Dual;#8208;Metal Interbonding as the Chemical Facilitator for Single;#8208;Atom Dispersions
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Zhou, Yao↗
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Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Atomic Drill Bit: Precision Controlled Atomic Fabrication of 2D Materials
The ability to deterministically fabricate nanoscale architectures with atomic precision is the central goal of nanotechnology, whereby highly localized changes in the atomic structure can be exploited to control device properties at their fundamental physical limit. Here, an automated, feedback-controlled atomic fabrication method is reported and the formation of 1D–2D heterostructures in MoS 2 is demonstrated through selective transformations along specific crystallographic orientations. The atomic-scale probe of an aberration-corrected scanning transmission electron microscope (STEM) is used, and the shape and symmetry of the scan pathway relative to the sample orientation are controlled. The focused and shaped electron beam is used to reliably create Mo 6 S 6 nanowire (MoS-NW) terminated metallic-semiconductor 1D–2D edge structures within a pristine MoS 2 monolayer with atomic precision. From these results, it is found that a triangular beam path aligned along the zig-zag sulfur terminated (ZZS) direction forms stable MoS-NW edge structures with the highest degree of fidelity without resulting in disordering of the surrounding MoS 2 monolayer. Density functional theory (DFT) calculations and ab initio molecular dynamic simulations (AIMD) are used to calculate the energetic barriers for the most stable atomic edge structures and atomic transformation pathways. These discoveries provide an automated method to improve understanding of atomic-scale transformations while opening a pathway toward more precise atomic-scale engineering of materials.
2D materials↗
Unraveling the Intermediate Reaction Complexes and Critical Role of Support-Derived Oxygen Atoms in CO Oxidation on Single-Atom Pt/CeO 2
CeO 2 -supported Pt single-atom catalysts have been extensively studied due to their relevance in automobile emission control and for the fundamental understanding of CeO 2 -based catalysts. Though CeO 2 -supported Pt nanoparticles are often more active than their single-atom counterparts, the former could easily redisperse to Pt single atom under oxidizing diesel conditions. Therefore, to maximize the reactivity of every Pt atom, it is important to fully understand the reaction mechanism of CeO 2 -supported Pt single atoms. Here, we report a CO oxidation study on a Pt/CeO 2 single-atom catalyst, where we can account for all of the neighbors using in situ and operando spectroscopy techniques and microcalorimetric measurements. Coupled with density functional theory calculations, we present a comprehensive picture of the dynamics of the surface species, the role of surface intermediates, and explain the observed reaction kinetics. We started with a catalyst containing exclusively single atoms and used in situ/operando spectroscopy to provide evidence for their stability during the reaction and to identify the Pt 1 complexes before and during the reaction and their binding to CO. The results reveal that in the precatalyst, Pt is present as Pt(O) 4 on the CeO 2 (111) step edge sites, but during CO oxidation, we find that two Pt 1 complexes coexist, representing two states of the same active site in the reaction cycle. The dominant state/complex remains Pt(O) 4 , which adsorbs CO very weakly as shown by CO microcalorimetry. The second, minority state/complex, Pt(CO)(O) 3 is generated through the reaction of Pt(O) 4 with CO, and CO is bound strongly to Pt 1 . Labile oxygen adatoms from the CeO 2 surface play a major role in the regeneration of Pt(O) 4 either directly from Pt(O) 3 or by reaction with the strongly adsorbed CO in Pt(CO)(O) 3 . We show that the formation of an oxygen vacancy and generation of a labile O* are not barrierless, which explains the long lifetime of Pt(CO)(O) 3 and its detectability despite being a minority complex. The results help to develop a comprehensive view of the dynamic evolution of Pt 1 complexes along the reaction cycle and provide mechanistic insights to guide the design of Pt-based single-atom catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Disentangling Pauli Blocking of Atomic Decay from Cooperative Radiation and Atomic Motion in a 2D Fermi Gas
The observation of Pauli blocking of atomic spontaneous decay via direct measurements of the atomic population requires the use of long-lived atomic gases where quantum statistics, atom recoil, and cooperative radiative processes are all relevant. In this work, we develop a theoretical framework capable of simultaneously accounting for all these effects in the many-body quantum degenerate regime. We apply it to atoms in a single 2D pancake or arrays of pancakes featuring an effective Λ level structure (one excited and two degenerate ground states). We identify a parameter window in which a factor of 2 extension in the atomic lifetime clearly attributable to Pauli blocking should be experimentally observable in deeply degenerate gases with ~10 3 atoms. We experimentally observe a suppressed excited-state decay rate, fully consistent with the theory prediction of an enhanced excited-state lifetime, on the 1 S 0 – 3 P 1 transition in 87 Sr atoms.
