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Davide Donadio

University of California, Davis, Chemistry, Faculty Member

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Papers by Davide Donadio

Trends in the Adsorption and Dissociation of Water Clusters on Flat and Stepped Metallic Surfaces

The Journal of Physical Chemistry C, 2014

Understanding the structure and chemical reactivity of water adsorbed at metallic surfaces is ver... more Understanding the structure and chemical reactivity of water adsorbed at metallic surfaces is very important in many processes such as catalysis, corrosion, and electrochemistry. Using density functional theory calculations, we investigate the adsorption and dissociation of water clusters on flat and stepped surfaces of several transition metals: Rh, Ir, Pd, and Pt. We find that water binds preferentially to the step edges than to terrace sites, thus linear clusters or one-dimensional water wires can be isolated by differential desorption. The clusters formed at the step are stabilized by the cooperative effect of chemical bonds with the metal and hydrogen bonding. The enhanced reactivity of the step edges and the cooperative effect of hydrogen bonding improve the chances of partial dissociation of water clusters. We assess the correlations between adsorption and dissociation energies, observing that they are increased on stepped surfaces. We present a detailed interpretation of water dissociation by analyzing changes in the electronic structure of both water and metals. The identification of trends in the energetics of water dissociation at transition metals is expected to aid the design of better materials for catalysis and fuel cells, where the density of steps at surfaces would be a relevant additional parameter.

Lattice thermal conductivity of nanostructured semiconductors from atomistic simulations

by Davide Donadio and Yuping He

We present an atomistic analysis of the thermal conductivity (k) of nanoporous silicon (np-Si) [1... more We present an atomistic analysis of the thermal conductivity (k) of nanoporous silicon (np-Si) [1, 2], and we compare our results with those obtained for bulk crystalline (c-Si) and amorphous Si. We computed k using equilibrium molecular dynamics and Green Kubo relations; we then analyzed our results by solving the Boltzmann Transport Equation in the single mode relaxation time approximation, and by using an approach devised [3] to describe thermal transport in disordered semiconductors. We observe that in np-Si the phonon mean free path is reduced by up to a factor of 10 with respect to c-Si, yielding a reduction of the k of about 2 orders of magnitude. The predominant phonon scattering processes contributing to k can be modeled by the same non-perturbative [3] approach that describes thermal transport in a-Si. [0pt] [1] J-H. Lee, et al. Appl. Phys. Lett, 91, 223110 (2007)[0pt] [2] J-H. Lee, et al., Nano. Lett., 8(11), 3750 (2008)[0pt] [3] P, B. Allen and J. L. Feldman, Phys. Rev. ...

Atomistic study of heat transport in SiGe alloys

Semiconductor alloys, e.g. SiGe, are considered as promising materials to build efficient thermoe... more Semiconductor alloys, e.g. SiGe, are considered as promising materials to build efficient thermoelectric devices [1], and atomistic modeling of heat transport in these systems may help complement and guide experiments in optimizing their efficiency. We analyze strengths and weaknesses of several atomistic approaches in modeling the thermal conductivity of SiGe alloys, and we analyze in detail their range of validity. In particular, we focus on equilibrium molecular dynamics [2], an approach based on the solution of the Boltzmann transport equation [3] and Green function techniques [4]. Applications to both bulk and nanostructured SiGe will be presented. [4pt] [1] A. J. Minnich, M. S. Dresselhaus, Z. F. Ren, and G. Chen, Energy Environ. Sci. 2, 466 (2009). [2] See e.g. D. Donadio and G. Galli, Phys. Rev. Lett. 102, 195901 (2009); Nano Lett. 10, 847 (2010). [3] See e.g. J. E. Turney, E. S. Landry, A. J. J. McGaughey, and C. H. Amon, Phys. Rev. B, 79, 064301 (2009). [4] See e.g. I. Sav...

Nuclear Quantum Effects in Water: A Multiscale Study

by Davide Donadio and Raffaello Potestio

We outline a method to investigate the role of nuclear quantum effects in liquid water making use... more We outline a method to investigate the role of nuclear quantum effects in liquid water making use of a force field derived from ab initio simulations. Starting from a first-principles molecular dynamics simulation we obtain an effective force field for bulk liquid water using the force-matching technique. After validating that our effective model reproduces the key structural and dynamic properties of the reference system, we use it to perform path integral simulations to investigate the role played by nuclear quantum effects on bulk water, probing radial distribution functions, vibrational spectra and hydrogen bond fluctuations. Our approach offers a practical route to derive ab initio quality molecular models to study quantum effects at a low computational cost.

