Unanswered Questions

18
votes
0answers
462 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 $\alpha$- ...
9
votes
0answers
260 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 ...
8
votes
0answers
104 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 ...
7
votes
0answers
55 views

Is greater relative AA battery capacity at high currents indicative of greater capacity at low currents?

I originally posted this on EE.SE but might be better here: Battery showdown compared the mAh and mWh capacity of different AA batteries discharged at 200mA. Would the relative capacities of each ...
7
votes
0answers
127 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 ...
7
votes
1answer
124 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 ...
7
votes
0answers
68 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 ...
6
votes
0answers
160 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. ...
6
votes
0answers
27 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 ...
6
votes
0answers
232 views

Is there an energy cost associated with flipping the spin of an electron?

THE STORY: A common example used to illustrate the limitations of restricted Hartree-Fock (RHF) theory is the H$_2$ dissociation energy ($D_e$) curves. RHF enforces electrons to be paired into spin ...
6
votes
0answers
189 views

Understanding moseley's law from the rydberg-type equation?

To explain the characteristic X-ray emission peaks for various elemental targets, a formula was developed which was similar in construct to the rydberg equation for H-atom as derived by the ...
5
votes
0answers
20 views

Is there a catalyst that will reduce an alcohol to an alkane?

There are many reduction methods of going from an alcohol to an alkane: http://www.transtutors.com/chemistry-homework-help/hydrocarbons/reduction-of-alcohols.aspx And there are catalytic methods of ...
5
votes
0answers
185 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 ...
5
votes
0answers
109 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 ...
5
votes
0answers
100 views

How can normal potentials be explained?

For example (for reductions) $$ \ce{2e-} + \ce{Cd^{2+}} \rightarrow \ce{Cd}:\mbox{ } E^0 = -0.403 V\\ \ce{2e-} + \ce{Ni^{2+}} \rightarrow \ce{Ni}:\mbox{ } E^0 = -0.25 V $$ How can I rationalize this ...

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