Lessons Learned from Organic Lessons Learned from Organic SynthesisSynthesis

Joshua J. Nyman Joshua J. Nyman Howard Hughes Medical Institute Summer Scholar Research ProjectHoward Hughes Medical Institute Summer Scholar Research Project

Mentor: Dr. Yan Zhang, Department of Medicinal Chemistry, VCU School of Pharmacy

BackgroundBackground Anibamine is a natural product, but Anibamine is a natural product, but

recently it has been successfully recently it has been successfully synthesized in the laboratory. synthesized in the laboratory.

Anibamine can be used as an anti-HIV Anibamine can be used as an anti-HIV drug drug

It has a unique chemical structure.It has a unique chemical structure.

N+

AnibamineAnibamineTFA

_

The Research ProjectThe Research Project

The objective of the research project was The objective of the research project was to synthesize the ring system of to synthesize the ring system of anibamine; and then to alter the anibamine; and then to alter the stereochemistry of its side-chains.stereochemistry of its side-chains.

N+

AnibamineAnibamineTFA

_

My Synthesis RouteMy Synthesis RouteO O

NH2

O

CN

NCH3 OH

CH3

CN

N Br

O

O

NCH3 OH

CH3

CNBr

NCH3 OH

CH3

CNNC

NCH3 Br

CH3

CNNC

acetylacetone

+

cyanoacetamide

K2CO3

3-cyano-4,6-dimethyl-2-hydroxypyridine(2-hydroxy-4,6-dimethyl-nicotinonitrile)

, TFA, H2SO4

5-bromo-2-hydroxy-4,6-dimethyl-nicotinonitrile

CuCN, DMF

under nitrogen gas

1,2-dihydro-4,6-dimethyl-2-oxopyridine-3,5-dicarbonitrile

Tetrabutylammonium bromide, P2O5

2-bromo-4,6-dimethylpyridine-3,5-dicarbonitrile

Forming the Pyridine RingForming the Pyridine Ring

An aqueous solution of potassium carbonate was An aqueous solution of potassium carbonate was prepared. prepared.

Acetylacetone and cyanoacetamide were added Acetylacetone and cyanoacetamide were added to the solution.to the solution.

A stir bar was placed into the resulting mixture A stir bar was placed into the resulting mixture and the mixture was allowed to stir at room and the mixture was allowed to stir at room temperature for 24 hours.temperature for 24 hours.

O O

NH2

O

CN

NCH3 OH

CH3

CN

acetylacetone cyanoacetamide

3-cyano-4,6-dimethyl-2-hydroxypyridine

K2CO3

Forming the Pyridine RingForming the Pyridine Ring

After 24 hours of stirring, the mixture was vacuum filtrated, yielding After 24 hours of stirring, the mixture was vacuum filtrated, yielding a white powder.a white powder.

Melting point was on the high end of the literature melting point, and Melting point was on the high end of the literature melting point, and the thin-layer chromatography provided a positive presumptive test the thin-layer chromatography provided a positive presumptive test for the pyridine ring product. for the pyridine ring product.

A proton-NMR was also done on the resultant compound, but was A proton-NMR was also done on the resultant compound, but was later to found to be of little value based on the solvent used to later to found to be of little value based on the solvent used to dissolve the sample.dissolve the sample.

Images: Barnard College Organic Chemistry Lab

Brominating the Pyridine RingBrominating the Pyridine Ring

The product of the previous reaction was dissolved in concentrated The product of the previous reaction was dissolved in concentrated sulfuric acid and trifluoracetic acid, while in an ice bath. N-sulfuric acid and trifluoracetic acid, while in an ice bath. N-bromosuccinimide was then added. **bromosuccinimide was then added. **

This reaction was run multiple times with varying degrees of purity. This reaction was run multiple times with varying degrees of purity. Melting points taken of the product(s) were 10 to 15 degrees too high in Melting points taken of the product(s) were 10 to 15 degrees too high in

a couple of cases.a couple of cases. Thin-layer chromatography suggested some compounds were impure.Thin-layer chromatography suggested some compounds were impure. Product appeared to be a light yellow in the more impure products and Product appeared to be a light yellow in the more impure products and

white in the purer products.white in the purer products.

NCH3 OH

CH3

CNN Br

O

O

NCH3 OH

CH3

CNBr, TFA, H2SO4

Brominating the Pyridine RingBrominating the Pyridine Ring

It seems the purity of this reaction could have It seems the purity of this reaction could have been affected by certain techniques.been affected by certain techniques. For example:For example:

Removing the reaction mixture from the ice bath: Exothermic Removing the reaction mixture from the ice bath: Exothermic reactionreaction

Rate of addition: Adding the NBS too quickly likely resulted in Rate of addition: Adding the NBS too quickly likely resulted in an undesired side reaction.an undesired side reaction.

Acid-Base reaction.Acid-Base reaction.

