Synthetic, Mechanistic and Theoretical Studies Related to the Kinamycin Antibiotics

525 Pages·2011·7.09 MB·English

by  Glenn Lee Abbott

Synthetic, Mechanistic and Theoretical
Studies Related to the Kinamycin
Antibiotics

by

Glenn Lee Abbott

A thesis
presented to the University of Waterloo
in fulfillment of the
thesis requirement for the degree of
Doctor of Philosophy
in
Chemistry

Waterloo, Ontario, Canada, 2011

©Glenn Lee Abbott 2011
AUTHOR'S DECLARATION
I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any
required final revisions, as accepted by my examiners.
I understand that my thesis may be made electronically available to the public.

Glenn Lee Abbott
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Abstract
The synthesis of an isosteric-isoelectronic analogue of prekinamycin, an N-
cyanobenzo[b]carbazoloquinone 2.1, is described. The key steps include a Vilsmeier-Haack
formylation, a regioselective bromination, a Buchwald-Hartwig cross-coupling, a palladium
mediated oxidative cyclization and N-cyanation to furnish the target in fifteen steps in an
overall yield of 1.6%. Subsequent bioactivity studies were conducted in which the
cytotoxicity of various compounds on K562 cells, a human erythroleukemic cell line,
revealed that the analogue had a similar bioactivity profile to prekinamycin. These results
suggest that the diazo functionality may not be an absolute requirement for bioactivity.
A study of the reactivity of nitric oxide with diphenyldiazomethane, kinamycin A and
isoprekinamycin diacetate was undertaken. Three products were isolated from the reaction
with diphenyldiazomethane: a nitrimine 3.7, benzophenone and, for the first time,
dinitrodiphenylmethane 3.9. The source of the two nitrogens in the nitrimine and
dinitrodiphenylmethane was elucidated through isotopic labeling experiments with 15N-
labeled diphenyldiazomethane. Results suggest that two separate 1,3-dipolar cycloadditions
generating two different 5-membered intermediates via two separate [3+2] cycloadditions,
furnishing the nitrimine and benzophenone, are occurring. Subsequent theoretical studies
reveal that the [3+2] cycloadditions are in accord with experimental results. Further
calculations show that the proposed intermediates and transition state structures are in good
agreement with the product distribution and isotopic labeling studies. The kinamycins were
found to be unresponsive to NO exposure in which theoretical calculations reveal that the
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free energy of activation for the 1,3 dipolar cycloadditions is significantly higher for the
natural products than for diphenyldiazomethane.
A comprehensive theoretical study on the chemistry of the N-acetyl indole-2,3-
quinodimethanes (N-Ac IQDM 5.1) at the DFT B3LYP 6-31 G(d) level is described.
Investigation of amide conformations of N-Ac IQDM in which good agreement between
experimental and theoretical results is shown. Subsequent studies addressing regioselectivity
and stereoselectivity of Diels-Alder (DA) reactions are described. FMO theory does not
provide a rationalization for the regioselectivity observed in DA reactions of N-Ac IQDM.
Transition state calculations were carried out to probe the regioselectivity of DA reactions of
this system. For acrolein, Δ‡G was found not to be predictive of regiochemistry as observed
experimentally. However, the calculated barriers, Δ‡E and Δ‡H, are in qualitative agreement
with experimental trends in which the major regioisomer is predicted to be C-2 DA adduct.
Methacrolein and crotonaldehyde were also examined. On comparison to acrolein, Δ‡G
predicts that both α-substitution (i.e. methacrolein) and β-substitution (i.e. crotonaldehyde)
increases regioselectivity for the C-2 regioisomer. Furthermore, the Δ‡E and Δ‡H data sets
for methacrolein predicts increased regioselectivity for the C-2 adduct; the Δ‡E and Δ‡H data
sets for crotonaldehyde predicts decreased C-2 regioselectivity.
Efforts towards the synthesis of tetrahydrofluorenes via DA reactions of ethyl 2,3-
dimethylene-2,3-dihydro-1H-indene-1-carboxylate (6.20) and diethyl 2,3-dimethylene-2,3-
dihydro-1H-indene-1,1-dicarboxylate (6.36) are described and were generated from the
corresponding ethyl 2-(2-(1-acetoxybuta-2,3-dien-2-yl)phenyl)acetate (6.18) and the diethyl
2-(2-(1-acetoxybuta-2,3-dien-2-yl)phenyl)malonate (6.35), respectively. Employing various
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solvents and bases, the carboxylate 6.20 failed to provide the desired DA adduct with methyl
acrylate. The malonate 6.35 was synthesized by carboxyalkylation followed by a Stille cross
coupling reaction. DA reactions with methyl acrylate were carried out in which evidence of a
DA adduct was observed in the 1H NMR spectrum but attempts of its purification proved
futile. DA reactions with N-phenylmaleimide provided the corresponding DA adduct in 77%
yield. Quantum chemical calculations reveal that the two dienes 6.20 and 6.36 have termini
that are significantly different and would suggest that FMO interactions would be a
determining factor in the regioselectivity of Diels-Alder cycloadditions. In the case of
acrolein, inspection of the MO coefficients predicts that the C-2 cycloadducts would be the
major regioisomer. TS calculations agree with the qualitative interpretation that FMO
arguments provide.