74 ATOMIC AND MOLECULAR PHYSICS↗
Long-Range Ordered Amorphous Atomic Chains as Building Blocks of a Superconducting Quasi-One-Dimensional Crystal
Crystalline and amorphous structures are two of the most common solid-state phases. Crystals having orientational and periodic translation symmetries are usually both short-range and long-range ordered, while amorphous materials have no long-range order. Short-range ordered but long-range disordered materials are generally categorized into amorphous phases. In contrast to the extensively studied crystalline and amorphous phases, the combination of short-range disordered and long-range ordered structures at the atomic level is extremely rare and so far has only been reported for solvated fullerenes under compression. Here, a report on the creation and investigation of a superconducting quasi-1D material with long-range ordered amorphous building blocks is presented. Using a diamond anvil cell, monocrystalline (TaSe4)(2)I is compressed and a system is created where the TaSe(4)atomic chains are in amorphous state without breaking the orientational and periodic translation symmetries of the chain lattice. Strikingly, along with the amorphization of the atomic chains, the insulating (TaSe4)(2)I becomes a superconductor. The data provide critical insight into a new phase of solid-state materials. The findings demonstrate a first ever case where superconductivity is hosted by a lattice with periodic but amorphous constituent atomic chains.
combination of crystalline and amorphous structure↗
Neighboring Pd single atoms surpass isolated single atoms for selective hydrodehalogenation catalysis
Single atom catalysts have been found to exhibit superior selectivity over nanoparticulate catalysts for catalytic reactions such as hydrogenation due to their single-site nature. However, improved selectively is often accompanied by loss of activity and slow kinetics. Here we demonstrate that neighboring Pd single atom catalysts retain the high selectivity merit of sparsely isolated single atom catalysts, while the cooperative interactions between neighboring atoms greatly enhance the activity for hydrogenation of carbon-halogen bonds. Experimental results and computational calculations suggest that neighboring Pd atoms work in synergy to lower the energy of key meta-stable reactions steps, i.e., initial water desorption and final hydrogenated product desorption. The placement of neighboring Pd atoms also contribute to nearly exclusive hydrogenation of carbon-chlorine bond without altering any other bonds in organohalogens. The promising hydrogenation performance achieved by neighboring single atoms sheds light on a new approach for manipulating the activity and selectivity of single atom catalysts that are increasingly studied in multiple applications.
36 MATERIALS SCIENCE↗
Quantum dynamics of the temporary capture of light atoms by superfluid helium nanodroplets at very low collision energies (≈1–13 meV): the case of the hydrogen atom and its isotopes
The capture dynamics of a H atom and isotopic variants [D, T and Q (hypothetical isotope of mass equal to four times the mass of H)] by a superfluid helium nanodroplet (HeND) has been investigated theoretically. The HeND (T = 0.37 K) is ( 4 He) N=400 and a mean field quantum hybrid approach [TDDFT (helium) + quantum wave packet (H, D, T or Q)] at zero angular momentum, is used to explore a rather wide range of very low initial kinetic energies (E k,0 ≈ 10–150 K). The analysis of the capture mechanism shows the existence of a dynamical barrier and a dynamical minimum that play key roles to understand the time evolution of the capture, especially the former property. In general, the H atom shows a different behavior from the other isotopes, with the behavior of T and Q being very similar to each other and the D atom behaving inbetween H and T. Besides, it is worth noting that, in principle, at the very low initial kinetic energies considered only “short” and “long” lived atom⋯HeND collision complexes are formed, i.e., in the atom-helium nanodroplet collision only the temporary capture of the atom takes place. The different behaviors observed have been interpreted considering the faster motion of the H atom when colliding with ( 4 He) N=400 and the more quantum character of the H behavior both due to its significantly lower mass. As far as we know, this is the first quantum dynamics study carried out on the collision of light atoms with HeNDs at very low energies.
