Jeremy N. Harvey
YOU?
Author Swipe
View article: A New Fragment‐Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of <scp>SARS</scp> ‐ <scp>CoV</scp> ‐2 <scp>NSP13</scp> Helicase
A New Fragment‐Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of <span>SARS</span> ‐ <span>CoV</span> ‐2 <span>NSP13</span> Helicase Open
Herein we report the in silico discovery of 13 novel micromolar potent inhibitors of the SARS‐CoV‐2 NSP13 helicase validated in cellular antiviral and biophysical ThermoFluor assays. The compounds, discovered using a novel fragment‐based p…
View article: Halving the Barrier to Gas-Phase Oxidation of Bromide by Ozone
Halving the Barrier to Gas-Phase Oxidation of Bromide by Ozone Open
Recent atmospheric measurements have indicated that bromine and iodine may be responsible for up to 72% of halogen-induced ozone loss near the tropopause. Whilst the neutral bromine and iodine radicals have well-described reaction pathways…
View article: Conformational analysis of macrocyclic compounds using a machine-learned interatomic potential
Conformational analysis of macrocyclic compounds using a machine-learned interatomic potential Open
Macrocyclic compounds play a vital role in many chemical and biological systems, yet their conformational analysis remains a significant challenge. In this work, we investigate the conformational landscape of macrocyclic compounds using a …
View article: Breakdown and Salvation of Statistical Rate Theory in Biomolecular Photoinduced Electron Transfer
Breakdown and Salvation of Statistical Rate Theory in Biomolecular Photoinduced Electron Transfer Open
Quantifying rates of photoinduced electron transfer (PET) is crucial to understand the remarkable efficiency of biological photosystems involved in photosynthesis and DNA repair. The ability to distinguish between specific PET channels and…
View article: Ligand Design for Aerobic Pd-Catalyzed Styrene Production via the One-Step C–H/C–H Coupling of Benzene and Ethylene
Ligand Design for Aerobic Pd-Catalyzed Styrene Production via the One-Step C–H/C–H Coupling of Benzene and Ethylene Open
sponsorship: We thank J. Dallenes for fruitful discussions and B. Van Huffel for ESI-MS measurements. XAS measurements were conducted at the SAMBA beamline of Synchrotron SOLEIL, Saint-Aubin, France. F.M., H.P.-R. and D.E.D.V. would like t…
View article: Photoinduced decarboxylation in fluorescent proteins: charge-transfer states and structure–function relationship
Photoinduced decarboxylation in fluorescent proteins: charge-transfer states and structure–function relationship Open
Computational exploration of charge-transfer states elucidates photoinduced decarboxylation mechanisms and structure–function relationships in fluorescent proteins.
View article: DARWEN: Data-driven Algorithm for Reduction of Wide Exoplanetary Networks
DARWEN: Data-driven Algorithm for Reduction of Wide Exoplanetary Networks Open
Context . Exoplanet atmospheric modeling is advancing toward complex coupled circulation-chemistry models, from chemically diverse 1D models to 3D global circulation models (GCMs). These models are crucial for interpreting observations fro…
View article: Understanding Substrate Binding and Reactivity of Stearoyl-CoA Desaturase (SCD1) through Classical and Multiscale Molecular Dynamics Simulations
Understanding Substrate Binding and Reactivity of Stearoyl-CoA Desaturase (SCD1) through Classical and Multiscale Molecular Dynamics Simulations Open
Stearoyl-CoA desaturase (SCD1) plays an important role in the metabolism of fatty acids and is a promising therapeutic target. However, the underlying mechanism of SCD1, as well as other transmembrane non-heme diiron enzymes, remains poorl…
View article: Transfer learning based on atomic feature extraction for the prediction of experimental ¹³C chemical shifts
Transfer learning based on atomic feature extraction for the prediction of experimental ¹³C chemical shifts Open
Forecasting experimental chemical shifts of organic compounds is a long-standing challenge in organic chemistry. Recent advances in machine learning (ML) have led to routines that surpass the accuracy of ab initio Density Functional Theory…
View article: The Fe-MAN Challenge: Ferrates–Microkinetic Assessment of Numerical Quantum Chemistry
The Fe-MAN Challenge: Ferrates–Microkinetic Assessment of Numerical Quantum Chemistry Open
Organometallic species, such as organoferrate ions, are prototypical nucleophiles prone to reacting with a wide range of electrophiles, including proton donors. In solution, the operation of dynamic equilibria and the simultaneous presence…
View article: Highly Ordered Co‐Assembly of Bisurea Functionalized Molecular Switches at the Solid‐Liquid Interface
Highly Ordered Co‐Assembly of Bisurea Functionalized Molecular Switches at the Solid‐Liquid Interface Open
Immobilization of stimulus‐responsive systems on solid surfaces is beneficial for controlled signal transmission and adaptive behavior while allowing the characterization of the functional interface with high sensitivity and high spatial r…
View article: Crystal structures of potassium and cesium salts of adenine: the role of alkali cations
Crystal structures of potassium and cesium salts of adenine: the role of alkali cations Open
The structures of alkali-salts of adenine and guanine are described from the perspective of the cations. Their relative affinity for interaction with oxygen or nitrogen of the nucleobase or with water governs the crystallisation of the sal…
View article: Exploration of biochemical reactivity with a QM/MM growing string method
Exploration of biochemical reactivity with a QM/MM growing string method Open
This work highlights a novel method for obtaining QM/MM reaction pathways which are of high-quality, quickly obtainable, and require minimal user intervention. Testing for the Claisen rearrangement in chorismate mutase shows the value of t…
View article: On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface
On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface Open
By synergy of STM results and statistical thermodynamics, we provide a novel framework for free energy assessment of monolayer formation at the liquid/solid interface.
