The seventh blind test of crystal structure prediction: structure generation methods.

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern.

Consistent and low is the only way to go: A polynomial regression approach to the effect of abusive supervision inconsistency.

The literature on abusive supervision largely presumes that employees respond to abuse in a relatively straightforward way: When abuse is present, outcomes are unfavorable, and when abuse is absent, outcomes are favorable (or, at least less unfavorable). Yet despite the recognition that abusive supervision can vary over time, little consideration has been given to how past experiences of abuse may impact the ways employees react to it (or, its absence) in the present. This is a notable oversight, as it is widely acknowledged that past experiences create a context against which experiences in the present are compared.

Frequency of Occurrence of the Rat Lungworm Parasite in the Invasive Island Apple Snail in South Carolina, USA.

The rat lungworm Angiostrongylus cantonensis is a nematode parasite that can cause potentially fatal eosinophilic meningitis in humans. The life cycle of A. cantonensis involves multiple hosts, with the most common terminal hosts being rodents and intermediate hosts comprising gastropods.

Interpersonal-level discrimination indices, sociodemographic factors, and telomere length in African-Americans and Whites.

Objective: Studies have linked self-reported discrimination to telomere attrition, a biological marker of accelerated cellular aging. However, it is unknown whether intersections between social categories-race, socioeconomic status (SES), sex, and age-influence the association of varying forms of discrimination with telomere length. We examined these associations in a socioeconomically and racially/ethnically diverse urban sample.

Everyday Discrimination Prospectively Predicts Blood Pressure Across 10 Years in Racially/Ethnically Diverse Midlife Women: Study of Women's Health Across the Nation.

Background: Interpersonal discrimination is linked to greater risk for cardiovascular disease (CVD) and this association varies by race/ethnicity.

Purpose: To examine whether exposure to everyday discrimination prospectively predicts elevated blood pressure (BP), whether this association differs by race/ethnicity, and is mediated by adiposity indices.

Methods: Using data for 2,180 self-identified White, Black, Chinese, Japanese, and Hispanic participants from the Study of Women's Health Across the Nation, we examined associations among exposure to (higher vs.

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

The use of advanced polarizable potentials in quantum mechanical/molecular mechanical (QM/MM) simulations has been shown to improve the overall accuracy of the calculation. We have developed a density-based potential called the Gaussian electrostatic model (GEM), which has been shown to provide very accurate environments for QM wave functions in QM/MM. In this contribution we present a new implementation of QM/GEM that extends our implementation to include all components (Coulomb, exchange-repulsion, polarization, and dispersion) for the total intermolecular interaction energy in QM/MM calculations, except for the charge-transfer term.

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia.

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive.

Corrigendum to "Obesity in a model of gpx4 haploinsufficiency uncovers a causal role for lipid-derived aldehydes in human metabolic disease and cardiomyopathy" [Mol Metab 4 (6) (2015) 493-506].

[This corrects the article DOI: 10.1016/j.molmet.

Obesity in a model of gpx4 haploinsufficiency uncovers a causal role for lipid-derived aldehydes in human metabolic disease and cardiomyopathy.

Objective: Lipid peroxides and their reactive aldehyde derivatives (LPPs) have been linked to obesity-related pathologies, but whether they have a causal role has remained unclear. Glutathione peroxidase 4 (GPx4) is a selenoenzyme that selectively neutralizes lipid hydroperoxides, and human gpx4 gene variants have been associated with obesity and cardiovascular disease in epidemiological studies. This study tested the hypothesis that LPPs underlie cardio-metabolic derangements in obesity using a high fat, high sucrose (HFHS) diet in gpx4 haploinsufficient mice (GPx4(+/-)) and in samples of human myocardium.

Diet composition and feeding ecology of the naked goby Gobiosoma bosc (Gobiidae) from four western Atlantic estuaries.

