Harmonising the human biobanking consent process: an Irish experience.

Biobanks are repositories of human biological samples and data. They are an important component of clinical research in many disease areas and often represent the first step toward innovative treatments. For biobanks to operate, researchers need human participants to give their samples and associated health data. In Ireland, research participants must provide their freely given informed consent for their samples and data to be taken and used for research purposes. Biobank staff are responsible for communicating the relevant information to participants prior to obtaining their consent, and this communication process is supported by documentation in the form of Participant Information Leaflets and Informed Consent Forms (PILs/ICFs). PILs/ICFs should be concise, intelligible, and contain relevant information. While not a substitute for layperson and research staff discussions, PILs and ICFs ensure that a layperson has enough information to make an informed choice to participate or not. However, PILs/ICFs are often lengthy, contain technical language and can be complicated and onerous for a layperson to read. The introduction of the General Data Protection Regulation (GDPR) and the related Irish Health Research Regulation (HRR) presented additional challenges to the Irish biobank community. In May 2019, the National Biobanking Working Group (NBWG) was established in Ireland. It consists of members from diverse research backgrounds located in universities, hospitals and research centres across Ireland and a public/patient partner. The NBWG aimed to develop a suite of resources for health research biobanks via robust and meaningful patient engagement, which are accessible, GDPR/HRR-compliant and could be used nationally, including a PIL/ICF template. This open letter describes the process whereby this national biobank PIL/ICF template was produced. The development of this template included review by the Patient Voice in Cancer Research, led by Professor Amanda McCann at University College Dublin and the Health Research Data Protection Network.

Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants.

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R2(O)P-link-P(O)R2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theory and the performance of known bis-phosphine oxide extractants. For the case where the link is -CH2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the "anomalous aryl strengthening" effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.

Benchmarking Continuum Solvent Models for Keto-Enol Tautomerizations.

Experimental free energies of tautomerization, ΔGT, were used to benchmark the gas-phase predictions of 17 different quantum mechanical methods and eight basis sets for seven keto-enol tautomer pairs dominated by their enolic form. The G4 method and M06/6-31+G(d,p) yielded the most accurate results, with mean absolute errors (MAE's) of 0.95 and 0.71 kcal/mol, respectively. Using these two theory levels, the solution-phase ΔGT values for 23 unique tautomer pairs composed of aliphatic ketones, ß-dicarbonyls, and heterocycles were computed in multiple protic and aprotic solvents. The continuum solvation models, namely, polarizable continuum model (PCM), polarizable conductor calculation model (CPCM), and universal solvation model (SMD), gave relatively similar MAE's of ∼1.6-1.7 kcal/mol for G4 and ∼1.9-2.0 kcal/mol with M06/6-31+G(d,p). Partitioning the tautomer pairs into their respective molecular types, that is, aliphatic ketones, ß-dicarbonyls, and heterocycles, and separating out the aqueous versus nonaqueous results finds G4/PCM utilizing the UA0 cavity to be the overall most accurate combination. Free energies of activation, ΔG(‡), for the base-catalyzed keto-enol interconversion of 2-nitrocyclohexanone were also computed using six bases and five solvents. The M06/6-31+G(d,p) reproduced the ΔG(‡) with MAE's of 1.5 and 1.8 kcal/mol using CPCM and SMD, respectively, for all combinations of base and solvent. That specific enolization was previously proposed to proceed via a concerted mechanism in less polar solvents but shift to a stepwise mechanism in more polar solvents. However, the current calculations suggest that the stepwise mechanism operates in all solvents.

Ionic liquid effects on nucleophilic aromatic substitution reactions from QM/MM simulations.

Nucleophilic aromatic substitution (SNAr) reactions are particularly sensitive to medium effects and have been reported to benefit from ionic liquids. The SNAr reaction between cyclic secondary amines (i.e., piperidine, pyrrolidine, and morpholine) and the 2-L-5-nitrothiophene (para-like) and 2-L-3-nitrothiophene (ortho-like) isomers, where L = bromo, methoxy, phenoxy, and 4-nitrophenoxy, has been computationally investigated in 1-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate [BMIM][BF4] and [BMIM][PF6], respectively. QM/MM Monte Carlo simulations utilizing free-energy perturbation theory were used to characterize the solute-solvent interactions over the addition-elimination reaction pathway. Energetic and structural analyses determined that the improved SNAr reactivity in [BMIM][BF4] and [BMIM][PF6] can be attributed to (1) an enhanced nucleophilicity of the cyclic amines in the ionic liquids with an order of Pyr ≥ Pip > Mor, (2) beneficial π(+)-π interactions between the BMIM cations and the aromatic rings present on the substrate that enhanced coplanarity between the thiophene ring and the aromatic substituents, resulting in a larger positive charge on the reacting ipso carbon, and (3) a highly ordered ionic liquid clathrate formation that, despite an entropy penalty, provided reduced activation free-energy barriers derived from an increasing number of solvent ions favorably interacting with the emerging charge separation at the rate-limiting addition step.

