Unanswered Questions
5,587 questions with no upvoted or accepted answers
42
votes
0answers
879 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 ...
25
votes
2answers
738 views
Is hybridization used in ab initio valence 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 ...
24
votes
1answer
368 views
Synthesis Golf X: TAK-457
I shall try to revive this!
A full FAQ post has been written on chemistry.meta.SE, explaining the premise of synthesis golf and the 'rules'. Please take a look at this before answering (if you haven't ...
21
votes
0answers
348 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 ...
17
votes
0answers
632 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 ...
15
votes
0answers
278 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 ...
15
votes
0answers
2k 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 ...
14
votes
0answers
10k views
Melting and boiling point trend in Group II
The following picture shows the melting and boiling point trends down group II elements.
I have added question marks where the variability in data was rather disturbing (over two hundred degrees ...
14
votes
1answer
530 views
Why does a Diels–Alder reaction not occur here?
I have recently come across this organic chemistry problem.
I thought it would undergo simple Diels–Alder reaction
But it didn't turn out to be. The product to me looks like a nucleophilic attack ...
13
votes
1answer
1k views
Explanation of the strength of phosphorus-oxygen bond
When discussing the Wittig reaction, Clayden's Organic Chemistry cites the strength of the $\ce{P=O}$ formed in triphenylphosphine oxide as a driver of the reaction through enthalpy:
The $\ce{P=O}$ ...
13
votes
1answer
3k views
In rovibrational spectra, when exactly is the Q branch forbidden?
I'm aware that the Q branch ($\Delta j = 0$) is usually not observed in rotational-vibrational spectra of diatomic molecules in the gas state, however, I've heard different things about when exactly ...
13
votes
1answer
2k views
Why is the endo product the major product in a Diels-Alder reaction?
I understand that the endo product is, at least in all cases in my textbook, the major product in a Diels-Alder reaction. However, I don't understand why this is the case.
The explanation in my ...
13
votes
1answer
366 views
How to treat pressure in computational chemistry?
I have a reaction where a gas at high pressure and a solution with all kinds of species is involved. How do I take pressure correctly into account to get reasonable values for $G$?
Do I calculate ...
12
votes
0answers
109 views
Can pi backdonation occur on non-metal centers?
The common example of back-donation is the interaction of a CO molecule with a metal center (d-orbitals) on a surface.
Can a similar mechanism occur between CO and a non-metal center, like oxygen on ...
12
votes
0answers
128 views
Calculating Triplet-Triplet Spin-Orbit Coupling
According to the Q-Chem manual [1], the singlet-triplet spin-orbit couplings between a singlet excited state $I$ and a triplet excited state state $J$ is:
$$\langle\Phi_\text{singlet}^I|\hat{\mathrm H}...
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