Lucio Colombi Ciacchi

Publications of Lucio Colombi Ciacchi

• Adsorption and reduction of glutathione disulfide on α-Al2O3 nanoparticles: experiments and modeling.

  Authors: Ralf Dringen, Yvonne Koehler, Ludmilla Derr, Giulia Tomba, Maike M Schmidt, Laura Treccani, Lucio Colombi Ciacchi, Kurosch Rezwan

  Langmuir : the ACS journal of surfaces and colloids. 06/2011; 27(15):9449-57.

  Glutathione disulfide (GSSG; γ-GluCysGly disulfide) was used as a physiologically relevant model molecule to investigate the fundamental adsorption mechanisms of polypeptides onto α-aluminaGlutathione disulfide (GSSG; γ-GluCysGly disulfide) was used as a physiologically relevant model molecule to investigate the fundamental adsorption mechanisms of polypeptides onto α-alumina nanoparticles. Its adsorption/desorption behavior was studied by enzymatic quantification of the bound GSSG combined with zeta potential measurements of the particles. The adsorption of GSSG to alumina nanoparticles was rapid, was prevented by alkaline pH, was reversed by increasing ionic strength, and followed a nearly ideal Langmuir isotherm with a standard Gibbs adsorption energy of -34.7 kJ/mol. Molecular dynamics simulations suggest that only one of the two glutathionyl moieties contained in GSSG binds stably to the nanoparticle surface. This was confirmed experimentally by the release of GSH from the bound GSSG upon reducing its disulfide bond with dithiothreitol. Our data indicate that electrostatic interactions via the carboxylate groups of one of the two glutathionyl moieties of GSSG are predominantly responsible for the binding of GSSG to the alumina surface. The results and conclusions presented here can provide a base for further experimental and modeling studies on the interactions of biomolecules with ceramic materials.

• Atomically smooth stress-corrosion cleavage of a hydrogen-implanted crystal.

  Authors: Gianpietro Moras, Lucio Colombi Ciacchi, Christian Elsässer, Peter Gumbsch, Alessandro De Vita

  Physical review letters. 08/2010; 105(7):075502.

  We present a quantum-accurate multiscale study of how hydrogen-filled discoidal "platelet" defects grow inside a silicon crystal. Dynamical simulations of a 10-nm-diameter platelet reveal that H2We present a quantum-accurate multiscale study of how hydrogen-filled discoidal "platelet" defects grow inside a silicon crystal. Dynamical simulations of a 10-nm-diameter platelet reveal that H2 molecules form at its internal surfaces, diffuse, and dissociate at its perimeter, where they both induce and stabilize the breaking up of highly stressed silicon bonds. A buildup of H2 internal pressure is neither needed for nor allowed by this stress-corrosion growth mechanism, at odds with previous models. Slow platelet growth up to micrometric sizes is predicted as a consequence, making atomically smooth crystal cleavage possible in implantation experiments.

• Dissociative adsorption of methane on surface oxide structures of Pd-Pt alloys

  Authors: Arezoo Dianat, Nicola Seriani, Lucio Colombi Ciacchi, Wolfgang Pompe, Gianaurelio Cuniberti, Manfred Bobeth

  03/2010;

  The dissociative adsorption of methane on variously oxidized Pd, Pt and Pd-Pt surfaces is investigated using density-functional theory, as a step towards understanding the combustion of methane onThe dissociative adsorption of methane on variously oxidized Pd, Pt and Pd-Pt surfaces is investigated using density-functional theory, as a step towards understanding the combustion of methane on these materials. For Pd-Pt alloys, models of surface oxide structures are built on the basis of known oxides on Pd and Pt. The methane adsorption energy presents large variations depending on the oxide structure and composition. Adsorption is endothermic on the bare Pd(111) metal surface as well as on stable thin layer oxide structures such as the ($\sqrt{5}\times\sqrt{5}$) surface oxide on Pd(100) and the PtO$_2$-like oxide on Pt(111). Instead, large adsorption energies are obtained for the (100) surface of bulk PdO, for metastable mixed Pd$_{1-x}$Pt$_x$O$_{4/3}$ oxide layers on Pt(100), and for Pd-Pt(111) surfaces covered with one oxygen monolayer. In the latter case, we find a net thermodynamic preference for a direct conversion of methane to methanol, which remains adsorbed on the oxidized metal substrates via weak hydrogen-bond interactions.

• Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces.

  Authors: Daniel J Cole, Mike C Payne, Lucio Colombi Ciacchi

  Physical chemistry chemical physics : PCCP. 12/2009; 11(48):11395-9.

  The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourableThe adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect.

