Phillip Nguyen

Research Priorities and Projects

Spring-Summer 2017

Priority 1—Me1(NitroPhenol)1-CB-Cyclen

  1. Delgado, Dalton 2013, 42, 6149-6160
  2. Notebook pages from Josh Priddle and/or Megan Ayala

Priority 2—Bis-CB-(MethylPhenol)Cyclens

a.Fusi, Inorg. Chem. 2014, 53, 4560-4569.

b.Koskinen, Tet. Lett. 2006, 47, 2977-2980.

Priority 3—Me1(EtOH)1-CB-Cyclen

  1. Wainwright,Inorganica Chimica Acta(1997),255(1),29-34.
  2. Wong, Tetrahedron Letters(2002),43(17),3217-3220.

Priority 4—Me1(Phosphonate)1-CB-Cyclen

  1. Yoo, ACS Med Chem Lett, 2015, 6, 1162-1166.

Priority 5 (Actually Priority #1)—Thiol Pendant Arms and Linking to Maleimide Lipids

Kovacs, JACS, 2006, 128, 14448-14449

6/5/17

  1. Crystallize all PTN metal complexes
  2. Mass spec all PTN metal complexes
  3. Set up Finkelstine replacement reaction from Kovacs paper for thiol pendant arm

Synthesis of 3-iodopropylthioacetate (IPTA). 3-chloropropylthioacetate (10 g, 66 mmol) was dissolved in 300 ml of acetone. The Finkelstein exchange reaction was performed by adding sodium iodide (30 g, 200 mmol) and refluxing overnight. The reaction was cooled to ambient temperature and the insoluble salts were filtered. Solvent was removed in vacuoaffording a red-orange solid. The solid was redissolved in dichloromethane (150 ml), and the insoluble white solid was filtered from the solution. Solvent was removed in vacuo, affording a red-orange oil, which was passed over a silica plug (95:5 hexanes/acetone) to afford the desired product (13.65 g) as a pale yellow oil (yield = 85%). 1H-NMR (ppm): 2.1 (m, 2H), 2.34 (s, 3H), 2.96 (t, J= 7.0 Hz, 2H), 3.21 (t, 2H, J= 6.9).

  1. Add protected thiol arm to mono-NH cross-bridged cyclen.

Dissolve 1.00g [(1.00 g)(1 mol/212.34g) = 0.0047 mol]of Me1H1-CB-Cyclen in 50 ml of dry acetonitrile. Add 0.01 mol of NaI [(0.01 mol)(149.89 g/mol) = 1.50 g NaI] and 0.001 mol of Na2CO3 [(0.01 mol)(105.99 g/mol) = 1.06 g Na2CO3]. While stirring this mixture, add 0.005 mol [(0.005mol)(152.64 g/mol) = 0.763 g) of 3-chloropropylthioacetate. Stopper and stir for 4-7 days at room temperature. Filter off solids and rotovap filtrate to give the product.

  1. Make cyclen tetracycle from cyclen and glyoxal

Bis-aminal1, 2 syntheses. A methanolic solution of 50 mmol of glyoxal (40% aqueous; make methanol to glyoxal volume 1:1) was added dropwise, between -5 and 0 oC, to a cooled 100 ml methanolic solution of 50mmol ofthe tetraazamacrocycle (cyclen, cyclam or homocyclam). Themixture was stirred for 3 h at room temperature after addition was complete. After solventevaporation, the residue was dissolved in minimum Diethyl Ether and the solution filtered through celite on a fine frit to remove polymers. Rinse with additional ether. After evaporation of thesolvent, bis-aminals were isolated as white solids and used as such in the following steps

Bis-aminal1: perhydro-2a,4a,6a,8a-tetraazacyclopenta[f,g]acenaphthylene (cyclen glyoxal). 95% yield, mp = 94 oC, 13C NMR (CDCl3): 77.5(Caminal), 51.1, 50.3 (CH2N).

  1. Monomethylate cyclen tetracycle from spring semester
  1. Make Cyclam Tetracycle from Procter and Gamble method (made starting material last semester)

6/12/17

  1. Mass Spec, NMR of Finkelstine reaction #3 above
  2. Mass Spec of continuing reaction #4 above. If no product has formed, set this reaction to reflux.
  3. Work up, Mass Spec, NMR reactions #5, #6, #7 above. We need to make sure we have the correct products before moving on.
  4. Completely bring up-to-date your notebook: Table of contents, all spectra copied and taped into notebook. This is a high priority to get everything current!
  5. Try adding IPTA arm according to Kovacs procedure.

