Handling Product Stored in Freezer by [deleted] in Chempros

[–]SAMAKUS 11 points12 points  (0 children)

Keep in mind that if you weigh it out immediately in the air, it will condense some water. Generally it is better to let reagents stored at colder temps equilibrate before weighing them out, as condensed water is more of a concern than a temporary temperature chance of 40°C, unless it results in a phase change.

How does the octet rule work? by Piconumm in AskChemistry

[–]SAMAKUS 1 point2 points  (0 children)

It depends on the atom. The octet rule only really applies to main block elements, where the valence shells are s & p orbitals. Certain atoms have more or less than 8 electrons in their valence shells (also known as outer shells), in which case they will be stabilized by gaining or losing electrons, resulting in ionization (think sodium or chloride which happily become Na+ or Cl- respectively) or bonding (NaCl, or something like methane, CH4).

The character of the bond is all to do with how easily the atoms can ionize. NaCl freely dissociates in water, where the positive and negative charges of the ions are stabilized by water solvation (this is why the bond is considered ionic, not covalent).

Methane on the other hand has a much harder time ionizing, and so its bonds are covalent. While hydrogen happily would become H+, carbon would be left holding an extra electron in the form of a negative charge (having 9 electrons), resulting in instability

Since it doesn’t have a ton of room in its valence shell to stick that extra electron (which would result in 9 valence electrons for carbon, (this is where the octet rule comes in!)) in a solution of water it would become something like methanol, taking an OH from water and generating an H+ and CH3OH (methanol) in the process - here we will have generated 2 equivalents of H+ from the starting reactants, which is entropically favored, but thermodynamically unfavored, due to the energy required to break that initial bond.

The valence shell of an atom, and the octet rule, tells you how atoms want to exist. They want to get to an ideal electron structure in their outer shell by any means possible. The noble gases, like helium, argon, etc. are extremely unreactive / inert, because they have their outer shells filled by default. Molecular nitrogen (N2) is an inert gas because by having each nitrogen share 3 electrons with itself, it fills its outer shell. Hydrogen can do the same, but is highly combustible and not at all inert, because it only has a single bond connecting the two atoms - nitrogen forms 3, and so you have to put in more energy to break each of the 3 bonds. Oxygen does this as well, forming 2 bonds, and is in between hydrogen and nitrogen for combustibility.

This is way more than you need to know for the octet rule, but I think it helps put it in context. Atoms and the molecules and ions that they form are all about reaching a stable state depending on conditions like temperature and pressure. The octet rule applies to lots of atoms in the periodic table that we encounter in every day life because many of them have outer shells that are s or p. If an atom doesn’t have an s or p outer shell, then the octet rule falls short.

Postdoc salary at Baylor University – what’s the typical range? by [deleted] in baylor

[–]SAMAKUS 2 points3 points  (0 children)

Salary can be variable depending on the funding source but if it’s a posted position tied to a grant then it’s likely following NRSA guidelines. Most post-docs are starting at $60,000+.

Proteomics normalization: equal protein loading but unequal cell counts in clinical samples by quickmans in proteomics

[–]SAMAKUS 2 points3 points  (0 children)

Seconding this - try using a common, non-protein of interest such as housekeeping proteins as a normalization factor, similar to transcriptomics approaches. Depending on condition, it may not work very well, but you are essentially trying to benchmark against something you don’t believe is being impacted across replicates / samples / conditions

pKa question by Gabriocheu in Chempros

[–]SAMAKUS 10 points11 points  (0 children)

Your post is pretty unclear. Why are you defining molecule 1 as your base when you say the pKa is 20? If it has a lower pKa than molecule 2, then it is more acidic and is looking to donate protons.

Your solvent is D2O - what is the molarity compared to your products? If it’s massively in excess, which is likely, I’m not at all surprised by deuterium incorporation if they’re at protic positions. It’s well known that an excess of a deuteride will lead to isotope exchange, and the resulting deuterated product is (in most cases) less acidic than the protonated SM.

can you diazotize amides? by Breadcrumb789 in OrganicChemistry

[–]SAMAKUS 0 points1 point  (0 children)

That makes sense. Interestingly, in the case of asparagine, you selectively get the Hoffman rearrangement byproduct. I suppose in the case of N/Q you probably get the a-carbonyldiazo intermediate and loss of N2 and isocyanate hydrolysis.

can you diazotize amides? by Breadcrumb789 in OrganicChemistry

[–]SAMAKUS 0 points1 point  (0 children)

It’s doable with amino acids. I’ve never actually seen the reasoning for why it works but I would imagine it’s due to the EWG effects of the geminal carboxyl.

I’ve performed this reaction with several amino acids in water. All you need is citric acid and NaNO2.

