Thermal conductivity decomposition in two-dimensional materials: Application to graphene

Two-dimensional materials have unusual phonon spectra due to the presence of flexural (out-of-plane) modes. Although molecular dynamics simulations have been extensively used to study heat transport in such materials, conventional formalisms treat the phonon dynamics isotropically. Here, we decompose the microscopic heat current in atomistic simulations into in-plane and out-of-plane components, corresponding to in-plane and out-of-plane phonon dynamics, respectively. This decomposition allows for direct computation of the corresponding thermal conductivity components in two-dimensional materials. We apply this decomposition to study heat transport in suspended graphene, using both equilibrium and nonequilibrium molecular dynamics simulations. We show that the flexural component is responsible for about two-thirds of the total thermal conductivity in unstrained graphene, and the acoustic flexural component is responsible for the logarithmic divergence of the conductivity when a sufficiently large tensile strain is applied

Dissociative Adsorption of Water at (211) Stepped Metallic Surfaces by First-Principles Simulations

Steps at high-index metallic surfaces display higher chemical reactivity than close-packed surfaces and may give rise to selective adsorption and partial dissociation of water. Inspired by differential desorption experiments, we have studied the adsorption and dissociation of water clusters and one-dimensional wires on Pt(211) by density functional theory and molecular dynamics simulations. These calculations reveal that water at the step edges of Pt(211) adsorbs more weakly than at Pt(221), but partial dissociation of adsorbed water clusters is energetically competitive. We observe that the one-dimensional structure proposed experimentally can be realized only by partially dissociated water wires. In addition, weaker adsorption allows the formation of structures in which a number of water molecules detach from the step and form weak hydrogen bonds with the terrace. This study is further extended to the energetics of small water clusters on (211) surfaces of Ir, Rh, and Pd

Tuning the Adsorption of Aromatic Molecules on Platinum via Halogenation

The interaction of aromatic molecules with metal surfaces is of key relevance for the functionality of molecular electronics and organic electronics devices. One way to control and tune the binding properties of molecules to metals is chemical functionalization. The adsorption of halogenated benzene molecules on the (111) surface of platinum is here investigated by density functional theory calculations with nonlocal van der Waals correlation functional. It is found that these systems exhibit a bistable adsorption energy profile with (meta)­stable chemisorption and physisorption states separated by a potential energy barrier. The relative stability of these states can be tuned by functionalizing benzene with a different number or type of halogen atoms. Our results suggest a simple rational molecular design to achieve the desired interfacial binding in organic electronic devices and in composites with interfaces between large aromatic molecules and metals

Autocatalytic and Cooperatively Stabilized Dissociation of Water on a Stepped Platinum Surface

Water–metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires

Autocatalytic and Cooperatively Stabilized Dissociation of Water on a Stepped Platinum Surface

Water–metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires

Nuclear Quantum Effects in Water: A Multiscale Study

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

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

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

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM′). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system

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

Many well-established classical biomolecular force fields, 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 also be 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 amino-acid 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 force fields, 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

Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles

Thermal decomposition is a promising route for the synthesis of highly monodisperse magnetite nanoparticles. However, the apparent simplicity of the synthesis is counterbalanced by the complex interplay of the reagents with the reaction variables that determine the final particle size and dispersity. Here, we present a combined experimental and theoretical study on the influence of the heating rate on crystal growth, size, and monodispersity of iron oxide nanoparticles. We synthesized monodisperse nanoparticles with sizes varying from 6.3 to 27 nm simply by controlling the heating rate of the reaction. The nanoparticles show size-dependent superparamagnetic behavior. Using numerical calculations based on the classical nucleation theory and growth model, we identified the relative time scales associated with the heating rate and precursor-to-monomer (growth species) conversion rate as a decisive factor influencing the final size and dispersity of the nanoparticles