Dissociation Time, Quantum Yield, and Dynamic Reaction Pathways in the Thermolysis of -3,4-Dimethyl-1,2-dioxetane.

The thermolysis of -3,4-dimethyl-1,2-dioxetane is studied by trajectory surface hopping. The significant difference between long and short dissociation times is rationalized by frustrated dissociations and the time spent in triplet states. If the C-C bond breaks through an excited state channel, then the trajectory passes over a ridge of the potential energy surface of that state.

The System of Self-Consistent Models: The Case of Henry's Law Constants.

Data on Henry's law constants make it possible to systematize geochemical conditions affecting atmosphere status and consequently triggering climate changes. The constants of Henry's law are desired for assessing the processes related to atmospheric contaminations caused by pollutants. The most important are those that are capable of long-term movements over long distances.

The validation of predictive potential via the system of self-consistent models: the simulation of blood-brain barrier permeation of organic compounds.

Context: To apply the quantitative relationships "structure-endpoint" approach, the reliability of prediction is necessary but sometimes challenging to achieve. In this work, an attempt is made to accomplish the reliability of forecasts by creating a set of random partitions of data into training and validation sets, followed by constructing random models. A system of random models for a helpful approach should be self-consistent, giving a similar or at least comparable statistical quality of the predictions for models obtained using different splits of available data into training and validation sets.

Development of Self-Consistency Models of Anticancer Activity of Nanoparticles under Different Experimental Conditions Using Quasi-SMILES Approach.

Algorithms of the simulation of the anticancer activity of nanoparticles under different experimental conditions toward cell lines A549 (lung cancer), THP-1 (leukemia), MCF-7 (breast cancer), Caco2 (cervical cancer), and hepG2 (hepatoma) have been developed using the quasi-SMILES approach. This approach is suggested as an efficient tool for the quantitative structure-property-activity relationships (QSPRs/QSARs) analysis of the above nanoparticles. The studied model is built up using the so-called vector of ideality of correlation.

CORAL: Model of Ecological Impact of Heavy Metals on Soils via the Study of Modification of Concentration of Biomolecules in Earthworms (Eisenia fetida).

The traditional application for quantitative structure-property/activity relationships (QSPRs/QSARs) in the fields of thermodynamics, toxicology or drug design is predicting the impact of molecular features using data on the measurable characteristics of substances. However, it is often necessary to evaluate the influence of various exposure conditions and environmental factors, besides the molecular structure. Different enzyme-driven processes lead to the accumulation of metal ions by the worms.

Theoretical DFT Study on the Mechanisms of CO/CO Conversion in Chemical Looping Catalyzed by Calcium Ferrite.

The CO/CO conversion mechanism on the calcium ferrite (CFO) surface in chemical looping was explored by a computational study using the density functional theory approach. The CFO catalytic reaction pathway of 2CO + O → 2CO conversion has been elucidated. Our results show that the Fe center in CFO plays the key role as a catalyst in the CO/CO conversion.

Application of quasi-SMILES to the model of gold-nanoparticles uptake in A549 cells.

Cell death is critical to human health and is associated with a variety of medical conditions. Therefore, new controllers of cell death are needed for the treatment of diverse diseases. In particular, nanoparticles (NP) are now regularly used in various applications, including a variety of products and medicines.

Single site Fe on the (110) surface of γ-AlO: insights from a DFT study including the periodic boundary approach.

Examination of the stable (110) surface of γ-alumina reveals that there are three different types of sites available to host a single Fe atom. With the carefully calibrated density functional approach (M12-L/SV), three types of Fe single sites on the (110) surface of γ-alumina have been investigated under the periodic boundary conditions. The most stable Fe replacement site on the (110) surface of γ-alumina has been found to be represented by the tri-coordinated Fe position with the quartet spin state.

How the CORAL software can be used to select compounds for efficient treatment of neurodegenerative diseases?

Recommendations on the efficient application of CORAL software (http://www.insilico.eu/coral) to establish quantitative structure-property/activity relationships (QSPRs/QSARs) are provided.

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for nanosafety assessment.

Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals.

Adsorption of nitrogen-containing compounds on hydroxylated α-quartz surfaces.

Adsorption energies of various nitrogen-containing compounds (specifically, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAn), and 3-nitro-1,2,4-triazole-5-one (NTO)) on the hydroxylated (001) and (100) α-quartz surfaces are computed. Different density functionals are utilized and both periodic as well as cluster approaches are applied. From the adsorption energies, partition coefficients on the considered α-quartz surfaces are derived.

Accurate and transferable multitask prediction of chemical properties with an atoms-in-molecules neural network.

Atomic and molecular properties could be evaluated from the fundamental Schrodinger's equation and therefore represent different modalities of the same quantum phenomena. Here, we present AIMNet, a modular and chemically inspired deep neural network potential. We used AIMNet with multitarget training to learn multiple modalities of the state of the atom in a molecular system.

"Ideal correlations" for biological activity of peptides.

Sequences of one-symbol abbreviations of amino acids are applied as the basis to build up predictive model of Angiotensin converting enzyme (ACE) inhibitory activity of dipeptides and antibacterial activity of group of polypeptides. The developed models are one-variable correlations between biological activity and descriptors calculated with so-called correlation weights of amino acids. The numerical data on the correlation weights are obtained by the Monte Carlo method.

Is clay-polycation adsorbent future of the greener society? In silico modeling approach with comprehensive virtual screening.

