Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jpca.6b04527 | DOI Listing |
J Clin Med
December 2024
Department of Cardiology, Umberto I Hospital, 84014 Nocera Inferiore, Italy.
Heart and lung sharing the same anatomical space are influenced by each other. Spontaneous breathing induces dynamic changes in intrathoracic pressure, impacting cardiac function, particularly the right ventricle. In intensive care units (ICU), mechanical ventilation (MV) and therefore positive end-expiratory pressure (PEEP) are often applied, and this inevitably influences cardiac function.
View Article and Find Full Text PDFMaterials (Basel)
December 2024
School of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, China.
Damage mechanisms are a key factor in materials science and are essential for understanding and predicting the behavior of materials under complex loading conditions. In this paper, the influence of different directions, different rates and different model parameters on the mechanical behavior of AZ31 magnesium alloy during the tensile process is investigated based on the secondary development of the VUMAT user subroutine based on the GTN damage model and verified by the tensile experiments at different loading rates and in different directions. The results show that AZ31 magnesium alloy exhibits significant differences in mechanical properties in radial and axial stretching, where the yield strength is lower in the radial direction than in the axial direction, and the elongation is the opposite.
View Article and Find Full Text PDFPlants (Basel)
December 2024
Plant Sciences Unit, ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Caritasstraat 39, 9090 Melle, Belgium.
Quinoa () cultivation has become increasingly popular in NW Europe but little is known about the performance of contract-free varieties in this region. In this study, we phenotyped 25 quinoa varieties on a single-plant basis in a field trial in Belgium. In addition, we optimized breeding tools such as NIRS (near-infrared reflectance spectroscopy) to estimate the seed crude protein content and a multiplex PCR set to identify true F progeny from pair crosses.
View Article and Find Full Text PDFMolecules
December 2024
Institute of Earth Sciences, Faculty of Natural Sciences, University of Silesia in Katowice, 60, Będzińska, 41-200 Sosnowiec, Poland.
Cathinone and its synthetic derivatives belong to organic compounds with narcotic properties. Their structural diversity and massive illegal use create the need to develop new analytical methods for their identification in different matrices. NMR spectroscopy is one of the most versatile methods for identifying the structure of organic substances.
View Article and Find Full Text PDFBMC Ecol Evol
January 2025
College of Life Sciences, Qufu Normal University, Qufu, 273165, China.
Background: Semi-aquatic mammals represent a transitional phase in the evolutionary spectrum between terrestrial and aquatic mammals. The sense of balance is crucial for mammalian locomotion, and in semi-aquatic mammals, the structural foundation of this sense (the vestibular system) shows distinct morphological adaptations to both aquatic and terrestrial environments compared to their terrestrial counterparts. Despite this, the precise molecular mechanisms driving these adaptations remain elusive.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!