Wikipedia:Wiki Ed/University of Ontario Institute of Technology/CHEM 4041U Advanced Topics in Inorganic Chemistry (Fall 2015)

CHEM 4041U Course Description.
This course is separated into two sections, coordination chemistry theory and bioinorganic chemistry. Description for the bioinorganic section: Survey of metalloenzymes highlighting their biological occurrence and function, structure-function relationships, and current chemistry research with biomimetic complexes; also biological metal ion specificity (chaperoning) and introduction to specialized inorganic analysis techniques (esr, EXAFS, magnetochem etc) used to study metalloenzymes. Metalloenzyme examples including (as time permits): Photosystem II, biological iron transport and storage, haemoglobin, nitrogenase, cytochrome P450, high potential iron proteins (HPIP), vitamin B12, CO2 fixation in methanogens and cofactor F430, superoxide dismutase, CO dehydrogenase, blue copper proteins.

Introduction (Wikipedia Assignment)
Google searches for scientific information routinely return Wikipedia articles in the top five search results, and more and more scientists are recognizing the worthiness of Wikipedia content. As a chemist, I have continually been impressed with the accuracy, quality and range of Wikipedia scientific content, and now use it so much that I have recently made a donation out of appreciation. Every chemistry or physics article I have read so far has been reasonably or very well written and accurate, not only content for which I already have the relevant expertise to pass judgement, but also for content that is new to me which I was later able to verify, for example by reading the primary references listed in the Wikipedia article.

Although Wikipedia does not use the explicit expert peer-review process employed by reputable scientific journals, it does have a reasonably effective mechanism to ensure quality and accuracy due to the tireless efforts from the community of many thousands of volunteer editors that not only contribute content but also assess the quality of articles and discuss the best ways to improve them, and from the Wiki Education Foundation staff that assist new editors.

The range of topics covered is impressive, making Wikipedia a preferred resource. While there are other high quality online chemistry information resources, they are either highly specialized or only have a relatively small number of topics/articles, because a small group of chemists at a particular institution can not contribute anywhere near as much content and range of topics as Wikipedia with its many thousands of editors contributing from all over the world. Furthermore, Wikipedia can be relied on to always be there for you, whereas numerous online chemistry information resources that I relied on in the past would at some point disappear off the internet as the staff maintaining the resource either moved on or lost funding that was supporting the resource.

Learning Outcomes


 * Gain experience with writing a scientific article in the neutral encyclopedic style for a general (worldwide) audience, not just for one instructor who is an expert in the field. Your assignment will not just end up archived on your hard drive where no one will see it, instead it will live on as a valuable contribution to a high quality worldwide online encyclopedia read by millions of people.


 * Gain experience with interacting with other editors and experts regarding:


 * feedback on how to improve your content


 * reaching a consensus opinion on how to improve the content of an article


 * justifying your intended contributions with primary source references from peer-reviewed scientific journals


 * objective (and cordial) analysis of existing content from other editors


 * Gain an understanding of the fundamentals of contributing to Wikipedia, and how it involves a large community of editors and volunteers working together to ensure high quality articles and a broad range and depth of content. As future chemistry professionals, this experience may entice you to become a Wikipedia volunteer editor and help contribute quality content in the areas of your expertise.

''“With a traditional assignment, your only audience is often your professor, or at most your professor and your classmates. I really liked the fact that this assignment gave me an opportunity to write for a broader audience and make a valuable contribution to a resource that I often use myself.” — Joseph Lapka, San Francisco State University''

''“Writing for Wikipedia has engaged my students like nothing else. They are some of the most pedagogically powerful assignments I’ve incorporated into my classes.” — Adeline Koh, instructor, Stockton University''

''“Students do use Wikipedia, and they need to understand what it is and how to trace back to the [cited] sources. It is a valuable tool that is dismissed by too many people.” Faculty participant''

Online video –

Wiki Education Foundation organization

Wikipedia Assignment (50% of total Ass#2 mark)
Outline (see timeline below for detailed instructions and resources)


 * Complete the Wikipedia orientation and student training
 * Create a Wikipedia account, user page and sandbox
 * Choose a subtopic (see &quot;Metalloenzyme subtopics&quot; below) and the type of Wikipedia contribution you wish to make, both choices must be pre-approved by your instructor before beginning to work on it.
 * Link your username and sandbox to this CHEM 4041 student assignment page
 * Contribute a minimum 300 words of original content, supported by good quality literature references from reputable peer-reviewed scientific journals, to the Wikipedia article for your chosen subtopic (create a new Wikipedia article if one does not already exist for your topic).
 * Alternatively, you can contribute references and/or media (figures and diagrams) to existing content or edit poorly written or inaccurate content, or any combination of these including contribution of original content.
 * The total contribution (any combination of original text, editing, references and/or diagrams) must be entered into the student’s user page sandbox and the username provided for the instructor to verify.
 * use the talk page of the article(s) to which you intend to contribute to identify and justify your intended edits to other Wikipedia editors, and (hopefully) reach a consensus of approval for the edits before making them to the live article.
 * The content should first be created in the user’s sandbox, and not be placed in the live article until after your instructor has reviewed it and made recommendations, and you have completed any revisions required by your instructor.

