407 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 $\alpha$- ...
247 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 ...
599 views

### Stoichiometric defects in ionic crystal?

The stoichiometric defects (Schottky and Frenkel defects) in ionic crystals are formed due to irregularities in ionic arrangement all the while maintaining the stoichiometry and electric neutrality. ...
98 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 ...
45 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 ...
108 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 ...
111 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 ...
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 ...
51 views

### How does the crystal know where to stop stacking the unit cells?

I tried to make different crystals in the cubic system by stacking cubes in a 3d software. However I need to tell the software where to skip rows or stop stacking the unit cells in a specific ...
183 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 ...
14 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 ...
127 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 ...
205 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 ...
### difference in the functioning of Alkaline and Acidified $\ce{KMnO4}$
What is the difference in the functioning of alkaline and acidified $\ce{KMnO4}$ as a reagent in organic chemistry? For e.g., in the oxidation of a primary alcohol to carboxylic acid, we use ...