Mauro Boero

University of Strasbourg - CNRS · Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS)

Nanostructures, fabricated by locating molecular building blocks in well-defined positions, for example, on a lattice, are ideal platforms for studying atomic-scale quantum effects. In this context, STM data obtained from self-assembled Bis(phthalocyaninato) Terbium (III) (TbPc2) single-molecule magnets on various substrates have raised questions a...

Poly(3-hexylthiophene) (P3HT) is a polymer used in organic solar cells as a light absorber and an electron donor. Photogenerated excitons diffuse and dissociate into free charge carriers provided they reach the absorber boundaries. The device efficiency is therefore dependent on the exciton diffusion. Although measurements can be performed for exam...

Enantiomeric excesses (ee) of L-amino acids in meteorites are higher than 10%, especially for isovaline (Iva). This suggests the existence of some kind of triggering mechanism responsible for the amplification of the ee from an initial small value. Here, we investigate the dimeric molecular interactions of alanine (Ala) and Iva in solution as an in...

Aldehydes and carboxylic acids are widely used as catalysts for efficient racemization process of amino acids. However, the detailed reaction mechanism remains unclear. This work aims to clarify the racemization mechanism of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid by using computational approaches. Density functional theory...

High enantiomeric excesses (ee's) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H...

The structural phase transition of the high-symmetry cubic phase of antiperovskite Na3OCl is investigated by computing the phonon band structures of 14 different polymorphs with distinct types of ONa6 octahedral tilting. The resulting P-T phase diagram shows that, at high temperature and low pressure, the high-symmetry cubic structure with Pm3¯m sy...

Thermal properties are expected to be sensitive to the network topology and yet no clearcut information is available on how the thermal conductivity of amorphous systems is affected by details of the atomic structure. To address this issue we use as a target system a phase change amorphous material (GST, i.e. Ge 2 Sb 2 Te 5 ) simulated by first-pri...

First-principles molecular dynamics (FPMD) calculations were performed on liquid GeSe4 with the aim of inferring the impact of dispersion (van der Waals, vdW) forces on the structural properties. Different expressions for the dispersion forces were employed, allowing us to draw conclusions on their performances in a comparative fashion. These resul...

Ionic liquids (ILs) feature a tailorable and wide range of structural, chemical and electronic properties that make this class of materials suitable to a broad variety of forefront applications in next-generation electronics. Yet, their intrinsic complexity call for special attention and experimental probes have still limitations in unraveling the...

We present an atomistic insight into the processes leading to the formation of graphene on SiC(0001) surfaces by resorting to first-principles molecular dynamics empowered by free-energy sampling methods. Based on the experimental surface, consisting of terraces bordered by a sequence of steps, we find that Si atoms are dislodged from step edges an...

Copper amine oxidase from Arthrobacter globiformis (AGAO) catalyses the oxidative deamination of primary amines via a large conformational change of a topaquinone (TPQ) cofactor during the semiquinone formation step. This conformational change of TPQ occurs in the presence of strong hydrogen bonds and neighboring bulky amino acids, especially the c...

Enantiomeric excesses of l-amino acids have been detected in meteorites; however, their molecular mechanism and prebiotic syntheses are still a matter of debate. To elucidate the origin of homochirality, alanine and the chiral precursors formed in prebiotic processes were investigated with regard to their stabilities among their isomers by employin...

First-principles molecular dynamics is employed to describe the atomic structure of amorphous SiN, a non-stoichiometric compound belonging to the SixNy family. To produce the amorphous state via the cooling of the liquid, both the Car–Parrinello and the Born–Oppenheimer approaches are exploited to obtain a system featuring sizeable atomic mobility....

Precursor molecules (NH3 and Ga compounds) along with carrier gas (H2 or N2) used to grow GaN structures bring a large amount of hydrogen atoms which affect the growing mechanism of GaN. This has a non-negligible effect of the chemistry and diffusivity of precursors and dissociation products. To encompass the experimentally difficulty in of unravel...

First-principles molecular dynamics is employed to describe the atomic structure of amorphous SiN, a non-stoichiometric compound belonging to the Si$_x$N$_{y}$ family. To produce the amorphous state via the cooling of the liquid, both the Car-Parrinello and the Born-Oppenheimer approaches are exploited to obtain a system featuring sizeable atomic m...

