Author Archives: Jessie Key

About Jessie Key

Jessie joined the VIU Faculty in the fall of 2012. He has previously taught Organic Chemistry as a sessional lecturer at UBC-Okanagan and was an instructor for Academic Upgrading and Chemical Technology at the Northern Alberta Institute of Technology (NAIT). Jessie’s main area of interest is Chemical Biology; with a focus on fluorophore synthesis, labelling and bioassay development. Jessie is currently teaching first year (Chem 140 and 142), Engineering Chemistry (Chem 150) and Organic Chemistry (Chem 231 and 232). Jessie can be reached at Jessie.Key@viu.ca

Monthly Video Blog Progress Update

Hi Everyone,

Around 9 months ago I started to contribute monthly video blog posts, with the aim of showcasing interesting aspects of Chemistry, or highlighting the chemistry of phenomena from everyday life. I thought this would be a great way to increase scientific and chemical literacy, and the Chemical Institute of Canada  (http://www.cheminst.ca/) seemed to agree as they funded the purchase of my screen capture software (Camtasia Studio 8). It hasn’t always been easy finding the time to research and make these videos with a full teaching load, and service on several committees/councils at VIU, but I have produced 8 videos so far, one for every month except December 2014 (due to final exams and the holiday break).  To date the 8 videos have been viewed over 1300 times total, and one is incorporated into the open textbook: Introductory Chemistry – 1st Canadian Edition (http://opentextbc.ca/introductorychemistry/). As a product of a smaller university, that has received no funding beyond the initial software purchase, no direct advertising, and is not seeking ad revenue by being listed on YouTube: I am counting this as a win.

Four more videos to go until the year-long project comes to completion!

– Jessie

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The Chemistry of Lava Lamps

A video which describes the chemistry behind the novelty devices known as Lava Lamps. This video is a part of the monthly chemistry video blog series.

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January 8, 2015 · 10:27 am

10 Moustached Chemists who Changed the World

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November 28, 2014 · 2:07 pm

The 2014 Nobel Prize in Chemistry

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October 30, 2014 · 3:58 pm

Happy Birthday Open Textbook Project/My Adventures Adapting a Chemistry Textbook

This is probably a very long overdue blog post, but as I am currently procrastinating from/avoiding the giant pile of marking on my desk I thought I should put it out there in the blog-o-verse.

 

Today is the second birthday of the BC campus open textbook project (http://bccampus.ca/2014/10/16/open-textbook-project-2012-2014/), and I have been involved with this project in a few different capacities. Avid readers of this blog may remember seeing a post about my experience reviewing an organic chemistry open textbook (http://wordpress.viu.ca/key2chem/2014/01/14/some-thoughts-on-textbooks-open-textbooks-and-reviewing-for-bc-campus/). There I made some points about what a great thing open textbooks could be for students, and then subsequently complained of the quality of the open text I reviewed. Some issues with spelling/editing, diagram/figure quality and lack of instructor resources were among my main complaints. Naturally, while reviewing this text I was always thinking to myself “If I wrote the textbook, I would include this… or make sure my diagram had that…”

 

Earlier in 2014, the opportunity to adapt an introductory chemistry textbook into a general chemistry textbook (as part of the open textbook project) arose and I got the chance to put my thoughts into practice. At first I was a little overwhelmed at the scope of the project, and the short amount of time I was given to perform the adaptation. The introductory textbook was set at a relatively low level (the US liberal arts college “non-major” level, or perhaps an upgrading/basic education course).The reviews from other faculty across BC were accurate and detailed, pointing out many of the major deficiencies found in the original text. For this book  to be actually used by instructors in BC, I figured it needed two additional chapters written from scratch, a glossary, expansion of the appendix materials, almost all chemical structures in the organic chapter needed redrawing in proper bond-line format, and several chapter sections were needed in a couple other chapters. I also chose to add six of my existing video tutorials into the textbook, available for viewing directly in the electronic version or with a QR code link in the print copy.

