5,237 questions with no upvoted or accepted answers
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### 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 ...
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### 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 ...
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### 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 ...
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 $\ce{... 0answers 181 views ### Single-molecule magnet with electrically-controlled permeability: How does the Titan Shield from Deus Ex work? In a recent installment of Deus Ex game series there is an augmentation called "Titan Shield" (it has nothing to do with$\ce{Ti}$element): A neodymium skin underlay matrix built of nano-meshed ... 0answers 208 views ### f-electrons in chemistry of heavy transition metals In one lecture on recent MCR-X conference I was puzzled by a side-note "f-hole is critical to describe DoS of$\ce{IrO2}$correctly." The context was DFT periodic plane-wave calculations with ... 0answers 349 views ### Ambimodal transition states in some organic reaction pathways In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ... 0answers 108 views ### Is there a consensus on whether amber can seal in air bubbles for millions of years? I read about deriving the oxygen content in the atmosphere in the Cretaceous by analyzing the air trapped in bubbles in amber from that period, but I have also found papers disputing the study's ... 0answers 1k views ### How to Calculate Transition Dipole Moment from Two Known Wavefunctions I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ... 0answers 6k views ### Melting and boiling point trend in Group II The following picture shows the melting and boiling point trends down group II elements. I have added question marks where the variability in data was rather disturbing (over two hundred degrees ... 0answers 671 views ### Neighbouring group participation with and without retention of configuration in nucleophilic substitution of 2,6-dichloro-9-thiabicyclo[3.3.1]nonane Treatment of the dichloride A under the conditions indicated gives B with retention of configuration, while treatment of dichloride C gives D with inversion of configuration. I am having ... 1answer 755 views ### In rovibrational spectra, when exactly is the Q branch forbidden? I'm aware that the Q branch ($\Delta j = 0$) is usually not observed in rotational-vibrational spectra of diatomic molecules in the gas state, however, I've heard different things about when exactly ... 1answer 896 views ### Why is the endo product the major product in a Diels-Alder reaction? I understand that the endo product is, at least in all cases in my textbook, the major product in a Diels-Alder reaction. However, I don't understand why this is the case. The explanation in my ... 1answer 117 views ### Mechanism of a Gold catalyzed organometallic reaction: Confusion regarding the last step I needed to draw the reaction mechanism for this reaction: So, after consulting some literature I drew this mechanism: But, I am not sure about the last step. Does the$\ce{H+}$just substitute the$...
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 ...