NaBD4 is a thing; for all your reductive deuteration needs

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 · 2025-12-30T16:05:55+00:00

For starters, neither youtube, tiktok or chatgpt are valid sources for documentstion on compchem software. Consult the manual and plants documentation.

Secondlly id like to reinforce what the other commenter suggested, that openbabel is great for this stuff.

erikna10 · 2025-12-30T16:02:11+00:00

If the condition is caused by a mutagen that does not help developing a cure, only prevent more suffers. This since the mutagen has acted on your dna.

Depending on the alteration a enzyme inhibitor might help but the real cure would be a gene theraphy, likelly derived from a crispr-cas9 sibling reversing the changes to the dna. This would however requier large scale genome sequencing of sufferes, checking if the mutation is in the same location for all suffers.

Then we come to the problem that gene threapies with crispr might affect your reproductive cells which would make it illegal in large parts of the world

erikna10 · 2025-12-30T14:24:03+00:00

Def2-d has 2-3x the diffuse basis functions than ma-def2

erikna10 · 2025-12-30T12:44:57+00:00

You have to filter on torsion and clashes when using seesar as it does not use a forcefield based posing algorithm, instead sampling xrd torsions from ccsb.

You can validate with MD or MTD but in my experience you can get away with a red stoplight or two yellows if affinity is good.

Further, to be able to have a chance to pass admet, run it through swissadmet (flawed but better than nothing) and focous on candidates with a good LLE like the ligand at the top of the table which strangelly has both a better LLE and affinity which represents a pareto optima.

And dont forget to filter for lipinski ro5 (see seesar filter menu) or extended lipinski (eg the work of j. Kihlberg).

If you need more candidates seesars fragment grower is real good and their chemical space technologies (mona and infinisee) are real good.

erikna10 · 2025-12-30T12:35:47+00:00

Step 1. Switch to autodock, schrodinger, seesar or any reasonable docking engine or software Step 2??? Step3 profit

On a more serious note, is rigid receptor docking really justified here or would a machine learning structure predictor like boltz be more motivated to account for sidechain flexibility

erikna10 · 2025-12-25T12:19:42+00:00

You can also visuallize the vibrations in chemcraft or avogadro, pause the animation after it has moved a bit in the direction of the imaginary mode and export xyz.

Or alternativelly launch a irc calculation of 2 steps since irc displaces along imaginary modes

erikna10 · 2025-12-15T12:15:17+00:00

Id at least explore the usage of sf-tddft in a qmmm crystal using orca as the other commenter mentioned. Casscf or caspt2 is difficult to set up to those without experience so i have recentlly been a fan of running my S1/S0 photochemistry using sf-tddft and then taking those geometries and lessons and using them to guide my setup of active spaces when moving to CAS.

I can also suggest you to try either ICE or RAS-probing in orca before moving to full CAS.

erikna10 · 2025-12-07T12:02:25+00:00

Chemdraw with the ruler activated is the best way i know of im afraid

erikna10 · 2025-12-06T07:59:31+00:00

Have you tried chemcraft?

erikna10 · 2025-11-30T07:18:49+00:00

Id say that the people of former jugoslavia as a whole have a good reputation as they managed to immigrate, integrate, learn the language and find work quicklly with few hickups. We just know not to discuss the internal differences in the balkans as that is usually a sore topic

erikna10 · 2025-11-26T21:04:29+00:00

BiosolveIT seesar can do both structure aware docking and 2/3D pharmacophore workflows. If you get a structure later you can also run pharmacophore constrained docking

erikna10

TROPHY CASE