Porosity evolution of mafic crystal mush during reactive flow.

The emergence of the "mush paradigm" has raised several questions for conventional models of magma storage and extraction: how are melts extracted to form eruptible liquid-rich domains? What mechanism controls melt transport in mush-rich systems? Recently, reactive flow has been proposed as a major contributing factor in the formation of high porosity, melt-rich regions. Yet, owing to the absence of accurate geochemical simulations, the influence of reactive flow on the porosity of natural mush systems remains under-constrained. Here, we use a thermodynamically constrained model of melt-mush reaction to simulate the chemical, mineralogical, and physical consequences of reactive flow in a multi-component mush system. Our results demonstrate that reactive flow within troctolitic to gabbroic mushes can drive large changes in mush porosity. For example, primitive magma recharge causes an increase in the system porosity and could trigger melt channelization or mush destabilization, aiding rapid melt transfer through low-porosity mush reservoirs.

Computational investigation of the radical-mediated mechanism of formation of difluoro methyl oxindoles: Elucidation of the reaction selectivity and yields.

Oxindoles are an important class of heterocyclic alkaloids with demonstrated pharmacological activity at multiple biological targets. Preparation of new analogs through novel synthetic routes is therefore highly attractive. In this work, we report a computational study to investigate the synthesis of ethoxycarbonyldifluoromethylated oxindoles from N-arylmethacrylamides. The reaction tolerates a diverse range of acrylamides, shows yields ranging from approximately 38%-96%. We have applied density functional theory (DFT) to explore the reaction mechanism, kinetics and thermodynamics to gain further understanding. We demonstrate that a radical-based ring closure reaction is energetically more favorable than a heterolytic process, that the rate-determining step is the formation of the arylmethacrylamide radical, and that the product yields and selectivities are consistent with experiment. The results demonstrate that theoretical methods can prove useful to understand how such reaction and could be potentially employed to rapidly explore the reaction scope further.

Circular Polarization Conversion in Single Plasmonic Spherical Particles.

Temporal and spectral behaviors of plasmons determine their ability to enhance the characteristics of metamaterials tailored to a wide range of applications, including electric-field enhancement, hot-electron injection, sensing, as well as polarization and angular momentum manipulation. We report a dark-field (DF) polarimetry experiment on single particles with incident circularly polarized light in which gold nanoparticles scatter with opposite handedness at visible wavelengths. Remarkably, for silvered nanoporous silica microparticles, the handedness conversion occurs at longer visible wavelengths, only after adsorption of molecules on the silver. Finite element analysis (FEA) allows matching the circular polarization (CP) conversion to dominant quadrupolar contributions, determined by the specimen size and complex susceptibility. We hypothesize that the damping accompanying the adsorption of molecules on the nanostructured silver facilitates the CP conversion. These results offer new perspectives in molecule sensing and materials tunability for light polarization conversion and control of light spin angular momentum at submicroscopic scale.

A Piezoelectric Ionic Cocrystal of Glycine and Sulfamic Acid.

Cocrystallization of two or more molecular compounds can dramatically change the physicochemical properties of a functional molecule without the need for chemical modification. For example, coformers can enhance the mechanical stability, processability, and solubility of pharmaceutical compounds to enable better medicines. Here, we demonstrate that amino acid cocrystals can enhance functional electromechanical properties in simple, sustainable materials as exemplified by glycine and sulfamic acid. These coformers crystallize independently in centrosymmetric space groups when they are grown as single-component crystals but form a noncentrosymmetric, electromechanically active ionic cocrystal when they are crystallized together. The piezoelectricity of the cocrystal is characterized using techniques tailored to overcome the challenges associated with measuring the electromechanical properties of soft (organic) crystals. The piezoelectric tensor of the cocrystal is mapped using density functional theory (DFT) computer models, and the predicted single-crystal longitudinal response of 2 pC/N is verified using second-harmonic generation (SHG) and piezoresponse force microscopy (PFM). The experimental measurements are facilitated by polycrystalline film growth that allows for macroscopic and nanoscale quantification of the longitudinal out-of-plane response, which is in the range exploited in piezoelectric technologies made from quartz, aluminum nitride, and zinc oxide. The large-area polycrystalline film retains a damped response of ≥0.2 pC/N, indicating the potential for application of such inexpensive and eco-friendly amino acid-based cocrystal coatings in, for example, autonomous ambient-powered devices in edge computing.

