Independent Electron Research Articles

Rotamer libraries of spin labelled cysteines for protein studies

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.

Phenanthro[9,10-d]imidazole as a new building block for blue light emitting materials

The blue light emitting compound, BPPI, based on a phenanthro[9,10-d]imidazole group, is prepared by a facial synthetic process and exhibits excellent thermal stability, highly efficient fluorescence and balanced carrier injection. The double-layered device based on BPPI shows a higher maximum luminance and a lower turn-on voltage than the multi-layered one with an independent electron injection layer. The results suggest that the phenanthroimidazole unit is an excellent building block for tuning the carrier injection properties as well as blue emission.

Doubly excited states resulting in H(2p) formation in the photoexcitation of water

The cross sections for the emission of Lyman-α fluorescence in the photoexcitation of H2O have been measured as a function of the incident photon energy in the 14–60 eV range, i.e. the outer- and inner-valence ranges. Four superexcited states have been found, two of which are doubly excited states, one is a singly excited state and one a state including electron configurations of both single and double excitations. The gross feature of the superexcited states of H2O resulting in the formation of excited hydrogen atoms has been obtained by combining the present results and the cross section curves of the Balmer fluorescences (Kato et al 2004 J. Phys. B: At. Mol. Opt. Phys. 37 3127). The breakdown of the independent electron model has been indicated in the inner-valence range of H2O, and the degree of breakdown has been compared among CH4, NH3 and H2O ten-electron molecules.

Modeling direct electron transfer to a multi-redox center protein: Cytochrome c oxidase

Direct electron transfer to Cytochrome c Oxidase (CcO) was investigated using fast scan cyclic voltammetry. The enzyme was tethered to the electrode in a strict orientation by means of a histidine-tag with Cu A, the first electron acceptor, directed towards the electrode. A lipid bilayer was then reconstituted in situ around the bound proteins, forming a protein-tethered bilayer lipid membrane. Cyclic voltammograms were measured under anaerobic conditions at different scan rates with CcO in the non-activated and the activated state. The activated state was attained after catalytic turnover of the enzyme in the presence of oxygen. A four-electron transfer model was developed to analyze the data. This enables us to discriminate between the mechanisms of sequential and independent electron transfer to the four redox centers Cu A, heme a, heme a 3 and Cu B. Moreover, values of parameters such as standard redox potentials and kinetic coefficients of electron transfer could be obtained. Based on these results we conclude that direct electron transfer to CcO most likely follows the sequential mechanism, thus mimicking the electron transfer form cytochrome c, the genuine electron donor of CcO.

Parallel fabrication of monolithic nanoscopic tunnel junctions for molecular devices

Nanoelectrode tunneling devices for molecular level measurements have been grown using atomic layer deposition. These devices are two-terminal nanostructures separated by a free space region on the order of one to several nanometers where molecules can adsorb and be probed with electrical measurements including electron tunneling spectroscopy. Successful fabrication of parallel devices arranged in arrays is achieved by exploiting a nanofeedback mechanism that aids in the convergence of independent devices to tunneling. Independent devices are shown to behave similarly for thermal expansion, adsorption, desorption, and tunneling spectroscopy measurements. Adsorption is shown to be strongly influenced by the large electric fields in the nanoscopic tunnel junctions, and a model based on electric field forces qualitatively captures these effects. Desorption events are observed as stochastic processes for the independent devices and parallel inelastic electron tunneling spectroscopy measurements show features that are similar between independent devices. These data demonstrate parallel operation of nanoelectrode devices and suggest that it may be possible to scale the devices to have many nanojunctions operating in parallel.

Spin-orbit effects on electronic delocalization. Aromaticity in a discrete square tetrapalladium sandwich complex

In this article, we report the relativistic electronic structure, including spin-orbit interaction, employing all-electron density functional theory calculations on the multimetallic sandwich compound [(CNT)Pd(4)(COT)](1+) (1), which can be considered as a [Pd(4)](2+) fragment flanked by two ring-ligands, namely, cyclononatetraenyl (CNT(1-)) and cyclooctatetraene (COT), as well as the dimer of 1, hereafter 2. The calculations suggest that the Pd(4)-ligand interaction is mainly electrostatic, being the main responsible term for the stabilization of the almost fully occupied 4d shell [Pd(4)](2+) fragment. The ring currents and electronic delocalization estimated via the nuclear independent chemical shifts indices and electron localization function, allow us to describe a significant sigma-aromaticity at the center of the Pd(4) square in 1, which in conjunction with the aromaticity arising from the ligands induce considerable aromatic character inside of the multimetallic metallocene.

The Ornstein–Zernike equation in molecular electronic structure theory

The Ornstein–Zernike equation expresses a simple relationship between direct and full correlation effects of a many-body system. Although it was introduced in the context of fluids, it can be derived through simple physical arguments that are equally applicable to the electrons in a molecule. Direct correlation effects account for the correlation between two particles at a time. If a simple model for direct correlation can be found, the Ornstein–Zernike equation can be used to convert it into a treatment of the full correlation effect. We show that the independent electron pair approximation (IEPA) is a reasonable model for the description of direct correlation effects. IEPA followed by our Ornstein–Zernike treatment is closer to CCSD(T) than is CCSD for valence correlation energies of small molecules.

Exothermic Rate Restrictions in Long-Range Photoinduced Charge Separations in Rigid Media

Glycerol/methanol (9:1) mixtures at 255 K behave as rigid media for photoinduced electron transfers that take place within a few hundred nanoseconds. This media also provides enough polarity and plasticity to accommodate charge separations with reaction free energies ranging from +3 to -34 kcal/mol. The distance dependence of the electron transfer rates from electronically excited aromatic hydrocarbons to nitriles in this medium is accurately described by an exponential decay constant of 1.65 per angstrom. These photoinduced electron transfers display, for the first time in charge separations between independent electron donors and acceptors, a free-energy relationship with a maximum rate followed by a decrease in the rate for more exothermic reactions. According to this free-energy relationship, Franck-Condon factors are maximized at DeltaG(0) approximately -15 kcal/mol. It is suggested that the inverted region observed for these first-order photoinduced charge separations originates from a slower increase of their reorganization energies with DeltaG(0) than that of the analogous second-order photoinduced charge separations, for which inverted regions have never been clearly observed.

Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.

Projectile scattering and electron-electron interaction in ion-atom collisions

One- and two-electron processes involving electron transfer and excitation are considered for a few basic ion-atom collision systems at intermediate impact energies. We have used the two-center basis generator method in the framework of the independent electron model for orbital propagation and the eikonal approximation for the calculation of scattering-angle differential cross sections. Our results shed some light on the roles of the nucleus-nucleus and the electron-electron interactions in these collisions.

JPL/USC GAIM: On the impact of using COSMIC and ground‐based GPS measurements to estimate ionospheric parameters

The University of Southern California (USC) and the Jet Propulsion Laboratory (JPL) have jointly developed the Global Assimilative Ionospheric Model (GAIM) to monitor space weather, study storm effects, and provide ionospheric calibration for space weather applications. JPL/USC GAIM is a physics‐based 3‐D data assimilation model that uses both four‐dimensional variational analysis and Kalman‐filter techniques to solve for the ion and electron density state and key drivers such as equatorial electrodynamics, neutral winds, and production terms. Here we report on GAIM Kalman filter‐based assimilation results using ground‐based GPS and COSMIC‐derived total electron count (TEC) measurements. We find that assimilating COSMIC measurements into GAIM improves critical ionospheric parameters such as NmF2 and HmF2. Assimilating COSMIC data produces higher‐accuracy vertical electron density profile “shapes,” as verified by comparisons to independent electron density profiles measured at Arecibo, Jicamarca, and Millstone Hill incoherent scatter radar (ISR). We also find significant improvement in global vertical TEC (VTEC) maps when assimilating COSMIC measurements, verified by comparing GAIM output with VTEC measurements from the Jason ocean altimeter. For 3 days in June 2006, improvement in accuracy compared to ground‐data‐only assimilation is found to be 30%, 28%, and 44%, respectively.

