Nathalie Tarrat

French National Centre for Scientific Research | CNRS · Centre d'Elaboration de Matériaux et d'Etudes Structurales CEMES

The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system and to evaluate the probability flows between them....

Up to date, the influence of ambient air exposure on the energetics and stability of silver clusters has rarely been investigated and compared to clusters in vacuum. Silver clusters up to 3000 atoms in size, on an amorphous carbon film, have been exposed to ambient air and investigated by atomic-resolution imaging in the aberration-corrected Scanni...

Silver nanoparticles have been modeled by density functional theory calculations and ab initio molecular dynamics simulations to explore their stability in air at room temperature. The role of contaminants is...

Dehydrogenation and deprotonation of sucrose and trehalose molecules in vacuum is theoretically studied by using ab initio calculations in the framework of the density functional theory. The differences in the structural, electronic, energetic and vibrational properties of dehydrogenated and deprotonated molecules are discussed, depending on the si...

Silver clusters up to 1000 atoms in size, on an amorphous carbon film, have been exposed to ambient air and investigated by atomic resolution imaging in the aberration-corrected Scanning Transmission Electron Microscope (ac-STEM). Ordered structures comprise more than half the population, the rest are amorphous. Of ordered isomer structures the mos...

Despite the frequent use of silver nanoparticles (Ag NPs) embedded in materials for medical or optical applications, the effect of the matrix on the nanoparticle properties remains largely unknown. This study aims to shed light on the effect of an amorphous silica matrix on the structure and charge distribution of 55- and 147-atom silver nanopartic...

The interest for properties of clusters deposited on surfaces has grown in recent years. In this framework, the Density Functional based Tight Binding (DFTB) method appears as a promising tool due to its ability to treat extended systems at the quantum level with a low computational cost. We report the implementation of periodic boundary conditions...

We report the combination of the threshold algorithm with the Density Functional-based Tight Binding method allowing for the exploration of complex potential energy surfaces and the evaluation of probability flows between their regions, at the quantum level. This original scheme is used to explore the energy landscape of an anionic 20-atom gold clu...

Scanning transmission electron microscopy experiments indicate that face-centered cubic (FCC) is the predominant ordered structure for Ag309 ± 7 nanoclusters, synthesized in vacuum. Historically, experiments do not present a consensus on the morphology at these sizes, whereas theoretical studies find the icosahedral symmetry for Ag309 and the decah...

8-hydroxyquinoline (8Hq) is known to efficiently inhibit the corrosion of aluminium by forming metal-organic layers (8Hq forms complexes with aluminium atoms). In the present work, the atomic scale structure and the energetics of 8-hydroxyquinoline complexes (Alq3) adsorbed on an aluminium surface are investigated by dispersion-corrected DFT comput...

The equilibrium shape of nanoparticles is investigated to elucidate the various core–shell morphologies observed in a bimetallic system associating two immiscible metals, iron and gold, that crystallize in the bcc and fcc lattices, respectively. Fe–Au core–shell nanoparticles present a crystalline Fe core embedded in a polycrystalline Au shell, wit...

Lamb modes describe the vibrations of an object as a whole from the stellar scale to the nanometer one. Lamb description has been built from the linear elasticity theory and considers a homogeneous elastic sphere. Our work tries to determine the minimum scale where this description remains valid by studying the vibration of quantum sized gold clust...

The adsorption of a methoxy radical (\(\hbox {OCH}_3\)) on the low-energy flat gold surfaces Au(111), Au(100) and Au(110) and on surface defects (adatoms) was compared with those of methanethiol (\(\hbox {SCH}_3\)) and methylamine (\(\hbox {NHCH}_3\)) radicals. Using dispersion-corrected DFT, we showed that the adsorption energy of \(\hbox {OCH}_3\...

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to...

Many applications as optical spectroscopy, photothermal therapy, photovoltaics or photocatalysis take advantage of localized surface plasmon resonance of noble metal nanoparticles. Among them, Ag nanoparticles are multi‐functionnal nano‐objects that can be used as efficient plasmonic antennae but also as electron reservoirs for charge transfer or i...

Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important c...

The present work highlights the links between melting properties and structural excitation spectra of small gold and silver clusters. The heat capacity curves are computed for Ag20, Au20, Ag55, Au55 and their ions, using a Parallel-Tempering Molecular Dynamics scheme to explore the Density Functional based Tight Binding (DFTB) potential energy surf...

Silver nanoparticles (AgNPs) are widely used in health-care sector and industrial applications because of their outstanding antibacterial activity. This bactericidal effect is mainly attributed to the release of Ag⁺ ions in the aqueous medium, the first step of which is the dissolution of the AgNP via the oxidation of its surface by O2. With the ai...

We introduce the concept of Convertible and Constrained Nucleic Acid (C2NA). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set...

Süße Oberfläche: Durch Elektrospray‐Ionenstrahlabscheidung kann nichtflüchtige Sucrose auf sauberen Oberflächen abgelagert werden. S. Abb et al. präsentieren in ihrer Zuschrift (DOI: 10.1002/ange.201901340) eine kristalline 2D‐Anordnung von Sucrose auf einer Cu(100)‐Oberfläche. Mit einer Kombination aus Rastertunnelmikroskopie und mehrstufiger Mode...

