Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

PubMed

Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

2014-02-15

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space.

PubMed

Jakobsen, Sofie; Jensen, Frank

2014-12-09

We assess the accuracy of force field (FF) electrostatics at several levels of approximation from the standard model using fixed partial charges to conformational specific multipole fits including up to quadrupole moments. Potential-derived point charges and multipoles are calculated using least-squares methods for a total of ∼1000 different conformations of the 20 natural amino acids. Opposed to standard charge fitting schemes the procedure presented in the current work employs fitting points placed on a single isodensity surface, since the electrostatic potential (ESP) on such a surface determines the ESP at all points outside this surface. We find that the effect of multipoles beyond partial atomic charges is of the same magnitude as the effect due to neglecting conformational dependency (i.e., polarizability), suggesting that the two effects should be included at the same level in FF development. The redundancy at both the partial charge and multipole levels of approximation is quantified. We present an algorithm which stepwise reduces or increases the dimensionality of the charge or multipole parameter space and provides an upper limit of the ESP error that can be obtained at a given truncation level. Thereby, we can identify a reduced set of multipole moments corresponding to ∼40% of the total number of multipoles. This subset of parameters provides a significant improvement in the representation of the ESP compared to the simple point charge model and close to the accuracy obtained using the complete multipole parameter space. The selection of the ∼40% most important multipole sites is highly transferable among different conformations, and we find that quadrupoles are of high importance for atoms involved in π-bonding, since the anisotropic electric field generated in such regions requires a large degree of flexibility.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

MC3, Version 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cawkwell, Marc Jon

2016-09-09

The MC3 code is used to perform Monte Carlo simulations in the isothermal-isobaric ensemble (constant number of particles, temperature, and pressure) on molecular crystals. The molecules within the periodic simulation cell are treated as rigid bodies, alleviating the requirement for a complex interatomic potential. Intermolecular interactions are described using generic, atom-centered pair potentials whose parameterization is taken from the literature [D. E. Williams, J. Comput. Chem., 22, 1154 (2001)] and electrostatic interactions arising from atom-centered, fixed, point partial charges. The primary uses of the MC3 code are the computation of i) the temperature and pressure dependence of lattice parameters andmore » thermal expansion coefficients, ii) tensors of elastic constants and compliances via the Parrinello and Rahman’s fluctuation formula [M. Parrinello and A. Rahman, J. Chem. Phys., 76, 2662 (1982)], and iii) the investigation of polymorphic phase transformations. The MC3 code is written in Fortran90 and requires LAPACK and BLAS linear algebra libraries to be linked during compilation. Computationally expensive loops are accelerated using OpenMP.« less

The effect of various quantum mechanically derived partial atomic charges on the bulk properties of chloride-based ionic liquids

NASA Astrophysics Data System (ADS)

Zolghadr, Amin Reza; Ghatee, Mohammad Hadi; Moosavi, Fatemeh

2016-08-01

Partial atomic charges using various quantum mechanical calculations for [Cnmim]Cl (n = 1, 4) ionic liquids (ILs) are obtained and used for development of molecular dynamics simulation (MD) force fields. The isolated ion pairs are optimized using HF, B3LYP, and MP2 methods for electronic structure with 6-311++G(d,p) basis set. Partial atomic charges are assigned to the atomic center with CHELPG and NBO methods. The effect of these sets of partial charges on the static and dynamic properties of ILs is evaluated by performing a series of MD simulations and comparing the essential thermodynamic properties with the available experimental data and available molecular dynamics simulation results. In contrast to the general trends reported for ionic liquids with BF4, PF6, and iodide anions (in which restrained electrostatic potential (RESP) charges are preferred), partial charges derived by B3LYP-NBO method are relatively good in prediction of the structural, dynamical, and thermodynamic energetic properties of the chloride based ILs.

Interactions of atomic hydrogen with amorphous SiO2

NASA Astrophysics Data System (ADS)

Yue, Yunliang; Wang, Jianwei; Zhang, Yuqi; Song, Yu; Zuo, Xu

2018-03-01

Dozens of models are investigated by the first-principles calculations to simulate the interactions of an atomic hydrogen with a defect-free random network of amorphous SiO2 (a-SiO2) and oxygen vacancies. A wide variety of stable configurations are discovered due to the disorder of a-SiO2, and their structures, charges, magnetic moments, spin densities, and density of states are calculated. The atomic hydrogen interacts with the defect-free a-SiO2 in positively or negatively charged state, and produces the structures absent in crystalline SiO2. It passivates the neutral oxygen vacancies and generates two neutral hydrogenated E‧ centers with different Si dangling bond projections. Electron spin resonance parameters, including Fermi contacts, and g-tensors, are calculated for these centers. The atomic hydrogen interacts with the positive oxygen vacancies in dimer configuration, and generate four different positive hydrogenated defects, two of which are puckered like the Eγ‧ centers. This research helps to understand the interactions between an atomic hydrogen, and defect-free a-SiO2 and oxygen vacancies, which may generate the hydrogen-complexed defects that play a key role in the degeneration of silicon/silica-based microelectronic devices.

Atomic masses 1993. The 1993 atomic mass evaluation

NASA Astrophysics Data System (ADS)

Audi, G.; Wapstra, A. H.

1993-11-01

The 1993 atomic mass evaluation by G. Audi and A.H. Wapstra is documented. The resulting data files containing recommended values of atomic masses, obtained by experiment of systematics, and related data such as reaction and separation energies are described. The data files can be obtained through online services from several nuclear data centers or on magnetic tape, free of charge.

A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges.

PubMed

Berente, Imre; Czinki, Eszter; Náray-Szabó, Gábor

2007-09-01

We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods. Copyright 2007 Wiley Periodicals, Inc.

Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

PubMed

Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

1995-03-01

We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain < 11% acidic lipid, the -25 mV equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase.

Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

PubMed Central

Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

1995-01-01

We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain < 11% acidic lipid, the -25 mV equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:7756540

An assessment for the erosion rate of DEMO first wall

NASA Astrophysics Data System (ADS)

Tokar, M. Z.

2018-01-01

In a fusion reactor a significant fraction of plasma particles lost from the confined volume will reach the vessel wall. The recombination of these charged species, electrons and ions of hydrogen isotopes, is a source of neutral molecules and atoms, recycling back into the plasma. Here they participate, in particular, in charge-exchange (c-x) collisions with the plasma ions and, as a result, atoms of high energies with chaotically oriented velocities are generated. A significant fraction of these hot neutrals will hit the wall, leading, as well as the outflowing fuel and impurity ions, to its erosion, limiting the reactor operation time. The rate of the wall erosion in DEMO is assessed by applying a one-dimensional model which takes into account the transport of charged and neutral species across the flux surfaces in the main part of the scrape-off layer, beyond the X-point vicinity and divertor, and by considering the shift of the centers of flux surfaces, their elongation and triangularity. Atoms generated by c-x of recycling neutrals are modeled kinetically to define firmly their energy spectrum, being of particular importance for the erosion assessment. It is demonstrated the erosion rate of the DEMO wall armor of tungsten will have a pronounced ballooning character with a significant maximum of 0.3 mm per full power year at the low field side, decreasing with an increase in the anomalous perpendicular transport in the ‘far’ SOL or the plasma density at the separatrix.

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

Multipolar electrostatics.

PubMed

Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

2014-06-14

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

Sc-Decorated Porous Graphene for High-Capacity Hydrogen Storage: First-Principles Calculations.

PubMed

Chen, Yuhong; Wang, Jing; Yuan, Lihua; Zhang, Meiling; Zhang, Cairong

2017-08-02

The generalized gradient approximation (GGA) function based on density functional theory is adopted to investigate the optimized geometrical structure, electron structure and hydrogen storage performance of Sc modified porous graphene (PG). It is found that the carbon ring center is the most stable adsorbed position for a single Sc atom on PG, and the maximum number of adsorbed H₂ molecules is four with the average adsorption energy of -0.429 eV/H₂. By adding a second Sc atom on the other side of the system, the hydrogen storage capacity of the system can be improved effectively. Two Sc atoms located on opposite sides of the PG carbon ring center hole is the most suitable hydrogen storage structure, and the hydrogen storage capacity reach a maximum 9.09 wt % at the average adsorption energy of -0.296 eV/H₂. The adsorption of H₂ molecules in the PG system is mainly attributed to orbital hybridization among H, Sc, and C atoms, and Coulomb attraction between negatively charged H₂ molecules and positively charged Sc atoms.

Sc-Decorated Porous Graphene for High-Capacity Hydrogen Storage: First-Principles Calculations

PubMed Central

Chen, Yuhong; Wang, Jing; Yuan, Lihua; Zhang, Meiling

2017-01-01

The generalized gradient approximation (GGA) function based on density functional theory is adopted to investigate the optimized geometrical structure, electron structure and hydrogen storage performance of Sc modified porous graphene (PG). It is found that the carbon ring center is the most stable adsorbed position for a single Sc atom on PG, and the maximum number of adsorbed H2 molecules is four with the average adsorption energy of −0.429 eV/H2. By adding a second Sc atom on the other side of the system, the hydrogen storage capacity of the system can be improved effectively. Two Sc atoms located on opposite sides of the PG carbon ring center hole is the most suitable hydrogen storage structure, and the hydrogen storage capacity reach a maximum 9.09 wt % at the average adsorption energy of −0.296 eV/H2. The adsorption of H2 molecules in the PG system is mainly attributed to orbital hybridization among H, Sc, and C atoms, and Coulomb attraction between negatively charged H2 molecules and positively charged Sc atoms. PMID:28767084

Geometry-dependent distributed polarizability models for the water molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.

2016-01-21

Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successivelymore » occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.« less

High-energy e- /e+ spectrometer via coherent interaction in a bent crystal

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo; Howard, Alexander

2018-01-01

We propose a novel spectrometer based on the crystal channeling effect capable of discriminating between positive and negative particles well beyond the TeV energy scale. The atomic order of a crystalline structure generates an electrostatic field built up by all the atoms in the crystals, which confines charged particle trajectories between neighbouring atomic planes. Through such an interaction in a tiny curved crystal, the same dynamical action on the highest energy particles as that of a huge superconducting magnet is achieved. Depending on the charge sign, points of equilibrium of the oscillatory motion under channeling lie between or on atomic planes for positive and negative particles, respectively, forcing positive particles to stably oscillate far from the planes, while negative ones repeatedly cross them. The different interaction rate with atomic planes causes a tremendous discrepancy between the deflection efficiency of positive and negative particles under channeling. We suggest the use of interactions between charged particles and oriented bent crystals as a novel non-cryogenic passive charge spectrometer to aid the search for dark matter in the Universe in satellite-borne experiment. The limited angular acceptance makes this technique particularly suited for directional local sources of energetic charged particles.

Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa.

PubMed

Chamorro, Ester R; Sequeira, Alfredo F; Zalazar, M Fernanda; Peruchena, Nélida M

2008-09-15

In the present work, the distribution of the electronic charge density of the natural sex pheromone, the (Z)-13-hexadecen-11-ynyl acetate, in the female processionary moth, Thaumetopoea pytiocampa, and its nine analogue derivatives was studied within the framework of the Density Functional Theory and the Atoms in Molecules (AIM) Theory at B3LYP/6-31G *//B3LYP/6-31++G * * level. Additionally, molecular electrostatic potential (MEP) maps of the previously mentioned compounds were computed and compared. Furthermore, the substitution of hydrogen atoms from the methyl group in the acetate group by electron withdrawing substituents (i.e., halogen atoms) as well as the replacement effect of hydrogen by electron donor substituents (+I effect) as methyl group, were explored. The key feature of the topological distribution of the charge density in analogue compounds, such as the variations of the topological properties encountered in the region formed by neighbouring atoms from the substitution site were presented and discussed. Using topological parameters, such as electronic charge density, Laplacian, kinetic energy density, and potential energy density evaluated at bond critical points (BCP), we provide here a detailed analysis of the nature of the chemical bonding of these molecules. In addition, the atomic properties (population, charge, energy, volume, and dipole moment) were determined on selected atoms. These properties were analyzed at the substitution site (with respect to the natural sex pheromone) and related to the biological activity and to the possible binding site with the pheromone binding protein, (PBP). Moreover, the Laplacian function of the electronic density was used to locate electrophilic regions susceptible to be attacked (by deficient electron atoms or donor hydrogen). Our results indicate that the change in the atomic properties, such as electronic population and atomic volume, are sensitive indicators of the loss of the biological activity in the analogues studied here. The crucial interaction between the acetate group of the natural sex pheromone and the PBP is most likely to be a hydrogen bonding and the substitution of hydrogen atoms by electronegative atoms in the pheromone molecule reduces the hydrogen acceptor capacity. This situation is mirrored by the diminish of the electronic population on carbon and oxygen atoms at the carbonylic group in the halo-acetate group. Additionally, the modified acetate group (with electronegative atoms) shows new charge concentration critical points or regions of concentration of charge density in which an electrophilic attack can also occur. Finally, the use of the topological analysis based in the charge density distribution and its Laplacian function, in conjunction with MEP maps provides valuable information about the steric volume and electronic requirement of the sex pheromone for binding to the PBP.

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE PAGES

Tillack, Andreas F.; Robinson, Bruce H.

2017-06-05

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tillack, Andreas F.; Robinson, Bruce H.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Charged dopants in neutral supercells through substitutional donor (acceptor): nitrogen donor charging of the nitrogen-vacancy center in diamond

NASA Astrophysics Data System (ADS)

Löfgren, Robin; Pawar, Ravinder; Öberg, Sven; Larsson, J. Andreas

2018-02-01

Charged defects are traditionally computed by adding (subtracting) electrons for negative (positive) impurities. When using periodic boundary conditions this results in artificially charged supercells that also require a compensating background charge of the opposite sign, which makes slab supercells problematic because of an arbitrary dependence on the vacuum thickness. In this work, we test the method of using neutral supercells through the use of a substitutional electron donor (acceptor) to describe charged systems. We use density functional theory (DFT) to compare the effects of charging the well-studied NV-center in diamond by a substitutional donor nitrogen. We investigate the influence of the donor-N on the NV-center properties as a function of the distance between them, and find that they converge toward those obtained when adding an electron. We analyze the spin density and conclude that the donor-N has a zero magnetic moment, and thus, will not be seen in electron spin resonance. We validate our DFT energies through comparison to GW simulations. Charging the NV-center with a substitutional donor-N enables accurate calculations of slabs, without the ambiguity of using charged supercells. Implantation of donor-N atoms opens up the possibility to engineer NV-centers with the desired charge state for future ICT and sensor applications.

A valence bond study of three-center four-electron pi bonding: electronegativity vs electroneutrality.

PubMed

DeBlase, Andrew; Licata, Megan; Galbraith, John Morrison

2008-12-18

Three-center four-electron (3c4e) pi bonding systems analogous to that of the ozone molecule have been studied using modern valence bond theory. Molecules studied herein consist of combinations of first row atoms C, N, and O with the addition of H atoms where appropriate in order to preserve the 3c4e pi system. Breathing orbital valence bond (BOVB) calculations were preformed at the B3LYP/6-31G**-optimized geometries in order to determine structural weights, pi charge distributions, resonance energies, and pi bond energies. It is found that the most weighted VB structure depends on atomic electronegativity and charge distribution, with electronegativity as the dominant factor. By nature, these systems are delocalized, and therefore, resonance energy is the main contributor to pi bond energies. Molecules with a single dominant VB structure have low resonance energies and therefore low pi bond energies.

Parametrization of semiempirical models against ab initio crystal data: evaluation of lattice energies of nitrate salts.

PubMed

Beaucamp, Sylvain; Mathieu, Didier; Agafonov, Viatcheslav

2005-09-01

A method to estimate the lattice energies E(latt) of nitrate salts is put forward. First, E(latt) is approximated by its electrostatic component E(elec). Then, E(elec) is correlated with Mulliken atomic charges calculated on the species that make up the crystal, using a simple equation involving two empirical parameters. The latter are fitted against point charge estimates of E(elec) computed on available X-ray structures of nitrate crystals. The correlation thus obtained yields lattice energies within 0.5 kJ/g from point charge values. A further assessment of the method against experimental data suggests that the main source of error arises from the point charge approximation.

Effects of external stress field on the charge stability of nitrogen vacancy centers in diamond

NASA Astrophysics Data System (ADS)

Yao, Miao-Miao; Zhu, Tian-Yuan; Shu, Da-Jun

2017-07-01

The interaction of the atom-like defects in semiconductors with external fields provides an avenue to quantum information processing and nanoscale sensors. Meanwhile, external fields may induce instability of the desired charge state of the defects. It is essential to understand how the charge state of a defect is affected by external fields that introduced in diverse applications. In this letter, we explore the stability of the negatively charged state (NV-) and the neutral state (NV0) of the nitrogen vacancy (NV) center in diamond under stress by first-principles calculations. We find that the relative stability of NV- to NV0 is always reduced by the stress if the NV center is free to relax its orientation. Once the NV center has formed and retains its orientation, however, the relative stability of NV- can be always enhanced by compressive stress along its trigonal symmetry axis. We believe that the results are not only significant for control of the charge stability of NV center but also enlightening for applications based on specific charge states of other kinds of defects in the stress field.

Two-parameter partially correlated ground-state electron density of some light spherical atoms from Hartree-Fock theory with nonintegral nuclear charge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cordero, Nicolas A.; March, Norman H.; Alonso, Julio A.

2007-05-15

Partially correlated ground-state electron densities for some spherical light atoms are calculated, into which nonrelativistic ionization potentials represent essential input data. The nuclear cusp condition of Kato is satisfied precisely. The basic theoretical starting point, however, is Hartree-Fock (HF) theory for the N electrons under consideration but with nonintegral nuclear charge Z{sup '} slightly different from the atomic number Z (=N). This HF density is scaled with a parameter {lambda}, near to unity, to preserve normalization. Finally, some tests are performed on the densities for the atoms Ne and Ar, as well as for Be and Mg.

Piezospectroscopy and first-principles calculations of the nitrogen-vacancy center in gallium arsenide

NASA Astrophysics Data System (ADS)

Kovac, Nicola; Künneth, Christopher; Alt, Hans Christian

2018-04-01

The nitrogen-vacancy (NV) center occurs in GaAs bulk crystals doped or implanted with nitrogen. The local vibration of nitrogen gives rise to a sharp infrared absorption band at 638 cm-1, exhibiting a fine structure due to the different masses of neighboring 69Ga and 71Ga host isotopes. Piezospectroscopic investigations in the crystallographic ⟨ 100 ⟩ direction prove that the center has C3v point symmetry, which is weakly perturbed by the isotope effect. The stress-induced shifts of some band components show an unusual non-linear behavior that can be explained by coupling between the isotope and the stress splitting. First-principles density-functional theory calculations are in full accordance with the experiments and confirm the C3v symmetry, caused by relaxation of the nitrogen atom from the anion lattice site towards the nearest-neighbor Ga plane. Furthermore, the calculations indicate the -3 charge state of the center as the most stable one for nearly all Fermi level positions. The NV center in GaAs is structurally analogous to the same center in diamond.

Surface charge features of kaolinite particles and their interactions

NASA Astrophysics Data System (ADS)

Gupta, Vishal

Kaolinite is both a blessing and a curse. As an important industrial mineral commodity, kaolinite clays are extensively used in the paper, ceramic, paint, plastic and rubber industries. In all these applications the wettability, aggregation, dispersion, flotation and thickening of kaolinite particles are affected by its crystal structure and surface properties. It is therefore the objective of this research to investigate selected physical and surface chemical properties of kaolinite, specifically the surface charge of kaolinite particles. A pool of advanced analytical techniques such as XRD, XRF, SEM, AFM, FTIR and ISS were utilized to investigate the morphological and surface chemistry features of kaolinite. Surface force measurements revealed that the silica tetrahedral face of kaolinite is negatively charged at pH>4, whereas the alumina octahedral face of kaolinite is positively charged at pH<6, and negatively charged at pH>8. Based on electrophoresis measurements, the apparent iso-electric point for kaolinite particles was determined to be less than pH 3. In contrast, the point of zero charge was determined to be pH 4.5 by titration techniques, which corresponds to the iso-electric point of between pH 4 and 5 as determined by surface force measurements. Results from kaolinite particle interactions indicate that the silica face--alumina face interaction is dominant for kaolinite particle aggregation at low and intermediate pH values, which explains the maximum shear yield stress at pH 5-5.5. Lattice resolution images reveal the hexagonal lattice structure of these two face surfaces of kaolinite. Analysis of the silica face of kaolinite showed that the center of the hexagonal ring of oxygen atoms is vacant, whereas the alumina face showed that the hexagonal surface lattice ring of hydroxyls surround another hydroxyl in the center of the ring. High resolution transmission electron microscopy investigation of kaolinite has indicated that kaolinite is indeed composed of silica/alumina bilayers with a c-spacing of 7.2 A. The surface charge densities of the silica face, the alumina face and the edge surface of kaolinite all influence particle interactions, and thereby affect the mechanical properties of kaolinite suspensions. The improved knowledge of kaolinite surface chemistry from this dissertation research provides a foundation for the development of improved process strategies for both the use and disposal of clay particles such as kaolinite.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richard, P.

