Topics for Group Projects

General Topics with possible subtopics / examples

  1. Polymerization Catalysis
    • Ziegler-Natta
    • Ring Opening Metathsis Polymerization (ROMP)
  2. Bioinorganic Chemistry
  3. Artificial Photosynthesis
  4. Solid-state / Nanochemistry Chemistry
    • Superconducting materials
    • Semiconducting materials
    • Quantum Dots
  5. Supramolecular Chemistry
    • Metal Organic Framework Materials (MOFs)
    • Zeolites
  6. Nuclear Chemistry
    • Radioimaging agents
    • Boron neutron capture agents
  7. Environmental Chemistry
  8. Descriptive / Main Group Chemistry
    • Ammonia borane for H2 storage
    • Compounds of the Nobel Gases
    • Main group multiple bonding
  9. Medicinal Chemistry
    • Pt drugs
    • Transition metal complexes as therapeutics
  10. Catalysis
    • Metal oxides as catalysts
    • Hydrogenation
    • Oxidation catalysis

This list should you started thinking about a topic for your group. The paper you choose will be much more focused and fit into one of the broader categories (the numbered items). I will update the list over the week.

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F’14 MotW Assignment – Part II

Esipova Motw example v2

Tasks for Part II of the MotW Assignment: Due Wednesday 09/17/2014

  1. Choose a paper from those approved.
  2. Share the citation in the group ChemWorx library.
  3. Deposit a pdf of the paper in the Reference folder in the group drive.
  4. Obtain the cif file (crystallographic information file) associated with the molecule you chose. The cif file is often available as supplementary material associated with a specific journal article, otherwise it can be obtained from the CSD.
  5. Deposit a copy of the cif file in the MotW folder and append your last names to the file name (e.g. Fairfield-Kassel-ciffilename.cif).
  6. Use Mercury to create a representative view of the molecule, and export a picture as a png or jpg to the MotW folder using the naming scheme described above. This is the picture that will be displayed in your post and link to the 3D model of the molecule.
  7. Create a Google Document in the MotW folder using lastnames-MotW to name your document; include a link to the full-text (HTML) article at the top of the document.

Write a brief description of the molecule using Science & Technology Concentrates from Chemical & Engineering News as a model. Focus on using simple and clear language when writing. Your summary should be approximately 250 to 300 words in length and include the full article citation using the ACS Style.

A few questions to consider as you begin your draft:

  • What is significant about the molecule?
  • How does it fit in the broader context of the research presented in the paper?
  • What interests you about the molecule/topic?

Use these suggestions to help craft and focus your writing while putting the molecule, the research, and your interest in context. Be as specific as possible and do not just ‘answer’ these questions. Let your responses guide the direction of your writing and ask yourself additional questions as you progress.

I suggest you consider using/creating a flat outline to get started. You may also need to refer to additional resources (i.e., articles referenced in the paper) to answer questions or fill any gaps in information/understanding. Cite these in your document using the ACS style as well.

Please do not hesitate to include questions in your draft that you can try to answer yourself or bring to me for help.

Above all, have fun!!

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F’14 MotW Assignment – Part I

Choose three recent papers (within the last 18 months) that contain at least one compound/complex that: contains a transition metal (Lanthanides and Actinides are allowed), is molecular or is a molecular ion (inorganic polymers, metal-organic frameworks, or metal containing proteins are not appropriate), and has a crystallographically determined structure.

Please review the examples provided below and browse the current contents of Inorganic Chemistry, Journal of the American Chemical Society, Angewandte Chemie International Edition, Dalton Transactions, Organometallics, Polyhedron, Inorganica Chimica Acta, and/or the Journal of Inorganic Biochemistry for ideas. While this is far from a comprehensive list, it should get you started. Post links to the papers on the ChemWorx wall. Remember to include your partner’s name in the post.

Examples of papers that are appropriate for the MotW assignment

Magnetic and Luminescent Binuclear Double-Stranded Helicates

(Phenoxyimidazolyl-salicylaldimine)iron complexes: synthesis, properties and iron catalysed ethylene reactions

Two water-soluble copper(II) complexes: Synthesis, characterization, DNA cleavage, protein binding activities and in vitro anticancer activity studies

Examples of papers that are not appropriate for the MotW assignment

High-Valent Chromium–Oxo Complex Acting as an Efficient Catalyst Precursor for Selective Two-Electron Reduction of Dioxygen by a Ferrocene Derivative – does not include a crystal structure

Theoretical Investigation on Multiple Bonds in Terminal Actinide Nitride Complexes – theoretical (computational) study

Versatile Mesoporous DyIII Coordination Framework for Highly Efficient Trapping of Diverse Pollutants – framework / supramolecular structure (i.e., not molecular)

Dinuclear Ru/Ni, Ir/Ni, and Ir/Pt Complexes with Bridging Phenanthroline-5,6-dithiolate: Synthesis, Structure, and Electrochemical and Photophysical Behavior – a ‘communication’ not a ‘full’ paper

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Molecule of the Week (MotW) Assignment

! Note: We will discuss specific deadlines in class. !

Choose three papers (from January 2012 to the present) that contain at least one molecule that meets the following criteria and email me with links to each – it must contain a metal, it must be molecular (no inorganic polymers, metal-organic frameworks, or metal containing enzymes), and it must have a crystallographically determined structure. I suggest browsing the current contents of Inorganic Chemistry, the Journal of the American Chemical Society, Angewandte Chemie, Dalton Transactions, Organometallics, Polyhedron, Inorganica Chimica Acta, and the Journal of Inorganic Biochemistry for ideas.

