Unanswered Questions

19
votes
0answers
506 views

Is there a general consensus on the causes of the alpha-effect?

There have been various explanations posited for the $\alpha$-effect. The $\alpha$-effect refers to a phenomenon wherein nucleophiles with lone pairs on atoms adjacent (i.e., in the $\alpha$- ...
12
votes
0answers
277 views

What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
10
votes
0answers
126 views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
8
votes
0answers
38 views

Can a multi-species system oscillate around equilibrium?

In reading about chemical oscillations such as those that occur in the Belousov–Zhabotinsky reaction (BZ), it's often reported that these reactions were initially not taken seriously, because of a ...
8
votes
0answers
149 views

Why does depurination happen at a higher pH (or under less harsh conditions) than depyrimidation?

I've always wondered why the N-glycosidic bond, which connects the adenine or guanine purine bases to their sugars, was the easiest to cleave via acid hydrolysis, or why purines have the lowest ...
8
votes
0answers
150 views

Is there any relationship between ultrasonication and temperature

In chemistry we use ultrasonication for cleaning vessels ,synthesis of chemical compounds (sonochemistry) etc.I know that during ultrasonication high temperature and pressure is formed "locally".But I ...
8
votes
0answers
70 views

When measuring avidity should you use the ligand concentration or the nanoparticle concentration?

Looking at avidity between a ligand-receptor, you're looking at an enhancement of the $K_d$ compared to a lone ligand. Is it more appropriate to compare the $K_d$ using the concentration of the ...
7
votes
0answers
179 views

Influence of Temperature on Biochemical Reactions

Short question How (quantitatively speaking) does temperature influences rate of decay of proteins? I am looking for some general number/function, the influence of temperature on an average protein. ...
7
votes
0answers
148 views

Can Entropy Increase During Bond Formation?

Recently the question was asked, "Is Bond Formation “Strictly” Exothermic?" As a corollary to that question, what is the relationship between entropy and bond formation? Does the entropy of the bond ...
6
votes
0answers
58 views
+50

What general uses do beta-lactam functional groups have?

I am currently working on a mechanistic study that deals with stereoselective $\beta$-lactam formation. I am well aware that there is a class of antibiotics, that involve this particular functional ...
6
votes
0answers
43 views

Hosoya Z Index and Correlation with Boiling Point

I have recently read about the Z topological index found by Hosoya. The papers/sources The Z index is the sum of the coefficients of the matching polynomials (no. of ways to choose an independent edge ...
6
votes
1answer
137 views

rate determination by 1H NMR spectroscopy

Currently I investigate a reaction where a starting material A reacts with an excess of thiophenol B towards products C and D. As shown by recurrent TLC analysis of the reaction, the formation of D ...
6
votes
0answers
76 views

Finding the number of cyclic isomers algorithmically

Is there an algorithm for finding the number of cyclic isomers a given compound might have? I've found a general algorithm for all isomers: http://www-jmg.ch.cam.ac.uk/data/isomercount/isojava.html, ...
5
votes
0answers
35 views

Salt concentration and electrical permittivity of water

We know that the electric flux density $D$ can be related to electric field intensity $E$ as $D=\epsilon(\omega) E$ $\epsilon(\omega) = \epsilon_0 \epsilon_r(\omega) $ where $\epsilon_0$ is the ...
5
votes
0answers
50 views

Bicycle tube inflation with 16g CO2 cartridge

How much pressure will a 16 gram cartridge of $\ce{CO2}$ (carbon dioxide) provide in a bicycle tire? Remembering my high school chemistry (forty years ago) and googling, I came up with this answer: ...

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