NCH3 OH

CH3

CNN Br

O

O

NCH3 OH

CH3

CNBr, TFA, H2SO4

Adding a Cyano- Group to the Pyridine Adding a Cyano- Group to the Pyridine RingRing

This reaction had some special considerations:This reaction had some special considerations:

One of the chemicals used in this reaction is a highly One of the chemicals used in this reaction is a highly toxic compound called cuprous cyanide (a.k.a. copper (I) toxic compound called cuprous cyanide (a.k.a. copper (I) cyanide).cyanide). Handling the cyanide required great careHandling the cyanide required great care

NCH3 OH

CH3

CNBr

NCH3 OH

CH3

CNNCCuCN, DMF

under nitrogen gas

Adding a Cyano- Group to the Pyridine RingAdding a Cyano- Group to the Pyridine Ring

All reactants had to be very dry!!!All reactants had to be very dry!!!

Oil PumpOil Pump

Adding a Cyano- Group to the Adding a Cyano- Group to the Pyridine RingPyridine Ring

The cuprous cyanide was dissolved in The cuprous cyanide was dissolved in dimethylformamide along with the product dimethylformamide along with the product from the previous reaction.from the previous reaction.

The mixture was then refluxed for 48 The mixture was then refluxed for 48 hours under nitrogen gas.hours under nitrogen gas.

NCH3 OH

CH3

CNBr

NCH3 OH

CH3

CNNCCuCN, DMF

under nitrogen gas

Adding a Cyano- Group to the Pyridine RingAdding a Cyano- Group to the Pyridine Ring

My compound being refluxed under My compound being refluxed under nitrogen protectionnitrogen protection

Adding a Cyano- Group to the Adding a Cyano- Group to the Pyridine RingPyridine Ring

This reaction gave me multiple problemsThis reaction gave me multiple problems Proton NMR, Thin-Layer Chromatograhy Proton NMR, Thin-Layer Chromatograhy

tests, and melting point tests = impure. tests, and melting point tests = impure. Because of this, I wasn’t able to proceed Because of this, I wasn’t able to proceed

further before the end of this program.further before the end of this program.

NCH3 OH

CH3

CNBr

NCH3 OH

CH3

CNNCCuCN, DMF

under nitrogen gas

Lessons LearnedLessons Learned

Organic synthesis can be very tricky, especially Organic synthesis can be very tricky, especially when trying to form natural products.when trying to form natural products.

I learned not only to think about the products I I learned not only to think about the products I am trying to synthesize, but also about which am trying to synthesize, but also about which products I do not want to synthesize (i.e. products I do not want to synthesize (i.e. impurities) and how to prevent them.impurities) and how to prevent them.

It’s not just what chemicals you add, but how It’s not just what chemicals you add, but how you add them. Temperature, rate of addition, you add them. Temperature, rate of addition, and other factors can have a considerable and other factors can have a considerable impact on the overall synthesis. impact on the overall synthesis.

References and References and AcknowledgementsAcknowledgements

A special thanks to Dr. Yan Zhang (my mentor) A special thanks to Dr. Yan Zhang (my mentor) for sharing his expertise, his laboratory, and for for sharing his expertise, his laboratory, and for making this an exceptional research learning making this an exceptional research learning experience.experience.

Also a special thanks to Dr. Guo Li and Kendra Also a special thanks to Dr. Guo Li and Kendra Haney, for generously sharing their time and for Haney, for generously sharing their time and for their guidance.their guidance.

And to all of the others brilliant individuals in Dr. And to all of the others brilliant individuals in Dr. Zhang’s lab whose efforts contributed to my Zhang’s lab whose efforts contributed to my learning experience.learning experience.

References and References and AcknowledgementsAcknowledgements

Literature (the primary source for my Literature (the primary source for my research project and background research project and background information presented in this presentation):information presented in this presentation): Guo Li, Karen Watson, Robert W. Buckheit, Guo Li, Karen Watson, Robert W. Buckheit,

and Yan Zhang: Total Synthesis of and Yan Zhang: Total Synthesis of Anibamine, a Novel Natural Product as a Anibamine, a Novel Natural Product as a Chemokine Receptor CCR5 Antagonist Chemokine Receptor CCR5 Antagonist Organic LettersOrganic Letters 2007. Vol 9. 10: 2043-2046. 2007. Vol 9. 10: 2043-2046.

References and References and AcknowledgementsAcknowledgements

Pictures and Graphics:Pictures and Graphics: Title Slide: Erlenmeyer Flasks –Title Slide: Erlenmeyer Flasks –

Department of Chemistry & BiochemistryDepartment of Chemistry & BiochemistryNorthern Arizona UniversityNorthern Arizona University

www.nau.edu/~chem/Images/flasks.jpgwww.nau.edu/~chem/Images/flasks.jpg

Slide 10: Reflux Apparatus and White Compound in Erlenmeyer Flask –Slide 10: Reflux Apparatus and White Compound in Erlenmeyer Flask –

Barnard College Organic Chemistry Lab Barnard College Organic Chemistry Lab

http://www.barnard.edu/chem/orgolab/lab2.htmhttp://www.barnard.edu/chem/orgolab/lab2.htm