Category for MotW

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


And a few more…

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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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MotW 15: Promising Ruthenium Complexes as Anticancer Drugs

Organoruthenium complexes, of the form of [(η6-arene)RuII(YZ)X]+ (Inorg. Chem., 2008, 47, 11470–11486, DOI: 10.1021/ic801361m), are increasingly being studied for use in medicine. The arene is usually a phenyl derivative, YZ is usually a chelating ligand, and X is usually a halide, such as Cl. This type of compound has been studied to be used against cancer. Using the exmple with x=Cl, the Ru-Cl bond can be hydrolyzed and then act as a binding site for DNA, while the arene is a hydrophobic site of the complex, which protects the RuII from oxidizing to RuIII. The chelating ligand provides stability and as the size of the arene increases, the cytotoxicity to the cancer cells increases.


The complex pictured, [(η6-Tha)Ru(bipy(OH)O)(9-EtG-N7)][PF6], contains the bipy(OH)O chelating ligand, and showed a large increase in the cytotoxicity toward human ovarian and human lung cancer cells. The tetrahydroanthracene (tha) “faces” protect the RuII against oxidation. Examining the crystal structures shows CH/π interactions between the bipyridine ligand and tetrahydroanthracene are important for stabilizing the interaction between [(η6-Tha)Ru(bipy(OH)O)(9-EtG-N7)][PF6] and proteins. Although this complex was not tested for activity against ovarian and lung cancer cell lines, A2780 and A549 respectively, other complexes with the tetrahydroanthracene (tha) moity were tested and proved to be most active against the ovarian cancer cell line. Ruthenium complexes such as [(η6-Tha)Ru(bipy(OH)O)(9-EtG-N7)][PF6] have been shown to mimic iron binding in the human body and the ligand, bipy(OH)O, helps the complex bind to DNA in ways that another antitumor compound, cisplatin, cannot. This shows extreme promise as a therapeutic as cisplatin tumor toxicity is not as high with some types of tumors.

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If you are struggling with your Molecule of the Week topics…

Updated F 09.03.10 – As a reminder, you need to find three examples from the chemical literature (full papers, 2009 to present) that minimally include a molecular metal-ligand complex and a crystal structure. Send me links to the papers, or, better yet, share a Google Doc with me so I can comment on the examples you provide. That’s it! The subject/area/topic is completely up to you.

As you search for relevant examples / topics for your MotW assignment, it is important to recognize that there is not a ‘correct’ way to search. Ultimately, the correct method is the one that leads to an answer or solution. Notice I didn’t say the answer, rather an answer, as the question will likely evolve during the search process (and it is a process). The more paths / methods you can employ for gathering information and ideas the better, and like most everything worth doing, deliberate practice is required.

If you are having difficulties finding appropriate examples, try using Google Scholar ( to investigate a topic you have some interest in learning more about. I provide a couple examples below (all Scholar searches excluded patents were limited from 2009 to the present).

Browse your ‘hit lists’ beyond the first page and then look at specific journals to narrow the range of your chosen topic. Is a transition metal involved? Is the compound molecular? Is a cif available for download or will you have to request it from the CCDC? While these are simple examples, you should take it as far as your interest, time, and patience allow!

One final tip for now. As soon as we have chosen an article for your MotW assignment, start writing. You may find it necessary to change topics only after you begin writing. Have a backup plan and please, have fun with it!

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MotW14 – A nonreducible, high-valent Mn(V) complex

MotW14-ic0609251-mol02wResearch involving the formation and characterization of high-valent Mn complexes has been slow. They are proposed to be active intermediates in biological and synthetic reactions, such as epoxidations and hydroxylations. They are also important intermediates in NR group transfer reactions, or pericyclic reactions in which a pi bond is  transformed into a sigma bond while another sigma bond migrates.

At John Hopkins University, a manganese(V) imido complex [(TBP8Cz)MnV(NMes)] was synthesized from the Mn(III) complex [(TBP8Cz)MnMIII]  (Lansky, D.; Kosack, J.; Narducci Sarjeant, A.; Goldberg, D. Inorg. Chem. 2006, 45, 8477-8479). Even with a high-valent MnV center, the complex is very resistant to reduction. The 1H-NMR spectrum showed a diamagnetic molecule, indicating a low-spin MnV (d2) species. The structure was confirmed via X-ray crystallography. The crystal contains two independent molecules, with the imido axial ligands pointing away from each other. A short Mn-N imido distance suggests a stronger pi overlap between the terminal imido ligand and the empty metal dxz/dyz orbitals. The metal ion is 0.55 Angstroms above the average plan of the four pyrrole N atoms.

