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". The developed NNP is able to produce, with excellent agreement, the structure, energy, and forces obtained at the DFT level. Finally, the calculated stability of various borophene polymorphs, including those not initially included in the training data set, shows better stabilization for ν ∼ 0.1 hole density, and in particular for the allotrope α (ν=1/9). The stability of borophene on the metal surface is shown to depend on its orientation, implying structural corrugation patterns that can be observed only from long-time simulations on extended systems. The NNP also demonstrates its ability to simulate vibrational densities of states and produce realistic structures with simulated STM images closely matching the experimental ones.

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. Classical molecular dynamics simulations of diazepam and the two forms of oxazepam on the external surface of Na+-montmorillonite highlighted the better coordination of the oxazepam-chair conformation, compared to its boat counterpart and diazepam. This has been confirmed through DFT calculations, from which a coordination energy that is greater by 10 kcal·mol-1 is observed. This strongly suggests that the experimentally observed intercalation of oxazepam occurs only in the chair form because of the strong coordination with the Na+ cation present in the Na-Mt interlayer. Classical MD simulations of the intercalated oxazepam chair molecule in the Na-Mt interlayer allowed the evaluation of the interlayer spacing d001, which was in very good agreement with the experimental XRD measurement.

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. The Au 4f photoelectron spectra with a depth profiling investigation are used to evaluate the degree of nanoparticle surface oxidation. In alkaline water, the results preclude any surface oxidation contrary to the case of nanoparticles produced in NaBr solution. In addition, the analysis of Br 3d core-level photoelectron spectra agrees with a clear signature of Br on the nanoparticle surface, which is confirmed by a specific valence band feature. This experimental study is supported by DFT calculations, evaluating the energy balance of halide adsorption on different configurations of gold surfaces including oxidation or adsorbed salts.

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 2.146 eV for ZnPc to 2.050 eV for ZnPcR4, in agreement with the experimental trend, and indicating the reliability of the electrochemical evaluation of LUMO and HOMO energy levels. Optical transitions computed at the CAM-B3LYP-D3 with triple zeta basis sets were found to be in good agreement with experimental values for both the B and Q bands. Subsequently, structures were also characterized for NO2 adsorbed complexes, in order to assess the potential role of ZnPc as a NO2 sensor. A clear sigma bonding chemisorption of NO2 on Zn atom is observed for all derivatives, followed by a charge transfer from the π Pc conjugated system to the Zn-NO2 moiety. More importantly, after NO2 chemisorption on ZnPc derivative a remarkable red-shift is observed in the optical spectra, particularly for NO2/ZnPcR4 complex, thus offering a good index to detect the binding of NO2. The optical spectra and the vibrational spectra can therefore be used to detect the presence of NO2 and ZnPc derivatives show appropriate properties to constitute good NO2 sensors.

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, Au2H+, prevents its dissociation and allows for adsorption of CO. Reaction kinetics are measured by employing a radio frequency ion trap, where Au2+ and CO interact for a given reaction time. The effect of a hydrogen atom is evaluated by comparing reaction rate constants measured for Au2+ and Au2H+. The theoretical results for the adsorption of CO molecules and their reaction characteristics with Au2+ and Au2H+ are found to agree with the experimental findings. The joint investigations provide insights into hydrogen atom adsorption effects and consequent reaction mechanisms.

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. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.

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. It is believed to be helpful for organometallic chemists, since it allows a deep understanding and may be used as a predictive tool of the coordinating properties of ligands.

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. It is reported that N(3)-C(4) and N(1)-C(2) bonds are more easily cleaved than the C(5)-C(6) bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C(5)-C(6) bond cleavage almost prohibited. Among all possible formed fragments, the formation of the OCN(+) fragment for the peak at m/z = 42 Da is excluded because of an intermediate that was not observed experimentally and too a large free energy barrier. Based on the required free energy, it is observed that two fragment derivatives: C(2)H(4)N(+) and C(2)H(2)O˙(+) may be formed, with a small preference for C(2)H(4)N(+). This latter product is not formed through a retro Diels Alder reaction in contrast to C(2)H(2)O˙(+). The following sequence is proposed for the peak at 42 Da: C(2)H(4)N(+) (from N(1)-C(2), C(4)-C(5) cleavages) > C(2)H(2)O˙(+) (from N(3)-C(4), N(1)-C(2) and C(5)-C(6) cleavages) > C(2)H(4)N(+) (from N(1)-C(2), N(3)-C(4) and C(4)-C(5)) > C(2)H(2)O˙(+) (from C(5)-C(6), N(1)-C(2) and N(3)-C(4) cleavages) > NCO(+) (from N(1)-C(2), C(4)-C(5) and N(3)-C(4) cleavages). Finally the peak at 28 Da is assigned to CNH(2)(+) derivatives that can be formed through two different paths, the easiest one requiring 5.4 eV.

