Hendrik Heinz | The University of Akron (original) (raw)

Papers by Hendrik Heinz

Journal of the American Chemical Society, Jul 9, 2003

We use molecular dynamics as a tool to understand the structure and phase transitions [Osman et. al.

arXiv (Cornell University), Jul 29, 2021

The Interface force field (IFF) enables accurate simulations of bulk and interfacial properties o... more The Interface force field (IFF) enables accurate simulations of bulk and interfacial properties of compounds and multiphase materials. However, the simulation of reactions and mechanical properties up to failure remains challenging and expensive. Here we introduce the Reactive Interface Force Field (IFF-R) to analyze bond breaking and failure of complex materials using molecular dynamics simulations. IFF-R uses a Morse potential instead of a harmonic potential as typically employed in molecular dynamics force fields to describe the bond energy, which can render any desired bond reactive by specification of the curve shape of the potential energy and the bond dissociation energy. This facile extension of IFF and other force fields that utilize a harmonic bond energy term allows the description of bond breaking without loss in functionality, accuracy, and speed. The method enables quantitative, on-the-fly computations of bond breaking and stress-strain curves up to failure in any material. We illustrate accurate predictions of mechanical behavior for a variety of material systems, including metals (iron), ceramics (carbon nanotubes), polymers (polyacrylonitrile and cellulose Iβ), and include sample parameters for common bonds based on using experimental and high-level (MP2) quantum mechanical reference data. Computed structures, surface energies, elastic moduli, and tensile strengths are in excellent agreement with available experimental data. Non-reactive properties are shown to be essentially identical to IFF values. Computations are approximately 50 times faster than using ReaxFF and require only a single set of parameters. Compatibility of IFF and IFF-R with biomolecular force fields allows the quantitative analysis of the mechanics of proteins, DNA, and other biological molecules.

Encyclopedia of Polymer Blends, 2016

Journal of Chemical Theory and Computation, 2021

Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, p... more Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.

Surfaces and Interfaces, 2020

While Li-ion cells show outstanding electrochemical performance, their poor thermal transport cha... more While Li-ion cells show outstanding electrochemical performance, their poor thermal transport characteristics result in reduced performance as well as significant safety concerns. The heterogeneous interface between cathode and separator plays a vital role in the process of thermal conduction in a Li-ion cell. Recent experiments have shown that the cathode-separator interfacial thermal resistance contributes significantly to total thermal resistance within the cell. In this paper, thermal conductance across the cathode-separator interface is calculated using molecular dynamics (MD) simulations with IFF-CVFF force field. Thermal transport in a pristine heterogeneous interface as well as when bridged with 3-Aminopropyl triethoxysilane (APTES), n-Butyl trimethoxysilane (nBTMS) and 3-Mercaptopropyl trimethoxysilane (MPTMS) molecules is computed. It is shown that molecular bridging at the interface results in up to 250% improvement in interfacial thermal conductance for the APTES case, which is consistent with recent experimental data. These results quantify the key role of the cathode-separator interface in thermal transport within the Li-ion cell, as well as the potential improvement in interfacial thermal transport by molecular bridging. The techniques and results discussed here may help downselect molecular species for interfacial thermal transport enhancement in Li-ion cells.

Science Advances, 2021

The adsorption of oxygen molecules to Pt nanostructures in solution is shown to predict the relat... more The adsorption of oxygen molecules to Pt nanostructures in solution is shown to predict the relative ORR activity in fuel cells.

Chemical Science, 2020

We introduce a cutting-edge force field for molybdenum disulfide and use it to uncover mechanisms... more We introduce a cutting-edge force field for molybdenum disulfide and use it to uncover mechanisms of peptide recognition and design.

