Jonathan M. Goodman
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View article: Advancing Structure Elucidation with a Flexible Multi‐Spectral AI Model
Advancing Structure Elucidation with a Flexible Multi‐Spectral AI Model Open
Validating chemical synthesis success requires confirming the desired product using various analytical techniques. While spectroscopic data collection is increasingly automated, interpreting results remains a major bottleneck, often requir…
View article: Advancing Structure Elucidation with a Flexible Multi-Spectral AI Model
Advancing Structure Elucidation with a Flexible Multi-Spectral AI Model Open
Validating chemical synthesis success requires confirming the desired product using various analytical techniques. While spectroscopic data collection is increasingly automated, interpreting results remains a major bottleneck often requiri…
View article: Enhancing Molecular Structure Elucidation with Reasoning-Capable LLMs
Enhancing Molecular Structure Elucidation with Reasoning-Capable LLMs Open
We introduce a novel workflow integrating reasoning-capable language models with specialized chemical analysis tools to enhance molecular structure determination using nuclear magnetic resonance spectroscopy. Generally, structure elucidati…
View article: Uncertainty-aware machine learning to predict non-cancer human toxicity for the global chemicals market
Uncertainty-aware machine learning to predict non-cancer human toxicity for the global chemicals market Open
Humans are exposed to many chemicals, yet limited toxicity data hinder effectively managing their impact on human health. High-performing machine learning models hold potential for addressing this gap, but their uncharacterized prediction …
View article: Towards automatically verifying chemical structures: the powerful combination of <sup>1</sup> H NMR and IR spectroscopy
Towards automatically verifying chemical structures: the powerful combination of <sup>1</sup> H NMR and IR spectroscopy Open
Experimental 1 H NMR and IR spectra can be scored against calculated data to verify candidate molecules. We show that combining these techniques is significantly more powerful for automated structure verification than using either one indi…
View article: Enhancing Molecular Structure Elucidation: MultiModalTransformer for both simulated and experimental spectra
Enhancing Molecular Structure Elucidation: MultiModalTransformer for both simulated and experimental spectra Open
We present MultiModalTransformer (MMT), a novel deep learning architecture that directly predicts molecular structures from diverse spectroscopic data (1H-NMR, 13C-NMR, HSQC, COSY, IR, and mass spectrometry (MS). Utilizing a modified Trans…
View article: Towards automatically verifying chemical structures: the powerful combination of ¹H NMR and IR spectroscopy
Towards automatically verifying chemical structures: the powerful combination of ¹H NMR and IR spectroscopy Open
Human interpretation of spectroscopic data remains key to confirming new structures; the quest for speed and resource-efficiency suggests automating structure verification. We report that the combination of NMR and easily accessible IR dat…
View article: Leveraging Language Model Multitasking To Predict C–H Borylation Selectivity
Leveraging Language Model Multitasking To Predict C–H Borylation Selectivity Open
C-H borylation is a high-value transformation in the synthesis of lead candidates for the pharmaceutical industry because a wide array of downstream coupling reactions is available. However, predicting its regioselectivity, especially in d…
View article: HSQC Spectra Simulation and Matching for Molecular Identification.
HSQC Spectra Simulation and Matching for Molecular Identification. Open
In the pursuit of improved compound identification and database search tasks, this study explores heteronuclear single quantum coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerpri…
View article: Suppressing <i>Cis</i>/<i>Trans</i> ‘Ring‐Flipping’ in Organoaluminium(III)‐2‐Pyridyl Dimers–Design Strategies Towards Lewis Acid Catalysts for Alkene Oligomerisation
Suppressing <i>Cis</i>/<i>Trans</i> ‘Ring‐Flipping’ in Organoaluminium(III)‐2‐Pyridyl Dimers–Design Strategies Towards Lewis Acid Catalysts for Alkene Oligomerisation Open
Owing to its high natural abundance compared to the commonly used transition (precious) metals, as well as its high Lewis acidity and ability to change oxidation state, aluminium has recently been explored as the basis for a range of singl…
View article: Every atom counts: predicting sites of reaction based on chemistry within two bonds
Every atom counts: predicting sites of reaction based on chemistry within two bonds Open
How much chemistry can be described by looking only at each atom, its neighbours and its next-nearest neighbours?
