Silver-functionalized silica aerogel for iodine capture: Adsorbent aging by NO[subscript 2] in spent
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Shen, Ziheng↗
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Results for “functions”
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Structural and Functional Studies of Ig[alpha beta] and Its Assembly with the B Cell Antigen Receptor
The B cell antigen receptor (BCR) plays an essential role in all phases of B cell development. Here we show that the extracellular domains of murine and human Ig{beta} form an I-set immunoglobulin-like structure with an interchain disulfide between cysteines on their G strands. Structural and sequence analysis suggests that Ig{alpha} displays a similar fold as Ig{beta}. An Ig{alpha}{beta} heterodimer model was generated based on the unique disulfide-bonded Ig{beta} dimer. Solution binding studies showed that the extracellular domains of Ig{alpha}{beta} preferentially recognize the constant region of BCR with chain specificity, suggesting a role for Ig{alpha}{beta} to enhance BCR chain signaling. Cluster mutations on Ig{alpha}, Ig{beta}, and a membrane-bound form of immunoglobulin (mIgM) based on the structural model identified distinct areas of potential contacts involving charged residues on both subunits of the coreceptor and the C4 domain of mIgM. These studies provide the first structural model for understanding BCR function.
60 APPLIED LIFE SCIENCES↗
Crystallographic and Functional Analysis of the ESCRT-I /HIV-1 Gag PTAP Interaction
Budding of HIV-1 requires the binding of the PTAP late domain of the Gag p6 protein to the UEV domain of the TSG101 subunit of ESCRT-I. The normal function of this motif in cells is in receptor downregulation. Here, we report the 1.41.6 {angstrom} structures of the human TSG101 UEV domain alone and with wild-type and mutant HIV-1 PTAP and Hrs PSAP nonapeptides. The hydroxyl of the Thr or Ser residue in the P(S/T)AP motif hydrogen bonds with the main chain of Asn69. Mutation of the Asn to Pro, blocking the main-chain amide, abrogates PTAP motif binding in vitro and blocks budding of HIV-1 from cells. N69P and other PTAP binding-deficient alleles of TSG101 did not rescue HIV-1 budding. However, the mutant alleles did rescue downregulation of endogenous EGF receptor. This demonstrates that the PSAP motif is not rate determining in EGF receptor downregulation under normal conditions.
08 HYDROGEN↗
Covalency of Trivalent Actinide Ions with Different Donor Ligands: Do Density Functional and Multiconfigurational Wavefunction Calculations Corroborate the Observed “Breaks”?
A comprehensive ab initio study of periodic actinide–ligand bonding trends for trivalent actinides is performed. Relativistic density functional theory (DFT) and complete active-space (CAS) self-consistent field wavefunction calculations are used to dissect the chemical bonding in the [AnCl 6 ] 3– , [An(CN) 6 ] 3– , [An(NCS) 6 ] 3– , [An(S 2 PMe 2 ) 3 ], [An(DPA) 3 ] 3– , and [An(HOPO)] – series of actinide (An = U–Es) complexes. Except for some differences for the early actinide complexes with DPA, bond orders and excess 5f-shell populations from donation bonding show qualitatively similar trends in 5f n active-space CAS vs DFT calculations. The influence of spin–orbit coupling on donation bonding is small for the tested systems. Along the actinide series, chemically soft vs chemically harder ligands exhibit clear differences in bonding trends. There are pronounced changes in the 5f populations when moving from Pu to Am or Cm, which correlate with previously noted “breaks” in chemical trends. As a result, bonding involving 5f becomes very weak beyond Cm/Bk. We propose that Cm(III) is a borderline case among the trivalent actinides that can be meaningfully considered to be involved in ground-state 5f covalent bonding.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Practical Approach to Wave Function Propagation, Hopping Probabilities, and Time Steps in Surface Hopping Calculations
We compare several established approaches for propagating wave functions and calculating hopping probabilities within the fewest switches surface hopping (FSSH) algorithm for difficult cases with many electronic states and many trivial crossings. If only a single time step (Δt c ) is employed, we find that no published approach can accurately capture the dynamics correctly unless Δt c → 0 (which is not computationally feasible). If multiple time steps are employed, for a fixed classical time step (Δt c ), a robust scheme can be found for dynamically choosing quantum time steps (δt q1 and δt q2 ) and calculating hopping probabilities so that one can systematically reduce all errors and achieve maximally efficient accuracy; scattering calculations confirm that one can choose a fairly large classical time step. Furthermore, the robust scheme presented here uses both the “local diabatic” and adiabatic interpolation and thus borrows elements from both the Granucci/Persico and Meek/Levine algorithms. Our findings should be broadly applicable in the future.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Synthetic Approach to β-Functionalized Naphtho[2,3]porphyrins
A concise synthetic method has been developed to access functionalized naphtho[2,3]porphyrins through combining two sequence reactions involving a Heck–electrocyclization–aromatization sequence and a Wittig–Knovenegal sequence. Using this method, mononaphtho[2,3]porphyrin (NP-1), opp-dinaphtho[2,3]porphyrin (NP-2), and push–pull naphtho[2,3]porphyrin (NP-3) have been prepared. These naphtho[2,3]porphyrins displayed interesting optical and electrochemical properties. As a result, excellent efficiencies of singlet oxygen generation were obtained for these naphtho[2,3]porphyrins.
