Themed collection Most popular 2021 physical and theoretical chemistry articles, 2021

30 items
Open Access Perspective

Automation isn't automatic

The process of automating chemistry involves a wide variety of considerations that are often overlooked.

Graphical abstract: Automation isn't automatic
Open Access Review Article

Conceptual density functional theory based electronic structure principles

In this review article, we intend to highlight the basic electronic structure principles and various reactivity descriptors as defined within the premise of conceptual density functional theory (CDFT).

Graphical abstract: Conceptual density functional theory based electronic structure principles
Open Access Review Article

Can we predict materials that can be synthesised?

Materials discovery is a crucial yet experimentally slow and wasteful process. We discuss how discovery can be accelerated by focusing on making predictions that are synthetically realisable.

Graphical abstract: Can we predict materials that can be synthesised?
Open Access Edge Article

Fine-tuning the spike: role of the nature and topology of the glycan shield in the structure and dynamics of the SARS-CoV-2 S

The N-glycans structures affect the mechanistic properties of the SARS-CoV-2 S, fine-tuning the glycoprotein. The evolution of the glycan shield led to the loss of N370 glycosylation in SARS-CoV-2 S, where the RBD cleft can bind host-cell glycans.

Graphical abstract: Fine-tuning the spike: role of the nature and topology of the glycan shield in the structure and dynamics of the SARS-CoV-2 S
From the themed collection: 2021 ChemSci Pick of the Week Collection
Open Access Edge Article

Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding

The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target. In silico methods reveal structural aspects of how it binds to its 11 natural cleavage sites, the design of novel peptide inhibitors, and insights into drug design.

Graphical abstract: Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding
From the themed collection: 2021 Chemical Science HOT Article Collection
Open Access Edge Article

Real-time prediction of 1H and 13C chemical shifts with DFT accuracy using a 3D graph neural network

From quantum chemical and experimental NMR data, a 3D graph neural network, CASCADE, has been developed to predict carbon and proton chemical shifts. Stereoisomers and conformers of organic molecules can be correctly distinguished.

Graphical abstract: Real-time prediction of 1H and 13C chemical shifts with DFT accuracy using a 3D graph neural network
Open Access Edge Article

Temperature artifacts in protein structures bias ligand-binding predictions

Temperature artifacts in protein structures impact the utility of structural information in computation by misleading validation and application of computational methods in discovering bioactive molecules.

Graphical abstract: Temperature artifacts in protein structures bias ligand-binding predictions
From the themed collection: 2021 ChemSci Pick of the Week Collection
Open Access Edge Article

Sensitization-initiated electron transfer via upconversion: mechanism and photocatalytic applications

A full picture of a new multi-photon excitation mechanism relying on sTTA upconversion is provided, together with selected photocatalytic applications. All mechanistic steps are investigated and the catalytically active species is observed directly.

Graphical abstract: Sensitization-initiated electron transfer via upconversion: mechanism and photocatalytic applications
From the themed collection: 2021 Chemical Science HOT Article Collection
Open Access Edge Article

A color-tunable single-component luminescent molecule with multiple emission centers

Color tunable luminescent materials with multiple emission centers showing delayed fluorescence, single molecular phosphorescence and aggregated molecular phosphorescence are achieved, along with time-dependent and excitation-dependent properties.

Graphical abstract: A color-tunable single-component luminescent molecule with multiple emission centers
Open Access Edge Article

Predicting enzymatic reactions with a molecular transformer

The enzymatic transformer was trained with a combination of patent reactions and biotransformations and predicts the structure and stereochemistry of enzyme-catalyzed reaction products with remarkable accuracy.

Graphical abstract: Predicting enzymatic reactions with a molecular transformer
Open Access Edge Article

DeepFrag: a deep convolutional neural network for fragment-based lead optimization

DeepFrag is a machine-learning model designed to assist with lead optimization. It recommends appropriate fragment additions given the 3D structures of a protein receptor and bound small-molecule ligand.

Graphical abstract: DeepFrag: a deep convolutional neural network for fragment-based lead optimization
Open Access Edge Article

Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES

Interpolation and exploration within the chemical space for inverse design.

Graphical abstract: Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES
Open Access Edge Article

Efficient and organic host–guest room-temperature phosphorescence: tunable triplet–singlet crossing and theoretical calculations for molecular packing

Molecular dynamics simulations were used to simulate the molecular conformation and interaction between hosts and guests. This work provides a new concept for the study of molecular packing for the investigation of the luminescence mechanism.

Graphical abstract: Efficient and organic host–guest room-temperature phosphorescence: tunable triplet–singlet crossing and theoretical calculations for molecular packing
Open Access Edge Article

Calculation of absolute molecular entropies and heat capacities made simple

A novel scheme for the automated calculation of the conformational entropy together with a modified thermostatistical treatment provides entropies with unprecedented accuracy even for large, complicated molecules.

Graphical abstract: Calculation of absolute molecular entropies and heat capacities made simple
From the themed collection: 2021 ChemSci Pick of the Week Collection
Open Access Edge Article

Accelerated AI development for autonomous materials synthesis in flow

A surrogate model is designed to represent a microfluidic material synthesis system using 1000 automatically conducted experiments. With this model, over 600 000 experiments are simulated to optimize an AI-guided material synthesis algorithm.