Parents' understanding of and accuracy in using measuring devices to administer liquid oral pain medication.

BACKGROUND: Dentists recommend over-the-counter medications for postoperative pain in children, and parents often make dosing errors when administering these medications. The authors compared the dosing accuracy when parents used various measuring devices and aimed to identify risk factors associated with dosing errors. METHODS: The authors recruited parent-child pairs visiting the Pediatric Clinic at the College of Dentistry at The University of Tennessee Health Science Center, Memphis, and three private dental offices. The parents completed a survey and a liquid measuring exercise. The authors instructed parents to measure 5 milliliters of liquid by using a medicine cup with clear markings, a medicine cup with printed markings, a cylindrical measuring spoon and an oral syringe. For the medicine cup with printed markings, the authors placed the parents randomly into one of two groups: those receiving text-only instructions or those receiving text-pictogram instructions. The authors weighed each device before and after the measuring exercise and compared the difference in weight with a reference weight of 5 mL. RESULTS: A total of 120 parent-child pairs participated. The results of a McNemar test revealed a significant difference in parents' ability to measure accurate doses with the various devices. The results of a Pearson χ(2) test showed no statistically significant difference between the control and study groups for dosing accuracy. The χ(2) analysis results showed no significant differences in risk factors that could be associated with dosing errors. CONCLUSIONS: Medicine cups were the devices parents reported using most frequently. Medicine cups had a higher occurrence of dosing errors when compared with the other devices. No sociodemographic factors were associated with dosing errors. Practical Implications. Dentists can improve pain management in pediatric patients by educating parents about accurate measuring devices, weight-based dosing and correct interpretation of medication dosing charts.

Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids.

Room temperature ionic liquid calculations require extensive sampling due to the large degree of localized structuring in the liquid phase relative to conventional solutions. Consequently, a large amount of computer time is required for the convergence of solvent properties, much of which is spent evaluating long-range electrostatics via Ewald summations. The damped Coulomb potential and cutoff-neutralized method of Wolf et al. (J. Chem. Phys.1999, 110, 8254) provides the framework for an accurate, linear-scaling alternative to Ewald in the ionic liquid simulations. The method has been the subject of multiple modifications for improved accuracy, including the damped Coulombic potential of Zahn et al. (J. Phys. Chem. B2002, 106, 10725), the damped shifted force method of Fennell and Gezelter (J. Chem. Phys.2006, 124, 234104), and the shifted force gradient of Kale and Herzfeld (J. Chem. Theory Comput.2011, 7, 3620). These pairwise electrostatic interaction alternatives along with the CHARMM shifted force potential and a new method proposed herein, the shifted force third derivative (SF3), have been examined on 59 unique ionic liquid combinations of 1-alkyl-3-methylimidazolium [RMIM] (R = M (methyl), E (ethyl), B (butyl), H (hexyl), and O (octyl)) and N-alkylpyridinium [RPyr] cations, along with Cl(-), PF6(-), BF4(-), NO3(-), AlCl4(-), Al2Cl7(-), and TfO(-) anions. Monte Carlo simulations utilizing our custom OPLS-AA ionic liquid force field and employing the pairwise alternatives with multiple cutoff distances and electrostatic damping values are compared to the energetics from full Ewald sums.

Inter- and intramolecular mechanisms for chlorine rearrangements in trimethyl-substituted N-chlorohydantoins.

The antimicrobial compounds 1-chloro-3,5,5-trimethylhydantoin and 3-chloro-1,5,5-trimethylhydantoin (1 and 2, respectively) have been synthesized and examined via a joint experimental and computational study. The measured rate of loss of oxidative chlorine in the absence and presence of exposure to UVA irradiation determined 2 to be less stable than 1. An interesting migration reaction was observed during UVA irradiation that featured the production of chlorine rearrangement and dechlorinated compounds. Two novel hydrogen atom transfer reaction (HATR) mechanisms have been proposed: (1) an intramolecular process in which a hydrogen atom undergoes a series of sigmatropic shifts, and (2) an intermolecular pathway in which a radical abstracts a hydrogen atom from a neighboring molecule. Density functional theory (DFT) calculations at the UB3LYP/6-311G++(2d,p) theory level have been employed to elucidate the preferred reaction pathway. Both proposed HATR mechanisms predicted 2 to possess a lower free energy of activation, ΔG(‡), relative to 1 in accordance with the experimental stability measurements. However, the intermolecular route had an overall lower absolute ΔG(‡) and was more consistent with measured product ratios in solution. The intermolecular reaction pathway, unlike the intramolecular route, also predicted the lack of formation of a migration product featuring a Cl covalently bonded to a methylene group at the 5-position of the hydantoin moiety, which was verified by NMR experiments.