Sternberg, Michael [Argonne National Laboratory (A↗
A Sensitive Technique Using Atomic Force Microscopy to Measure the Low Earth Orbit Atomic Oxygen Erosion of Polymers
Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene) are commonly used spacecraft materials due to their desirable properties such as flexibility, low density, and in the case of FEP low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low Earth orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen erosion of polymers occurs in LEO and is a threat to spacecraft durability. It is therefore important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data is rare and very costly, short-term exposures such as on the shuttle are often relied upon for atomic oxygen erosion determination. The most common technique for determining E is through mass loss measurements. For limited duration exposure experiments, such as shuttle experiments, the atomic oxygen fluence is often so small that mass loss measurements can not produce acceptable uncertainties. Therefore, a recession measurement technique has been developed using selective protection of polymer samples, combined with postflight atomic force microscopy (AFM) analysis, to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences. This paper discusses the procedures used for this recession depth technique along with relevant characterization issues. In particular, a polymer is salt-sprayed prior to flight, then the salt is washed off postflight and AFM is used to determine the erosion depth from the protected plateau. A small sample was salt-sprayed for AFM erosion depth analysis and flown as part of the Limited Duration Candidate Exposure (LDCE-4,-5) shuttle flight experiment on STS-51. This sample was used to study issues such as use of contact versus non-contact mode imaging for determining recession depth measurements. Error analyses were conducted and the percent probable error in the erosion yield when obtained by the mass loss and recession depth techniques has been compared. The recession depth technique is planned to be used to determine the erosion yield of 42 different polymers in the shuttle flight experiment PEACE (Polymer Erosion And Contamination Experiment) planned to fly in 2002 or 2003.
deGroh, Kim K.↗
Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties
The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.
NASA Discipline Number 52-20↗
The Radical Atom: Mechanosynthetic 3D Printing of an Atomically Precise SPM Tip
This research effort sought to overcome current limitations in scanning probe-based atomic manipulation to enable atomically precise manufacturing (APM). Previous theoretical and experimental works on atom by atom and molecule by molecule fabrication of precise structures are limited to essentially to two-dimensions. APM will enable a paradigm shift in 21st century manufacturing practices in which every single atom in a electronic chip, device or machine can be placed in an exact and predefined position in three-dimensions. By providing a general method for generating reproducible SPM tip structure, this project will drive forward the entire field of atomically precise scanning probe microscopy, opening the door to positional control of nearly arbitrary covalent chemistry. Such control could, for example, be used in applications such as novel 2.5 or 3D microchip fabrication. The creation of a unique manufacturing method through APM has the potential to impact technologies at the theoretical limits of performance, weight, and utility including: solid-state quantum and spintronic computing systems, high efficiency optical antenna, solar power systems, defect engineered materials and extremely efficient catalysts. Although this experiment focused on pick-and-place non-scalable APM, the better understanding of the chemistry is crucial to the eventual goal of scalable APM. To place individual atoms into a specified location is a seminal aspiration of researchers and engineers in the many fields and may have early premium applications in medical devices and microelectronics.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Atom Interferometry with Floquet Atom Optics
Floquet engineering offers a compelling approach for designing the time evolution of periodically driven systems. We implement a periodic atom-light coupling to realize Floquet atom optics on the strontium 1 S 0 - 3 P 1 transition. These atom optics reach pulse efficiencies above 99.4% over a wide range of frequency offsets between light and atomic resonance, even under strong driving where this detuning is on the order of the Rabi frequency. Moreover, we use Floquet atom optics to compensate for differential Doppler shifts in large momentum transfer atom interferometers and achieve state-of-the-art momentum separation in excess of 400 ℏk. In conclusion, this technique can be applied to any two-level system at arbitrary coupling strength, with broad application in coherent quantum control.