Caldera resurgence during the 2018 eruption of Sierra Negra volcano, Galápagos Islands.

Recent large basaltic eruptions began after only minor surface uplift and seismicity, and resulted in caldera subsidence. In contrast, some eruptions at Galápagos Island volcanoes are preceded by prolonged, large amplitude uplift and elevated seismicity. These systems also display long-term intra-caldera uplift, or resurgence. However, a scarcity of observations has obscured the mechanisms underpinning such behaviour. Here we combine a unique multiparametric dataset to show how the 2018 eruption of Sierra Negra contributed to caldera resurgence. Magma supply to a shallow reservoir drove 6.5 m of pre-eruptive uplift and seismicity over thirteen years, including an Mw5.4 earthquake that triggered the eruption. Although co-eruptive magma withdrawal resulted in 8.5 m of subsidence, net uplift of the inner-caldera on a trapdoor fault resulted in 1.5 m of permanent resurgence. These observations reveal the importance of intra-caldera faulting in affecting resurgence, and the mechanisms of eruption in the absence of well-developed rift systems.

Quantitative Polarization-Resolved Second-Harmonic-Generation Microscopy of Glycine Microneedles.

Second-harmonic generation (SHG) is a nonlinear optical process that can provide disease diagnosis through characterization of biological building blocks such as amino acids, peptides, and proteins. The second-order nonlinear susceptibility tensor χ(2) of a material characterizes its tendency to cause SHG. Here, a method for finding the χ(2) elements from polarization-resolved SHG microscopy in transmission mode is presented. The quantitative framework and analytical approach that corrects for micrometer-scale morphology and birefringence enable the determination and comparison of the SHG susceptibility tensors of ß- and γ-phase glycine microneedles. The maximum nonlinear susceptibility coefficients are d33  = 15 pm V-1 for the ß and d33  = 5.9 pm V-1 for the γ phase. The results demonstrate glycine as a useful biocompatible nonlinear material. This combination of the analytical model and polarization-resolved SHG transmission microscopy is broadly applicable for quantitative SHG material characterization and diagnostic imaging.

Cryptic evolved melts beneath monotonous basaltic shield volcanoes in the Galápagos Archipelago.

Many volcanoes erupt compositionally homogeneous magmas over timescales ranging from decades to millennia. This monotonous activity is thought to reflect a high degree of chemical homogeneity in their magmatic systems, leading to predictable eruptive behaviour. We combine petrological analyses of erupted crystals with new thermodynamic models to characterise the diversity of melts in magmatic systems beneath monotonous shield volcanoes in the Galápagos Archipelago (Wolf and Fernandina). In contrast with the uniform basaltic magmas erupted at the surface over long timescales, we find that the sub-volcanic systems contain extreme heterogeneity, with melts extending to rhyolitic compositions. Evolved melts are in low abundance and large volumes of basalt flushing through the crust from depth overprint their chemical signatures. This process will only maintain monotonous activity while the volume of melt entering the crust is high, raising the possibility of transitions to more silicic activity given a decrease in the crustal melt flux.

Towards reproducible computational drug discovery.

The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.

Investigation of Factors Affecting the Performance of in silico Volume Distribution QSAR Models for Human, Rat, Mouse, Dog & Monkey.

Volume of distribution (Vdss ) is a measure of how effectively a drug molecule is distributed throughout the body. Along with the clearance, it determines the half-life and therefore the drug dosing interval. A number of different pre-clinical approaches are available to predict the Vdss in human including quantitative structure activity relationship (QSAR) models. Vdss QSAR models have been reported for human and rat, but not important pre-clinical species including dog, mouse and monkey. In this study, we have generated Vdss QSAR model on the human and commonly used pre-clinical species, each of which differs in terms of size, chemical diversity and data quality. We discuss the model performance by species, assess the effect the domain of applicability and the relative merits of building chemical series-specific models. In addition, we compare the intrinsic variability of the experimental logVdss data (∼1.2 fold error) to in-vivo interspecies differences (∼2 fold error) and in silico based models (∼3 fold error). This prompted us to explore whether one species could be used to predict another, particularly where little data for that species is available. i. e. does the expansion in domain of applicability prove beneficial over and above any deterioration due to the use of response values from an alternative species.

In silico identification and in vitro validation of nogalamycin N-oxide (NSC116555) as a potent anticancer compound against non-small-cell lung cancer cells.

