Observing crystal nucleation in four dimensions using atomic electron tomography.

Nucleation plays a critical role in many physical and biological phenomena that range from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases1-3. However, nucleation is a challenging process to study experimentally, especially in its early stages, when several atoms or molecules start to form a new phase from a parent phase. A number of experimental and computational methods have been used to investigate nucleation processes4-17, but experimental determination of the three-dimensional atomic structure and the dynamics of early-stage nuclei has been unachievable. Here we use atomic electron tomography to study early-stage nucleation in four dimensions (that is, including time) at atomic resolution. Using FePt nanoparticles as a model system, we find that early-stage nuclei are irregularly shaped, each has a core of one to a few atoms with the maximum order parameter, and the order parameter gradient points from the core to the boundary of the nucleus. We capture the structure and dynamics of the same nuclei undergoing growth, fluctuation, dissolution, merging and/or division, which are regulated by the order parameter distribution and its gradient. These experimental observations are corroborated by molecular dynamics simulations of heterogeneous and homogeneous nucleation in liquid-solid phase transitions of Pt. Our experimental and molecular dynamics results indicate that a theory beyond classical nucleation theory1,2,18 is needed to describe early-stage nucleation at the atomic scale. We anticipate that the reported approach will open the door to the study of many fundamental problems in materials science, nanoscience, condensed matter physics and chemistry, such as phase transition, atomic diffusion, grain boundary dynamics, interface motion, defect dynamics and surface reconstruction with four-dimensional atomic resolution.

Amyloid-like amelogenin nanoribbons template mineralization via a low-energy interface of ion binding sites.

Protein scaffolds direct the organization of amorphous precursors that transform into mineralized tissues, but the templating mechanism remains elusive. Motivated by models for the biomineralization of tooth enamel, wherein amyloid-like amelogenin nanoribbons guide the mineralization of apatite filaments, we investigated the impact of nanoribbon structure, sequence, and chemistry on amorphous calcium phosphate (ACP) nucleation. Using full-length human amelogenin and peptide analogs with an amyloid-like domain, films of ß-sheet nanoribbons were self-assembled on graphite and characterized by in situ atomic force microscopy and molecular dynamics simulations. All sequences substantially reduce nucleation barriers for ACP by creating low-energy interfaces, while phosphoserines along the length of the nanoribbons dramatically enhance kinetic factors associated with ion binding. Furthermore, the distribution of negatively charged residues along the nanoribbons presents a potential match to the Ca­Ca distances of the multi-ion complexes that constitute ACP. These findings show that amyloid-like amelogenin nanoribbons provide potent scaffolds for ACP mineralization by presenting energetically and stereochemically favorable templates of calcium phosphate ion binding and suggest enhanced surface wetting toward calcium phosphates in general.

Hierarchically structured bioinspired nanocomposites.

Next-generation structural materials are expected to be lightweight, high-strength and tough composites with embedded functionalities to sense, adapt, self-repair, morph and restore. This Review highlights recent developments and concepts in bioinspired nanocomposites, emphasizing tailoring of the architecture, interphases and confinement to achieve dynamic and synergetic responses. We highlight cornerstone examples from natural materials with unique mechanical property combinations based on relatively simple building blocks produced in aqueous environments under ambient conditions. A particular focus is on structural hierarchies across multiple length scales to achieve multifunctionality and robustness. We further discuss recent advances, trends and emerging opportunities for combining biological and synthetic components, state-of-the-art characterization and modelling approaches to assess the physical principles underlying nature-inspired design and mechanical responses at multiple length scales. These multidisciplinary approaches promote the synergetic enhancement of individual materials properties and an improved predictive and prescriptive design of the next era of structural materials at multilength scales for a wide range of applications.

Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth?

Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.

Adsorption and Diffusion of Oxygen on Pure and Partially Oxidized Metal Surfaces in Ultrahigh Resolution.

