ChemSemBlog

Wendell P. Griffith, an analytical chemist, presented his findings and analysis on mass spectrometry of proteins.  Mass spectrometry??? Yes, mass spectrometry. I mean, what chemist or chemistry student hasn’t heard of mass spectrometry, or already know what it is, as well as its applications.  Surprisingly, mass spec can be applied and used to analyze a lot of biochemically composed structures.  I did not realize this until Griffith came to make a presentation on using mass spectrometry to analyze proteins.

His presentation was very interesting.  It left me wondering if he has presented at a Christian private university before, especially since he came to us as a professor from a public school – University of Toledo.  I mean, his work and research was quite understandable and easy to follow, but his choice of words and examples startled us a little and might have actually distracted us somewhat.  However, regardless, I still believe the students and teachers in the audience gained some knowledge on how mass spec is used to further understanding of the structure and function of proteins. Griffith is currently using an electrospray ionization mass spectrometry (ESI-MS) to study the structural information of the proteins and their macromolecular interactions.

Some things that I found very interesting from the seminar were Griffith’s studies in hemoglobin and their interactions.  He is especially interested in the structure of heptoglobin and how it interacts with hemoglobin and other biomolecules.  This portion of the lecture captured my attention because hemoglobin is an essential part of human biology, so I specifically wanted to know why these biomolecules interested him so much.  Griffith explained that he was concerned about haptoglobin because it is a binding protein, all higher organisms have it, and now bacteria are evolving with receptors for haptoglobin and hemoglobin complexes.  I wish a lot of success to Griffith and that some time in the near future he will be able to come back and inform us of his progress in his studies. I am very thankful for Griffith’s seminar which highlighted the importance of mass spectrometry in the field of  chemical and biochemical analysis.

Post This To My

Hide Sites

This Thursday, Wendell Griffith, an assistant professor of Chemistry at the University of Toledo, made a presentation about mass spectrometry (MS) and hemoglobin. His presentation was very interesting because during biochemistry class I recently learned about proteins, specifically hemoglobin.  So this presentation increased my understanding of hemoglobin and hemoglobin-binding proteins.

In addition to the subject about hemoglobin and hemoglobin-binding proteins, I learned a lot of information about mass spectrometry as well as his recent research project. He said he usually uses mass spectrometry as an alternative analytical tool rather than NMR and X-Ray crystallography.  MS provides mass information based on m/z ratio by vaporizing analytes, ionizing them, and generating charged molecules or molecule fragments. Especially, an electrospray ionization mass spectrometry (ESI-MS) gives wonderful protein images such as structural information of proteins and their macromolecular interactions. It was very interesting that a denatured protein has a larger range of charge distribution in ESI-MS than a normal protein.

Another thing that I would like to learn more about is the hemoglobin assembly/dissociation pathway. Hemoglobin consists of two alpha and two beta globins and four hemo. Beta globin chins are very flexible for the efficient accommodation to alpha chains. When hemoglobins are made, a form of an alpha globin combining with hemo and a beta globin without binding hemo works as an important intermediate in the hemoglobin assembly/dissociation pathway.  On the other hand, there is a new concept that I couldn’t understand very well. I wondered what haptoglobin is and why haptoglobin-hemoglobin binding protein is important.

For my ‘non-science’ friend this presentation was about mass spectrometry, which is a great analytical technique generally used for determination of the composition of organic compounds, but it can also give us a deeper understanding of protein structure and function.

Post This To My

Hide Sites

The topic in ChemSem this week was Total Synthesis from Silas Cook of Indiana University. Specifically he discussed his five year project regarding 11-O-Debenzointashironin which was a recently isolated natural product that has been shown to increase the health of neurons. Ideally speaking, this drug could aid in the fight against Alzheimer’s disease if successfully synthesized. Though much of the presentation followed this specific synthesis, the overall goal of the seminar was to educate on the purposes and possibilities total synthesis laboratories offer. Beyond the fact that they give unparalleled opportunities for experimentation and procedural skill development, they are also useful in terms of the products they produce. Though many syntheses fail, the overall potential leads to the broadening of Chemistry as a science and the discovery of reagents that could be useful in the medical fields.

Cook did an excellent job of laying the ground work for his seminar with his discussion of the purpose and methodology of total synthesis. Among the things I learned was a host of material regarding various reactions. The presentation went very quickly and it was difficult to absorb much of the information he discussed, but the overview was well received.

