afranceschem.bsky.social
@afranceschem.bsky.social
🧪⚡️☀️⏰️ Photochemistry and chemical dynamics. Chemist at University of Valencia #Photochemistry #ExcitedStates #MolecularDynamics
Pinned
🔎easyPARM is officially presented in JCTC!! ✅️ Check out the validation and new capabilities 🔆 Great work of A. Abdelgawwad, code developer.
doi.org/10.1021/acs....
#JCTC #CompChem #MetalComplex #MolecularDynamics
easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms
The dynamics of metal centers are challenging to describe due to the vast variety of ligands, metals, and coordination spheres, hampering the existence of general databases of transferable force field parameters for classical molecular dynamics simulations. Here, we present easyPARM, a Python-based tool that can calculate force field parameters for a wide range of metal complexes from routine frequency calculations with electronic structure methods. The approach is based on a unique labeling strategy, in which each ligand atom that coordinates the metal receives a unique atom type. This design prevents parameter shortage, labeling duplication, and the necessity to post-process output files, even for very complicated coordination spheres, whose parametrization process remain automatic. The program requires the Cartesian Hessian matrix, the geometry xyz file, and the atomic charges to provide reliable force-field parameters extensively benchmarked against density functional theory dynamics in both the gas and condensed phases. The procedure allows the classical description of metal complexes at a low computational cost with an accuracy as good as the quality of the Hessian matrix obtained by quantum chemistry methods. easyPARM v2.00 reads vibrational frequencies and charges in Gaussian (version 09 or 16) or ORCA (version 5 or 6) format and provides refined force-field parameters in Amber format. These can be directly used in Amber and NAMD molecular dynamics engines or converted to other formats. The tool is available free of charge in the GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).
doi.org
It is a pleasure to have Alessandra G. Ritacca presenting her results at @icmoluv.bsky.social today. Very interesting science and discussions 💡🔬 #icmoltalks #moleculardynamics #compchem #anticancer #Alzheimer
October 17, 2025 at 1:33 PM
The outstanding photocatalytic properties of metallacarboranes in water have been published in CRPS. An interesting dependence on the excitation wavelength is discussed with ab initio calculations! @icmoluv.bsky.social @icmabcsic.bsky.social
www.cell.com/cell-reports...
Low-load Θ-metallacarboranes as safe and efficient photoredox catalysts for UVA-driven oxidation in water
Guerrero et al. report two efficient 3d6 and 3d5 metallacarborane photoredox catalysts with identical structures that selectively oxidize alcohols and alkenes in water at low catalyst loadings. UVA irradiation enhances performance despite weak absorption, demonstrating that earth-abundant metals can rival precious metal catalysts in photoredox applications.
www.cell.com
September 10, 2025 at 3:26 PM
Deeply honored to the ESP for the young investigator award #ESPcongress2025
@photobiologyeurope.bsky.social
August 28, 2025 at 7:34 AM
Listening to Sherri McFarland's plenary lecture. Top science! #ESPcongress2025
August 26, 2025 at 7:13 AM
All ready to start the #ESPcongress2025. Hi Bari!!
August 24, 2025 at 4:50 PM
June 27, 2025 at 4:17 PM
Deeply honoured to receive this award. Thank you @photobiologyeurope.bsky.social !!! See you in Bari
🥁 Drum roll........the 2025 Young Investigator Awardees have been selected! Congratulations to Nicoletta Liguori @nikinikki87.bsky.social and Antonio Francés-Monerris @afranceschem.bsky.social 🎉 They will deliver the Young Investigator Award Lectureship at the #ESPCongress2025. See you all there!
June 11, 2025 at 8:38 AM
Reposted
18 positions with one more in theory!
📣📣📣
Fancy theory, catalysis , excellent research, and working in the most liveable city of the world?
🖥️☀️🎓🇦🇹
Apply now!
#phdjobs
Vienna Doctoral School in #Chemistry offers 17 fully funded #PhD positions. 🧪 #phdsky #academicsky 👩‍🔬👨‍🔬
📅 Application deadline: April 21, 2025.
For more information & how to apply: ⤵️
doschem.univie.ac.at/application/...