Reactions of the Mn(V) complex with alkenes were unsuccessful. H-atom abstraction should be able to occur in this molecule, but it was completely unreactive toward even a highly reactive H-atom donor. This lack of reactivity shows that the complex cannot undergo even weak H abstraction. The explanation could be that the rate-determining step is the reduction of MnV to MnIV which is not easily reached, and therefore the thermodynamics do not favor the H abstraction. The complex is also very resistant to reduction, even as a high-valent species, as shown by the electochemical data.

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MotW13 – A Potential Metal-Free Cancer Drug


Metal-DNA adducts are popular molecules for cancer treatment.  However, the metal-based drugs have been associated with unwanted side effects such as nausea, nephrotoxicity (toxicity to kidney cells), and myelosuppression (suppression of bone marrow activity).  Researchers have therefore been geared toward synthesizing metal-free cancer drugs.  A research team at the Indian Institute of Technology in Bombay  has created a new bis(phosphite) ligand) and corresponding complexes of selenium and gold with thioether functionalities (D. Suresh, Maravanji S. Balakrishna, Krishnan Rathinasamy, Dulal Panda and Joel T. Mague Dalton Trans., 2008, 2285 – 2292).

All three compounds were examined for cytotoxic activity in a HeLa (human cervix epitheloid carcinoma) cell line.  While the bis(phosphite) ligand and bis(sulfide) derivative of the ligand significantly inhibited growth of the HeLa cells, the selenium and gold complexes did not.  By testing both the bis(phosphite) ligand and bis(sulfide) derivative in the HeLa line with annexin V and a propidium iodide apoptosis detection kit, the researchers discovered that both compounds caused cell death by apoptosis, using specialized mechanisms within the cell to shed membrane-bound particles.  The creation of a cancer drug that could potentially reduce or eliminate the side effects of metal-based drugs could help make treatment more bearable for patients as well as possibly attack resistant cells more effectively.

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MotW12 – potential prodrugs for Alzheimer’s disease

MotW12-b815404j-co340wThe molecule for this week comes from research out of the Medicinal Inorganic Chemistry Group at the University of British Columbia in Vancouver and concerns altering pyridinone N-substituents to optimize activity as potential prodrugs for Alzheimer’s disease (Lauren E. Scott, Brent D. G. Page, Brian O. Patrick and Chris Orvig. Dalton Trans., 2008, 6364 – 6367). The research focuses on using metal-binding pyridinone prodrugs for Alzheimer’s disease treatment because of their brain targeting abilities as well as their antioxidant characteristics. Pyridinones are already approved for therapeutic purposes in some areas of the world and, since hydroxypridinones are good at binding to metals, the N-substituent can be modified which in turn alters the structure without changing metal binding capabilities.

In previous research, it was found that molecules that contain a glucose moiety can easily target the brain. Based on this, the researchers aimed to attach a glucose moiety at the 3-hydroxyl oxygen.  This glucose moiety can then be enzymatically removed once the molecule reaches the target leaving the metal binding agent. The copper complexes 3-Hydroxy-2-methyl-1-phenyl-4(1H)-pyridinone (Hppp) and 3-hydroxy-2-methyl-4(1H)-pyridinone (Hnbp) were synthesized. Copper was used as it is one of the redox active metals involved in Alzheimer’s disease and because it has a higher affinity for amerliorate toxic beta-amyloid deposits, which are found in the brains of affected patients.  It was found that the Hppp and Hnbp significantly reduced the amount of amerliorate toxic beta-amyloid deposits and there was no significant difference between the Hppp copper complex and the Hnbp copper complex in efficiency.

I found this research both interesting and important as there is currently no cure for Alzheimer’s disease. It is also interesting to see how inorganic chemistry can be applied to solving problems in medical and biological settings . I am hopeful that in a few years we will see a similar drug or concept that will help cure Alzheimer’s disease.