Acta Materialia, 2020

Oxidation and corrosion have a significant economic footprint. Mo-based alloys are a strong candi... more Oxidation and corrosion have a significant economic footprint. Mo-based alloys are a strong candidate for structural materials with oxidation resistance at high temperatures. However, understanding of the mechanisms remains limited as experimental techniques do not reach atomic-scale resolution. We examined the mechanism of oxidation of Mo 3 Si (A15 phase) in MoÀSiÀB alloys, the emergence of a superficial silica scale, and explain available experimental data up to the large nanometer scale using chemically detailed reactive simulations. We introduce new simulation protocols for layer-by-layer oxidation and simple force fields for the reactants, intermediates, and products. Growth of thin superficial silica layers as a function of temperature and oxidation rate on the (001) surface involves the formation of silica clusters, rings, and chains with pore sizes of 0 to 2 nm. An increase in temperature from 800 to 1000°C slightly decreased the pore size and lead to less accumulation of Mo oxides at the interface, consistent with observations by electron tomography and energy dispersive X-ray spectroscopy (EDS). The elimination of gaseous MoO x is essential to form open channels and much larger pores up to 100 nm size as observed by 3D tomography, in-situ transmission electron microscopy (TEM) and scanning electron microscopy (SEM) as the oxide phase grows. According to the simulation, these large pores would otherwise be closed. The rate of oxidation, represented by successive oxidation of layers of variable thickness per unit time, influences the structure and cohesion of silica layers. High rates of oxidation can destabilize and break apart the silica layer, supported by a very wide pore size distribution in electron tomography. Limitations of the simulations in time scale currently restrict the analysis to few-layer oxidation. Within these bounds, the proposed simulation protocols can provide insight into the oxidation of (hkl) surfaces, grain boundaries, and various alloys compositions up to the 100 nm scale in atomic-level detail.

The Journal of Physical Chemistry C, 2019

Zinc and stannous ions are commonly used in oral care to reduce tooth enamel degradation. However... more Zinc and stannous ions are commonly used in oral care to reduce tooth enamel degradation. However, mechanistic understanding of the role of the ions in the protection of enamel against acid insults remains inadequate due to limitations of experimental techniques to validate interfacial interactions at the atomic scale. We overcome this problem by the examination of adsorption and sub-surface exchange of the ions on common hydroxyapatite (001) and (010) surfaces in contact with electrolytes at pH values of 5 and 7 using molecular dynamics simulations in unprecedented accuracy. The surface chemistry under these conditions is characterized by the presence of dihydrogenphosphate ions and a 70/30 mixture of dihydrogenphosphate ions and monohydrogenphosphate ions, respectively. Zn(II) and Sn(II) ions favorably adsorb and coat the surfaces under all conditions, with stronger attraction at pH 5 than at pH 7 and a preference for the prismatic (010) surface over the basal (001) surface. Subsurface substitution is only significant for Zn(II) ions at pH 7 in small concentrations up to 6 mol % with free energies between 0 and-20 kcal/mol on both surfaces, and largely unfavorable for Sn(II) ions. Zn(II) and Sn(II) ions can therefore coat the enamel surface and it is likely that Zn 2+ ions incorporate below the surface and play a role to stabilize apatite surfaces from dissolution. Computed substitution free energies, lattice strains up to 1.5%, and changes in X-ray data agree very well with available experimental data for bulk apatites. The results provide first quantitative insights into enamel surface stabilization and the methods can be applied to other mineral phases.

Nanoscale, 2019

We describe the dynamics of gellan strands in solution, the interaction mechanisms with clay plat... more We describe the dynamics of gellan strands in solution, the interaction mechanisms with clay platelets of different composition, and design principles to tune the attraction.