“Site Binding” of Ca2+ Ions to Polyacrylates in Water: A Molecular Dynamics Study of Coiling and Aggregation

by Davide Donadio and Alessandro Laio

ABSTRACT The interaction of Ca2+ ions with short polyacrylate chains (NaPA) in water is investiga... more ABSTRACT The interaction of Ca2+ ions with short polyacrylate chains (NaPA) in water is investigated using molecular dynamics simulations, accelerated with the recently developed metadynamics algorithm. The much discussed “site binding” of calcium ions to these industrially relevant polymers is driven by an entropy gain as water molecules are released into the solution. At high NaPA concentrations, increased Ca2+−PA monomer ratios will not result in strong coiling of PA oligomers. This is due to the local rigidity induced by the binding of many Ca2+ ions to the polymer. Because the uncoiled state of the crowded chain obstructs formation of high Ca2+−COO- coordination numbers, interchain interactions will become favorable, and formation of PA aggregates can be expected. On the other hand, at low NaPA concentrations, introduction of Ca2+ ions to the solution leads to the formation of very stable coiled configurations, with local crystal-like structures, in which the Ca2+ ions cluster together. It is the sharing of carboxylate groups among the metal ions that leads to the formation of these crystal-like conformations, inducing desolvation and precipitation of the chain at threshold Ca2+ concentrations.

Simulation of the grafting of organosilanes at the surface of dry amorphous silica

We have performed first principles metadynamics simulations of the grafting process of tetraethox... more We have performed first principles metadynamics simulations of the grafting process of tetraethoxysilane (TEOS) at two surface sites of dry amorphous silica: the two-membered silicon ring and the isolated silanol. The ab initio activation energies for the grafting reaction are 0.2 eV and 1.4 eV, at the 2M and SiOH sites, respectively. The simulations support the experimental evidence based on IR vibrational spectroscopy that the ring is more reactive than the surface SiOH group for the grating of organosilanes.

Crystal structure transformations in SiO2 from classical and ab initio metadynamics

S ilica is the main component of the Earth's crust and is also of great relevance in many branche... more S ilica is the main component of the Earth's crust and is also of great relevance in many branches of materials science and technology. Its phase diagram is rather intricate and exhibits many different crystalline phases 1-6 . The reported propensity to amorphization and the strong influence on the outcome of the initial structure and of the pressurization protocol 1,7 indicate the presence of metastability and large kinetic barriers. As a consequence, theory is also faced with great difficulties and our understanding of the complex transformation mechanisms is still very sketchy despite a large number of simulations 8-13 . Here, we introduce a substantial improvement of the metadynamics method 14,15 , which finally brings simulations in close agreement with experiments. We unveil the subtle and non-intuitive stepwise mechanism of the pressure-induced transformation of fourfold-coordinated α-quartz into sixfold-coordinated stishovite at room temperature. We also predict that on compression fourfoldcoordinated coesite will transform into the post-stishovite α-PbO 2 -type phase. The new method is far more efficient than previous methods, and for the first time the study of complex structural phase transitions with many intermediates is within the reach of molecular dynamics simulations. This insight will help in designing new experimental protocols capable of steering the system towards the desired transition.

Cluster expansion and optimization of thermal conductivity in SiGe nanowires

Physical Review B - Condensed Matter and Materials Physics, 2010

We investigate the parametrization and optimization of thermal conductivity in silicon-germanium ... more We investigate the parametrization and optimization of thermal conductivity in silicon-germanium alloy nanowires by the cluster-expansion technique. Si 1−x Ge x nanowires are of interest for thermoelectric applications and the reduction in lattice thermal conductivity ͑ L ͒ is desired for enhancing the thermoelectric figure of merit. We seek the minimization of L with respect to arrangements of Si and Ge atoms in 1.5 nm diameter ͓111͔ Si 1−x Ge x nanowires, by obtaining L from equilibrium classical molecular-dynamics ͑MD͒ simulations via the Green-Kubo formalism, and parametrizing the results with a coarse-grained cluster expansion. Using genetic algorithm optimization with the coarse-grained cluster expansion, we are able to predict configurations that significantly decrease L as verified by subsequent MD simulations. Our results indicate that superlatticelike configurations with planes of Ge show drastically lowered L .