Synthesis of 3Boc-cyclam-11-propylthioacetate (3Boc-cyclam-PrAc). (0.615 g, 1.23 mmol) and Cs2CO3 (0.327 g, 2.46 mmol) were dissolved in DMF (3 ml) at ambient temperature. IPTA (0.600 g, 0.0025 mol) was added dropwise while stirring. The solution was stirred for 5 days, until TLC showed product formation to be complete. Water (~100 ml) was added and the solution was extracted by ethyl acetate (3x30 ml). The organic extracts were combined and washed with brine (3x30 ml). The organic layer was dried over MgSO4, filtered, and solvent was removed in vacuoto afford the crude product as a yellow oil. Column chromatography on silica gel (CH2Cl2:methanol – gradient 0-4% methanol) afforded the pure product (0.665 g, 1.08 mmol) as a pale yellow sticky residue (yield = 88%). 1H-NMR (ppm in CDCl3): 1.46 (s, 27H), 1.71 (bm, 4H), 1.80 (t, J= 7.2 Hz, 2H), 2.32 (s, 3H), 2.35-2.43 (m, 4H), 2.86 (bm, 2H), 2.83 (t, J= 7.1 Hz, 2H), 3.21-3.35 (bm, 12H). ESI-MS (M+1) calcd for C30H56N4O7S: 616.39. found: 617.7.

  1. Addition of nitrophenol arm to monomethyl-cyclam-tetracycle. Follow same procedure as we did during Spring 2017 (PTN03). This time, use all of the large batch of monomethyl-cyclen-tetracycle made in #6 above.
  1. Make more Me1H1Bcyclam.
  1. Monobenzylation of Cyclam Tetracycle: 2 equivalents of BnBr + 1 equivalent of cyclam tetracycle in CH3CN (20 ml solvent per gram of tetracycle), for 4 hours, at room temperature. Filter solid product on fine frit. Wash with ethyl acetate to remove BnBr from the solid product. Then wash with ether to remove the ethyl acetate. Dry on vac line.
  1. Methylation of monobenzylated cyclam-tetracycle: 10 eq. of idodomethane was added to the stirring monobenzylated cyclam-tetracycle in 20 ml of CH3CN per gram of starting material. Stir 4 day with stopper at room temp. Filter (IN HOOD), off the white solid product. Wash with ether to remove excess iodomethane. A second fraction may be obtained by ether addition to the filtrate
  1. Sodium Borohydride reduction to Bn1Me1-CB-Cyclam: 14.694g (0.025 mol) of this intermediate was dissolved in 1250 ml 95% EtOH and reacted with 15 equivalents (14.00 g, 0.37 mol) of NaBH4 for 6 days at room temperature under nitrogen. 6 M HCl was then slowly added until a pH of ~1-2 was reached. Following removal of the EtOH under vacuum, 30% aqueous KOH was added until a pH of ~14 was reached, then an additional 10 g KOH was added. After extraction with chloroform (5 x 100 mL fractions), the choroform layer was dried over Na2SO4 overnight, and the solvent evaporated. After drying, 4 was isolated as a yellow oil. Yield = 6.886g, 90%.1H NMR (400 MHz, CDCl3) 1.49 (m, 4H N-β-CH2), 2.19 (s, 3H, CH3), 2.28 (m, 3H, N-α-CH2), 2.42 (m, 8H, N-α-CH2), 2.68 (m, 2H, N-α-CH2), 2.89 (m, 1H, N-α-CH2), 3.11 (m, 3H, N-α-CH2), 3.78 (m, 2H, H2Cbenzylic), 3.98 (m, 1H, N-α-CH2), 7.26 (m, 5H, CHaromatic). 13C{1H} NMR (100 MHz, CDCl3) 26.91 (N-β-CH2), 27.82 (N-β-CH2), 42.83 (N-α-CH3), 51.90 (N-α-CH2), 52.08 (N-α-CH2), 54.01 (N-α-CH2), 54.94 (N-α-CH2), 55.98 (N-α-CH2), 56.15 (N-α-CH2), 56.55 (N-α-CH2), 56.66 (N-α-CH2), 57.77 (N-α-CH2), 59.39 (N-α-CH2), 59.93 (N-α-CH2), 126.41 (CHaromatic), 127.91 (CHaromatic), 128.81 (CHaromatic), 140.93 (Caromatic). MS (ES)m/z 330 [MH]+, 239 [M-Bn]+.Elemental analysis(%)calcd.C20H34N4.0.2C6H6.0.2H2O:C 72.81, H 10.26, N 16.02; Found C 72.46,H 10.41, N 16.29.
  1. Debenzylation with Pd/C to make Me1H1-CB-Cyclam:

1. 11.0 g of Bn2Bcyclam (0.0271 mol) was stirred in 1375 ml of 85% Acetic Acid (1169ml Glacial Acetic Acid + 206ml H2O) in a 2L roundbottom flask.

