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42
votes
0answers
855 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 ...
24
votes
1answer
310 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 ...
18
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0answers
289 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
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0answers
602 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
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262 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
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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 ...
15
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2answers
289 views

Disproportionation of Au(II)

Cu(II) and Ag(II) complexes are known to exist while Au(II) is unstable and disproportionates to Au(I) and Au(III). My guess as to possible reasons to this effect is that Au(II) like Cu(II) and Ag(II)...
14
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0answers
9k 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
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0answers
441 views

What was the lithium concentration in 1940's 7-Up?

I just came across this article in the New York Times, where lithium (or more correctly, lithium salts), a known anti-depressant had been added to beverages in the 1940's. They also mention that a ...
14
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1answer
477 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
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1answer
2k 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
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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
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1answer
357 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
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0answers
106 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
1answer
940 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 $\ce{P=O}$ ...
12
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0answers
122 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}...
12
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0answers
139 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 ...
12
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0answers
238 views

Why is Diiron nonacarbonyl so exceptional?

My textbooks says: With exception of $\ce{Fe2(CO)9}$, all other metal carbonyls are soluble in hydrocarbon solvents. Weller, M.; Overton, T.; Rourke, J.; Armstrong, F. Inorganic Chemistry, 6th ed. ...
12
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1answer
162 views

Products formed on cleavage of epoxides using HI

There seems to be multiple forms of HI used to cleave epoxides: conc. HI, anhydrous HI, cold HI, hot HI, cold conc. HI, hot conc. HI, etc. So, does concentration of HI and temperature have any ...
11
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0answers
133 views

Why does the exchange interaction in Hartree-Fock theory lower the total energy?

In Hartree-Fock theory, the expectation value of the total energy can be written as $$E = \langle\Psi| H |\Psi\rangle = \sum_{a} \langle a| h |a \rangle + \frac{1}{2}\sum_{ab} \big( [aa |bb] - [ab|ba]...
11
votes
1answer
153 views

Importance of higher order exchange terms?

The MP2 ground state energy of a molecule or solid can be written as $$E^{(2)} = \frac{1}{2}\sum^{\text{occ.}}_{ij}\sum^{\text{virt.}}_{ab} \frac{\langle ij | ab \rangle [\langle ab|ij \rangle - \...
11
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1answer
535 views

What are these “certain chemical compounds” denser than osmium?

The Wikipedia entry for density states Osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. I ...
11
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0answers
127 views

Tetrahedrane Properties and Analogs

I took a look into some tetrahedrane (C4H4) analogs, platonic hydrocarbon, basically very strained tetrahedral geometry at every carbon. I was wondering what will be the predicted delta H of ...
11
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0answers
269 views

Rotation around CC bond in 1,2-dioxetane: transition states and local minimum structures

TLDR: What: Potential energy surface associated with rotation around CC bond in the ring-opened version of 1,2-dioxetane. How: State average(4)-CASSCF(12,10)/VTZP constrained geometry optimizations ...
11
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0answers
9k views

How does VB theory explain the bond angles in SiO2?

Silicon dioxide has a huge variety of structures. Most of them have a tetrahedral $\ce{SiO2}$ unit cell — the $\ce{O–Si–O}$ angle is $109.5°$, accordingly. The VB/hybridization approach to this ...
11
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0answers
209 views

Density Functional Theory with Generalized Gradient Approxmations (GGA) - What Happens if the Electron Density Shows a “Kink” at the Ion Position?

My question may be stupid, so please correct me if you find anything which is obviously erroneous. In the following I will place a question mark (?) besides points/steps I consider doubtful. My ...
10
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0answers
149 views

Why are palladium and platinum carbonyls unstable at room temperature?

By palladium and platinum carbonyls, I mean the mononuclear, homoleptic, charge-neutral, binary carbonyl complexes of the form $\ce{M(CO)_n}$ and not any heteroleptic complexes like $\ce{Pd(CO)(PPh3)3}...
10
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0answers
135 views

What happens when para-water ice is suddenly melted?

Background (hydrogen) In the case of recently liquified hydrogen (which is quite cold of course) it must be re-equilibrated before loading on to a rocket as fuel to avoid a sudden exothermic ...
10
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0answers
345 views

Understanding two-electron integrals in Gaussian 09

I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
10
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0answers
129 views

Does this binary compound of C and N - isoelectronic with carbon suboxide - exist?

I am a mathematician not a chemist, so my questions are naive and rather combinatorial. I am intrigued by the possibility of the following compound: $$\ce{N- = N+ = C = N+ = N-}$$ which ought to ...
10
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0answers
213 views

Were gold(II) complexes synthesized for the first time in 2017?

