# Unanswered Questions

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### 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 $\alpha$- ...
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### 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 ...
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### CO2 removal from mushroom growing tent

I'm trying to grow oyster mushrooms that like high temperatures. They look great in an indoor terrarium, and can eventually yield several tasty meals :) However oyster mushrooms are hard to grow ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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. ...
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### 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 ...
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### 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, ...
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### 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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333 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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### 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 ...
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### 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 ...
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### 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 ...

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