As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1).
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1016/j.saa.2013.10.059 | DOI Listing |
ACS Appl Mater Interfaces
January 2025
School of Materials Science and Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, P. R. China.
The emerging step (S)-scheme heterojunction systems became a powerful strategy in promoting photogenerated charge separation while maintaining their high redox potentials. However, the weak interfacial interaction limits the charge migration rate in S-scheme heterojunctions. Herein, we construct a unique S-scheme carbon nitride (CN) homojunction with boron (B)-doped CN and phosphorus (P)-doped CN (B-CN/P-CN) for hydrogen peroxide (HO) photosynthesis.
View Article and Find Full Text PDFBiophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFJ Colloid Interface Sci
January 2025
Engineering Research Center of Advanced Functional Material Manufacturing of Ministry of Education, School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001 Henan, China; National Key Laboratory of Coking Coal Green Process Research, Zhengzhou University, Zhengzhou 450001, Henan, China. Electronic address:
Hydrogen production via electrocatalytic water splitting has garnered significant attention, due to the growing demand for clean and renewable energy. However, achieving low overpotential and long-term stability of water splitting catalysts at high current densities remains a major challenge. Herein, a CoP@CoNi layered double hydroxide (LDH) electrode was synthesized via a two-step electrodeposition process, demonstrating oxygen evolution reaction, with an overpotential (ƞ) of 373 mV and a Tafel slope of 64.
View Article and Find Full Text PDFComput Biol Chem
January 2025
National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Pakistan. Electronic address:
A major threat to world health is the high death rate from gastrointestinal (GI) cancer, especially in Asia, South America, and Europe. The new approaches are needed because of the complexity and heterogeneity of gastrointestinal (GI) cancer, which has made the development of effective treatments difficult. To investigate the potential of peptide-based therapies that target the P21 Activated Kinase 1 (PAK1) in GI cancer, we are using the DBsORF database to predict peptides from the genomes of two bacterial strains: Lactobacillus plantarum and Pediococcus pentosaceus.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
The local electric field (LEF) plays an important role in the catalytic process; however, the precise construction and manipulation of the electric field microenvironment around the active site remains a significant challenge. Here, we have developed a supramolecular strategy for the implementation of a LEF by introducing the host macrocycle 18-crown-6 (18C6) into a cobalt phthalocyanine (CoPc)-containing covalent organic framework (COF). Utilizing the supramolecular interaction between 18C6 and potassium ion (K), a locally enhanced K concentration around CoPc can be built to generate a LEF microenvironment around the catalytically active Co site.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!