Atomic Core Research Articles

Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone-Pair and Bond Orbital Contributions.

NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance-assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero-point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J-coupling is performed in terms of "chemist's orbitals", that is, localized molecular orbitals (LMOs) representing lone-pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de-shielding of the protons in resonance-assisted hydrogen bonds with delocalization involving the π-backbone. Resonance is also shown to be an important factor causing de-shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J-couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra- and intermolecular resonance.

Momentum partition between constituents of exotic atoms during laser-induced tunneling ionization

The tunneling ionization of exotic atoms such as muonic hydrogen, muonium and positronium in a strong laser field of circular polarization is investigated taking into account the impact of the motion of the center of mass on the the tunneling ionization dynamics. The momentum partition between the ionization products is deduced. The effect of the center of mass motion for the momentum distribution of the ionization components is determined. The effect scales with the ratio of the electron (muon) to the atomic core masses and is nonnegligible for exotic atoms, while being insignificant for common atoms. It is shown that the electron (muon) momentum shift during the under-the-barrier motion due to the magnetically induced Lorentz force has a significant impact on the momentum distribution of the atomic core and depends on the ratio of the electron to the atomic core masses.

Machine Learning for Quantum Mechanical Properties of Atoms in Molecules

We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling of computational cost in system size is demonstrated for saturated polymers with up to sub-mesoscale lengths.

Surface elasticity and size effect on the vibrational behavior of silicon nanoresonators

Predominance of nano-scale effects observed in material behavior at small scales requires implementation of new simulation methods which are not merely based on classical continuum mechanic. On the other hand, although the atomistic modeling methods are capable of modeling nano-scale effects, due to the computational cost, they are not suitable for dynamic analysis of nano-structures. In this research, we aim to develop a continuum-based model for nano-beam vibrations which is capable of predicting the results of molecular dynamics (MD) simulations with considerably lower computational effort. In this classical-based modeling, the surface and core regions are taken to have different mechanical properties, where core atoms are assumed to have macroscale properties whereas surface layer is showing a different elastic modulus from the core components. By estimating physical parameters of proposed classical model using molecular dynamics results and the genetic algorithm, calibrated classical Euler–Bernoulli and Timoshenko beam models are developed. The results demonstrates that a Timoshenko beam model incorporating surface effects and having calibrated parameters, is able to provide almost the same results as molecular dynamics method which can be used to predict the vibrational behavior of nano-beams at different scales from nano to macro.

Molecular materials - towards quantum properties.

Molecular materials are promising candidates for the expression of quantum properties, mainly due to the inherent monodispersity of their building blocks and the unique possibility to tailor the local environments of (natural) atoms. Both artificial as well as natural atoms have been proposed as quantum objects in the realisation of quantum information schemes. As a result of their confinement, electrons in both natural atoms and in quantum dots, so-called artificial atoms, are characterized by the formation of discrete energy levels. Similarly, in the case of a Josephson junction, Cooper pairs are confined in the potential well of the Josephson coupling energy leading to a discrete distribution of energy levels. Hence, the junction can be considered as a superconducting artificial atom. With regard to magnetism, single spins of impurities in semiconductors as well as molecular nanomagnets have been proposed as solid-state candidates for quantum bits (qubits). The used quantum correlations (e.g., entanglement, coherence) are usually observed only on the nanometer scale and have long been recognized as an information resource for quantum communication and processing. In particular, there is a considerable motivation to produce quantum computers, and a great deal of interest from scientists working in materials science, chemistry, physics, and nanofabrication technologies has been attracted. For example, the company D-wave has demonstrated a quantum annealer that performs certain calculations sufficiently rapidly to have a consortium, which involves Google and NASA, investing staggering sums of money in one such device [1]. The main advantage of the use of the molecular approach here is that molecules are quantum objects that can be produced by synthetic tools in a large number of atomically precise copies – a requirement for the scalable exploitation of the quantum properties. Devices based on single, or small numbers of, molecules, could speed up information treatment or allow for processing schemes that have not been possible to date. In a series of recent publications, it could be shown that magnetic molecules, in particular lanthanide complexes can be considered to be spin-qubits [2] or spin qugates [3]. Moreover, it was shown that molecule-based nuclear spins are extremely well insulated from environmental perturbations, rendering them less prone to decoherence. By means of synthetic engineering the central fine-tuning of the delicate trade-off between decoupling of the quantum object for low decoherence and connecting it for the electrical read-out could be achieved [2]. Quantum computing, the manipulation of data encoded in qubits instead of bits of information such as spin states of electrons or of an atomic nucleus, has been a long standing goal of scientists. In principle, if the qubits can maintain their coherence, without being perturbed by the noise of the surrounding environments (e.g., neighbouring atoms), quantum computers could be powered to find the best solutions far more quickly than current conventional computers. In some of the proposed device materials, quantum information is carried by the spin and the orbital degree of freedom of the electron. The challenge consists in circumventing the strong coupling of the latter one with the environment in order to achieve the needed long coherence times to carry out quantum operations. In this context, molecular quantum materials offer the additional advantage that the active quantum processing elements comprise an atomic core of one to a few open-spin ions surrounded by a shell of organic material. At low temperatures, the behavior of such molecular spin objects can be well described by simple few-level systems. Moreover, their spin degree of freedom can be sufficiently decoupled from environmental perturbations to attain long coherence times, thus making them the ideal candidates for the implementation of qubits. The organic shell can be used to fine-tune the coupling between molecular qubits as required by scalability for logical quantum gate operations. We have gathered in the Thematic Series contributions dealing with the magnetic properties of molecules, partially under use of lanthanide metal ions und their coordination under surface confinement. By the same token, the needed surface attachment and positioning of molecular materials by self-assembly techniques is addressed – an important prerequisite for the electrical addressing of molecules by lateral graphene electrodes or vertical scanning tunnelling microscopy set-ups or e-beam lithographed gold or Prussian blue nano-arrays. Complementary, quantum chemical calculations have addressed lanthanide complexes and metal-organic frameworks. This Thematic Series is part of a subsession of the same title, which took place at the E-MRS spring meeting in May 2014 in Lille, France. I would like to kindly thank Prof. G. Aromi (Barcelona) and Prof. A. Bousseksou (Toulouse) for co-chairing this event. Mario Ruben Karlsruhe, June 2015

Simultaneous melting of shell and core atoms, a molecular dynamics study of lithium–copper nanoalloys

Melting of nanoalloys originates from the alloy surface and gradually propagates into the interior region. The thermal stability of Li cores and Cu shells nanoalloy with size of 3.5 nm is studied through molecular dynamics and embedded atom method with the use of potential energy, Lindemann index, and radial distribution function. Results show that the shell and core Li atoms are melted in two steps: first, some Li atoms in the core migrate to the nanoalloy surface and maintain a typical solid state despite that the system temperature is higher than the bulk melting point of Li because of Li solidification in the solid–liquid interface; second, the shell and core Li atoms are simultaneously melted at high temperatures. A comparative study of Li@Cu nanoalloys with different Li atomic numbers shows that thermal stability is enhanced with the decreasing number of Li atoms within the nanoalloys because of weak binding for Cu thin shells.

Crystal structure of bis-(N-methyl-N-phenyl-amino)-tris-ulfane.

The title compound, C14H16N2S3, crystallized with two independent mol-ecules [(1 a ) and (1 b )] in the asymmetric unit. Both mol-ecules display a pseudo-trans conformation. The two consecutive S-S bond lengths of the tris-ulfane unit of mol-ecule (1 a ) are 2.06 (3) and 2.08 (3) Å, and 2.08 (3) and 2.07 (2) Å for mol-ecule (1 b ). Torsion angles about each of the two S-S bonds are 86.6 (2) and 87.0 (2)° for (1 a ), and -84.6 (2) and -85.9 (2)° for (1 b ). The core atoms, viz. the N-S-S-S-N moiety, of the two mol-ecules superimpose well if one is inverted on the other, but the phenyl groups do not. Thus, the two units are essentially conformational enanti-omers. In mol-ecule (1 a ), the two phenyl rings are inclined to one another by 86.7 (3)°, and in mol-ecule (1 b ), by 81.1 (3)°. In the crystal, mol-ecules are linked via C-H⋯π inter-actions, forming sheets lying parallel to (010).

Soft X‐ray Spectromicroscopic Investigation of Synthetic C‐S‐H and C3S Hydration Products

Calcium silicate hydrates (C‐S‐H), the primary binding phase in concrete, is the most prominent physiochemical factor controlling the mechanical and chemical properties in the production of concrete. This paper reports the local‐binding structure and morphological details of C‐S‐H as determined by high‐resolution X‐ray spectromicroscopy. Hydrated tricalcium silicate (C3S) was used to determine the properties and role of the outer products (Op) of C3S. C‐S‐H with different molar ratios of Ca/Si, were synthesized (Syn‐CSH) to quantitatively evaluate the effect of silicate polymerization on Ca L and Si K edge of C‐S‐H. Near edge X‐ray absorption fine structure (NEXAFS) spectroscopy of Syn‐CSH showed no variation in peak positions and energy separation for CaLIII, II edge for the Ca/Si ratios investigated. Compared to Syn‐CSH, C3S, when hydrated for 17 d, had a similar local structure around Ca. Si K edge NEXAFS analysis on Syn‐CSH showed a tendency for the peak positions of both the Si K edge and the peak induced by multiple scattering to shift to higher energy levels. The results also indicated that the distance between the two peaks increased with a decrease of the Ca/Si ratio in Syn‐CSH. Silicate polymerization influenced the multiple scattering of distant shell atoms more than the binding energy of the core atoms. Op of C3S had a uniform and higher degree of silicate polymerization compared to the core area. The results imply that Op reduces the hydration process of C3S into the core area thereby playing a key role on the properties of concrete upon formation.

Terminal Fluorinated Nitroxide Radical Liquid Crystalline Compounds

We have synthesized a new series of all-organic paramagnetic liquid crystalline (LC) compounds, which include a five-membered ring nitroxide radical (NR) moiety in the mesogen core and fluorine atoms as terminal substituents. These new compounds are the structural analogs of the previously reported NR-LC compounds, and showed remarkable fluorine substituent effects. The introducing fluorine atom into terminal unit stabilizes nematic phase. However, an excess of fluorination leads to the destabilization of nematic phase.

ChemInform Abstract: Structural and Bonding Patterns in Gold Clusters

AbstractReview: 85 refs.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field.

Site preference and alloying effect of Re atoms in the edge dislocation cores in Ni3Al

Using Cambridge sequential total energy package method based on the density functional theory, we investigated the site preference and alloying effect of Re atoms in the [1 0 0] (0 1 0) edge dislocation cores in Ni3Al. Due to the introduction of a Re atom, the energetic and electronic structure of dislocation core systems have been changed a lot. The binding energy results suggest Re atom prefers Al site, especially the centre site in the centre-Al system, which can be explained by the results of Mulliken orbital population and density of states. When Re atom occupies the centre site in the centre-Al system, the DC system has the highest stability and stronger bonds formed between the Re atom and its nearest neighbouring atom due to hybridization of the Re-5d and Ni-3d orbitals.

The adiabatic potentials of low-lying electronic states of the NaRb molecule

Adiabatic potential energy curves and spectroscopic constants have been calculated for the NaRb molecule. The results of ten states of the symmetry , six states of the symmetry Π, and two states of the symmetry Δ are obtained by the nonrelativistic quantum chemical method used with pseudopotentials describing the interaction of valence electrons with atomic cores. Analysis is based on a comparison with the results of other theoretical and experimental studies.