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Acknowledgements
My gratitude goes to my adviser, Dr. Gary I. Dmitrienko, who provided myself with a great
opportunity to conduct research studies in his laboratory. From the very beginning, Gary
gave me carte blanche on my projects and allowed me to flesh out my own ideas. I couldn't
begin to imagine all that I have learned through my research projects. What I have realized is
I have learned much about organic synthesis, medicinal chemistry, biochemistry, physical
organic chemistry and theoretical/computational chemistry.
I thank my committee members, Dr. William Tam, Dr. Eric Fillion, and Dr. J. Michael
Chong for their help and constructive advice throughout the course of my research.
Past and present members of the Dmitrienko lab are acknowledged for their help and
discussions about chemistry. Mr. Darryl Evanoff, Dr. Muhong Shang, Dr. Oedayo Adidayo,
Dr. Nan Chen, Dr. Anthony Krismanich, Dr. Ahmad Ghavami, Mr. Timothy Rasmusson, Mr.
Timothy Ramadhar, Mrs. Miriam Heynen, Mrs. Valerie Goodfellow, Dr. Laura Marrone, Dr.
Thammaiah Viswanatha and Mr. Taras Rybak. In particular, a special acknowledgement goes
towards Dr. Nan Chen and Dr. Ahmad Ghavami. I have known Nan or "Coke" since my
early days at Waterloo and he has never ceased to entertain me. Nan is quite unconventional,
especially the manner in which he has demonstrated his use of the English language. His
innate ability to coin phrases from the far reaches of the English lexicon will remain a
mystery to me. There is not a soul on this planet that has described beer as "portable
AC"...what a lovely thought. Nan and I share a love of wine as well and this has fuelled
many conversations. In February 2007, Dr. Ahmad Ghavami came to us as a postdoctoral
fellow and immediately the lab became a better place to work. Ahmad's enthusiasm and love
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for life are beyond words. There is not a kinder, more sincere and genuine person on this
earth. An office mate for the last three years, my life has been enriched tremendously of
which I'm lost for words to describe. A friend whose friendship has been unwavering.
Together, Nan, Ahmad and I have had many dinners and BBQ's over the years. Our
discussions on topics not just of chemistry but of art, music, literature, religion, cooking and
cuisine, culture and pop culture...the list is never ending. It is these things that bind us. Their
cultural influences on various topics were evident and refreshing and have given me insight
and perspective that I would of otherwise never acquired. These experiences have provided
an informal education far beyond what any text book could offer. Taras, an undergraduate
student who worked on the naphthoquinone project, gave me everything he had and more.
Taras' work ethic was outstanding and by the end of that year, I believe he taught me more
about chemistry then I taught him. I wish him well. The girls down the hall, Val and Laura,
are another part of the family for which the lab could not be functional. Laura's baking and
other delights she has brought to the office have been great. Val was one of the very first
people I met at UW and she has also entertained us with BBQs at her place in the summer.
During the course of my research, it is with great sadness that Dr. Thammaiah Viswanatha
or "TV" as we affectionately called him, left us. TV was on my PhD oral comprehensive
committee. I will never forget his reaction to my answers. With his head bowed, he listened
to me intensely and nodded at each answer I made about enzyme kinetics and particularly,
my derivation of the Michaelis-Menton equation. He left with me some very powerful words
which I will never forget. He told me not to be discouraged if one has read something several
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times before you understand it. And then he said to me the most poetic words "...Repetition is
