Several standard semiempirical methods as well as the MMFF94 force field approximation have been tested in reproducing 8 DLPNO-CCSD(T)/cc-pVTZ level conformational energies and spatial structures for 37 organic molecules representing pharmaceuticals, drugs, catalysts, synthetic precursors, industry-related chemicals (37conf8 database). All contemporary semiempirical methods surpass their standard counterparts resulting in more reliable conformational energies and spatial structures, even though at significantly higher computational costs. However, even these methods show unexpected failures in reproducing energy differences between several conformers of the crown ether 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6). Inexpensive force field MMFF94 approximation groups with contemporary semiempirical methods in reproducing the correct order of conformational energies and spatial structures, although the performance in predicting absolute conformational energies compares to standard semiempirical methods. Based on these findings, we suggest a two-step strategy for reliable yet feasible conformational search and sampling in realistic-size flexible organic molecules: i) geometry optimization/preselection of relevant conformers using the MMFF94 force field; ii) single-point energy evaluations using a contemporary semiempirical method. We expect that developed database 37conf8 is going to be useful for development of semiempirical methods.
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http://dx.doi.org/10.1002/cphc.201801063 | DOI Listing |
Rev Med Virol
January 2025
United States Department of Agriculture, Exotic & Emerging Avian Viral Diseases Research, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA.
Avian influenza viruses are ubiquitous in the Anatinae subfamily of aquatic birds and occasionally spill over to poultry. Infection with low pathogenicity avian influenza viruses generally leads to subclinical or mild clinical disease. In contrast, highly pathogenic avian influenza viruses emerge from low pathogenic forms and can cause severe disease associated with extraordinarily high mortality rates.
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December 2024
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China. Electronic address:
The inhibition of the TIGIT/PVR interaction demonstrates considerable anticancer properties by enhancing the cytotoxic activity of natural killer (NK) and CD8+ T cells. However, the development of small molecule inhibitors that target TIGIT is currently limited. In this study, small molecules with the capacity to bind TIGIT and block the TIGIT/PVR interaction were screened through an advanced computational process, subsequently confirmed by blocking assays.
View Article and Find Full Text PDFJ Xenobiot
December 2024
Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa.
The direct discharge of cationic surfactants into environmental matrices has exponentially increased due to their wide application in many products. These compounds and their degraded products disrupt microbial dynamics, hinder plant survival, and affect human health. Therefore, there is an urgent need to develop electroanalytical assessment techniques for their identification, determination, and monitoring.
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December 2024
Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Medicine, University of Debrecen, 4032 Debrecen, Hungary.
Hydrogels like agarose have long been used as sieving media for the electrophoresis-based analysis of biopolymers. During gelation, the individual agarose strands tend to form hydrogen-bond mediated double-helical structures, allowing thermal reversibility and adjustable pore sizes for molecular sieving applications. The addition of tetrahydroxyborate to the agarose matrix results in transitional chemical cross-linking, offering an additional pore size adjusting option.
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November 2024
Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, UAE.
Disordered single-stranded RNA (ssRNA) molecules, like their well-folded counterparts, have crucial functions that depend on their structures. However, since native ssRNAs constitute a highly heterogeneous conformer population, their structural characterization poses challenges. One important question regards the role of sequence in influencing ssRNA structure.
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