Quasi Temperature Independent Electron Mobility in Hexagonal Columnar Mesophases of an H-Bonded Benzotristhiophene Derivative

Reported here are the unique properties of N,N′,N′′-(3,4,5-tridodecyloxyphenyl)benzo[b,b′,b′′]tristhiophene-2,2′,2′′-tricarboxamide 3 as a new H-bonded discotic liquid crystal. Polarized optical microscopy and thermal analysis as well as variable temperature IR spectroscopy and X-ray diffraction confirm the presence of two thermotropic H-bonded hexagonal columnar mesophases that cover a temperature range from <−50 to 280 °C. Intermediate lyotropic mesophases of the highly viscous material aid the alignment of the hexagonal columnar mesophases, which is essential for a detailed structural characterization and applications. Solutions of 3 in heptane at concentrations as low as 1 wt % display isotropic organo-gel phases that consist of H-bonded networks of 3 but do not contain columnar stacks. 2D-X-ray diffraction studies on aligned samples of the thermotropic hexagonal columnar mesophases and DFT calculations on a tetramer of 3 reveal a helical columnar stacking of the individual benzotristhiophene units. C...

Projectile angular-differential cross sections for electron transfer processes in ion-helium collisions: Evidence for the applicability of the independent electron model

The electron dynamics in $p\text{-He}$ and ${\text{He}}^{2+}\text{-He}$ collisions have been investigated on the level of the independent electron model by using the two-center basis generator method. Projectile angular-differential cross sections for various one- and two-electron processes involving electron transfer have been calculated with the eikonal approximation. Overall, the calculated cross sections are in good agreement with the most recent experimental cold target recoil ion momentum spectroscopy data taken at impact energies in the range from 40 to 630 keV/amu. This demonstrates, somewhat surprisingly, that electron correlations play but a minor role for the processes and the energies considered.

An Atomic Counterpoise Method for Estimating Inter- and Intramolecular Basis Set Superposition Errors.

An atomic counterpoise method is proposed to calculate estimates of inter- and intramolecular basis set superposition errors. The method estimates the basis set superposition error as a sum of atomic contributions and can be applied for both independent particle and electron correlation models. It is shown that the atomic counterpoise method provides results very similar to the molecular counterpoise method for intermolecular basis set superposition errors at both the HF and MP2 levels of theory with a sequence of increasingly larger basis sets. The advantage of the atomic counterpoise method is that it can be applied with equal ease to estimate intramolecular basis set superposition errors, for which few other methods exist. The atomic counterpoise method is computationally quite efficient, requiring typically double the amount of computer time as required for calculating the uncorrected energy.

Angular differential cross section calculations for ion-helium collisions

We have calculated projectile angular-differential cross sections for various processes in ion-helium collisions. Key ingredients of our approach are the independent electron model, the two-center basis generator method for orbital propagation, and the eikonal approximation for the extraction of angular-differential scattering amplitudes. In general, we find good agreement with measurements; in some cases even for two-electron processes, although correlation effects are not taken into account.

Bloch electron spontaneous emission from a single energy band in a classical ac field

A theory for the spontaneous emission of radiation for a Bloch electron in a single superlattice (SL) energy band under the influence of an external, spatially homogeneous, classical ac electric field is presented. The classical external ac electric field is described in the vector-potential gauge. The quantum radiation field is described by the free-space quantized electromagnetic field in the Coulomb gauge. Utilizing the instantaneous eigenstates of the Bloch Hamiltonian as the basis states, the Bloch electron dynamics is described to all orders in the classical ac electric field. It is shown that the spontaneous emission occurs with frequencies equal to integral multiples of the classical ac electric field frequency; this is due to the imposition of temporal periodic motion of the Bloch electrons in the SL miniband from the external periodic ac field. From appropriately derived selection rules for photon frequency and wave-vector transitions, the total spontaneous-emission probability (TSEP) is derived to first-order perturbation theory in the quantized radiation field. A general expression is obtained for the TSEP in terms of arbitrary SL miniband parameters; further, the TSEP is analyzed in detail based on the band model for the nearest-neighbor tight-binding approximation, and results show multiharmonic behavior and ac electric field tuning properties. In the nearest-neighbor tight-binding approximation, specific results for single Bloch electron manifest distinct plateaulike step structure in the analysis of normalized TSEP as a function of the ratio ${\ensuremath{\omega}}_{0}/\ensuremath{\omega}$, where ${\ensuremath{\omega}}_{0}$ is the characteristic frequency, proportional to the ac electric field amplitude, and $\ensuremath{\omega}$ is the ac electric field frequency; the plateau centers of gravity are found to be defined by the Stark delocalization condition established in ac-field transport. Further, the influence of a microcavity waveguide is established and shows enhancement as well as harmonic tuning of the TSEP due to coupling to the microcavity modal environment. Finally, the one-electron TSEP is extended, within the independent electron approximation, so as to include fractional band filling along with a constant-temperature-dependent and electron-density-dependent analysis; from this analysis, TSEP numerical estimates are projected at terahertz external field frequencies for a half-filled GaAs/AlGaAs SL miniband at zero temperature.