The study of inelastic collision phenomena with highly charged projectile ions and the interpretation of spectral features resulting from these collisions remain as the major focal points in the atomic physics research at the J.R. Macdonald Laboratory, Kansas State University, Manhattan, Kansas. The title of the research project, ``Atomic Physics with Highly Charged Ions,`` speaks to these points. The experimental work in the past few years has divided into collisions at high velocity using the primary beams from the tandem and LINAC accelerators and collisions at low velocity using the CRYEBIS facility. Theoretical calculations have been performed to accurately describemore » inelastic scattering processes of the one-electron and many-electron type, and to accurately predict atomic transition energies and intensities for x rays and Auger electrons. Brief research summaries are given for the following: (1) electron production in ion-atom collisions; (2) role of electron-electron interactions in two-electron processes; (3) multi-electron processes; (4) collisions with excited, aligned, Rydberg targets; (5) ion-ion collisions; (6) ion-molecule collisions; (7) ion-atom collision theory; and (8) ion-surface interactions.« less

Ab initio scanning tunneling spectroscopy simulation of graphene with metal adatoms: weak and strong coupling regimes

NASA Astrophysics Data System (ADS)

Kim, Gunn; Parq, Jae-Hyeon; Yu, Jaejun; Kwon, Young-Kyun; Kyung Hee University Collaboration; Seoul National University Collaboration

2011-03-01

Metal atoms on graphene, when ionized, can act as a point-charge impurity to probe a charge response of graphene with the Dirac cone band structure. To understand charge and spin polarization in graphene, we present scanning tunneling spectroscopy STS simulations based on density-functional theory calculations. We find that a Cs atom on graphene is fully ionized with a significant band-bending feature in the STS whereas the charge and magnetic states of Ba and La atoms on graphene appear to be complicated due to orbital hybridization and Coulomb interaction. By applying external electric field, we observe changes in charge donations and spin magnetic moments of the metal adsorbates on graphene. This work was supported by the National Research Foundation of Korea through the ARP (Grant No. R17-2008-033- 01000-0) (J.Y.) and the Basic Science Research Program through the NRF of Korea (Grant No. 2010-0007805) (G.K.).

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Lattice distortion and electron charge redistribution induced by defects in graphene

DOE PAGES

Zhang, Wei; Lu, Wen -Cai; Zhang, Hong -Xing; ...

2016-09-14

Lattice distortion and electronic charge localization induced by vacancy and embedded-atom defects in graphene were studied by tight-binding (TB) calculations using the recently developed three-center TB potential model. We showed that the formation energies of the defects are strongly correlated with the number of dangling bonds and number of embedded atoms, as well as the magnitude of the graphene lattice distortion induced by the defects. Lastly, we also showed that the defects introduce localized electronic states in the graphene which would affect the electron transport properties of graphene.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

PubMed

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase

NASA Astrophysics Data System (ADS)

Golden, Emily; Yu, Li-Juan; Meilleur, Flora; Blakeley, Matthew P.; Duff, Anthony P.; Karton, Amir; Vrielink, Alice

2017-01-01

The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.

Long-range Coulomb forces and localized bonds.

PubMed

Preiser; Lösel; Brown; Kunz; Skowron

1999-10-01

The ionic model is shown to be applicable to all compounds in which the atoms carry a net charge and their electron density is spherically symmetric regardless of the covalent character of the bonding. By examining the electric field generated by an array of point charges placed at the positions of the ions in over 40 inorganic compounds, we show that the Coulomb field naturally partitions itself into localized regions (bonds) which are characterized by the electric flux that links neighbouring ions of opposite charge. This flux is identified with the bond valence, and Gauss' law with the valence-sum rule, providing a secure theoretical foundation for the bond-valence model. The localization of the Coulomb field provides an unambiguous definition of coordination number and our calculations show that, in addition to the expected primary coordination sphere, there are a number of weak bonds between cations and the anions in the second coordination sphere. Long-range Coulomb interactions are transmitted through the crystal by the application of Gauss' law at each of the intermediate atoms. Bond fluxes have also been calculated for compounds containing ions with non-spherical electron densities (e.g. cations with stereoactive lone electron pairs). In these cases the point-charge model continues to describe the distant field, but multipoles must be added to the point charges to give the correct local field.

Fission gas in thoria

NASA Astrophysics Data System (ADS)

Kuganathan, Navaratnarajah; Ghosh, Partha S.; Galvin, Conor O. T.; Arya, Ashok K.; Dutta, Bijon K.; Dey, Gautam K.; Grimes, Robin W.

2017-03-01

The fission gases Xe and Kr, formed during normal reactor operation, are known to degrade fuel performance, particularly at high burn-up. Using first-principles density functional theory together with a dispersion correction (DFT + D), in ThO2 we calculate the energetics of neutral and charged point defects, the di-vacancy (DV), different neutral tri-vacancies (NTV), the charged tetravacancy (CTV) defect cluster geometries and their interaction with Xe and Kr. The most favourable incorporation point defect site for Xe or Kr in defective ThO2 is the fully charged thorium vacancy. The lowest energy NTV in larger supercells of ThO2 is NTV3, however, a single Xe atom is most stable when accommodated within a NTV1. The di-vacancy (DV) is a significantly less favoured incorporation site than the NTV1 but the CTV offers about the same incorporation energy. Incorporation of a second gas atom in a NTV is a high energy process and more unfavourable than accommodation within an existing Th vacancy. The bi-NTV (BNTV) cluster geometry studied will accommodate one or two gas atoms with low incorporation energies but the addition of a third gas atom incurs a high energy penalty. The tri-NTV cluster (TNTV) forms a larger space which accommodates three gas atoms but again there is a penalty to accommodate a fourth gas atom. By considering the energy to form the defect sites, solution energies were generated showing that in ThO2-x the most favourable solution equilibrium site is the NTV1 while in ThO2 it is the DV.

Topology of charge density of flucytosine and related molecules and characteristics of their bond charge distributions.

PubMed

Murgich, Juan; Franco, Héctor J; San-Blas, Gioconda

2006-08-24

The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.

The role of the anionic and cationic pt sites in the adsorption site preference of water and ethanol on defected Pt4/Pt(111) substrates: A density functional theory investigation within the D3 van der waals corrections

NASA Astrophysics Data System (ADS)

Seminovski, Yohanna; Amaral, Rafael C.; Tereshchuk, Polina; Da Silva, Juarez L. F.

2018-01-01

Platinum (Pt) atoms in the bulk face-centered cubic structure have neutral charge because they are equivalent by symmetry, however, in clean Pt surfaces, the effective charge on Pt atoms can turn slightly negative (anionic) or positive (cationic) while increasing substantially in magnitude for defected (low-coordinated) Pt sites. The effective charge affect the adsorption properties of molecular species on Pt surfaces and it can compete in importance with the coupling of the substrate-molecule electronic states. Although several studies have been reported due to the importance of Pt for catalysis, our understanding of the role played by low-coordinated sites is still limited. Here, we employ density functional theory within the Perdew-Burke-Ernzerhof exchange-correlation functional and the D3 van der Waals (vdW) correction to investigate the role of the cationic and anionic Pt sites on the adsorption properties of ethanol and water on defected Pt4/Pt(111) substrates. Four substrates were carefully selected, namely, two two-dimensional (2D) Pt4 configurations (2D-strand and 2D-island) and two tri-dimensional (3D) Pt4 (3D-fcc and 3D-hcp), to understand the role of coordination, effective charge, and coupling of the electronic states in the adsorption properties. From the Bader charge analysis, we identified the cationic and anionic sites among the Pt atoms exposed to the vacuum region in the Pt4/Pt(111) substrates. We found that ethanol and water bind via the anionic O atoms to the low-coordinated defected Pt sites of the substrates, where the angle PtOH is nearly 100° for most configurations. In the 3D-fcc or 3D-hcp defected configurations, the lowest-coordinated Pt atoms are anionic, hence, those Pt sites are not preferable for the adsorption of O atoms. The charge transfer from water and ethanol to the Pt substrates has similar magnitude for all cases, which implies similar Coulomb contribution to the adsorption energy. Moreover, we found a correlation of the adsorption energy with the shift of the center of gravity of the occupied d-states of Pt sites.

Excess-Si related defect centers in buried SiO2 thin films

NASA Astrophysics Data System (ADS)

Warren, W. L.; Fleetwood, D. M.; Shaneyfelt, M. R.; Schwank, J. R.; Winokur, P. S.; Devine, R. A. B.

1993-06-01

Using electron paramagnetic resonance (EPR) and capacitance-voltage measurements we have investigated the role of excess-silicon related defect centers as charge traps in separation by the implantation of oxygen materials. Three types of EPR-active centers were investigated: oxygen vacancy Eγ' centers (O3≡Si• +Si≡O3), delocalized Eδ' centers, and D centers (Si3≡Si•). It was found that all of these paramagnetic centers are created by selective hole injection, and are reasonably ascribed as positively charged when paramagnetic. These results provide the first experimental evidence for (1) the charge state of the Eδ' center, and (2) that the D center is an electrically active point defect in these materials.

Experimental observation of charge-shift bond in fluorite CaF2.

PubMed

Stachowicz, Marcin; Malinska, Maura; Parafiniuk, Jan; Woźniak, Krzysztof

2017-08-01

On the basis of a multipole refinement of single-crystal X-ray diffraction data collected using an Ag source at 90 K to a resolution of 1.63 Å -1 , a quantitative experimental charge density distribution has been obtained for fluorite (CaF 2 ). The atoms-in-molecules integrated experimental charges for Ca 2+ and F - ions are +1.40 e and -0.70 e, respectively. The derived electron-density distribution, maximum electron-density paths, interaction lines and bond critical points along Ca 2+ ...F - and F - ...F - contacts revealed the character of these interactions. The Ca 2+ ...F - interaction is clearly a closed shell and ionic in character. However, the F - ...F - interaction has properties associated with the recently recognized type of interaction referred to as `charge-shift' bonding. This conclusion is supported by the topology of the electron localization function and analysis of the quantum theory of atoms in molecules and crystals topological parameters. The Ca 2+ ...F - bonded radii - measured as distances from the centre of the ion to the critical point - are 1.21 Å for the Ca 2+ cation and 1.15 Å for the F - anion. These values are in a good agreement with the corresponding Shannon ionic radii. The F - ...F - bond path and bond critical point is also found in the CaF 2 crystal structure. According to the quantum theory of atoms in molecules and crystals, this interaction is attractive in character. This is additionally supported by the topology of non-covalent interactions based on the reduced density gradient.

Photoelectron spectroscopy of color centers in negatively charged cesium iodide nanocrystals

NASA Astrophysics Data System (ADS)

Sarkas, Harry W.; Kidder, Linda H.; Bowen, Kit H.

1995-01-01

We present the photoelectron spectra of negatively charged cesium iodide nanocrystals recorded using 2.540 eV photons. The species examined were produced using an inert gas condensation cluster ion source, and they ranged in size from (CsI)-n=13 to nanocrystal anions comprised of 330 atoms. Nanocrystals showing two distinct types of photoemission behavior were observed. For (CsI)-n=13 and (CsI)-n=36-165, a plot of cluster anion photodetachment threshold energies vs n-1/3 gives a straight line extrapolating (at n-1/3=0, i.e., n=∞) to 2.2 eV, the photoelectric threshold energy for F centers in bulk cesium iodide. The linear extrapolation of the cluster anion data to the corresponding bulk property implies that the electron localization in these gas-phase nanocrystals is qualitatively similar to that of F centers in extended alkali halide crystals. These negatively charged cesium iodide nanocrystals are thus shown to support embryonic forms of F centers, which mature with increasing cluster size toward condensed phase impurity centers. Under an alternative set of source conditions, nanocrystals were produced which showed significantly lower photodetachment thresholds than the aforementioned F-center cluster anions. For these species, containing 83-131 atoms, a plot of their cluster anion photodetachment threshold energies versus n-1/3 gives a straight line which extrapolates to 1.4 eV. This value is in accord with the expected photoelectric threshold energy for F' centers in bulk cesium iodide, i.e., color centers with two excess electrons in a single defect site. These nanocrystals are interpreted to be the embryonic F'-center containing species, Cs(CsI)-n=41-65.

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

A numerical study on liquid charging inside electrostatic atomizers

NASA Astrophysics Data System (ADS)

Kashir, Babak; Perri, Anthony; Sankaran, Abhilash; Staszel, Christopher; Yarin, Alexander; Mashayek, Farzad

2016-11-01

The charging of the dielectric liquid inside an electrostatic atomizer is studied numerically by developing codes based on the OpenFOAM platform. Electrostatic atomization is an appealing technology in painting, fuel injection and oil coating systems due to improved particle-size distribution, enhanced controlability of droplets' trajectories and lower power consumption. The numerical study is conducted concurrently to an experimental investigation to facilitate the validation and deliver feedback for further development. The atomizer includes a pin electrode that is placed at the center of a converging chamber. The chamber orifice is located at a known distance from the electrode tip. The pin electrode is connected to a high voltage that leads to the charging of the liquid. In the present work, the theoretical foundations of separated treatment of the polarized layer and the electronuetral bulk flow are set by describing the governing equations, relevant boundary conditions and the matching condition between these two domains. The resulting split domains are solved numerically to find the distribution of velocity and electrostatic fields over the specified regions. National Science Foundation Award Number: 1505276.

Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline.

PubMed

Jarzembska, Katarzyna N; Kamiński, Radosław; Durka, Krzysztof; Woźniak, Krzysztof

2018-05-10

This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å -1 ) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.

Numerology, hydrogenic levels, and the ordering of excited states in one-electron atoms

NASA Astrophysics Data System (ADS)

Armstrong, Lloyd, Jr.

1982-03-01

We show that the observed ordering of Rydberg states of one-electron atoms can be understood by assuming that these states are basically hydrogenic in nature. Much of the confusion concerning this point is shown to arise from the failure to differentiate between hydrogenic ordering as the nuclear charge approaches infinity, and hydrogenic ordering for an effective charge of one. The origin of κ ordering of Rydberg levels suggested by Sternheimer is considered within this picture, and the predictions of κ ordering are compared with those obtained by assuming hydrogenic ordering.

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Quantized conductance operation near a single-atom point contact in a polymer-based atomic switch

NASA Astrophysics Data System (ADS)

Krishnan, Karthik; Muruganathan, Manoharan; Tsuruoka, Tohru; Mizuta, Hiroshi; Aono, Masakazu

2017-06-01

Highly-controlled conductance quantization is achieved near a single-atom point contact in a redox-based atomic switch device, in which a poly(ethylene oxide) (PEO) film is sandwiched between Ag and Pt electrodes. Current-voltage measurements revealed reproducible quantized conductance of ˜1G 0 for more than 102 continuous voltage sweep cycles under a specific condition, indicating the formation of a well-defined single-atom point contact of Ag in the PEO matrix. The device exhibited a conductance state distribution centered at 1G 0, with distinct half-integer multiples of G 0 and small fractional variations. First-principles density functional theory simulations showed that the experimental observations could be explained by the existence of a tunneling gap and the structural rearrangement of an atomic point contact.

Quantum Error Correction with a Globally-Coupled Array of Neutral Atom Qubits

DTIC Science & Technology

2013-02-01

magneto - optical trap ) located at the center of the science cell. Fluorescence...Bottle beam trap GBA Gaussian beam array EMCCD electron multiplying charge coupled device microsec. microsecond MOT Magneto - optical trap QEC quantum error correction qubit quantum bit ...developed and implemented an array of neutral atom qubits in optical traps for studies of quantum error correction. At the end of the three year

Resolution of identity approximation for the Coulomb term in molecular and periodic systems.

PubMed

Burow, Asbjörn M; Sierka, Marek; Mohamed, Fawzi

2009-12-07

A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 muhartree per atom, for both molecular and periodic systems.

Resolution of identity approximation for the Coulomb term in molecular and periodic systems

NASA Astrophysics Data System (ADS)

Burow, Asbjörn M.; Sierka, Marek; Mohamed, Fawzi

2009-12-01

A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Jia, E-mail: jia-zhu@jxnu.edu.cn, E-mail: zhangyf@fzu.edu.cn; Zhang, Hui; Tong, Yawen

The structures and electronic properties of bimetallic oxide CrW{sub 2}O{sub 9} clusters supported on the perfect and defective MgO(001) surfaces with three different color centers, F{sub S}{sup 0}, F{sub S}{sup +}, and F{sub S}{sup 2+} centers, respectively, have been investigated by density functional theory calculations. Our results show that the configurations, adsorption energies, charge transfers, and bonding modes of dispersed CrW{sub 2}O{sub 9} clusters are sensitive to the charge states of the F{sub S} centers. Compared with the gas-phase configuration, the CrW{sub 2}O{sub 9} clusters supported on the defective surfaces are distorted dramatically, which exhibit different chain structures. On themore » perfect MgO surface, the depositions of clusters do not involve obvious charge transfer, while the situation is quite different on the defective MgO(001) surfaces in which significant electron transfer occurs from the surface to the cluster. Interestingly, this effect becomes more remarkable for electron-rich oxygen vacancies (F{sub S}{sup 0} center) than that for electron-poor oxygen vacancies (F{sub S}{sup +} and F{sub S}{sup 2+} centers). Furthermore, our work reveals a progressive Brønsted acid sites where spin density preferentially localized around the Cr atoms not the W atoms for all kinds of F{sub S}-centers, indicating the better catalytic activities can be expected for CrW{sub 2}O{sub 9} cluster on defective MgO(001) surfaces with respect to the W{sub 3}O{sub 9} cluster.« less

Molybdenum-oxide based unique polyprotic nanoacids showing different deprotonations and related assembly processes in solution.

PubMed

Kistler, Melissa L; Liu, Tianbo; Gouzerh, Pierre; Todea, Ana Maria; Müller, Achim

2009-07-14

We report the self-assembly processes in solution of three Keplerate-type molybdenum-oxide based clusters {Mo72V30}, {Mo72Cr30} and {Mo72Fe30} (all with diameters of approximately 2.5 nm). These clusters behave as unique weak polyprotic acids owing to the external water ligands attached to the non-Mo metal centers. Whereas the Cr and Fe clusters have 30 water ligands attached at the 30 M3+ centers pointing outside, {Mo72V30} has 20 water ligands coordinated to vanadium atoms, of which only 10 are pointing outside. The self-assembly processes of the Keplerates leading to supramolecular blackberry-type structures are influenced by the effective charge densities on the cluster surfaces, which can be tuned by the pH values and solvent properties. As expected, {Mo72Cr30} and {Mo72Fe30} behave similarly in aqueous solution due to their analogous structures and in both cases the self-assembly follows the partial deprotonation of the external water ligands attached to the non-Mo metal centers. However, the M-OH2 functionalities differ not only in acidity but also lability, i.e. in different residence times of the H2O ligands. In contrast to {Mo72Cr30} and {Mo72Fe30}, the {Mo72V30} clusters carry a rather large number of negative charges so that their solution properties are different. They exist as discrete macroions in dilute aqueous solution, and form only in mixed water/organic solvent (like acetone) blackberry-type structures whose size increases with acetone content. The comparison of the properties of the clusters allows more general information about the interesting self-assembly phenomenon to be unveiled.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations. PMID:25290376

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.

Atomic-scale diffractive imaging of sub-cycle electron dynamics in condensed matter

PubMed Central

Yakovlev, Vladislav S.; Stockman, Mark I.; Krausz, Ferenc; Baum, Peter

2015-01-01

For interaction of light with condensed-matter systems, we show with simulations that ultrafast electron and X-ray diffraction can provide a time-dependent record of charge-density maps with sub-cycle and atomic-scale resolutions. Using graphene as an example material, we predict that diffraction can reveal localised atomic-scale origins of optical and electronic phenomena. In particular, we point out nontrivial relations between microscopic electric current and density in undoped graphene. PMID:26412407

Atomic-scale diffractive imaging of sub-cycle electron dynamics in condensed matter

DOE PAGES

Yakovlev, Vladislav S.; Stockman, Mark I.; Krausz, Ferenc; ...

2015-09-28

For interaction of light with condensed-matter systems, we show with simulations that ultrafast electron and X-ray diffraction can provide a time-dependent record of charge-density maps with sub-cycle and atomic-scale resolutions. Using graphene as an example material, we predict that diffraction can reveal localised atomic-scale origins of optical and electronic phenomena. Here, we point out nontrivial relations between microscopic electric current and density in undoped graphene.

Interaction of a magnet and a point charge: Unrecognized internal electromagnetic momentum

NASA Astrophysics Data System (ADS)

Boyer, Timothy H.

2015-05-01

Whereas nonrelativistic mechanics always connects the total momentum of a system to the motion of the center of mass, relativistic systems, such as interacting electromagnetic charges, can have internal linear momentum in the absence of motion of the system's center of energy. This internal linear momentum of a system is related to the controversial concept of "hidden momentum." We suggest that the term "hidden momentum" be abandoned. Here, we use the relativistic conservation law for the center of energy to give an unambiguous definition of the "internal momentum of a system," and then we exhibit this internal momentum for the system of a magnet (modeled as a circular ring of moving charges) and a distant static point charge. The calculations provide clear illustrations of this system for three cases: (a) the moving charges of the magnet are assumed to continue in their unperturbed motion; (b) the moving charges of the magnet are free to accelerate but have no mutual interactions; and (c) the moving charges of the magnet are free to accelerate and also interact with each other. When the current-carrying charges of the magnet are allowed to interact, the magnet itself will contain internal electromagnetic linear momentum, something that has not been described clearly in the research and teaching literature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orlenko, E. V., E-mail: eorlenko@mail.ru; Evstafev, A. V.; Orlenko, F. E.

