Nonadiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems. Consequently, simulations are often performed on simplified models to interpret the experimental results. In this context, a variety of techniques have been developed to perform NAMD using approximate methods, particularly density functional tight binding (DFTB). Despite the use of these techniques on large systems, where ab initio methods are computationally prohibitive, a comprehensive validation has been lacking. In this work, we present a new implementation of trajectory surface hopping combined with DFTB, utilizing nonadiabatic coupling vectors. We selected the methaniminium cation and furan systems for validation, providing an exhaustive comparison with the higher-level electronic structure methods. As a case study, we simulated a system from the class of molecular motors, which has been extensively studied experimentally but remains challenging to simulate with ab initio methods due to its inherent complexity. Our approach effectively captures the key photophysical mechanism of dihedral rotation after the absorption of light. Additionally, we successfully reproduced the transition from the bright to dark states observed in the time-dependent fluorescence experiments, providing valuable insights into this critical part of the photophysical behavior in molecular motors.
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http://dx.doi.org/10.1021/acs.jctc.4c01263 | DOI Listing |
CNS Neurosci Ther
January 2025
Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, the First Dongguan Affiliated Hospital, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China.
Aims: Neuron death is caused primarily by apoptosis after spinal cord injury (SCI). Autophagy, as a cellular response, can maintain cellular homeostasis to reduce apoptosis. We aimed to investigate the effect and the mechanism of vimentin knockdown on autophagy and neural recovery after SCI.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous biological processes. Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. However, MSMs face challenges in identifying transition states, as they partition MD conformations into discrete metastable states (or free energy minima), lacking description of transition states located at the free energy barriers.
View Article and Find Full Text PDFAm J Hum Genet
January 2025
Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Center for Rare Disease, University of Tübingen, 72076 Tübingen, Germany; Genomics for Health in Africa (GHA), Africa-Europe Cluster of Research Excellence (CoRE).
Inborn errors of selenoprotein expression arise from deleterious variants in genes encoding selenoproteins or selenoprotein biosynthetic factors, some of which are associated with neurodegenerative disorders. This study shows that bi-allelic selenocysteine tRNA-specific eukaryotic elongation factor (EEFSEC) variants cause selenoprotein deficiency, leading to progressive neurodegeneration. EEFSEC deficiency, an autosomal recessive disorder, manifests with global developmental delay, progressive spasticity, ataxia, and seizures.
View Article and Find Full Text PDFAquat Toxicol
December 2024
School of Emergency Management, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., Zhenjiang, Jiangsu 212013, China. Electronic address:
Monoethylhexyl phthalate (MEHP) is the primary metabolite of di(2-ethylhexyl) phthalate (DEHP), the most prevalent phthalate plasticiser globally. It has been demonstrated that MEHP exerts more potent toxic effects than DEHP. Nevertheless, the full extent of the toxicity of MEHP to neurodevelopmental organisms remains unclear.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust, University of Cambridge, Cambridge, United Kingdom.
Background: Frontotemporal dementia (FTD) and Progressive Supranuclear Palsy (PSP) have distinct molecular pathologies, with Tau and TDP43 aggregation, and distinct patterns of regional brain atrophy. However, they share the synaptotoxicity of protein aggregation, and neurotransmitter loss (including GABA), which contribute to clinical and neurophysiological similarities. Defining the relationships between synaptic loss, network physiology and cognition builds bridges between preclinical and clinical studies, and facilitates early phase trials.
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