W. Stephen McNeil Stephen McNeil
Department of Chemistry
UBC Okanagan
3247 University Way, Fipke 352
Kelowna, BC, Canada
V1V 1V7
Office: Fipke 352
Phone: 250.807.8751
s.mcneil@ubc.ca
@wsmcneil


Dr. W. Stephen McNeil is an Associate Professor in the Department of Chemistry at UBC Okanagan, in Kelowna, British Columbia. Information regarding Dr. McNeil's research interests and publications may be found on his faculty research page.

Dr. McNeil often teaches courses such as Chem 220 (Atomic Structure and Molecular Bonding), Chem 335 (Bioinorganic Chemistry), and he occasionally forays into general, main group, and organometallic chemistries. If you're planning on taking one of those courses, then you might be here looking for a document or web page relating to them. In Term 1 of the 2016/17 academic year, he is teaching Chemistry 220, and in Term 2, he is teaching Chemistry 123 and Chemistry 335.

Course Documents [top]

Chemistry 113/123
Review Session: Sun Apr 9, 9:30AM - 2:30PM, FIP 204
Final Exam:Mon Apr 10, 9AM - noon, GYM

Handouts
Syllabus (yellow)
Summary: Reaction Rates and Kinetics
Summary: Chemical Equilibrium
Summary: Thermodynamics
Summary: Acid Base Equilibria
Summary: Organic Chemistry
Chemical Fuels Guided Inquiry Assignment
pKa Trends Guided Inquiry Assignment
nomenclature of organic compounds
organic steroisomer nomenclature

Learning Objectives
kinetics
equilibrium
thermodynamics
acid base equilbria
organic chemistry (revised)

Class Slides
reaction rates
collision theory
reaction mechanisms
catalysts
equilbrium vs resonance
Haber Bosch process
solution enthalpy
spontaneous change
acid base introduction
table of acid and base strengths
acid base calculations guide
organic spectroscopy
curved arrows
electrostatic potential maps
acid-base properties of amino acids
nucleophilic substitution reaction mechanisms

Clicker Questions
Class Pre-readings (to March 13)
Kinetics
Equilbrium
Thermodynamics
Chemical Fuels guided inquiry exercise (Feb 6)
Acid Base Chemistry
Organic Chemistry (to March 13)
pKa trends guided inquiry exercise (Mar 17)

Supplemental Learning Sessions
• Tuesday: 9:30-11 am, UNC 316, Jordan
• Tuesday: 3-4:30 pm, UNC 316, Katie
• Wednesday: 2:00-3:30 pm, UNC 316, Riley
• Friday: 2:00-3:30 pm, UNC 316, Riley

BIOC 305 / BIOL 319
• Download a zip file of pdbs and scripts.
• Download UBCMol

Chemistry 335
Review Session: Tue Apr 11, 1 - 4PM, ART 386
Final Exam: Thu Apr 13, 6 - 9PM, LIB 306


Handouts
Syllabus (pink)
• Information about metalloproteins and element abundances (yellow)
• Information about amino acids and protein structure (green)
• Various organic and metal cofactors (goldenrod)
• Matters pertaining to Hard Soft Acid Base Theory, ionic radii, and complex stability (blue)
• A primer on crystal field theory (purple)
siderophores
transferrin
electron Transfer and Marcus Theory (salmon)
electron transfer proteins (pink)
mitochondrial electron transport (goldenrod)
photosynthetic electron transport (yellow)
dioxygen transport proteins (greeen)
• definitions about oxidases and oxygenases
cytochromes P450 and soluble methane monooxygenase
aromatic amino acid hydroxylases (AAAHs) and Rieske dioxygenases
catechol dioxygenases
information about N2 and the nitrogen cycle
nitrogenase
nitrate reductases
Cu and cd1 nitrite reductases
cytochrome c nitrite reductase
hydrogenases
carbon monoxide dehydrogenase / acetyl CoA synthase
peroxidases and catalases
zinc enzymes
tyrosinase

Problem Sets/Exams/Presentations
Problem Sets: PS#1 PS#2 PS#3 PS#4
Web page for Problem Set #1
Web page for Problem Set #2
Web page for Problem Set #3
Papers for PS#2: Science95 JACS96 JACS98

PS and Exam Answer Keys:
PS#1Key, PS#2Key, PS#3Key

Midterm answer key

Oral presentation topics list
Oral presentation grading rubric
Oral presentation schedule and topics list.


Lab Materials
C335 Lab Schedule
revised lab manual Page 1
Spartan files for Experiment #1
Reference for Experiment #1

Computer Stuff
• A Brief Guide to Using Spartan
• Download UBCMol, a self-contained Java applet for the exploration and visualization of molecular and protein structure.
• Download a User's Guide for UBCMol
• A script for UBCMol, useful to display things that bioinorganic chemists care about.
• Explore protein structures at the Protein Data Bank


Course Pages [top]

Chemistry 111/121 and 113/123
• Chemistry simulations at The King's Centre for Visualization in Science, including
   • atomic weight calculator
   • mass spectrometer
• Chemistry simulations at PhET at the University of Colorado Boulder, including
   • Gas Properties
   • Photoelectric Effect
   • Molecules and Light
   • Beer's Law
   • Molecular Polarity
   • States of Matter
   • Reversible Reactions
• Java applet illustrating the electromagnetic wave nature of light
• Mark Winter's Orbitron Gallery of atomic orbitals, at Sheffield
• Richard Spinney's Hydrogen Atomic Orbitals, at Ohio State
• Robert Hanson's hydrogenic orbital wavefunction viewer, at St. Olaf's College
Molecular geometries as predicted by VSEPR
• Animation of thin layer chromatography at the Royal Society for Chemistry's Interactive Lab Primer
representations of organic molecules
conformations of organic molecules
enantiomers and R/S nomenclature
• Alison Flynn's outstanding organic nomenclature tutorial and quiz site at uOttawa, Nomenclature101
• Richard Spinney's database of animated IR, 1H NMR, 13C NMR, and MS spectra, at Ohio State