A formalism of exchange perturbation theory (EPT) is developed for the case of interactions that explicitly depend on time. Corrections to the wave function obtained in any order of perturbation theory and represented in an invariant form include exchange contributions due to intercenter electron permutations in complex multicenter systems. For collisions of atomic systems with an arbitrary type of interaction, general expressions are obtained for the transfer (T) and scattering (S) matrices in which intercenter electron permutations between overlapping nonorthogonal states belonging to different centers (atoms) are consistently taken into account. The problem of collision of alpha particles with lithiummore » atoms accompanied by the redistribution of electrons between centers is considered. The differential and total charge-exchange cross sections of lithium are calculated.« less

Theoretical assessment of the disparity in the electrostatic forces between two point charges and two conductive spheres of equal radii

NASA Astrophysics Data System (ADS)

Kolikov, Kiril

2016-11-01

The Coulomb's formula for the force FC of electrostatic interaction between two point charges is well known. In reality, however, interactions occur not between point charges, but between charged bodies of certain geometric form, size and physical structure. This leads to deviation of the estimated force FC from the real force F of electrostatic interaction, thus imposing the task to evaluate the disparity. In the present paper the problem is being solved theoretically for two charged conductive spheres of equal radii and arbitrary electric charges. Assessment of the deviation is given as a function of the ratio of the distance R between the spheres centers to the sum of their radii. For the purpose, relations between FC and F derived in a preceding work of ours, are employed to generalize the Coulomb's interactions. At relatively short distances between the spheres, the Coulomb force FC, as estimated to be induced by charges situated at the centers of the spheres, differ significantly from the real force F of interaction between the spheres. In the case of zero and non-zero charge we prove that with increasing the distance between the two spheres, the force F decrease rapidly, virtually to zero values, i.e. it appears to be short-acting force.

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

PubMed

Yang, Zhong-Zhi; Wu, Yang; Zhao, Dong-Xia

2004-02-08

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

Effects of axial coordination on immobilized Mn(salen) catalysts.

PubMed

Teixeira, Filipe; Mosquera, Ricardo A; Melo, André; Freire, Cristina; Cordeiro, M Natália D S

2014-11-13

The consequences of anchoring Mn(salen) catalysts onto a supporting material using one of the vacant positions of the metal center are tackled by studying several Mn(salen) complexes with different axial ligands attached. This is accomplished using Density Functional Theory at the X3LYP/Triple-ζ level of theory and the Atom In Molecules formalism. The results suggest that both Mn(salen) complexes and their oxo derivatives should lie in a triplet ground state. Also, the choice of the axial ligand bears a moderate effect on the energy involved in the oxidation of the former to oxo-Mn(salen) complexes, as well as in the stability of such complexes toward ligand removal by HCl. AIM analysis further suggests that the salen ligand acts as a "charge reservoir" for the metal center, with strong correlations being obtained between the charge of salen and the electron population donated by the axial ligand to the metal center. Moreover, the results suggest that the Mn atom in Mn(salen) complexes holds different hybridization of its valence orbitals depending on the type of axial ligand present in the system.

A method to obtain static potential for electron-molecule scattering

NASA Astrophysics Data System (ADS)

Srivastava, Rajesh; Das, Tapasi; Stauffer, Allan

2014-05-01

Electron scattering from molecules is complicated by the fact that molecules are a multi-centered target with the nuclei of the constituent atoms being a center of charge. One of the most important parts of a scattering calculation is to obtain the static potential which represents the interaction of the incident electron with the unperturbed charge distribution of the molecule. A common way to represent the charge distribution of molecules is with Gaussian orbitals centered on the various nuclei. We have derived a way to calculate spherically-averaged molecular static potentials using this form of molecular wave function which is mostly analytic. This method has been applied to elastic electron scattering from water molecules and we obtained differential cross sections which are compared with previous experimental and theoretical results. The method can be extended to more complex molecules. One of us (RS) is thankful to IAEA, Vienna, Austria and DAE-BRNS, Mumbai, India for financial support.

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development

PubMed Central

Lu, Zhenyu; Zhou, Nengjie; Wu, Qin; Zhang, Yingkai

2011-01-01

One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding. PMID:22267958

A method to estimate statistical errors of properties derived from charge-density modelling

PubMed Central

Lecomte, Claude

2018-01-01

Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This ‘SSD methodology’ procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling. PMID:29724964

Modification of the G-phonon mode of graphene by nitrogen doping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lukashev, Pavel V., E-mail: pavel.lukashev@uni.edu; Hurley, Noah; Zhao, Liuyan

2016-01-25

The effect of nitrogen doping on the phonon spectra of graphene is analyzed. In particular, we employ first-principles calculations and scanning Raman analysis to investigate the dependence of phonon frequencies in graphene on the concentration of nitrogen dopants. We demonstrate that the G phonon frequency shows oscillatory behavior as a function of nitrogen concentration. We analyze different mechanisms which could potentially be responsible for this behavior, such as Friedel charge oscillations around the localized nitrogen impurity atom, the bond length change between nitrogen impurity and its nearest neighbor carbon atoms, and the long-range interactions of the nitrogen point defects. Wemore » show that the bond length change and the long range interaction of point defects are possible mechanisms responsible for the oscillatory behavior of the G frequency as a function of nitrogen concentration. At the same time, Friedel charge oscillations are unlikely to contribute to this behavior.« less

Phonon-assisted changes in charge states of deep level defects in germanium

NASA Astrophysics Data System (ADS)

Markevich, A. V.; Litvinov, V. V.; Emtsev, V. V.; Markevich, V. P.; Peaker, A. R.

2006-04-01

Electronic processes associated with changes in the charge states of the vacancy-oxygen center (VO or A center) and vacancy-group-V-impurity atom (P, As, Sb or Bi) pairs (E centers) in irradiated germanium crystals have been studied using deep level transient spectroscopy (DLTS), high-resolution Laplace DLTS and Hall effect measurements. It is found that the electron emission and capture processes related to transitions between the doubly and the singly negatively charged states of the A center and the E centers in Ge are phonon-assisted, i.e., they are accompanied by significant vibrations and re-arrangements of atoms in the vicinity of the defects. Manifestations of the phonon involvements are: (i) temperature-dependent electron capture cross-sections which are well described in the frame of the multi-phonon-assisted capture model; (ii) large changes in entropy related to the ionization of the defects and, associated with these, temperature-dependent positions of energy levels; and (iii) electron emission via phonon-assisted tunneling upon the application of electric field. These effects have been considered in detail for the vacancy-oxygen and the vacancy-donor complexes. On the basis of a combined analysis of the electronic processes a configuration-coordinate diagram of the acceptor states of the A and E centers is plotted. It is found that changes in the entropy of ionization and the energy for electron emission for these traps follow the empirical Meyer-Neldel rule. A model based on multi-phonon-assisted carrier emission from defects is adapted for the explanation of the origin of this rule for the case of electronic processes in Ge.

Geometry, bonding and magnetism in planar triangulene graphene molecules with D3h symmetry: Zigzag Cm∗∗2+4m+1H3m+3 (m = 2, …, 15)

NASA Astrophysics Data System (ADS)

Philpott, Michael R.; Cimpoesu, Fanica; Kawazoe, Yoshiyuki

2008-12-01

Ab initio plane wave based all valence electron DFT calculations with geometry optimization are reported for the electronic structure of planar zigzag edged triangular shaped graphene molecules CH where the zigzag ring number m = 2, …, 15. The largest molecule C 286H 48 has a 3.8 nm side length and retains D3h symmetric geometry. The zone in the middle of the molecules, where the geometry and electronic properties resemble infinite single sheet graphite (graphene), expands with increasing ring number m, driving deviations in geometry, charge and spin to the perimeter. If a molecule is viewed as a set of nested triangular rings of carbon, then the zone where the lattice resembles an infinite sheet of graphene with CC = 142 pm, extends to the middle of the penultimate ring. The radial bonds joining the perimeter carbon atoms to the interior are long CC = 144 pm, except near the three apexes where the bonds are shorter. Isometric surfaces of the total charge density show that the two bonds joined at the apex have the highest valence charge. The perimeter CC bonds establish a simple pattern as the zigzag number increases, which shares some features with the zigzag edges in the D2h linear acenes C 4m+2H 2m+4 and the D6h hexangulenes CH6m but not the D6h symmetric annulenes (CH). The two CC bonds forming each apex are short (≈139 pm), next comes one long bond CC ≈ 142 pm and a middle region where all the CC bonds have length ≈141 pm. The homo-lumo gap declines from 0.53 eV at m = 2 to approximately 0.29 V at m = 15, the latter being larger than found for linear or hexagonal shaped graphenes with comparable edge lengths. Across the molecule the charge on the carbon atoms undergoes a small oscillation following the bipartite lattice. The magnitude of the charge in the same nested triangle decreases monotonically with the distance of the row from the center of the molecule. These systems are predicted to have spin polarized ground states with S = ½( m - 1), in accord with the theorems of Lieb for a bipartite lattice with unequal numbers of sub-lattice carbon atoms. The magnitude of the spin on the atoms increases monotonically from the center to the edges, this effect being greatest on the majority A-sub lattice atoms. The spins are delocalized, not confined to specific atoms as might result in geometries stabilized by islands of aromatic resonance. In the largest systems the magnetic non-bonding levels (NBL) occur as a narrowly distributed set of homos close to the Fermi level, separated from the lower lying valence bond manifold by a gap of about 1 eV. The NBL are a set of disjoint radical orbitals having charge only on atoms belonging to the A-lattice and this charge is concentrated on the perimeter and penultimate row atoms.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

Cold atoms in one-dimensional rings: a Luttinger liquid approach to precision measurement

NASA Astrophysics Data System (ADS)

Ragole, Stephen; Taylor, Jacob

Recent experiments have realized ring shaped traps for ultracold atoms. We consider the one-dimensional limit of these ring systems with a moving weak barrier, such as a blue-detuned laser beam. In this limit, we employ Luttinger liquid theory and find an analogy with the superconducting charge qubit. In particular, we find that strongly-interacting atoms in such a system could be used for precision rotation sensing. We compare the performance of this new sensor to the state of the art non-interacting atom interferometry. Funding provided by the Physics Frontier Center at the JQI and by DARPA QUASAR.

Atomic charges of sulfur in ionic liquids: experiments and calculations.

PubMed

Fogarty, Richard M; Rowe, Rebecca; Matthews, Richard P; Clough, Matthew T; Ashworth, Claire R; Brandt, Agnieszka; Corbett, Paul J; Palgrave, Robert G; Smith, Emily F; Bourne, Richard A; Chamberlain, Thomas W; Thompson, Paul B J; Hunt, Patricia A; Lovelock, Kevin R J

2017-12-14

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra, X-ray photoelectron (XP) spectra and Auger electron spectra are reported for sulfur in ionic liquids (ILs) with a range of chemical structures. These values provide experimental measures of the atomic charge in each IL and enable the evaluation of the suitability of NEXAFS spectroscopy and XPS for probing the relative atomic charge of sulfur. In addition, we use Auger electron spectroscopy to show that when XPS binding energies differ by less than 0.5 eV, conclusions on atomic charge should be treated with caution. Our experimental data provides a benchmark for calculations of the atomic charge of sulfur obtained using different methods. Atomic charges were computed for lone ions and ion pairs, both in the gas phase (GP) and in a solvation model (SMD), with a wide range of ion pair conformers considered. Three methods were used to compute the atomic charges: charges from the electrostatic potential using a grid based method (ChelpG), natural bond orbital (NBO) population analysis and Bader's atoms in molecules (AIM) approach. By comparing the experimental and calculated measures of the atomic charge of sulfur, we provide an order for the sulfur atoms, ranging from the most negative to the most positive atomic charge. Furthermore, we show that both ChelpG and NBO are reasonable methods for calculating the atomic charge of sulfur in ILs, based on the agreement with both the XPS and NEXAFS spectroscopy results. However, the atomic charges of sulfur derived from ChelpG are found to display significant, non-physical conformational dependence. Only small differences in individual atomic charge of sulfur were observed between lone ion (GP) and ion pair IL(SMD) model systems, indicating that ion-ion interactions do not strongly influence individual atomic charges.

The theoretical current-voltage dependence of a non-degenerate disordered organic material obtained with conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Woellner, Cristiano F.; Freire, José A.; Guide, Michele; Nguyen, Thuc-Quyen

2011-08-01

We develop a simple continuum model for the current voltage characteristics of a material as measured by the conducting atomic force microscopy, including space charge effects. We address the effect of the point contact on the magnitude of the current and on the transition voltages between the different current regimes by comparing these with the corresponding expressions obtained with planar electrodes.

An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

NASA Astrophysics Data System (ADS)

Poursina, Mohammad; Anderson, Kurt S.

2014-08-01

This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

Nanoscale Charge Balancing Mechanism in Calcium-Silicate-Hydrate Gels: Novel Complex Disordered Materials from First-principles

NASA Astrophysics Data System (ADS)

Ozcelik, Ongun; White, Claire

Alkali-activated materials which have augmented chemical compositions as compared to ordinary Portland cement are sustainable technologies that have the potential to lower CO2 emissions associated with the construction industry. In particular, calcium-silicate-hydrate (C-S-H) gel is altered at the atomic scale due to changes in its chemical composition. Here, based on first-principles calculations, we predict a charge balancing mechanism at the molecular level in C-S-H gels when alkali atoms are introduced into their structure. This charge balancing process is responsible for the formation of novel structures which possess superior mechanical properties compared to their charge unbalanced counterparts. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these charge balancing effects on the structures is assessed by analyzing their formation energies, local bonding environments, diffusion barriers and mechanical properties. These results provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental mechanisms that play a crucial role in these complex disordered materials. We acknowledge funding from the Princeton Center for Complex Materials, a MRSEC supported by NSF.

CO oxidation on Ru-Pt bimetallic nanoclusters supported on TiO2(101): The effect of charge polarization

NASA Astrophysics Data System (ADS)

Jia, Chuanyi; Zhong, Wenhui; Deng, Mingsen; Jiang, Jun

2018-03-01

Pt-based catalyst is widely used in CO oxidation, while its catalytic activity is often undermined because of the CO poisoning effect. Here, using density functional theory, we propose the use of a Ru-Pt bimetallic cluster supported on TiO2 for CO oxidation, to achieve both high activity and low CO poisoning effect. Excellent catalytic activity is obtained in a Ru1Pt7/TiO2(101) system, which is ascribed to strong electric fields induced by charge polarization between one Ru atom and its neighboring Pt atoms. Because of its lower electronegativity, the Ru atom donates electrons to neighboring Pt. This induces strong electric fields around the top-layered Ru, substantially promoting the adsorption of O2/CO + O2 and eliminating the CO poisoning effect. In addition, the charge polarization also drives the d-band center of the Ru1Pt7 cluster to up-shift to the Fermi level. For surface O2 activation/CO oxidation, the strong electric field and d-band center close to the Fermi level can promote the adsorption of O2 and CO as well as reduce the reaction barrier of the rate-determining step. Meanwhile, since O2 easily dissociates on Ru1Pt7/TiO2(101) resulting in unwanted oxidation of Ru and Pt, a CO-rich condition is necessary to protect the catalyst at high temperature.

Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1992-01-01

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.

Electric field mill network products to improve detection of the lightning hazard

NASA Technical Reports Server (NTRS)

Maier, Launa M.

1987-01-01

An electric field mill network has been used at Kennedy Space Center for over 10 years as part of the thunderstorm detection system. Several algorithms are currently available to improve the informational output of the electric field mill data. The charge distributions of roughly 50 percent of all lightning can be modeled as if they reduced the charged cloud by a point charge or a point dipole. Using these models, the spatial differences in the lightning induced electric field changes, and a least squares algorithm to obtain an optimum solution, the three-dimensional locations of the lightning charge centers can be located. During the lifetime of a thunderstorm, dynamically induced charging, modeled as a current source, can be located spatially with measurements of Maxwell current density. The electric field mills can be used to calculate the Maxwell current density at times when it is equal to the displacement current density. These improvements will produce more accurate assessments of the potential electrical activity, identify active cells, and forecast thunderstorm termination.

Ion-atom charge-transfer reactions and a hot intercloud medium. [in interstellar space

NASA Technical Reports Server (NTRS)

Steigman, G.

1975-01-01

An investigation is conducted concerning the ionization equilibrium of carbon in a hot intercloud medium (ICM), taking into account various charge-transfer reactions. Attention is given to problems related to observations of carbon along the lines of sight to several unreddened stars. It is pointed out that the observed underabundance of C III and overabundance of C I can be consistent with the presence of a hot, partially ionized ICM, provided that two of the charge-transfer reactions considered are rapid at thermal energies.

Spectral Diagnostics of Galactic and Stellar X-Ray Emission from Charge Exchange Recombination

NASA Technical Reports Server (NTRS)

Wargelin, B.

2002-01-01

The proposed research uses the electron beam ion trap at the Lawrence Livermore National Laboratory (LLNL) to study X-ray emission from charge-exchange recombination of highly charged ions with neutral gases. The resulting data fill a void in existing experimental and theoretical understanding of this atomic physics process, and are needed to explain all or part of the observed X-ray emission from the soft X-ray background, stellar winds, the Galactic Center, supernova ejecta, and photoionized nebulae. Progress made during the first year of the grant is described, as is work planned for the second year.

Theoretical study on the photocatalytic properties of graphene oxide with single Au atom adsorption

NASA Astrophysics Data System (ADS)

Ju, Lin; Dai, Ying; Wei, Wei; Li, Mengmeng; Jin, Cui; Huang, Baibiao

2018-03-01

The photocatalytic properties of graphene oxide (GO) with single Au atom adsorption are studied via the first-principles calculations based on the density functional theory. The present study addresses the origin of enhancement in photocatalytic efficiency of GO derived from single Au atom depositing. Compared with the clean one, the work function of the single Au atom adsorbed GO is lowered due to the charge transfer from Au to GO, indicating enhanced surface activity. The Au atom plays as an electron trapping center and a mediating role in charge transfer from photon excited GO to target species. The photogenerated electron-hole pairs can be separated effectively. For the GO configuration with atomic Au dispersion, there are some states introduced in the band gap, which are predominantly composed of Au 6s states. Through the in-gap state, the photo-generated electron transfer from the valence band of clean GO to the conductive band more easily. In addition, the reduction of the gap in the system is also presented in the current work, which indicates that the single Au atom adsorption improves light absorption for the GO based photocatalyst. These theoretical results are valuable for the future applications of GO materials as photocatalyst for water splitting.

Resilience of the quantum Rabi model in circuit QED

NASA Astrophysics Data System (ADS)

E Manucharyan, Vladimir; Baksic, Alexandre; Ciuti, Cristiano

2017-07-01

In circuit quantum electrodynamics (circuit QED), an artificial ‘circuit atom’ can couple to a quantized microwave radiation much stronger than its real atomic counterpart. The celebrated quantum Rabi model describes the simplest interaction of a two-level system with a single-mode boson field. When the coupling is large enough, the bare multilevel structure of a realistic circuit atom cannot be ignored even if the circuit is strongly anharmonic. We explored this situation theoretically for flux (fluxonium) and charge (Cooper pair box) type multi-level circuits tuned to their respective flux/charge degeneracy points. We identified which spectral features of the quantum Rabi model survive and which are renormalized for large coupling. Despite significant renormalization of the low-energy spectrum in the fluxonium case, the key quantum Rabi feature—nearly-degenerate vacuum consisting of an atomic state entangled with a multi-photon field—appears in both types of circuits when the coupling is sufficiently large. Like in the quantum Rabi model, for very large couplings the entanglement spectrum is dominated by only two, nearly equal eigenvalues, in spite of the fact that a large number of bare atomic states are actually involved in the atom-resonator ground state. We interpret the emergence of the two-fold degeneracy of the vacuum of both circuits as an environmental suppression of flux/charge tunneling due to their dressing by virtual low-/high-impedance photons in the resonator. For flux tunneling, the dressing is nothing else than the shunting of a Josephson atom with a large capacitance of the resonator. Suppression of charge tunneling is a manifestation of the dynamical Coulomb blockade of transport in tunnel junctions connected to resistive leads.

Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

2015-12-01

A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

Charge transfer mechanism for the formation of metallic states at the KTaO3/SrTiO3 interface

NASA Astrophysics Data System (ADS)

Nazir, S.; Singh, N.; Schwingenschlögl, U.

2011-03-01

The electronic and optical properties of the KTaO3/SrTiO3 heterointerface are analyzed by the full-potential linearized augmented plane-wave approach of density functional theory. Optimization of the atomic positions points at subordinate changes in the crystal structure and chemical bonding near the interface, which is due to a minimal lattice mismatch. The creation of metallic interface states thus is not affected by structural relaxation but can be explained by charge transfer between transition metal and oxygen atoms. It is to be expected that a charge transfer is likewise important for related interfaces such as LaAlO3/SrTiO3. The KTaO3/SrTiO3 system is ideal for disentangling the complex behavior of metallic interface states, since almost no structural relaxation takes place.

Hidden topological constellations and polyvalent charges in chiral nematic droplets

NASA Astrophysics Data System (ADS)

Posnjak, Gregor; Čopar, Simon; Muševič, Igor

2017-02-01

Topology has an increasingly important role in the physics of condensed matter, quantum systems, material science, photonics and biology, with spectacular realizations of topological concepts in liquid crystals. Here we report on long-lived hidden topological states in thermally quenched, chiral nematic droplets, formed from string-like, triangular and polyhedral constellations of monovalent and polyvalent singular point defects. These topological defects are regularly packed into a spherical liquid volume and stabilized by the elastic energy barrier due to the helical structure and confinement of the liquid crystal in the micro-sphere. We observe, for the first time, topological three-dimensional point defects of the quantized hedgehog charge q=-2, -3. These higher-charge defects act as ideal polyvalent artificial atoms, binding the defects into polyhedral constellations representing topological molecules.