April 4, 2025 at 8:58 PM
Reposted
🧪📣❗ #PhDPosition to develop light-activated drugs for cancer phototherapy. We are seeking candidates with a strong background in #OrganicChemistry #ChemBio and #MedChem to apply for FI-STEP predoctoral fellowships #PDT #Metallodrugs #ScienceJobs
March 27, 2025 at 3:29 PM
Reposted
Job alert ! I am looking for a postdoc to work on "computational investigation of ion-effects in ribozyme catalysis" to work with me in Paris (France). 1-year contract funded by @agencerecherche.bsky.social, with possible 2nd year in collab. with P. Jungwirth @iocbprague.bsky.social #compchem #RNA
March 26, 2025 at 8:48 AM
Reposted
A PhD position in theoretical chemistry (2025-2028) is available in my group starting in October. Info&Apply: huixrotllant.github.io/openings.html #academicjobs #compchem Please RT
Openings
huixrotllant.github.io
March 20, 2025 at 6:00 PM
Glad to see our last collaboration on Ir metal complexes for anticancer photodynamic therapy published in Inorg. Chem. Front.!!! @inorgchemfront.rsc.org
doi.org/10.1039/D4QI...
Achieving red-light anticancer photodynamic therapy under hypoxia using Ir(III)-COUPY conjugates
Despite the potential of photodynamic therapy (PDT), this oxygen-dependent oncological treatment is greatly restricted in the clinic by the well-known hypoxic feature of solid tumors. Here we provide ...
doi.org
March 8, 2025 at 1:24 AM
My colleagues from the University of Geneva talking about a very interesting interleukin project. Many mysteries and therapeutic opportunities to be revealed!! #interleukin #biology #proteins #inflammation
www.linkedin.com/feed/update/...
Geneva Centre for Inflammation Research - UNIGE on LinkedIn: #psoriasis #interleukin #il38 #inflammation #cytokine #researcharticle…
🔬 What if IL-38 could unlock new ways to treat inflammatory diseases like #psoriasis? After the discovery of interleukin (IL)-38 in 2001, early studies…
www.linkedin.com
February 17, 2025 at 10:35 AM
⏬️ Potent Ru(III) photosensitizers with high anticancer activity in hypoxia conditions. Very happy to collaborate in such an interesting topic!! ✴️
February 15, 2025 at 8:50 PM
🔎easyPARM is officially presented in JCTC!! ✅️ Check out the validation and new capabilities 🔆 Great work of A. Abdelgawwad, code developer.
doi.org/10.1021/acs....
#JCTC #CompChem #MetalComplex #MolecularDynamics
easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms
The dynamics of metal centers are challenging to describe due to the vast variety of ligands, metals, and coordination spheres, hampering the existence of general databases of transferable force field parameters for classical molecular dynamics simulations. Here, we present easyPARM, a Python-based tool that can calculate force field parameters for a wide range of metal complexes from routine frequency calculations with electronic structure methods. The approach is based on a unique labeling strategy, in which each ligand atom that coordinates the metal receives a unique atom type. This design prevents parameter shortage, labeling duplication, and the necessity to post-process output files, even for very complicated coordination spheres, whose parametrization process remain automatic. The program requires the Cartesian Hessian matrix, the geometry xyz file, and the atomic charges to provide reliable force-field parameters extensively benchmarked against density functional theory dynamics in both the gas and condensed phases. The procedure allows the classical description of metal complexes at a low computational cost with an accuracy as good as the quality of the Hessian matrix obtained by quantum chemistry methods. easyPARM v2.00 reads vibrational frequencies and charges in Gaussian (version 09 or 16) or ORCA (version 5 or 6) format and provides refined force-field parameters in Amber format. These can be directly used in Amber and NAMD molecular dynamics engines or converted to other formats. The tool is available free of charge in the GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).
doi.org
February 7, 2025 at 2:00 PM
🚀 easyPARM V3.00 Release! 🚀New features:
✅ Force field parameterization for metalloproteins
✅ Support for GAMESS & RESP charges from ORCA & GAMESS
✅ Convert AMBER force fields to OpenMM & GROMACS
Check out the manual for details! 🔬📖
github.com/Abdelazim-Ab...
GitHub - Abdelazim-Abdelgawwad/easyPARM: easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems and to enable charge res...
easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems and to enable charge restraints on specific atoms. - Abdelazim...
github.com
February 1, 2025 at 10:45 AM
Here we introduce easyPARM, a free code to generate force field parameters for transition metal complexes. The program requires only the Gaussian/ORCA frequencies and the RESP charges. The output is in Amber format.
chemrxiv.org/engage/chemr...
December 1, 2024 at 1:16 PM