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. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.

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. The androstane derivative steroids considered in the present study have two functional groups at C(3) and C(17), which may interact with the methacrylic acid. These can be hydroxyl or ketone groups. Experimental results show that the steroids can be divided in three groups corresponding to the ketone type at C(3), the H-bond strength increasing with the number of double bonds. DFT calculations are in very good agreement with experimental results, showing increasing binding energy from no bonds, a single bond, and two double bond steroids. For steroids holding a hydroxyl group the binding energy obtained in the solvent model is comparable to the binding energy of single bond ketone steroids.

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 5.8 kcal mol(-1) in the micro-solvated model. This illustrates the high oxidising power of the [Fe(IV)O(H(2)O)(5)](2+) complex. On the other hand, the breaking of the Fe-O bond, leading to the formation of hydroquinone, is observed to be the rate-determining step of the reaction. The rather large free energy barrier corresponding to this bond cleavage amounts to 10.2 and 9.3 kcal mol(-1) in the gas-phase and micro-solvated models, respectively. Elsewhere, the lifetime of the HO˙ radical has previously been shown to be extremely small. These facts, combined with observations of oxo iron under certain experimental conditions, suggest that oxo iron is a highly plausible oxidative species of the reaction. In addition, a trigonal bipyramidal iron complex, coordinated either by hydroxyl groups and/or by water molecules, has been found in all described mechanisms. This structure appears to be a stable intermediate; and to our knowledge, it has not been characterised by previous studies.

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. In almost all considered cases, adsorption involved the spontaneous proton transfer to the nucleobase, with a more pronounced character in the Osub structures. The binding energy is about 10 kcal mol(-1) larger for Osub than for Tsub complexes mainly due to the larger acidity in Osub surfaces and due to the better stabilization by H-bond contacts between the negatively charged surface and the protonated base. The binding energy of coplanar orientations of the base is observed to be as large as the orthogonal ones due to a balance between electrostatic and dispersion contributions. Finally the binding of guanine and adenine on the acidic surface amounts to 50 kcal mol(-1) while that of cytosine rises to 44 kcal mol(-1).

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. In contrast, Li(+) tends to hydrate and coordinate to 4 water molecules in all cases, except for OT(sub), for which one of the two Li(+) cations remains bound to the oxygens close to the substituted tetrahedral site. Finally, Na(+) presents an intermediate behaviour, binding to the surface in T(sub) montmorillonite but being hydrated in O(sub). These simulations show that the hydration/adsorption behaviour of alkali cations in the swelling process of montmorillonite depends on the affinity of the cation for water and the surface, as well as on the type of substitution that controls the negative charge on surface oxygen atoms.

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. The strength of the stabilization is due to the number of stabilizing interactions increasing with the size of the cation and to the Lewis acidity of the alkali cations, which increases as the size of the cations decreases. In the product, NO(3)(-) interacts mainly with the cations and NO(+) with the basic oxygen atoms of the tetrahedral aluminium through its nitrogen atom. As the cation size increases, the NO(3)(-)...cation interaction increases. As a result, the negative charge of the framework is less well screened by the larger cations and the interaction between NO(+) and the basic oxygen atoms becomes stronger. NO(+) appears to be a good probe of zeolite basicity, in agreement with experimental observations.

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. The former involves the hardness of the alkaline cation. The latter reflects the charge density of the basic oxygen, well described by the "hard" descriptor: the molecular electrostatic potential. The harder is the alkali metal, the easier is the H3C-OH or H3C-I bond dissociation, and the lower is the basicity of the bridging oxygen, and thus the more difficult is the C-O-zeolite bond formation. The fact that these two processes compete has been established by comparing the energy profiles for the methylation with methyl iodide and methanol. For methanol the role of the alkaline metal on the bond dissociation prevails because of the larger hardness of the OH group as compared to that of the iodine atom. For methyl iodide the oxygen basicity prevails over the interaction of I with metal. This study clearly shows that in both experimental and theoretical studies the role of the Lewis acidity or hardness of the alkali metal ion and the role of the basicity of the framework oxygen have to be separated from each other for a good interpretation of zeolite basicity. Also, the hardness of the probe molecule is particularly important when considering the interaction with the alkali metal ion.

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. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA-DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.

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. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.