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Molecule of the Week (11): Organometallic carbon-oxygen bond cleavage

MotW11This article focuses on the synthesis of iron catalysts which are less toxic than those used in industry (Ryan J. Trovitch, Emil Lobkovsky, Marco W. Bouwkamp, Paul J. Chirik. Organometallics 2008 27, 6264-6278). Oxidative addition is a common process involved in organometallic chemistry. This process typically constitutes a two electron redox reaction and is more common when late transition metal complexes are involved. This molecule is part of continuing research as chemists strive to replace toxic and expensive precious metal catalysts with more cost effective and benign iron compounds. However, such research also requires a deeper understanding of the elementary steps involved in oxidative addition catalysis.

The Chirik laboratory at Cornell University has reported the synthesis of aryl-substituted bis(imino)pyridine iron dinitrogen compounds that have the capacity of functioning as efficient catalysts for hydrogenation and hydrosilylation of olefins and alkynes. Even more interesting is that some of these iron containing catalysts were able to promote catalytic cycloisomerizations. Fortunately, researchers have found a convenient way to synthesize four coordinate bis(imino)pyridine iron aklyls. One possible focus of future research may include extending this approach to sp2 hybridized alkenyl to allow the synthesis of the desired vinyl compound. One ongoing problem these researchers face is that many of the iron containing catalysts they attempt to synthesize are too unstable to perform organometallic bond cleavage. Overall, this research could provide advantages over those currently used in industry, especially when considering toxicity. I am hopeful that we will eventually reach a point where more reactions can be carried out with non-toxic catalysts.

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Molecule of the Week (10)

This week’s molecule comes from research at the University of Calabria, Italy about Pt(II) and Pd(II) complexes which may be active as anticancer agents (Pucci, D.; Bellusci, A.; Bernardini, S.; Bloise, R.; Crispini, A.; Federici, G.; Liguori, P.; Lucas, M.F.; Russo, N.; Valentini, A., Dalton Transactions, 2008, 5897-5904). The research focused on the synthesis of metal-complexes with two chelating ligands, 2-hydrocyclohepta-2,4,6-trienone (tropolone) and dihexadecyl-2,2′-bipyridine-4,4′-dicarboxylate (bipy), around either Pt(II) or Pd(II) metal centers. Pt is often used as a metal center in anti-cancer drugs, and Pd was introduced with the hope of reducing the toxicity of previous Pt drugs. Both compounds were successfully synthesized and analyzed by X-ray diffraction.

The geometry about the Pt(II) metal is distorted square planar and the molecule is essentially planar. The metal complexes were tested in vitro against the human prostate DU145 and hormone-sensitive LNCaPcell lines. The two chelating ligand system was more active at cell growth inhibition than other studied complexes. The complexes are known to inhibit tumor growth by binding to a cell’s DNA and inducing cell apoptosis or necrosis. These metal-based anticancer drugs are important because they seem to be more effective in lower doses, which would decrease toxicity. Also the specific bipy ligand which allows strong pi-pi bonds may cause further conformational changes in a cell’s DNA which might increase efficiency. The Calabria researchers plan to investigate the mechanisms of these inhibitory complexes in future work.

This molecule interested me because of its long, linear chains and near planar shape. It’s cool to take a look at the potential drugs of tomorrow.

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MotW09 – Catalytic Decomposition of Water

The molecule of the week comes from ongoing research by Dr. Randolf Thummel at the University of Houston (Zeping Deng, Huan-Wei Tseng, Ruifa Zong, Dong Wang, and Randolph Thummel. Inorg. Chem. 2008, 47, 1835 – 1848).  The article focuses on research done in the catalytic decomposition of water into hydrogen and oxygen using diruthenium complexes.  One of the major hurdles which must be overcome in order for hydrogen is the large scale production of hydrogen in an environmentally friedly way.  Currently, hydrogen is produced from hydrocarbons or through the electrolysis of water.  Using hydrocarbons does not solve the problems of oil dependency and using electrolysis requires large amounts of electricity, which would likely be produed by burning coal.  The ultimate goal of the Thummel group is to produce a photocatalyst which will use UV- light to carry out the redox reaction converting water into hydrogen gas and oxgyen gas. The ability to catalyze the decomposition of water is partly due to the presence of the two ruthenium centers so close to one another.  A molecule of water binds to each metal center and hydrogen is release through an oxidation process.  The oxgyen atoms are then within close enough proximity to react to form diatomic oxygen.  Currently, the diruthenium complex is able to catalyse the decomposition of water only in a highly acidic (pH=1) solution in the presence of Ce(IV).  The role of the Ce(IV) is as a sacrificial oxidant.  Future research by the Thummel group will focus on further understanding the specific mechanism involved in the catalysis reaction with the eventual goal of using UV-light to drive the reaction.