Some facts about total synthesis I did find interesting. For instance, most laboratory chemists working for pharmaceutical companies (likely greater than 90%) come from total synthesis graduate programs. Total synthesis, at least at Indiana University, focuses on neurological diseases, third world diseases, and other unknown synthetic procedures that potentially could improve the quality of life for people around the world. Finally, the total synthesis presentation highlighted how much of an introduction to organic chemistry the undergraduate course really is.

Overall Cook did a great job presenting his work. It was interesting and well received. It is certain from the lecture that to become a total synthesis chemist, one must have large amounts of patience and a good level of divergent thinking capable of continually finding detour routes around that which theoretically should work, but for some reason does not.

Post This To My

Hide Sites

Today’s guest speaker for chemistry seminar was Wendell P. Griffith. He earned a doctor’s degree in Analytical Chemistry at the University of Massachusetts.  Also, he conducted research at John Hopkins University School of Medicine.

His presentation title was “Breathing New Life into Old Protein.”   The main theme was a story of hemoglobin and hemoglobin binding protein. Before presenting about hemoglobin and its binding protein, he explained about Mass Spectrometry, or MS, which is used to analyze and determine the composition of molecules. It is a good instrument for efficient separation and high resolution.  The neutral molecule has to be converted to an ion to be analyzed and for its mass to be determined. After that, he talked about the application of MS to protein structure and dynamics, hemoglobin assembly and dissociation, heptoglobin, and band3.

I also learned that Dalton John is called the  father of atomic theory. He published the first atomic weight table, and did research on colour blindness, which  is also called Daltonism.  In addition, α helix chain of hemoglobin is made from number 16 chromosome, while β sheet chain of it is made from number 11 chromosome of DNA. Therefore, α globin and β globin have different roles in hemoglobin assembly.  α-Globin plays an important role as a rigid template when they are assembled into hemoglobin.  On the other hand, β globin is flexible enough to efficiently form the hemoglobin tetramer.

The presentation was interesting to me because it dealt with biochemistry.  As a biochemistry major, it was a good chance to learn the connection between our body system and chemistry. When we assemble new furniture and use it, we need to read the description to know how each part functions.   Similarly, to use our body better, we need to study, analyze and understand more knowledge about our body.  So, this seminar allowed me to understand more about hemoglobin.

Post This To My

Hide Sites

Just what in the world is total synthesis?

After listening to Professor Silas Cook, I think that I now have a better understanding of this area of organic chemistry, though I do admit I had to do a little Wikipedia search to fully comprehend what he was saying regarding total synthesis and methodology. Part of what confused me initially was the terminology he used. “Total synthesis” as well as “methodology” just sounded kind of ambiguous to me.  I mean I thought all organic synthesis was the same, right? You have the reaction and reagents that ultimately form a product. Well, apparently their are two main research areas in organic synthesis called total synthesis and methodology. As Wikipedia puts it, the former deals with “…complete chemical synthesis of complex organic molecules from simple, commercially available  or natural precursors”, while the latter focuses on getting good yield and pure product usually using reactions from the literature with less emphasis on “trying to reinvent the wheel”.

From his lecture I was able to gather that the goals of his total synthesis research was to synthesize needed molecules and demonstrate the limitations of current methods. He was able to illustrate very well the trials and hurdles associated with synthesizing these relatively complex molecules using commercially available precursors using total synthesis. He was so effective in fact that he could seemingly go on and on for hours about the complications that arose when making 11-o-debenzoyltashironin. After all, it did take 5 years and thousands of dollars to end up where they are now in the clinical trial phase. After viewing several slides of reactions, I found that I didn’t even remember what 11-o-debenzoyltashironin actually does. I could only remember the long epic journey of backtracking and climbing over mountains to find this novel way of synthesizing it.

Ok, so total synthesis is really complicated, what good can it bring us other than confusion and headache? Professor Cook was able to illustrate very well how the interests of his research team were a fitting match for total synthesis. He listed oncology, antibiotics, neurological disorders, and Third World ailments as primary choices of interest and gave justifications on how total synthesis can impact those areas for the greater good. He additionally reasoned that with organic synthesis the sky’s the limit on the areas of research you can do. I was able to learn a great deal from this lecture and found it quite interesting. I would advise my non-science friends that this presentation was about finding new and innovative ways to make complex, useful molecules.

Post This To My

Hide Sites

This week’s seminar was on Breathing New Life into Old Proteins: A Story of Hemoglobin and Hemoglobin-Binding Proteins.  The presenter was Wendell Peter Griffith, an analytical chemist.  He is an assistant professor for the chemistry department and the University of Toledo.  He got his bachelor’s degree from Grambling State University and then he completed a PhD in Analytical Chemistry at the University of Massachusetts.  He did some postdoctoral research at John Hopkins University School of Medicine.  The presentation was interesting and easy to follow.