The feeding ecology of the small-bodied benthic naked goby Gobiosoma bosc, a western Atlantic species that occurs in estuaries and other inshore habitats from Connecticut to Texas U.S.A.

Genetic population structure of spotted seatrout Cynoscion nebulosus along the south-eastern U.S.A.

Analyses of the genetic population structure of spotted seatrout Cynoscion nebulosus along the south-eastern U.S. coast using 13 microsatellites suggest significant population differentiation between fish in North Carolina (NC) compared with South Carolina (SC) and Georgia (GA), with New River, NC, serving as an area of integration between northern and southern C.

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles.

Do fish oil omega-3 fatty acids enhance antioxidant capacity and mitochondrial fatty acid oxidation in human atrial myocardium via PPARγ activation?

Abstract Studies in experimental models suggest that n-3 polyunsaturated fatty acids (PUFAs) improve metabolic and anti-inflammatory/antioxidant capacity of the heart, although the mechanisms are unclear and translational evidence is lacking. In this study, patients ingested a moderately high dose of n-3 PUFAs (3.4 g/day eicosapentaenoic (EPA) and doxosahexaenoic acid (DHA) ethyl-esters) for a period of 2-3 weeks before having elective cardiac surgery.

Monoamine oxidase is a major determinant of redox balance in human atrial myocardium and is associated with postoperative atrial fibrillation.

Background: Onset of postoperative atrial fibrillation (POAF) is a common and costly complication of heart surgery despite major improvements in surgical technique and quality of patient care. The etiology of POAF, and the ability of clinicians to identify and therapeutically target high-risk patients, remains elusive.

Methods And Results: Myocardial tissue dissected from right atrial appendage (RAA) was obtained from 244 patients undergoing cardiac surgery.

Genetic population structure of US atlantic coastal striped bass (Morone saxatilis).

Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions.

A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank.

A finite field method for calculating spherical tensor molecular polarizability tensors α(lm;l'm') = ∂Δ(lm)/∂ϕ(l'm')* by numerical derivatives of induced molecular multipole Δ(lm) with respect to gradients of electrostatic potential ϕ(l'm')* is described for arbitrary multipole ranks l and l'. Interconversion formulae for transforming multipole moments and polarizability tensors between spherical and traceless Cartesian tensor conventions are derived. As an example, molecular polarizability tensors up to the hexadecapole-hexadecapole level are calculated for water using the following ab initio methods: Hartree-Fock (HF), Becke three-parameter Lee-Yang-Parr exchange-correlation functional (B3LYP), Møller-Plesset perturbation theory up to second order (MP2), and Coupled Cluster theory with single and double excitations (CCSD).

Atomic forces for geometry-dependent point multipole and gaussian multipole models.

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models.

Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg(2+)-coordinating Thr of regulatory GTPases.

When G-protein alpha subunits binds GTP and Mg(2+), they transition from their inactive to their active conformation. This transition is accompanied by completion of the coordination shell of Mg(2+) with electrons from six oxygens: two water molecules, the ss and gamma phosphoryls of GTP, a helix-alpha1 Ser, and a switch I domain (SWI) Thr, and the repositioning of SWI and SWII domains. SWII binds and regulates effector enzymes and facilitates GTP hydrolysis by repositioning the gamma-carbonyl of a Gln.

Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis.

Following our previous study (Piquemal et al., New J. Chem.

Gaussian Multipole Model (GMM).

An electrostatic model based on charge density is proposed as a model for future force fields. The model is composed of a nucleus and a single Slater-type contracted Gaussian multipole charge density on each atom. The Gaussian multipoles are fit to the electrostatic potential (ESP) calculated at the B3LYP/6-31G* and HF/aug-cc-pVTZ levels of theory and tested by comparing electrostatic dimer energies, inter-molecular density overlap integrals, and permanent molecular multipole moments with their respective ab initio values.

Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations.

Conformations and free energy landscapes of polyproline peptides.

The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables.