The generation of surrogate potential energy functions (PEF) that are orders of magnitude faster to compute but as accurate as the underlying training data from high-level electronic structure methods is one of the most promising applications of fitting procedures in chemistry. In previous work, we have shown that transition state force fields (TSFFs), fitted to the functional form of MM3* force fields using the quantum guided molecular mechanics (Q2MM) method, provide an accurate description of transition states that can be used for stereoselectivity predictions of small molecule reactions. Here, we demonstrate the applicability of the method for fit TSFFs to the well-established Amber force field, which could be used for molecular dynamics studies of enzyme reaction. As a case study, the fitting of a TSFF to the second hydride transfer in Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase (PmHMGR) is used. The differences and similarities to fitting of small molecule TSFFs are discussed.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8912266 | PMC |
| http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0264960 | PLOS |
Publication Analysis
Top Keywords
Similar Publications
Influence of aluminium distribution on the diffusion mechanisms and pairing of [Cu(NH)] complexes in Cu-CHA.
Nat Commun
January 2025
Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, SE-412 96, Göteborg, Sweden.
The performance of Cu-exchanged chabazite (Cu-CHA) for the ammonia-assisted selective catalytic reduction of NO (NH-SCR) depends critically on the presence of paired complexes. Here, a machine-learning force field augmented with long-range Coulomb interactions is developed to investigate the effect of Al-distribution and Cu-loading on the mobility and pairing of complexes. Performing unbiased and constrained molecular dynamics simulations, we obtain unique information inaccessible to first-principle calculations and experiments.
View Article and Find Full Text PDFApplications of innovative synthetic strategies in anticancer drug Discovery: The Driving Force of new chemical reactions.
Bioorg Med Chem Lett
January 2025
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China. Electronic address:
The discovery of novel anticancer agents remains a critical goal in medicinal chemistry, with innovative synthetic methodologies playing a pivotal role in advancing this field. Recent breakthroughs in CH activation reactions, cyclization reactions, multicomponent reactions, cross-coupling reactions, and photo- and electro-catalytic reactions have enabled the efficient synthesis of new molecular scaffolds exhibiting potent biological activities, including anticancer properties. These methodologies have facilitated the functionalization of natural products, the modification of bioactive molecules, and the generation of entirely new compounds, many of which demonstrate strong antitumor activity.
View Article and Find Full Text PDFThe droplet dynamics of asymmetrical impingement on moving ridged surface.
J Colloid Interface Sci
January 2025
School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 China. Electronic address:
Hypothesis: The depth of research into the mechanism of droplet impacting structured surfaces dictates the efficacy of their applications. The impact stress generated when a droplet impacts a surface is a pivotal factor influencing the efficiency of surface applications, ultimately determining the extent of surface wear. Despite the systematic examination of impact force, there remains a scarcity of research on impact stress and its mitigation strategies.
View Article and Find Full Text PDFModeling and Elucidating the Behavior of a Thermoresponsive LCST Ionic Liquid.
J Chem Inf Model
January 2025
Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastián, Spain.
Desalination of seawater by forward osmosis is a technology potentially able to address the global water scarcity problem. The major challenge limiting its widespread practical application is the design of a draw solute that can be separated from water by an energetically efficient process and then reused for the next cycle. Recent experiments demonstrate that a promising draw solute for forward-osmosis desalination is tetrabutylphosphonium 2,4,6-trimethylbenzenesulfonate ([P][TMBS]).
View Article and Find Full Text PDFLive cell imaging of plant infection provides new insight into the biology of pathogenesis by the rice blast fungus Magnaporthe oryzae.
J Microsc
January 2025
The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases affecting rice cultivation around the world. During plant infection, M. oryzae forms a specialised infection structure called an appressorium.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!