In this seminar I learned about the mass analyzer, time of flight, where the smaller molecules moves faster than the larger ones and get to the detector first.  Another thing is that the parts of hemoglobin are made at different chromosomes.  And that haptoglobin binds free hemoglobin and takes it to the liver to be removed from the body.

The other students seemed to be pretty attentive during the seminar, though it was a little long and some seemed to be losing concentration towards the end.  The question and answer period was not very long since we were out of time.

The presentation definitely encouraged me to learn more about the subject.  I don’t think that this would be something that I would want to study in graduate school, but I would like to learn more about it.

I think the reason the seminar was interesting was because it was on a subject that has a lot to do with the medical field.

If I were to describe this seminar in one sentence it would be, “mass spectroscopy can be used to study the unstable configurations of proteins.”

Post This To My

Hide Sites

Silas P. Cook is a very fascinating young professor in the Chemistry Department of Indiana University, who has been interested in all types of chemistry since he started pursuing his undergrad at Reed College in Portland, Oregon.  Since those days, he has already accomplished a lot more than expected of a young fellow, and has published three papers along with Samuel J. Danishefsky.  With Danishefsky, Cook studied the total synthesis of 11-O-Debenzoyltashironin.  Cook’s experiences with Danishefsky sparked Cook’s love for total synthesis and its useful applications.  Now, Cook loves being a synthetic organic chemist and developing fancy new procedures and methods for synthesizing molecules and compounds.

Cook’s presentation was far from simple, but still very understandable.  He attempted to explain his work on the 11-O-Debenzoyltashironin in as simple of a way as possible.  However, at about two thirds through the synthesis of the compound I became a little lost.  Usually when I get lost during a process I find no need in paying attention to the rest of the lecture, however, Cook’s enthusiasm level (not to mention the prizes he was giving away) locked in my attention from beginning to end.  From his seminar, he has really convinced me that total synthesis is a very needed and fascinating field of research.  Honestly, maybe it was mostly the prizes he was giving away to students for correct answers that held my attention the most, but regardless, of whether it was the gifts or not, Cook definitely gave Andrews University an attention grabbing look into his studies with Danishefsky.

From my understanding of the seminar, total synthesis studies look at natural structures (in tiny amounts) with biological activity and tries to recreate them.  Total synthesis also practices methodology, which studies new conditions for synthesizing.  When you combining total synthesis with methodology you produce a study that strives to design new strategies and develop understanding.  Cook also stressed that total synthesis also trains a lot of outstanding chemists.

Therapeutically, Cook is interested in contributing to advances in oncology, antibiotics, neurological disorders, and Third World ailments such as malaria and chagas.  Currently, he is studying Artemisinin, which is an herbal treatment for parasitic infections and malaria that also protects against certain types of cancer.   The treatment that uses Artemisinin is called ATC treatment.  Cook hopes that his research will help develop a shorter, more efficient way of synthesizing and improving ATC treatment.

Lately I have been very interested in drug synthesis, especially drug hybrids.  So I asked Cook if he has looked into combining different drugs that help treat malaria to create a more potent and effective drug.   He replied that he is very interested in traveling that path to improve treatments against malaria, but currently he is still working on a more efficient method for synthesizing the compounds needed for malaria treatment.

Post This To My

Hide Sites

In the beginning of his seminar, Silas Cook made clear his intentions: explain what synthetic chemistry is, how awesome it is, and not to worry about all the chemistry that would be flying over our heads. And indeed, many of the reactions and reagents included in his slides were foreign to our ears. His slides weren’t explanatory, nor were they entertaining or mind-engaging. It was beyond our organic chemistry textbook and sky high above our knowledge. SO HOW DID I GET THROUGH THIS SEMINAR?

Again, the enthusiasm and energy of the speaker keeps you interested! When those all too hauntingly familiar organic chemistry reactions like “electrophilic aromatic substitution” and “diels-alder” began popping up, the speaker called me out for my petulant nodding! They are important; don’t wave it off just yet! Plus, if you answer his question right, he gave you the limited Indiana University water bottle, another of his interest-catching methods.

Paying closer attention (not enough to quickly process the water bottle prize spinning towards my direction), I sincerely believe that synthetic chemistry is pretty dang awesome. Some of its attractiveness that Cook pointed out was its wide range, the flexibility and control, and the significant impact it has and can have for improving life. From anti-cancer drugs to fuel cell membranes, whether making it better, cheaper, more efficient or something completely new, synthetic chemistry deals with a wide range of fields and their research mainly aims to benefit the human race. Combining the fundamentals with new strategies, synthetic chemists can be likened to the best martial artists.