View article: Potential for Machine Learning to Address Data Gaps in Human Toxicity and Ecotoxicity Characterization
Potential for Machine Learning to Address Data Gaps in Human Toxicity and Ecotoxicity Characterization Open
Machine Learning (ML) is increasingly applied to fill data gaps in assessments to quantify impacts associated with chemical emissions and chemicals in products. However, the systematic application of ML-based approaches to fill chemical da…
View article: HSQC Spectra Simulation and Matching for Molecular Identification
HSQC Spectra Simulation and Matching for Molecular Identification Open
In the pursuit of improved compound identification and database search tasks, this study explores Heteronuclear Single Quantum Coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerpri…
View article: CONFPASS: Fast DFT Re-Optimizations of Structures from Conformation Searches
CONFPASS: Fast DFT Re-Optimizations of Structures from Conformation Searches Open
CONFPASS (Conformer Prioritizations and Analysis for DFT re-optimizations) has been developed to extract dihedral angle descriptors from conformational searching outputs, perform clustering, and return a priority list for density functiona…
View article: Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions
Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions Open
The selectivity in a group of oxazaborolidinium ion-catalysed reactions between aldehyde and diazo compounds cannot be explained using transition state theory. VRAI-selectivity, developed to predict the outcome of dynamically controlled re…
View article: CONFPASS: fast DFT re-optimizations of structures from conformation searches
CONFPASS: fast DFT re-optimizations of structures from conformation searches Open
CONFPASS (Conformer Prioritizations & Analysis for DFT re-optimisations) has been developed to extract dihedral angle descriptors from conformational searching outputs, perform clustering and return a priority list for DFT re-optimisations…
View article: CONFPASS: fast DFT re-optimizations of structures from conformation searches
CONFPASS: fast DFT re-optimizations of structures from conformation searches Open
CONFPASS (Conformer Prioritizations & Analysis for DFT re-optimisations) has been developed to extract dihedral angle descriptors from conformational searching outputs, perform clustering and return a priority list for DFT re-optimisations…
View article: Selective Functionalisation of 5‐Methylcytosine by Organic Photoredox Catalysis
Selective Functionalisation of 5‐Methylcytosine by Organic Photoredox Catalysis Open
The epigenetic modification 5‐methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5‐methylcytosine methyl group is challenging. Currently, no such c…
View article: Selective Functionalisation of 5‐Methylcytosine by Organic Photoredox Catalysis
Selective Functionalisation of 5‐Methylcytosine by Organic Photoredox Catalysis Open
The epigenetic modification 5‐methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5‐methylcytosine methyl group is challenging. Currently, no such c…
View article: Quantitative <i>In Silico</i> Prediction of the Rate of Protodeboronation by a Mechanistic Density Functional Theory-Aided Algorithm
Quantitative <i>In Silico</i> Prediction of the Rate of Protodeboronation by a Mechanistic Density Functional Theory-Aided Algorithm Open
Computational reaction prediction has become a ubiquitous task in chemistry due to the potential value accurate predictions can bring to chemists. Boronic acids are widely used in industry; however, understanding how to avoid the protodebo…
View article: Interpreting Vibrational Circular Dichroism Spectra: the Cai•Factor for Absolute Configuration with Confidence
Interpreting Vibrational Circular Dichroism Spectra: the Cai•Factor for Absolute Configuration with Confidence Open
Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and…
View article: Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions
Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions Open
The selectivity in a group of oxazaborolidinium ion-catalysed reactions between aldehyde and diazo compounds cannot be explained using transition state theory.
View article: Analysing a billion reactions with the RInChI
Analysing a billion reactions with the RInChI Open
The RInChI is a canonical identifier for reactions which is widely used in reaction databases. It can be used to handle large collections of reactions and to link information from diverse data sources. How much information can it handle? S…
View article: RSC CICAG Open Chemical Science meeting: integrating chemical data from two symposia and a series of workshops
RSC CICAG Open Chemical Science meeting: integrating chemical data from two symposia and a series of workshops Open
In November 2020 the Royal Society of Chemistry Chemical Information and Computer Applications interest group (RSC CICAG) ran a five-day meeting entitled Open Chemical Science ( https://www.rsc.org/events/detail/42090/open-chemical-science…
View article: A review of molecular representation in the age of machine learning
A review of molecular representation in the age of machine learning Open
Research in chemistry increasingly requires interdisciplinary work prompted by, among other things, advances in computing, machine learning, and artificial intelligence. Everyone working with molecules, whether chemist or not, needs an und…
View article: The DP5 probability, quantification and visualisation of structural uncertainty in single molecules
The DP5 probability, quantification and visualisation of structural uncertainty in single molecules Open
Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra.
View article: MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations
MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations Open
New representations and machine learning calculate DFT minima from force field geometries.