The interaction of gas molecules with metal and oxide surfaces plays a critical role in corrosion, catalysis, sensing, and heterogeneous materials. However, insights into the dynamics of O2 from picoseconds to microseconds have remained unavailable to date. We obtained 3D potential energy surfaces for adsorption of O2 on 11 common pristine and partially oxidized (hkl) surfaces of Ni and Al in picometer resolution and high accuracy of 0.1 kcal/mol, identified binding sites, and surface mobility from 25 to 300 °C. We explain relative oxidation rates and parameters for oxide growth. We employed over 150 000 molecular mechanics and molecular dynamics simulations with the interface force field (IFF) using structural data from X-ray diffraction (XRD) and low-energy electron diffraction (LEED). The methods reach 10 to 50 times higher accuracy than possible before and are suited to analyze gas interactions with metals up to the micrometer scale including defects and irregular nanostructures.

Cement Interfaces: Current Understanding, Challenges, and Opportunities.

Cement and concrete are rapidly growing in demand and pose many unresolved chemistry questions at particle interfaces, during hydration reactions, regarding the role of electrolytes and organic additives. Solutions through developing greener, more sustainable formulations are needed to reduce the high carbon footprint that amounts to 11% of global CO2 emissions. Cement is a multiphase material composed of calcium silicates, aluminates, and other mineral phases, produced from natural and low-cost industrial sources, which undergoes complex hydration reactions. This perspective highlights current research challenges and opportunities for new chemistry insight, including intriguing colloid and interface science problems that involve mineral surfaces, electrolytes, polymers, and hydration reactions. Specifically, we discuss (1) characteristics of cement phases, supplementary cementitious materials, and other constituents, (2) hydration reactions and the characterization by imaging and NMR spectroscopy, (3) the structure of hydrated cement phases including calcium-silicate-hydrates at different scales, (4) quantitative simulation techniques from the atomic scale to microscale kinetic models, and (5) the function of organic additives. Focusing on new directions, we explain the benefits of integrating knowledge from inorganic chemistry, acid-base chemistry, polymer chemistry, reaction mechanisms, and theory to describe mesoscale cement properties and bulk properties upon manufacturing.

Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic-biotic interface.

A hydrophobic heptapeptide, with sequence AFILPTG, as part of a phage capsid protein binds effectively to silica particles carrying negative charge. Here, we explore the silica binding activity of the sequence as a short polypeptide with polar N and C terminals. To describe the structural changes that occur on binding, we fit experimental infrared, Raman and circular dichroism data for a number of structures simulated in the full configuration space of the hepta-peptide using replica exchange molecular dynamics. Quantum chemistry was used to compute normal modes of infrared and Raman spectra and establish a relationship to structures from MD data. To interpret the circular dichroism data, instead of empirical factoring of optical activity into helical/sheet/random components, we exploit natural transition orbital theory and specify the contributions of backbone amide units, side chain functional groups, water, sodium ions and silica to the observed transitions. Computed optical responses suggest a less folded backbone and importance of the N-terminal when close to silica. We further discuss the thermodynamics of the interplay of charged and hydrophobic moieties of the polypeptide on association with the silica surface. The outcomes of this study may assist in the engineering of novel artificial bio-silica heterostructures.

Peptide-Assisted 2-D Assembly toward Free-Floating Ultrathin Platinum Nanoplates as Effective Electrocatalysts.

We demonstrate the 2-D anisotropic formation of ultrathin free-floating Pt nanoplates from the assembly of small nanocrystals using T7 peptide (Ac-TLTTLTN-CONH2). As-formed nanoplates are rich in grain boundaries that can promote their catalytic activities. Furthermore, we demonstrate that a minor number of Pd atoms can selectively deposit on and stabilize the grain boundaries, which leads to enhanced structure stability. The Pd-enhanced Pt polycrystal nanoplates show great oxygen reduction reaction activities with 15.5 times higher specific activity and 13.7 times higher mass activity than current state-of-the-art commercial Pt/C electrocatalysts as well as 2.5 times higher mass activity for hydrogen evolution reaction compared with Pt/C.

Long-Range Hierarchical Nanocrystal Assembly Driven by Molecular Structural Transformation.