If I learned anything today, it is synthetic chemists are the Bear Grylls among science researchers. What organic chemistry students did in Independent Research Projects under Dr. Desmond Murray, these guys do a hundred times more intense. Most of us in IRP found our results undesirable, so we moaned and groaned to each other and Dr. Murray all semester long. How measly we are compared to these synthetic organic chemists! Putting in a minimum of four hours a week, for one semester (spring semester, at that), how are we to expect amazing results? Silas Cook worked on synthesizing 11-o-debenzoyltashironin for five years. This man obviously knows his organic chemistry, he’s no neophyte like us, and he still ran into problems. However, he overcame these obstacles, using the resources around him, no matter how many syntheses he ran without success. He even liked some of the botched results; he knows when something in organic chemistry is novel and interesting.

I could have asked loads of questions, but since most of them mainly have the format of “What is [insert reagent/reaction]” I thought it better to not waste everyone’s time, especially considering we had gone over the scheduled seminar time again. The only worthwhile question I had to ask was why is he not a full-time researcher, why is he teaching? For chemistry-related questions: well, as I said before, most of the chemistry was over my head.

Laymen’s Summary of Chemistry Seminar: Synthetic chemistry involves knowing how to make the desired product (limitless molecules to choose from), actually making it after countless trials-and-errors, patience, persistence, and a bit of awesomeness.

P.S. – Along with the water bottles, there were other IU goodies, such as highlighters, pens, and, my favorite, a periodic table card.

P.P.S. – If I could punch a hole through the card to fit on my key chain would it be nerdy? Maybe. Would it also be totally awesome? Most definitely!

Post This To My

Hide Sites

Our seminar presentation today was given by Dr. Silas Cook on “The Evolution of a Synthesis: 11-0-Debenzoyltashironin”. Dr. Cook works at Indiana University, and he made sure we would remember by bringing us much paraphernalia and information about IU.

He started his talk with defining and giving examples of what synthetic organic chemistry is, and what his area of work has led to. He talked about the advantages of being a synthetic organic chemist, and what total synthesis is. I learned that the goals of total synthesis are to synthesize much needed molecules, to demonstrate the limits of current methods, to highlight new methods in a complex setting, and to train outstanding synthetic chemists.

The presentation was very interesting, Dr. Cook was very personable and the seminar was very interactive. It was easy to pay attention and understand what was going on. Though I did feel like it was a presentation on Indiana University at some points, with him telling us why it would be good to do our graduate research there and become synthetic organic chemists. His information was very interesting, dealing a lot  with synthesizing naturally based molecules and pharmaceuticals.

He talked some of artemisinin, the best malaria medication on the market, and the problems with it as far as countries that really need it. The main focus of the presentation was on 11-0-debenzoyltashironin, which is being produced for testing in neurological diseases. He talked about the many problems in trying to cheaply synthesize this compound, and he was very honest with how much work goes into it with a lot of dead ends. To put it simply, this talk was about studies done with a chemical that will hopefully one day be used as a medication for Alzheimer’s and other neurological diseases.

Post This To My

Hide Sites

Today’s presentation was done by Silas Cook from Indiana University.  His presentation was on the process of synthesizing 11-o-Debenzoyltashironin.  Due to time constraints, Cook was unable to discuss all of the chemistry involved.  However, he was able to give plenty of insights into the life of a synthetic chemist.  In organic synthesis, the two main components are total synthesis and methodology.  Total synthesis is making a product found in nature and methodology is investigating ‘better’ more efficient reaction conditions.  Cook believes that in organic synthesis, these two components are intertwined.

He elaborated a bit more on total synthesis, saying that sixty three percent of pharmaceutical products were based on total synthesis.  The goals of total synthesis are to make molecules with potent biological functions, show limitations of current synthetic methods, highlight new synthetic methods, and train outstanding synthetic chemists.  Cook also discussed four therapeutic areas that he and other synthetic chemists are interested in.  They are oncology, antibiotics, neurological disorders, and Third World ailments.

The bulk of Cook’s presentation was his struggle to make 11-o-Debenzoyltashironin.  It has been shown to promote neural cell growth, but no one knows how yet.  It took Cook about 5 years to make the desired compound.  He accomplished his goal only by working backwards and redesigning his synthesis.  Ultimately, Cook’s redesigned synthesis produced a more efficient and successful result.  In the long run, 11-o-Debenzoyltashironin could be used to treat Alzheimer’s and Parkinson’s diseases.

