When plotting different orbitals with consistent contour values, one can create illusions about the relative extension of charge distributions. We suggest that the comparison is not biased when plots reproduce the same fraction of the total charge. We have developed an algorithm and software that facilitate this type of visualization. We propose superimposing molecules and associated orbitals, and creating cross-sections by selecting a particular part of the orbital limited by pre-defined planes.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/ct800043a | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis.
Nat Commun
January 2025
Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany.
Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing software solutions for MALDI MSI data analysis are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries. Here, we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data.
View Article and Find Full Text PDFThe multifaceted roles of retinoids in eye development, vision, and retinal degenerative diseases.
Curr Top Dev Biol
January 2025
Center for Translational Vision Research, Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, United States; Department of Chemistry, University of California Irvine, Irvine, CA, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States. Electronic address:
Vitamin A (all-trans-retinol; at-Rol) and its derivatives, known as retinoids, have been adopted by vertebrates to serve as visual chromophores and signaling molecules, particularly in the eye/retina. Few tissues rely on retinoids as heavily as the retina, and the study of genetically modified mouse models with deficiencies in specific retinoid-metabolizing proteins has allowed us to gain insight into the unique or redundant roles of these proteins in at-Rol uptake and storage, or their downstream roles in retinal development and function. These processes occur during embryogenesis and continue throughout life.
View Article and Find Full Text PDFInterDIA: Interpretable Prediction of Drug-induced Autoimmunity through Ensemble Machine Learning Approaches.
Toxicology
January 2025
Deparment of clinical pharmacy, Jieyang People's Hospital, 522000, China. Electronic address:
Drug-induced autoimmunity (DIA) is a non-IgE immune-related adverse drug reaction that poses substantial challenges in predictive toxicology due to its idiosyncratic nature, complex pathogenesis, and diverse clinical manifestations. To address these challenges, we developed InterDIA, an interpretable machine learning framework for predicting DIA toxicity based on molecular physicochemical properties. Multi-strategy feature selection and advanced ensemble resampling approaches were integrated to enhance prediction accuracy and overcome data imbalance.
View Article and Find Full Text PDFKirkendall Effect-Mediated Transformation of ZIF-67 to NiCo-LDH Nanocages as Oxidase Mimics for Multicolor Point-of-Care Testing of β-Galactosidase Activity and .
Anal Chem
January 2025
Yunnan Key Laboratory of Modern Separation Analysis and Substance Transformation, College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650500, Yunnan Province, P. R. China.
Early and portable detection of pathogenic bacteria is crucial for ensuring food safety, monitoring product quality, and tracing the sources of bacterial infections. Moving beyond traditional plate-culture counting methods, the analysis of active bacterial components offers a rapid means of quantifying bacteria. Here, metal-organic framework (MOF)-derived NiCo-layered double hydroxide nanosheets (LDHs), synthesized via the Kirkendall effect, were employed as highly effective oxidase mimics to generate reactive oxygen species (ROS).
View Article and Find Full Text PDFExpression and purification of recombinant proteins in is a bedrock technique in biochemistry and molecular biology. Expression optimization requires testing different combinations of solubility tags, affinity purification techniques, and site-specific proteases. This optimization is laborious and time consuming as these features are spread across different vector series and require different cloning strategies with varying efficiencies.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!