Stability of hydrocarbons at deep Earth pressures and temperatures

Proceedings of the National Academy of Sciences of the United States of America, 2011

Determining the thermochemical properties of hydrocarbons (HCs) at high pressure and temperature ... more Determining the thermochemical properties of hydrocarbons (HCs) at high pressure and temperature is a key step toward understanding carbon reservoirs and fluxes in the deep Earth. The stability of carbon-hydrogen systems at depths greater than a few thousand meters is poorly understood and the extent of abiogenic HCs in the Earth mantle remains controversial. We report ab initio molecular dynamics simulations and free energy calculations aimed at investigating the formation of higher HCs from dissociation of pure methane, and in the presence of carbon surfaces and transition metals, for pressures of 2 to 30 GPa and temperatures of 800 to 4,000 K. We show that for T ≥ 2,000 K and P ≥ 4 GPa HCs higher than methane are energetically favored. Our results indicate that higher HCs become more stable between 1,000 and 2,000 K and P ≥ 4 GPa. The interaction of methane with a transition metal facilitates the formation of these HCs in a range of temperature where otherwise pure methane would be metastable. Our results provide a unified interpretation of several recent experiments and a detailed microscopic model of methane dissociation and polymerization at high pressure and temperature. carbon cycle | Earth interior | numerical simulation T here is growing evidence that carbon-bearing compounds in the deep Earth contribute to the global carbon cycle (1, 2). We have limited knowledge of the role played by pressure and temperature on reactions in the C-O-H system under these conditions. In the case of methane, many open questions remain concerning its dissociation and possible polymerization under pressure, in spite of several experiments carried out in recent years (3-6).

Hyperbranched Unsaturated Polyphosphates as a Protective Matrix for Long-Term Photon Upconversion in Air

by Davide Donadio and Katharina Landfester

Journal of the American Chemical Society, 2014

The energy stored in the triplet states of organic molecules, capable of energy transfer via an e... more The energy stored in the triplet states of organic molecules, capable of energy transfer via an emissive process (phosphorescence) or a nonemissive process (triplet− triplet transfer), is actively dissipated in the presence of molecular oxygen. The reason is that photoexcited singlet oxygen is highly reactive, so the photoactive molecules in the system are quickly oxidized. Oxidation leads to further loss of efficiency and various undesirable side effects. In this work we have developed a structurally diverse library of hyperbranched unsaturated poly(phosphoester)s that allow efficient scavenging of singlet oxygen, but do not react with molecular oxygen in the ground state, i.e., triplet state. The triplet−triplet annihilation photon upconversion was chosen as a highly oxygen-sensitive process as proof for a long-term protection against singlet oxygen quenching, with comparable efficiencies of the photon upconversion under ambient conditions as in an oxygen-free environment in several unsaturated polyphosphates. The experimental results are further correlated to NMR spectroscopy and theoretical calculations evidencing the importance of the phosphate center. These results open a technological window toward efficient solar cells but also for sustainable solar upconversion devices, harvesting a broad-band sunlight excitation spectrum.

Electronic Effects in the IR Spectrum of Water under Confinement †

The Journal of Physical Chemistry B, 2009

We compare calculations of infrared (IR) spectra of water confined between nonpolar surfaces, obt... more We compare calculations of infrared (IR) spectra of water confined between nonpolar surfaces, obtained by molecular dynamics simulations with forces either computed using density functional theory or modeled by empirical potentials. Our study allows for the identification of important electronic effects, contributing to IR signals, that are not included in simulations based on empirical force fields, and cannot be extracted from the analysis of vibrational density of states. These effects originate from electronic charge fluctuations involving both surface and water molecules in close proximity of the interface. The implications of our findings for the interpretation of experimental data are discussed.

Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields

The Journal of Physical Chemistry B, 2014

Many well-established classical biomolecular forcefields, fitted on the solvation properties of s... more Many well-established classical biomolecular forcefields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion-pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion-pairing, but it may be also necessary to correctly capture structural details, such as the coordination mode. In this work we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion-pairing. Given the prominent role of the interactions of negatively charged aminoacid side chains and divalent cations in many biomolecular systems we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular forcefields, namely GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion-pairing.

Topological Defects and Bulk Melting of Hexagonal Ice

The Journal of Physical Chemistry B, 2005

We use classical molecular dynamics combined with the recently developed metadynamics method [A. ... more We use classical molecular dynamics combined with the recently developed metadynamics method [A. Laio and M. Parrinello, Procs. Natl. Acad. Sci. USA 99, 20 (2002)] to study the process of bulk melting in hexagonal ice. Our simulations show that bulk melting is mediated by the formation of topological defects which preserve the coordination of the tetrahedral network. Such defects cluster to form a defective region involving about 50 molecules with a surprisingly long life-time. The subsequent formation of coordination defects triggers the transition to the liquid state.