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Molecule of the Week(08): Cytotoxicity of Platinum(II) Compounds

The molecule of the week is fresh out of Leiden University in the Netherlands regarding the cytotoxicity of fluorescent platinum (II) compounds (Brouwer, J.; den Dulk, H.; Kooijman, H.; Marques-Gellego, P.; Reekijk, J.; Roubeau, O.; Spek, A.L.; Teat, S.J., Inorg. Chem., Articles ASAP).  Although the paper describes the synthesis of two platinum(II) compounds, I chose to focus on cis-[Pt(A9opy)Cl2] (molecule 1) because of the intricate way in which the planar ligand conforms itself to bind to the platinum metal ion.  The E-2-[1-(9-anthryl)-3-oxo-3-prop-2-enylpyridine] (aka A9opy in figure 1) ligand coordinates to platinum through three different bonds.  The carbons of the isomerizable carbon-carbon double bond coordinate perpendicularly in an organometallic bond to create a constrained and distorted square planar configuration.  The pyradinium nitrogen also coordinates to the metal ion to create a five-membered chelating ring with platinum and the carbon-carbon double bond.

However I didn’t choose this molecule because it looked “cool”.  I found the molecule’s ability to bind to cancerous cells and fluoresce to be particularly appealing.  Previously, most known platinum (II) anticancer compounds did not flouresce which was promblematic because the best way to study living cells was using a digital fluorescence microscopy technique.  Achieving a fluorescent metal-based molecule allows researchers to study the chemical processes platinum undergoes once it binds to tumor cells, providing better insight to fighting cancer.  In the case of cis-[Pt(A9opy)Cl2], studies showed that upon photolysis, the carbon-carbon double bond remained stable and did not isomerize.  Although the molecule is less effective than cisplatin, the most common metal-based chemotherapeutic drug, it proved to be fairly active against most tumor cells.  Further studies into the synthesis of related compounds and more in-depth biological research will be conducted in order to eventually find a drug that is less toxic and more active against a wider range of tumor lines.

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Trianionic Organoborate Triangles

Scientists at the University of Melbourne in Australia are currently doing research on Trianionic Organoborate triangles (Abrahams, B.F.; Boughton, B.A.; Choy, H.; Clarke, O.; Grannas, M.J.; Price, D.J.; Robson, R, Inorg. Chem. 2008, 47, 10.1021). Specifically, supramolecular systems containing the ligand 3,3,3?,3?-tetramethyl-1,1?spirobisindane-5,5?,6,6?-tetrol, or LH4.

Prior studies have been done on the anion L4-, resulting in boron derivatives with a square arrangement. Continued research has resulted in the Molecule of the Week, which is the new boron derivative, [B3L3]3- ligand. Although studies have been performed using the cations, C3H5N2+, and Et4N+, dabcoH+, I focused on the Et3NH+ cation. When solvated, the [B3L3](Et3NH)2? form stacks of alternating chirality. The overall effect of the overlap results in a Rhombus-like cross section when stacks are viewed from above.

What interested me in particular about this molecule was that the cations were actually located within the ligand, rather than the ligand attaching next to the cation. Also, there is something intrinsically aesthetically pleasing about the organization of the anions. Unfortunately the scientists do not offer any particular use for the development of these molecules beyond simply analyzing their organization.

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Mercury 101

So you’re working on your Molecule of the Week assignment and you’re looking at your molecule in Mercury and thinking Wow this is hideous. How am I going to make this look presentable? If you’re not familiar with Mercury, the program seems a bit complicated with letters and buttons all over the place. Hopefully some of these tips will help clear things up, and you’ll get a pretty picture in the end.

Let’s Start with a before picture:

