An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction energies for molecular systems with roughly 1000 atoms. The essential novelty in this so-called GFN2-xTB method is the inclusion of anisotropic second order density fluctuation effects via short-range damped interactions of cumulative atomic multipole moments. Without noticeable increase in the computational demands, this results in a less empirical and overall more physically sound method, which does not require any classical halogen or hydrogen bonding corrections and which relies solely on global and element-specific parameters (available up to radon, Z = 86). Moreover, the atomic partial charge dependent D4 London dispersion model is incorporated self-consistently, which can be naturally obtained in a tight-binding picture from second order density fluctuations. Fully analytical and numerically precise gradients (nuclear forces) are implemented. The accuracy of the method is benchmarked for a wide variety of systems and compared with other semiempirical methods. Along with excellent performance for the "target" properties, we also find lower errors for "off-target" properties such as barrier heights and molecular dipole moments. High computational efficiency along with the improved physics compared to its precursor GFN-xTB makes this method well-suited to explore the conformational space of molecular systems. Significant improvements are furthermore observed for various benchmark sets, which are prototypical for biomolecular systems in aqueous solution.
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http://dx.doi.org/10.1021/acs.jctc.8b01176 | DOI Listing |
ACS Chem Neurosci
January 2025
Departments of Psychiatry and Neurology, Division of Molecular Therapeutics, New York State Psychiatric Institute, Columbia University Medical Center, New York, New York 10032, United States.
Voluntary movement, motivation, and reinforcement learning depend on the activity of ventral midbrain neurons, which extend axons to release dopamine (DA) in the striatum. These neurons exhibit two patterns of action potential activity: low-frequency tonic activity that is intrinsically generated and superimposed high-frequency phasic bursts that are driven by synaptic inputs. acute striatal brain preparations are widely employed to study the regulation of evoked DA release but exhibit very different DA release kinetics than recordings.
View Article and Find Full Text PDFChilds Nerv Syst
January 2025
Ph.D. Human Genetics Program, Molecular Biology and Genomics Department, Human Genetics Institute "Dr. Enrique Corona-Rivera", University Center of Health Sciences, University of Guadalajara, Guadalajara, Mexico.
Background: Central nervous system tumors (CNSTs) represent a significant oncological challenge in pediatric populations, particularly in developing regions where access to diagnostic and therapeutic resources is limited.
Methods: This research investigates the epidemiology, histological classifications, and survival outcomes of CNST in a cohort of pediatric patients aged 0 to 19 years within a 25-year retrospective study at the Civil Hospital of Guadalajara, Mexico, from 1999 to 2024.
Results: Data was analyzed from 273 patients who met inclusion criteria, revealing a higher incidence in males (51.
Vet Res Commun
January 2025
Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.
Colostrum, the initial mammary secretion produced by various mammals following birth, is a conduit for maternal immunity transfer in diverse mammalian species. Concurrently, many cellular processes are occurring in the neonatal small intestine to prepare it to receive molecular signals from a superfood essential for the neonate's health and development. During the prepartum colostrum secretion, the newborn intestine undergoes transient alterations in the intestinal barrier, primarily regulating immunoglobulin absorption.
View Article and Find Full Text PDFMol Biol Rep
January 2025
Department of Cardiology, Ganzhou People's Hospital, Ganzhou, Jiangxi, China.
As multiple imaging modalities cannot reliably diagnose cardiac tumors, the molecular approach offers alternative ways to detect rare ones. One such molecular approach is CRISPR-based diagnostics (CRISPR-Dx). CRISPR-Dx enables visual readout, portable diagnostics, and rapid and multiplex detection of nucleic acids such as microRNA (miRNA).
View Article and Find Full Text PDFJACC Clin Electrophysiol
December 2024
Physiology, Amsterdam Cardiovascular Sciences, Heart Failure, and Arrhythmias, Amsterdam University Medical Center, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands. Electronic address:
Background: Atrial fibrillation (AF) persistence is associated with molecular remodeling that fuels electrical conduction abnormalities in atrial tissue. Previous research revealed DNA damage as a molecular driver of AF.
Objectives: This study sought to explore the diagnostic value of DNA damage in atrial tissue and blood samples as an indicator of the prevalence of electrical conduction abnormalities and stage of AF.
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