Joshua J. Nyman
Howard Hughes Medical Institute Summer Scholar Research Project
Lessons Learned from Organic
Synthesis
Mentor: Dr. Yan Zhang, Department of Medicinal Chemistry,
VCU School of Pharmacy
Background
 Anibamine is a natural product, but
recently it has been successfully
synthesized in the laboratory.
 Anibamine can be used as an anti-HIV
drug
 It has a unique chemical structure.
N
+
TFA
_
Anibamine
The Research Project
 The objective of the research project was
to synthesize the ring system of
anibamine; and then to alter the
stereochemistry of its side-chains.
N
+
TFA
_
Anibamine
My Synthesis Route
CH3
O
O
CN
K2CO3
acetylacetone
H3C
N
OH
3-cyano-4,6-dimethyl-2-hydroxypyridine
(2-hydroxy-4,6-dimethyl-nicotinonitrile)
+
O
O
CN
H2N
cyanoacetamide
N Br
, TFA, H2SO4
O
CH3
CN
Br
CuCN, DMF
CH3
CN
NC
H3C
N
under nitrogen gas
H3C
N
OH
5-bromo-2-hydroxy-4,6-dimethyl-nicotinonitrile
OH
1,2-dihydro-4,6-dimethyl-2-oxopyridine-3,5-dicarbonitrile
Tetrabutylammonium
bromide,
P2O5
CH3
CN
NC
H3C
N
Br
2-bromo-4,6-dimethylpyridine-3,5-dicarbonitrile
Forming the Pyridine Ring
O
O
O
H2N
acetylacetone
CH3
CN
cyanoacetamide
CN
K2CO3
H3C
N
OH
3-cyano-4,6-dimethyl-2-hydroxypyridine
 An aqueous solution of potassium carbonate
was prepared.
 Acetylacetone and cyanoacetamide were
added to the solution.
 A stir bar was placed into the resulting
mixture and the mixture was allowed to stir at
room temperature for 24 hours.
Forming the Pyridine Ring
 After 24 hours of stirring, the mixture was vacuum filtrated, yielding a
white powder.
 Melting point was on the high end of the literature melting point, and
the thin-layer chromatography provided a positive presumptive test
for the pyridine ring product.
 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
dissolve the sample.
Images: Barnard College Organic Chemistry Lab
Brominating the Pyridine Ring
O
CH3
CN
N Br
O
H3C
N
OH
, TFA, H2SO4
CH3
CN
Br
H3C
N
OH
 The product of the previous reaction was dissolved in concentrated
sulfuric acid and trifluoracetic acid, while in an ice bath. Nbromosuccinimide was then added. **
 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
a couple of cases.
 Thin-layer chromatography suggested some compounds were impure.
 Product appeared to be a light yellow in the more impure products and
white in the purer products.
Brominating the Pyridine Ring
O
CH3
CN
N Br
O
H3C
N
OH
, TFA, H2SO4
CH3
CN
Br
H3C
N
OH
 It seems the purity of this reaction could have
been affected by certain techniques.
 For example:
 Removing the reaction mixture from the ice bath: Exothermic
reaction
 Rate of addition: Adding the NBS too quickly likely resulted in
an undesired side reaction.
 Acid-Base reaction.
Adding a Cyano- Group to the Pyridine
Ring
CH3
CN
Br
H3C
CH3
N
OH
CuCN, DMF
CN
NC
under nitrogen gas
H3C
N
OH
 This reaction had some special considerations:
 One of the chemicals used in this reaction is a highly
toxic compound called cuprous cyanide (a.k.a. copper (I)
cyanide).
 Handling the cyanide required great care
Adding a Cyano- Group to the Pyridine Ring
Oil Pump
 All reactants had to be very dry!!!
Adding a Cyano- Group to the
Pyridine Ring
CH3
CN
Br
H3C
CH3
N
OH
CuCN, DMF
CN
NC
under nitrogen gas
H3C
N
OH
 The cuprous cyanide was dissolved in
dimethylformamide along with the product
from the previous reaction.
 The mixture was then refluxed for 48
hours under nitrogen gas.
Adding a Cyano- Group to the Pyridine Ring
 My compound being refluxed under
nitrogen protection
Adding a Cyano- Group to the
Pyridine Ring
CH3
CN
Br
H3C
CH3
N
OH
CuCN, DMF
CN
NC
under nitrogen gas
H3C
N
OH
 This reaction gave me multiple problems
 Proton NMR, Thin-Layer Chromatograhy
tests, and melting point tests = impure.
 Because of this, I wasn’t able to proceed
further before the end of this program.
Lessons Learned
 Organic synthesis can be very tricky, especially
when trying to form natural products.
 I learned not only to think about the products I
am trying to synthesize, but also about which
products I do not want to synthesize (i.e.
impurities) and how to prevent them.
 It’s not just what chemicals you add, but how
you add them. Temperature, rate of addition, and
other factors can have a considerable impact on
the overall synthesis.
References and
Acknowledgements
 A special thanks to Dr. Yan Zhang (my mentor)
for sharing his expertise, his laboratory, and for
making this an exceptional research learning
experience.
 Also a special thanks to Dr. Guo Li and Kendra
Haney, for generously sharing their time and for
their guidance.
 And to all of the others brilliant individuals in Dr.
Zhang’s lab whose efforts contributed to my
learning experience.
References and
Acknowledgements
 Literature (the primary source for my
research project and background
information presented in this presentation):
 Guo Li, Karen Watson, Robert W. Buckheit,
and Yan Zhang: Total Synthesis of Anibamine,
a Novel Natural Product as a Chemokine
Receptor CCR5 Antagonist Organic Letters
2007. Vol 9. 10: 2043-2046.
References and
Acknowledgements
 Pictures and Graphics:
 Title Slide: Erlenmeyer Flasks –
 Department of Chemistry & Biochemistry
Northern Arizona University
www.nau.edu/~chem/Images/flasks.jpg
 Slide 10: Reflux Apparatus and White Compound in Erlenmeyer Flask –
 Barnard College Organic Chemistry Lab
http://www.barnard.edu/chem/orgolab/lab2.htm