Additional data and results

We provide a microscopic insight, both structural and electronic, into the multifold interactions occurring in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [EMIM][TFSI] currently targeted for applications in next-generation low-power electronics and optoelectronic devices. To date, practical applications have remai...

The approach-to-equilibrium molecular dynamics (AEMD) methodology implemented within a first-principles molecular dynamics (FPMD) scheme is applied to amorphous SiO2. In this disordered material, measurements of the thermal conductivity indicate no reduction down to 10 nm. In view of these premises, we calculate the thermal conductivity of amorphou...

In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors (intermolecular structural factors), intermolecular center-to-c...

Metal carbene complexes represent an ubiquitous class of compounds in organomettalic chemistry able to trigger a wealth of catalytic reactions of both fundamental and industrial processes. By resorting to first principles approaches, we focus on the fundamental features of these complexes in which the metal center can be either Hf, Ti or Zr. These...

First-principles molecular dynamics, within the density functional theory framework, is employed to assess the structural properties of the chalcohalide glass Ge20Te73I7 (gGTI). The calculated total x-ray and neutron structure factors are in quantitative agreement with the experimental counterparts. Glassy gGTI features a predominantly Ge-centered...

Achieving a precise understanding of nanoscale thermal transport in phase change materials (PCMs), such as Ge2Sb2Te5 (GST), is the key of thermal management in nanoelectronics, photonic and neuromorphic applications using non-volatile memories. By resorting to a first-principles approach to calculate the thermal conductivity of amorphous GST, we fo...

Water pollution by heavy metals is of increasing concern due to its devastating effects on the environment and on human health. For the removal of heavy metals from water sources, natural materials, such as spent-coffee-grains or orange/banana/chestnut peels, appear to offer a potential cheap alternative to more sophisticated and costly technologie...

Achieving a precise understanding of nanoscale thermal transport in phase change materials (PCMs), such as Ge2Sb2Te5 (GST), is the key of thermal management in nanoelectronics, photonic and neuromorphic applications using non-volatile memories. By resorting to a first-principles approach to calculate the thermal conductivity of amorphous GST, we fo...

The atomic structure of glassy GeTe4 is obtained in the framework of first-principles molecular dynamics (FPMD) by considering five different approaches for the description of the electronic structure within density functional theory (DFT). Among these schemes, one is not corrected by accounting for the dispersion forces and it is based on the BLYP...

Heavy metals are captured by hemicellulose from water: modeling and simulations. Classical and ab initio molecular dynamics aided by metadynamics. Relevant to the understanding of removal of heavy metals from water sources with natural materials, e.g. spent coffee grains.

We report first-principles calculations based on the density-functional theory that clarify atomic reactions of ammonia decomposition and subsequent nitrogen incorporation during GaN epitaxial growth. We find that Ga-Ga weak bonds are ubiquitous on Ga-rich growing surface and responsible for the growth reactions. Furthermore, Car-Parrinello Molecul...

The oxidative deamination of biogenic amines, crucial in the metabolism of a wealth of living organisms, is catalyzed by copper amine oxidases (CAOs). In this work, on the ground of accurate molecular modeling, we provide a clear insight into the unique protonation states of the key catalytic aspartate residue Asp298 and the prosthetic group of top...

This paper focuses on a theoretical investigation of the peculiar properties of the chromophore in the C-phycocyanin (C-PC), phycocyanobilin (PCB). The scope is to unravel their key features upon light absorption and transmission occurring in natural photosynthesis. To this aim, by resorting to the time dependent density functional theory (TDDFT) a...

The approach-to-equilibrium molecular dynamics (AEMD) methodology is applied in combination with first-principles molecular dynamics to investigate the thermal transfer between two silicon blocks connected by a molecular layer. Our configuration consists of alkanes molecules strongly coupled to the silicon surfaces via covalent bonds. In phase 1 of...

DNA-stabilized silver clusters (Ag:DNAs) have attracted much attention due to their unique sequence-dependent fluorescence and many potential applications; however, the understandings of their atomic structures and functional properties are still limited, which hamper the further development of the novel nanoclusters. Using the advanced computation...