Graphical abstract: Accelerated AI development for autonomous materials synthesis in flow
Open Access Edge Article

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

Graphical abstract: High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling
Open Access Edge Article

A feasible approach for automatically differentiable unitary coupled-cluster on quantum computers

We develop computationally affordable and encoding independent gradient evaluation procedures for unitary coupled-cluster type operators, applicable on quantum computers.

Graphical abstract: A feasible approach for automatically differentiable unitary coupled-cluster on quantum computers
From the themed collection: Editor’s Choice – Jinlong Gong
Open Access Edge Article

Retrosynthetic accessibility score (RAscore) – rapid machine learned synthesizability classification from AI driven retrosynthetic planning

The retrosynthetic accessibility score (RAscore) is based on AI driven retrosynthetic planning, and is useful for rapid scoring of synthetic feasability and pre-screening of large datasets of virtual/generated molecules.

Graphical abstract: Retrosynthetic accessibility score (RAscore) – rapid machine learned synthesizability classification from AI driven retrosynthetic planning
Open Access Edge Article

Predicting glycosylation stereoselectivity using machine learning

A random forest algorithm, trained on a concise dataset and validated experimentally, accurately predicts the stereoselectivity of a complex organic coupling varying all reaction parameters as well as previously unknown mechanistic influences.

Graphical abstract: Predicting glycosylation stereoselectivity using machine learning
Open Access Edge Article

Insight into the drastically different triplet lifetimes of BODIPY obtained by optical/magnetic spectroscopy and theoretical computations

The electron spin polarization inversion and anisotropic decay of triplet substates explain the short triplet state lifetime of BODIPY derivatives.

Graphical abstract: Insight into the drastically different triplet lifetimes of BODIPY obtained by optical/magnetic spectroscopy and theoretical computations
Open Access Edge Article

Relating atomic energy, radius and electronegativity through compression

Compression is used to derive a long sought-after connection between two central chemical concepts – van-der-Waals (vdW) radii and electronegativity – and how these relate to the driving forces behind chemical and physical transformations.

Graphical abstract: Relating atomic energy, radius and electronegativity through compression
From the themed collection: 2021 ChemSci Pick of the Week Collection
Open Access Edge Article

How many water molecules are needed to solvate one?

How quantum spectroscopic simulations can explain water solvation by comparison with experimental spectra.

Graphical abstract: How many water molecules are needed to solvate one?
From the themed collection: 2021 Chemical Science HOT Article Collection
Open Access Edge Article

BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules

Prediction of bond dissociation energies for charged molecules with a graph neural network enabled by global molecular features and reaction difference features between products and reactants.

Graphical abstract: BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules
Open Access Edge Article

Consistent inclusion of continuum solvation in energy decomposition analysis: theory and application to molecular CO2 reduction catalysts

Extension of ALMO-EDA to include contributions from continuum solvent and application to electro- and photochemical CO2 reduction catalysts.

Graphical abstract: Consistent inclusion of continuum solvation in energy decomposition analysis: theory and application to molecular CO2 reduction catalysts
Open Access Edge Article

Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity

QM/MM simulations identify the mechanism of reaction of N3, a covalent peptidyl inhibitor of SARS-CoV-2 main protease. Modelling of two novel proposed compounds, B1 and B2, suggests that reversibility of covalent inhibition could be tailored.

Graphical abstract: Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity
Open Access Edge Article

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.

Graphical abstract: Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease
Open Access Edge Article

Universal quenching of common fluorescent probes by water and alcohols

Overtones and combinations of O–H vibrations in the solvent efficiently quench red-emitting fluorophores by resonant energy transfer.

Graphical abstract: Universal quenching of common fluorescent probes by water and alcohols
Open Access Edge Article

Machine learning meets mechanistic modelling for accurate prediction of experimental activation energies

Hybrid reactivity models, combining mechanistic calculations and machine learning with descriptors, are used to predict barriers for nucleophilic aromatic substitution.

Graphical abstract: Machine learning meets mechanistic modelling for accurate prediction of experimental activation energies
Open Access Edge Article

Unusual light-driven amplification through unexpected regioselective photogeneration of five-membered azaheterocyclic AIEgen

A multifunctional, AIE-based, fused five-membered azaheterocycle is photogenerated with light-driven amplification to combat the photobleaching issue and fabricate display materials.

Graphical abstract: Unusual light-driven amplification through unexpected regioselective photogeneration of five-membered azaheterocyclic AIEgen
Open Access Edge Article

Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

Using reversed allosteric communication, we performed MD simulations, MSMs, and mutagenesis experiments, to discover allosteric sites. It reproduced the known allosteric site for MDL-801 on Sirt6 and uncovered a novel cryptic allosteric Pocket X.

Graphical abstract: Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy
30 items

About this collection

This specially curated collection pulls together some of the most popular articles from 2021 in the field of physical and theoretical chemistry. The collection presents some outstanding contributions to the field, ranging from fundamental questions in the solvation chemistry of water, through to advances in machine learning and AI applied to diverse chemical problems such as retrosynthesis and predicting activation energies, and – as with all Chemical Science articles – they are all completely free to access and read. We hope you enjoy browsing through this collection.

If a particular article has inspired you, do feel free to share on social media using the buttons on each article landing page and use our hashtag: #ChemSciMostPopular

Spotlight

Advertisements