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Everything posted by BabcockHall

  1. Tutoring is not a replacement for studying on your own, IMO. It can fill in the gaps when you get stuck. My advice is to turn off all electronic distractions; short, intense studying is more effective than long periods of diffuse studying.
  2. If I recall correctly I once used bromocresol green to detect compounds containing a carboxylic acid group on a TLC plate. That is probably different from the sort of reaction that you were thinking about.
  3. A catalyst such as thiamine pyrophosphate can decarboxylate alpha-keto acids.
  4. Hi CharonY, Thank you for a very helpful answer. We used established antimicrobial substances as positive controls; we were not comparing our compounds to them in any other sense.
  5. Many covalent inhibitors are irreversible, but not all of them are. If each step to form a covalent bond is reversible, then the whole process is reversible. A good example is peptide aldehyde or trifluromethylketone binding to the nucleophile in a cysteine or serine proteases. Reversible, covalent inhibitors seem to be catching on, so it's a good topic.
  6. My suggestion is to rewrite the standard Michaelis-Menten equation in the form (velocity)/Vmax = and so forth. To do so is trivial from the point of view of the algebra involved.
  7. Good Morning, We are collaborating with a group that performs disk diffusion assays on compounds that we make. We would like to publish some disk diffusion data in addition to reporting on the syntheses and perhaps the in vitro behavior of a set of compounds. However, the area of whole-cell biological testing is generally unfamiliar to me, and I don't know how to present data in a manuscript. I also don't have a good feel for what information should or should not be included in reporting these data. Perhaps someone could suggest a model publication, for example. Thank you.
  8. In carbohydrate chemistry, my suggestion is generally to start with the HC-1 signal, because it verifies the configuration of this carbon. It is also simpler in appearance.
  9. We have tried both diethyl amine and 4-methylpiperidine in the deprotection. Most recently we removed the white precipitate with centrifugation in Corex centrifuge tubes. This was an improvement over having a bunch of precipitate sit on the top of the silica column.
  10. The carbon and oxygen are still present. What do you think happens to the hydrogen on the oxygen?
  11. Is there any point in repeating a successful disk diffusion assay at lower starting concentration of substance? Or would it make more sense to move to some form of minimum inhibitory concentration assays?
  12. We tried a silica column after using diethyl amine to deprotect. We obtained two pools, but we did not obtain our product. We are short on mass. It seems like time for a rethink regarding the best purification method.
  13. We have a tertiary-butyl protected amino acid in which nitrogen is protected with FMOC. We removed the FMOC group with diethyl amine, and we used rotary evaporation plus a toluene strip to remove the volatiles. We attempted to purify over a short column of silica. We were able to remove a fast-moving impurity (presumably dibenzofulvene or a derivative) using 40:60 EtOAc/hexanes, then switched to 99:1 hexanes/TEA in the hope of eluting the N-deprotected product, still bearing the carboxylate protecting group, but the product was not soluble in EtOAc or in DCM (it might have been a suspension). We eluted with 90:10 DCM/methanol and saw two products by TLC. They were not completely separated. I am interested in soliciting ideas for what we should do differently next time. In retrospect a lower percentage of methanol would have been an improvement. I wonder whether or not the solubility of the amine would have been better in chloroform than it was in DCM. I realize that some people do not purify at all at this stage, but instead couple the crude product with another amino acid. We also want to couple to another amino acid.
  14. https://doi.org/10.1002/chem.201101163 I am working on synthetic routes to a glucoside. The beta-trimethylsilylethoxymethyl (SEM) group has some attractive features (particularly in regards to deprotection), but I have only found one paper in which four SEM groups were used to protect the oxygen atoms at carbons 2-4 and 6 of a glycoside conjugated with a steroid. They did not deprotect to the best of my knowledge, but I assume that one would use a standard recipe. I did find a paper in which a glycoside was protected with several different groups, including one SEM. Are there disadvantages to using the SEM group as the protecting group? Are there reasons why it has been used more in carbohydrate chemistry? Should I be favoring other protecting groups instead?
  15. You might be able to do it using what is called the specific activity of the enzyme. Specific activity is given as units per milligram of protein. The denominator is a mass, not a concentration.
  16. Does anyone know of a web-based program for estimating retention times that is simple to use? I found one, but I struggled a bit with the output.
  17. Our interest is in LC/MS of the peptides, and we plan to work in water/acetonitrile/formic acid. We found a number of protocols for C-18 on line (I can provide links to these), and we are focusing on those protocols that specify formic acid (not TFA). Our Zip Tips use C-18. (1) Are Zip Tips necessary? (2) Given their capacity, does one obtain enough for material for one or for several LC/MS runs? (3) Are Zip Tips reusable? (4) Does anyone have a paper or protocol that is especially informative? Thank you very much.
  18. We are synthesizing the next generation of inhibitors, and they have increased water solubility.
  19. I don't know the answer to your question, but I am inclined to say that we will try to optimize the compounds. With regard to these compounds, we have in vitro data against a validated target enzyme. They are irreversible inhibitors with ligand binding efficiencies greater than 0.3. The second generation inhibitors that we are currently synthesizing were designed with transport across membranes as a consideration.
  20. Our collaborators used only volatile organic solvents to dissolve the compounds prior to the preparation of the disks. I am not sure whether or not this information is useful.
  21. I asked my institution to file a provisional patent, but I have not yet heard back.
  22. The enzyme has been shown to be essential in some pathogenic bacterial strains and also in Candida albicans. We are in the process of revising our first manuscript on our inhibitors. For the best compounds in this series, the ratios of binding energies to molecular weights are promising, among other possibly favorable properties. We envision either an antifungal or antibacterial compound, although at the moment we are more fungal-focused. What sort of near-term commercial applications do you mean?
  23. That is a helpful reference; thank you. We synthesized a family of compounds that are good inhibitors of an essential microbial enzyme. As a whole they are not very water-soluble, although there is variation in the group. One of the more hydrophilic ones is one of two that showed growth inhibition. Therefore, we are synthesizing the next generations of inhibitors that might be more water-soluble and thinking about what are the meanings of various test results.
  24. One other issue occurs to me. As the compound diffuses, the microorganisms are growing. So it is possible that the compound arrives at a certain place with a particular concentration only after growth has ceased for other reasons, such as buildup of waste or consumption of nutrients.
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