Neural Network Approach for a Rapid Prediction of Metal-Supported Borophene Properties.

We developed a high-dimensional neural network potential (NNP) to describe the structural and energetic properties of borophene deposited on silver. This NNP has the accuracy of density functional theory (DFT) calculations while achieving computational speedups of several orders of magnitude, allowing the study of extensive structures that may reveal intriguing moiré patterns or surface corrugations. We describe an efficient approach to constructing the training data set using an iterative technique known as the "adaptive learning approach".

Selective Adsorption of Organic Micro-Pollutants by Smectite Clays Revealed from Atomistic Simulations.

In this study, atomistic simulations were carried out to study the difference in the adsorption process between two similar molecules, diazepam and oxazepam, on Na-montmorillonite. Kinetic and XRD measurements showed a contrasting adsorption mechanism of these two molecules, differing only by the presence/absence of methyl and hydroxyl groups, with a larger adsorption amount and intercalation for the oxazepam. The structural characterization of these molecules was investigated through DFT calculations and showed the vicinity of hydroxyl and carbonyl groups for only the chair conformation of oxazepam compared to the boat conformation.

Surface Chemistry of Gold Nanoparticles Produced by Laser Ablation in Pure and Saline Water.

Pulsed laser ablation in liquid (PLAL) is a powerful method for producing nanoparticle colloids with a long-term stability despite the absence of stabilizing organic agents. The colloid stability involves different reactivities and chemical equilibria with complex ionic-specific effects at the nanoparticle/solvent interface which must be strongly influenced by their chemical composition. In this work, the surface composition of PLAL-produced gold nanoparticles in alkaline and saline (NaBr) water is investigated by X-ray photoelectron spectroscopy on free-flying nanoparticles, exempt from any substrate or radiation damage artifact.

New zinc phthalocyanine derivatives for nitrogen dioxide sensors: A theoretical optoelectronic investigation.

Zinc-phthalocyanines ZnPc derivatives including quinoleinoxy groups have been studied through DFT calculations. The most stable geometries were characterized for the unsubstituted to the tetra substituted ZnPcs. The energy gap decreased from 2.

Hydrogen-Induced Adsorption of Carbon Monoxide on the Gold Dimer Cation: A Joint Experimental and DFT Investigation.

It is demonstrated, using tandem mass spectrometry and radio frequency ion trap, that the adsorption of a H atom on the gold dimer cation, AuH, prevents its dissociation and allows for adsorption of CO. Reaction kinetics are measured by employing a radio frequency ion trap, where Au and CO interact for a given reaction time. The effect of a hydrogen atom is evaluated by comparing reaction rate constants measured for Au and AuH.

Fragmentation mechanisms of cytosine, adenine and guanine ionized bases.

The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks.

Dual descriptor and molecular electrostatic potential: complementary tools for the study of the coordination chemistry of ambiphilic ligands.

In this paper, we show that the ambiphilic properties of some organic ligands in organometallic complexes may be retrieved readily from simple calculations in the framework of conceptual density functional theory (C-DFT): namely, the dual descriptor (DD) and the molecular electrostatic potential (MEP) of the ligands afford a rather straightforward interpretation of experimental trends such as the bonding geometry and the electronic properties of complexes in terms of σ-, π- and back-bonding. The studied ligands were chosen to be representative of the wide variety organometallic chemistry offers, ranging from neutral to charged systems and from diatomic to polyatomic molecules. The present approach is general since all relevant parameters are retrieved from the electron density, obtained either from a DFT or post-Hartree-Fock calculation.

DFT study of the fragmentation mechanism of uracil RNA base.

The fragmentation process of the uracil RNA base has been investigated via DFT calculations in order to assign fragments to the ionisation mass spectrum obtained after dissociation induced by collision experiments. The analysis of the electronic distribution and geometry parameters of the cation allows selection of several bonds that may be cleaved and lead to the formation of various fragments. Differences are observed in the electronic behaviour of the bond breaking as well as the energy required for the cleavage.

Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study.

Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water.

Study of prepolymerization complex formation in the synthesis of steroid-based molecularly imprinted polymers.

The preparation of steroid-based molecularly imprinted polymers (MIPs) based upon noncovalent interaction is particularly suited for selective capture of steroid hormones in biological and environmental samples. The success of this method lies in the optimization of the interaction between steroids (template) and methacrylic acid (functional monomer) in the prepolymerization mixture. NMR techniques coupled with DFT calculations were used to evaluate the capacity of the methacrylic acid to bind a steroid for future applications.

Oxo iron(IV) as an oxidative active intermediate of p-chlorophenol in the Fenton reaction: a DFT study.

Debate continues over which active species plays the role of oxidative agent during the Fenton reaction-the HO˙ radical or oxo iron [Fe(IV)O](2+). In this context, the present study investigates the oxidation of p-chlorophenol by [Fe(IV)O(H(2)O)(5)](2+) using DFT calculations, within gas-phase and micro-solvated models, in order to explore the possible role of oxo iron as a reactant. The results show that the chlorine atom substitution of p-chlorophenol by oxo iron is a highly stabilising step (ΔH = -83 kcal mol(-1)) with a free energy barrier of 5.

Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite.

In the present study, DFT periodic plane wave calculations, at the PBE-D level of theory, were carried out to investigate the interaction of DNA nucleobases with acidic montmorillonite. The surface model was considered in its octahedral (Osub) and tetrahedral (Tsub) substituted forms, known to have different acidic properties. The adsorption of adenine, guanine and cytosine was considered in both orthogonal and coplanar orientations with the surface, interacting with the proton via a given heteroatom.

Ab initio molecular dynamics study of the hydration of Li(+), Na(+) and K(+) in a montmorillonite model. Influence of isomorphic substitution.

The present work reports ab initio molecular dynamics simulations, based on density functional theory using the PBE functional, of Li(+)- Na(+)- and K(+)-montmorillonites, considering three types of isomorphic substitutions in the montmorillonite layer: tetrahedral (T(sub)), octahedral (O(sub)) and both (OT(sub)). These simulations allow us to evaluate the effect of each type of substitution on the inner- outer-sphere complex formation of the alkali cations. It is observed that, for the three kinds of substituted montmorillonites, K(+) remains bound to the surface confirming its role as swelling inhibitor.

Understanding the reactivity and basicity of zeolites: a periodic DFT study of the disproportionation of N(2)O(4) on alkali-cation-exchanged zeolite Y.

The disproportionation of N(2)O(4) into NO(3)(-) and NO(+) on Y zeolites has been studied through periodic DFT calculations to unravel 1) the role of metal cations and the framework oxygen atoms and 2) the relationship between the NO(+) stretching frequency and the basicity of zeolites. We have considered three situations: adsorption on site II cations with and without a cation at site III and adsorption on a site III cation. We observed that cations at sites II and III cooperate to stabilize N(2)O(4) and that the presence of a cation at site III is necessary to allow the disproportionation reaction.

Understanding the concept of basicity in zeolites. A DFT study of the methylation of Al-O-Si bridging oxygen atoms.

DFT calculations on a 4-ring cluster and on ONIOM models of faujasite were carried out to assess the concept of basicity in zeolites, exchanged with alkali cations. The considered reaction is the methylation of the Si-O-Al bridging oxygen by methanol and methyl iodide. The reaction involves both the dissociation of the H3C-OH or H3C-I bonds and the formation of the C-O-zeolite bond.

Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.

The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes.

A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding.