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Brodie Bulcock

@brodiebulcock.bsky.social
23 followers 58 following 4 posts

PhD candidate at UWA researching fungal natural products chemistry ⚗️🧪 and biosynthesis 🧫🧬

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Brodie Bulcock @brodiebulcock.bsky.social · 06/08/2026
Really cool computational work uncovering the mechanism for mechanoluminescence in 1,2-dioxetanes doi.org/10.1021/jacs...
doi.org
The Force Awakens a Dormant Chemiluminescent Pathway in 1,2-Dioxetane
Abstract. 1,2-Dioxetanes are well-known for their chemiluminescent decomposition initiated by O–O bond scission. Under thermal conditions, this chemilumine
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Brodie Bulcock @brodiebulcock.bsky.social · 13/04/2026
Great detective work, finding trace impurities (0.5%, new structures) as the true source of antiviral activity for isoquercetin: pubs.acs.org/doi/10.1021/...
pubs.acs.org
Multilevel Residual Complexity Analysis Reveals Origin of Nanomolar Antiviral Bioactives of “Isoquercitrin”
The remarkable reported in vitro and in vivo antiviral activity of a commercial, naturally derived, isoquercitrin sample (IQC90) against Ebola (EBOV), Zika virus (ZIKV), and SARS-CoV-2 could not be co...
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Reposted by Brodie Bulcock
Avogadro Project @avogadro.cc · 01/04/2026
No fooling, Avogadro 2.0.0 is finally here! Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️ avogadro.cc/install/ discuss.avogadro.cc #opensource #openscience #compchem
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Reposted by Brodie Bulcock
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Reposted by Brodie Bulcock
Mehdi Beniddir @mehdibeni.bsky.social · 13/10/2025
Thrilled to share with you a recent work from our group: Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome | Journal of Natural Products pubs.acs.org/doi/10.1021/... Please have a look to the associated MassQL compendium.
pubs.acs.org
Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome
An advanced metabolomic workflow featuring expert knowledge-tailored mass spectral queries and multi-informative molecular networking was applied to French DNA-barcoded collections of Amanita species ...
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Brodie Bulcock @brodiebulcock.bsky.social · 04/07/2025
Crystal clear? Not quite! Our new paper explores how atoms with similar atomic numbers can be misidentified with X-ray crystallography, and revises the chemical structures of a series of nucleoside natural products. pubs.acs.org/doi/10.1021/...
pubs.acs.org
Reconsidering the Structures of Tetillapyrone, Nortetillapyrone, Ochraceopyronide, and Rhizoaspergillin A
In this study, we revise the structures of the marine sponge-derived pyrone-deoxyribosides tetillapyrone and nortetillapyrone, as well as the semisynthetic derivative tetillapyrone diacetate, to the n...
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Reposted by Brodie Bulcock
Thomas Froitzheim @thfroitzheim.bsky.social · 24/06/2025
After almost 3 years of development with @grimmelab.bsky.social, a first preliminary version of our next-generation general extended Tight-Binding (g-xTB) is now on ChemRxiv! Catch the details at #WATOC: my talk (Thu Session B1) and Stefan’s talk (Thu Session A2). #compchem doi.org/10.26434/che...
doi.org
g-xTB: A General-Purpose Extended Tight-Binding Electronic Structure Method For the Elements H to Lr (Z=1–103)
We present g-xTB, a next-generation semi-empirical electronic structure method derived from tight-binding (TB) approximations to Kohn–Sham density functional theory (KS-DFT). Designed to bridge the ga...
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Reposted by Brodie Bulcock
FACCTs @faccts.de · 19/02/2025
The paper on ORCA 6’s Global Optimization Algorithm GOAT is finally published at Angewandte Chemie! Feel free to try Bernardo's (@bernadsz.bsky.social) algorithm to generate conformer ensembles and much more. doi.org/10.1002/anie... Tutorial on GOAT: www.faccts.de/docs/orca/6.... #ORCAqc #ChemSky
doi.org
GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters
In this work, we propose a new Global Optimization Algorithm (GOAT) for molecules and clusters of atoms and show how it can find the global energy minima for both systems without resorting to molecul...
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Brodie Bulcock @brodiebulcock.bsky.social · 10/02/2025
Excited to share that SpectroIBIS, a tool for natural product DFT data processing, is now out in JNP! 🌿 Key features: 🔹Drag & drop Gaussian/ORCA output files to calculate Boltzmann-averaged ECD/UV/VCD/IR/NMR/OR data 🔹Removes redundant conformers 🔹Makes SI data tables pubs.acs.org/doi/10.1021/...
doi.org
SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations
Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of chemical structures, especially their stereochemical configurations. These calculations have become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks for many researchers. In this article, we introduce the SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered in this workflow. Through a simple graphical user interface, researchers can drag and drop Gaussian or ORCA output files to produce Boltzmann-averaged ECD, VCD, UV–vis and IR data, optical rotations, and/or 1H and 13C NMR chemical shifts in seconds. Also produced are formatted, publication-quality supplementary data tables containing conformer energies and atomic coordinates, saved to a DOCX file compatible with Microsoft Word and LibreOffice. Importantly, SpectroIBIS can assist researchers in finding common calculation issues by automatically checking for redundant conformers and imaginary frequencies. Additional useful features include recognition of conformer energy recalculations at a higher theory level, and automated generation of input files for quantum chemistry programs with optional exclusion of high-energy conformers. Lastly, we demonstrate the applicability of SpectroIBIS with spectroscopic calculations for five natural products. SpectroIBIS is open-source software available as a free desktop application (https://github.com/bbulcock/SpectroIBIS).
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