The epidermal growth factor receptor (EGFR) was found to be overexpressed in several cancers, especially in lung cancers. Finding new effective drug against EGFR is the key to cancer treatment. In this study, the GOLD docking algorithm was used to virtually screen for novel human EGFR inhibitors from the NCI database. Thirty-four hit compounds were tested for EGFR-tyrosine kinase (TK) inhibition. Two potent compounds, 1-amino-4-(4-[4-amino-2-sulfophenyl]anilino)-9,10-dioxoanthracene-2-sulfonic acid (NSC125910), and nogalamycin N-oxide (NSC116555) were identified with IC50 values against EGFR-TK comparable to gefitinib; 16.14 and 37.71 nM, respectively. However, only NSC116555 demonstrated cytotoxic effects against non-small-cell lung cancer, A549, shown in the cell cytotoxicity assay with an IC50 of 0.19 + 0.01 µM, which was more potent than gefitinib. Furthermore, NSC116555 showed cytotoxicity against A549 via apoptosis in a dose-dependent manner.

Surface plasmon propagation enhancement via bowtie antenna incorporation in Au-mica block waveguides.

The optimum geometry for waveguide propagation was determined by comparing bowtie and semicircle antenna cuts to a standard plain waveguide with a 635 nm laser. The results of both experimental data and COMSOL simulations proved that the bowtie antenna increased waveguide output in comparison to the plain waveguide with the semicircle pattern showing no enhancement. It was also determined that the propagation was highest when the polarization direction of the laser was perpendicular to the direction of the waveguide for all patterns, while polarization along the propagation direction led to little or no output in all antenna and plain waveguide cases. The waveguide output of the bowtie antenna and plain structures was then measured using a tunable laser for wavelengths from 570 nm to 958 nm under both parallel and perpendicular polarization conditions. The results indicated that the bowtie antenna performed better over the entire range with an average increase factor of 2.12±0.40 over the plain waveguide pattern when perpendicularly polarized to the waveguide direction, and 1.10±0.48 when parallel. The measured values indicate that the structure could have applications in broadband devices.

APTES Duality and Nanopore Seed Regulation in Homogeneous and Nanoscale-Controlled Reduction of Ag Shell on SiO2 Microparticle for Quantifiable Single Particle SERS.

Noble-metal nanoparticles size and packing density are critical for sensitive surface-enhanced Raman scattering (SERS) and controlled preparation of such films required to achieve reproducibility. Provided that they are made reliable, Ag shell on SiO2 microscopic particles (Ag/SiO2) are promising candidates for lab-on-a-bead analytical measurements of low analyte concentration in liquid specimen. Here, we selected nanoporous silica microparticles as a substrate for reduction of AgNO3 with 3-aminopropyltriethoxysilane (APTES). In a single preparation step, homogeneous and continuous films of Ag nanoparticles are formed on SiO2 surfaces with equimolar concentration of APTES and silver nitrate in ethanol. It is discussed that amine and silane moieties in APTES contribute first to an efficient reduction on the silica and second to capping the Ag nanoparticles. The high density and homogeneity of nanoparticle nucleation is further regulated by the nanoporosity of the silica. The Ag/SiO2 microparticles were tested for SERS using self-assembled 4-aminothiophenol monolayers, and an enhancement factor of ca. 2 × 106 is measured. Importantly, the SERS relative standard deviation is 36% when a single microparticle is considered and drops to 11% when sets of 10 microparticles are considered. As prepared, the microparticles are highly suitable for state-of-the-art quantitative lab-on-a-bead interrogation of specimens.

Control of piezoelectricity in amino acids by supramolecular packing.

Piezoelectricity, the linear relationship between stress and induced electrical charge, has attracted recent interest due to its manifestation in biological molecules such as synthetic polypeptides or amino acid crystals, including gamma (γ) glycine. It has also been demonstrated in bone, collagen, elastin and the synthetic bone mineral hydroxyapatite. Piezoelectric coefficients exhibited by these biological materials are generally low, typically in the range of 0.1-10 pm V-1, limiting technological applications. Guided by quantum mechanical calculations we have measured a high shear piezoelectricity (178 pm V-1) in the amino acid crystal beta (ß) glycine, which is of similar magnitude to barium titanate or lead zirconate titanate. Our calculations show that the high piezoelectric coefficients originate from an efficient packing of the molecules along certain crystallographic planes and directions. The highest predicted piezoelectric voltage constant for ß-glycine crystals is 8 V mN-1, which is an order of magnitude larger than the voltage generated by any currently used ceramic or polymer.