The Journal of Physical Chemistry C, 2018

Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and ... more Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and the origin of alloy formation energies, defect energies, and interfacial properties have not been well understood to date but are critical to material performance. In this contribution, we explain the polar nature of chemical bonding and an implementation in classical and reactive atomistic simulations to understand such properties more quantitatively. Electronegativity differences between metal atoms lead to polar bonding, and exothermic alloy formation energies are related to charge transfer between the different elements. These differences can be quantified by atomic charges using pairwise charge increments, determined by matching the computed alloy formation energy to experimentally measured alloy formation energies using pair potentials for the pure metals. The polar character of alloys is comparable to organic molecules and partially ionic minerals, for example, AlNi and AlNi 3 alloys assume significant atomic charges of ±0.40e and +0.60e/−0.20e, respectively. The subsequent analysis of defect sites and defect energies using force-field-based calculations shows excellent agreement with calculations using density functional theory and embedded atom models (EAM). The formation of vacancy and antisite defects is characterized by a redistribution of charge in the first shell of neighbor atoms in the classical models whereby electroneutrality is maintained and charge increments correlate with differences in electronegativity. The proposed atomic charges represent internal dipole and multipole moments, consistent with existing definitions for organic and inorganic compounds and with the extended Born model (Heinz, H.; Suter, U. W. J. Phys. Chem. B 2004, 108 (47), 18341−18352). The method can be applied to any alloy and has a reproducibility of ±10%. In contrast, quantum mechanical charge schemes remain associated with deviations exceeding ±100%. The atomic charges for alloys provide a simple initial measure for the internal electronic structure, surface adsorption of molecules, and reactivity in catalysis and corrosion. The models are compatible with the Interface force field (IFF), CHARMM, AMBER, OPLS-AA, PCFF, CVFF, and GROMOS for reliable atomistic simulations of alloys and their interfaces with minerals and electrolytes from the nanometer scale to the micrometer scale.

Nature Communications, 2018

Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging,... more Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard–Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, ...

ACS Nano, 2018

Core−shell nanoparticles find applications in catalysts, sensors, and theranostics. The full inte... more Core−shell nanoparticles find applications in catalysts, sensors, and theranostics. The full internal 3D atomic structure, however, cannot be resolved by current imaging and diffraction techniques. We analyzed the atomic positions and stress-release mechanism in a cubic Au−Pd core−shell nanoparticle in approximately 1000 times higher resolution than current experimental techniques using large-scale molecular dynamics simulation to overcome these limitations. The core− shell nanocube of 73 nm size was modeled similarly to solution synthesis by random epitaxial deposition of a 4 nm thick shell of Pd atoms onto a Au core of 65 nm side length using reliable interatomic potentials. The internal structure reveals specific deformations and stress relaxation mechanisms that are caused by the +4.8% lattice mismatch of gold relative to palladium and differential confinement of extended particle facets, edges, and corners by one, two, or three Au−Pd interfaces, respectively. The three-dimensional lattice strain causes long-range, arc-like bending of atomic rows along the faces and edges of the particle, especially near the Au−Pd interface, a bulging deformation of the Pd shell, and stacking faults in the Pd shell at the corners of the particle. The strain pattern and mechanism of stress release were further characterized by profiles of the atomic layer spacing in the principal crystallographic directions. Accordingly, strain in the Pd shell is several times larger in the extended facets than near the edges and corners of the nanoparticle, which likely affects adsorption, optical, and electrochemical properties. The findings are consistent with available experimental data, including 3D reconstructions of the same cubic nanoparticle by coherent diffractive imaging (CDI) and may be verified by more powerful experimental techniques in the future. The stress release mechanisms are representative for cubic core−shell nanoparticles with fcc structure and can be explored for different shapes by the same methods.

ACS applied materials & interfaces, Jan 12, 2017

Polyacrylonitrile (PAN)/carbon nanotube (CNT) composites are used as a precursor for ultrastrong ... more Polyacrylonitrile (PAN)/carbon nanotube (CNT) composites are used as a precursor for ultrastrong and lightweight carbon fibers. However, the mechanisms of formation and relationships of the nanoscale structure to mechanical and thermal properties have remained uncertain. This study reports on the impact of different degrees of PAN pre-orientation and CNT diameter on the composite properties using molecular dynamics simulation with accurate potentials and comparisons to experimental data. Relationships between the atomically resolved structure, thermal, and mechanical properties are derived. CNT inclusion in the matrix is favored for a medium degree of PAN orientation and small CNT diameter. The glass transition at the CNT/PAN interface involves the release of rotational degrees of freedom of nitrile side groups in contact with the carbon nanotubes. The glass transition temperature increases sharply in the presence of CNTs and for higher CNT volume fraction, in correlation with the a...

