Kohn-Sham density functional theory (DFT) is the workhorse method for calculating adsorbate binding energies relevant for catalysis. Unfortunately, this method is too computationally expensive to methodically and broadly search through catalyst candidate space. Here, we assess the promise of computational alchemy, a perturbation theory approach that allows for predictions of binding energies thousands of times faster than DFT. We first benchmark the binding energy predictions of oxygen reduction reaction intermediates on alloys of Pt, Pd, and Ni using alchemy against predictions from DFT. Far faster alchemical estimates yield binding energies within 0.1 eV of DFT values in many cases. We also identify distinct cases where alchemy performs significantly worse, indicating areas where modeling improvements are needed. Our results suggest that computational alchemy is a very promising tool that warrants further consideration for high-throughput screening of heterogeneous catalysts.
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http://dx.doi.org/10.1021/acs.jpclett.7b01974 | DOI Listing |
J Phys Chem B
January 2025
School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia.
A systematic series of QM cluster models has been developed to predict the trend in the carbonic anhydrase binding affinity of a structurally diverse dataset of ligands. Reference DLPNO-CCSD(T)/CBS binding energies were generated for a cluster model and used to evaluate the performance of contemporary density functional theory methods, including Grimme's "3c" DFT composite methods (rSCAN-3c and ωB97X-3c). It is demonstrated that when validated QM methods are used, the predictive power of the cluster models improves systematically with the size of the cluster models.
View Article and Find Full Text PDFMol Divers
January 2025
Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India.
Nanobodies or variable antigen-binding domains (VH) derived from heavy chain-only antibodies (HcAb) occurring in the Camelidae family offer certain superior physicochemical characteristics like enhanced stability, solubility, and low immunogenicity compared to conventional antibodies. Their efficient antigen-binding capabilities make them a preferred choice for next-generation small biologics. In the present work, we design an anti-SARS-CoV-2 bi-paratopic nanobody drug conjugate by screening a nanobody database.
View Article and Find Full Text PDFMikrochim Acta
January 2025
College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou, 363000, China.
The detection of cysteine (Cys) and homocysteine (Hcy) in biological fluids has great significance for early diagnosis, including Alzheimer's and Parkinson's disease. The simultaneous determination of Cys and Hcy with a single probe is still a huge challenge. To enlarge the differences in space structure (line and ring) and energy (-721.
View Article and Find Full Text PDFJ Biomol Struct Dyn
January 2025
Department of Chemistry, National Institute of Technology Silchar, Silchar, Assam, India.
A series of 2,6-di(pyrazine-2-yl)pyridine (dppy) ligands - of varying substituents of different electronic nature (-NMe, -OMe,-Me, and -Cl) in the 4-position of the pyridine moiety has been designed and synthesized to study the binding behavior of the dppy ligands towards Bovine Serum Albumin (BSA), a low-cost serum albumin protein. The interaction between ligands and BSA has been studied using UV-Visible and fluorescence spectroscopy and molecular docking studies. The fluorescence of BSA was found to be quenched in the presence of all the ligands , in which ligand , having the most electron donating group NMe exhibits the maximum binding affinity towards BSA.
View Article and Find Full Text PDFProtein Sci
February 2025
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
We have recently demonstrated a novel anaerobic NADH-dependent haem breakdown reaction, which is carried out by a range of haemoproteins. The Yersinia enterocolitica protein, HemS, is the focus of further research presented in the current paper. Using conventional experimental methods, bioinformatics, and energy landscape theory (ELT), we provide new insight into the mechanism of the novel breakdown process.
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