Unanswered Questions

5,777 questions with no upvoted or accepted answers
43
votes
0answers
903 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
771 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
384 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 ...
20
votes
0answers
360 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
664 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 ...
16
votes
1answer
11k 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 ...
15
votes
0answers
294 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
1answer
590 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 ...
14
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 ...
13
votes
1answer
2k 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
0answers
155 views

Mechanistic Explanation of Circular Dichroism

I'm wondering if someone can give me a physically motivated reason for why chiral molecules interact with left and right circularly polarized light (LCP) (RCP) differently. Particularly, a quantum ...
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
375 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
119 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 ...

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