2. Degas for 30 minutes by bubbling nitrogen through the solution with a long needle and hose-barb-to luer-lock adapter and a small needle outlet vent, both punctured through a septum.

3. 13.75 g of 10% Palladium on Activated Carbon catalyst was added with stirring. Degas an additional 10 minutes after addition is complete. CAUTION!!:Pd/C is potentially flammable in contact with organic liquids. Take care in handling (see safety handout on handling Pd/C attached).

4. Bubble H2 gas from a balloon through the solution using the same long/short needle system used for degassing. Simply replace the N2 tank source with the H2 balloon. (The balloon should be attached to a short piece of rubber tubing, taped around the fragile balloon with electrical tape, and held securely in place by a hose clamp.) Bubble 3-4 filled balloons through the solution to saturate it with H2. You may need to compress the balloon manually to force the last 1/3 of H2 out.

5. After bubbling through the last balloon, quickly replace the septum with a gas inlet valve in the off position. [CAUTION: sometimes grease obstructs the gas inlet valve, blocking the H2 from the reaction. Make sure the gas inlet opening is clear; 1atm of H2 will not “push through” any grease.] Refill the H2 balloon (twisting the balloon to keep full) then connect it to the gas inlet using the rubber tubing. Untwist the balloon and open the gas valve to introduce a 1atm H2 pressure above the stirring reaction.

6. Replace the balloon at least twice a day (7am/7pm) during the course of the 4-day rxn. Be sure to close the gas inlet valve before removing the balloon from it. Be sure to open the gas inlet valve once a new filled balloon has been attached.

Workup

7. Filter the Pd/C off the reaction using Celite in a medium glass frit. Rinse with water. Filtrate should be completely clear. Filter again if any gray/black Pd/C particles remain. [Caution: rinse Pd/C/Celite thoroughly with water. Transfer to a waste bottle specific to Pd/C only.

ALWAYS KEEP WET w/H2O]

8. Rotovap off solvent. Dissolve residue in 30% KOH (350ml) + additional KOH pellets (15 g). Extract into 5 x 250 ml benzene. Dry combined benzene layers over Na2SO4. Filter off Na2SO4, and rotovap benzene to obtain yellow oil / white solid product (5.6 g, 91% yield).

  1. Make more Me1H1Bcyclen
  2. Monomethylation of cyclen-tetracycle:
  1. Benzylation to make Bn1Me1-cyclen-tetracycle:
  1. Sodium Borohydride reduction to Bn1-Me1-CB-Cyclen:
  1. Debenzylation to make Me1H1Bcyclen: Same general method as for Cyclam above

6/26/17

  1. Work up CuCl2 complex of ThiolAcetate Armed Bcyclam as follows:
  2. Filter off any solid—shouldn’t be much and can discard
  3. Add 5 eq of NH4PF6 (dissolved in minimum of MeOH and filtered) with stirring. A precipitate should form. Set in freezer for ~1hr to finish precipitation.
  4. Filter on small disposable frit. Wash with 1 ml MeOH and then 10 ml ether.
  5. Dry on vac line. Get yield. Save 5 mg for elemental. Take another mass spec.
  6. Crystallize the product from MeCN, MeOH, Acetone, 2-butanone, MeNO2.
  1. Set up scaled-up reaction of IPTA + H1Me1Bcyclam (TJH sample) using the rest of this TJH batch.
  1. Work up Me1(NO2Phenol)1Bcyclen

7/5/17

  1. Make metal complexes with Me1(NO2Phenol)1Bcyclen as follows: 0.001 mol of ligand plus 0.001 mol of metal salt (MnCl2, FeCl2, CoCl2, NiCl2, CuCl2, ZnCl2) in acetonitrile. Use DMF only for NiCl2 complexation. Here is a set of procedures from Donnie’s complexation with a very similar ligand.

[M(PyMeEBC)Cl]PF6 where M = Mn2+, Fe2+, Co2+, Ni2+, and Zn2+. The general procedure for [Mn(PyMeEBC)Cl]Cl was followed using 0.001 mol (0.332 g) of PyMeEBC and 0.001 mol of the respective anhydrous divalent metal chloride salt. [Because NiCl2 has little solubility in acetonitrile, N,N-dimethylformamide (DMF) was used as the solvent for this reaction only. The reaction was removed from the glovebox and refluxed overnight before workup.] These reactions, other than manganese, gave little or no precipitation. All

were filtered to remove trace solids, which were discarded (other than manganese, which gave a copious white solid, which was filtered, dissolved in a minimum of MeOH, and precipitated with NH4PF6 as for the other metal ions). The filtrates were then evaporated under vacuum to give crude [M(PyMeEBC)Cl]Cl solid products that were dissolved in a minimum of MeOH in the glovebox. To each was added 0.815 g (0.005 mol, 5 equiv) of NH4PF6, likewise dissolved in a minimum of MeOH. Precipitation of the [M(PyMeEBC)Cl]PF6 products was immediate, but the suspensions were allowed to stir

approximately 1 h to complete precipitation. The solid [M-(PyMeEBC)Cl]PF6 products were filtered off, washed with diethyl ether, and allowed to dry overnight open to the glovebox atmosphere.

