Tag archive for noteworthy

Recommended reading F’13 Edition

Here is a collection of posts that may be useful as you work on your first writing assignment:

Molecule of the Week

Writing

And a few more…

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Google Reader and my current science feeds

As I mentioned in class, I use Google Reader to keep up with chemistry journals and many science (and non-science) websites. This is infinitely easier than visiting each individual website as the majority of the content is collected in one place. There are many resources available for getting started with Google Reader. Here are two to get you started: The Google Reader Getting Started Guide and Google Reader for Beginners. An updated list of some of the websites I subscribe to via RSS follows:

Chemistry journals I try to review regularly (weekly or biweekly if possible):

The ACS maintains a complete list of their journals and related RSS feeds.

Other science related feeds I review as time permits:

What are you reading online (science related of course)? Leave a link and why you read it in the comments!

Disclaimer: I assume no responsibility for the content of the listed websites.

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Chemical Information?

“A month in the laboratory can often save an hour in the library.”
Frank H. Westheimer

A wealth of information exists outside of Google, although both Google and Google Scholar are powerful tools. How do you search for chemistry related information, documents, references, and other literature?

What if you wanted…

  1. to find references related to your current laboratory experiment?
  2. to find references for your writing assignments?
  3. to find references for your research?
  4. to determine if the ‘science’ you are interested in pursuing is already known?
  5. to cultivate new research or project ideas?

Chemical Databases

Many databases exist that allow searching by author, keyword, title, structure, or even reaction! Most provide tools for exporting search results to text files, word docs (or rtf’s), or reference managers (e.g., RefWorks). The library maintains a current list of major resources. Those that I use most often follow (in no particular order):

  1. American Chemical Society (ACS) Publications (pubs.acs.org)
  2. Article1st and WorldCat (search journals and books, respectively – not chemistry specific)
  3. SciFinder Scholar + structure searching (ChemAbstracts search client)
  4. Reaxys + structure/reaction searching
  5. ScienceDirect (not chemistry specific)
  6. Cambridge Crystallographic Data Center (ConQuest – crystal structure search)
  7. Google Scholar (not chemistry specific)

Be careful…

Do not assume that each of these databases is comprehensive! As much as they would like to be the “one stop shop,” each will have omissions or exclusions of some sort. A good strategy is to use multiple searches of multiple databases. Also remember that a single search term is unlikely to provide comprehensive results. Small changes (additional terms, change in case, etc.) may give drastically different results. Remember to always put your search results in context with the ultimate question(s) asked, and that smaller, complementary searches are usually better than attempting one world beating search!

Searches to try… (use multiple databases as appropriate)

Author

  1. DeSimone, Joeseph
  2. Sorensen, Eric
  3. Trofimenko, S.
  4. Rabinovich, Daniel
  5. Riordan, C.

Topic

  1. organometallic (complex)
  2. olefin metathesis
  3. oxidation
  4. olefin oxidation
  5. epoxidation (styrene)
  6. asymmetric oxidation
  7. trispyrazoylborate (synthesis)

Structure

  1. Search using a simple ethylenediamineNi(II) fragment
  2. Search for both nitrito and nitro cobalt complexes, and other metal nitrito/nitro complexes
  3. Consider the salen ligand and derivatives
  4. Consider a fragment of the tris(pyrazolyl)borate ligand using different R groups (e.g., Me, t-Bu, Ph, halogens… use your imagination)

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So you’re writing your first post…

sharpie&paperYou found an article that really grabbed your attention and you cannot wait to share it. Great! So where do you begin? Start by choosing a specific idea, fact, or result and use it to focus your writing. Your enemy here is being overly broad and/or vague. Once you have a focus, prepare a list of 5-7 points/ideas/contexts/relationships/etc. that you may want to discuss. Do not concern yourself with order, length, or sentence structure as it is much more important to get your thoughts out of your head (I generally use a Sharpie and computation pad for this). Use your list to begin collecting appropriate references, links, images, etc. to support your argument(s). You may have to reframe your arguments in light of the information you collect. Use your research to rewrite each statement on your list into a clear and concise sentence. Consider these complete statements in the context of your topic and reorder (or eliminate) them in a coherent and logical sequence. Remember that there is not one correct way to arrange things – a little trial end error is warranted at this stage. Now that you have what amounts to a detailed outline, it is time to consider the length of your piece – is it a one paragraph summary, a five paragraph analysis, or should it be divided into a series? Once you have decided on length, use clear and concise language to layout and connect your statements/points; they should form a cohesive unit when combined. Construct strong and clear opening and closing statements to frame your work. Your reader may or may not continue reading on the basis of your opening statement so make it count. Review your piece as a whole and rewrite/edit as necessary. Reviewing and rewriting usually takes the most time and effort. You may want to consider having someone else read and comment on the work before submitting it for publication. When you are satisfied with your work, submit your post for review and publication, then sit back and bask in the accolades of a job well done!

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Assignment update

A table of completed assignments is available on the wiki. Please don’t wait until the last minute to complete your assignments. Nicole and I are available for help both subject wise and in getting your assignments published.

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still looking for suggestions…

I’m still looking for suggestions for this website now that we’ve been up and running for a couple of months. My goal is to make it as functional as possible without cluttering it up. A few ideas I have: an authors page where each of you can write a little blurb about yourself including anything interesting you’d like to add, personal websites, etc.; a links or commonplace page to publish interesting things that may not make for a decent post. We could consider doing something with delicious instead of a links/commonplace page. Do either of my ideas sound reasonable? How would you change/adapt them? What suggestions do you have?

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Week 2 review – character tables and representations

We built on our discussion of symmetry and introduction to character tables by ‘generating’ the character table for the C2v point group using the set of coordinate vectors (and the idea of ‘orthogonality’), and defined both irreducible and reducible representations. From there, we discussed groups and defined several terms and symbols associated with chemically relevant character tables. We ended the week by considering transform matrices associated with symmetry operations, their use in generating reducible representations, and the reduction of reducible representations.

C2v_CT

Some things to think about / consider:

  • symmetry with respect to (wrt) an operation is denoted by a 1, while -1 represents anti-symmetry wrt an operation
  • irreducible vs. reducible representations
  • the properties of groups
  • definitions associated with character tables: order, classes, orthogonality…
  • the meaning of symbols commonly encountered with character tables (A, E, T, u, g….)
  • the transform matrix
  • reducing reducible representations

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Week 1 review – molecular symmetry and an introduction to group theory

water w_sym.tiff

The focus this week has been on molecular symmetry, symmetry elements and operations, point groups and point group assignment, with a brief intro to character tables.

A few take home points:

  1. a molecule is considered to have symmetry if a transformation results in a new orientation indistinguishable from the original
  2. a symmetry element is an object (point, line, or plane) through which a symmetry operation is carried out, e.g., rotation (operation) about a proper axis (element)
  3. symmetry elements include: proper axis (Cn), mirror plane (s), inversion center (i), improper axis (Sn aka rotation/reflection), and the identity (E)
  4. molecules can be grouped and classified by symmetry elements (point groups)
  5. molecular and physical properties are often predicted and explained using symmetry and group theory
  6. character tables provide a mathematical basis for symmetry elements and operations

hydrazine w_sym.tiff

I hope that I have impressed upon you the importance of drawing accurate Lewis structures wrt to identifying symmetry elements and making point group assignments. The molecule in the upper right is water, which belongs to the C2v point group. The molecule to the left is hydrazine, which is in the C2h point group. The images were created using Bio-Rad’s KnowItAll software package. I have a site license for the software; please contact me if you are interested.

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