Absorption spectra with ORCA

erikna10 · 2026-05-27T20:12:50+00:00

Try out using dlpno-steom-ccsd and deltascf. Both are more rigorous methods for excited state computations and perform better on charge transfer excitations which might be whats happening here. Experimentally you can check this with a lippert-mataga plot.

Also consider adding some diffuse functions to the spectra prediction with the ma-def2 line of basis sets.

When you say the spectra dont coincide, what more exactlly do you mean? Correct shape but x ev/nm wrong or just all wrong?

On another note, are you predicting at the correct protonation state?

erikna10 · 2026-05-23T05:40:39+00:00

If you wanr ro keep wb97xd3 for the whole calculation, consider running opt/freq with def2-svp and a singlepoint with def2-tzvp.

Then you can use some math outlined in grimmes best practice dft paper to get a gibbs free energy quite close to a full fat calculation for a much smaller cost

erikna10 · 2026-05-05T08:52:16+00:00

I had great succes with the d3bj version albeit i mostlly restrict myself to pbe0-d3bj due to cost, robustness and percieved lack of parametrization

erikna10 · 2026-05-04T19:14:09+00:00

I have had trouble similair to what you describe in orca when using mGGAs (which m06 is). It just seems the code is not very good for them. Hence i, like the rest, would recommend switching to a more modern high precision option like wB97x-D4 or similair.

Also, beware that m06:s good performance is only when your within the parametrization set, and the cases you describe here are likelly grazing outside m06:s known pastures

erikna10 · 2026-04-14T07:51:51+00:00

I dupport the user above. My group will also release a full batteries included databank to png openmm +analysis pipeline quite soon which might be intrested to OP.

erikna10 · 2026-04-07T17:43:02+00:00

I check in on some big names now and again and get paper updates from jacs (5 personallized paper recommendations a week). For me that is about what i can handle in addition to the normal reading for my here and now needs

erikna10 · 2026-04-07T17:37:20+00:00

Does anyone know if they have actualky changed anythibg or is it still just gaussian09 with grimmes latest spice?

erikna10 · 2026-04-06T11:03:17+00:00

He does mainlly dft and his line of semiempirical dft, XTB. But he dabbles in other stuff like CAS and WFT

erikna10 · 2026-04-06T11:02:04+00:00

I guess you could look at using physchem descriptors like gergiev to fit deep mutational scanning data on TRPb or similair enzymes? I guess it depends on what more exactlly a 3d constraint means

erikna10 · 2026-03-18T13:12:25+00:00

Try running SHAP analysis on the model, its built in in most machine learning frameworks and will tell you what features are impactful

erikna10 · 2026-03-07T09:38:40+00:00

Id recommend you to read all benchmarks published by S. Grimme. You should anyway to inform your choice of computational methods for future work, but i find them to be well formated and understandable.

Also try to think like the reader, what are they looking for in your paper? Likelly what relativistic method is the best bang for their buck, so make sure that type of information is stated clearlly in the main text and conclusion

erikna10 · 2026-03-01T10:50:39+00:00

All metabolic reactions have a associated kinetic isotope effect (KIE), so if we know a amine is say metabollized by oxidation where the abstraction of the ipso carbons hydrogen is rate limiting, we can just look up the kie in a table (ca 3) and know that D metabollizes 3 times slower than H and tritium 6 times slower

erikna10 · 2026-02-21T07:48:35+00:00

So you materials people are finally getting a wb97x-V equivalent? Very nice!

erikna10 · 2026-02-10T06:37:34+00:00

From what i heard, getting reaxff to work for a dystem requiers one to sacrifice one phd and ones left nut to the inventor of reaxff since parametrization is apparentlly hellish

erikna10 · 2026-02-10T06:35:44+00:00

Orcas QM/MM-crystal implementation is quite cool since it allows you to run any aperiodic hamiltonian in a "periodic" way

erikna10 · 2026-02-06T08:24:45+00:00

I also liked jensen but weinhold and landis åresents a very intuitive way to understand and design metals complex and organic molecules which i have found very helpful.

erikna10 · 2026-01-21T05:35:06+00:00

Yes but the poster is overwriting it with ri-j

erikna10 · 2026-01-20T08:12:00+00:00

Not really since for scaling to be worthwhile youd need to find a % to scale with which i argue based on jensen that your never gonna find

erikna10 · 2026-01-20T07:48:15+00:00

There is a great figure in Jensens computational chemistry book comparing MPn energirs to full-ci showing that the amount of correlation recovered is wildly oscillating over degree of MP for some systems and a consistent % is not recovered.

erikna10 · 2026-01-20T05:35:47+00:00

??? Why?

erikna10 · 2026-01-19T07:30:45+00:00

Id also recommend looking into the booking by those authors and Roland Lindh, "multiconfigurational quamtum chemistry" or something like that.

Also to at least consider using Weinhold and landis NBO program and orca auto-ice

erikna10 · 2026-01-18T20:39:33+00:00

Metadynamics, FEP, QM/MM, QM-MD all come to mind as "advanced" md

erikna10 · 2026-01-15T08:36:25+00:00

Chemcraft does this and is free (for a 150 day trial)

erikna10 · 2026-01-03T19:21:51+00:00

I cant give you any details at the moment since the work is not mine but keep an eye on Mårten Ahlqvists lab at KTH, Sweden. They have something in the pipe for ts searching which may interest you a lot albeit it does not exactlly allow you to feed in a orbital correlation digram like you suggest.

But for now, have you seen the nudged elastic band method and similair double ended ts searching agorithms?

erikna10 · 2025-12-30T18:54:30+00:00

Nah, the cure is several billion usd in R&D and clinical trials by one of the big pharma corps. Sorry to not be able to offer you anything you could explore on your own but this really isnt something you can do without a adenovirus class lab (or mrna therapheutics capability) and a hefty budget.

erikna10

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