The hierarchical control in biogenic minerals, from precise nanomorphology control to subsequent macroscopic assembly, remains a formidable challenge in artificial synthesis. Studies in biomineralization, however, are largely limited to atomic andmolecular scale crystallization, devoting little attention to biomolecular higher-order structures (HOSs) which critically impact long-range assembly of biominerals. Here we demonstrate a biomimetic route and quantitative simulations that explore peptide HOSs on guiding nanocrystal formation and anisotropic assembly into hierarchical structures. It is found that the Pt{100}-specific peptide T7 (Ac-TLTTLTN-CONH2) adopts ST-turn secondary structure, promoting cubic Pt nanocrystal formation at low concentration, and spontaneously transforms into a ß-sheet with increased concentration. The ß-sheet T7-Pt{100} specificity drives cubic Pt nanocrystals to self-assemble into large-area, long-range, [100] linear assemblies. This study provides a robust demonstration for bio/nonbiogenic material specificity, nanoscale synthesis, and long-range self-organization with biomolecular HOSs and opens vast opportunities for multiscale programmable structures.

From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica.

Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following the identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous environment. Our approach relies on modelling infrared and Raman spectral responses using predictions of molecular dynamics simulations and quantum studies of the normal modes for several potential structures. By simultaneously fitting both infrared and Raman responses in the amide spectral region, we show that the main structural conformer has a beta-like central region and helix-twisted terminals. Classical simulations, as conducted previously (Chem. Mater., 2014, 26, 5725), predict that the association of the main structure with the interface is stimulated by electrostatic interactions though surface binding also requires spatially distributed sodium ions to compensate for negatively charged acidic silanol groups. Accordingly, diffusion of sodium ions would contribute to a stochastic character of the peptide association with the surface. Consistent with the described dynamics at the interface, the results obtained from isothermal titration calorimetry (ITC) confirm a significant enhancement of polypeptide binding to silica at higher concentrations of Na+. The results of this study suggest that the tertiary structure of a phage capsid protein plays a significant role in regulating the conformation of peptide LDHSLHS, increasing its binding to silica during the phage display process. The results presented here support design-led engineering of polypeptide-silica nanocomposites for bio-technological applications.

Constructing surface models of silicate glasses using molecular dynamics to understand the effect of pH on the hydration properties.

In this work, we use realistic silicate glass surface models, with molecular dynamics simulations, and present an algorithm for proper atomic partial charge assignment, consistent with measurable internal dipoles. The immersion energy is calculated for different silicate glass compositions in solutions of varying pH. We use molecular dynamics to elucidate the differences in the structure of water between mono- and divalent cations. The immersion energy of the glass surface is found to increase with an increase in ionic surface density and pH. This can be attributed to the stronger interaction between water and cations, as opposed to the interactions between water and silanol groups. The developed models and methods provide new insights into the structure of glass-solution interfaces and the effect of cation surface density in common nanoscale environments.

Interactions at the Silica-Peptide Interface: Influence of the Extent of Functionalization on the Conformational Ensemble.

In this contribution, the effect of silica particle size (28 and 210 nm) and surface chemistry (i.e., hydroxyl, methyl, or amino groups) on peptide binding response is studied with a specific emphasis on the effect of the extent of functionalization on binding. Exhaustive characterization of the silica surfaces was crucial for knowledge of the chemistry and topography of the solid surface under study and, thus, to understand their impact on adsorption and the conformational ensemble of the peptides. The extent of surface functionalization was shown to be particle-size dependent, a higher level of 3-aminopropyl functionality being obtained for smaller particles, whereas a higher degree of methyl group functionality was found for the larger particles. We demonstrated that peptide interactions at the aqueous interface were not only influenced by the surface chemistry but also by the extent of functionalization where a "switch" of peptide adsorption behavior was observed, whereas the changes in the conformational ensemble revealed by circular dichroism were independent of the extent of functionalization. In addition to electrostatic interactions and hydrogen bonding driving interaction at the silica-peptide interface, the data obtained suggested that stronger interactions such as hydrophobic and/or covalent interactions may moderate the interaction. The insights gained from this peptide-mineral study give a more comprehensive view of mechanisms concerning mineral-peptide interactions which may allow for the design and synthesis of novel (nano)materials with properties tailored for specific applications.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities.