Absorption↗
Electronic and magnetic properties of substituted BN sheets: A density functional theory study
Using density functional calculations, we investigate the geometries, electronic structures and magnetic properties of hexagonal BN sheets with 3d transition metal (TM) and nonmetal atoms embedded in three types of vacancies: VB, VN, and VB+N. We show that some embedded configurations, except TM atoms in VN vacancy, are stable in BN sheet and yield interesting phenomena. For instance, the band gaps and magnetic moments of BN sheet can be tuned depending on the embedded dopant species and vacancy type. In particular, embedment such as Cr in VB+N, Co in VB, and Ni in VB leads to half-metallic BN sheets interesting for spin filter applications. From the investigation of Mn-chain (CMn) embedments, a regular 1D structure can be formed in BN sheet as an electron waveguide, a metal nanometer wire with a single atom thickness.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
CO2 capture properties of alkaline earth metal oxides and hydroxides: A combined density functional theory and lattice phonon dynamics study
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Duan, Yuhua↗
Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics
We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electronic structure of C and N co-doped TiO{sub 2}: A combined hard x-ray photoemission spectroscopy and density functional theory study
We have studied the electronic structure of C and N co-doped TiO{sub 2} using hard x-ray photoelectron spectroscopy and first-principles density functional theory calculations. Our results reveal overlap of the 2p states of O, N, and C in the system which shifts the valence band maximum towards the Fermi level. Combined with optical data we show that co-doping is an effective route for band gap reduction in TiO{sub 2}. Comparison of the measured valence band with theoretical photoemission density of states reveals the possibility of C on Ti and N on O site.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Understanding density functional theory (DFT) and completing it in practice
We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A simple way to test for collinearity in spin symmetry broken wave functions: General theory and application to generalized Hartree Fock
We introduce a necessary and sufficient condition for an arbitrary wavefunction to be collinear, i.e., its spin is quantized along some axis. It may be used to obtain a cheap and simple computational procedure to test for collinearity in electronic structure theory calculations. We adapt the procedure for Generalized Hartree Fock (GHF), and use it to study two dissociation pathways in CO{sub 2}. For these dissociation processes, the GHF wave functions transform from low-spin Unrestricted Hartree Fock (UHF) type states to noncollinear GHF states and on to high-spin UHF type states, phenomena that are succinctly illustrated by the constituents of the collinearity test. This complements earlier GHF work on this molecule.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ion energy-angle distribution functions at the plasma-material interface in oblique magnetic fields
The ion energy-angle distribution (IEAD) at the wall of a magnetized plasma is of fundamental importance for the determination of the material processes occurring at the plasma-material interface, comprising secondary emissions and material sputtering. Here, we present a numerical characterization of the IEAD at the wall of a weakly collisional magnetized plasma with the magnetic field inclined at an arbitrary angle with respect to the wall. The analysis has been done using two different techniques: (1) a fluid-Monte Carlo method, and (2) particle-in-cell simulations, the former offering a fast but approximate method for the determination of the IEADs, the latter giving a computationally intensive but self-consistent treatment of the plasma behavior from the quasi-neutral region to the material boundary. The two models predict similar IEADs, whose similarities and differences are discussed. Data are presented for magnetic fields inclined at angles from normal to grazing incidence (0°–85°). We show the scaling factors of the average and peak ion energy and trends of the pitch angle at the wall as a function of the magnetic angle, for use in the correlation of fluid plasma models to material models.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