Chemistry 220
orientation of d-orbitals in various crystal fields, at the University of the West Indies
• A gallery of point groups
• Another page examining symmetry elements and operations, at Otterbein University
• William Coleman's continuum of ionic and covalent bonding in MO theory, at Wellesley College

Chemistry 335
• the Protein Data Bank
• representations of various levels of protein structure
• structures of various proteins and enzymes:
   • transferrin
   • ferritin, the protein used for iron storage
   • electron transfer proteins
   • mitochondrial electron transport chain
   • photosynthetic electron transport chain
   • dioxygen transport
   • oxygenase enzymes
   • nitrogenase enzymes
   • various zinc proteins

Chemistry 339
Structures of:
various boranes
various binary element hydrides
• some main group ring and cage compounds
• some organolithium compounds
• various ionic, associated covalent, and network solids
• various allotropes of carbon

Chemistry 422S
• structures of bovine rhodopsin, showing conformational change of the retinal chromophore
• structures of green and red fluorescent proteins

Links [top]

Need some help with chemistry? Visit the Chemistry Course Union in Sci 233B, attend a Supplemental Learning session, or drop by the Math and Science Centre in UNC 201.

If you're a chemistry or biochemistry student, you need a program to draw proper chemical structures.
MarvinSketch is Java-based, and will run on PC, Mac, or Linux.
• Both ACDLab's Chemsketch and Accelrys' Accelrys Draw are PC programs that are free for academic and personal use.

Need a periodic table? Of course you do. Your choice:
• A practical table with element names and molar masses, in either black and white or colour.
• Another attractive colour table, from ptable.com.
• Or, if none of those strikes your fancy, try one of these.

Looking for reference data for that lab write-up? Try these sites:
Webelements and PTable have more data on the elements than you could ever hope to use.
• The CRC Handbook of Chemistry and Physics
• The PubChem offers basic physical properties and bioloigcal / pharmacological activity information on small molecules.
• The NIST Chemistry WebBook
• The NIST Computational Chemistry Comparison and Benchmark Database has experimental physical data on over 1500 compounds, such as bond lengths and angles, vibrational frequencies, formation enthalpies, and dipole moments.
• Data tables at Franklin and Marshall College
Properties of Organic Compounds (over 29000 of them)
• The Spectral Database for Organic Compounds (SDBS)
• Nakamoto's Infrared and Raman Spectra of Inorganic and Coordination Compounds:
    • Part A is theory and main group compounds
    • Part B is coordination compounds, organometallics, and bioinorganic.
• Online Material Saftey Data Sheets (MSDS) at the Canadian Centre for OHS
Sigma-Aldrich can tell you the expected melting point, boiling point, flash point, and IR and NMR spectra of all your reagents and hoped-for products in your organic lab, and, if you screwed up the prep, they'll sell them to you.
• Do you have mysterious extra peaks in your NMR spectrum? You need this Organometallics paper and this J. Org. Chem. paper to figure out what they are. There, aren't those the most useful references ever?

Think those latex gloves protect your hands from the solvents you're handling? Yeah, not so much.

There are many databases of Jmol molecules to look at, including those at:
ChemTube3D, featuring models of hundreds of inorganic compounds. However, anaylze these structures critically before using them. Many models are based on qualitative idealized structures rather than experimental data (e.g. the bond angle in NF3 is not 109.5°), and many are simply wrong (e.g. [I5]+ isn't a W, Cl2O6 does not have equivalent Cl atoms, TeO4 doesn't exist, [NO2] and N2O4 do not have unequal N-O bond lengths, [Ni(CN)4]2– is not tetrahedral, etc.).
Purdue University (lots of simple organic and inorganic molecules, coordination complexes, and inorganic crystals)

The Royal Society is dedicated to furthering informed communication between media and the scientific community, and is an excellent source of reliable scientific discussion about matters of current importance. Want to know what scientists really think about genetically-modified foods, global warming, or human cloning, and why?

You need to know How Stuff Works.

Believe it or not, there are sometimes even interesting research articles published in fields other than chemistry.

Bio [top]

Dr. McNeil comes to UBC Okanagan by way of the other University of British Columbia, the University of Washington, and Douglas College, whereby he has acquired an inordinate fondness for organometallic reaction mechanisms, well-crafted Americanos, and active-learning teaching strategies. He is a member of the Canadian Society for Chemistry Inorganic Division, the American Chemical Society, the Society for Teaching and Learning in Higher Education, and Project Steve.

His ongoing interests include the use of new cobalt compounds as mediators for controlled radical polymerization and potential pharmaceutical agents, the development and assessment of innovative chemistry education student-engagement strategies, science communication and chemistry outreach, and esoteric and expensive board games. He likes a good hootenanny: chock full of hoot, just a little bit of nanny.

 

Learn about . . .
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Check . . .
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Read . . .
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This page is maintained and copyright by W. Stephen McNeil at UBC Okanagan.
All educational works available on this page are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Canada License.