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Energy-effective Grinding of Inorganic Solids Using Organic Additives.

We present our research findings related to new formulations of the organic additives (grinding aids) needed for the efficient grinding of inorganic solids. Even though the size reduction phenomena of the inorganic solid particles in a ball mill is purely a physical process, the addition of grinding aids in milling media introduces a complex physicochemical process. In addition to further gain in productivity, the organic additive helps to reduce the energy needed for grinding, which in the case of cement clinker has major environmental implications worldwide. This is primarily due to the tremendous amounts of cement produced and almost 30% of the associated electrical energy is consumed for grinding. In this paper, we examine the question of how to optimize these grinding aids linking molecular insight into their working mechanisms, and also how to design chemical additives of improved performance for industrial comminution.

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography.

Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. Here, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ∼19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field and the full strain tensor with a 3D resolution of ∼1 nm(3) and a precision of ∼10(-3), which are further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.

Tailoring molecular specificity toward a crystal facet: a lesson from biorecognition toward Pt{111}.

Surfactants with preferential adsorption to certain crystal facets have been widely employed to manipulate morphologies of colloidal nanocrystals, while mechanisms regarding the origin of facet selectivity remain an enigma. Similar questions exist in biomimetic syntheses concerning biomolecular recognition to materials and crystal surfaces. Here we present mechanistic studies on the molecular origin of the recognition toward platinum {111} facet. By manipulating the conformations and chemical compositions of a platinum {111} facet specific peptide, phenylalanine is identified as the dominant motif to differentiate {111} from other facets. The discovered recognition motif is extended to convert nonspecific peptides into {111} specific peptides. Further extension of this mechanism allows the rational design of small organic molecules that demonstrate preferential adsorption to the {111} facets of both platinum and rhodium nanocrystals. This work represents an advance in understanding the organic-inorganic interfacial interactions in colloidal systems and paves the way to rational and predictable nanostructure modulations for many applications.

Analyzing the Li-Al-O Interphase of Atomic Layer-Deposited Al2O3 Films on Layered Oxide Cathodes Using Atomistic Simulations.

Alumina surface coatings are commonly applied to layered oxide cathode particles for lithium-ion battery applications. Atomic layer deposition (ALD) is one such surface coating technique, and ultrathin alumina ALD films (<2 nm) are shown to improve the electrochemical performance of LiNixMnyCo1-x-yO2 materials, with groups hypothesizing that a beneficial Li-Al-O product is being formed during the alumina ALD process. However, the atomic structure of these films is still not well understood, and quantifying the interface of ultrathin (∼1 nm) ALD films is an arduous experimental task. Here, we perform molecular dynamics simulations of amorphous alumina films of varying thickness in contact with the (0001) LiCoO2 (LCO) surface to quantify the film nanostructure. We calculate elemental mass density profiles through the films and observe that the Li-Al-O interphase extends ∼2 nm from the LCO surface. Additionally, we observe layering of Al and O atoms at the LCO-film interface that extends for ∼1.5 nm. To access the short-range order of the amorphous film, we calculated the Al coordination numbers through the film. We find that while [4]Al is the prevailing coordination environment, significant amounts of [6]Al exist at the interface between the LiCoO2 surface and the film. Taken together, these principal findings point to a pseudomorphic Li-Al-O overlayer that approximates the underlying layered LiCoO2 lattice but does not exactly replicate it. Additionally, with sufficient thickness, the Li-Al-O film transitions to an amorphous alumina structure. We anticipate that our findings on the ALD-like, Li-Al-O film nanostructure can be applied to other layered LiNixMnyCo1-x-yO2 materials because of their shared crystal structure with LiCoO2. This work provides insight into the nanostructure of amorphous ALD alumina films to help inform their use as protective coatings for Li-ion battery cathode active materials.