Design, synthesis, and evaluation of the anticancer activity of 2-amino-aryl-7-aryl-benzoxazole compounds.

A series of 2-amino-aryl-7-aryl-benzoxazole derivatives have been designed, synthesized, and evaluated as anticancer agents. Fourteen of the compounds exhibited cytotoxic effects toward human A549 lung cancer cells. We found 12l was the most potent with an EC50 of 0.4 µm, equivalent to the anticancer drug doxorubicin, but had low selectivity following cross screening in monkey kidney Vero cells. Eight of the most potent or most selective compounds were further profiled in additional cell lines (MCF7, NCI-H187, and KB) to better understand their cytotoxic activity. Only compound 12l had a measurable EC50 in a single cell line (3.3 µm in the KB cell line). Taken together, this data suggest the series as a whole display specific cytotoxicity toward A549 cells. Cheminformatics searches pointed to JAK2 as a possible target. A subset of compounds assayed at this target showed IC50 s ranging from 10 to 0.08 µm; however, no clear correlation between JAK2 potency and A549 cytotoxicity was observed.

Towards Predicting the Cytochrome P450 Modulation: From QSAR to Proteochemometric Modeling.

Drug metabolism determines the fate of a drug when it enters the human body and is a critical factor in defining their absorption, distribution, metabolism, excretion and toxicity (ADMET) characteristics. Among the various drug metabolizing enzymes, cytochrome P450s (CYP450) constitute an important protein family that aside from functioning in xenobiotic metabolism, is also responsible for a diverse array of other roles encompassing steroid and cholesterol biosynthesis, fatty acid metabolism, calcium homeostasis, neuroendocrine functions and growth regulation. Although CYP450 typically converts xenobiotics into safe metabolites, there are some situations whereby the metabolite is more toxic than its parent molecule. Computational modeling has been instrumental in CYP450 research by rationalizing the nature of the binding event (i.e. inhibit or induce CYP450s) or metabolic stability of query compounds of interest. A plethora of computational approaches encompassing ligand, structure and systems based approaches have been utilized to model CYP450-ligand interactions. This review provides a brief background on the CYP450 family (i.e. its roles, advantages and disadvantages as well as its modulators) and then discusses the various computational approaches that have been used to model CYP450-ligand interaction. Particular focus was given to the use of quantitative structure-activity relationship (QSAR) and more recent proteochemometric modeling studies. Finally, a perspective on the current state of the art and future trends of the field is also provided.

A missense founder mutation in VLDLR is associated with Dysequilibrium Syndrome without quadrupedal locomotion.

BACKGROUND: Dysequilibrium syndrome is a genetically heterogeneous condition that combines autosomal recessive, nonprogressive cerebellar ataxia with mental retardation. The condition has been classified into cerebellar ataxia, mental retardation and disequilibrium syndrome types 1 (CAMRQ1), 2 (CAMRQ2) and 3 (CAMRQ3) and attributed to mutations in VLDLR, CA8 and WDR81 genes, respectively. Quadrupedal locomotion in this syndrome has been reported in association with mutations in all three genes. METHODS: SNP mapping and candidate gene sequencing in one consanguineous Omani family from the United Arab Emirates with cerebellar hypoplasia, moderate mental retardation, delayed ambulation and truncal ataxia was used to identify the mutation. In a second unrelated consanguineous Omani family, massively parallel exonic sequencing was used. RESULTS: We identified a homozygous missense mutation (c.2117 G > T, p.C706F) in the VLDLR gene in both families on a shared affected haplotype block.This is the first reported homozygous missense mutation in VLDLR and it occurs in a highly conserved residue and predicted to be damaging to protein function. CONCLUSIONS: We have delineated the phenotype associated with dysequilibrium syndrome in two Omani families and identified the first homozygous missense pathogenic mutation in VLDLR gene with likely founder effect in the southeastern part of the Arabian Peninsula.

Strategies for the generation, validation and application of in silico ADMET models in lead generation and optimization.

