Newcastle Chemistry

@chemistryncl.bsky.social

Official BlueSky feed from Chemistry at Newcastle University https://www.ncl.ac.uk/nes/our-disciplines/chemistry/

Check out our new paper on using approximate symmetry to simplify the asymmetric units of crystal structures with a large number of molecules in the asymmetric unit: pubs.acs.org/doi/full/10.... #crystallography #symmetry #chemsky

Close Enough: Approximate Symmetry in Recent Crystal Structures with Extreme Z′ (Z′ ≥ 12)

To further highlight the link between approximate symmetry and homomolecular structures that crystallize with large numbers of molecules in the asymmetric unit (Z′ ≥ 12), the most recent structures of this type have been analyzed, and the approximate symmetry identified. In most cases, when approximate symmetry is considered, a smaller approximate unit cell can be described, where the effective Z′ is lower than that of the original unit cell. For one example, defining an approximate cell was not appropriate, and the approximate symmetry in the structure was hence described using approximate layer and rod groups. Generally, it appears that though the molecules in the asymmetric units of these structures may not be related by crystallographic symmetry, symmetrical relationships appear to be retained as much as possible in cases where the packing is awkward and precise symmetry is not possible. Revealing the link between extreme-Z′ structures and theoretical structures with lower Z′ is of potential use to the field of crystal structure prediction with regard to the prediction of structures where Z′ > 1.

pubs.acs.org

Thanks to Dr Chris Russell for running the Future Leaders Programme for our PhD researchers last week! A fantastic 2 days where our researchers considered leadership, strategy, and decision making, helping prepare them for leadership roles in academia and industry in the future!

MoSMed PhD researchers taking part in the Future Leadership Programme

🌟 Applications are now open for the Next Generation of AI Chemists Programme, a funded opportunity for penultimate-year undergraduates from backgrounds under-represented in chemistry. 📍 Imperial London | 📅 6–7 July 2026 (in person) 👉 Apply here: buff.ly/MLfs9Zg

Bild

📢 Now out in #JCTC "A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules". Collaborative effort between @charlie-adams.bsky.social, @chemistryncl.bsky.social, @openforcefield.org & Kuano! #compchem pubs.acs.org/doi/10.1021/...

A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules

Common methods for assigning atom-centered partial charges in computational chemistry, such as RESP and AM1-BCC, rely on quantum mechanical or semiempirical calculations of the molecule of interest, which are expensive to compute and dependent on the choice of input molecular conformer(s). Graph neural network (GNN) based continuous atom embeddings have been shown to be a fast and flexible solution for partial charge assignment, but those developed so far for condensed phase modeling have usually been trained to reproduce AM1-BCC charges, which themselves seek to reproduce the HF/6-31G(d) molecular electrostatic potential. Here, we investigate the suitability of various common charge assignment schemes, including ESP and atoms-in-molecule (AIM) based approaches, as training targets for new GNN-based charge models. We show that the strengths of both approaches can be combined by cotraining GNN models to AIM charges and molecular dipoles and electrostatic potentials. We collect a data set of quantum mechanical AIM properties computed at a high level of theory (ωB97X-D/def2-tzvpp), in both vacuum and implicit solvent, and train new GNN charge models to each. Charges can be scaled between the vacuum and solvated charge sets, and combined with Lennard-Jones parameters optimized using the Open Force Field infrastructure, to yield force fields that are suitably polarized for condensed phase modeling. We further demonstrate that the charge models may be applied to explore electrostatics-driven structure–activity relationships in medicinal chemistry. The charge models are freely available at: https://github.com/cole-group/nagl-mbis/.

pubs.acs.org