CONCERNING THE EQUATION OF STATE FOR A PARTIALLY IONIZED SYSTEM

I will discuss the expansion of various thermodynamic quantities about the ideal gas in powers of the electric charge, and I will discuss some cellular models. The first type of cellular model is appropriate for hydrogen. The second type is for Z &gt; 1. It has the independent electron approximation within the atoms. These models are cross compared and minimal regions of validity are determined. The actual region of validity is expected to be larger. In the cellular models, the phase boundaries for liquid-gas transitions are found. For the second type of cellular model, in the part of the low-temperature, low-density region where there is not much expectation of validity of these methods, a non-thermodynamic region is found. I have devised a construction, similar in spirit to the Maxwell construction, to bridge this region so as to leave a thermodynamically valid equation of state. The non-thermodynamic region does not occur in hydrogen and it seems to be due to the inadequacy of the aforementioned approximation in that region.

On the incorporation of local correlation effects into ionic solids

Two distinct means of introducing local correlation effects are considered here. In the first we develop a one center pseudopotential method, and apply it to the lowest excitons of the F and U centers in KCl and the newly measured core (1s) excitonic spectra of NiO. While the results obtained at the lowest truncation level are in good agreement with experiment, convergence is poor as higher terms are added, thus precluding general use of the method. In the second method, the solid is replaced by a cluster with appropriate boundary conditions, and correlation effects are treated by the independent electron pair approximation (IEPA). Application to the lowest exciton of LiF produces an energy of 12.6 eV (to which correlation contributes 2.5 eV) in good agreement with the experimental value of 12.5 eV.

Independent pair-potential correlated wave functions

An approximation for calculating the correlation energy is proposed which lies intermediate between the independent electron pair approximation and the total pair-excited variational wave function. In this approximation the correlation contribution from each electron is calculated separately by constructing wave functions which include all the pair excitations of an electron occupying a particular reference orbital and the remaining electrons in the system. These fragments are then summed in order to obtain the total correlation energy. Some illustrative calculations on boron hydride are discussed.

Infinite‐order functional for nonlinear parameters optimization in explicitly correlated coupled cluster theory

AbstractCoupled cluster (CC) calculations with Gaussian geminals rely heavily on extensive optimizations of nonlinear parameters (exponents and positions) defining the geminal basis functions. As the CC method is not a variational theory, it provides no functional for such an optimization. The nonlinear parameters must therefore be supplied by some other theory, giving pair functions that can be expected to be close to those of the CC method. The conventional approach thus far was to use the second‐order many‐body perturbation theory with Møller–Plesset partition of the Hamiltonian (MP2) for this purpose and to minimize the corresponding Hylleraas‐type functional. We present a new functional, which goes beyond the second order, and can be applied in situations when the Møller–Plesset theory converges slowly. This functional does take a partial account of infinite‐order terms in the MP theory, but neglects the interpair coupling in the spirit of the independent electron pair approximation approach. The pair functions minimizing this new functional include the most important infinite‐order contributions from the point of view of the MP theory and are much closer to the CC pair functions than the first‐order ones. The nonlinear parameters obtained using this infinite‐order functional are then better suited for coupled cluster calculations than those obtained using the MP2 functional. The effectiveness of the new functional is demonstrated by performing coupled cluster doubles (CCD) calculations for the Be atom and Li− ion. The obtained energies are much better than those based on the MP2 optimizations and represent the most accurate CCD energies for these systems obtained thus far. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009