View article: Kinetic modelling of cobalt-catalyzed propene hydroformylation: a combined <i>ab initio</i> and experimental fitting protocol
Kinetic modelling of cobalt-catalyzed propene hydroformylation: a combined <i>ab initio</i> and experimental fitting protocol Open
The mechanism of propene hydroformylation is studied with quantum chemistry and kinetic modelling. This yields detailed insight into mechanisms, and reveals the essential role of a complex between hydridocobalttricabonyl and toluene.
View article: Transfer learning based on atomic feature extraction for the prediction of experimental <sup>13</sup> C chemical shifts
Transfer learning based on atomic feature extraction for the prediction of experimental <sup>13</sup> C chemical shifts Open
Atomic feature extraction as a solution for low-data regimes in chemistry.
View article: Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis
Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis Open
This work exemplifies the use of machine-learned 3D structure predictors combined with molecular docking to generate poses for atomistic study via molecular dynamics, ultimately enabling rapid insight into a novel biosynthetic cascade.
View article: Investigation of the temperature effect on the formation of a two-dimensional self-assembled network at the liquid/solid interface
Investigation of the temperature effect on the formation of a two-dimensional self-assembled network at the liquid/solid interface Open
In this work, we investigate the temperature effect on the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface, focusing on an alkylated achiral glycine derivative at the 1-phenyloctane/HOPG interface.
View article: Reaction pathways leading to HPALD intermediates in the OH-initiated oxidation of isoprene
Reaction pathways leading to HPALD intermediates in the OH-initiated oxidation of isoprene Open
The HPALD formation in the OH-initiated isoprene oxidation has been revisited. Vibrationally hot peroxy radicals from O 2 addition in the α-position of Z,Z′-OH-allyl radicals decompose in a chemically activated manner, efficiently yielding…
View article: Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase
Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase Open
This work investigates the signalling mechanism found in human CBS. Quantum chemical calculations give an atomistic insight into gas binding to heme, and molecular dynamics simulations show the allosteric signalling pathway initiated by ga…
View article: Exploration of Biochemical Reactivity with a QM/MM Growing String Method
Exploration of Biochemical Reactivity with a QM/MM Growing String Method Open
In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in t…
View article: Kinetic Modelling of Cobalt-Catalyzed Propene Hydroformylation: A Combined Ab Initio and Experimental Fitting Protocol
Kinetic Modelling of Cobalt-Catalyzed Propene Hydroformylation: A Combined Ab Initio and Experimental Fitting Protocol Open
Kinetic modelling of catalytic reaction systems can yield detailed insight into mechanisms, enabling in particular the identification of rate- and turnover-limiting steps. Empirical models fitted to observed kinetics do not always unambigu…
View article: Exploration of Biochemical Reactivity with a QM/MM Growing String Method
Exploration of Biochemical Reactivity with a QM/MM Growing String Method Open
In this work, we have implemented the single-ended growing string method within our in-house QM/MM package, QoMMMa. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to…
View article: Quantifying the Cooperative Process of Molecular Self-Assembly on Surfaces: A Case Study of Isophthalic Acids
Quantifying the Cooperative Process of Molecular Self-Assembly on Surfaces: A Case Study of Isophthalic Acids Open
sponsorship: The authors gratefully acknowledge financial support from the Research Foundation-Flanders (FWO) via EOS 40007495, and KU Leuven-Internal Funds (C14/19/079) . T.R. acknowl-edges financial support through a FWO Ph.D. fellowship…
View article: Stability profile of vimentin rod domain
Stability profile of vimentin rod domain Open
Intermediate filaments (IFs) form an essential part of the metazoan cytoskeleton. Despite a long history of research, a proper understanding of their molecular architecture and assembly process is still lacking. IFs self‐assemble from elon…
View article: Issue Information
Issue Information Open
A theory that includes both relativistic and solvent effects at a high level is crucial to elucidate the structure, properties, and reactions of molecules containing heavy elements in solution.We present a method that combines the Dirac-Ha…