Hidden topological constellations and polyvalent charges in chiral nematic droplets

PubMed Central

Posnjak, Gregor; Čopar, Simon; Muševič, Igor

2017-01-01

Topology has an increasingly important role in the physics of condensed matter, quantum systems, material science, photonics and biology, with spectacular realizations of topological concepts in liquid crystals. Here we report on long-lived hidden topological states in thermally quenched, chiral nematic droplets, formed from string-like, triangular and polyhedral constellations of monovalent and polyvalent singular point defects. These topological defects are regularly packed into a spherical liquid volume and stabilized by the elastic energy barrier due to the helical structure and confinement of the liquid crystal in the micro-sphere. We observe, for the first time, topological three-dimensional point defects of the quantized hedgehog charge q=−2, −3. These higher-charge defects act as ideal polyvalent artificial atoms, binding the defects into polyhedral constellations representing topological molecules. PMID:28220770

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

Mechanism of formation of the response of a hydrogen gas sensor based on a silicon MOS diode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaman, V. I.; Balyuba, V. I.; Gritsyk, V. Yu.

2008-03-15

Experimental data on the dependence of the flat-band voltage and relaxation time for the capacitance of the space-charge region in an MOS diode (Pd-SiO{sub 2}-n-Si) on the hydrogen concentration in a hydrogen/air gaseous mixture are discussed. It is assumed that variation in the flat-band voltage U{sub fb} in an MOS structure with the thickness d = 369 nm subjected to a hydrogen/air gaseous mixture can be accounted for by the formation of dipoles in the Pd-SiO{sub 2} gap due to polarization of hydrogen atoms (H{sub a}). An analytical expression describing the dependence of variation in the flat-band voltage {Delta}U{sub fb}more » on the hydrogen concentration n{sub H{sub 2}} was derived. In MOS structures with d {<=} 4 nm (or MOS diodes), the value of {Delta}U{sub fb} is mainly controlled by passivation of the centers responsible for the presence of the surface acceptor-type centers at the SiO{sub 2}-n-Si interface by hydrogen atoms. Analytical expressions describing the dependences of {Delta}U{sub fb} and the capacitance relaxation time in the space-charge region on n{sub H{sub 2}} are derived. The values of the density of adsorption centers and the adsorption heat for hydrogen atoms at the Pd-SiO{sub 2} and SiO{sub 2}-n-Si interfaces are found.« less

Mechanism of formation of the response of a hydrogen gas sensor based on a silicon MOS diode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaman, V. I.; Balyuba, V. I.; Gritsyk, V. Yu.

2008-03-15

Experimental data on the dependence of the flat-band voltage and relaxation time for the capacitance of the space-charge region in an MOS diode (Pd-SiO{sub 2}-n-Si) on the hydrogen concentration in a hydrogen/air gaseous mixture are discussed. It is assumed that variation in the flat-band voltage U{sub fb} in an MOS structure with the thickness d = 369 nm subjected to a hydrogen/air gaseous mixture can be accounted for by the formation of dipoles in the Pd-SiO{sub 2} gap due to polarization of hydrogen atoms (H{sub a}). An analytical expression describing the dependence of variation in the flat-band voltage {delta}U{sub fb}more » on the hydrogen concentration n{sub H2} was derived. In MOS structures with d {<=} 4 nm (or MOS diodes), the value of {delta}U{sub fb} is mainly controlled by passivation of the centers responsible for the presence of the surface acceptor-type centers at the SiO{sub 2}-n-Si interface by hydrogen atoms. Analytical expressions describing the dependences of {delta}U{sub fb} and the capacitance relaxation time in the space-charge region on n{sub H2} are derived. The values of the density of adsorption centers and the adsorption heat for hydrogen atoms at the Pd-SiO{sub 2} and SiO{sub 2}-n-Si interfaces are found.« less

Recent Livermore Excitation and Dielectronic Recombination Measurements for Laboratory and Astrophysical Spectral Modeling

NASA Technical Reports Server (NTRS)

Beiersdorfer, P.; Brown, G. V.; Gu, M.-F.; Harris, C. L.; Kahn, S. M.; Kim, S.-H.; Neill, P. A.; Savin, D. W.; Smith, A. J.; Utter, S. B.

2000-01-01

Using the EBIT facility in Livermore we produce definitive atomic data for input into spectral synthesis codes. Recent measurements of line excitation and dielectronic recombination of highly charged K-shell and L-shell ions are presented to illustrate this point.

Return on Investment Point of Service Computerized Provider Charge Entry

PubMed Central

Kiepek, Wendy; FitzHenry, Fern; Shultz, Edward K

2003-01-01

Provider charge entry systems offer many benefits to users and organizations. At Vanderbilt University Medical Center, a web-based provider charge entry system promises to deliver benefits in reducing days in accounts receivable, reducing labor required for claims and edit processing, and implementing business rules that deliver both strategic and financial benefits. PMID:14728396

Optical Lattice Bose-Einstein Condensates and the dd Fusion - Iwamura Connection

NASA Astrophysics Data System (ADS)

Chubb, Talbot

2003-03-01

My conjecture: LENR dd fusion occurs in PdDx when a subset of the interstitial deuterons occupy tetrahedral sites in a PdDx crystallite. The tetrahedral deuterons(d's), which occupy shallow potential wells, behave as a superfluid, similar to ultracold Na atoms in shallow-well optical traps, as modeled by Jaksch et al.(D. Jaksch, et al, Phys. Rev. Lett., 81, 3108 (1998).) The tetrahedral d's form a deuteron (d) subsystem, which is neutralized by an electron subsystem containing an equal number of electrons. In the superfluid all the properties of each quasiparticle d are partitioned among N_s_i_te equivalent sites. The partitioning of the d point charge reduces the Coulomb self-repulsion within each quasiparticle pair, which causes wave function overlap at large N_s_i_t_e, allowing d-d fusion. Similarly, partitioning of the point charge of each single quasiparticle d reduces the Coulomb repulsion between it and an obstructing impurity atom, which causes wave function overlap between quasiparticle and atom at large N_s_i_t_e, allowing transmutation of the impurity atom. The Iwamura reaction(Y. Iwamura, et al, Japan J. of Appl. Physics, 41A, 4642 (2002).) is 4 ^2D^+_B_l_o_ch + 4 e^-_B_l_o_ch + ^1^3^3Cs arrow ^1^4^1Pr, with the reaction energy incoherently transferred to the lattice.

Electrical control of charged carriers and excitons in atomically thin materials

NASA Astrophysics Data System (ADS)

Wang, Ke; De Greve, Kristiaan; Jauregui, Luis A.; Sushko, Andrey; High, Alexander; Zhou, You; Scuri, Giovanni; Taniguchi, Takashi; Watanabe, Kenji; Lukin, Mikhail D.; Park, Hongkun; Kim, Philip

2018-02-01

Electrical confinement and manipulation of charge carriers in semiconducting nanostructures are essential for realizing functional quantum electronic devices1-3. The unique band structure4-7 of atomically thin transition metal dichalcogenides (TMDs) offers a new route towards realizing novel 2D quantum electronic devices, such as valleytronic devices and valley-spin qubits8. 2D TMDs also provide a platform for novel quantum optoelectronic devices9-11 due to their large exciton binding energy12,13. However, controlled confinement and manipulation of electronic and excitonic excitations in TMD nanostructures have been technically challenging due to the prevailing disorder in the material, preventing accurate experimental control of local confinement and tunnel couplings14-16. Here we demonstrate a novel method for creating high-quality heterostructures composed of atomically thin materials that allows for efficient electrical control of excitations. Specifically, we demonstrate quantum transport in the gate-defined, quantum-confined region, observing spin-valley locked quantized conductance in quantum point contacts. We also realize gate-controlled Coulomb blockade associated with confinement of electrons and demonstrate electrical control over charged excitons with tunable local confinement potentials and tunnel couplings. Our work provides a basis for novel quantum opto-electronic devices based on manipulation of charged carriers and excitons.

The estimation of H-bond and metal ion-ligand interaction energies in the G-Quadruplex ⋯ Mn+ complexes

NASA Astrophysics Data System (ADS)

Mostafavi, Najmeh; Ebrahimi, Ali

2018-06-01

In order to characterize various interactions in the G-quadruplex ⋯ Mn+ (G-Q ⋯ Mn+) complexes, the individual H-bond (EHB) and metal ion-ligand interaction (EMO) energies have been estimated using the electron charge densities (ρs) calculated at the X ⋯ H (X = N and O) and Mn+ ⋯ O (Mn+ is an alkaline, alkaline earth and transition metal ion) bond critical points (BCPs) obtained from the atoms in molecules (AIM) analysis. The estimated values of EMO and EHB were evaluated using the structural parameters, results of natural bond orbital analysis (NBO), aromaticity indexes and atomic charges. The EMO value increase with the ratio of ionic charge to radius, e/r, where a linear correlation is observed between EMO and e/r (R = 0.97). Meaningful relationships are also observed between EMO and indexes used for aromaticity estimation. The ENH value is higher than EOH in the complexes; this is in complete agreement with the trend of N⋯Hsbnd N and O⋯Hsbnd N angles, the E (2) value of nN → σ*NH and nO → σ*NH interactions and the difference between the natural charges on the H-bonded atom and the hydrogen atom of guanine (Δq). In general, the O1MO2 angle becomes closer to 109.5° with the increase in EMO and decrease in EHB in the presence of metal ion.

Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation.

PubMed

Konermann, Lars

2017-08-31

Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase. Here, we describe a mobile proton algorithm that considers the electrostatic contributions from all atoms, such that charge solvation is explicitly included. MD runs were broken down into 50 ps fixed-charge segments. After each segment, the electrostatics was reanalyzed and protons were redistributed. Challenges associated with computational cost were overcome by devising a streamlined method for electrostatic calculations. Avidin (a 504-residue protein complex) maintained a nativelike fold over 200 ns. Proton transfer and side chain rearrangements produced extensive salt bridge networks at the protein surface. The mobile proton technique introduced here should pave the way toward future studies on protein folding, unfolding, collapse, and subunit dissociation in the gas phase.

Charge Sharing and Charge Loss in a Cadmium-Zinc-Telluride Fine-Pixel Detector Array

NASA Technical Reports Server (NTRS)

Gaskin, J. A.; Sharma, D. P.; Ramsey, B. D.; Six, N. Frank (Technical Monitor)

2002-01-01

Because of its high atomic number, room temperature operation, low noise, and high spatial resolution a Cadmium-Zinc-Telluride (CZT) multi-pixel detector is ideal for hard x-ray astrophysical observation. As part of on-going research at MSFC (Marshall Space Flight Center) to develop multi-pixel CdZnTe detectors for this purpose, we have measured charge sharing and charge loss for a 4x4 (750micron pitch), lmm thick pixel array and modeled these results using a Monte-Carlo simulation. This model was then used to predict the amount of charge sharing for a much finer pixel array (with a 300micron pitch). Future work will enable us to compare the simulated results for the finer array to measured values.

The interactions of high-energy, highly-charged ions with fullerenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ali, R.; Berry, H.G.; Cheng, S.

1996-03-01

In 1985, Robert Curl and Richard Smalley discovered a new form of carbon, the fullerene, C{sub 60}, which consists of 60 carbon atoms in a closed cage resembling a soccer ball. In 1990, Kritschmer et al. were able to make macroscopic quantities of fullerenes. This has generated intense activity to study the properties of fullerenes. One area of research involves collisions between fullerenes and atoms, ions or electrons. In this paper we describe experiments involving interactions between fullerenes and highly charged ions in which the center-of-mass energies exceed those used in other work by several orders of magnitude. The highmore » values of projectile velocity and charge state result in excitation and decay processes differing significantly from those seen in studies 3 at lower energies. Our results are discussed in terms of theoretical models analogous to those used in nuclear physics and this provides an interesting demonstration of the unity of physics.« less

Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces.

PubMed

Rogers, T Ryan; Wang, Feng

2017-10-28

An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about -0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE PAGES

Huang, Jing; Mei, Ye; König, Gerhard; ...

2017-01-24

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

PubMed

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jing; Mei, Ye; König, Gerhard

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

QTAIM charge-charge flux-dipole flux interpretation of electronegativity and potential models of the fluorochloromethane mean dipole moment derivatives.

PubMed

Silva, Arnaldo F; da Silva, João V; Haiduke, R L A; Bruns, Roy E

2011-11-17

Infrared fundamental vibrational intensities and quantum theory atoms in molecules (QTAIM) charge-charge flux-dipole flux (CCFDF) contributions to the polar tensors of the fluorochloromethanes have been calculated at the QCISD/cc-pVTZ level. A root-mean-square error of 20.0 km mol(-1) has been found compared to an experimental error estimate of 14.4 and 21.1 km mol(-1) for MP2/6-311++G(3d,3p) results. The errors in the QCISD polar tensor elements and mean dipole moment derivatives are 0.059 e when compared with the experimental values. Both theoretical levels provide results showing that the dynamical charge and dipole fluxes provide significant contributions to the mean dipole moment derivatives and tend to be of opposite signs canceling one another. Although the experimental mean dipole moment derivative values suggest that all the fluorochloromethane molecules have electronic structures consistent with a simple electronegativity model with transferable atomic charges for their terminal atoms, the QTAIM/CCFDF models confirm this only for the fluoromethanes. Whereas the fluorine atom does not suffer a saturation effect in its capacity to drain electronic charge from carbon atoms that are attached to other fluorine and chlorine atoms, the zero flux electronic charge of the chlorine atom depends on the number and kind of the other substituent atoms. Both the QTAIM carbon charges (r = 0.990) and mean dipole moment derivatives (r = 0.996) are found to obey Siegbahn's potential model for carbon 1s electron ionization energies at the QCISD/cc-pVTZ level. The latter is a consequence of the carbon mean derivatives obeying the electronegativity model and not necessarily to their similarities with atomic charges. Atomic dipole contributions to the neighboring atom electrostatic potentials of the fluorochloromethanes are found to be of comparable size to the atomic charge contributions and increase the accuracy of Siegbahn's model for the QTAIM charge model results. Substitution effects of the hydrogen, fluorine, and chlorine atoms on the charge and dipole flux QTAIM contributions are found to be additive for the mean dipole derivatives of the fluorochloromethanes.

Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

PubMed

Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A

2011-10-14

The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.

Atomic spectroscopy with twisted photons: Separation of M 1 -E 2 mixed multipoles

NASA Astrophysics Data System (ADS)

Afanasev, Andrei; Carlson, Carl E.; Solyanik, Maria

2018-02-01

We analyze atomic photoexcitation into the discrete states by twisted photons, or photons carrying extra orbital angular momentum along their direction of propagation. From the angular momentum and parity considerations, we are able to relate twisted-photon photoexcitation amplitudes to their plane-wave analogs, independently of the details of the atomic wave functions. We analyze the photoabsorption cross sections of mixed-multipolarity E 2 -M 1 transitions in ionized atoms and found fundamental differences coming from the photon topology. Our theoretical analysis demonstrates that it is possible to extract the relative transition rates of different multipolar contributions by measuring the photoexcitation rate as a function of the atom's position (or impact parameter) with respect to the optical vortex center. The proposed technique for separation of multipoles can be implemented if the target's atom position is resolved with subwavelength accuracy; for example, with Paul traps. Numerical examples are presented for Boron-like highly charged ions.

Electronic levels and charge distribution near the interface of nickel

NASA Technical Reports Server (NTRS)

Waber, J. T.

1982-01-01

The energy levels in clusters of nickel atoms were investigated by means of a series of cluster calculations using both the multiple scattering and computational techniques (designated SSO) which avoids the muffin-tin approximation. The point group symmetry of the cluster has significant effect on the energy of levels nominally not occupied. This influences the electron transfer process during chemisorption. The SSO technique permits the approaching atom or molecule plus a small number of nickel atoms to be treated as a cluster. Specifically, molecular levels become more negative in the O atom, as well as in a CO molecule, as the metal atoms are approached. Thus, electron transfer from the nickel and bond formation is facilitated. This result is of importance in understanding chemisorption and catalytic processes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Bu; Yu, Yingtian; Bauchy, Mathieu, E-mail: bauchy@ucla.edu

Although quartz (α-form) is a mineral used in numerous applications wherein radiation exposure is an issue, the nature of the atomistic defects formed during radiation-induced damage has not been fully clarified. Especially, the extent of oxygen vacancy formation is still debated, which is an issue of primary importance as optical techniques based on charged oxygen vacancies have been utilized to assess the level of radiation damage in quartz. In this paper, molecular dynamics simulations are applied to study the effects of ballistic impacts on the atomic network of quartz. We show that the defects that are formed mainly consist ofmore » over-coordinated Si and O, as well as Si–O connectivity defects, e.g., small Si–O rings and edge-sharing Si tetrahedra. Oxygen vacancies, on the contrary, are found in relatively low abundance, suggesting that characterizations based on E′ centers do not adequately capture radiation-induced structural damage in quartz. Finally, we evaluate the dependence on the incident energy, of the amount of each type of the point defects formed, and quantify unambiguously the threshold displacement energies for both O and Si atoms. These results provide a comprehensive basis to assess the nature and extent of radiation damage in quartz.« less

Adsorption of Atoms of 3 d Metals on the Surfaces of Aluminum and Magnesium Oxide Films

NASA Astrophysics Data System (ADS)

Ramonova, A. G.; Kibizov, D. D.; Kozyrev, E. N.; Zaalishvili, V. B.; Grigorkina, G. S.; Fukutani, K.; Magkoev, T. T.

2018-01-01

The adsorption and formation of submonolayer structures of Ti, Cr, Fe, Ni, Cu on the surfaces of aluminum and magnesium oxide films formed on Mo(110) under ultrahigh vacuum conditions are studied via X-ray, ultraviolet photo-, and Auger electron spectroscopy (XPS, UVES, AES); spectroscopy of energy losses of high-resolution electrons (SELHRE); spectroscopy of the backscattering of low-energy ions (SBSLEI); infrared absorption spectroscopy (IAS); and the diffraction of slow electrons (DSE). Individual atoms and small clusters of all the investigated metals deposited on oxides acquire a positive charge, due presumably to interaction with surface defects. As the concentration of adatoms increases when the adsorption centers caused by defects are filled, charge transfer from adatoms to substrates is reduced. This is accompanied by further depolarization caused by the lateral interaction of adatoms.

Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms

NASA Astrophysics Data System (ADS)

Tokar, M. Z.

2016-12-01

Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 % - 30 % . This discrepancy can be significantly reduced if after the convergence of coupled plasma-neutral calculations, the final computation for c-x atoms is done kinetically.

Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments.

PubMed

Darley, Michael G; Handley, Chris M; Popelier, Paul L A

2008-09-09

Intramolecular polarization is the change to the electron density of a given atom upon variation in the positions of the neighboring atoms. We express the electron density in terms of multipole moments. Using glycine and N-methylacetamide (NMA) as pilot systems, we show that neural networks can capture the change in electron density due to polarization. After training, modestly sized neural networks successfully predict the atomic multipole moments from the nuclear positions of all atoms in the molecule. Accurate electrostatic energies between two atoms can be then obtained via a multipole expansion, inclusive of polarization effects. As a result polarization is successfully modeled at short-range and without an explicit polarizability tensor. This approach puts charge transfer and multipolar polarization on a common footing. The polarization procedure is formulated within the context of quantum chemical topology (QCT). Nonbonded atom-atom interactions in glycine cover an energy range of 948 kJ mol(-1), with an average energy difference between true and predicted energy of 0.2 kJ mol(-1), the largest difference being just under 1 kJ mol(-1). Very similar energy differences are found for NMA, which spans a range of 281 kJ mol(-1). The current proof-of-concept enables the construction of a new protein force field that incorporates electron density fragments that dynamically respond to their fluctuating environment.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

PubMed

Ionescu, Crina-Maria; Sehnal, David; Falginella, Francesco L; Pant, Purbaj; Pravda, Lukáš; Bouchal, Tomáš; Svobodová Vařeková, Radka; Geidl, Stanislav; Koča, Jaroslav

2015-01-01

Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.

Importance of Unit Cells in Accurate Evaluation of the Characteristics of Graphene

NASA Astrophysics Data System (ADS)

Sabzyan, Hassan; Sadeghpour, Narges

2016-04-01

Effects of the size of the unit cell on energy, atomic charges, and phonon frequencies of graphene at the Γ point of the Brillouin zone are studied in the absence and presence of an electric field using density functional theory (DFT) methods (LDA and DFT-PBE functionals with Goedecker-Teter-Hutter (GTH) and Troullier-Martins (TM) norm-conserving pseudopotentials). Two types of unit cells containing nC=4-28 carbon atoms are considered. Results show that stability of graphene increases with increasing size of the unit cell. Energy, atomic charges, and phonon frequencies all converge above nC=24 for all functional-pseudopotentials used. Except for the LDA-GTH calculations, application of an electric field of 0.4 and 0.9 V/nm strengths does not change the trends with the size of the unit cell but instead slightly decreases the binding energy of graphene. Results of this study show that the choice of unit cell size and type is critical for calculation of reliable characteristics of graphene.

Deep eutectic solvents: similia similibus solvuntur?