Monomeric sarcosine oxidase (MSOX) is a fundamental - yet one of the simplest - member of a family of flavoenzymes able to catalyze the oxidation of sarcosine (N-methylglycine) and other secondary amines. MSOX is one of the best characterized members of the amine oxidoreductases (AOs), however, its reaction mechanism is still controversial. A singl...

We show that in nanoscale disordered networks the thermal conductivity reduces with respect to the bulk value in a way remindful of the analogous behavior in nanocrystalline systems. Our rationale is based on the analogy with nanostructured crystalline silicon and is substantiated by results obtained (experimentally, analytically and by atomic scal...

First-principles molecular dynamics (FPMD) is a well-established method to study materials at the atomic scale by taking advantage of three ingredients: the laws of statistical mechanics, the theoretical foundations of density functional theory and powerful computers. FPMD does its best when the atomic structures are unknown or poorly known and whe...

Modelling gas adsorption of porous materials is nowadays an undeniable necessary in order to complement experiment findings with the purpose to enrich our fundamental understanding of adsorption mechanisms as well as develop better performing materials for gas mixture separation. In this contribution, we explore the possibility to use first-princip...

First-principles molecular dynamics is employed to investigate thermal transport in glassy GeTe4, a subsystem of several ternary phase-change materials. As a first result, we found modes localized on a few atoms in the vibrational density of states. The thermal transport is further rationalized by calculating the thermal conductivity for a range of...

Bis(phthalocyaninato)lanthanide (LnPc2) double-decker-based devices have recently raised a great deal of interest for data encoding purposes. Although the 4f-electrons of lanthanide ions play a key role in the experimental methodology, their localized character, deeper in energy than 3d ones of transition metals, hampers a detailed investigation. H...

Quantum chemistry based simulations were used to examine the excited state of porphyra-334, one of the fundamental mycosporine-like amino acids present in a wide variety of aqueous organisms. Our calculations reveal three characteristic aspects of porphyra-334 related to either its ground or excited state. Specifically, (i) the ground state (S0) st...

An overview of the major first-principles methods used to simulate condensed phases is presented, with special emphasis on chalcogenide glasses. The scope of this review article is to offer a survey of fundamental algorithms and techniques, accompanied by a few recent examples particularly representative of computational materials science applied t...

The vibrational excitation related transport properties of a manganese phthalocyanine molecule suspended between the tip of a scanning tunneling microsope (STM) and a surface are investigated by combining the local manipulation capabilities of the STM with inelastic electron tunneling spectroscopy. By attachment of the molecule to the probe tip, th...

The vibrational excitation related transport properties of a MnPc molecule suspended between the tip of an STM and a surface is investigated by combining the local manipulation capabilities of STM with inelastic electron tunneling spectroscopy. By attachment of the molecule to the probe tip, the intrinsic physical properties similar to those exhibi...

Hydrogen storage mechanism and diffusion in metal-organic frameworks We report a detailed investigation of diffusion processes and storage mechanisms of H 2 inside both MOF-5 and IRMOF-6 utilizing Car-Parrinello molecular dynamics simulations. These insights provide precious guidelines for the design of effective MOF systems via the control of the...

A comparative turnover frequency (TOF) study for structure-sensitive CO–NO reactions between overlayer (thin-film) and nanoparticle Rh catalysts was performed using a combined experimental and theoretical approach. Two types of honeycomb catalysts were prepared: one by the arc-plasma deposition of a 3-nm Rh overlayer having a (111) preferential ori...

Diffusion and storage of hydrogen molecules in metal organic frameworks are crucial for the de- velopment of next-generation energy storage devices. By resorting to first principles modeling, we compute the diffusion coefficient of molecular hydrogen in these systems in a range of tempera- tures where MOF–based devices are expected to operate. The...

The inclusion of dispersion (van der Waals, vdW) forces in first-principles modeling of disordered chalcogenides is analyzed and critically discussed in view of their impact on the atomic structure. To this purpose we considered the case of glassy GeTe4. We selected a vdW correction (termed vdWG hereafter) introduced by Grimme (2006) and, as an alt...

