Unanswered Questions

25
votes
0answers
687 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
161 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 ...
11
votes
0answers
243 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
73 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
113 views

Mechanism of dehydrogenation with Nosylate

What is the mechanism of the attached reaction? How could nosylate do the dehydrogenation? The reaction is from this synthesis (46th IChO preparatory problem 26):
7
votes
0answers
226 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
67 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 ...
7
votes
0answers
124 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, ...
7
votes
0answers
123 views

Molecular Imaging - Any surprises to be had?

Molecular imaging, using STM and AFM technologies, appear so far to visually prove most of what we already know about chemical structures, such as VSEPR theory. For instance, here are the ideal ...
6
votes
1answer
63 views

How to express uncertainty containing values with error progression?

A student reported the mass of 10 glass beads as $2.507 \pm 0.015~\mathrm{g}$. What should the student report as the mass of one bead? A student reported the density of ten glass beads as ...
6
votes
2answers
110 views

Why no thermal expansion for camping tents?

I know that solid materials expand when heated, which is called thermal expansion. But what is happening to tent square or tent canvas of (plastic?) camping tents? I have noticed, that during the ...
6
votes
0answers
40 views

How to get defect-energy level diagram from PL data

I am reading this article Phys. Chem. Chem. Phys. , 2011, 13, 14902-14905 and seen that the authors have drawn a image of defect level using PL data Can you explain me how this diagram can be drawn ...
6
votes
0answers
144 views

Is hybridization used in ab-initio valance bond calculation?

Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing ...
6
votes
0answers
394 views

Deliquescence/efflorescence: How can I convert between salt concentration and RH?

I am looking at two phase diagrams, one has axes of $T$ and $\%\ce{MgClO4}$ in a $\ce{H2O-MgClO4}$ mix, and the other has axes of $T$ and relative humidity. The authors of the second phase diagram say ...
5
votes
0answers
468 views

Natural Bond Orbital (NBO) analyses: Physical significance/interpretation of E(2) 'stabilization energy'?

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...

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