Assistance from the Wiki Education Foundation Staff

Ian, an on-staff content expert from the Wiki Education Foundation, will follow the students work throughout the term and provide them with feedback as they edit. He is signed up on our course page as Ian (Wiki Ed).

Topics - Guidelines and Suggested Subtopics
Choose one or more metalloenzyme subtopics, or general bio-inorganic topic as per the examples below, for which the Wikipedia article has either:


 * missing reasonably important content amounting to a minimum ~ 300 words


 * insufficient supporting references for the existing content


 * insufficient figures and/or schemes for the existing content


 * inaccurate or poorly written existing content

you can choose any metalloenzyme, metalloprotein or bioinorganic topic, even if it is already discussed in the lecture notes.

note: the “Suggested Topics” section below lists specific topics for which the Wikipedia articles are in need of new (subtopic) contributions.

BEFORE BEGINNING: obtain approval from your instructor regarding:


 * 1) which topic(s)/subtopic(s) you wish to work on and the associated Wikipedia article(s)


 * in the case two or more students choose the same subtopic, only the first student to contact their instructor will get the approval, the others will have to find another subtopic.

 what type(s) of Wikipedia contribution you wish to make (adding new text content with supporting references is highly recommended but it can be any combination of the following items subject to instructor pre-approval)


 * contribute new text content,


 * add citations to existing content


 * add media (figures and diagrams)


 * edit/improve existing content


 * evaluate article quality

Metalloenzyme subtopics


 * biological occurrence and function (including conditions needed for proper function)
 * catalytic rate (turnover number and frequency)
 * how the metalloenzyme is isolated and structurally characterized (including conditions needed to stabilize it)
 * structure and electronic properties


 * protein subunits: size, shape, conformation(s), subunit binding


 * active site(s): metals, ligands, overall charge oxidation states and high vs. low spin states


 * other binding sites


 * structure-function relationships
 * biomimetic complexes
 * any other relevant and important subtopic (subject to approval from your instructor)

General Bioinorganic topics (ie. applicable to multiple metalloenzymes)

focus on a specific topic that is fundamental to multiple metalloenzymes and has sufficient theoretical detail (ie. not just an introductory level survey of examples)


 * metal chaperoning
 * medicinal inorganic chemistry
 * entatic state hypothesis
 * e- transfer theory


 * Marcus theory


 * long range e- transfer in metalloproteins


 * macrocyclic stabilization of uncommon oxidation states

Marking Scheme (100 marks total which count as 50% of Ass2 mark)

 * creation of Wikipedia account and user page (username submitted to instructor and enrolled on the Wikipedia course page) - 10 marks
 * completion of the online training for students - 10 marks
 * learning how to edit and using sandbox to practice editing the contribution - 10 marks
 * use of talk page to identify and justify your intended edits to other Wikipedia editors - 10 marks
 * quality of original text contribution:


 * follows Wikipedia’s core policies and guidelines including the five pillars - 10 marks


 * uses proper Wikipedia editing and syntax - 10 marks


 * written well enough to be worthy of the Wikipedia article - 25 marks


 * sufficient and appropriate referencing to support the content; pdf files of references must be submitted to your instructor - 15 marks

.....................................................

editing / referencing / diagrams equivalencies (to original text contributions)


 * 1) editing existing content:


 * if more than 50% of a sentence is edited, then count all the words in the sentence


 * if less than 50% of sentence is edited, then count only the number of new words added


 * there must be a valid reason for each edit and it must be explained in the talk page

 adding references to existing content:


 * adding one reference will be considered equivalent to 20 words of text content, ie. adding 15 references will count as equivalent to contributing 300 words of original text content
 * pdf files of all references must be submitted to the instructor to verify their appropriateness

 adding diagrams


 * the equivalency of each diagram will be decided by the instructor depending on the complexity and relevance of the diagram, students must therefore consult (email) with the instructor to determine the equivalency allowed for a diagram.

Suggested Topics
Bioinorganic Chemistry (definition and overview)


 * add new examples of metalloenzymes and/or metal cofactors to the Wikipedia Bioinorganic Chemistry article and/or the Wikipedia metalloprotein and metalloenzymes article; perhaps make new linked article that gives a comprehensive list, should discuss that with the other editors.