Presence of organic pollutants in the wastewater and aquatic environment is one of the serious concerns worldwide. Superior adsorption of organic pollutants on modified clays with organocations is well approved nowadays. Among hybrid materials, clay-polyelectrolyte nanocomposites (CPN) are one of the specifically designed materials for the efficient adsorption of diverse organic pollutants.

Virtual Screening of Anti-Cancer Compounds: Application of Monte Carlo Technique.

Possibility and necessity of standardization of predictive models for anti-cancer activity are discussed. The hypothesis about rationality of common quantitative analysis of anti-cancer activity and carcinogenicity is developed. Potential of optimal descriptors to be used as a tool to build up predictive models for anti-cancer activity is examined from practical point of view.

Toward comprehension of multiple human cells uptake of engineered nano metal oxides: quantitative inter cell line uptake specificity (QICLUS) modeling.

To address the nanomaterial exposure threat, it is imperative to understand how nanomaterials are recognized, internalized, and distributed within diverse cell systems. Targeting of nanomaterials to a specific cell type is generally attained through the modification of the nanoparticle (NP) surface leading to required cellular uptake. The enhanced cellular uptake to normal cells can direct to the higher interaction of NPs with subcellular organelles resulting the provocation of various signaling pathways.

Helical Multi-walled Carbon Nanotubes as an Efficient Material for the Dispersive Solid-Phase Extraction of Low and High Molecular Weight Polycyclic Aromatic Hydrocarbons from Water Samples: Theoretical Study.

The differences in effectiveness of multi-walled carbon nanotubes (MWCNTs) as the dispersive solid-phase extraction (dSPE) sorbent for the selective extraction of polycyclic aromatic hydrocarbons (PAHs) were explained on the basis of theoretical study. It was observed that for low molecular weight PAHs, the recoveries using non-helical and helical MWCNTs were similar. In contrary, for PAHs containing five or more aromatic rings, the extraction efficiency was higher using HMWCNTs than for non-helical ones.

Semi-correlations combined with the index of ideality of correlation: a tool to build up model of mutagenic potential.

Mutagenicity is the ability of a substance to induce mutations. This hazardous ability of a substance is decisive from point of view of ecotoxicology. The number of substances, which are used for practical needs, grows every year.

Single or mixture halogenated chemicals? Risk assessment and developmental toxicity prediction on zebrafish embryos based on weighted descriptors approach.

Halogenated chemicals including perfluoroalkyl substances (PFASs) represent an emerging class of endocrine-disrupting pollutants for human populations across the globe. Distress related to their environmental fate and toxicity has initiated several research projects, but the amount of experimental data available for these pollutants is limited. The objective of this study is to assess the toxicity of potentially "safer" alternatives, in relation to their existing counterparts.

Prediction of antimicrobial activity of large pool of peptides using quasi-SMILES.

The purpose of this study was the estimation of ability of the so-called optimal descriptors calculated to be a tool to predict the antimicrobial activity of large pool of peptides. Traditional simplified molecular input-line entry system (SMILES) is an efficient tool to represent the molecular structure of different compounds. Quasi-SMILES represents an extension of traditional SMILES.

Structure and Energetics of (111) Surface of γ-AlO: Insights from DFT Including Periodic Boundary Approach.

The (111) surface of γ-alumina has been reexamined, and a new (111) surface model has been suggested. The local structure of this new surface of γ-alumina, (111), has been optimized by the density functionals along with the full electron basis sets by using periodic boundary condition. This newly modeled (111) surface is characterized by the same stability as that of the (110) surface, and its surface energy amounts to 2.

CompNanoTox2015: novel perspectives from a European conference on computational nanotoxicology on predictive nanotoxicology.

A first European Conference on Computational Nanotoxicology, CompNanoTox, was held in November 2015 in Benahavís, Spain with the objectives to disseminate and integrate results from the European modeling and database projects (NanoPUZZLES, ModENPTox, PreNanoTox, MembraneNanoPart, MODERN, eNanoMapper and EU COST TD1204 MODENA) as well as to create synergies within the European NanoSafety Cluster. This conference was supported by the COST Action TD1204 MODENA on developing computational methods for toxicological risk assessment of engineered nanoparticles and provided a unique opportunity for cross fertilization among complementary disciplines. The efforts to develop and validate computational models crucially depend on high quality experimental data and relevant assays which will be the basis to identify relevant descriptors.

CORAL and Nano-QFAR: Quantitative feature - Activity relationships (QFAR) for bioavailability of nanoparticles (ZnO, CuO, CoO, and TiO).

Quantitative feature - activity relationships (QFAR) approach was applied to prediction of bioavailability of metal oxide nanoparticles. ZnO, CuO, CoO, and TiO nanoxides were considered. The computational model for bioavailability of investigated species is asserted.

Origin of Substituent Effect on Tautomeric Behavior of 1,2,4-Triazole Derivatives: Combined Spectroscopic and Theoretical Study.

The reaction of 2-aryl-[1,2,4]triazolo[1,5-c]quinazolines with nucleophilic reagents (hydrazine hydrate, sodium hydroxide, sodium methoxide, hydrochloric acid) under acidic conditions leads to formation of compounds that tend to tautomerize. The products of the transformation are distinguished by the position (ortho-, meta-, para-) of the OCH group in the aryl moiety. To assign their structures we used the combined approach: experiment and theoretical modeling.