PubMed

Zahn, Stefan

2017-02-01

Deep eutectic solvents, mixtures of an organic compound and a salt with a deep eutectic melting point, are promising cheap and eco-friendly alternatives to ionic liquids. Ab initio molecular dynamics simulations of reline, a mixture consisting of urea and choline chloride, reveal that not solely hydrogen bonds allow similar interactions between both constituents. The chloride anion and the oxygen atom of urea also show a similar spatial distribution close to the cationic core of choline due to a similar charge located on both atoms. As a result of multiple similar interactions, clusters migrating together cannot be observed in reline which supports the hypothesis similia similibus solvuntur. In contrast to previous suggestions, the interaction of the hydroxyl group of choline with a hydrogen bond acceptor is overall rigid. Fast hydrogen bond acceptor dynamics is facilitated by the hydrogen atoms in the trans position to the carbonyl group of urea which contributes to the low melting point of reline.

Characterization of heterocyclic rings through quantum chemical topology.

PubMed

Griffiths, Mark Z; Popelier, Paul L A

2013-07-22

Five-membered rings are found in a myriad of molecules important in a wide range of areas such as catalysis, nutrition, and drug and agrochemical design. Systematic insight into their largely unexplored chemical space benefits from first principle calculations presented here. This study comprehensively investigates a grand total of 764 different rings, all geometry optimized at the B3LYP/6-311+G(2d,p) level, from the perspective of Quantum Chemical Topology (QCT). For the first time, a 3D space of local topological properties was introduced, in order to characterize rings compactly. This space is called RCP space, after the so-called ring critical point. This space is analogous to BCP space, named after the bond critical point, which compactly and successfully characterizes a chemical bond. The relative positions of the rings in RCP space are determined by the nature of the ring scaffold, such as the heteroatoms within the ring or the number of π-bonds. The summed atomic QCT charges of the five ring atoms revealed five features (number and type of heteroatom, number of π-bonds, substituent and substitution site) that dictate a ring's net charge. Each feature independently contributes toward a ring's net charge. Each substituent has its own distinct and systematic effect on the ring's net charge, irrespective of the ring scaffold. Therefore, this work proves the possibility of designing a ring with specific properties by fine-tuning it through manipulation of these five features.

Charge-screening role of c -axis atomic displacements in YBa 2 Cu 3 O 6 + x and related superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Božin, E. S.; Huq, A.; Shen, Bing

2016-02-01

The importance of charge reservoir layers for supplying holes to the CuO 2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers. We address this issue in the case of YBa 2 Cu 3 O 6 + x , where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this modelmore » to the temperature-dependent shifts of ions along the c axis, we infer a charge transfer of 5–10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c -axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. This line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi 2 Sr 2 CaCu 2 O 8 + δ .« less

Charge-screening role of c -axis atomic displacements in YBa 2 Cu 3 O 6 + x and related superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Božin, E. S.; Huq, A.; Shen, Bing

2016-02-01

The importance of charge reservoir layers for supplying holes to the CuO2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers.We address this issue in the case of YBa2Cu3O6+x , where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this model to the temperature-dependent shifts of ions along the cmore » axis, we infer a charge transfer of 5–10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c-axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. This line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi2Sr2CaCu2O8+δ .« less

Charge-screening role of c-axis atomic displacements in YBa 2Cu 3O 6+x and related superconductors

DOE PAGES

E. S. Bozin; Huq, A.; Shen, Bing; ...

2016-02-29

The importance of charge reservoir layers for supplying holes to the CuO 2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers. We address this issue in the case of YBa 2Cu 3O 6+x, where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this model to the temperature-dependent shifts ofmore » ions along the c axis, we infer a charge transfer of 5-10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c-axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. Furthermore, this line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi 2Sr 2CaCu 2O 8+δ.« less

Impacts of oxidants in atomic layer deposition method on Al2O3/GaN interface properties

NASA Astrophysics Data System (ADS)

Taoka, Noriyuki; Kubo, Toshiharu; Yamada, Toshikazu; Egawa, Takashi; Shimizu, Mitsuaki

2018-01-01

The electrical interface properties of GaN metal-oxide-semiconductor (MOS) capacitors with an Al2O3 gate insulator formed by atomic layer deposition method using three kinds of oxidants were investigated by the capacitance-voltage technique, Terman method, and conductance method. We found that O3 and the alternate supply of H2O and O3 (AS-HO) are effective for reducing the interface trap density (D it) at the energy range of 0.15 to 0.30 eV taking from the conduction band minimum. On the other hand, we found that surface potential fluctuation (σs) induced by interface charges for the AS-HO oxidant is much larger than that for a Si MOS capacitor with a SiO2 layer formed by chemical vapor deposition despite the small D it values for the AS-HO oxidant compared with the Si MOS capacitor. This means that the total charged center density including the fixed charge density, charged slow trap density, and charged interface trap density for the GaN MOS capacitor is higher than that for the Si MOS capacitor. Therefore, σs has to be reduced to improve the performances and reliability of GaN devices with the Al2O3/GaN interfaces.

Tuning charge and correlation effects for a single molecule on a graphene device

DOE PAGES

Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; ...

2016-11-25

The ability to understand and control the electronic properties of individual molecules in a device environment is crucial for developing future technologies at the nanometre scale and below. Achieving this, however, requires the creation of three-terminal devices that allow single molecules to be both gated and imaged at the atomic scale. We have accomplished this by integrating a graphene field effect transistor with a scanning tunnelling microscope, thus allowing gate-controlled charging and spectroscopic interrogation of individual tetrafluoro-tetracyanoquinodimethane molecules. We observe a non-rigid shift in the molecule’s lowest unoccupied molecular orbital energy (relative to the Dirac point) as a function ofmore » gate voltage due to graphene polarization effects. Our results show that electron–electron interactions play an important role in how molecular energy levels align to the graphene Dirac point, and may significantly influence charge transport through individual molecules incorporated in graphene-based nanodevices.« less

Attractive non-DLVO forces induced by adsorption of monovalent organic ions.

PubMed

Smith, Alexander M; Maroni, Plinio; Borkovec, Michal

2017-12-20

Direct force measurements between negatively charged colloidal particles were carried out using an atomic force microscope (AFM) in aqueous solutions containing monovalent organic cations, namely tetraphenylarsonium (Ph 4 As + ), 1-hexyl-3-methylimidazolium (HMIM + ), and 1-octyl-3-methylimidazolium (OMIM + ). These ions adsorb to the particle surface, and induce a charge reversal. The forces become attractive at the charge neutralization point, but they are stronger than van der Waals forces. This additional and unexpected attraction decays exponentially with a decay length of a few nanometers, and is strikingly similar to the one previously observed in the presence of multivalent ions. This attractive force probably originates from coupled spontaneous charge fluctuations on the respective surfaces as initially suggested by Kirkwood and Shumaker.

Photoelectron wave function in photoionization: plane wave or Coulomb wave?

PubMed

Gozem, Samer; Gunina, Anastasia O; Ichino, Takatoshi; Osborn, David L; Stanton, John F; Krylov, Anna I

2015-11-19

The calculation of absolute total cross sections requires accurate wave functions of the photoelectron and of the initial and final states of the system. The essential information contained in the latter two can be condensed into a Dyson orbital. We employ correlated Dyson orbitals and test approximate treatments of the photoelectron wave function, that is, plane and Coulomb waves, by comparing computed and experimental photoionization and photodetachment spectra. We find that in anions, a plane wave treatment of the photoelectron provides a good description of photodetachment spectra. For photoionization of neutral atoms or molecules with one heavy atom, the photoelectron wave function must be treated as a Coulomb wave to account for the interaction of the photoelectron with the +1 charge of the ionized core. For larger molecules, the best agreement with experiment is often achieved by using a Coulomb wave with a partial (effective) charge smaller than unity. This likely derives from the fact that the effective charge at the centroid of the Dyson orbital, which serves as the origin of the spherical wave expansion, is smaller than the total charge of a polyatomic cation. The results suggest that accurate molecular photoionization cross sections can be computed with a modified central potential model that accounts for the nonspherical charge distribution of the core by adjusting the charge in the center of the expansion.

The spatial variations of lightning during small Florida thunderstorms

NASA Technical Reports Server (NTRS)

Oram, Timothy D.; Krider, E. Philip

1991-01-01

Networks of field mills (FM's) and lightning direction finders (LDF's) were used to locate lightning over the NASA KSC on three storm days. Over 90 percent of all cloud-to-ground (CG) flashes that were detected by the LDF's in the study area were also detected by the LDF's. About 17 percent of the FM CG events could be fitted to either a monopole or a dipole charge model. These projected FM charge locations are compared to LDF locations, i.e., the ground strike points. It was found that 95 percent of the LDF points are within 12 km of the FM charge, 75 percent are within 8 km, and 50 percent are within 4 km. For a storm on 22 Jul. 1988, there was a systematic 5.6 km shift between the FM charge centers and the LDF strike points that might have been caused by the meteorological structure of the storm.

Two novel mixed-ligand complexes containing organosulfonate ligands.

PubMed

Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

2008-07-01

The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

Carbon Dioxide Electroreduction into Syngas Boosted by a Partially Delocalized Charge in Molybdenum Sulfide Selenide Alloy Monolayers.

PubMed

Xu, Jiaqi; Li, Xiaodong; Liu, Wei; Sun, Yongfu; Ju, Zhengyu; Yao, Tao; Wang, Chengming; Ju, Huanxin; Zhu, Junfa; Wei, Shiqiang; Xie, Yi

2017-07-24

Structural parameters of ternary transition-metal dichalcogenide (TMD) alloy usually obey Vegard law well, while interestingly it often exhibits boosted electrocatalytic performances relative to its two pristine binary TMDs. To unveil the underlying reasons, we propose an ideal model of ternary TMDs alloy monolayer. As a prototype, MoSeS alloy monolayers are successfully synthesized, in which X-ray absorption fine structure spectroscopy manifests their shortened Mo-S and lengthened Mo-Se bonds, helping to tailor the d-band electronic structure of Mo atoms. Density functional theory calculations illustrate an increased density of states near their conduction band edge, which ensures faster electron transfer confirmed by their lower work function and smaller charge-transfer resistance. Energy calculations show the off-center charge around Mo atoms not only benefits for stabilizing COOH* intermediate confirmed by its most negative formation energy, but also facilitates the rate-limiting CO desorption step verified by CO temperature programmed desorption and electro-stripping tests. As a result, MoSeS alloy monolayers attain the highest 45.2 % Faradaic efficiency for CO production, much larger than that of MoS 2 monolayers (16.6 %) and MoSe 2 monolayers (30.5 %) at -1.15 V vs. RHE. This work discloses how the partially delocalized charge in ternary TMDs alloys accelerates electrocatalytic performances at atomic level, opening new horizons for manipulating CO 2 electroreduction properties. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Charge dynamics of 57Fe probe atoms in La2Li0.5Cu0.5O4

NASA Astrophysics Data System (ADS)

Presniakov, I. A.; Sobolev, A. V.; Rusakov, V. S.; Moskvin, A. S.; Baranov, A. V.

2018-06-01

The objective of this study is to characterize the electronic state and local surrounding of 57Fe Mössbauer probe atoms within iron-doped layered perovskite La2Li0.5Cu0.5O4 containing transition metal in unusual formal oxidation states "+3". An approach based on the qualitative energy diagrams analysis and the calculations within the cluster configuration interaction method have been developed. It was shown that a large amount of charge is transferred via Cu-O bonds from the O: 2p bands to the Cu: 3d orbitals and the ground state is dominated by the d9L configuration ("Cu2+-O-" state). The dominant d9L ground state for the (CuO6) sublattice induces in the environment of the 57Fe probe cations a charge transfer Fe3+ + O-(L) → Fe4+ + O2-, which transforms "Fe3+" into "Fe4+" state. The experimental spectra in the entire temperature range 77-300 K were described with the use of the stochastic two-level model based on the assumption of dynamic equilibrium between two Fe3+↔Fe4+ valence states related to the iron atom in the [Fe(1)O4]4- center. The relaxation frequencies and activation energies of the corresponding charge fluctuations were estimated based on Mössbauer data. The results are discussed assuming a temperature-induced change in the electronic state of the [CuO4]5- clusters in the layered perovskite.

Nanometer scale composition study of MBE grown BGaN performed by atom probe tomography

NASA Astrophysics Data System (ADS)

Bonef, Bastien; Cramer, Richard; Speck, James S.

2017-06-01

Laser assisted atom probe tomography is used to characterize the alloy distribution in BGaN. The effect of the evaporation conditions applied on the atom probe specimens on the mass spectrum and the quantification of the III site atoms is first evaluated. The evolution of the Ga++/Ga+ charge state ratio is used to monitor the strength of the applied field. Experiments revealed that applying high electric fields on the specimen results in the loss of gallium atoms, leading to the over-estimation of boron concentration. Moreover, spatial analysis of the surface field revealed a significant loss of atoms at the center of the specimen where high fields are applied. A good agreement between X-ray diffraction and atom probe tomography concentration measurements is obtained when low fields are applied on the tip. A random distribution of boron in the BGaN layer grown by molecular beam epitaxy is obtained by performing accurate and site specific statistical distribution analysis.

A Scanning Quantum Cryogenic Atom Microscope

NASA Astrophysics Data System (ADS)

Lev, Benjamin

Microscopic imaging of local magnetic fields provides a window into the organizing principles of complex and technologically relevant condensed matter materials. However, a wide variety of intriguing strongly correlated and topologically nontrivial materials exhibit poorly understood phenomena outside the detection capability of state-of-the-art high-sensitivity, high-resolution scanning probe magnetometers. We introduce a quantum-noise-limited scanning probe magnetometer that can operate from room-to-cryogenic temperatures with unprecedented DC-field sensitivity and micron-scale resolution. The Scanning Quantum Cryogenic Atom Microscope (SQCRAMscope) employs a magnetically levitated atomic Bose-Einstein condensate (BEC), thereby providing immunity to conductive and blackbody radiative heating. The SQCRAMscope has a field sensitivity of 1.4 nT per resolution-limited point (2 um), or 6 nT / Hz1 / 2 per point at its duty cycle. Compared to point-by-point sensors, the long length of the BEC provides a naturally parallel measurement, allowing one to measure nearly one-hundred points with an effective field sensitivity of 600 pT / Hz1 / 2 each point during the same time as a point-by-point scanner would measure these points sequentially. Moreover, it has a noise floor of 300 pT and provides nearly two orders of magnitude improvement in magnetic flux sensitivity (down to 10- 6 Phi0 / Hz1 / 2) over previous atomic probe magnetometers capable of scanning near samples. These capabilities are for the first time carefully benchmarked by imaging magnetic fields arising from microfabricated wire patterns and done so using samples that may be scanned, cryogenically cooled, and easily exchanged. We anticipate the SQCRAMscope will provide charge transport images at temperatures from room to \\x9D4K in unconventional superconductors and topologically nontrivial materials.

Scanning Quantum Cryogenic Atom Microscope

NASA Astrophysics Data System (ADS)

Yang, Fan; Kollár, Alicia J.; Taylor, Stephen F.; Turner, Richard W.; Lev, Benjamin L.

2017-03-01

Microscopic imaging of local magnetic fields provides a window into the organizing principles of complex and technologically relevant condensed-matter materials. However, a wide variety of intriguing strongly correlated and topologically nontrivial materials exhibit poorly understood phenomena outside the detection capability of state-of-the-art high-sensitivity high-resolution scanning probe magnetometers. We introduce a quantum-noise-limited scanning probe magnetometer that can operate from room-to-cryogenic temperatures with unprecedented dc-field sensitivity and micron-scale resolution. The Scanning Quantum Cryogenic Atom Microscope (SQCRAMscope) employs a magnetically levitated atomic Bose-Einstein condensate (BEC), thereby providing immunity to conductive and blackbody radiative heating. The SQCRAMscope has a field sensitivity of 1.4 nT per resolution-limited point (approximately 2 μ m ) or 6 nT /√{Hz } per point at its duty cycle. Compared to point-by-point sensors, the long length of the BEC provides a naturally parallel measurement, allowing one to measure nearly 100 points with an effective field sensitivity of 600 pT /√{Hz } for each point during the same time as a point-by-point scanner measures these points sequentially. Moreover, it has a noise floor of 300 pT and provides nearly 2 orders of magnitude improvement in magnetic flux sensitivity (down to 10-6 Φ0/√{Hz } ) over previous atomic probe magnetometers capable of scanning near samples. These capabilities are carefully benchmarked by imaging magnetic fields arising from microfabricated wire patterns in a system where samples may be scanned, cryogenically cooled, and easily exchanged. We anticipate the SQCRAMscope will provide charge-transport images at temperatures from room temperature to 4 K in unconventional superconductors and topologically nontrivial materials.

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Comparison of graphite, aluminum, and TransHab shielding material characteristics in a high-energy neutron field

NASA Technical Reports Server (NTRS)

Badhwar, G. D.; Huff, H.; Wilkins, R.; Thibeault, Sheila

2002-01-01

Space radiation transport models clearly show that low atomic weight materials provide a better shielding protection for interplanetary human missions than high atomic weight materials. These model studies have concentrated on shielding properties against charged particles. A light-weight, inflatable habitat module called TransHab was built and shown to provide adequate protection against micrometeoroid impacts and good shielding properties against charged particle radiation in the International Space Station orbits. An experiment using a tissue equivalent proportional counter, to study the changes in dose and lineal energy spectra with graphite, aluminum, and a TransHab build-up as shielding, was carried out at the Los Alamos Nuclear Science Center neutron facility. It is a continuation of a previous study using regolith and doped polyethylene materials. This paper describes the results and their comparison with the previous study. Published by Elsevier Science Ltd.

Covalent Co–O–V and Sb–N Bonds Enable Polyoxovanadate Charge Control

PubMed Central

2017-01-01

The formation of [{CoII(teta)2}{CoII2(tren)(teta)2}VIV15SbIII6O42(H2O)]·ca.9H2O [teta = triethylenetetraamine; tren = tris(2-aminoethyl)amine] illustrates a strategy toward reducing the molecular charge of polyoxovanadates, a key challenge in their use as components in single-molecule electronics. Here, a V–O–Co bond to a binuclear Co2+-centered complex and a Sb–N bond to the terminal N atom of a teta ligand of a mononuclear Co2+ complex allow for full charge compensation of the archetypal molecular magnet [V15Sb6O42(H2O)]6–. Density functional theory based electron localization function analysis demonstrates that the Sb–N bond has an electron density similar to that of a Sb–O bond. Magnetic exchange coupling between the VIV and CoII spin centers mediated via the Sb–N bridge is comparably weakly antiferromagnetic. PMID:28541697

Charge Induced Dynamics of Water in a Graphene–Mica Slit Pore

PubMed Central

2017-01-01

We use atomic force microscopy to in situ investigate the dynamic behavior of confined water at the interface between graphene and mica. The graphene is either uncharged, negatively charged, or positively charged. At high humidity, a third water layer will intercalate between graphene and mica. When graphene is negatively charged, the interface fills faster with a complete three layer water film, compared to uncharged graphene. As charged positively, the third water layer dewets the interface, either by evaporation into the ambient or by the formation of three-dimensional droplets under the graphene, on top of the bilayer. Our experimental findings reveal novel phenomena of water at the nanoscale, which are interesting from a fundamental point of view and demonstrate the direct control over the wetting properties of the graphene/water interface. PMID:28985466

O-shell emission of heavy atoms in an optically thin tokamak plasma

NASA Astrophysics Data System (ADS)

Finkenthal, M.; Lippmann, S.; Huang, L. K.; Zwicker, A.; Moos, H. W.; Goldstein, W. H.; Osterheld, A. L.

1992-04-01

Heavy atoms Au (Z=79), Pb (Z=82), Bi (Z=83), and U (Z=92) have been introduced in the low-density (ne~1013 cm-3) high-temperature (Te>=1 keV) TEXT tokamak (Fusion Research Center, University of Texas at Austin) plasma. The emission has been measured in the 50-200-Å range using a photometrically calibrated, time-resolving grazing-incidence spectrometer. The O-shell ion emission has been identified by comparison with ab initio energy-level calculations and line-intensity predictions of collisional radiative models for various charge states with 5p65dk ground-state configurations.

Interactions of hydrogen with amorphous hafnium oxide

NASA Astrophysics Data System (ADS)

Kaviani, Moloud; Afanas'ev, Valeri V.; Shluger, Alexander L.

2017-02-01

We used density functional theory (DFT) calculations to study the interaction of hydrogen with amorphous hafnia (a -HfO2 ) using a hybrid exchange-correlation functional. Injection of atomic hydrogen, its diffusion towards electrodes, and ionization can be seen as key processes underlying charge instability of high-permittivity amorphous hafnia layers in many applications. Hydrogen in many wide band gap crystalline oxides exhibits negative-U behavior (+1 and -1 charged states are thermodynamically more stable than the neutral state) . Our results show that in a -HfO2 hydrogen is also negative-U, with charged states being the most thermodynamically stable at all Fermi level positions. However, metastable atomic hydrogen can share an electron with intrinsic electron trapping precursor sites [Phys. Rev. B 94, 020103 (2016)., 10.1103/PhysRevB.94.020103] forming a [etr -+O -H ] center, which is lower in energy on average by about 0.2 eV. These electron trapping sites can affect both the dynamics and thermodynamics of the interaction of hydrogen with a -HfO2 and the electrical behavior of amorphous hafnia films in CMOS devices.

Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holden, Zachary C.; Richard, Ryan M.; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu

2013-12-28

An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect tomore » the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.« less

Thermal equilibrium concentrations and effects of negatively charged Ga vacancies in n-type GaAs

NASA Astrophysics Data System (ADS)

Tan, T. Y.; You, H.-M.; Gösele, U. M.