Recent first-principles molecular dynamics simulations (FPMD) results on two chalcogenide glasses (glassy GeS4 and GeSe4) are revisited by accounting explicitly for van der Waals (vdW) dispersion forces. This effort is motivated by the observation that such contributions were found to be important in the case of glassy GeTe4 while they were negligi...

A detailed insight into the catalytic reduction of NO operated by Cr-Cu nanostructures embedded in a CeO 2 surface A synergy between experiments and theoretical modeling enables us to propose a comprehensive scenario of the reaction mechanism for the CO-NO reactions on the surface of a Cr-Cu/CeO 2 catalyst for the first time. These insights provide...

A detailed insight into the catalytic reduction of NO operated by Cr-Cu nanostructures embedded in a CeO 2 surface A synergy between experiments and theoretical modeling enables us to propose a comprehensive scenario of the reaction mechanism for the CO-NO reactions on the surface of a Cr-Cu/CeO 2 catalyst for the first time. These insights provide...

Replacing rare and expensive elements, such as Pt, Pd, and Rh commonly used in catalytic devices, with more abundant and less expensive ones is a mandatory issue to realize efficient, sustainable and economically appealing three–way catalysts. In this context, the surface of a Cr–Cu/CeO2 system represents a versatile catalyst for the conversion of...

Due the broad range of application of iron oxide nanoparticles (NPs), the control of their size and shape on demand remains a great challenge as these parameters are of upmost importance to provide NPs with magnetic properties tailored to the targeted application. One promising synthesis process to tune their size and shape is the thermal decomposi...

The thermal conductivity of a glass can be obtained by first-principles molecular dynamics provided we exploit a methodology that has been termed the “approach-to-equilibrium” molecular dynamics (AEMD) [1,2, Chap. 8]. In the present work, we investigate the occurrence of size effects by comparing the thermal conductivity of two g-GeTe4 atomic model...

A thorough understanding of the interactions of CO2 with the hosting porous network is crucial for the design of new adsorbent materials with enhanced gas adsorption capacity and selectivity. In this paper, first-principles molecular dynamics simulations are performed to assess the interactions of CO2 adsorbed in a nanoporous glassy chalcogenide (i...

First-principles molecular dynamics have been employed to highlight the structural properties of glassy Ga10Ge15Te75 (GGT), a promising disordered system for infrared applications. Our approach relies entirely on the predictive power of density functional theory, in combination with a careful choice of the exchange-correlation functional and the ac...

Thermal decomposition is a practical and reliable tool to synthesize nanoparticles with monodisperse size distribution and reproducible accuracy. The nature of the precursor molecules and their interaction with the environment during the synthesis process have a direct impact on the resulting nanoparticles. Our study focuses on widely used transiti...

The amorphous structure of the phase change material Ge2Sb2Te5 (GST) has been the object of controversial structural models. By employing first-principles molecular dynamics within density functional theory, we are able to obtain quantitative agreement with experimental structural findings for the topology of glassy GST. To this end, we take full a...

Developing cost-effective and high performance oxygen reduction reaction (ORR) catalysts is a fundamental issue in fuel cells and metal-air batteries. To this aim, carbon materials catalysts (CMCs) are extensively investigated because of their performance comparable to noble metal based catalysts in alkaline solution. Yet, acidic solutions are desi...

When single molecule magnets (SMMs) self-assemble into 2D networks on a surface they interact via the π-electrons of their ligands. This interaction is relevant to the quantum entanglement between molecular qubits, a key issue in quantum computing. Here we examine the role played by the unpaired radical electron in the upper ligand of Tb double-dec...

Copper- and cobalt-based layered simple hydroxides (LSH) are successfully functionalized by a series of fluorene mono- and diphosphonic acids, using anionic exchange reactions and a preintercalation strategy. The lateral functionalization of the fluorene moieties has only little impact on the overall structure of the obtained layered hybrid materia...

A set of structural properties of liquid GeSe2 are calculated by using first-principles molecular dynamics and including, for the first time, van der Waals dispersion forces. None of the numerous atomic-scale simulations performed in the past on this prototypical disordered network-forming material had ever accounted for dispersion forces in the ex...

We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function,...