Recently in the Google news feed, I discovered this news: Gold stabilized in very rare oxidation state +II Missing golden link found: Divalent gold complex isolated for the first time in a ...
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0answers
78 views

Oxide content description

From time to time, I come by to see what people do with my mhchem package. Here, I came across a notation that I did not know yet: $\ce{K2O-nSiO2-xH2O}$ and $\ce{K2O - 3.2SiO2 - 2.7H2O}$ What is this?...
10
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0answers
101 views

In a molecular dynamics context, is the methyl rotation in propene a symmetric or asymmetric internal rotor?

In a prior question, I asked about the (a)symmetry of the potential energy surface of the methyl rotation of propene. In that context, the kinetic energy of the nuclear motions is of course assumed ...
10
votes
1answer
257 views

What might serve as an initial starting photocatalyst for this large water-splitting solar simulator?

The Gizmodo article Insane Light System Blasts the Energy of 10,000 Suns and Phys.org's Let there be light: German scientists test 'artificial sun' both describe the large, powerful concentrated light ...
10
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0answers
82 views

Is there a structured data source containing information on the World Health Organisation's Stability Testing Policies?

Hoping to automate some product testing guidance software, I've been attempting to find a (hopefully live, up-to-date) Database, Web-service, or other structured data source containing the ...
10
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0answers
135 views

Color of methoxy substituted phenyl rings when heated in the presence of acid

Anyone who's familiar with organic synthesis will probably have came across the DMB and PMB protecting groups. When TLC-ing compounds containing these protecting groups using common stains like ...
10
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0answers
926 views

What makes a compound a dehydrating agent?

When a carboxylic acid with low molecular weight is heated with $\ce{P2O5}$ we get the corresponding anhydride. My book says that this reaction happens with dehydrating agents such as $\ce{P2O5}$. I ...
10
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0answers
251 views

Does liquids that emit light when vibrated exist?

I am looking for a liquid that illuminates when vibrations are added. It does not have to be strictly chemical, it might as well be something else as well. Maybe a crystal in powder form mixed with ...
10
votes
1answer
2k views

Calculation of Atomic weight percentage in AAS

I am currently doing doping studies in a system similar to this ($\ce{A_{x}B_{1-x}}$) and I have to find atomic weight percentage of $\ce{B}$ element using atomic absorption spectroscopy(AAS). I have ...
10
votes
1answer
604 views

Nucleophilicity with respect to the solvent

I am currently studying nucleophilicity of molecules and am getting a set of conflicting information, so I wanted to clarify nucleophilicity trends with respect to solvent. Master Organic Chemistry ...
9
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0answers
209 views

What is the largest coupled cluster calculation that has ever been done (as of March 2019)?

I am doing some research and trying to make sure the numbers I am reporting are accurate. I found that the paper by Sylvetsky et. al. says:[1] We were, however, able to complete a ...
9
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0answers
53 views

Does the alpha effect apply to third row elements?

Alkylperoxy anions are stronger nucleophiles than alkoxides (the so-called alpha effect), but would an alkyldisulfide anion be a better nucleophile than an alkylthiolate anion?
9
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0answers
79 views

Polymers that aren't brittle at the cryogenic temperatures found on Titan?

For entertainment purposes, I'm imagining a colony on a non-terraformed Titan, and wondering what is achievable. Hydrocarbons are incredibly plentiful there, while metals and even silicon would be ...
9
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0answers
205 views

Aza-enolates: why no reaction at N

My understanding is that aza-enolates have an advantage over enamines in enolate-type alkylations because the reaction at N is less likely. As a result, unactivated electrophiles can be used (i.e. ...
9
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0answers
136 views

Some materials emit more photoelectrons than others - why?

Again, I'm a physicist turning to chemists (so bear with me). So I've been measuring some materials by changing the wavelength of the incident light on the material and I have a detecting tip like in ...
9
votes
0answers
217 views

Does a zinc metal coating react with coffee in a coffee grinder?

I'm restoring an old coffee grinder and I want to give the grinder mechanism a nice zinc / silver coating. But I read it is not safe for zinc to be in contact with acidic foods. When I look at the ...
9
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0answers
2k views

Synthesis of Anthracene: Mechanism

Recently, I happened to find a problem that involved the synthesis of anthracene from bromobenzene in the presence of tert-butyl lithium, using THF as the solvent, and at room temperature. I am ...
9
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0answers
533 views

Are all monomers in a polymer covalently bonded?

I'm approaching chemistry and I read on Wikipedia that The modern concept of polymers as covalently bonded macromolecular structures was proposed in 1920 by Hermann Staudinger" But then the ...
9
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0answers
118 views

Newer ionic radii data than Shannon's 1976 compilation?

Shannon, R. D., 1976, Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides: Acta Crystallographica Section A, v. 32, p. 751–767. DOI: 10.1107/...
9
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0answers
111 views

How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...

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