The Two Bioinorganic Projects of Research Methodology Fall 2012

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The Two Bioinorganic Projects of Research Methodology Fall 2012. Ligand synthesis. MeOH 20 h or so. in NaOH pH ~11. Solvent : aqueous ethylene glycol. What is the significance of this project? Tris - chelate Ru compexes bind to DNA… - PowerPoint PPT Presentation

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The Two Bioinorganic Projects of Research Methodology Fall 2012

Ligand synthesisin NaOH pH ~11MeOH

20 h or soSolvent : aqueous ethylene glycol

What is the significance of this project?

Tris-chelate Ru compexes bind to DNA

where the strength of binding corresponds to a match of chirality between the Ru complex and DNA

Look at how snugly this red complex fits into the groove:B-DNA is a right hand helix andthat red complex is right-handed too!

How can that be?


Simplify first to see chiralityWhat is the point symmetry?Simplify againto see handedness

To have complex oriented properly to see this, arrange complex so that one end of each chelate makes a triangle.

delta isomer, right handedlambda isomer, left handed

- [Ru(bpy)2(DPPZ)]2+ - [Ru(bpy)2(DPPZ)]2+ - [Ru(bpy)3]2+ - [Ru(bpy)3]2+

What we could see for [Ru(bpy)3]2+ Is also true for [Ru(bpy)2(DPPZ)]2+And also for all the other [Ru(bpy)2(L)]2+ complexes you will make

Bioinorganic Research in the Burgmayer Labsthen we add them to DNA and see what happens . . . . .

Intercalation modeGroove binding modeDo they bind to DNA?


Are they able to damage DNA?

What aspect of Ru complexes causes DNA damage?Metals Work with DNAUniversity of Richmond, November 2010DNA is the target of anti-cancer metal drugscis-Platin, the most famous example, used since 1977

binds to DNA, distorts,prevents DNA repair, leads to cell death

10Pteridines meet RuUniversity of Richmond, November 2010Why we decide to jump into the game

So lets see ifwe can make this,and see what happenswith DNA11

Some questions about the reaction:Why are Cl- ligands on Ru replaced?What role do Cl- ions play after step 1?Why is the reaction heated?

Theses two complexes are special;They are made from different ligands that undergoes a reaction on the metal during heating.Theses two complexes are special;The ligand undergoes a reaction on the metal during heating.

How will we know when reactions are done?ESI-MSElectrospray Ionization Mass Spectrometry ESI-MSblack boxmassdetectormagnetic fieldseparates light and heavymass ionsMolecules in gas phase as ions + or -16



Electrospray ionization methodmakes tiny dropletsVacuum removes solventElectric potential creates + and - ions19For discussion:

What did you think about the two very different procedure formats last week?Reaction scale is 2.0 mmol using reagents in an equimolar ratio.Phen dione is dissolved in 15 mL MeOH.Diamine reagent is dissolved in either MeOH or water made basic with dilute NaOH.Two reagent solutions combined in round bottom flask.Mixture is stirred overnight.Product is isolated by filtration (Hirsch funnel, filter paper).Product is washed with water, methanol and diethylether.**All manipulations including isolation of the product must be performed in a hood.**A stir bar and 0.3L propionic acid are added to a 500-mL three-neck, round-bottom flask fitted with a reflux condenser. Put the addition funnel in the center neck, the condensor on a side neck and a septum on the third neck. The acid is brought to a reflux and 0.1 mol of the appropriate substituted benzaldehyde is added. Quantities of aldehydes: benzaldehyde [for TPP synthesis] = 10.16 mLp-tolualdehyde [for TTP synthesis] = 11.8 mL4-chlorobenzaldehyde [for TClPP synthesis] = 14.06 gTo the refluxing solution, 10 mL (0.1 mol) freshly distilled pyrrole is cautiously added via a dropping funnel. A recommended rate is about 1 drop/sec. Caution! The condensation reaction of the pyrrole with the aldehyde is extremely exothermic, and the rate of pyrrole addition must be continuously monitored. The solution is refluxed for 30 min, cooled to ambient temperature, and chilled in an ice bath before vacuum filtering off the purple, crystalline product. [Note: Filtrations can be slow. Try adding small volumes of Pteridinyl PhenanthrolinePorphyrinFor discussion:

What did you think about the two very different procedure formats last week?2) Why were there two ligand synthesis methods?3) How best to clean glassware?Brief Outline of Ru reaction steps:

Purge reactants in solution with N2 gas.Heat / reflux / cause reaction to occurCool then filter to remove unwanted solidsAdd NH4PF6 in excess to ppt the complex, [Ru(bpy)y(L-)]2+ (PF6)25) Filter to isolate next weekChart of Complex Reaction Conditions

Group #1234567

Ligand name DPPZL-alloxL-aminoL-ketoL-aapL-UNL-alap


Ru synthesisReflux 3-4 hours at ~150 degReflux 3-4 hours at ~150 degReflux 1 hour at ~110 degReflux 2-3 hours at ~110 degReflux 2-3 hours at ~110 deg then increase to 140 deg 2 hours(not made)Aqueous 2 hour refluxNote: H2O only!!

scheduleSynth 9/19Isolate -9/25Synth 9/19Isolate -9/25Synth 9/19Isolate -9/25Synth 9/19Isolate -9/25Synth 9/19Isolate -9/25Synth 9/19Isolate -9/25

Scale = 0.5 to 0.3 mmol in RuUse 1:1 ration of Ru:ligandSolvent = 2:1 v/v ethylene glycol/H2O;Volume = 30 mL

Group #1234567