How interesting this presentation was depends largely on what kind of chemist one is.  I was not really interested in the organic chemistry.  Cook didn’t go into a lot of detail, and there were far too many steps to remember.  Although I lost interest in the chemistry portion of the presentation, I was intrigued by the perseverance required of synthetic chemists.  I learned about some new organic reactions, such as the Baeyer-Villiger and the Still-Gennari reactions.  I also learned about the areas of interest for synthetic chemists and some of their problems.

Cook mentioned that intellectual property issues often arise with antibiotics.  A synthetic chemist not only needs to know chemistry, but also needs to know how to get around the trademark issues.  Finally, I learned that synthesis can take dozens of steps.  I asked Cook what was the greatest number of steps he had ever seen in a synthetic process.  His answer was about 200, and it wasn’t even a complete synthesis!  For me, the biggest points of interest in the presentation were not from the chemistry itself, but from the insights into how a synthetic chemist works.  If I had to sum up this presentation for a layperson, I would say it was about how a synthetic chemist goes about solving problems in order to make a desired product.

Post This To My

Hide Sites

On Thursday, September 24, 2009, Professor Silas Cook of Indiana University came to Andrews University and gave an amazing account of what takes place in creating an 11-O-Debenzoyltashironin molecule.  Professor Cook used a mixture of Total Synthesis and Methodology to create and develop this molecule.  Synthetic Organic Chemistry is specifically what Professor Cook uses and this is gives us the ability to make molecules that already exist naturally.

Professor Cook creates natural product molecules in his lab through a process of synthesis. He starts out with a very simple substance and design reaction sequences to obtain the desired target.  Professor Cook uses Methodology to develop new ways in which to get the same results but with a goal of getting the same product with less synthesis steps and with fewer dollars.  In the case of Debenzoyltashironin it took Professor Cook roughly twenty-three sythesis steps to obtain the desired product. It also took Professor Cook nearly 5 years to complete this project and get his product. There were many, many trials that he went through and obstacles that he had to get around but was able to finally get the results that he desired. And if I am not mistaken I believe Professor Cook mentioned that this particular product is being tested at this time to see if it can help with a strain of cancer.

Professor Cook was very knowledgeable about the topic he presented. Aside from the fact that I have not completed Organic Chemistry yet and was not able to pick up and understand everything that was being presented I found the speaker very informative and very interesting. He spoke very well and gave a lot of information about the different routes that he took to create this product. He did not just come in and show us the way that finally worked he came and showed us that in synthetic chemistry there are problems and snags that you can run into. He showed us various routes that he tried to take in order to get the desired results and why each result failed. I feel that even though I do not know a whole lot about the topic that I still learned a lot and was able to gleen information.

I was very impressed with how well he spoke and with the way that he was able to interact with the audience. He did not just talk at the audience but he also asked questions of the audience and interacted with the audience. He was a wonderful speaker and I would love to hear more about the background behind the synthesis processes that he has done. The presentation was the best so far this semester.

Post This To My

Hide Sites

This week’s seminar was on The Evolution of a Synthesis: 11-O-Debenzoyltashironin and the speaker was Silas Cook, an organic chemist.  He is currently an assistant professor at Indiana University.  He got his bachelor’s degree from Reed College in Portland.  He then took a job at Genomics Institute of Novartis Research Foundation in San Diego, CA.  He did his graduate studies in total synthesis at Columbia University in New York under Professor Samuel J. Danishefsky.  He did post-doctoral research with Professor Eric Jacobsen at Harvard University.  He was a very interesting speaker and was easy to follow.

One of the new things I learned in this seminar was that total synthesis is making molecules that nature already made.  I learned that Maoecrystal V is highly selective against cervical cancer.  And that neurotrophins bind to TRK receptors and promote cell growth.

The other students seemed to be pretty interested in the presentation.  The question and answer period went well, there were a lot of questions and the speaker was very knowledgeable and was able to answer all of the questions quite well.

The speaker encouraged me to learn more about the subject, though maybe from a biochemical aspect rather than a total synthesis aspect.  The speaker also was very encouraging about attending his school for graduate studies; he seemed very excited about Indiana University and made lots of comments on it.

The presentation was interesting because the speaker was excited about the topic and was very clear on the practical aspects of his topic.  If I had to summarize the seminar in one sentence it would be “The synthesis of 11-O-Debenzoyltashironin.”

Post This To My

Hide Sites

This week’s speaker was Silas Cook, a synthetic organic chemist, currently at Indiana University. He did undergraduate studies at Reed College in Portland, OR. While doing his studies he recognized the importance of organic chemistry in a wide range of disciplines from cell biology to nuclear chemistry. Cook’s research focuses on the synthesis of biologically relevant small molecules inspired by complex natural products. His work seeks to uncover new strategies in synthesis, catalysis, and molecular pharmacology.

