal Processing à Mass Spectrum

* indicates under vacuum conditions

14.2 Ion Sources * Electron Impact (Hard) Fragmentation * Chemical Ionization (Soft) MW information * Ionization of solid and nonvolatiles * Field Desorption * Fast Atom Bombardment * Matrix-Assisted Laser Desorption/Ionization (MALDI) * Direct Probe * Electrospray2002 Nobel Prize for John B. Fenn of Virginia Commonwealth University (video) * Atmospheric Pressure Chemical Ionization

14.3 Recent Developments in Ionization Techniques * Direct Analysis in Real Time (DART, Video) * Desorption Electrospray Ionization (DESI, Video) * Atmospheric Pressure Photoionization Source (APPI)

Desorption atmospheric pressure photoionization (DAPPI) * Summary from Aglient

14.4 Mass Analyzers * Resolution * Magnetic Sector * Double Focusing * Quadrapole, a tutorial from LCGC magazine * Time of Flight * Ion Trap * Orbitrap (A review publication) * MS-MS systems * Quad-Quad * QTOF * Electron Multiplier

14.5 ICP-MS * Agilent ICP-MS diagram

14.6 Guides to MS * I-mass guides * Spectroscopy Now * ASMS * Ion Sources

12. Ion Exchange, Ion, and Molecular Exclusion Chromatographies (IEC, IC, MEC)

15.1 IEC and IC Background from Wikipedia * IEC from Amersham Biosciences

15.2 Anion Exchangers * Quaternary and tertiary ammonium groups * Cation Exchangers * Sulfonate and carboxyl groups * Resins

Ion Exchange Selectivity

X- A+ + B+ = X- B+ + A+

        

15.3 Analytical Ion Chromatography * IC vs. IEC what’s the difference? * Suppression columns

15.4 Molecular Exclusion Chromatography * Wikipedia * Gel Filtration * Gel Permeation

13. Interpretation of MS Spectra

Book by Fred W. McLaffery * Isotope Abundances * Isotope Distribution and Mass Spectrum Calculator * Calculation of Isotope Abundances

Fragmentation * From Michigan State * From Chemguide

General Rules Regarding Interpretation * From Cal State Bakersfield 

14. Electrochemistry

2.1 Review * Daniell Cell * Video * The Nernst Equation

2.2 Standard Electrode Potentials * Electrochemical Series (Link 2)

2.3 Connection between Ecell, ∆G, and K

2.4 Single Electrode Potentials, Precipitation Reactions on Electrodes

2.5 Significant Figures and pH.

2.6 Reference Electrodes (SHE, SCE, Ag/AgCl)

15. Potentiometric Membrane Electrodes

3.1 Ion Selective Electrodes From Warsaw University of Technology

3.2 Beginner’s Guide From Nico2000   Glass pH Electrode

3.3 Latest Review Literature on ISE's from Google Scholar

16. Voltammetry

4.1 Analytical Electrochemistry*ASDL*CV in J.Chem.Ed * CV in Libretext

4.2 Background: Capacitive Current (Biologic)

4.3 Voltammetry  Cyclic Voltammetry: J. Chem Ed. 2018,95,197

4.4 CV Modeling Programs

Open Source: J.Chem.Ed. 2015,92,1490*J. Chem. Educ., 2016,93,1326. (2)*J.Chem.Ed 2017,94,1567 (requires Matlab Runtime see Wang Shou’s Comment, also 2)*Another CV Simulator

Commercial: DigiSim CV simulation*DigiElch CV and titration simulation

4.5 Dopamine EC electrode mechanism-Dopamine in the brain - Wikipedia - DOPAC Implantable Electrodes

4.6 A Study of an EC’ Mechanism from my research group

4.7 Chronoamperometry (2), ASL,

            The glucose sensor by my Ph.D. advisor (1, 2)

4.8 Modern Hg drop Electrode System Links - 1, 2

4.9 ASV from Wikipedia, A Theoretical Treatment AC 1987, 59, 386-389,

4.10 Analysis of Pb in Blood*Forensic Analysis of Ba and Pb in Gunshot residue* EPA Method 7063 analysis of As by Anodic Stripping Voltammetry

 

17. Exam Dates for Spring 2021

·       Exam 1 (100 points), February 17

·       Exam 2 (100 points), March 10

·       Exam 3 (100 points), April 28

·       Final Exam May 14, 10:15 (150 points) (UI Registrar)

·       Laboratory (150 points) 

 Class Averages on American Chemical Society Instrumental Analysis Exams

Year- National Percentile Avg, 2018- 69th, 2011-82nd, 2010-63rd, 2009-74th, 2008-66th, 2007-69th, 2006-60th, 2005-74th, 2003-86th, 2002-86th

 

19. Old Exam Files – Please note that the exams from previous years may not correspond to this year's course materials or exam subject matter. They can provide you with an idea as to the exam format and additional homework assignments.

1998, 19992000, 2002, 2005, 2006, 2007,2008, 2009 , 2010, 2011

2018 Exam 1, Exam 2, Exam 3

2019 Exam 1, Exam 2, Exam3

20.

Forensic Science Journals & Books

 

Analytical Chemistry Journals

 

    

Forensic Magazine      

Journal of Forensic Sciences

Forensic Science International

Forensic Science International: Genetics

Forensic Toxicology

Forensic Analysis: Weighing Bullet Lead Evidence

 

Analytical Chemistry

Analytica Chimica Acta

Microchemical Journal

Fresenius' journal of analytical chemistry

Analytical biochemistry

Journal of electroanalytical chemistry

Electroanalysis

Electrochimica acta

Applied spectroscopy

 

21. Other Resources

MIT Courseware Advance Chemical Experimentation and Instrumentation

Analytical Sciences Digital Library