 

After discussion with my BCcampus project manager Amanda, a schedule was set and I had myself a significant summer project. To accomplish these goals, I approached the problem in the following series of steps:

 

  1. For each chapter section/chapter I looked at 3-4 existing textbooks and identified what I thought were the common important concepts discussed.
  2. In Microsoft word I wrote up drafts of each chapter section, then pasted this into the PressBooks platform.
  3. Equations were typed out and put into PressBooks. This was the most problematic step! PressBooks uses a programming language known as LaTex to display mathematical equations, but I am no programmer. I ended up using a converter software to go from Microsoft word equations into LaTex, then imputing those into PressBooks with the help of Amanda. Let’s just say that the converter and PressBooks did not always play nice together, and both Amanda and I spent hours tweaking bits of code here and there.

 

  1. Figures and diagrams were either generated by myself using various softwares (from Microsoft paint, to ChemDraw Pro 13.0) or I scoured through creative commons image repositories (http://commons.wikimedia.org/wiki/Main_Page) for decent images I could use.

 

  1. I proofread my chapter sections, and they were then sent away for professional editing. Several weeks later I would receive an email from the editor, via the project manager, noting occasional mistakes and asking me to double check or correct them. As with most publications, it seemed formatting (particularly with the equations) was the most common mistake.

 

The finished product is now available for adoption, and can be found here (http://opentextbc.ca/introductorychemistry/). I still feel there is room for improvement in many of the chapters which were untouched, and also additional resources like more end of chapter questions/a testbank, and an instructors powerpoint slide series would greatly help adoption of this resource. However, I feel I did the best I could to bring this text up to the level of a first year university general chemistry course with the time and resources available.

 

I am currently working with the BCcampus team as a Faculty Fellow (http://bccampus.ca/2014/10/09/improving-adoption-of-open-textbooks-through-faculty-advocates/), to advise, promote and research open textbooks and open resources. I was really impressed with the rest of the Faculty Fellows, and look forward to working with them over the next year.

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The Chemistry of Bioluminescence

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September 24, 2014 · 4:06 pm

ChemTrix Chemistry Calculator for iPad

The kind folks at Black Rhino have supplied me with a copy of ChemTrix Chemistry Calculator for the iPad (https://itunes.apple.com/ca/app/chemtrix-chemistry-calculator/id605236459?mt=8). It is currently listed for $3.99 CAD. It has been evaluated on an iPad mini.

ChemTrix_Logo

First Impressions:

The ChemTrix Chemistry Calculator app is exactly as the name advertises, an app to calculate typical chemistry values.

 

Context:

All undergraduate chemistry courses require that some fundamental calculations are performed, both in the lecture and lab. Most calculations are fairly straight forward, as long as students possess the basic skills of unit conversion (dimensional analysis).

 

The App:

The opening screen features a large periodic table and number keypad. Simply choose the elements you want and punch in how many, then hit the orange checkmark button!

photo 2 (2)

 

It will list the molecular weight on the main page, but clicking on the information button ( a lowercase “i” in a circle),  it shows things such as the empirical formula, average mass,  monoisotopic mass,  percent composition (by mass) and converts between grams and moles. There is also a concentration calculator in the top right corner.

photo 1 (2)

 

 

 

 

 

All units in the mass-mole conversion/concentration calculators can be changed to the most common SI prefixes from nano to giga.

photo 2 (3)

A mass distribution plot is also present, but is disappointing as it does not have axis titles/values. However, a peak table is given by clicking the arrow at the bottom right corner.

photo 1 (3)


Back in the main screen, clicking on the icon that looks like two pieces of paper brings up a menu featuring the history of your previous searches, and surprisingly large lists of commonly used organic groups, ions, ligands.

photo 2

Clicking the right arrow button opens up a menu of programmable buttons, which would be handy for commonly used moieties.

 

A help menu is available and is well written.

photo 3 (3)

Final Impressions:

Overall, this app can quickly determine molecular weight and perform some commonly used conversions, and has a surprisingly large amount of groups, ions and ligands programmed in. However, the conversions it can perform could be done fairly quickly by a relatively competent grade 11 student with a calculator, pen and paper.

 

Disclosure:

The author received a copy of the software, but received no other compensation.