ACS nano, Dec 29, 2017

Debundling and dispersion of carbon nanotubes (CNTs) in polymer solutions play a major role in th... more Debundling and dispersion of carbon nanotubes (CNTs) in polymer solutions play a major role in the preparation of carbon nanofibers due to early effects on interfacial ordering and mechanical properties. A roadblock toward ultrastrong fibers is the difficulty to achieve homogeneous dispersions of CNTs in polyacrylonitrile (PAN) and poly(methyl methacrylate) (PMMA) precursor solutions in solvents such as dimethyl sulfoxide (DMSO), N,N-dimethylacetamide (DMAc), and N,N-dimethylformamide (DMF). In this contribution, molecular dynamics simulations with accurate interatomic potentials for graphitic materials that include virtual π electrons are reported to analyze the interaction of pristine single wall CNTs with the solvents and polymer solutions at 25 °C. The results explain the barriers toward dispersion of SWCNTs and quantify CNT-solvent, polymer-solvent, as well as CNT-polymer interactions in atomic detail. Debundling of CNTs is overall endothermic and unfavorable with dispersion en...

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Current Opinion in Chemical Engineering, 2016

Silicates, glasses, and oxides are widely used in everyday applications such as surfaces of cell ... more Silicates, glasses, and oxides are widely used in everyday applications such as surfaces of cell phones and tablets as well as in nanostructured form for therapeutics, catalysts, and composites. Modeling of the inorganic-organic interfaces at the 1 to 100 nm scale has recently become more viable as suitable force fields and molecular models including details of oxide surface chemistry and pH dependent ionization have been introduced. Here we describe computational models for glasses, silica, and common oxides for simulations at high temperatures and at room temperature, including necessary chemical specificity to analyze surfaces and organic interfaces. The bulk structure of glasses, surface chemistry and type of molecular interactions governing adsorption, as well as the feasible accuracy is illustrated by examples. Applications and opportunities of simulation methods are discussed.

The Journal of Physical Chemistry C, 2016

Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. A... more Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior models for atomistic simulations are limited in the representation of chemical bonding, surface chemistry, and interfacial interactions. This work introduces an accurate force field along with pH-resolved surface models for hydroxyapatite to represent chemical bonding, structural, surface, interfacial, and mechanical properties in quantitative agreement with experiment. The accuracy is orders of magnitude higher in comparison to earlier models to facilitate quantitative monitoring of inorganic-biological assembly. The force field is integrated into the CHARMM, AMBER, OPLS-AA, PCFF, and INTERFACE force fields to enable realistic simulations of apatite-biological systems of any composition and ionic strength. Specifically, the parameters reproduce lattice constants (<0.5% deviation), IR spectrum, cleavage energies, immersion energies in water (<5% deviation), and elastic constants (<10% deviation) of hydroxyapatite in comparison to experiment. Interactions between mineral, water, and organic compounds are represented by standard combination rules in the force field without additional adjustable parameters and shown to achieve quantitative accuracy. Surface models for common (001), (010), (020), (101) facets and nanocrystals are introduced as a function of pH on the basis of extensive experimental data. New insight into surface and immersion energies, the structure of aqueous interfaces, density profiles, and superficial dissolution is described. Mechanisms of specific binding of peptides, drugs, and mineralization can be analyzed and the force field is extensible to substituted and defective apatites as well as to other calcium phosphate phases.

Molecular Simulation, 2017

The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recogni... more The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metalorganic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo 3 Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation-pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time.