Cook specializes in total synthesis, which deals with making molecules nature’s already made and methodology, which deals with figuring out new reaction conditions to develop new products. For example a + b= c, then you find out that a +b = d.

During the presentation, Cook made eye-contact with the audience, was very informative, and spoke in an understandable way. He would also ask questions and give out prizes which kept things interesting and people from falling asleep. The topic was very interesting and brought back memories of the mechanisms and reactions I learned in organic chemistry.

Some new things I learned were the goals of total synthesis: to synthesize much needed molecules, demonstrate the limitations of current methods, highlight new methods in a complex setting, and train outstanding synthetic chemists. There are also some therapeutic areas of interest: oncology, antibiotics, neurological disorders, and Third World ailments, meaning malaria, chagas, e.t.c.

Cook was once working on Artemisinin which is the best malaria treatment, which is now produced via semi-synthesis from plant materials. Then his group became interested in neurotrophic factors that are responsible for the growth, maintenance, and survival of neurons. It was thought that they may be a key in treating neurodegenerative diseases such as Alzheimer’s and Parkinsons. Nonpeptidyl small molecule neurotrophic factor mimetics have the potential of avoiding these pitfalls. While they still feature neurotrophic activity, they may also be orally bioavailable, blood-brain barrier permeable, and more specific in their target receptor activation. One such small molecule is 11-O-debenzoyltashironin. When working with this molecule, Cook went through various reaction sequences to find the one that gave the desired results.

The desired result was to succeed in isolating the 11-O-Debenzoyltashironin from the ester. He used many methods: Retrosynthetic Analysis, Phenol Synthesis, Alkene Diels-Alder, Aromatic transformation, and an enol ether approach. This whole process took about five years, showing that Cook was very dedicated and hardworking. This topic also made me wonder if there are any molecules that are closely related to 11-O-Debenzoyltashirionin or even artemisinin that performs close to same performance and has been found to have any effect on the diseases mentioned. Are there different conformations of this molecule that may give adverse effects?

During the question and answer period, Cook was able to answer the questions well, and many students enjoyed this presentation, and seemed to be interested in learning new things about the topic.

Post This To My

Hide Sites

This week’s seminar title was  “The Evolution of a Synthesis: 11-O-Debenzoyltashironin”.   The speaker was Silas Cook, an organic chemist.  He is currently an assistant professor of Chemistry at Indiana University.  Dr. Silas received his bachelor’s degree from Reed College located in Portland, Oregon.   He then later accepted a job position at Genomics Institute of Novartis Research Foundation in San Diego, CA.  After this he did graduate and postdoctoral studies at the renowned Columbia University in New York.

His current area of research specifically is in the area of Synthetic Organic Chemistry.  According to Dr. Silas, synthetic organic encompasses two major ideas: total synthesis and Methodology.  When these both are taken into consideration then one is able to formulate new strategies and develop fundamental understanding.  Some specific areas of interest to Cook that uses synthetic organic chemistry extensively are Oncology, Antibiotics, Neurological Disorders, and Third World Ailments such as Malaria.  As a result of these areas of research, medications has been discovered or developed.  For example Artemisinin (for malaria), Maoecrystal V (cervical cancer), and Englerin A (renal cancer).

Dr. Silas then went on to explain the structure of 11-O-debenzoyltashironin and the tedious process through which he synthesized this substance.  11-O-debenzoyltashironin is a tetracyclic sesquiterpene consisting of a (2,2,2)-bicyclic core, a cyclopentane ring, and a five-membered acetal. It has two tertiary methyl groups, one secondary methyl group, two hydroxyl groups, a ketone group, and six stereogenic bridgehead centers anchoring the faces together.

The synthesis of 11-O-debenzoyltashironin and its analogs depends on two major steps which are capable of generating all four rings at once: a Pelter-Tamura oxidative dearomatization involving the intramolecular trapping of a tethered, allylic alcohol, followed by a spontaneous Diels-Alder reaction. The key substrate, transformed from commercially available vanillyl alcohol, can be either a tetrasubstituted enol ether to yield all four rings or a terminal alkyne to yield the bicyclic core and cyclopentane ring. If only those three rings are formed, then the 5-membered acetal is closed afterwards.

As a side note, I personally found it humorous when Dr. Silas explained the great lengths he went to to synthesize 11-0-Debenzoyltashironin using a Diels-Alder reaction, sometimes to no avail.  This helped me to realize the immense patience it takes to be a synthetic chemist, expecially at the high level of difficulty of the reactions they work with.  After today’s seminar, I can say that I have truly gained a new respect for synthetic organic chemists and their research.

