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Isomerism

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Sodium adduct formation with graph-based machine learning can aid structural elucidation in non-targeted LC/ESI/HRMS.

Analytica chimica acta
Non-targeted screening with LC/ESI/HRMS aims to identify the structure of the detected compounds using their retention time, exact mass, and fragmentation pattern. Challenges remain in differentiating between isomeric compounds. One untapped possibil...

Utilization of Machine Learning for the Differentiation of Positional NPS Isomers with Direct Analysis in Real Time Mass Spectrometry.

Analytical chemistry
The differentiation of positional isomers is a well established analytical challenge for forensic laboratories. As more novel psychoactive substances (NPSs) are introduced to the illicit drug market, robust yet efficient methods of isomer identificat...

A Neural Network Approach for Property Determination of Molecular Solar Cell Candidates.

The journal of physical chemistry. A
The dihydroazulene/vinylheptafulvene (DHA/VHF) photocouple is a promising candidate for molecular solar heat batteries, storing and releasing energy in a closed cycle. Much work has been done on improving the energy storage capacity and the half-life...

Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI).

The Journal of chemical physics
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing the product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates usi...

Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials.

Journal of chemical information and modeling
Computational programs accelerate the chemical discovery processes but often need proper three-dimensional molecular information as part of the input. Getting optimal molecular structures is challenging because it requires enumerating and optimizing ...

Transition state search and geometry relaxation throughout chemical compound space with quantum machine learning.

The Journal of chemical physics
We use energies and forces predicted within response operator based quantum machine learning (OQML) to perform geometry optimization and transition state search calculations with legacy optimizers but without the need for subsequent re-optimization w...

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.

The Journal of chemical physics
Modern semiempirical electronic structure methods have considerable promise in drug discovery as universal "force fields" that can reliably model biological and drug-like molecules, including alternative tautomers and protonation states. Herein, we c...

In vitro metabolic studies and machine learning analysis of mass spectrometry data: A dual strategy for differentiating alpha-pyrrolidinohexiophenone (α-PHP) and alpha-pyrrolidinoisohexanophenone (α-PiHP) in urine analysis.

Forensic science international
Synthetic cathinones are some of the most prevalent new psychoactive substances (NPSs) globally, with alpha-pyrrolidinoisohexanophenone (α-PiHP) being particularly noted for its widespread use in the United States, Europe, and Taiwan. However, the an...

Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach.

Journal of chemical information and modeling
Unraveling the reaction pathway of photoinduced reactions poses a great challenge owing to its complexity. Recently, graph theory-based machine learning combined with nonadiabatic molecular dynamics (NAMD) has been applied to obtain the global reacti...

Fast and Accurate Prediction of Tautomer Ratios in Aqueous Solution via a Siamese Neural Network.

Journal of chemical theory and computation
Tautomerization plays a critical role in chemical and biological processes, influencing molecular stability, reactivity, biological activity, and ADME-Tox properties. Many drug-like molecules exist in multiple tautomeric states in aqueous solution, c...