the mother of learning..." Indeed, this has always been a metaphor for my life. Thank you.
Dr Nicholas Taylor, the departments X-ray crystallographer, left us as well. Nick procured
the very first single crystal X-ray structure for me, that of the nitrimine, presented in this
thesis. I remember with great fondness, discussions with him about his art at his favorite
smoking post. In a moment of intellectual discourse, he and I returned to his office, to
retrieve a rather old book on the subject and upon returning to his post, he communicated to
me various aspects of his art. His passion was evident and profound.
As well I acknowledge the help and support of many of the support staff within the
department and include the following. From Chemistry Stores; Ms. Lena Zepf, Ms. Maya
Bernier, Mrs. Suhair Ammouri, Mrs. Slavica Bogdanovic, Mr. Ken Gosselink, Mr. Matt
Sternbauer and Mr. Luke Bott. From the Chemistry office, Mrs. Cathy van Esch. Cathy has
always been a tremendous help throughout my years at UW. Technical staff including Mrs.
Janet Venne, Mr. Mike Ditty, Dr. Jalil Assoud and Dr. Richard W. Smith are acknowledged.
Jan, Mike, Jalil and Richard always gave me their best on solving my problems. Their
professionalism cannot be overstated.
Dr. Leonardo and Mrs. Josephine Simon have extended their hospitality to me through the
many dinners and BBQ's at their place and is acknowledged here. Thanks to Mr. Ryan
Bonfield who has gifted me with fine scotch and cigars...Montreal here I come...full house:
aces over kings!
My world outside the chemistry department could largely be affiliated with the Graduate
House on campus. The "Grad House" has become a second home to me. Who to thank and
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acknowledge? Staff, coworkers and patrons many of which became good friends all too
numerous to mention. Special mention goes to Rose Vogt. Rose, a tireless, enthusiastic,
professional and engaging individual...(need I say more?) whose name and face is
synonymous with the GH. Rose's dedication and passion for the GH is evident and I share
that passion with her. We have shared dialogue through the years over many topics and she
has become a great friend grown out of our mutual respect and admiration for one another.
My promotion to a supervisory role this past fall (September 2010) would seem to be the
high point for my years of service at the GH. Thank you Rose! As well, my passion for
athletics soon found me on the soccer team (GHFC) and before I knew it, I was running the
practices and training hard. Reluctant to accept titles, my teammates soon cast the title of
coach upon me. But if their declaration is an acknowledgement for my enthusiasm, passion
and dedication, than I am a willing acceptor. This past fall (November 2010), for the first
time, the GHFC won the intermediate level of the intramural soccer league on campus and
finally, one my dreams came to fruition...champions! Some of my best friends come from the
football team. Miroslav Koprnicky, Elodie Fourquet, Jeff Dicker, Matt Houlahan, Ryan Sim,
Eric Camm, Vlad Ciubo, Jamil Absoula, Jay Murray and Patrick Roh. Thanks to Miro, Jay,
Lori and Pat for the lodging when I needed it most. Jeff has furnished me many a cigar, fine
beers and scotch...thanks. Special thanks to Miro and Elodie...you have become two of my
best friends. We are three explorers on a discovery mission about life. I will not forget our
road trip to Boston (April 2010) to see Jeff and it is nice to see that we have already made a
quick few road trips to London to see him again. Rock n' roll babies.....let the good times
roll...Go GHFC!!!
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Dedication

For my family.

For my mother and father whose endless love and support came by unspoken words.

For my grandmother whose words provided the inspiration.

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