In-operando synchronous time-multiplexed O K-edge x-ray absorption spectromicroscopy of functioning tantalum oxide memristors
Memristors are receiving keen interest because of their potential varied applications and promising large-scale information storage capabilities. Tantalum oxide is a memristive material that has shown promise for high-performance nonvolatile computer memory. The microphysics has been elusive because of the small scale and subtle physical changes that accompany conductance switching. In this study, we probed the atomic composition, local chemistry, and electronic structure of functioning tantalum oxide memristors through spatially mapped O K-edge x-ray absorption. We developed a time-multiplexed spectromicroscopy technique to enhance the weak and possibly localized oxide modifications with spatial and spectral resolutions of <30 nm and 70 meV, respectively. During the initial stages of conductance switching of a micrometer sized crosspoint device, the spectral changes were uniform within the spatial resolution of our technique. When the device was further driven with millions of high voltage-pulse cycles, we observed lateral motion and separation of ∼100 nm-scale agglomerates of both oxygen interstitials and vacancies. We also demonstrate a unique capability of this technique by identifying the relaxation behavior in the material during electrical stimuli by identifying electric field driven changes with varying pulse widths. In addition, we show that changes to the material can be localized to a spatial region by modifying its topography or uniformity, as against spatially uniform changes observed here during memristive switching. The goal of this report is to introduce the capability of time-multiplexed x-ray spectromicroscopy in studying weak-signal transitions in inhomogeneous media through the example of the operation and temporal evolution of a memristor.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Spin orientations of the spin-half Ir{sup 4+} ions in Sr{sub 3}NiIrO{sub 6}, Sr{sub 2}IrO{sub 4}, and Na{sub 2}IrO{sub 3}: Density functional, perturbation theory, and Madelung potential analyses
The spins of the low-spin Ir{sup 4+} (S = 1/2, d{sup 5}) ions at the octahedral sites of the oxides Sr{sub 3}NiIrO{sub 6}, Sr{sub 2}IrO{sub 4}, and Na{sub 2}IrO{sub 3} exhibit preferred orientations with respect to their IrO{sub 6} octahedra. We evaluated the magnetic anisotropies of these S = 1/2 ions on the basis of density functional theory (DFT) calculations including spin-orbit coupling (SOC), and probed their origin by performing perturbation theory analyses with SOC as perturbation within the LS coupling scheme. The observed spin orientations of Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4} are correctly predicted by DFT calculations, and are accounted for by the perturbation theory analysis. As for the spin orientation of Na{sub 2}IrO{sub 3}, both experimental studies and DFT calculations have not been unequivocal. Our analysis reveals that the Ir{sup 4+} spin orientation of Na{sub 2}IrO{sub 3} should have nonzero components along the c- and a-axis directions. The spin orientations determined by DFT calculations are sensitive to the accuracy of the crystal structures employed, which is explained by perturbation theory analyses when interactions between adjacent Ir{sup 4+} ions are taken into consideration. There are indications implying that the 5d electrons of Na{sub 2}IrO{sub 3} are less strongly localized compared with those of Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4}. This implication was confirmed by showing that the Madelung potentials of the Ir{sup 4+} ions are less negative in Na{sub 2}IrO{sub 3} than in Sr{sub 3}NiIrO{sub 6} and Sr{sub 2}IrO{sub 4}. Most transition-metal S = 1/2 ions do have magnetic anisotropies because the SOC induces interactions among their crystal-field split d-states, and the associated mixing of the states modifies only the orbital parts of the states. This finding cannot be mimicked by a spin Hamiltonian because this model Hamiltonian lacks the orbital degree of freedom, thereby leading to the spin-half syndrome. The spin-orbital entanglement for the 5d spin-half ions Ir{sup 4+} is not as strong as has been assumed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