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Unanswered Questions

41
votes
0answers
729 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 ...
19
votes
1answer
302 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
317 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 ...
17
votes
1answer
202 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
167 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 ...
15
votes
0answers
191 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
303 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
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
0answers
90 views

Is there a consensus on whether amber can seal in air bubbles for millions of years?

I read about deriving the oxygen content in the atmosphere in the Cretaceous by analyzing the air trapped in bubbles in amber from that period, but I have also found papers disputing the study's ...
13
votes
0answers
615 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 ...
13
votes
1answer
578 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
116 views

Mechanism of a Gold catalyzed organometallic reaction: Confusion regarding the last step

I needed to draw the reaction mechanism for this reaction: So, after consulting some literature I drew this mechanism: But, I am not sure about the last step. Does the $\ce{H+}$ just substitute the $...
13
votes
1answer
308 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
158 views

Verifying data acquired from a molecular dynamics simulation

This question is about verifying a system simulated with MD. I am currently building a model of a two phase gas-liquid system, where I initially have $\ce{N2}$, $\ce{CO2}$, $\ce{Ar}$, $\ce{He}$ and $\...
12
votes
0answers
6k 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 ...

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