Vapor-phase transport deposition, characterization, and applications of large nanographenes.

Recently, chemical synthesis of a range of large nanographene molecules with various shapes and sizes opened a new path to utilize them in various applications and devices. However, due to their extended aromatic cores and high molecular weight, film formation of large nanographene molecules, bearing more than 90 sp(2) carbon atoms in aromatic cores, is very challenging, which has prevented their applications such as in thin-film transistors. Here, we developed an effective approach to prepare films of such large nanographene molecules using a vapor-phase transport (VPT) technique based on molecule sublimation. The VPT of these molecules was made possible by combining the molecules and the target substrate in a small confinement of vacuum-sealed glass tube, so that a small amount of sublimation can be utilized to create films. Surprisingly, such heavy and large molecules can be deposited on any substrate by this method to create films of assembled large nanographene molecules while maintaining their aromatic cores intact, which was confirmed using mass spectrometry measurements. Moreover, field-effect transistors based on these films are depleted and show significantly improved current on/off ratio compared to previous large nanographene-based transistors fabricated using liquid-phase-based process. Our work shows that VPT deposition can be a viable technique to prepare films based on large nanographene molecules and potentially other high molecular weight compounds, which may find exciting applications in electronics and optoelectronics.

Skeletal octahedral nanoframe with Cartesian coordinates via geometrically precise nanoscale phase segregation in a Pt@Ni core-shell nanocrystal.

Catalytic properties of nanoparticles can be significantly enhanced by controlling nanoscale alloying and its structure. In this work, by using a facet-controlled Pt@Ni core-shell octahedron nanoparticle, we show that the nanoscale phase segregation can have directionality and be geometrically controlled to produce a Ni octahedron that is penetrated by Pt atoms along three orthogonal Cartesian axes and is coated by Pt atoms along its edges. This peculiar anisotropic diffusion of Pt core atoms along the ⟨100⟩ vertex, and then toward the ⟨110⟩ edges, is explained via the minimum strain energy for Ni-Ni pair interactions. The selective removal of the Ni-rich phase by etching then results in structurally fortified Pt-rich skeletal PtNi alloy framework nanostructures. Electrochemical evaluation of this hollow nanoframe suggests that the oxygen reduction reaction (ORR) activity is greatly improved compared to conventional Pt catalysts.

Non-resonant elastic scattering of low-energy photons by atomic sodium confined in quantum plasmas

The non-resonant elastic scattering of low-energy photons by the bound valence electron in the ground state 3s of atomic sodium confined in quantum plasmas is investigated theoretically. The incident photon energy is assumed to be much smaller than the 3s-3p excitation energy. The alkali atom sodium is first formulated as an effective one-electron problem in which the attractive interaction between the valence electron and the atomic ion core is simulated by a spherically symmetric model potential. The Shukla-Eliasson oscillatory exponential cosine screened-Coulomb potential model is then used to mimic the effective two-body (valence-core) interaction within quantum plasmas. Non-relativistic calculations performed within the electric dipole approximation indicate that the non-resonant elastic photon scattering cross-section undergoes a dramatic growth by several orders of magnitude as the quantum wave number increases. A qualitative explanation of this phenomenon is presented. In the absence of the oscillatory cosine screening term, a similar growth is observed at larger values of the quantum wave number. Our computed relevant atomic data are in very good agreement with the experimental as well as the previous theoretical data for the zero-screening (free atom) case, and with the very limited, accurate theoretical results available for the case of exponential screened-Coulomb two-body interaction, without the cosine screening term.

Determining and visualizing flexibility in protein structures.

