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Unanswered Questions

41
votes
0answers
698 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 ...
22
votes
1answer
222 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 "...
19
votes
1answer
875 views

What is the nature of the bonding in cyclotriphosphazene?

The bonding in $\ce{(NPCl2)3}$ (and other compounds of the form $\ce{(NPR2)3}$) has historically been described using the ‘Dewar island model’. By analogy to benzene, $\ce{(NPCl2)3}$ is π-electron ...
19
votes
1answer
272 views

Why are lithides not known?

In the last few decades, many alkalides - anions of alkali metals - have been synthesised. The most famous is undoubtedly that of sodium: $\ce{[Na(\text{2.2.2-cryptand})]+Na-}$, but the alkalides $\ce{...
18
votes
2answers
274 views

(Computationally) finding similarity between two organic compounds

I have been struggling to find an acceptable answer for this question for my purposes. There are many ways to find similarity between two organic compounds - some of which are particularly popular ...
16
votes
1answer
178 views

Why don't alkynes undergo preferential anti bromination to the degree that alkenes do?

Alkenes, for the most part (unless there is a phenyl group or highly ionising solvent) undergo almost exclusively anti addition of bromine. However, under similar conditions alkynes, although undergo ...
16
votes
0answers
166 views

Similarities and Differences between Resonance and MCSCF treatments

Recently, there has been a question by Voldemort concerning different resonance structures of $\ce{NCO-}$, requesting an explanation why one resonance structure would be more preferred than another. ...
15
votes
0answers
216 views

What is three dimensional aromaticity?

I have recently come across a statement which states: The relative stability of the 1,3-dehydro-5,7-adamantanediyl dication is ascribed to its three-dimensional aromaticity. [1] My ...
15
votes
0answers
148 views

Single-molecule magnet with electrically-controlled permeability: How does the Titan Shield from Deus Ex work?

In a recent installment of Deus Ex game series there is an augmentation called "Titan Shield" (it has nothing to do with $\ce{Ti}$ element): A neodymium skin underlay matrix built of nano-meshed ...
14
votes
0answers
284 views

Hellmann-Feynman Forces with Hartree-Fock

The energy in the Hartree-Fock approximation is given as: $$E_{HF}=\left<\psi_{HF} \left| \hat{H} \right| \psi_{HF} \right>=\sum_{i,j}P_{i,j}H_{i,j}^{core}+\frac{1}{2}\sum_{i,j,k,l}P_{i,j}P_{l,...
14
votes
0answers
272 views

Ambimodal transition states in some organic reaction pathways

In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
14
votes
0answers
171 views

f-electrons in chemistry of heavy transition metals

In one lecture on recent MCR-X conference I was puzzled by a side-note "f-hole is critical to describe DoS of $\ce{IrO2}$ correctly." The context was DFT periodic plane-wave calculations with ...
14
votes
0answers
1k views

How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
13
votes
1answer
189 views

Why is the bond dissociation energy of C-H bond higher than that of a N-H bond?

Looking at a chart of BDEs (bond dissociation energies) regarding elements bonded with hydrogen, the general trend seems to be that the BDE increases as we go to the top and to the right. This can be ...
13
votes
0answers
583 views

Neighbouring group participation with and without retention of configuration in nucleophilic substitution of 2,6-dichloro-9-thiabicyclo[3.3.1]nonane

Treatment of the dichloride A under the conditions indicated gives B with retention of configuration, while treatment of dichloride C gives D with inversion of configuration. I am having ...

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