1993-03-01

We have calculated the thermal equilibrium concentrations of the various negatively charged Ga vacancy species in GaAs. The triply-negatively-charged Ga vacancy, V {Ga/3-}, has been emphasized, since it dominates Ga self-diffusion and Ga-Al interdiffusion under intrinsic and n-doping conditions, as well as the diffusion of Si donor atoms occupying Ga sites. Under strong n-doping conditions, the thermal equilibrium V {Ga/3-}concentration, C_{V_{_{Ga} }^{3 - } }^{eq} (n), has been found to exhibit a temperature independence or a negative temperature dependence, i.e., the C_{V_{_{Ga} }^{3 - } }^{eq} (n) value is either unchanged or increases as the temperature is lowered. This is quite contrary to the normal point defect behavior for which the point defect thermal equilibrium concentration decreases as the temperature is lowered. This C_{V_{_{Ga} }^{3 - } }^{eq} (n) property provides explanations to a number of outstanding experimental results, either requiring the interpretation that V {Ga/3-}has attained its thermal equilibrium concentration at the onset of each experiment, or requiring mechanisms involving point defect non-equilibrium phenomena.

PHEPS: web-based pH-dependent Protein Electrostatics Server

PubMed Central

Kantardjiev, Alexander A.; Atanasov, Boris P.

2006-01-01

PHEPS (pH-dependent Protein Electrostatics Server) is a web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pKa,i) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points. The speed of calculation is based on fast determination of distance-dependent pair charge-charge interactions as empirical three exponential function that covers charge–charge, charge–dipole and dipole–dipole contributions. After atomic coordinates input, all standard parameters are used as defaults to facilitate non-experienced users. Special attention was given to interactive addition of non-polypeptide charges, extra ionizable groups with intrinsic pKas or fixed ions. The output information is given as plain-text, readable by ‘RasMol’, ‘Origin’ and the like. The PHEPS server is accessible at . PMID:16845042

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

PubMed

Zhurova, Elizabeth A; Zhurov, Vladimir V; Pinkerton, A Alan

2007-11-14

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

Experimental validation of calculated atomic charges in ionic liquids

NASA Astrophysics Data System (ADS)

Fogarty, Richard M.; Matthews, Richard P.; Ashworth, Claire R.; Brandt-Talbot, Agnieszka; Palgrave, Robert G.; Bourne, Richard A.; Vander Hoogerstraete, Tom; Hunt, Patricia A.; Lovelock, Kevin R. J.

2018-05-01

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.

Optical patterning of trapped charge in nitrogen-doped diamond

NASA Astrophysics Data System (ADS)

Jayakumar, Harishankar; Henshaw, Jacob; Dhomkar, Siddharth; Pagliero, Daniela; Laraoui, Abdelghani; Manson, Neil B.; Albu, Remus; Doherty, Marcus W.; Meriles, Carlos A.

2016-08-01

The nitrogen-vacancy (NV) centre in diamond is emerging as a promising platform for solid-state quantum information processing and nanoscale metrology. Of interest in these applications is the manipulation of the NV charge, which can be attained by optical excitation. Here, we use two-colour optical microscopy to investigate the dynamics of NV photo-ionization, charge diffusion and trapping in type-1b diamond. We combine fixed-point laser excitation and scanning fluorescence imaging to locally alter the concentration of negatively charged NVs, and to subsequently probe the corresponding redistribution of charge. We uncover the formation of spatial patterns of trapped charge, which we qualitatively reproduce via a model of the interplay between photo-excited carriers and atomic defects. Further, by using the NV as a probe, we map the relative fraction of positively charged nitrogen on localized optical excitation. These observations may prove important to transporting quantum information between NVs or to developing three-dimensional, charge-based memories.

Optical patterning of trapped charge in nitrogen-doped diamond.

PubMed

Jayakumar, Harishankar; Henshaw, Jacob; Dhomkar, Siddharth; Pagliero, Daniela; Laraoui, Abdelghani; Manson, Neil B; Albu, Remus; Doherty, Marcus W; Meriles, Carlos A

2016-08-30

The nitrogen-vacancy (NV) centre in diamond is emerging as a promising platform for solid-state quantum information processing and nanoscale metrology. Of interest in these applications is the manipulation of the NV charge, which can be attained by optical excitation. Here, we use two-colour optical microscopy to investigate the dynamics of NV photo-ionization, charge diffusion and trapping in type-1b diamond. We combine fixed-point laser excitation and scanning fluorescence imaging to locally alter the concentration of negatively charged NVs, and to subsequently probe the corresponding redistribution of charge. We uncover the formation of spatial patterns of trapped charge, which we qualitatively reproduce via a model of the interplay between photo-excited carriers and atomic defects. Further, by using the NV as a probe, we map the relative fraction of positively charged nitrogen on localized optical excitation. These observations may prove important to transporting quantum information between NVs or to developing three-dimensional, charge-based memories.

Optical patterning of trapped charge in nitrogen-doped diamond

PubMed Central

Jayakumar, Harishankar; Henshaw, Jacob; Dhomkar, Siddharth; Pagliero, Daniela; Laraoui, Abdelghani; Manson, Neil B.; Albu, Remus; Doherty, Marcus W.; Meriles, Carlos A.

2016-01-01

The nitrogen-vacancy (NV) centre in diamond is emerging as a promising platform for solid-state quantum information processing and nanoscale metrology. Of interest in these applications is the manipulation of the NV charge, which can be attained by optical excitation. Here, we use two-colour optical microscopy to investigate the dynamics of NV photo-ionization, charge diffusion and trapping in type-1b diamond. We combine fixed-point laser excitation and scanning fluorescence imaging to locally alter the concentration of negatively charged NVs, and to subsequently probe the corresponding redistribution of charge. We uncover the formation of spatial patterns of trapped charge, which we qualitatively reproduce via a model of the interplay between photo-excited carriers and atomic defects. Further, by using the NV as a probe, we map the relative fraction of positively charged nitrogen on localized optical excitation. These observations may prove important to transporting quantum information between NVs or to developing three-dimensional, charge-based memories. PMID:27573190

Ferrocene-decorated nanocrystalline cellulose with charge carrier mobility.

PubMed

Eyley, Samuel; Shariki, Sara; Dale, Sara E C; Bending, Simon; Marken, Frank; Thielemans, Wim

2012-04-24

Ferrocene-decorated cellulose nanowhiskers were prepared by the grafting of ethynylferrocene onto azide functionalized cotton-derived cellulose nanowhiskers using azide-alkyne cycloaddition. Successful surface modification and retention of the crystalline morphology of the nanocrystals was confirmed by elemental analysis, inductively coupled plasma-atomic emission spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The coverage with ferrocenyl is high (approximately 1.14 × 10(-3) mol g(-1) or 4.6 × 10(13) mol cm(-2) corresponding to a specific area of 61 Å(2) per ferrocene). Cyclic voltammetry measurements of films formed by deposition of ferrocene-decorated nanowhiskers showed that this small spacing of redox centers along the nanowhisker surface allowed conduction hopping of electrons. The apparent diffusion coefficient for electron (or hole) hopping via Fe(III/II) surface sites is estimated as Dapp = 10(-19) m(2)s(-1) via impedance methods, a value significantly less than nonsolvated ferrocene polymers, which would be expected as the 1,2,3-triazole ring forms a rigid linker tethering the ferrocene to the nanowhisker surface. In part, this is believed to be also due to "bottleneck" diffusion of charges across contact points where individual cellulose nanowhiskers contact each other. However, the charge-communication across the nanocrystal surface opens up the potential for use of cellulose nanocrystals as a charge percolation template for the preparation of conducting films via covalent surface modification (with applications similar to those using adsorbed conducting polymers), for use in bioelectrochemical devices to gently transfer and remove electrons without the need for a solution-soluble redox mediator, or for the fabrication of three-dimensional self-assembled conducting networks.

Topological Triply Degenerate Points Induced by Spin-Tensor-Momentum Couplings

NASA Astrophysics Data System (ADS)

Hu, Haiping; Hou, Junpeng; Zhang, Fan; Zhang, Chuanwei

2018-06-01

The recent discovery of triply degenerate points (TDPs) in topological materials has opened a new perspective toward the realization of novel quasiparticles without counterparts in quantum field theory. The emergence of such protected nodes is often attributed to spin-vector-momentum couplings. We show that the interplay between spin-tensor- and spin-vector-momentum couplings can induce three types of TDPs, classified by different monopole charges (C =±2 , ±1 , 0). A Zeeman field can lift them into Weyl points with distinct numbers and charges. Different TDPs of the same type are connected by intriguing Fermi arcs at surfaces, and transitions between different types are accompanied by level crossings along high-symmetry lines. We further propose an experimental scheme to realize such TDPs in cold-atom optical lattices. Our results provide a framework for studying spin-tensor-momentum coupling-induced TDPs and other exotic quasiparticles.

Quasiparticles and charge transfer at the two surfaces of the honeycomb iridate Na2IrO3

NASA Astrophysics Data System (ADS)

Moreschini, L.; Lo Vecchio, I.; Breznay, N. P.; Moser, S.; Ulstrup, S.; Koch, R.; Wirjo, J.; Jozwiak, C.; Kim, K. S.; Rotenberg, E.; Bostwick, A.; Analytis, J. G.; Lanzara, A.

2017-10-01

Direct experimental investigations of the low-energy electronic structure of the Na2IrO3 iridate insulator are sparse and draw two conflicting pictures. One relies on flat bands and a clear gap, the other involves dispersive states approaching the Fermi level, pointing to surface metallicity. Here, by a combination of angle-resolved photoemission, photoemission electron microscopy, and x-ray absorption, we show that the correct picture is more complex and involves an anomalous band, arising from charge transfer from Na atoms to Ir-derived states. Bulk quasiparticles do exist, but in one of the two possible surface terminations the charge transfer is smaller and they remain elusive.

Direct measurement of electrostatic fields using single Teflon nanoparticle attached to AFM tip

PubMed Central

2013-01-01

Abstract A single 210-nm Teflon nanoparticle (sTNP) was attached to the vertex of a silicon nitride (Si3N4) atomic force microscope tip and charged via contact electrification. The charged sTNP can then be considered a point charge and used to measure the electrostatic field adjacent to a parallel plate condenser using 30-nm gold/20-nm titanium as electrodes. This technique can provide a measurement resolution of 250/100 nm along the X- and Z-axes, and the minimum electrostatic force can be measured within 50 pN. PACS 07.79.Lh, 81.16.-c, 84.37. + q PMID:24314111

Direct Observation of Charge Transfer at a MgO(111) Surface

NASA Astrophysics Data System (ADS)

Subramanian, A.; Marks, L. D.; Warschkow, O.; Ellis, D. E.

2004-01-01

Transmission electron diffraction (TED) combined with direct methods have been used to study the √(3)×√(3)R30° reconstruction on the polar (111) surface of MgO and refine the valence charge distribution. The surface is nonstoichiometric and is terminated by a single magnesium atom. A charge-compensating electron hole is localized in the next oxygen layer and there is a nominal charge transfer from the oxygen atoms to the top magnesium atom. The partial charges that we obtain for the surface atoms are in reasonable agreement with empirical bond-valence estimations.

Submolecular Gates Self-Assemble for Hot-Electron Transfer in Proteins.

PubMed

Filip-Granit, Neta; Goldberg, Eran; Samish, Ilan; Ashur, Idan; van der Boom, Milko E; Cohen, Hagai; Scherz, Avigdor

2017-07-27

Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific polarizability perpendicular to the molecular plane enhances the hot-electron transport. Maximal transport efficiency is predicted for a specific, ∼5 Å, distance above the center of the metalized BChl, which is in remarkably close agreement with the distance and mutual orientation of corresponding native cofactors. These findings provide new metrics and guidelines for analysis of biological redox centers and for designing charge mobilizing machines such as artificial photosynthesis.

Characterization of an Atomic Hydrogen Source for Charge Exchange Experiments

NASA Technical Reports Server (NTRS)

Leutenegger, M. A.; Beierdorfer, P.; Betancourt-Martinez, G. L.; Brown, G. V.; Hell, N; Kelley, R. L.; Kilbourne, C. A.; Magee, E. W.; Porter, F. S.

2016-01-01

We characterized the dissociation fraction of a thermal dissociation atomic hydrogen source byinjecting the mixed atomic and molecular output of the source into an electron beam ion trapcontaining highly charged ions and recording the x-ray spectrum generated by charge exchangeusing a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchangestate-selective capture cross sections are very different for atomic and molecular hydrogen incidenton the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

Atomic and electronic structure of trilayer graphene/SiC(0001): Evidence of Strong Dependence on Stacking Sequence and charge transfer.

PubMed

Pierucci, Debora; Brumme, Thomas; Girard, Jean-Christophe; Calandra, Matteo; Silly, Mathieu G; Sirotti, Fausto; Barbier, Antoine; Mauri, Francesco; Ouerghi, Abdelkarim

2016-09-15

The transport properties of few-layer graphene are the directly result of a peculiar band structure near the Dirac point. Here, for epitaxial graphene grown on SiC, we determine the effect of charge transfer from the SiC substrate on the local density of states (LDOS) of trilayer graphene using scaning tunneling microscopy/spectroscopy and angle resolved photoemission spectroscopy (ARPES). Different spectra are observed and are attributed to the existence of two stable polytypes of trilayer: Bernal (ABA) and rhomboedreal (ABC) staking. Their electronic properties strongly depend on the charge transfer from the substrate. We show that the LDOS of ABC stacking shows an additional peak located above the Dirac point in comparison with the LDOS of ABA stacking. The observed LDOS features, reflecting the underlying symmetry of the two polytypes, were reproduced by explicit calculations within density functional theory (DFT) including the charge transfer from the substrate. These findings demonstrate the pronounced effect of stacking order and charge transfer on the electronic structure of trilayer or few layer graphene. Our approach represents a significant step toward understand the electronic properties of graphene layer under electrical field.

On-Demand Generation of Neutral and Negatively Charged Silicon-Vacancy Centers in Diamond

NASA Astrophysics Data System (ADS)

Dhomkar, Siddharth; Zangara, Pablo R.; Henshaw, Jacob; Meriles, Carlos A.

2018-03-01

Point defects in wide-band-gap semiconductors are emerging as versatile resources for nanoscale sensing and quantum information science, but our understanding of the photoionization dynamics is presently incomplete. Here, we use two-color confocal microscopy to investigate the dynamics of charge in type 1b diamond hosting nitrogen-vacancy (NV) and silicon-vacancy (SiV) centers. By examining the nonlocal fluorescence patterns emerging from local laser excitation, we show that, in the simultaneous presence of photogenerated electrons and holes, SiV (NV) centers selectively transform into the negative (neutral) charge state. Unlike NVs, 532 nm illumination ionizes SiV- via a single-photon process, thus hinting at a comparatively shallower ground state. In particular, slower ionization rates at longer wavelengths suggest the latter lies approximately ˜1.9 eV below the conduction band minimum. Building on the above observations, we demonstrate on-demand SiV and NV charge initialization over large areas via green laser illumination of variable intensity.

Electronic Structure and Bonding in Transition Metal Inorganic and Organometallic Complexes: New Basis Sets, Linear Semibridging Carbonyls and Thiocarbonyls, and Oxidative Addition of Molecular Hydrogen to Square - Iridium Complexes.

NASA Astrophysics Data System (ADS)

Sargent, Andrew Landman

Approximate molecular orbital and ab initio quantum chemical techniques are used to investigate the electronic structure, bonding and reactivity of several transition metal inorganic and organometallic complexes. Modest-sized basis sets are developed for the second-row transition metal atoms and are designed for use in geometry optimizations of inorganic and organometallic complexes incorporating these atoms. The basis sets produce optimized equilibrium geometries which are slightly better than those produced with standard 3-21G basis sets, and which are significantly better than those produced with effective core potential basis sets. Linear semibridging carbonyl ligands in heterobimetallic complexes which contain a coordinatively unsaturated late transition metal center are found to accept electron density from, rather than donate electron density to, these centers. Only when the secondary metal center is a coordinatively unsaturated early transition metal center does the semibridging ligand donate electron density to this center. Large holes in the d shell around the metal center are more prominent and prevalent in early than in late transition metal centers, and the importance of filling in these holes outweighs the importance of mitigating the charge imbalance due to the dative metal-metal interaction. Semibridging thiocarbonyl ligands are more effective donors of electron density than the carbonyl ligands since the occupied donor orbitals of pi symmetry are higher in energy. The stereoselectivity of H_2 addition to d^8 square-planar transition metal complexes is controlled by the interactions between the ligands in the plane of addition and the concentrations of electronic charge around the metal center as the complex evolves from a four-coordinate to a six-coordinate species. Electron -withdrawing ligands help stabilize the five-coordinate species while strong electron donor ligands contribute only to the destabilizing repulsive interactions. The relative thermodynamic stabilities of the final complexes can be predicted based on the relative orientations of the strongest sigma-donor ligands.

Photoelectron wave function in photoionization: Plane wave or Coulomb wave? [Does photoionization of neutral targets produce Coulomb or plane waves?

DOE PAGES

Gozem, Samer; Gunina, Anastasia O.; Ichino, Takatoshi; ...

2015-10-28

The calculation of absolute total cross sections requires accurate wave functions of the photoelectron and of the initial and final states of the system. The essential information contained in the latter two can be condensed into a Dyson orbital. We employ correlated Dyson orbitals and test approximate treatments of the photoelectron wave function, that is, plane and Coulomb waves, by comparing computed and experimental photoionization and photodetachment spectra. We find that in anions, a plane wave treatment of the photoelectron provides a good description of photodetachment spectra. For photoionization of neutral atoms or molecules with one heavy atom, the photoelectronmore » wave function must be treated as a Coulomb wave to account for the interaction of the photoelectron with the +1 charge of the ionized core. For larger molecules, the best agreement with experiment is often achieved by using a Coulomb wave with a partial (effective) charge smaller than unity. This likely derives from the fact that the effective charge at the centroid of the Dyson orbital, which serves as the origin of the spherical wave expansion, is smaller than the total charge of a polyatomic cation. Finally, the results suggest that accurate molecular photoionization cross sections can be computed with a modified central potential model that accounts for the nonspherical charge distribution of the core by adjusting the charge in the center of the expansion.« less

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Modeling the Partial Atomic Charges in Inorganometallic Molecules and Solids and Charge Redistribution in Lithium-Ion Cathodes

DOE PAGES

Wang, Bo; Li, Shaohong L.; Truhlar, Donald G.

2014-10-30

Partial atomic charges are widely used for the description of charge distributions of molecules and solids. These charges are useful to indicate the extent of charge transfer and charge flow during chemical reactions in batteries, fuel cells, and catalysts and to characterize charge distributions in capacitors, liquid-phase electrolytes, and solids and at electrochemical interfaces. However, partial atomic charges given by various charge models differ significantly, especially for systems containing metal atoms. In the present study, we have compared various charge models on both molecular systems and extended systems, including Hirshfeld, CM5, MK, ChElPG, Mulliken, MBS, NPA, DDEC, LoProp, and Badermore » charges. Their merits and drawbacks are compared. The CM5 charge model is found to perform well on the molecular systems, with a mean unsigned percentage deviation of only 9% for the dipole moments. We therefore formulated it for extended systems and applied it to study charge flow during the delithiation process in lithium-containing oxides used as cathodes. Our calculations show that the charges given by the CM5 charge model are reasonable and that during the delithiation process, the charge flow can occur not only on the transition metal but also on the anions. The oxygen atoms can lose a significant density of electrons, especially for deeply delithiated materials. We also discuss other methods in current use to analyze the charge transfer and charge flow in batteries, in particular the use of formal charge, spin density, and orbital occupancy. Here, we conclude that CM5 charges provide useful information in describing charge distributions in various materials and are very promising for the study of charge transfer and charge flows in both molecules and solids.« less

Modeling the Partial Atomic Charges in Inorganometallic Molecules and Solids and Charge Redistribution in Lithium-Ion Cathodes.

PubMed

Wang, Bo; Li, Shaohong L; Truhlar, Donald G

2014-12-09

Partial atomic charges are widely used for the description of charge distributions of molecules and solids. These charges are useful to indicate the extent of charge transfer and charge flow during chemical reactions in batteries, fuel cells, and catalysts and to characterize charge distributions in capacitors, liquid-phase electrolytes, and solids and at electrochemical interfaces. However, partial atomic charges given by various charge models differ significantly, especially for systems containing metal atoms. In the present study, we have compared various charge models on both molecular systems and extended systems, including Hirshfeld, CM5, MK, ChElPG, Mulliken, MBS, NPA, DDEC, LoProp, and Bader charges. Their merits and drawbacks are compared. The CM5 charge model is found to perform well on the molecular systems, with a mean unsigned percentage deviation of only 9% for the dipole moments. We therefore formulated it for extended systems and applied it to study charge flow during the delithiation process in lithium-containing oxides used as cathodes. Our calculations show that the charges given by the CM5 charge model are reasonable and that during the delithiation process, the charge flow can occur not only on the transition metal but also on the anions. The oxygen atoms can lose a significant density of electrons, especially for deeply delithiated materials. We also discuss other methods in current use to analyze the charge transfer and charge flow in batteries, in particular the use of formal charge, spin density, and orbital occupancy. We conclude that CM5 charges provide useful information in describing charge distributions in various materials and are very promising for the study of charge transfer and charge flows in both molecules and solids.

Surface energy of talc and chlorite: Comparison between electronegativity calculation and immersion results.