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Odyssey Atomic Orbitals – Chemistry App Review

The kind folks at Wavefunction Inc. have supplied me with their full Odyssey general chemistry app suite and I will be reviewing each of these apps throughout the remainder of 2014.

atomic_orbitals_logo

This is the fourth of these reviews, and I will be discussing the Atomic Orbitals app which is available for purchase in the app store for $3.99 CAD (https://itunes.apple.com/ca/app/odyssey-atomic-orbitals/id830980902?mt=8)

 

Context:

At VIU in our CHEM 140 class, and most other General Chemistry courses elsewhere, atomic orbitals are examined and explained in terms of the quantum theory. The topic of atomic orbitals and hybridization can be very visual, and yet also abstract with a lot of theory. An app that can help student understanding in this tricky topic would be a great benefit in the CHEM 140 course.

The App:

The interface is very similar to the other Odyssey apps previously reviewed. There is a portion where the orbitals are featured for manipulation and a portion which lists examples and has tabs for a glossary, some additional comments, and questions.  As well, some guidelines towards how students should approach using the app are given in the OBSERVE! tab.

photo 1

The shapes of the orbitals can be clearly observed by clicking on each of the orbitals. Pinch-to-zoom and swiping to rotate gives a full three-dimensional perspective on the orbitals.

Under the Shell Structure of the Atom, the shell number can be chosen, showing the impact of the principal quantum number on the size of the atoms (compare the picture below at n=5, to that above at n=3).

photo 2

 

By selecting any of the 22 main group Chemical Elements provided, a list detailing the number of electrons, number of occupied orbitals, electron pairs/unpaired electrons, electron configuration (with shorthand) and magnetism appears, as well as buttons for each orbital of the atom.

photo 2 (2)

The glossary has a list of helpful definitions, and multiple choice questions are available under the question section.

photo 3 (2)

Final Impressions:

I think this is a really helpful app to get across the 3-D nature of the atomic orbitals beyond the scope of the 2-D textbook, and emphasize certain aspects of the quantum theory behind orbitals. For instance, I plan to use this app to show the effect changing the principal quantum number has on the orbital size during my lecture this fall. My main critique is that hybridized orbitals are not included, which are often a trickier subject for students. Hybrid orbitals are also taught in this type of General Chemistry course following atomic orbitals.

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ChemTrix Chemistry Calculator for iPhone – Chemistry App Review

I have downloaded the app ChemTrix Chemistry Calculator by Black Rhino for the iPhone (https://itunes.apple.com/ca/app/chemtrix-chemistry-calculator/id549708598?mt=8) while it was briefly free in the appstore. It is currently listed for $3.99 CAD. It has been evaluated on an iPad mini.

ChemTrix_Logo

First Impressions:

The ChemTrix Chemistry Calculator iphone app is exactly as the name advertises, an app to calculate typical chemistry values.

 

Context:

All undergraduate chemistry courses require that some fundamental calculations are performed, both in the lecture and lab. Most calculations are fairly straight forward, as long as students possess the basic skills of unit conversion (dimensional analysis).

 

The App:

It can calculate things like molecular weight, monoisotopic weight, percent composition (by mass) and convert between grams and moles. It is fairly intuitive and easy to use, like a normal calculator, just punch in the number of each element in the molecule and hit enter to view the molecular weight and percent composition.
photo 3

At first it appears that you can only choose from some of the more common elements (C, H, N, O, P, S, Cl), but a swipe from right to left gives a complete alphabetical list. As well, it lists a surprisingly large number of commonly used organic groups, ions, ligands and the history of your previous calculations. Embarrassingly, this swipe feature eluded me at first! When in doubt, carefully consult the help menu or contact the Black Rhino support team, who were very quick to respond to my query. I have also been informed that if  ChemTrix is run on a 4″ iOS device,  a row of four programmable buttons will also be available (this review was performed on an iPad mini).

photo 5

Tap on the formula again and it opens up the mass/moles/molar mass converter where you can enter a mass or number of moles to convert between the two. There is also a concentration calculator, allowing you to determine the concentration.