• Density functional theory study of Fe(II) adsorption and oxidation on goethite surfaces

  Authors: Benedict Russell, Mike C Payne, Lucio Colombi Ciacchi

  05/2009;

  We study the interactions between Fe(II) aqua complexes and surfaces of goethite (alpha-FeOOH) by means of density functional theory calculations including the so-called Hubbard U correction to theWe study the interactions between Fe(II) aqua complexes and surfaces of goethite (alpha-FeOOH) by means of density functional theory calculations including the so-called Hubbard U correction to the exchange-correlation functional. Using a thermodynamic approach, we find that (110) and (021) surfaces in contact with aqueous solutions are almost equally stable, despite the evident needlelike shape of goethite crystals indicating substantially different reactivity of the two faces. We thus suggest that crystal anisotropy may result from different growth rates due to virtually barrierless adsorption of hydrated ions on the (021) but not on the (110) surface. No clear evidence is found for spontaneous electron transfer from an adsorbed Fe(II) hex-aqua complex to a defect-free goethite substrate. Crystal defects are thus inferred to play an important role in assisting such electron transfer processes observed in a recent experimental study. Finally, goethite surfaces are observed to enhance the partial oxidation of adsorbed aqueous Fe(II) upon reaction with molecular oxygen. We propose that this catalytic oxidation effect arises from donation of electronic charge from the bulk oxide to the oxidizing agent through shared hydroxyl ligands anchoring the Fe(II) complexes on the surface.

• Stress-driven oxidation chemistry of wet silicon surfaces

  Authors: Lucio Colombi Ciacchi, Daniel J. Cole, Mike C Payne, Peter Gumbsch

  05/2009;

  The formation of a hydroxylated native oxide layer on Si(001) under wet conditions is studied by means of first principles molecular dynamics simulations. Water molecules are found to adsorb andThe formation of a hydroxylated native oxide layer on Si(001) under wet conditions is studied by means of first principles molecular dynamics simulations. Water molecules are found to adsorb and dissociate on the oxidised surface leading to rupture of Si-O bonds and producing reactive sites for attack by dissolved dioxygen or hydrogen peroxide molecules. Tensile strain is found to enhance the driving force for the dissociative adsorption of water, suggesting that similar reactions could be responsible for environmentally-driven sub-critical crack propagation in silicon.

• Vacancy segregation in the initial oxidation stages of the TiN(100) surface.

  Authors: Janina Zimmermann, Mike W Finnis, Lucio Colombi Ciacchi

  The Journal of chemical physics. 05/2009; 130(13):134714.

  The well-known corrosion resistance and biocompatibility of TiN depend on the structural and chemical properties of the stable oxide film that forms spontaneously on its surface after exposure toThe well-known corrosion resistance and biocompatibility of TiN depend on the structural and chemical properties of the stable oxide film that forms spontaneously on its surface after exposure to air. In the present work, we focus on the atomistic structure and stability of the TiN(100) surface in contact with an oxidizing atmosphere. The early oxidation stages of TiN(100) are investigated by means of first-principles molecular dynamics (FPMD). We observe selective oxidation of Ti atoms and formation of an ultrathin Ti oxide layer, while Ti vacancies are left behind at the metal/oxide interface. Within the formalism of ab initio thermodynamics we compute the segregation energies of vacancies and vacancy clusters at the metal/oxide interface, comparing the stability of the system obtained by FPMD simulations with ideally reconstructed models. We find that the localization of Ti vacancies in the thin oxide layer and at the TiN/oxide interface is thermodynamically stable and may account for the early removal of N atoms from the interface by segregation of N vacancies from the bulk reservoir. We suggest that superficial oxidation may proceed along two distinct possible pathways: a thermodynamically stable path along the potential energy minimum surface and a metastable, kinetically driven path that results from the high heat release during the dissociation of O(2).

• Stress Development and Impurity Segregation during Oxidation of the Si(100) Surface

  Authors: Daniel J. Cole, Mike C Payne, Lucio Colombi Ciacchi

  08/2008;

  We have studied the segregation of P and B impurities during oxidation of the Si(100) surface by means of combined static and dynamical first-principles simulations based on density functionalWe have studied the segregation of P and B impurities during oxidation of the Si(100) surface by means of combined static and dynamical first-principles simulations based on density functional theory. In the bare surface, dopants segregate to chemically stable surface sites or to locally compressed subsurface sites. Surface oxidation is accompanied by development of tensile surface stress up to 2.9 N/m at a coverage of 1.5 monolayers of oxygen and by formation of oxidised Si species with charges increasing approximately linearly with the number of neighbouring oxygen atoms. Substitutional P and B defects are energetically unstable within the native oxide layer, and are preferentially located at or beneath the Si/SiOx interface. Consistently, first-principles molecular dynamics simulations of native oxide formation on doped surfaces reveal that dopants avoid the formation of P-O and B-O bonds, suggesting a surface oxidation mechanism whereby impurities remain trapped at the Si/SiOx interface. This seems to preclude a direct influence of impurities on the surface electrostatics and, hence, on the interactions with an external environment.