Post This To My

Hide Sites

Today’s guest speaker was Silas Cook who is one of the faculty members in the Chemistry Department of Indiana University.

His presentation title was “The Evolution of a Synthesis: 11-o-Debenzoyltashironin. This compound affects on TRK receptor and is used to treat Alzheimer’s disease.

At first, he told us the difference between total synthesis and methodology in synthetic organic chemistry, which I did not know before. Total synthesis focuses on natural products, structure determination, biological activity and pharmaceuticals. In methodology, scientists study new conditions and their effects on existing reactions and also synthesis of new products using same reagents. Therefore, number of steps, yield, control/selectivity, purification and cost are important things to consider in methodology. He used both ways, which give him new strategies and fundamental understanding.

Cook also spoke about and introduced us to some other drugs. of interest to him. For example, Artemisinin is used for treating malaria. He said that  it is cheap in  the U.S. but not in the Third World, where it is needed most. In addition, Maoecrystal V and Englerin A are used to treat cancer.

He mainly explained about the steps to synthesize 11-o-Debenzoyltashironin. I was impressed when I heard that the compound was made in 12 steps and in the steps, there were some reactions which I learned in Organic Chemistry class. Moreover, it is interesting that a new compound, made by synthetic organic chemistry, gives hope to people who have a tough time because of a chronic disease. I would tell my friends that we can make useful compounds which are able to treat fatal diseases by using various organic reactions.

Post This To My

Hide Sites

Chemistry Seminar on “The Evolution of a Synthesis” by Dr. Silas Cook, from Indiana University, was definitely a reminder of organic chemistry. Dr. Silas Cook did a wonderful job of explaining a topic that can normally be very confusing and dull. He was confident in his knowledge, entertaining and informative. Even though he was highly knowledgeable, Dr. Cook made the presentation relatable for university students.

In this seminar I learned that total synthesis is the process of reproducing molecules that nature has already made. This process has to be linked with synthetic methodology, the science of method and arrangement. Dr. Cook talked about his study of the synthesis of 11-O-Debenzoyltashironin. He described that neurotrophins are natural proteins found in the body that bind to TRK receptors and cause cell growth.

I appreciate that Dr. Cook took the time to describe his work to us including his failures in synthesizing his desired compound. I was reminded of the independent research projects we did in organic chemistry. In that class we were so flustered by one element of our product not turning out and having to devise a new plan. I can’t imagine the work and time it would take to do total synthesis and rearranging reactions and compounds multiple times to find your product. I appreciate the amount of patience and dedication this type of work takes.

In describing this seminar to friends and family I would say we discussed the process and challenges of creating new kinds of pharmaceutical drugs.

Post This To My

Hide Sites

The title of seminar held on September 24, 2009 was “The Evolution of Synthesis: 11-O-Debenzoyltashironin.” The speaker, Silas Cook was from the chemistry department of Indiana University. In his presentation, he focused on synthetic organic chemistry, especially total synthesis. Not only this, he also has researched on new strategies and methods in synthesis.

Total synthesis can be defined as making molecules that nature already has. This research can lead to treatments for cancer, malaria, Alzheimer and Parkinson, for example.  The goals of  total synthesis research are to synthesize much needed molecules, demonstrate the limitation of current methods, highlight new methods in a complex setting and train outstanding synthetic chemists.

In the seminar, Dr. Cook shared about his research on 11-O-Debenzolyltashironin by showing his work step by step.  There are a lot of steps involved such as retrosynthetic analysis, phenol synthesis, Allene Diels-Alder, Aromatic Transformation, and Enol Ether Approach.  However, he said that it encountered a lot of problems, with several steps not providing the product that he needed.  So,  he had to new methods to continue his research. For instance, in one step he had to change a methyl protecting group to a benzyl group.  This often meant starting over and having to do over a lot of synthetic steps.

This presentation was really interesting because Cook related some of his topic to our real life and it made me feel more comfortable. Some of them are sort of familiar that I have learned from organic chemistry class. Also, there are a lot of things that I did not know such as 63% of pharmaceutical products came from total synthesis. Products like Artemisinin, maoecrystal V and englenin A, used as treatment for malaria and cancer, are made through total synthesis.

As I was listening to the seminar, I had some questions: “was there any new or interesting compound found?”,  “is there any other compound for treating cancer or malaria?” and “how many people were involved in the synthesis and how long did it take ?”

Overall, I was very interested in the total synthesis and it was easy to understand. The speaker was really enthusiastic about his research. So, the total synthesis, which makes small molecules inspired from nature, is really connected to our life, because it helps us find treatment for specific diseases.