Particle Formation in the Emulsion-Solvent Evaporation Process

Small, 2013

Growth of Nanostructured Carbon Films by Cluster Assembly

Physical Review Letters, 1999

The structural properties of nanostructured films obtained by deposition of supersonic beams of c... more The structural properties of nanostructured films obtained by deposition of supersonic beams of carbon clusters are investigated by classical molecular dynamics simulations and compared to experiments. Simulations are shown to predict how the structural properties of the deposited film depend on the actual growth protocol. In particular, it is shown that the assembly of small linear clusters can lead to the formation of random schwarzite structures. 81.05.Tp, Supersonic cluster beam deposition (SCBD) has recently emerged as a powerful technique for the growth of nanostructured carbon thin films . When the incident energy of clusters accelerated in a supersonic expansion is small enough to prevent massive fragmentation, films are obtained in a large, albeit controllable variety of morphologies. Such films, as it appears from various experimental characterizations , are shown to retain a memory of the precursor clusters and to display a disordered graphitelike character with a prevalent threefold coordination. Transmission electron microscopy (TEM) shows a porous structure with a density of ϳ1 g͞cm 3 , consisting of closed graphitic particles and curved graphene foils embedded in an amorphous matrix (see ). The inhomogeneity is observed at different length scales up to the macroscopic one and appears to be self-affine . This makes these systems appealing for possible applications, e.g., in gas sensing and gettering [3,6-8]. Moreover, carbon cluster assembling has been suggested as a possible route to the formation of negatively curved graphitic carbon (random schwarzites) [9,10]. Unlike fullerenes, tubulenes, and graphite, whose tridimensional solids are partially bound by van der Waals forces, schwarzites are entirely sp 2 covalent tridimensional structures . As such they would constitute a further fundamental allotropic form of carbon, combining a high porosity with a robust crystalline structure.

Influence of Temperature and Anisotropic Pressure on the Phase Transitions in α-Cristobalite

Physical Review Letters, 2008

The role of temperature and anisotropy of the applied load in the pressure-induced transformation... more The role of temperature and anisotropy of the applied load in the pressure-induced transformations of -cristobalite is investigated by means of first principles molecular dynamics combined with the metadynamics algorithm for the study of solid-solid phase transitions. We reproduce the transition to -PbO 2 as found in experiments and we observe that the transition paths are qualitatively different and yield different products when a nonhydrostatic load is applied, giving rise to a new class of metastable structures with mixed tetrahedral and octahedral coordination.

Metadynamics Simulations of the High-Pressure Phases of Silicon Employing a High-Dimensional Neural Network Potential

Physical Review Letters, 2008

We study in a systematic way the complex sequence of the high-pressure phases of silicon obtained... more We study in a systematic way the complex sequence of the high-pressure phases of silicon obtained upon compression by combining an accurate high-dimensional neural network representation of the density-functional theory potential-energy surface with the metadynamics scheme. Starting from the thermodynamically stable diamond structure at ambient conditions we are able to identify all structural phase transitions up to the highest-pressure fcc phase at about 100 GPa. The results are in excellent agreement with experiment. The method developed promises to be of great value in the study of inorganic solids, including those having metallic phases.

Hamiltonian Adaptive Resolution Simulation for Molecular Liquids

by Davide Donadio, Raffaello Potestio, and Rafael Delgado-buscalioni

Physical Review Letters, 2013

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously dif... more Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well defined statistical ensembles can be generated making use of all standard Molecular Dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

Polyamorphism of Ice at Low Temperatures from Constant-Pressure Simulations

Physical Review Letters, 2004

We report results of MD simulations of amorphous ice in the pressure range 0 -22.5 kbar. The high... more We report results of MD simulations of amorphous ice in the pressure range 0 -22.5 kbar. The high-density amorphous ice (HDA) prepared by compression of I h ice at T = 80 K is annealed to T = 170 K at intermediate pressures in order to generate relaxed states. We confirm the existence of recently observed phenomena, the very high-density amorphous ice and a continuum of HDA forms. We suggest that both phenomena have their origin in the evolution of the network topology of the annealed HDA phase with decreasing volume, resulting at low temperatures in the metastability of a range of densities.

From four- to six-coordinated silica: Transformation pathways from metadynamics

Physical Review B, 2007

Prediction of the stable crystal structure on the basis of only the chemical composition is one o... more Prediction of the stable crystal structure on the basis of only the chemical composition is one of the central problems of condensed matter physics, which for a long time remained unsolved. The recently developed evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography) made an important progress in this field, enabling efficient and reliable prediction of structures with up to 30-40 atoms in the unit cell using ab initio methods (or up to 100-200 atoms/cell with classical forcefields). Here we review this methodology, illustrating its variation operators and visualising evolutionary runs using specifically formulated similarity matrices. We also show several recent applications -(1) prediction of new high-pressure phases of CaCO 3 , (2) search for the structure of the polymeric phase of CO 2 ("phase V"), (3) search for new phases of transition metals, (4) high-pressure phases of oxygen, (4) new highpressure phases of FeS and FeO, (5) exploration of possible stable compounds in the Xe-C system at high pressures, (6) investigation of previously proposed cluster-based insulators Al 13 K and Al 12 C. state), while a number of applications to systems where the stable structure is unknown are presented in section IV. This review contains both new results and those published previously ([13][14][30][32][69][73]).