This was my Molecule of the Week before any editing

This picture is chaotic and extremely confusing. So now what…

  1. You can hide all of the hydrogens on your molecule in one simple click. In the bottom right hand corner (directly below the picture) under options uncheck “Show Hydrogens.”
  2. You can change how the atoms/bonds look. In the upper left hand corner next to “Style” there’s a drop down menu giving you 4 different options. If you have nothing highlighted the entire molecule’s style will change when you select any of these. However, you can change atoms individually or as groups. Just click the center of the atom(s) and then choose which style you like. There’s no need to hold down any keys when selecting multiple atoms, and you may have to rotate the molecule slightly to be able to select the atoms. Don’t worry, your previously selected atoms will not be deselected by this action, rotate away.
  3. You can hide atoms. Select the atoms you don’t want to see. Go to Display > Show/Hide > Atoms > Select Hide > Okay. The atoms magically disappear, it’s fantastic, and gets rid of “floaters” in your image instantly clearing things up. If you made a mistake, you can go to Edit > Undo, or you can go to Display > Show All and start over.
  4. You can rotate the image without having to click and move the cursor. Up at the top right above the actual image there is a set of buttons “a b c a* b* c*” These are comparable to the x,y,z axes and when you click them your molecule is aligned accordingly. To the right of these commands are x- x+ y- etc… These nudge your molecule slightly in either the positive/negative x y or z direction. The last commands rotate the molecule 90 degrees with respect to the axes. You can also translate your molecule to the left, right, up, or down by clicking on the arrows.
  5. You’ll probably want to zoom in to make your molecule as clear as possible. Just click the zoom buttons on the upper right.

After these 5 steps you’ll end up with a beautiful molecule:

These are just a few simple little tricks that should help you create a professional looking picture. Clearly there are many other things Mercury has to offer, however I am not familiar with the program entirely. Therefore, I would like to ask all of you to comment here when you discover new tricks. Good luck, and don’t be afraid to click things. I discovered a lot of tricks simply by trial and error.

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Molecule of the Week (06)

The molecule of the week originates from research at the Indian Institute of Science dealing with the photoactivation of oxovanadium complexes for photodynamic therapy (Sasmal, P.K.; Patra, A.K.; Nethaji, M. Chakravarty, A.R. Inorg. Chem. 2007, 46, 11112 – 11121). Photodynamic Therapy (PDT) is an anti-tumor therapy where the anti-tumor drug is activated by irradiation of the tumor with light. There are a couple of characteristics necessary for a potential PDT drug. The first is that it cannot exhibit any ‘dark’ activity; that is, it cannot be active without first being irradiated with light. The second is that the excitation wavelength should be as close to IR as possible. This allows for the light to penetrate the skin without damaging the healthy cells, which UV light would do. The oxovanadium complex in this research is the first vanadium complex to fulfill both of these requirements.

The mechanism of action is extremely interesting. The ligands on the vanadium first bind to the minor groove of the DNA. The complex is then irradiated with light, which activates the metal complex. The activation of the metal complex allows it to transform triplet oxygen, 3O2, into singlet oxygen, 1O2. Singlet oxygen is highly reactive and will react with any molecule in proximity, which in this case is DNA. The destruction of DNA by singlet oxygen leads to cell death even in tumor cells, allowing for the targeted destruction of tumors while leaving healthy cells intact. The only question I have is how molecules like this are metabolized in vivo. Would they stay bound to the DNA of healthy cells for an indefinite period of time and how would their presence affect the activity of cell machinery? Questions such as this need to be addressed, but the groundbreaking research done here is still vital to the search for anti-tumor drugs.

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Molecule of the Week (05)

This week’s molecule comes out of recent research at Iowa State University focused on the catalytic activity of zirconium (IV) complexes involving a new class of scorpionate ligands (Dunne, J.F.; Su, J.; Ellern, A.; Sadow, A.D., Organometallics, 2008, 27, 2399-2401).  I found this to be of particular interest since the Zubris lab has also been investigating the catalytic activity of zirconium complexes with new and interesting ligands.  First developed by DuPont chemist Swiatoslav Trofimenko in the 1960s, the tridentate tris(pyrazolyl)borate (“Tp,” “scorpionate”) ligands coordinate to a metal in a facial manner creating steric bulk on one side, partially shielding the metal center and preventing unwanted side reactions.  The chemists at ISU have been exploring the reactivity of a similar class of complexes in olefin catalysis.  What makes these ligands significant is their ability to withstand the high energy of a reactive, cationic zirconium during polymerization.  The carbon-boron bonds, the researchers believe, allow the ligand to withstand decomposition and isomerization tendencies, thereby maintaining its structural integrity in the presence of cationic zirconium.  Previous research has shown that the nitrogen-boron bonds found in the traditional Tp ligands, are subject to isomerization and cleavage in many transition metal complexes.  The ISU chemists anticipate that the bulk of these ligands will protect and stabilize the zirconium complex, allowing the polymerization of olefins and possible stereoselective polymerizations with analogous chiral zirconium complexes they hope to synthesize.

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