PubMed

Douillard, Jean-Marc; Salles, Fabrice; Henry, Marc; Malandrini, Harold; Clauss, Frédéric

2007-01-15

The surface energies of talc and chlorite is computed using a simple model, which uses the calculation of the electrostatic energy of the crystal. It is necessary to calculate the atomic charges. We have chosen to follow Henry's model of determination of partial charges using scales of electronegativity and hardness. The results are in correct agreement with a determination of the surface energy obtained from an analysis of the heat of immersion data. Both results indicate that the surface energy of talc is lower than the surface energy of chlorite, in agreement with observed behavior of wettability. The influence of Al and Fe on this phenomenon is discussed. Surface energy of this type of solids seems to depend more strongly on the geometry of the crystal than on the type of atoms pointing out of the surface; i.e., the surface energy depends more on the physics of the system than on its chemistry.

Carbon Nanotube Devices Engineered by Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Prisbrey, Landon

This dissertation explores the engineering of carbon nanotube electronic devices using atomic force microscopy (AFM) based techniques. A possible application for such devices is an electronic interface with individual biological molecules. This single molecule biosensing application is explored both experimentally and with computational modeling. Scanning probe microscopy techniques, such as AFM, are ideal to study nanoscale electronics. These techniques employ a probe which is raster scanned above a sample while measuring probe-surface interactions as a function of position. In addition to topographical and electrostatic/magnetic surface characterization, the probe may also be used as a tool to manipulate and engineer at the nanoscale. Nanoelectronic devices built from carbon nanotubes exhibit many exciting properties including one-dimensional electron transport. A natural consequence of onedimensional transport is that a single perturbation along the conduction channel can have extremely large effects on the device's transport characteristics. This property may be exploited to produce electronic sensors with single-molecule resolution. Here we use AFM-based engineering to fabricate atomic-sized transistors from carbon nanotube network devices. This is done through the incorporation of point defects into the carbon nanotube sidewall using voltage pulses from an AFM probe. We find that the incorporation of an oxidative defect leads to a variety of possible electrical signatures including sudden switching events, resonant scattering, and breaking of the symmetry between electron and hole transport. We discuss the relationship between these different electronic signatures and the chemical structure/charge state of the defect. Tunneling through a defect-induced Coulomb barrier is modeled with numerical Verlet integration of Schrodinger's equation and compared with experimental results. Atomic-sized transistors are ideal for single-molecule applications due to their sensitivity to electric fields with very small detection volumes. In this work we demonstrate these devices as single-molecule sensors to detect individual N-(3-Dimethylaminopropyl)- N'-ethylcarbodiimide (EDC) molecules in an aqueous environment. An exciting application of these sensors is to study individual macromolecules participating in biological reactions, or undergoing conformational change. However, it is unknown whether the associated electrostatic signals exceed detection limits. We report calculations which reveal that enzymatic processes, such as substrate binding and internal protein dynamics, are detectable at the single-molecule level using existing atomic-sized transistors. Finally, we demonstrate the use of AFM-based engineering to control the function of nanoelectronic devices without creating a point defect in the sidewall of the nanotube. With a biased AFM probe we write charge patterns on a silicon dioxide surface in close proximity to a carbon nanotube device. The written charge induces image charges in the nearby electronics, and can modulate the Fermi level in a nanotube by +/-1 eV. We use this technique to induce a spatially controlled doping charge pattern in the conduction channel, and thereby reconfigure a field-effect transistor into a pn junction. Other simple charge patterns could be used to create other devices. The doping charge persists for days and can be erased and rewritten, offering a new tool for prototyping nanodevices and optimizing electrostatic doping profiles.

Atomic resolved phase map of monolayer MoS2 retrieved by spherical aberration-corrected transport of intensity equation.

PubMed

Zhang, Xiaobin; Oshima, Yoshifumi

2016-10-01

An atomic resolution phase map, which enables us to observe charge distribution or magnetic properties at an atomic scale, has been pointed out to be retrieved by transport of intensity equation (TIE) when taking two atomic-resolved transmission electron microscope (TEM) images of small defocus difference. In this work, we firstly obtained the atomic-resolved phase maps of an exfoliated molybdenum disulfide sheet using spherical aberration-corrected transmission electron microscope. We successfully observed 60° grain boundary of mechanically exfoliated monolayer molybdenum disulfide sheet. The relative phase shift of a single molybdenum atomic column to the column consisting of two sulfur atoms was obtained to be about 0.01 rad on average, which was about half lower than the simulated TIE phase map, indicating that the individual atomic sites can be distinguished qualitatively. The appropriate condition for retrieving atomic-resolved TIE phase maps was briefly discussed. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ionization equilibrium at the transition from valence-band to acceptor-band migration of holes in boron-doped diamond

NASA Astrophysics Data System (ADS)

Poklonski, N. A.; Vyrko, S. A.; Poklonskaya, O. N.; Kovalev, A. I.; Zabrodskii, A. G.

2016-06-01

A quasi-classical model of ionization equilibrium in the p-type diamond between hydrogen-like acceptors (boron atoms which substitute carbon atoms in the crystal lattice) and holes in the valence band (v-band) is proposed. The model is applicable on the insulator side of the insulator-metal concentration phase transition (Mott transition) in p-Dia:B crystals. The densities of the spatial distributions of impurity atoms (acceptors and donors) and of holes in the crystal are considered to be Poissonian, and the fluctuations of their electrostatic potential energy are considered to be Gaussian. The model accounts for the decrease in thermal ionization energy of boron atoms with increasing concentration, as well as for electrostatic fluctuations due to the Coulomb interaction limited to two nearest point charges (impurity ions and holes). The mobility edge of holes in the v-band is assumed to be equal to the sum of the threshold energy for diffusion percolation and the exchange energy of the holes. On the basis of the virial theorem, the temperature Tj is determined, in the vicinity of which the dc band-like conductivity of holes in the v-band is approximately equal to the hopping conductivity of holes via the boron atoms. For compensation ratio (hydrogen-like donor to acceptor concentration ratio) K ≈ 0.15 and temperature Tj, the concentration of "free" holes in the v-band and their jumping (turbulent) drift mobility are calculated. Dependence of the differential energy of thermal ionization of boron atoms (at the temperature 3Tj/2) as a function of their concentration N is calculated. The estimates of the extrapolated into the temperature region close to Tj hopping drift mobility of holes hopping from the boron atoms in the charge states (0) to the boron atoms in the charge states (-1) are given. Calculations based on the model show good agreement with electrical conductivity and Hall effect measurements for p-type diamond with boron atom concentrations in the range from 3 × 1017 to 3 × 1020 cm-3, i.e., up to the Mott transition. The model uses no fitting parameters.

Prediction of another semimetallic silicene allotrope with Dirac fermions

NASA Astrophysics Data System (ADS)

Wu, Haiping; Qian, Yan; Du, Zhengwei; Zhu, Renzhu; Kan, Erjun; Deng, Kaiming

2017-11-01

Materials with Dirac point are so amazing since the charge carriers are massless and have an effective speed of light. However, among the predicted two-dimensional silicon allotropes with Dirac point, no one has been directly proved by experiment. This fact motivates us to search for other two-dimensional silicon allotropes. As a result, another stable single atomic layer thin silicon allotrope is found with the help of CALYPSO code in this work. This silicene allotrope is composed of eight-membered rings linked by Si-Si bonds with buckling formation. The electronic calculation reveals that it behaves as a nodal line semimetal with the linear energy dispersion relation near the Fermi surface. Notably, the ab initio molecular dynamics simulations display that the original atomic configuration can be remained even at an extremely high temperature of 1000 K. Additionally, hydrogenation could induce a semimetal-semiconductor transition in this silicene allotrope. We hope this work can expand the family of single atomic layer thin silicon allotropes with special applications.

Atomic charge transfer-counter polarization effects determine infrared CH intensities of hydrocarbons: a quantum theory of atoms in molecules model.

PubMed

Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E

2014-11-14

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Characterization of an atomic hydrogen source for charge exchange experiments

DOE PAGES

Leutenegger, M. A.; Beiersdorfer, P.; Betancourt-Martinez, G. L.; ...

2016-07-02

Here, we characterized the dissociation fraction of a thermal dissociation atomic hydrogen source by injecting the mixed atomic and molecular output of the source into an electron beam ion trap containing highly charged ions and recording the x-ray spectrum generated by charge exchange using a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchange state-selective capture cross sections are very different for atomic and molecular hydrogen incident on the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokoyama, Hideshi, E-mail: h-yokoya@u-shizuoka-ken.ac.jp; Tsuruta, Osamu; Akao, Naoya

2012-06-15

Highlights: Black-Right-Pointing-Pointer Structures of a metal-bound Helicobacter pylori neutrophil-activating protein were determined. Black-Right-Pointing-Pointer Two zinc ions were tetrahedrally coordinated by ferroxidase center (FOC) residues. Black-Right-Pointing-Pointer Two cadmium ions were coordinated in a trigonal-bipyramidal and octahedral manner. Black-Right-Pointing-Pointer The second metal ion was more weakly coordinated than the first at the FOC. Black-Right-Pointing-Pointer A zinc ion was found in one negatively-charged pore suitable as an ion path. -- Abstract: Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn{sup 2+}-more » or Cd{sup 2+}-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.« less

IBEX-Lo Observations of Secondary Interstellar Helium and Oxygen Distributions

NASA Astrophysics Data System (ADS)

Park, J.; Kucharek, H.; Moebius, E.; Kubiak, M. A.; Bzowski, M.; Galli, A.; McComas, D. J.

2015-12-01

Observations of the Interstellar Boundary EXplorer (IBEX) show, among other features, the pristine interstellar neutral gas flow and additional populations associated with neutral helium and oxygen. Kubiak et al. (2014, ApJS, 213, 29) discovered the "Warm Breeze", or additional He component, which is slower and warmer than the primary interstellar He population and its flow direction differs by about 19° from the interstellar neutral (ISN) flow. Park et al. (2015, ApJS, In Press) studied the combined count rate maps of heavy neutral atoms with three statistical analysis methods and found an extended tail of the ISN O flow, centered around 190° in ecliptic longitude and +15° in ecliptic latitude, or approximately 38° from the ISN O and Ne flow peak. The most likely sources for the Warm Breeze and the extended O tail may be secondary populations of interstellar He and O, created by charge exchange between ISN atoms and interstellar ions in the outer heliosheath. The charge exchange between interstellar He atoms and He+ ions is the most important reaction to generate the secondary neutral He in the outer heliosheath, with a reaction rate of 1.7×10-10 s-1 and a mean free path of ~950 AU. For O+, the charge exchange with interstellar H atoms with a rate ~1.0×10-9 s-1 and a mean free path of ~100 AU is most important. Because the differences in the reaction rates and atomic masses for He and O result in different velocity distributions in the outer heliosheath, the directional distributions of these populations at Earth orbit are not identical. In this study, we use the IBEX flux maps of the observed helium and oxygen atoms to compare their directional distributions. These observed distributions may provide constraints and information to improve our current understanding of the interactions in the outer heliosheath.

Renormalization shielding effect on the Wannier-ridge mode for double-electron continua in partially ionized dense hydrogen plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Myoung-Jae; Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr; Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180-3590

2016-01-15

The influence of renormalization shielding on the Wannier threshold law for the double-electron escapes by the electron-impact ionization is investigated in partially ionized dense plasmas. The renormalized electron charge and Wannier exponent are obtained by considering the equation of motion in the Wannier-ridge including the renormalization shielding effect. It is found that the renormalization shielding effect reduces the magnitude of effective electron charge, especially, within the Bohr radius in partially ionized dense plasmas. The maximum position of the renormalized electron charge approaches to the center of the target atom with an increase of the renormalization parameter. In addition, the Wanniermore » exponent increases with an increase of the renormalization parameter. The variations of the renormalized electron charge and Wannier exponent due to the renormalization shielding effect are also discussed.« less

Spin properties of charged Mn-doped quantum dota)

NASA Astrophysics Data System (ADS)

Besombes, L.; Léger, Y.; Maingault, L.; Mariette, H.

2007-04-01

The optical properties of individual quantum dots doped with a single Mn atom and charged with a single carrier are analyzed. The emission of the neutral, negatively and positively charged excitons coupled with a single magnetic atom (Mn) are observed in the same individual quantum dot. The spectrum of the charged excitons in interaction with the Mn atom shows a rich pattern attributed to a strong anisotropy of the hole-Mn exchange interaction slightly perturbed by a small valence-band mixing. The anisotropy in the exchange interaction between a single magnetic atom and a single hole is revealed by comparing the emission of a charged Mn-doped quantum dot in longitudinal and transverse magnetic field.

Interstellar Chemistry Gets More Complex With New Charged-Molecule Discovery

NASA Astrophysics Data System (ADS)

2007-07-01

Astronomers using data from the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) have found the largest negatively-charged molecule yet seen in space. The discovery of the third negatively-charged molecule, called an anion, in less than a year and the size of the latest anion will force a drastic revision of theoretical models of interstellar chemistry, the astronomers say. Molecule formation Formation Process of Large, Negatively-Charged Molecule in Interstellar Space CREDIT: Bill Saxton, NRAO/AUI/NSF Click on image for page of graphics and detailed information "This discovery continues to add to the diversity and complexity that is already seen in the chemistry of interstellar space," said Anthony J. Remijan of the National Radio Astronomy Observatory (NRAO). "It also adds to the number of paths available for making the complex organic molecules and other large molecular species that may be precursors to life in the giant clouds from which stars and planets are formed," he added. Two teams of scientists found negatively-charged octatetraynyl, a chain of eight carbon atoms and one hydrogen atom, in the envelope of gas around an old, evolved star and in a cold, dark cloud of molecular gas. In both cases, the molecule had an extra electron, giving it a negative charge. About 130 neutral and about a dozen positively-charged molecules have been discovered in space, but the first negatively-charged molecule was not discovered until late last year. The largest previously-discovered negative ion found in space has six carbon atoms and one hydrogen atom. "Until recently, many theoretical models of how chemical reactions evolve in interstellar space have largely neglected the presence of anions. This can no longer be the case, and this means that there are many more ways to build large organic molecules in cosmic environments than have been explored," said Jan M. Hollis of NASA's Goddard Space Flight Center (GSFC). Ultraviolet light from stars can knock an electron off a molecule, creating a positively-charged ion. Astronomers had thought that molecules would not be able to retain an extra electron, and thus a negative charge, in interstellar space for a significant time. "That obviously is not the case," said Mike McCarthy of the Harvard-Smithsonian Center for Astrophysics. "Anions are surprisingly abundant in these regions." Remijan and his colleagues found the octatetraynyl anions in the envelope of the evolved giant star IRC +10 216, about 550 light-years from Earth in the constellation Leo. They found radio waves emitted at specific frequencies characteristic of the charged molecule by searching archival data from the GBT, the largest fully-steerable radio telescope in the world. Another team from the Harvard-Smithsonian Center for Astrophysics (CfA) found the same characteristic emission when they observed a cold cloud of molecular gas called TMC-1 in the constellation Taurus. These observations also were done with the GBT. In both cases, preceding laboratory experiments by the CfA team showed which radio frequencies actually are emitted by the molecule, and thus told the astronomers what to look for. "It is essential that likely interstellar molecule candidates are first studied in laboratory experiments so that the radio frequencies they can emit are known in advance of an astronomical observation," said Frank Lovas of the National Institute of Standards and Technology (NIST). Both teams announced their results in the July 20 edition of the Astrophysical Journal Letters. "With three negatively-charged molecules now found in a short period of time, and in very different environments, it appears that many more probably exist. We believe that we can discover more new species using very sensitive and advanced radio telescopes such as the GBT, once they have been characterized in the laboratory," said Sandra Bruenken of the CfA. "Further detailed studies of anions, including astronomical observations, laboratory studies, and theoretical calculations, will allow us to use them to reveal new information about the physical and chemical processes going on in interstellar space," said Martin Cordiner, of Queen's University in Belfast, Northern Ireland. "The GBT continues to take a leading role in discovering, identifying and mapping the distribution of the largest molecules ever found in astronomical environments and will continue to do so for the next several decades," said Phil Jewell of NRAO. In addition to Hollis, Lovas, Cordiner and Jewell, Remijan worked with Tom Millar of Queen's University in Belfast, Northern Ireland, and Andrew Markwick-Kemper of the University of Manchester in the UK. Bruenken worked with McCarthy, Harshal Gupta, Carl Gottlieb, and Patrick Thaddeus, all of the Harvard-Smithsonian Center for Astrophysics. The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc. Headquartered in Cambridge, Mass., the Harvard-Smithsonian Center for Astrophysics is a joint collaboration between the Smithsonian Astrophysical Observatory and the Harvard College Observatory. CfA scientists, organized into six research divisions, study the origin, evolution and ultimate fate of the universe.

Polaronic effects on the off-center donor impurity in AlAs/GaAs/SiO2 spherical core/shell quantum dots

NASA Astrophysics Data System (ADS)

El Haouari, M.; Feddi, E.; Dujardin, F.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.

2017-11-01

The ground state of a conduction electron coupled to an off-center impurity donor in a AlAS/GaAs spherical core/shell quantum dot is investigated theoretically. The image-charge effect and the influence of the electron-polar-LO-phonon interaction are considered. The electron-impurity binding energy is calculated via a variational procedure and is reported both as a function of the shell width and of the radial position of the donor atom. The polaronic effects on this quantity are particularly discussed.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Fast calculator for X-ray emission due to Radiative Recombination and Radiative Electron Capture in relativistic heavy-ion atom collisions

NASA Astrophysics Data System (ADS)

Herdrich, M. O.; Weber, G.; Gumberidze, A.; Wu, Z. W.; Stöhlker, Th.

2017-10-01

In experiments with highly charged, fast heavy ions the Radiative Recombination (RR) and Radiative Electron Capture (REC) processes have significant cross sections in an energy range of up to a few GeV / u . They are some of the most important charge changing processes in collisions of heavy ions with atoms and electrons, leading to the emission of a photon along with the formation of the ground and excited atomic states. Hence, for the understanding and planning of experiments, in particular for X-ray spectroscopy studies, at accelerator ring facilities, such as FAIR, it is crucial to have a good knowledge of these cross sections and the associated radiation characteristics. In the frame of this work a fast calculator, named RECAL, for the RR and REC process is presented and its capabilities are demonstrated with the analysis of a recently conducted experiment at the Experimental Storage Ring (ESR) at the GSI Helmholtz Center for Heavy Ion Research in Darmstadt, Germany. A method is presented to determine unknown X-ray emission cross sections via normalization of the recorded spectra to REC cross sections calculated by RECAL.

Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

PubMed Central

Baker, Nathan A.; McCammon, J. Andrew

2008-01-01

The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew

2007-10-01

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560ns of simulation time. A finite, positive potential of 13-24 kbTec-1 (where T =300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0Å from the solute surface, on average 0.008ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.

Proton trapping in SiO 2 layers thermally grown on Si and SiC

NASA Astrophysics Data System (ADS)

Afanas'ev, V. V.; Ciobanu, F.; Pensl, G.; Stesmans, A.

2002-11-01

Positive charging of thermal SiO 2 layers on (1 0 0)Si and (0 0 0 1)6H-, 4H-SiC related to trapping of protons is studied using low-energy proton implantation into the oxide, and compared to the trapping of holes generated by 10-eV photons. Proton trapping has an initial probability close to 100% and shows little sensitivity to the annealing-induced oxygen deficiency of SiO 2. In contrast to protons, hole trapping in as-grown SiO 2 shows a much lower efficiency which increases upon oxide annealing, in qualitative correlation with the higher density of O 3Si• defects (E' centers) detected by electron spin resonance after hole injection. Despite these differences, the neutralization of positive charges induced by holes and protons has the same cross-section, and in both cases is accompanied by liberation of atomic H suggesting that protons account for positive charge in both cases. The rupture of Si-O bonds in the oxide observed upon proton injection suggests, as a first basic step, the bonding of a proton to a bridging oxygen atom in SiO 2 network.

Communication: Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

NASA Astrophysics Data System (ADS)

Vanfleteren, Diederik; Van Neck, Dimitri; Bultinck, Patrick; Ayers, Paul W.; Waroquier, Michel

2010-12-01

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.

Existence of Hartree-Fock excited states for atoms and molecules

NASA Astrophysics Data System (ADS)

Lewin, Mathieu

2018-04-01

For neutral and positively charged atoms and molecules, we prove the existence of infinitely many Hartree-Fock critical points below the first energy threshold (that is, the lowest energy of the same system with one electron removed). This is the equivalent, in Hartree-Fock theory, of the famous Zhislin-Sigalov theorem which states the existence of infinitely many eigenvalues below the bottom of the essential spectrum of the N-particle linear Schrödinger operator. Our result improves a theorem of Lions in 1987 who already constructed infinitely many Hartree-Fock critical points, but with much higher energy. Our main contribution is the proof that the Hartree-Fock functional satisfies the Palais-Smale property below the first energy threshold. We then use minimax methods in the N-particle space, instead of working in the one-particle space.

NOVA SCIENCE UNIT 15, FUNDAMENTAL PARTICLES 4.

ERIC Educational Resources Information Center

1964

THE PRINCIPLES OF ATOMIC STRUCTURE WHICH ARE STRESSED ARE THAT ATOMS ARE MADE UP OF A NUCLEUS WITH A POSITIVE CHARGE, SURROUNDED BY ELECTRONS WITH A NEGATIVE CHARGE, AND THAT THERE IS NO CHANGE IN THE ATOM WHEN THE POSITIVE AND NEGATIVE CHARGES ARE EQUAL. EXPERIMENTS ILLUSTRATE THAT CURRENT ELECTRICITY IS ACTUALLY ELECTRONS IN MOTION, THAT THERE…

Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.