How to compare the structures of an ensemble of protein conformations is a fundamental problem in structural biology. As has been previously observed, the widely used RMSD measure due to Kabsch, in which a rigid-body superposition minimizing the least-squares positional deviations is performed, has its drawbacks when comparing and visualizing a set of flexible protein structures. Here, we develop a method, fleximatch, of protein structure comparison that takes flexibility into account. Based on a distance matrix measure of flexibility, a weighted superposition of distance matrices rather than of atomic coordinates is performed. Subsequently, this allows a consistent determination of (a) a superposition of structures for visualization, (b) a partitioning of the protein structure into rigid molecular components (core atoms), and (c) an atomic mobility measure. The method is suitable for highlighting both particularly flexible and rigid parts of a protein from structures derived from NMR, X-ray diffraction or molecular simulation.

Calculations of rates for strong-field ionization of alkali-metal atoms in the quasistatic regime

Tunneling and over-the-barrier ionization of alkali-metal atoms in strong electromagnetic fields are studied using the single-electron model (valence electron plus atomic core) and the frozen-core approximation. The lowest-state energies and widths (ionization rates) at different values of applied field, obtained using the Stark shift expansion and the Ammosov-Delone-Krainov formula, respectively, are compared with the corresponding values determined numerically by the complex rotation method. Good agreement for the energies is obtained at the field strengths corresponding to the tunneling regime. In contrast, the rates obtained by the Ammosov-Delone-Krainov formula significantly overestimate numerical results. After introducing a correction in the formula that accounts for the dependence of the binding energy on the field strength, good agreement in the tunneling regime is obtained for the rates too. A disagreement that still remains in the over-the-barrier ionization regime indicates that at stronger fields further corrections of the rate formula, such as those related to the form of the bound-state wave function, are required. Finally, it is demonstrated that numerically determined ionization rates are not too sensitive to the choice of model for the effective core potential and good results can be obtained using a simple local pseudopotential.

Oxygen-atom transfer chemistry and thermolytic properties of a di-tert-butylphosphate-ligated Mn4O4 cubane.

[Mn4O4{O2P(OtBu)2}6] (1), an Mn4O4 cubane complex combining the structural inspiration of the photosystem II oxygen-evolving complex with thermolytic precursor ligands, was synthesized and fully characterized. Core oxygen atoms within complex 1 are transferred upon reaction with an oxygen-atom acceptor (PEt3), to give the butterfly complex [Mn4O2{O2P(OtBu)2}6(OPEt3)2]. The cubane structure is restored by reaction of the latter complex with the O-atom donor PhIO. Complex 1 was investigated as a precursor to inorganic Mn metaphosphate/pyrophosphate materials, which were studied by X-ray absorption spectroscopy to determine the fate of the Mn4O4 unit. Under the conditions employed, thermolyses of 1 result in reduction of the manganese to Mn(II) species. Finally, the related butterfly complex [Mn4O2{O2P(pin)}6(bpy)2] (pin = pinacolate) is described.

Characterization of the thickness and distribution of latex coatings on polyvinylidene chloride beads by backscattered electron imaging.

Polyvinylidene chloride (PVDC) co-polymer resins are commonly formulated with a variety of solid additives for the purpose of processing or stabilization. A homogeneous distribution of these additives during handling and processing is important. The Dow Chemical Company developed a process to incorporate solid materials in latex form onto PVDC resin bead surfaces using a coagulation process. In this context, we present a method to characterize the distribution and thickness of these latex coatings. The difference in backscattered electron signal from the higher mean atomic number PVDC core and lower atomic number latex coating in conjunction with scanning electron microscopy (SEM) imaging using a range of accelerating voltages was used to characterize latex thickness and distribution across large numbers of beads quickly and easily. Monte Carlo simulations were used to quantitatively estimate latex thickness as a function of brightness in backscatter electron images. This thickness calibration was validated by cross-sectioning using a focused ion-beam SEM. Thicknesses from 100 nm up to about 1.3 µm can be determined using this method.