74 ATOMIC AND MOLECULAR PHYSICS↗
Economizing on Precious Metals in Three-Way Catalysts: Thermally Stable and Highly Active Single-Atom Rhodium on Cera for NO Abatement under Dry and Industrially Relevant Conditions
We show for the first time that atomically dispersed Rh cations on ceria, prepared via high-temperature atom trapping synthesis, are the active species for (CO+NO) reaction. This provides a direct link with the organometallic homogeneous Rh(I) complexes capable of catalyzing dry (CO+NO) reaction but without the stability concern. In particular, thermally stable Rh cations in 0.1wt% Rh1/CeO2 achieve full NO conversion with a TOF of ~ 330 hr-1 per Rh atom at 120 °C. Under dry conditions, the main product above 100 °C is N2 with N2O being the minor product. The presence of water promotes low-temperature activity of 0.1wt% Rh1/CeO2 starting at 50 °C with full NO conversion at ~120 °C. In the case with the wet stream, however, ammonia and nitrogen are the main products with only minor N2O amounts. NH3 formation at such low temperatures is attractive because of the potential to use this as a passive SCR system. Because of the uniformity of Rh ions on the support, we are able to observe the intermediates of (CO+NO) reaction via infrared measurements on Rh cations on zeolite and ceria. Furthermore, we show that ammonia formation correlates with the WGS activity of the material and thus, rhodium hydride Rh-H species are involved in this reaction: we detect Rh(CO)Hx species on ceria using isotopic IR measurements. These findings provide new mechanistic understanding for the catalytically active species in TWC catalysis and open up a new avenue for the synthesis of novel emissions control catalysts with 100% atom economy of ultra-expensive precious metals such as Rh.
Khivantsev, Konstantin↗
Doping transition-metal atoms in graphene for atomic-scale tailoring of electronic, magnetic, and quantum topological properties
Atomic-scale fabrication is an outstanding challenge and overarching goal for the nanoscience community. The practical implementation of moving and fixing atoms to a structure is non-trivial considering that one must spatially address the positioning of single atoms, provide a stabilizing scaffold to hold structures in place, and understand the details of their chemical bonding. Free-standing graphene offers a simplified platform for the development of atomic-scale fabrication and the focused electron beam in a scanning transmission electron microscope can be used to locally induce defects and sculpt the graphene. In this scenario, the graphene forms the stabilizing scaffold and the experimental question is whether a range of dopant atoms can be attached and incorporated into the lattice using a single technique and, from a theoretical perspective, we would like to know which dopants will create technologically interesting properties. Here in this paper, we demonstrate that the electron beam can be used to selectively and precisely insert a variety of transition metal atoms into graphene with highly localized control over the doping locations. We use first-principles density functional theory calculations with direct observation of the created structures to reveal the energetics of incorporating metal atoms into graphene and their magnetic, electronic, and quantum topological properties.
36 MATERIALS SCIENCE↗
Observation of electron orbital signatures of single atoms within metal-phthalocyanines using atomic force microscopy
Resolving the electronic structure of a single atom within a molecule is of fundamental importance for understanding and predicting chemical and physical properties of functional molecules such as molecular catalysts. However, the observation of the orbital signature of an individual atom is challenging. We report here the direct identification of two adjacent transition-metal atoms, Fe and Co, within phthalocyanine molecules using high-resolution noncontact atomic force microscopy (HR-AFM). HR-AFM imaging reveals that the Co atom is brighter and presents four distinct lobes on the horizontal plane whereas the Fe atom displays a “square” morphology. Pico-force spectroscopy measurements show a larger repulsion force of about 5 pN on the tip exerted by Co in comparison to Fe. Our combined experimental and theoretical results demonstrate that both the distinguishable features in AFM images and the variation in the measured forces arise from Co’s higher electron orbital occupation above the molecular plane. The ability to directly observe orbital signatures using HR-AFM should provide a promising approach to characterizing the electronic structure of an individual atom in a molecular species and to understand mechanisms of certain chemical reactions.
36 MATERIALS SCIENCE↗
A diagnostic to measure time-resolved atom column density and Doppler temperature in atomic vapors produced by laser ablation
We report on the development of a diagnostic to measure the time-resolved column density and Doppler temperature of atomic vapors produced by laser ablation. The diagnostic is based on the strong frequency dependence of the atomic susceptibility near an electronic transition in the interrogated atomic species. Interference on the face of a fast photodetector between the several frequency components present in a sinusoidally phase-modulated probe beam will produce a time signature uniquely determined by the column density of atoms in the probed atomic state and the Doppler temperature of the atomic vapor. With the extensive, high precision atomic spectroscopy data available in the literature, it is possible to model the vapor and extract the desired parameters through comparison of the model result with the experimental data.
47 OTHER INSTRUMENTATION↗
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer
Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.
59 BASIC BIOLOGICAL SCIENCES↗