Post This To My

Hide Sites

The Evolution of Synthesis: 11-O-Debenzoyltashironin by Silas Cook

Our chemistry seminar speaker this week was Silas Cook, who is an assistant Professor of Chemistry Department at Indiana University.

Through his seminar, I now have new knowledge of Synthetic Organic Chemistry., which the speaker said is divided into total synthesis and methodology.  Dr. Cook’s research purpose is to discover new strategies in total synthesis, catalysis and study the molecular pharmacology of the compounds made.

I learned about the importance of synthetic organic chemistry, especially in the area of pharmaceutical research.  I also understand better that there are many useful natural compounds to treat disorders, but they are often very complex and expensive to synthesize.

So Dr. Cook is devoted to developing new methods to make natural compounds. For example, he found the synthetic ‘tools’ needed to synthesize 11-O-Debenzoyltashironin from phenols and allenes.

On the other hand, I am wondering how 11-O-Debenzoyltashironin can be applied to the invention of medicines that allow real patients to get healthier.

Also I would like to know more about the speaker’s most recent research area that he is working on.

In generally, I was interested in his presentation very much because I was overwhelmed  by his enthusiasm for his research, and I also got involved in his presentation by giving responses to his questions.

In addition, although I understood the mechanisms involved in the synthesis of 11-O-Debenzoyshironin, I learned a lot about how many researchers, including Dr. Cook,  invests so much time, knowledge, and passion to achieve a successful synthesis. I was surprised that he spent five years and  used more than twenty three steps to get his desired product.

To my friend lacking scientific information, I’d like to introduce Synthetic Organic Chemistry, a field of study to synthesize needed molecules, demonstrate the limitation of current methods and develop new methods.

Post This To My

Hide Sites

As far as content goes, I would have to say that I enjoyed this lecture the most out of all the lectures so far in the semester. The format in which the information was presented was well organized and the information was enlightening as well as interesting.

The reason I found it interesting was the fact that this lecture was about the process of making the chemicals and not the theories behind processes. I find hands-on work and formulas much more interesting than theory and posturing. It was kinda cool to find out that around sixty-three percent of all pharmaceuticals on the market today are based on compounds found in nature. I knew that some were natural based, but I did not realize that so much was based on natural products.

It was also interesting to find out what total synthesis was. Before this lecture I had never heard of it, but now it seems like an interesting field of study. According to the speaker, total synthesis is “the art of making stuff that nature has already made.”

One thing that confused me was something that the speaker said. He said that not many groups get involved with antibiotics research anymore because even if they come up with something new, chances are it’s already been patented or something like that. It confuses me as to how something that doesn’t exist can be claimed as property. But with the way our government works, it doesn’t surprise me all that much.

And if I had to explain this lecture to one of my non-science friends I would say that this lecture was about the process of making medicines and other nature-based chemicals. The speaker’s style was smooth and understandable, and I really appreciate his being aware of our time, even though I would have been able to listen for longer if I hadn’t had to go to Wind Symphony practice.

Post This To My

Hide Sites

I thought “The Evolution of a Synthesis” presentation by Professor Silas Cook was pretty interesting although many of the reactions were above my head, since I have forgotten so many of the reactions I learned in Organic Chemistry class. I am not saying that it was interesting because I saw a whole bunch of reactions, but I am saying that learning about synthetic organic chemistry was interesting. His presentation would have been better and more informative to us, if he focused on telling us more about Synthetic Organic Chemistry rather than about tons of reactions he worked on.

Three new things I learned during this seminar were that 1) two branches of synthetic organic chemistry are total synthesis and methodology. Each branch is just as important as the other branch,  2) In total synthesis, researchers look at the structures discovered and retrieved from biological sources, and they try to synthesize the same structure chemically via reactions, and 3) In methodology, researchers try to make the existing reactions ‘better’ by shortening the reaction steps, reducing expensive chemicals used in reactions, or increasing the yield.

I also learned that Artemisinin is the best malaria treatment out there but can be unaffordable for those who need it most.  It currently requires 12 steps, which is research group is trying to shorten by  synthetic methodology. A substance Professor Cook synthesized was 11-o-Debenzoyltashironin, which promotes neural growth in fatal neurons, was the main topic of his presentation.

If I were to describe this presentation to my ‘non-science’ friend or family so that they could understand it, I would say “The Evolution of a Synthesis” presentation by Professor Silas Cook explains about synthetic organic chemistry and tells about how he synthesized 11-0-Debenzoyltashironin.

Post This To My

Hide Sites