A new article - An Ab Initio Metadynamics Study Reveals Multiple Mechanisms of Reactivity by a Primal Carbon Cluster Toward Hydrogen and Ammonia in Space

#quantum #chemistry #science #compchem #theochem #chemsky #reaction #mechanism #metadynamics #dynamics #CP2K #carbon

doi.org/10.3390/nano...

Some initial results on the reactivity of a primal carbon cluster towards ammonia in space - IOPscience Some initial results on the reactivity of a primal carbon cluster towards ammonia in space, Kalchevski, Dobromir Antonov, Trifonov, Dimitar, Kolev, Stefan Kolev, Popov, Valentin, Aleksandrov, Hristiyan, Dimov, Dimitar Angelov, Milenov, Teodor Ivanov

A new article - Some initial results on the reactivity of a primal carbon cluster towards ammonia in space

#quantum #chemistry #theoretical #science #compchem #theochem #chemsky #theory #reaction #mechanism #metadynamics #dynamics #CP2K

iopscience.iop.org/article/10.1...

Electronic density through the plane of the reactive C- - -H- - -C atomic formation of a [1,5] sigmatropic H-shift.

#theoretical #chemistry #quantum #metadynamics #dynamics #abinitio #chemsky #theochem #compchem #organic #sigmatropic #mechanism #reaction #CP2K

Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and noncanonical base pairs that require protonation events to stabilize or perturb these interactions. Constant pH molecular dynamics (CpHMD) methods provide a reliable framework to explore the conformational and protonation spaces of dynamic structures and to perform robust calculations of pH-dependent properties, such as the pKa of titratable sites. Despite growing biological evidence concerning pH regulation of certain motifs and its role in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. This work extends the stochastic titration CpHMD method to include RNA parameters from the standard χOL3 AMBER force field. We demonstrate its capability to capture titration events of nucleotides in single-stranded RNAs. We validate the method using trimers and pentamers with a single central titratable site while integrating a well-tempered metadynamics approach into the st-CpHMD methodology (CpH-MetaD) using PLUMED. This approach enhances the convergence of the conformational landscape and enables more efficient sampling of protonation-conformation coupling. Our pKa estimates are in agreement with experimental data, validating the method’s ability to reproduce electrostatic changes around a titratable nucleobase in single-stranded RNA. These findings provide molecular insight into intramolecular phenomena, such as nucleobase stacking and phosphate interactions, that dictate the experimentally observed pKa shifts between different strands. Overall, this work validates both the st-CpHMD method and the metadynamics integration as reliable tools for studying biologically relevant RNA systems.

Constant pH #metadynamics simulation of #RNA oligomers now published on @acs.org JCIM! Work done by @tf-silva.bsky.social with some help from @bussigio.bsky.social . doi.org/10.1021/acs.jcim.4c02185

Και φυσικά... Περήφανα, αναφέρω την προσθήκη νέου "υψηλού" πελατολογίου σε Αυτοδιοίκηση και Κεντρική Πολιτική σκηνή. Η #Metadynamics με εμπειρία και τεχνογνωσία κάνει βήματα Meta...

Εμπιστευτείτε μας και εδώ στο #Bluesky 🤟

Intermediate Workshop: December 19th 2024 at ULisboa

Our work presented at the 3D-BIOINFO-PT workshop 3d-bioinfo-pt.github.io/workshops/wo... and meeting 3d-bioinfo-pt.github.io/annual_meeti...! @tf-silva.bsky.social will give a @plumed.org tutorial on constant pH #metadynamics and show our latest results on #RNA oligomers (arxiv.org/abs/2410.16064)

mfmaterials.com

We combine advanced experimental and theoretical approaches in the design, synthesis and characterization of Multifunctional Materials.

#chemistry #quantum #theory #experiment #reaction #mechanism #metadynamics #dynamics #qmmm #materials #CP2K #MOLCAS #theochem #compchem

My first Bluesky post!

Using #metadynamics and #python? Try our Metadynminer.py doi.org/10.1093/bioi...