7/17/17

  1. Finish workup of metal complexes from #19 above. Mn and Fe in glovebox should be filtered to give “A” fraction. “B” fraction will be obtained by allowing solvent to evaporate in the Glovebox.
  1. Make sure some of each complex fraction is kept for Elemental Analysis (which will probably happen after the summer session.
  1. Set up crystallization of all metal complexes from #19 above.
  1. Mass Spec and NMR Characterization of Bn1Me1Bcyclam from #14 above. If they look good for the correct product, proceed with De-Benzylation using Pd/C.
  1. Debenzylation with Pd/C to make Me1H1-CB-Cyclam:

1. 11.0 g of Bn2Bcyclam (0.0271 mol) was stirred in 1375 ml of 85% Acetic Acid (1169ml Glacial Acetic Acid + 206ml H2O) in a 2L roundbottom flask.

2. Degas for 30 minutes by bubbling nitrogen through the solution with a long needle and hose-barb-to luer-lock adapter and a small needle outlet vent, both punctured through a septum.

3. 13.75 g of 10% Palladium on Activated Carbon catalyst was added with stirring. Degas an additional 10 minutes after addition is complete. CAUTION!!:Pd/C is potentially flammable in contact with organic liquids. Take care in handling (see safety handout on handling Pd/C attached).

4. Bubble H2 gas from a H2 gas cylinder through the solution using the same long/short needle system used for degassing. Typically, completion of the reaction takes ~4 days. You can check for completion by taking a small amount of the reaction solution out, filtering of Pd/C, and obtaining a mass spectrum. Look for product as 100% peak and none of starting material. Keep H2 going until all starting material is gone.

Workup

5. Filter the Pd/C off the reaction using Celite in a medium glass frit. Rinse with water. Filtrate should be completely clear. Filter again if any gray/black Pd/C particles remain. [Caution: rinse Pd/C/Celite thoroughly with water. Transfer to a waste bottle specific to Pd/C only. ALWAYS KEEP WET w/H2O]

6. Rotovap off solvent. Dissolve residue in 30% KOH (350ml) + additional KOH pellets (15 g). Extract into 5 x 250 ml CH2Cl2. Dry combined CH2Cl2 layers over Na2SO4. Filter off Na2SO4, and rotovap to obtain yellow oil / white solid product (5.6 g, 91% yield).

  1. Mass Spec and NMR Characterization of Bn1Me1Bcyclen from #15 above. If they look good for the correct product, proceed with De-Benzylation using Pd/C following same procedure directly above.
  1. If good H1Me1Byclen is obtained, IPTA can be reacted with it to form the thiol acetate pendant armed ligand. Use Cable’s IPTA if you need more than you have.
  1. Make more IPTA if you need to.

Synthesis of 3-iodopropylthioacetate (IPTA). 3-chloropropylthioacetate (10 g, 66 mmol) was dissolved in 300 ml of acetone. The Finkelstein exchange reaction was performed by adding sodium iodide (30 g, 200 mmol) and refluxing overnight. The reaction was cooled to ambient temperature and the insoluble salts were filtered. Solvent was removed in vacuoaffording a red-orange solid. The solid was redissolved in dichloromethane (150 ml), and the insoluble white solid was filtered from the solution. Solvent was removed in vacuo, affording a red-orange oil, which was passed over a silica plug (95:5 hexanes/acetone) to afford the desired product (13.65 g) as a pale yellow oil (yield = 85%). 1H-NMR (ppm): 2.1 (m, 2H), 2.34 (s, 3H), 2.96 (t, J= 7.0 Hz, 2H), 3.21 (t, 2H, J= 6.9).

  1. If/When new batches of H2Bcyclam and H2Bcyclen are obtained (Zane and Donnie are working on this; Zane’s are currently in last step Pd/C), attempt to add 1 IPTA arm to each of these ligands. Procedures would be very similar to the IPTA addition reactions above. We would want only 1 arm added initially, so 1:1 stoichiometry would be used. Later, we may try to add 2 of these arms to the ligand as well.

Phillip Nguyen