Edgardo De Leon
edlalio.bsky.social
Edgardo De Leon
@edlalio.bsky.social
Computational chemist:)

Graduate student at utrgv

Studies on nuclear receptors
Reposted by Edgardo De Leon
Interesting paper that challenges alkyl group electronic effects in standard organic chemistry textbooks.

#ChemSky

pubs.acs.org/doi/10.1021/...
Rethinking Organic Chemistry: The Dual Electronic Behavior of the Alkyl Group
A unified framework for understanding the electronic nature of alkyl substituents is presented, resolving the contradiction between spectroscopic data and reactivity patterns typically found in organic chemistry textbooks. This framework is based on the distinct interactions of alkyl groups with σ frameworks and π systems. When attached to an sp3-hybridized atom, as in alkanes, amines, and ethers, the alkyl group acts as an inductive electron-withdrawing substituent (relative to hydrogen). This behavior reflects the greater electronegativity of carbon than hydrogen, as evidenced by NMR chemical shifts and dipole moments. The stability trends observed for aliphatic carbanions and free radicals (ethyl < isopropyl < tert-butyl in both cases) are due to this electron-withdrawing character. The acidity trend of alcohols in aqueous mixtures (methanol > ethanol > 2-propanol > tert-butanol) correlates with the decreasing permittivities of the pure alcohols. Apparent electron-donating effects inferred from Gibbs free energy acidities of ammonium ions and substituted acetic acids arise from entropic artifacts caused by hydrophobic effects. When the alkyl group is bonded to an sp2-hybridized atom, as in alkenes, arenes, carbonyl compounds, carboxylic acids, amides, heterocycles, and carbocations, or to an sp-hybridized atom, as in alkynes, concurrent hyperconjugative electron donation occurs, which overcomes the inductive electron-withdrawing effect in the tert-butyl cation. This work calls for revising textbooks to emphasize both electronic effects and to replace the misinterpreted reactivity examples with spectroscopically validated models, thereby providing a consistent framework essential for educating students and training AI systems in chemistry.
pubs.acs.org
November 11, 2025 at 4:48 AM
I wish I could keep working on this cool protein:(
September 27, 2025 at 11:10 PM
Tiny paraben goes bye-bye
September 26, 2025 at 2:32 AM
Reposted by Edgardo De Leon
Excited to share our new ChemPhysChem paper 🎉
🔗 doi.org/10.1002/cphc...
MD simulations reveal how glycan fluctuations impact water networks & proton shuttle dynamics in this cancer-linked enzyme.

#CompChem #MolecularDynamics #EnzymeCatalysis #Glycosylation
Effect of Glycosylation on the Reorganization at the Active Site of Human Carbonic Anhydrase IX
Coupled dynamics of a distal glycan chain and active site reorganization is reported from simulations of catalytic domain of human carbonic anhydrase IX in water. Glycan conformations, extended away ....
doi.org
September 20, 2025 at 6:27 PM
Reposted by Edgardo De Leon
Watch how the calcium pump moves ions across cell membranes allowing the synchronized contraction of muscle cells.
Calcium Pump (from PDB-101)
This animation is an excerpt from the "What is a Protein?" video available here: http://pdb101.rcsb.org/learn/videos/what-is-a-protein-video Animation by Maria Voigt
www.youtube.com
September 1, 2025 at 4:22 PM
Reposted by Edgardo De Leon
Many plant stress responses are mediated by a signaling pathway activated by abscisic acid (ABA), a small-molecule hormone synthesized by plant tissue under drought conditions.
More at September's Molecule of the Month:
PDB101: Molecule of the Month: Abscisic Acid Receptor
Regulating drought tolerance in plants
pdb101.rcsb.org
September 2, 2025 at 3:48 PM
She is looking over my script🙂‍↕️
August 14, 2025 at 3:41 PM
Reposted by Edgardo De Leon
July 7, 2025 at 5:29 AM
Reposted by Edgardo De Leon
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...
June 30, 2025 at 7:45 PM
what a cool paper!
Don't miss Christo Z. Christov et al's recent article

#ChemSciCovers
#chemsky

'Revealing the nature of the second branch point in the catalytic mechanism of the Fe(ii)/2OG-dependent ethylene forming enzyme'

🔗 doi.org/10.1039/D4SC...
May 12, 2025 at 12:52 AM
Reposted by Edgardo De Leon
Applications are open for the CECAM - @mddbeu.bsky.social workshop on the role of MD in drug discovery!
➡️ www.cecam.org/workshop-det...
Join us to explore how #MolecularDynamics simulations support and accelerate drug discovery!