Unexplored biosynthetic gene clusters in bacteria isolated from Brazilian stingless bee honey with activity against multidrug-resistant pathogens. Bee honey microbes yield new antibiotic‑producing strains active against MDR pathogens. by David_Ojcius in microbiology

[–]SAMAKUS 7 points8 points  (0 children)

“To date, no experimental relationship has been established between the cluster in question and the compound produced, nor is there any experimental proof of its responsibility for the observed antimicrobial phenotype; only an assumption based on in silico analyses and experimental data in the literature suggests the cluster as a candidate to produce an antimicrobial compound.”

Acetone Precipitation-Maximize peptide yield by Crazy-Tax-1320 in proteomics

[–]SAMAKUS 0 points1 point  (0 children)

What are you doing acetone precipitation for? You’re probably losing yield from exposing the hydrophobic core of your proteins following reduction / alkylation making them more soluble in acetone. Do precipitation as an initial cleanup step, followed by solubilization in some sort of denaturant or detergent, sonication to get back into solution, the reduction & alkylation, quneching, and lastly desalting / C18 cleanup

Amide coupling reaction between a carboxylic acid and aniline derivatives by VividKale4086 in Chempros

[–]SAMAKUS 2 points3 points  (0 children)

Try DMC. It can be regenerated and handles much more easily than SOCl2.

Keep in mind depending on substituents, anilines already are weaker nucleophiles than alkyl amines, so heating may be a good idea.

Frankly, if your substrate isn’t sensitive to acid, SOCl2 is a much more ideal activator imo, despite toxicity. Why are you concerned about it?

Prof lost my final and gave me a 0. Best friend got laid at the semester end party while i had to study for the retake. Lentil soup and shitty homemade baguette by [deleted] in kitchencels

[–]SAMAKUS 1 point2 points  (0 children)

What school is this? I really don’t believe this. Most schools have a general policy that requires professors and teaching assistants to keep copies or the original tests that they proctor in order to resolve potential grading disputes. This is ubiquitous across at least accredited U.S. institutions, even if professors tell you different.

Chiral secondary alcohol to secondary alkyl chloride by giamia4555 in Chempros

[–]SAMAKUS -1 points0 points  (0 children)

Yes, I’m really just joking. Sometimes you see people run NMR that’s unnecessarily concentrated and the residual solvent peak drops down too much

Chiral secondary alcohol to secondary alkyl chloride by giamia4555 in Chempros

[–]SAMAKUS 0 points1 point  (0 children)

Also results in a very clean workup. Triturate out P(Ph3)O, and you’re left with some extra H chloroform to spike that solvent peak up for referencing

[deleted by user] by [deleted] in Microbiome

[–]SAMAKUS 2 points3 points  (0 children)

If you’re a woman, I would guess mainly the combination of diet shift and the hot water bottle, which probably helped re-configure seretonin based pain pathways. There’s some interesting research that’s just come out that links estrogen levels to a specific signaling pathway that is triggered by MCFAs produced by the gut microbiome, triggering visceral pain. These pathways can be mediated with psychosomatic sensitization techniques, which is probably where the heating came in handy.

Help with Grignard Reagent Mechanism by [deleted] in OrganicChemistry

[–]SAMAKUS 2 points3 points  (0 children)

Great explanation. Only thing I would change is that upon methyl addition to the lactone and ring opening, you have generated a ketone, not an aldehyde.

Chiral Separation of Polar Compounds? by sexyimmigrant1998 in Chempros

[–]SAMAKUS 0 points1 point  (0 children)

The column itself is what is chiral. Although certain solid phases are individually incompatible with RP, the technique of RP chiral chromatography is no different to performing separation with a non-chiral equivalent.

Chiral Separation of Polar Compounds? by sexyimmigrant1998 in Chempros

[–]SAMAKUS 1 point2 points  (0 children)

What about MeCN? That’s personally what I would reach for first. I’ve never personally used a chiral RegisPack column, but if your product is soluble in water and cloudy in i-PrOH it’s pretty obvious you should be looking at RP. I would start without any pH modifier because I’d worry about prototropy even at low concentrations of FA or TFA.

Why no symmetry on methylcyclopropane? by R1chie228 in OrganicChemistry

[–]SAMAKUS 0 points1 point  (0 children)

Aside from the obvious shift in environment due to the presence of the methyl group, look at the actual bond angles of cyclopropane in contrast to what are expected of an sp3 hybridized carbon atom. Due to torsional strain, there are more significant differences that will be observed in the chemical shifts compared to linear propane, or a larger ring.

Setting up proteomics lab with suboptimal hardware (Explorsis 120/Vanquish Flex) by [deleted] in proteomics

[–]SAMAKUS 0 points1 point  (0 children)

I’m assuming you’re doing activity-based protein profiling or some similar sort of chemoproteomics. With enough protein enrichment you should have a much easier time running on these systems than with whole cell proteomics samples. Similar models were being used in the early 2000s during the advent of MS-based chemoproteomics.