Bonded radii and the contraction of the electron density of the oxygen atom by bonded interactions.

The bonded radii for more than 700 bonded pairs of atoms, comprising more than 50 oxide crystals, extracted from experimental and theoretical electron density distributions, are averaged and compared with the ionic radii for first, second, and third row atoms. At odds with the assumption of a "fixed" ionic radius of 1.40 Å for the oxide anion, the bonded radius for the anion, r(b)(O), decreases systematically from 1.40 to 0.65 Å as the electron density distribution of the atom is progressively polarized and contracted by its bonded interactions. The radii for the more electropositive metal atoms agree with the ionic radii when the electron density distribution of the anion is largely unpolarized by its bonded interactions. However, those for the more electronegative metal atoms are progressively larger than the ionic radii as the electron density distribution of the anion is progressively polarized and contracted along the bond vectors with decreasing bond length. The progressive decrease of r(b)(O) indicates that the compilation of sets of ionic radii, based on a fixed radius for the oxide anion, is problematic and impacts the accuracy of the ionic radii for the metal atoms. The assumption of a "fixed" radius for the anion, made in the derivation of sets of radii, not only results in unrealistic negative ionic radii for the more electronegative atoms but also in ionic radii that are as much as 0.5 Å smaller than the bonded radii, particularly for the more electronegative M atoms. The lack of agreement between the ionic and the bonded radii for the more shared bonded interactions is ascribed to the progressive increase in the polarization and contraction of the electron density of the oxide anion by the bonded interactions with a concomitant decrease in the radius of the anion, a factor that was largely neglected in the compilation of the ionic radii for fluoride, oxide, sulfide, and nitride crystals. The close agreement of the bonded radii and procrystal bonded radii is consistent with the argument that the chemical forces that govern the electron density distributions and bonded radii are largely atomic in nature, resulting in comparable electron density distributions.

Association of medication-assisted treatment and short acting opioids with newborn head circumference and birth weight.

OBJECTIVE: We compared the association of methadone, buprenorphine, and short-acting opioid exposure with newborn head circumference (HC) and birth weight (BW), and evaluated gestational age (GA) as a mediator. STUDY DESIGN: We included newborns born 2013-2018 identified by neonatal abstinence syndrome diagnosis code (N = 572) and birthday-matched unexposed controls (N = 571). Linear regressions of opioid exposure with HC and BW controlled for tobacco, marijuana, cocaine, gabapentin, cesarean section, Medicaid, and newborn sex, with mediation analysis by GA. RESULT: Methadone was associated with 0.81 cm lower HC (95% CI = -1.22, -0.40) and 0.23 kg lower BW (95% CI = -0.35, -0.10) with approximately 24% and 41% mediated by GA, respectively. Buprenorphine and short acting opioids were not associated with HC or BW. CONCLUSION: Methadone exposed newborns have smaller HC and lower BW not fully attributable to younger GA, suggesting a direct effect of methadone on intrauterine growth. Exploration of potential developmental consequences of this is urgently needed.

Genomic imprinting of DIO3, a candidate gene for the syndrome associated with human uniparental disomy of chromosome 14.

Individuals with uniparental disomy of chromosome 14 (Temple and Kagami-Ogata syndromes) exhibit a number of developmental abnormalities originating, in part, from aberrant developmental expression of imprinted genes in the DLK1-DIO3 cluster. Although genomic imprinting has been reported in humans for some genes in the cluster, little evidence is available about the imprinting status of DIO3, which modulates developmental exposure to thyroid hormones. We used pyrosequencing to evaluate allelic expression of DLK1 and DIO3 in cDNAs prepared from neonatal foreskins carrying single-nucleotide polymorphisms (SNPs) in the exonic sequence of those genes, and hot-stop PCR to quantify DIO3 allelic expression in cDNA obtained from a skin specimen collected from an adult individual with known parental origin of the DIO3 SNP. In neonatal skin, DLK1 and DIO3 both exhibited a high degree of monoallelic expression from the paternal allele. In the adult skin sample, the allele preferentially expressed is that inherited from the mother, although a different, larger DIO3 mRNA transcript appears the most abundant at this stage. We conclude that DIO3 is an imprinted gene in humans, suggesting that alterations in thyroid hormone exposure during development may partly contribute to the phenotypes associated with uniparental disomy of chromosome 14.

A tool for the interactive 3D visualization of electronic structure in molecules and solids.

This paper presents the Vienna ab initio simulation package (VASP) data viewer, a desktop 3D visualization application for the analysis of valence electronic structure information derived from first-principles quantum-mechanical density functional calculations. This tool allows a scientist to directly view and manipulate the calculated charge density or electron localization function (ELF) from an electronic structure calculation, providing insight into the nature of chemical bonding. Particular attention was given to the design and implementation of the user interface (UI) for the data viewer. It provides for expert and novice usage, and both natural direct manipulation and precise numerical control. The data viewer has proven useful to chemical scientists for understanding the results of electronic structure calculations.