Saccharides are ubiquitous biomolecules but little is known about their interaction with and assembly at surfaces. Combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self-assembly of the disaccharide sucrose on the Cu(100) surface with subunit-level imaging. By combining a m...

Süße Oberfläche: Mittels präparativer Massenspektrometrie und Rastertunnelmikroskopie gelang es, das Disaccharid Sucrose auf einer Cu(100)‐Oberfläche mit einer Auflösung auf Untereinheiten‐Ebene abzubilden. Mithilfe eines mehrstufigen Modellierungsansatzes konnte die Konformation des Disaccharids an der Oberfläche sowie die Wechselwirkungen zwische...

Saccharides are ubiquitous biomolecules but little is known about their interaction with and assembly on surfaces. Combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self‐assembly of the disaccharide sucrose on the Cu(100) surface with subunit‐level imaging. By combining a m...

The fight against antibiotic resistance has become a major public health issue in recent years. In this context, nano-antibiotics composed of gold nanoparticles with antibiotics grafted on their surface often exhibit outstanding properties, sometimes even bypassing bacterial resistance mechanisms. Among these nano-antibiotics, gold nanoparticles/am...

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical proper...

Structural aspects of the Au147 cluster have been investigated through a density functional based tight binding global optimization involving a parallel tempering molecular dynamics scheme with quenching followed by geometries relaxation at the Density Functional Theory (DFT) level. The focus is put on the competition between relaxed ordered regula...

A gold/water interface has been investigated with the DFT-based self-consistent-charge density-functional tight-binding (SCC-DFTB) method using a cluster model. Born-Oppenheimer molecular-dynamics simulations for mono-, bi-, and trilayers of water on the surface of a Au55 cluster have been computed. We have demonstrated the applicability of this me...

We investigate the dependence upon charge of the heat capacities of the magic gold cluster Au20 obtained from density functional based tight binding theory within parallel tempering molecular dynamics and the multiple histogram method. The melting temperatures, determined from heat capacity curves, are found to be 1102 K for neutral Au20 and only 8...

The adsorption of the iron tetraphenylporphyrin (FeTPP) molecule in its deckchair conformation was investigated on Au(111), Ag(111) and Cu(111) surfaces by performing spin-polarized density functional theory (DFT) calculations taking into account both van der Waals (vdW) interaction and on-site Coulomb repulsion. The deckchair conformation of the m...

2,4-Dihydroxybutyric acid (DHB) is a molecule with considerable potential as a versatile chemical synthon. Notably, it may serve as a precursor for chemical synthesis of the methionine analogue 2-hydroxy-4-(methylthio)butyrate, thus, targeting a considerable market in animal nutrition. However, no natural metabolic pathway exists for the biosynthes...

The global optimization of metallic clusters is an important topic because nanoclusters exhibit structure-dependent properties. In this paper, we present a global optimization study of , , and in their neutral and charge states (-1, 0, +1) conducted using a Parallel-Tempering Molecular Dynamics algorithm at the DFTB level without pre-screening. For...

Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest. In this article, we ha...

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters with N =...

Whereas the bulk equiatomic FeRh alloy with B2 structure is antiferromagnetic (AFM) below 370 K, we demonstrate that the surface configuration can stabilize the low-temperature ferromagnetic (FM) state in FeRh nanoparticles in the 6-10 nm range. The most stable configuration for FM nanoparticles, predicted through first-principles calculations, is...

Core-shell Fe@Au crystalline NPs, particularly suitable for biomedical applications, have been successfully synthesized by sequential deposition from two elemental targets in a ultrahigh vacuum sputtering device. The size of the NPs, in the 8–15 nm range, is controlled by the deposited Fe volume. The obtained NPs adopt an original polyhedral core-s...

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) atomic parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters w...

State-of-the-art van der Waals (vdW) corrected density functional theory (DFT) is routinely used to overcome the failure of standard DFT in the description of molecule/surface long range interactions. However, the systematic use of dispersion forces to model metallic surfaces could lead to less accurate results than the standard DFT and the effect...

The adsorption of several small molecules on different gold surfaces, Au(001), strained Au(001) and Au(001) epitaxied on Fe(001), has been characterized using density functional theory. The surface strain leads to a less energetically favourable adsorption for all studied molecules. Moreover, the presence of the iron substrate induces an additional...

Chemo-enzymatic strategies hold great potential for the development of stereo- and regioselective syntheses of structurally-defined bioactive oligosaccharides. Herein, we illustrate the potential of the appropriate combination of a planned chemo-enzymatic pathway and an engineered biocatalyst for the multi-step synthesis of an important decasacchar...

In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this...

An extensive DFT search of (meta)stable structures of the screw dislocation in hcp-Ti is presented. It reveals that the stable core structures are never basal but always prismatic. This prismatic core dissociates into two partial dislocations in the same or neighboring prismatic planes depending on the initial position of the dislocation line, lead...