• Structure and energetics of diphenylalanine self-assembling on Cu(110).

  Authors: Giulia Tomba, Magalí Lingenfelder, Giovanni Costantini, Klaus Kern, Florian Klappenberger, Johannes V Barth, Lucio Colombi Ciacchi, Alessandro De Vita

  The journal of physical chemistry. A. 01/2008; 111(49):12740-8.

  We investigate the dynamical features of the adsorption of diphenylalanine molecules on the Cu(110) surface and of their assembling into supramolecular structures by a combination of quantum andWe investigate the dynamical features of the adsorption of diphenylalanine molecules on the Cu(110) surface and of their assembling into supramolecular structures by a combination of quantum and classical atomistic modeling with dynamic scanning tunneling microscopy and spectroscopic experiments. Our results reveal a self-assembling mechanism in which isolated adsorbed molecules change their conformation and adsorption mode as a consequence of their mutual interactions. In particular, the formation of zwitterions after proton transfer between initially neutral molecules is found to be the key event of the assembling process, which stabilizes the supramolecular structures. Because of the constraints on the intermolecular bonds exerted by the surface-molecule interactions, the assembly process is strictly stereoselective, and may suggest a general model for patterning and functionalization of bare metal surfaces with short chiral peptides.

• Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding.

  Authors: Daniel J. Cole, Mike C Payne, Gábor Csányi, S. Mark Spearing, Lucio Colombi Ciacchi

  The Journal of chemical physics. 12/2007; 127(20):204704.

  We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination andWe have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.

• Tracking the chiral recognition of adsorbed dipeptides at the single-molecule level.

  Authors: Magalí Lingenfelder, Giulia Tomba, Giovanni Costantini, Lucio Colombi Ciacchi, Alessandro De Vita, Klaus Kern

  Angewandte Chemie (International ed. in English). 02/2007; 46(24):4492-5.

• Catalytic oxidation activity of Pt3O4 surfaces and thin films.

  Authors: Nicola Seriani, Wolfgang Pompe, Lucio Colombi Ciacchi

  The journal of physical chemistry. B. 09/2006; 110(30):14860-9.

  The catalytic oxidation activity of platinum particles in automobile catalysts is thought to originate from the presence of highly reactive superficial oxide phases which form under oxygen-richThe catalytic oxidation activity of platinum particles in automobile catalysts is thought to originate from the presence of highly reactive superficial oxide phases which form under oxygen-rich reaction conditions. Here we study the thermodynamic stability of platinum oxide surfaces and thin films and their reactivities toward oxidation of carbon compounds by means of first-principles atomistic thermodynamics calculations and molecular dynamics simulations based on density functional theory. On the Pt(111) surface the most stable superficial oxide phase is found to be a thin layer of alpha-PtO2, which appears not to be reactive toward either methane dissociation or carbon monoxide oxidation. A PtO-like structure is most stable on the Pt(100) surface at oxygen coverages of one monolayer, while the formation of a coherent and stress-free Pt3O4 film is favored at higher coverages. Bulk Pt3O4 is found to be thermodynamically stable in a region around 900 K at atmospheric pressure. The computed net driving force for the dissociation of methane on the Pt3O4(100) surface is much larger than that on all other metallic and oxide surfaces investigated. Moreover, the enthalpy barrier for the adsorption of CO molecules on oxygen atoms of this surface is as low as 0.34 eV, and desorption of CO2 is observed to occur without any appreciable energy barrier in molecular dynamics simulations. These results, combined, indicate a high catalytic oxidation activity of Pt3O4 phases that can be relevant in the contexts of Pt-based automobile catalysts and gas sensors.

• Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations.

  Authors: Lucy Heady, Marivi Fernandez-Serra, Ricardo L Mancera, Sian Joyce, Ashok R Venkitaraman, Emilio Artacho, Chris-Kriton Skylaris, Lucio Colombi Ciacchi, Mike C Payne

  Journal of medicinal chemistry. 09/2006; 49(17):5141-53.

