Design of New Dispersants Using Machine Learning and Visual Analytics.

Artificial intelligence (AI) is an emerging technology that is revolutionizing the discovery of new materials. One key application of AI is virtual screening of chemical libraries, which enables the accelerated discovery of materials with desired properties. In this study, we developed computational models to predict the dispersancy efficiency of oil and lubricant additives, a critical property in their design that can be estimated through a quantity named blotter spot.

Dissolving Hydroxyolite: A DNA Molecule into Its Hydroxyapatite Mold.

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double-stranded DNA has been investigated at the atomistic level using computer simulations.

An experimental-computer modeling study of inorganic phosphates surface adsorption on hydroxyapatite particles.

The adsorption of orthophosphate, pyrophosphate, triphosphate and a trisphosphonate onto hydroxyapatite has been examined using experiments and quantum mechanical calculations. Adsorption studies with FTIR and X-ray photoelectron spectroscopies have been performed considering both crystalline hydroxyapatite (HAp) and amorphous calcium phosphate particles, which were specifically prepared and characterized for this purpose. Density functional theory (DFT) calculations have been carried out considering the (100) and (001) surfaces of HAp, which were represented using 1 × 2 × 2 and 3 × 3 × 1 slab models, respectively.

Synergistic approach to elucidate the incorporation of magnesium ions into hydroxyapatite.

Although the content of Mg(2+) in hard tissues is very low (typically ≤1.5 wt %), its incorporation into synthetic hydroxyapatite (HAp) particles and its role in the mineral's properties are still subject of intensive debate. A combined experimental-computational approach is used to answer many of the open questions.

DNA adsorbed on hydroxyapatite surfaces.

Hydroxyapatite (HAp) particles with very different surface charges and compositions (i.e. different Ca/P and CO /PO ratios) have been obtained by varying the experimental conditions used during the chemical precipitation process.

Modeling biominerals formed by apatites and DNA.

Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations.

Mineralization of DNA into nanoparticles of hydroxyapatite.

Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca(2+), PO4(3-) and OH(-)-containing aqueous solutions in the presence and absence of B-DNA has been used to conclude that the backbone of the double helix acts as a template for HAp growth. More specifically, results reveal the formation of calcium phosphate clusters at the first stages of the simulations, which subsequently re-organize to nucleate HAp.

Factors governing the conformational tendencies of C(α)-ethylated α-amino acids: chirality and side-chain size effects.

The intrinsic conformational properties of the N-acetyl-N'-methylamide derivatives of d-C(α)-ethylglycine (Abu), d-C(α)-methyl-C(α)-ethylglycine (Iva), and C(α,α)-diethylglycine (Deg) have been investigated using quantum mechanical calculations in the gas phase and in chloroform, dichloromethane and aqueous solutions. Although the large number of flexible dihedral angles results in many minimum energy conformations, only a few of them are energetically representative because of the repulsive interactions between the ethyl groups and the backbone atoms. The conformational restrictions imposed by such repulsions increase as follows: Abu < Iva < Deg.

Intermolecular interactions in electron transfer through stretched helical peptides.

The helical peptide Cys-Ala-Lys-(Glu-Ala-Ala-Ala-Lys)(2)-Ala-NH-(CH(2))(2)-SH has been organized forming a self-assembled monolayer on gold (0.602 peptides per nm(2)), its conductance behavior under stretching conditions being studied using scanning tunnelling microscopy and current sensing atomic force microscopy. The helical conformation of the peptide has been found to play a fundamental role in the conductance.

Conformational profile of a proline-arginine hybrid.

The intrinsic conformational preferences of a new nonproteinogenic amino acid have been explored by computational methods. This tailored molecule, named ((β)Pro)Arg, is conceived as a replacement for arginine in bioactive peptides when the stabilization of folded turn-like conformations is required. The new residue features a proline skeleton that bears the guanidilated side chain of arginine at the C(β) position of the five-membered pyrrolidine ring, in either a cis or a trans orientation with respect to the carboxylic acid.