The POLYFIT rigid-body algorithm for automated global pairwise and multiple protein structural alignment is presented. Smith-Waterman local alignment is used to establish a set of seed equivalences that are extended using Needleman-Wunsch dynamic programming techniques. Structural and functional interaction constraints provided by evolution are enc...

Introduction Structural comparison and alignment play a pivotal role in the understanding of evolutionary and functional relations in proteins, providing the material basis of both hierarchical protein classification systems and continuous descriptions of protein fold space. Methods for protein structural alignment and superposition of equivalenced...

We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the...

Bulk properties of hcp-Ti, relevant for the description of dislocations, such as elastic constants, stacking faults and γ-surface, are computed using density functional theory (DFT) and two central force embedded atom interaction models (Zope and Mishin 2003 Phys. Rev. B 68 024102, Hammerschmidt et al 2005 Phys. Rev. B 71 205409). The results are c...

With increasing interest in the control of the conformations of nucleic acids to define active riboswitch or siRNA, we present herein our efforts towards the stereocontrolled synthesis and conformational analysis of ribodinucleotides in which α and β torsional angles are constrained within a dioxaphosphorinane structure (ribo-α,β-D-CNA). The crysta...

Properties of hcp-Ti such as elastic constants, stacking faults and γ−surfaces are computed using Density Functional Theory (DFT) and two central force Embedded Atom interaction Models (EAM) [1, 2]. The results are compared to previously published calculations and to predicting models. Their implications on the plastic properties of hcp-Ti are disc...

P-CNAs are dinucleotide building blocks in which the torsional angles α and β of the sugar/phosphate backbone are constrained to non-canonical values within a cyclic phosphonate structure (phostone) synthesised by diastereoselective intramolecular Arbuzov reaction. The reaction has been improved through the use of microwave activation and addition...

α,β-D-CNA building blocks featuring either canonical gauche(−) or noncanonical gauche(+) values of the nucleic acidssugar phosphate backbone torsional angle α have been introduced into oligonucleotides, and provide new insight on conformational restriction impact on duplex formation ability by means of UV experiments and molecular dynamics simulati...

We have studied the alkaline hydrolysis mechanism for six different dimethylphosphate triesters. According to our calculations, we can conclude that for esters with poor leaving groups (pKalg>8) the reaction occurs via a stepwise mechanism, whereas for good leaving groups, it occurs via a concerted mechanism. The attack of the hydroxide anion has t...

Core structure of (a/3)<11-20>screw dislocations in alpha-Ti has been studied in the cluster approach with ab initio DFT-GGA, and in both the cluster and quadrupole approaches with a recently highly optimized EAM central force potential. With the EAM potential we have shown that finite-size effects, in the cluster approach, are negligible down to t...

Introduction of alpha,beta-D-CNA featuring canonical values of the torsional angles alpha and beta within oligonucleotides leads to an overall stabilization and improved rigidity of the duplex DNA as demonstrated by UV experiments, circular dichroism and corroborated by molecular dynamics simulations.

We have investigated the performance of DFT in U(VI) chemistry. A large, representative selection of functionals has been tested, in combination with two ECPs developed in Stuttgart that have different-sized cores (60 and 78 electrons for U). In addition, several tests were undertaken with another 14 electron pseudopotential, which was developed in...

It has been proposed that the driving force for the initial phosphoryl transfer step of protein tyrosine phosphatases (PTPases) could be activation of the substrate ROPO32- by means of an enforced hydrogen-bonding interaction between an aspartic general acid and the bridging oxygen atom O (Zhang et al. Biochemistry 1995, 34, 16088-16096). The poten...

A DFT study of the isostructural compounds [UO2L5](n-) with n=3-5 and linear [Cp2UL5](m-) with m=1-3 has been carried out for two different anionic ligands. Structurally stable structures are obtained for all systems. The coordination competition between cyanide (CN(-)) and isocyanide (NC(-)) as well as between cyanate (OCN(-)) and isocyanate (NCO(...

Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prio...

(Chemical Equation Presented) Constrained nucleic acids (α,β-D-CNAs) have an ethylene bridge that locks the α and β backbone torsion angles of DNA in the canonical (gauche(-),trans) conformation, as in B-form DNA (see picture), or in the noncanonical (gauche(+),trans) conformation. Canonical α,β-D-CNAs enhance the duplex-forming ability of oligonuc...

Konformativ eingeschränkte Nucleinsäuren (α,β-D-CNAs) enthalten eine Ethylenbrücke, die die Rückgratwinkel α und β einer DNA in der kanonischen (gauche(−),trans) oder in der nichtkanonischen Konformation (gauche(+), trans) arretiert. Kanonische α,β-D-CNAs verstärken die Duplexbildung von Oligonucleotiden mit komplementärer DNA, während nichtkanonis...

DFT calculations and dielectric continuum methods have been employed to map out the lowest activation free-energy profiles for the alkaline hydrolysis of representative phosphate triesters and diesters, including trimethyl phosphate (TMP), dimethyl 4-nitrophenyl phosphate (DMNPP), dimethyl hydrogen phosphate (DMHP), and the dimethyl phosphate anion...