INTRODUCTION: The most desirable chemical starting point in drug discovery is a hit or lead with a good overall profile, and where there may be issues; a clear SAR strategy should be identifiable to minimize the issue. Filtering based on drug-likeness concepts are a first step, but more accurate theoretical methods are needed to i) estimate the biological profile of molecule in question and ii) based on the underlying structure-activity relationships used by the model, estimate whether it is likely that the molecule in question can be altered to remove these liabilities. AREAS COVERED: In this paper, the authors discuss the generation of ADMET models and their practical use in decision making. They discuss the issues surrounding data collation, experimental errors, the model assessment and validation steps, as well as the different types of descriptors and statistical models that can be used. This is followed by a discussion on how the model accuracy will dictate when and where it can be used in the drug discovery process. The authors also discuss how models can be developed to more effectively enable multiple parameter optimization. EXPERT OPINION: Models can be applied in lead generation and lead optimization steps to i) rank order a collection of hits, ii) prioritize the experimental assays needed for different hit series, iii) assess the likelihood of resolving a problem that might be present in a particular series in lead optimization and iv) screen a virtual library based on a hit or lead series to assess the impact of diverse structural changes on the predicted properties.

Insight into the reaction mechanism of cis,cis-muconate lactonizing enzymes: a DFT QM/MM study.

MLEs derived from mycobacterium smegmatis and seudomonas fluorescens share ∼76% identity and have a very similar arrangement of catalytic residues in their active site configuration. However, while they catalyze the conversion of cis,cis-muconate to the same achiral product, muconolactone, studies in deuterated solvent surprisingly show that the cyclo-isomerization proceeds with the formation of a chiral product. In this paper we discuss the application of DFT QM/MM calculations on both MLEs, to our knowledge the first reported in the literature on this protein. We investigate the proposal that the base involved in the catalytic reaction is the lysine residue found at the end of the 2(nd) strand given: (a) that the lysine residue at the end of the 6(th) strand is in an apparently equally effective position to catalyze reaction and (b) that the structural related epimerase in-fact achieve their stereo-specific outcomes by relying on either the base from the 2(nd) or 6(th) strand.

Application of drug efficiency index in drug discovery: a strategy towards low therapeutic dose.

INTRODUCTION: The ultimate objective of optimizing adsorption, distribution, metabolism and excretion (ADME) parameters in drug discovery is to maximize the unbound concentration at the site of action for a given dose level. This has the added benefit of minimizing the efficacious dose, reducing the potential for attrition related to drug burden and direct organ toxicity. The concept of drug efficiency was formulated as a tool to obtain a balanced profile between target affinity and ADME properties during lead optimization. AREAS COVERED: The authors discuss how it is possible to maximize the in vivo pharmacological potential addressing whether drug efficiency adds value to the decision-making process and whether it is possible to introduce a single optimization parameter, the drug efficiency index (DEI), linking target affinity and ADME properties, as a marker of in vivo efficacy. EXPERT OPINION: In the absence of a clear hypothesis-driven approach at the beginning of the program (i.e., pharmacokinetic-pharmacodynamic link), the objective to select molecules with a low therapeutic dose is still a major hurdle in drug discovery. The authors believe that a greater strategic focus on mechanistically relevant measures of the determinants of receptor occupancy would help the optimization and selection process. In this respect, the introduction of the DEI, which can be seen as a correction of target affinity by the in vivo pharmacokinetic potential, may help drug discovery to select and promote those molecules with the highest probability to interact with the biological target and with the best balance between target affinity and ADME properties.

Molecular dynamics investigation of psalmopeotoxin I. Probing the relationship between 3D structure, anti-malarial activity and thermal stability.

PcFK1 is a member of the cysteine knot inhibitor family that displays anti-malarial properties. The naturally occurring molecule is ∼ 40 amino acids in length and forms a highly constrained 3D structure due to the presence of 3 disulfide and multiple intra-molecular H-bonds. Recent experimental studies on PcFK1 wild-type and mutants, where the cystiene residues of each disulfide bond were mutated into serine residues, suggest that alterations to these structural constraints can give rise to sizeable differences in SAR. To better understand the relationship between the dynamic inhibitor 3D structure, biophysical and biological properties we have performed solution based molecular dynamics calculations over 150 ns using the CHARMM forcefield. We have analyzed the theoretical trajectory in a systematic way using principal components analysis, which allows us to identify the correlated nature of the protein loop, turn and sheet movements. We have identified the key molecular motions that give rise to the differing SAR which has helped to more precisely direct our ongoing SAR studies in this important therapeutic area.