I will review each of the papers and approve one or more for you to consider using. After you choose a paper from those approved, obtain the cif file (crystallographic information file) associated with the molecule you chose. It is often available as supplementary material associated with a specific journal article, otherwise it can be obtained from the CSD. Email the cif to me.

Use Mercury (installed as part of the CSD) to open the cif file, manipulate the structure to get a representative view, export a picture as a png or jpg, and email the picture to me. This is the picture that will be displayed in your post and link to the 3D model of the molecule.

Create and share a Google Document with me. Use lastnames-MotW draft to name your document and paste a link to the article at the top of the document. Write a brief description of your molecule using Science & Technology Concentrates from C&EN as a model. Focus on using simple and clear language when writing. Your summary will be between 250 and 300 words in length and should include the full article reference following ACS Guidelines. Begin your draft by considering the following questions:

  • What is significant about the molecule you chose?
  • How does it fit in the broader context of the research presented?
  • What interests you about the molecule/topic?

Use these suggestions to help you craft and focus your writing while putting the molecule, the research, and your interest in context. Do not just ‘answer’ these questions. Be as specific as possible. Let your responses guide the direction of your writing and ask yourself additional questions as you progress.

I suggest you consider using/creating a flat outline to get started. You may also need to refer to additional resources (articles referenced in the paper you chose, or others) to answer questions or fill any gaps. Cite these in your document using the ACS guidelines. Please do not hesitate to include questions in your draft that you can try to answer yourself or bring to me for help.

Above all, I hope you enjoy the writing as it comes together!

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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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Friday Science Spree 09/13/13

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Friday Science Spree 01/21/13

nl-2012-039162_0006

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Friday Science Spree 09/30/11

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Basic Newswriting Tips

From Prof. Ksiazek‘s visit on W 09/21/11 (and the annotated pdf of his example from yahoo news.):

Audience analysis

  • Who is your audience?
  • What sources of information can I use to better understand my audience?
  • What is their prior knowledge of my topic?
  • How can I make the story accessible to a wide audience?

Story structure: The “Inverted Pyramid”

Getting started: Writing the “lead” and “nut graph”

  • 5 W’s and H – Who, What, Where, When, Why and How
  • So What? (The “hook”)
  • Tips for writing leads:
    1. Be brief
    2. Don’t bury the lead
    3. Use active voice
      • “Researchers conducted experiments…” (Active)
      • “Experiments were conducted by researchers…” (Passive)
    4. Use subject-verb-object format
    5. Balance breadth and specificity
    6. Avoid jargon, unnecessary words, and “it”

Resources:

And his annotated pdf of his example from yahoo news.

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Friday Science Spree 09/23/11

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Friday Science Spree 09/16/11

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Friday Science Spree 09/09/11

As always, leave your links in the comments!

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Some examples to help you find topics for your writing assignments

Obviously, these examples are off-limits…

Example of a MotW paper/topic

Examples of “Science in the News”

Examples of Press Releases (which are off-limits as well)

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Friday Science Spree 09/02/11

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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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Recommended reading

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

Writing

Molecule of the Week

And a few more…

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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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MotW16: Anticancer properties of Ruthenium(II) complexes

Ruthenium(II) complexes of the general formula [(η6-arene)Ru(XY)Z]+ were studied for their anticancer properties in A2780 human ovarian cancer cells and A549 human lung cancer cells (Inorg. Chem. 2009, 48, 9444–9453, DOI: 10.1021/ic9013366). The specific arenes used included p-cymene, hexamethylbenzene, and biphenyl), XY denotes o-phenylenediamine, o-benzoquinonediimine or 4,5-dimethyl-o-phenylenediamine, and Z denotes Cl, Br, or I. In particular, redox-active diamine ligands were tested for their inhibitory growth properties for those cancer cells.

The researchers found that when the oxidized ligand (o-bqdi) was present in the Ruthenium complex, it showed no activity in inhibiting the growth of cancer cells. While the ligand (o-pda) showed the highest inhibitory activity against A2780 ovarian cancer cells, none of the complexes showed any activity against the A549 lung cancer cells. The paper states that the presence of GSH in 15-mol equiv reduced complex 4 completely to o-pda from o-bqdi. The o-bqdi chelating ligand, when reduced to an o-pda chelating ligand, acts as an inhibitory complex. However, in human cells, GSH is naturally present in 2-10mM concentrations, which is significantly lower than the 15-mol equiv concentration. Because there was no activity in complex 4 in either cancerous cell, the paper concludes that the reduction process from GSH is too slow. Also, reoxidation from oxygen (air) prevents the reduction to o-pda from taking place.

The authors also state that the low activity of the oxidized chelated ligand may be the result of the stabilizing effect the π-acceptor o-bqdi has on the Ruthenium complex, making it more difficult for Cl- to leave the complex. The Ru-Cl bond does not break as readily resulting in low hydrolysis that is required for reactions with DNA. The hydrolysis of Ru-Cl results in a [(η6-arene)Ru(II)(en)H2O]2+ that binds to DNA and forms a monofunctional adduct. The paper concludes that the low activity of the complexes in inhibiting cancer cells could be a result of a lack of hydrolysis. Hydrolysis allows the complex to form an adduct with the guanine. The ligands and complexes presented are interesting because of their potential cytotoxicity towards cancer cells.

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