 

photo 2 (2)

 

The units can be changed between 4 SI prefix options (eg. mol, mmol, µmol and nmol).

photo 3 (2)

However, this app is fairly limited, as you can only choose 7 of the more common elements (C, H, N, O, P, S, Cl), which may work for many simple organic molecules, but that is about it. You can select certain R-groups (like methyl, ethyl, phenyl etc.)

 

I was disappointed in the “Mass Distribution” plot, as there are no axis present. For example, I put in the simple molecule C2H3Cl: Chlorine has two common isotopes 35C and 37C, in a roughly 3:1 ratio. Therefore a signal should be present at approximately 62 and at 64, in a 3:1 ratio. This is not clearly shown in the spectrum provided below, but can be found by clicking upon it to pull up a peak intensities menu.

photo 4

A help menu is available and is well written.

photo 1 (2)

Final Impressions:

Overall, this app can quickly determine molecular weight and perform some conversions, and has a surprisingly large amount of groups, ions and ligands programmed in. However, the conversions it can perform could be done fairly quickly by a relatively competent grade 11 student with a calculator, pen and paper. There is an iPad version of ChemTrix available, which appears to have expanded functionality, but I know many of my students use their iPhones (as a calculator particularly for quick calculations). I will be reviewing the iPad version in the near future.

 

Disclosure:

The author downloaded the software from the app store while it was briefly free, and received no other compensation.

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Odyssey Electron Sharing – Chemistry ipad App Review

The kind folks at Wavefunction Inc. have supplied me with their full Odyssey general chemistry app suite and I will be reviewing each of these apps throughout the remainder of 2014.

odyssey_electron_sharing

This is the third of these reviews, and I will be discussing the Electron Sharing app which is available for purchase in the app store for $3.99 CAD (https://itunes.apple.com/ca/app/odyssey-electron-sharing/id849135421?mt=8)

 

First Impressions:

At first, I was very curious what this app could bring to the table that the previously reviewed VSEPR (http://wordpress.viu.ca/key2chem/2014/07/03/odyssey-vsepr-app-chemistry-ipad-app-review/)  and Polar Bonds (http://wordpress.viu.ca/key2chem/2014/07/28/odyssey-polar-bonds-and-molecules-chemistry-ipad-app-review/)  apps could not. Unfortunately, I was a bit let down, as discussed in my final impressions.

Context:

Most first year general chemistry courses spend time discussing orbitals, electron density and bonding theories. At VIU our CHEM 140 is no exception.

 

The App:

The interface is very similar to the other Odyssey apps previously reviewed. There is a portion where the molecules are featured for manipulation and a portion which lists examples and has tabs for a glossary, some additional comments, and questions.  As well, some guidelines towards how students should approach using the app are given in the OBSERVE! tab.

photo 1

In this app, the molecules are only displayed as nuclei and electron clouds. Molecules can be rotated with a finger swipe, and expanded/shrunk with the pinch of the thumb and index finger. Nuclei can be shown as small spheres, medium-size spheres or the molecule can be shown as a space filling model.

photo 3

 

As well, the internuclear distance, and angle tools which have been featured in the two previously reviewed apps are also available.

photo 2

The main novel feature of this app is that the user may adjust the electron density shown, from very low where almost all (99.9%) of the electrons are enclosed by the isosurface, to very high where only 30% of the electrons are enclosed by the isosurface. There are 30 example molecules that can be examined, and some multiple choice questions are pre-loaded into the app. Similar to the previous apps reviewed, the questions can be scored automatically by the app.

photo 6

Final Impressions:

Ultimately, I believe the goal of this app is to provide students/users with a view of molecules beyond the simple ball and stick model. It does this by focusing on nuclei and electron clouds, and does allow for the manipulation of the electron density shown. However, it seems the other Odyssey apps accomplish this already with electrostatic potential maps etc., and almost all modern textbooks include electron cloud and electrostatic potential diagrams already (granted, they are static in nature).

I do not believe there is enough to this app to justify the $3.99 pricetag, and I think many students would lose interest after a few minutes. This app was a little disappointing after reviewing the previous Odyssey apps.

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