Iron Transport


 * Ferrichrome ; Wikipedia article https://en.wikipedia.org/wiki/Ferrichrome has only two sentences.
 * Dmt1 Fe2+ transporter (humans) ; Wikipedia article https://en.wikipedia.org/wiki/DMT1 only discusses the “role in neurodegenerative diseases”, so could add structure and mechanism
 * Irt1 Fe2+ transporter in plants ; Wikipedia has no article.
 * Ferrireductase ; Wikipedia article has only two sentences https://en.wikipedia.org/wiki/Ascorbate_ferrireductase_%28transmembrane%29
 * Transferrin ; Wikipedia article https://en.wikipedia.org/wiki/Transferrin has multiple subtopics but discussions are too short with no diagrams; also several grammatical errors
 * Tranferrin receptor ; Wikipedia article https://en.wikipedia.org/wiki/Transferrin is too short with no diagrams

Metal Chaperones



Inorganic Medicinal Chemistry



Hydrolase and Lyase Enzymes


 * Carbonic Anhydrase: Wikipedia article https://en.wikipedia.org/wiki/Carbonic_anhydrase only gives a short written description of the mechanism, should have a diagram with a detailed description and references

Iron sulfur clusters:


 * Wikipedia article has only one sentence and two references https://en.wikipedia.org/wiki/Iron-sulfur_cluster

Electron Transfer Proteins



Nitrogenase:


 * Wikipedia Nitrogenase article does not discuss:


 * the latest Xray structure of the FeMoco cluster with the central carbide atom


 * the oxidation states of the Mo and Fe ions


 * the P-cluster location and Xray structure


 * that 1 mole of H2 is released for every 1 N2 reacted is shown in the reaction equation but is not discussed in the text, also the implications to the mechanism could be discussed as well.

methanogens


 * cofactor F430: https://en.wikipedia.org/wiki/Cofactor_F430


 * only one sentence describing the reaction catalyzed, mechanism is not given


 * gives one paragraph describing the “corphin” ligand, however the ligand is commonly referred to as a “porphinoid” ligand in the chemical literature which should be discussed, the term “corphin” should be removed unless a literature reference can be found or supplied by the original editor.

Week 1

 * Overview of the Assignment
 * Understanding Wikipedia as a community, we'll discuss its expectations and etiquette.

Handout (for interest's sake):


 * 1) Complete the interactive online training for students. During this training, you will:


 * create a Wikipedia account and user page


 * practice editing in your sandbox and learn the basic formatting and markup for Wikipedia text and references.

Resources: Online Training for Students


 * note: select the “resources” tab to access guides, tutorials, help resources and other info: Training Resources


 * online training for students: creating an account


 * why you need to create an account

User Page: Log in to your account and it will say “to start a page called User:XXXX, type in the box below. When you are done, preview the page to check for errors and then save it.”


 * About User pages

Sandboxes: about Sandboxes the sandbox is your own page (ie. not a live article) where you can practice editing and enter your intended contributions, then when you are ready, your edits can be moved from your sandbox to the main (live) article page. Although other users can view and edit your sandbox, it is considered a serious violation of Wikipedia's policy that users must not edit other users sandboxes (editing someone else's sandbox can result in a suspension or permanent block on your account)

“To start a page called User:XXXX/sandbox, type in the box below. When you are done, preview the page to check for errors and then save it.”


 * how to make multiple sandboxes (ie. subpages on your user page)


 * about subpages to create a user subpage, see user pages

Editing and Markup: About Editing Wikipedia (a downloadable pdf file that is also posted to the BB Ass2 folder)


 * a quick reference on wiki syntax

How to Upload images and diagrams:


 * Introduction to Uploading Images


 * Uploading Images, includes the &quot;Illustrating Wikipedia&quot; Guide (a downloadable pdf file that is also posted to the BB Ass2 folder)

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 Enroll your username and sandbox on the CHEM 4041 course page; instructions will be given in the Blackboard Ass2 file.

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<ol start="3" style="list-style-type: decimal;"> <li>Begin Looking for a Topic</li></ol>

Week 2

 * 1) Decide on a Topic (subtopic) and Obtain Instructor Approval
 * 2) Begin Searching the Literature and Reading References.


 * Perform a literature search for the most relevant literature articles from reputable peer-reviewed scientific journals on the topic. Best to use SciFinder Scholar (instructions in the Course Syllabus on BB). Remember the literature articles must be submitted to your instructor. Check the course textbook (BGSV-06) for literature references (if the topic is discussed in the course textbook).


 * Be sure to look for the most recent articles also, to be sure the content of earlier articles is still considered accurate and relevant. Many bioinorganic topics involve very active areas of research where fundamental aspects such as the structure or mechanism are still not known or proven, such that new experiments and insights are being reported every year. For example, the exact structure of the CaMn4O5 cluster in photosystem II has only been determined as of 2011 (well after the current edition of the textbook BGSV-06) and the mechanism is not &quot;settled&quot; with several different proposed mechanisms in the recent literature, likewise the structure of the FeMoco (MoFe7S9C) cofactor in nitrogenase was not fully resolved until 2011 and currently the mechanism is still not known, even the initial binding site of the N2 substrate is not known.

<ol start="3" style="list-style-type: decimal;"> <li>Learn the Basics of how to Contribute to Wikipedia</li></ol>


 * About Contributing to Wikipedia


 * About Wikipedia Policies and Guidelines