🗓️ Sep 29 - Oct 1
📍 Montelino (PG), Umbria, Italy

Read more and register ➡️ bit.ly/3GFShFs

#MDDB #DrugDiscovery #FAIRdata #OpenScience
May 8, 2025 at 11:35 AM
Reposted by Edgardo De Leon
Okay hear me out, what if building your protein model was a first person horror survival experience??

#MolecularNodes #b3d #GeometryNodes 🧪
April 29, 2025 at 9:43 AM
Reposted by Edgardo De Leon
🧪Holy shit. The Covid.gov website directs to the WH website claiming that covid came from a lab leak. And they are blaming Anthony Fauci. And calling the NIH a failure. I am utterly speechless. Anti-science propaganda running its wheels in real time.
Lab Leak: The True Origins of Covid-19
THE ORIGIN “The Proximal Origin of SARS-CoV-2” publication — which was used repeatedly by public health officials and the media to discredit the lab leak
Covid.gov
April 19, 2025 at 12:19 AM
Reposted by Edgardo De Leon
AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 17, 2025 at 7:11 PM
Reposted by Edgardo De Leon
RIP quantum mechanics, you were too woke for this world #chemsky 🧪
woke is when equations
April 3, 2025 at 5:31 PM
Reposted by Edgardo De Leon
We are, quite literally, held together by collagen. But the protein's twisted ropes aren't stable at our body temp—so what keeps us from falling apart? That story and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪
April 2, 2025 at 12:07 AM
Reposted by Edgardo De Leon
Our study of Mad2 conformational changes is out in final form.

A fun collaborative project to work that uses NMR and MD. @connyyu.bsky.social

onlinelibrary.wiley.com/doi/full/10....
Molecular mechanism of Mad2 conformational conversion promoted by the Mad2‐interaction motif of Cdc20
During mitosis, unattached kinetochores trigger the spindle assembly checkpoint by promoting the assembly of the mitotic checkpoint complex, a heterotetramer comprising Mad2, Cdc20, BubR1, and Bub3. ...
onlinelibrary.wiley.com
March 31, 2025 at 9:56 AM
Reposted by Edgardo De Leon
Asgard Arf GTPases can act as membrane-associating molecular switches with the potential to function in organelle biogenesis www.nature.com/articles/s41... #jcampubs
Asgard Arf GTPases can act as membrane-associating molecular switches with the potential to function in organelle biogenesis - Nature Communications
The formation of organelles was a pivotal point in eukaryotic evolution. Here they show that Archaea possess Arf-like GTPases that can perform key organelle-producing mechanisms when expressed in a eu...
www.nature.com
March 18, 2025 at 12:42 AM
Reposted by Edgardo De Leon
Next up in the ProSE Seminar Series: Devlina Chakravarty (@devlinac.bsky.social) presents "Mutations Switch Folds in Proteins".
Join us to explore how mutations reshape protein structures!

April 8, 3PM GMT
Register here: tinyurl.com/prose-seminar3

#ProSESeminar #ProteinEvolution #StructuralBiology
March 26, 2025 at 2:27 PM
Reposted by Edgardo De Leon
For readers interested in how functional dynamics studies of G-protein-coupled receptors can reveal new routes for drug discovery, here's a recent review nature.com/articles/s41...
rdcu.be/ee1cN
March 25, 2025 at 3:13 PM
Getting a structure ready for MD:)
March 20, 2025 at 7:10 PM
Amazing presentation!
March 18, 2025 at 4:31 PM
Reposted by Edgardo De Leon
I am pleased to share my eLife Insight related to an outstanding manuscript by Nahas et al. This manuscript discusses the assembly of the Herpes simplex virus through a combination of light microscopy and X-ray tomography. You can find my Insight here: elifesciences.org/articles/106....
Viruses: How herpes is assembled
A combination of imaging techniques reveals how herpes simplex virus type 1 assembles within infected cells, highlighting the roles of essential viral proteins in viral assembly and exit.
elifesciences.org
March 17, 2025 at 5:09 PM
So im guessing something went wrong with my simulation
March 14, 2025 at 1:18 PM
Really liking this book so far:D
March 13, 2025 at 8:30 PM