  The rational development of specific inhibitors for the approximately 500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity andThe rational development of specific inhibitors for the approximately 500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP binding. Combining classical dynamic simulations with a novel ab initio computational approach linear-scalable to molecular interactions involving thousands of atoms, we have investigated the binding of five distinct inhibitors to the cyclin-dependent kinase CDK2. We report here that polarization and dynamic hydrogen bonding effects, so far undetected by crystallography, affect both their activity and selectivity. The effects arise from the specific solvation patterns of water molecules in the ATP binding pocket or the intermittent formation of hydrogen bonds during the dynamics of CDK/inhibitor interactions and explain the unexpectedly high potency of certain inhibitors such as 3-(3H-imidazol-4-ylmethylene)-5-methoxy-1,3-dihydro-indol-2-one (SU9516). The Lys89 residue in the ATP-binding pocket of CDK2 is observed to form temporary hydrogen bonds with the three most potent inhibitors. This residue is replaced in CDK4 by Thr89, whose shorter side-chain cannot form similar bonds, explaining the relative selectivity of the inhibitors for CDK2. Our results provide a generally applicable computational method for the analysis of biomolecular structures and reveal hitherto unrecognized features of the interaction between protein kinases and their inhibitors.

• First-principles molecular-dynamics study of native oxide growth on Si(001).

  Authors: Lucio Colombi Ciacchi, Mike C Payne

  Physical review letters. 12/2005; 95(19):196101.

  Through first-principles molecular dynamics we study the low-temperature oxidation of the Si(001) surface from the initial adsorption of an O2 molecule to the formation of a native oxide layer.Through first-principles molecular dynamics we study the low-temperature oxidation of the Si(001) surface from the initial adsorption of an O2 molecule to the formation of a native oxide layer. Peculiar features of the oxidation process are the early, spontaneous formation of Si4+ species, and the enhanced reactivity of the surface while the reactions proceed, until saturation is reached at a coverage of 1.5 ML. The channels for barrierless oxidation are found to be widened in the presence of both boron and phosphorous impurities.

• "Hot-atom" O2 dissociation and oxide nucleation on Al(111).

  Authors: Lucio Colombi Ciacchi, Mike C Payne

  Physical review letters. 05/2004; 92(17):176104.

  We propose an atomistic model for the nucleation of aluminum oxide on the Al(111) surface derived from first principles molecular dynamics simulations. The process begins with the dissociativeWe propose an atomistic model for the nucleation of aluminum oxide on the Al(111) surface derived from first principles molecular dynamics simulations. The process begins with the dissociative adsorption of O2 molecules on the metal surface, which occurs via a "hot-atom" mechanism driven by the partial filling of the sigma* antibonding molecular orbital of O2. During the subsequent hyperthermal motion, O atoms can be spontaneously incorporated underneath the topmost Al surface layer, initiating the nucleation of the oxide far below the saturation coverage of one (1 x 1) O adlayer.

• The entry pathway of O2 into human ferritin

  Authors: Lucio Colombi Ciacchi, Mike C Payne

  Chemical Physics Letters.

  We study the entry pathway of dioxygen into human ferritin by means of both first principles and classical molecular dynamics techniques. Oxygen molecules, which behave hydrophobically in the waterWe study the entry pathway of dioxygen into human ferritin by means of both first principles and classical molecular dynamics techniques. Oxygen molecules, which behave hydrophobically in the water solvent, are found to interact with the Tyr 29 residue of human ferritin both directly via weak interactions and indirectly via hydrophobic forces. These interactions drive O2 toward a narrow hydrophobic channel which connects the ferroxidase site of ferritin with the external environment. Diffusion of O2 through the channel is observed using locally enhanced sampling techniques, and the enthalpy barrier to diffusion is calculated from first principles.

• Ab initio study of element segregation and oxygen adsorption on PtPd and CoCr binary alloy surfaces

  Authors: Arezoo Dianat, Janina Zimmermann, Nicola Seriani, Manfred Bobeth, Wolfgang Pompe, Lucio Colombi Ciacchi

  Surface Science.

  The segregation behavior of the bimetallic alloys PtPd and CoCr in the case of bare surfaces and in the presence of an oxygen ad-layer has been studied by means of first-principles modeling based onThe segregation behavior of the bimetallic alloys PtPd and CoCr in the case of bare surfaces and in the presence of an oxygen ad-layer has been studied by means of first-principles modeling based on density-functional theory (DFT). For both systems, change of the d-band filling due to charge transfer between the alloy components, resulting in a shift of the d-band center of surface atoms compared to the pure components, drives the surface segregation and governs the chemical reactivity of the bimetals. In contrast to previous findings but consistent with analogous PtNi alloy systems, enrichment of Pt atoms in the surface layer and of Pd atoms in the first subsurface layer has been found in Pt-rich PtPd alloy models, despite the lower surface energy of pure Pd compared to pure Pt. Similarly, Co surface and Cr subsurface segregation occurs in Co-rich CoCr alloys. However, in the presence of adsorbed oxygen, Pd and Cr occupy preferentially surface sites due to their lower electronegativity and thus stronger oxygen affinity compared to Pt and Co, respectively. In either cases, the calculated oxygen adsorption energies on the alloy surfaces are larger than on the pure components when the more noble components are present in the subsurface layers.