PubMed

Parandekar, Priya V; Hratchian, Hrant P; Raghavachari, Krishnan

2008-10-14

Hybrid QM:QM (quantum mechanics:quantum mechanics) and QM:MM (quantum mechanics:molecular mechanics) methods are widely used to calculate the electronic structure of large systems where a full quantum mechanical treatment at a desired high level of theory is computationally prohibitive. The ONIOM (our own N-layer integrated molecular orbital molecular mechanics) approximation is one of the more popular hybrid methods, where the total molecular system is divided into multiple layers, each treated at a different level of theory. In a previous publication, we developed a novel QM:QM electronic embedding scheme within the ONIOM framework, where the model system is embedded in the external Mulliken point charges of the surrounding low-level region to account for the polarization of the model system wave function. Therein, we derived and implemented a rigorous expression for the embedding energy as well as analytic gradients that depend on the derivatives of the external Mulliken point charges. In this work, we demonstrate the applicability of our QM:QM method with point charge embedding and assess its accuracy. We study two challenging systems--zinc metalloenzymes and silicon oxide cages--and demonstrate that electronic embedding shows significant improvement over mechanical embedding. We also develop a modified technique for the energy and analytic gradients using a generalized asymmetric Mulliken embedding method involving an unequal splitting of the Mulliken overlap populations to offer improvement in situations where the Mulliken charges may be deficient.

Polarization pattern of vector vortex beams generated by q-plates with different topological charges.

PubMed

Cardano, Filippo; Karimi, Ebrahim; Slussarenko, Sergei; Marrucci, Lorenzo; de Lisio, Corrado; Santamato, Enrico

2012-04-01

We describe the polarization topology of the vector beams emerging from a patterned birefringent liquid crystal plate with a topological charge q at its center (q-plate). The polarization topological structures for different q-plates and different input polarization states have been studied experimentally by measuring the Stokes parameters point-by-point in the beam transverse plane. Furthermore, we used a tuned q=1/2-plate to generate cylindrical vector beams with radial or azimuthal polarizations, with the possibility of switching dynamically between these two cases by simply changing the linear polarization of the input beam.

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0).

PubMed

Hellström, Matti; Spångberg, Daniel; Hermansson, Kersti

2015-12-15

We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10(1)0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10(1)0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.

Genetics Home Reference: SLC4A1-associated distal renal tubular acidosis

MedlinePlus

... exchanger 1 (AE1) protein, which transports negatively charged atoms (anions) across cell membranes. Specifically, AE1 exchanges negatively charged atoms of chlorine (chloride ions) for negatively charged bicarbonate ...

Saturn Ring

NASA Image and Video Library

2007-12-12

Like Earth, Saturn has an invisible ring of energetic ions trapped in its magnetic field. This feature is known as a "ring current." This ring current has been imaged with a special camera on Cassini sensitive to energetic neutral atoms. This is a false color map of the intensity of the energetic neutral atoms emitted from the ring current through a processed called charged exchange. In this process a trapped energetic ion steals and electron from cold gas atoms and becomes neutral and escapes the magnetic field. The Cassini Magnetospheric Imaging Instrument's ion and neutral camera records the intensity of the escaping particles, which provides a map of the ring current. In this image, the colors represent the intensity of the neutral emission, which is a reflection of the trapped ions. This "ring" is much farther from Saturn (roughly five times farther) than Saturn's famous icy rings. Red in the image represents the higher intensity of the particles, while blue is less intense. Saturn's ring current had not been mapped before on a global scale, only "snippets" or areas were mapped previously but not in this detail. This instrument allows scientists to produce movies (see PIA10083) that show how this ring changes over time. These movies reveal a dynamic system, which is usually not as uniform as depicted in this image. The ring current is doughnut shaped but in some instances it appears as if someone took a bite out of it. This image was obtained on March 19, 2007, at a latitude of about 54.5 degrees and radial distance 1.5 million kilometres (920,000 miles). Saturn is at the center, and the dotted circles represent the orbits of the moon's Rhea and Titan. The Z axis points parallel to Saturn's spin axis, the X axis points roughly sunward in the sun-spin axis plane, and the Y axis completes the system, pointing roughly toward dusk. The ion and neutral camera's field of view is marked by the white line and accounts for the cut-off of the image on the left. The image is an average of the activity over a (roughly) 3-hour period. http://photojournal.jpl.nasa.gov/catalog/PIA10094

Charge Dynamics in near-Surface, Variable-Density Ensembles of Nitrogen-Vacancy Centers in Diamond.

PubMed

Dhomkar, Siddharth; Jayakumar, Harishankar; Zangara, Pablo R; Meriles, Carlos A

2018-06-13

Although the spin properties of superficial shallow nitrogen-vacancy (NV) centers have been the subject of extensive scrutiny, considerably less attention has been devoted to studying the dynamics of NV charge conversion near the diamond surface. Using multicolor confocal microscopy, here we show that near-surface point defects arising from high-density ion implantation dramatically increase the ionization and recombination rates of shallow NVs compared to those in bulk diamond. Further, we find that these rates grow linearly, not quadratically, with laser intensity, indicative of single-photon processes enabled by NV state mixing with other defect states. Accompanying these findings, we observe NV ionization and recombination in the dark, likely the result of charge transfer to neighboring traps. Despite the altered charge dynamics, we show that one can imprint rewritable, long-lasting patterns of charged-initialized, near-surface NVs over large areas, an ability that could be exploited for electrochemical biosensing or to optically store digital data sets with subdiffraction resolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozlovski, V. V.; Lebedev, A. A.; Bogdanova, E. V.

The model of conductivity compensation in SiC under irradiation with high-energy electrons is presented. The following processes are considered to cause a decrease in the free carrier concentration: (i) formation of deep traps by intrinsic point defects, Frenkel pairs produced by irradiation; (ii) 'deactivation' of the dopant via formation of neutral complexes including a dopant atom and a radiation-induced point defect; and (iii) formation of deep compensating traps via generation of charged complexes constituted by a dopant atom and a radiation-induced point defect. To determine the compensation mechanism, dose dependences of the deep compensation of moderately doped SiC (CVD) undermore » electron irradiation have been experimentally studied. It is demonstrated that, in contrast to n-FZ-Si, moderately doped SiC (CVD) exhibits linear dependences (with a strongly nonlinear dependence observed for Si). Therefore, the conductivity compensation in silicon carbide under electron irradiation occurs due to deep traps formed by primary radiation defects (vacancies and interstitial atoms) in the silicon and carbon sublattices. It is known that the compensation in silicon is due to the formation of secondary radiation defects that include a dopant atom. It is shown that, in contrast to n-SiC (CVD), primary defects in only the carbon sublattice of moderately doped p-SiC (CVD) cannot account for the compensation process. In p-SiC, either primary defects in the silicon sublattice or defects in both sublattices are responsible for the conductivity compensation.« less

Quantum theory of atoms in molecules charge-charge flux-dipole flux models for the infrared intensities of X(2)CY (X = H, F, Cl; Y = O, S) molecules.

PubMed

Faria, Sergio H D M; da Silva, João Viçozo; Haiduke, Roberto L A; Vidal, Luciano N; Vazquez, Pedro A M; Bruns, Roy E

2007-08-16

The molecular dipole moments, their derivatives, and the fundamental IR intensities of the X2CY (X = H, F, Cl; Y = O, S) molecules are determined from QTAIM atomic charges and dipoles and their fluxes at the MP2/6-311++G(3d,3p) level. Root-mean-square errors of +/-0.03 D and +/-1.4 km mol(-1) are found for the molecular dipole moments and fundamental IR intensities calculated using quantum theory of atoms in molecules (QTAIM) parameters when compared with those obtained directly from the MP2/6-311++G(3d,3p) calculations and +/-0.05 D and 51.2 km mol(-1) when compared with the experimental values. Charge (C), charge flux (CF), and dipole flux (DF) contributions are reported for all the normal vibrations of these molecules. A large negative correlation coefficient of -0.83 is calculated between the charge flux and dipole flux contributions and indicates that electronic charge transfer from one side of the molecule to the other during vibrations is accompanied by a relaxation effect with electron density polarization in the opposite direction. The characteristic substituent effect that has been observed for experimental infrared intensity parameters and core electron ionization energies has been applied to the CCFDF/QTAIM parameters of F2CO, Cl2CO, F2CS, and Cl2CS. The individual atomic charge, atomic charge flux, and atomic dipole flux contributions are seen to obey the characteristic substituent effect equation just as accurately as the total dipole moment derivative. The CH, CF, and CCl stretching normal modes of these molecules are shown to have characteristic sets of charge, charge flux, and dipole flux contributions.

Local electric dipole moments: A generalized approach.

PubMed

Groß, Lynn; Herrmann, Carmen

2016-09-30

We present an approach for calculating local electric dipole moments for fragments of molecular or supramolecular systems. This is important for understanding chemical gating and solvent effects in nanoelectronics, atomic force microscopy, and intensities in infrared spectroscopy. Owing to the nonzero partial charge of most fragments, "naively" defined local dipole moments are origin-dependent. Inspired by previous work based on Bader's atoms-in-molecules (AIM) partitioning, we derive a definition of fragment dipole moments which achieves origin-independence by relying on internal reference points. Instead of bond critical points (BCPs) as in existing approaches, we use as few reference points as possible, which are located between the fragment and the remainder(s) of the system and may be chosen based on chemical intuition. This allows our approach to be used with AIM implementations that circumvent the calculation of critical points for reasons of computational efficiency, for cases where no BCPs are found due to large interfragment distances, and with local partitioning schemes other than AIM which do not provide BCPs. It is applicable to both covalently and noncovalently bound systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

FUSE spectra of Lyman series emissions from the interplanetary medium

NASA Astrophysics Data System (ADS)

Clarke, John

Neutral atoms from the local ISM flow into the solar system producing diffuse emissions through resonant scattering of solar emissions. This wind contains the velocity distribution of the local ISM, plus modifications by solar gravity and radiation pressure near the Sun. In addition, the H atom motions are modified by charge exchange collisions with fast protons in the heliospheric interface region, while He atoms are little affected by charge exchange. Recent observations of the He and H flows in the solar system suggest that the He velocity of 26 km s-1 is that of the local ISM cloud, while the lower H velocity of 18-21 km s-1 and greatly increased velocity dispersion in the flow direction are due to an interface modification of the H flow. Remote observations of the H flow thereby provide a method to remotely study the heliospheric interface. The H flow has been studied from H Lyα line profiles at high spectral resolution observed by Copernicus, IUE, and HST, using the Earth orbital motion to Doppler shift the ISM from the geocoronal emission. One serious ambiguity in the interpretation of these data results from the optically thick Lyα emission, leading to uncertainties in derived values of the H density. Using FUSE to observe the brightness and line profile of the optically thin H Lyβ line, close in time to SOHO observations of the Lyα emission, we can determine accurately the optical depth and density n(H) along lines of sight upwind, downwind, and cross-flow. Comparing n(H) with the heliospheric helium density, and with the interstellar cloud HI/HeI ratio measured recently by the EUVE, will give the fraction of H atoms removed by charge exchange at the entrance to the heliosphere, and then the Local Cloud (or ambient ISM) electron density which governs the size of the heliosphere. We request FUSE sky aperture spectra in the two narrow science apertures obtained during other pointed observations, through cooperation in scheduling pointed observations in the correct look directions at the proper times of year.

Search for light scalar dark matter with atomic gravitational wave detectors

NASA Astrophysics Data System (ADS)

Arvanitaki, Asimina; Graham, Peter W.; Hogan, Jason M.; Rajendran, Surjeet; Van Tilburg, Ken

2018-04-01

We show that gravitational wave detectors based on a type of atom interferometry are sensitive to ultralight scalar dark matter. Such dark matter can cause temporal oscillations in fundamental constants with a frequency set by the dark matter mass and amplitude determined by the local dark matter density. The result is a modulation of atomic transition energies. We point out a new time-domain signature of this effect in a type of gravitational wave detector that compares two spatially separated atom interferometers referenced by a common laser. Such a detector can improve on current searches for electron-mass or electric-charge modulus dark matter by up to 10 orders of magnitude in coupling, in a frequency band complementary to that of other proposals. It demonstrates that this class of atomic sensors is qualitatively different from other gravitational wave detectors, including those based on laser interferometry. By using atomic-clock-like interferometers, laser noise is mitigated with only a single baseline. These atomic sensors can thus detect scalar signals in addition to tensor signals.

Cathodic Corrosion at the Bismuth-Ionic Liquid Electrolyte Interface under Conditions for CO 2 Reduction

DOE PAGES

Medina Ramos, Jonnathan; Zhang, Weiwei; Yoon, Kichul; ...

2018-03-08

Bismuth electrodes undergo distinctive electrochemically induced structural changes in nonaqueous imidazolium ([Im])(+))-based ionic liquid solutions under cathodic polarization. In situ X-ray reflectivity (XR) studies have been undertaken to probe well-ordered Bi (001) films which originally contain a native Bi 2O 3 layer. This oxide layer gets reduced to Bi(0)during the first cyclic voltammetry (CV) scan in acetonitrile solutions containing 1-butyl-3-methylimidazolium ([BMIM](+)) electrolytes. Approximately 60% of the Bi (001) Bragg peak reflectivity is lost during a potential sweep between -1.5 and -1.9 V vs Ag/AgCI due to a similar to 4-10% thinning and a similar to 40% decrease in lateral sizemore » of Bi (001) domains, which are mostly reversed during the anodic scan. Repeated potential cycling enhances the thinning and roughening of the films, suggesting that partial dissolution of Bi ensues during negative polarization. The mechanism of this behavior is understood through molecular dynamics simulations using ReaxFF and density functional theory (DFT) calculations. Both approaches indicate that [Im] + cations bind to the metal surface more strongly than tetrabutylammonium (TBA +) as the potential and the charge on the Bi surface become more negative. ReaxFF simulations predict a higher degree of disorder for a negatively charged Bi (001) slab in the presence of the [Im](+)cations and substantial migration of Bi atoms from the surface. DFT simulations show the formation of Bi center dot center dot center dot[Im] + complexes that lead to the dissolution of Bi atoms from step edges on the Bi (001) surface at potentials between -1.65 and -1.95 V. Bi desorption from a flat terrace requires a potential of approximately -2.25 V. Together, these results suggest the formation of a Bi center dot center dot center dot[Im] + complex through partial cathodic corrosion of the Bi film under conditions (potential and electrolyte composition) that favor the catalytic reduction of CO 2 .« less

Cathodic Corrosion at the Bismuth-Ionic Liquid Electrolyte Interface under Conditions for CO 2 Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medina Ramos, Jonnathan; Zhang, Weiwei; Yoon, Kichul

Bismuth electrodes undergo distinctive electrochemically induced structural changes in nonaqueous imidazolium ([Im])(+))-based ionic liquid solutions under cathodic polarization. In situ X-ray reflectivity (XR) studies have been undertaken to probe well-ordered Bi (001) films which originally contain a native Bi 2O 3 layer. This oxide layer gets reduced to Bi(0)during the first cyclic voltammetry (CV) scan in acetonitrile solutions containing 1-butyl-3-methylimidazolium ([BMIM](+)) electrolytes. Approximately 60% of the Bi (001) Bragg peak reflectivity is lost during a potential sweep between -1.5 and -1.9 V vs Ag/AgCI due to a similar to 4-10% thinning and a similar to 40% decrease in lateral sizemore » of Bi (001) domains, which are mostly reversed during the anodic scan. Repeated potential cycling enhances the thinning and roughening of the films, suggesting that partial dissolution of Bi ensues during negative polarization. The mechanism of this behavior is understood through molecular dynamics simulations using ReaxFF and density functional theory (DFT) calculations. Both approaches indicate that [Im] + cations bind to the metal surface more strongly than tetrabutylammonium (TBA +) as the potential and the charge on the Bi surface become more negative. ReaxFF simulations predict a higher degree of disorder for a negatively charged Bi (001) slab in the presence of the [Im](+)cations and substantial migration of Bi atoms from the surface. DFT simulations show the formation of Bi center dot center dot center dot[Im] + complexes that lead to the dissolution of Bi atoms from step edges on the Bi (001) surface at potentials between -1.65 and -1.95 V. Bi desorption from a flat terrace requires a potential of approximately -2.25 V. Together, these results suggest the formation of a Bi center dot center dot center dot[Im] + complex through partial cathodic corrosion of the Bi film under conditions (potential and electrolyte composition) that favor the catalytic reduction of CO 2 .« less

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

Quantum crystallographic charge density of urea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Fe Isolated Single Atoms on S, N Codoped Carbon by Copolymer Pyrolysis Strategy for Highly Efficient Oxygen Reduction Reaction.

PubMed

Li, Qiheng; Chen, Wenxing; Xiao, Hai; Gong, Yue; Li, Zhi; Zheng, Lirong; Zheng, Xusheng; Yan, Wensheng; Cheong, Weng-Chon; Shen, Rongan; Fu, Ninghua; Gu, Lin; Zhuang, Zhongbin; Chen, Chen; Wang, Dingsheng; Peng, Qing; Li, Jun; Li, Yadong

2018-06-01

Heteroatom-doped Fe-NC catalyst has emerged as one of the most promising candidates to replace noble metal-based catalysts for highly efficient oxygen reduction reaction (ORR). However, delicate controls over their structure parameters to optimize the catalytic efficiency and molecular-level understandings of the catalytic mechanism are still challenging. Herein, a novel pyrrole-thiophene copolymer pyrolysis strategy to synthesize Fe-isolated single atoms on sulfur and nitrogen-codoped carbon (Fe-ISA/SNC) with controllable S, N doping is rationally designed. The catalytic efficiency of Fe-ISA/SNC shows a volcano-type curve with the increase of sulfur doping. The optimized Fe-ISA/SNC exhibits a half-wave potential of 0.896 V (vs reversible hydrogen electrode (RHE)), which is more positive than those of Fe-isolated single atoms on nitrogen codoped carbon (Fe-ISA/NC, 0.839 V), commercial Pt/C (0.841 V), and most reported nonprecious metal catalysts. Fe-ISA/SNC is methanol tolerable and shows negligible activity decay in alkaline condition during 15 000 voltage cycles. X-ray absorption fine structure analysis and density functional theory calculations reveal that the incorporated sulfur engineers the charges on N atoms surrounding the Fe reactive center. The enriched charge facilitates the rate-limiting reductive release of OH* and therefore improved the overall ORR efficiency. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Spin Multiplicity in O2 Adsorption and Dissociation on Small Bimetallic AuAg Clusters.

PubMed

García-Cruz, Raúl; Poulain, Enrique; Hernández-Pérez, Isaías; Reyes-Nava, Juan A; González-Torres, Julio C; Rubio-Ponce, A; Olvera-Neria, Oscar

2017-08-17

To dispose of atomic oxygen, it is necessary the O 2 activation; however, an energy barrier must be overcome to break the O-O bond. This work presents theoretical calculations of the O 2 adsorption and dissociation on small pure Au n and Ag m and bimetallic Au n Ag m (n + m ≤ 6) clusters using the density functional theory (DFT) and the zeroth-order regular approximation (ZORA) to explicitly include scalar relativistic effects. The most stable Au n Ag m clusters contain a higher concentration of Au with Ag atoms located in the center of the cluster. The O 2 adsorption energy on pure and bimetallic clusters and the ensuing geometries depend on the spin multiplicity of the system. For a doublet multiplicity, O 2 is adsorbed in a bridge configuration, whereas for a triplet only one O-metal bond is formed. The charge transfer from metal toward O 2 occupies the σ* O-O antibonding natural bond orbital, which weakens the oxygen bond. The Au 3 ( 2 A) cluster presents the lowest activation energy to dissociate O 2 , whereas the opposite applies to the AuAg ( 3 A) system. In the O 2 activation, bimetallic clusters are not as active as pure Au n clusters due to the charge donated by Ag atoms being shared between O 2 and Au atoms.

The Primary Break-up Instabilities in a gas-liquid coaxial atomizer combined with electro-spray

NASA Astrophysics Data System (ADS)

Osuna, Rodrigo; Machicoane, Nathanael; Aliseda, Alberto

2017-11-01

We present an experimental study of a canonical coaxial gas-liquid atomizer, balancing the physics of gas-assisted atomization and electro-sprays. The laminar liquid stream is injected through a long straight metallic pipe at the center of the turbulent gas jet. The liquid needle is used as the anode, while the cathode is formed by a ring located on the streamwise face of the coaxial gas chamber. The gas Reynolds number ranges from 104-106, while keeping the liquid Reynolds number constant at 103. The electrospray voltage applied is varied from 100 to 5000 V and the resulting negative charge transferred to the liquid jet spans from O(10-3 - 10-1) Coulomb per cubic meter. The relative influence of the high speed gas to the liquid electric charge on the primary instability and jet break-up is studied. The effect of the electric field on the atomization process is characterized by high speed visualization at the nozzle exit, complemented with the resulting droplet size distribution in the mid field after break-up has ended. The quantitative visualization captures the fast dynamics of the interface de-stabilization and clearly shows the changes in the liquid stream instabilities caused by the electric field. These instabilities control the liquid droplet sizes and their spatio-temporal distribution in the spray, as measured from light interferometry.

Atomic charges of individual reactive chemicals in binary mixtures determine their joint effects: an example of cyanogenic toxicants and aldehydes.

PubMed

Tian, Dayong; Lin, Zhifen; Yin, Daqiang; Zhang, Yalei; Kong, Deyang

2012-02-01

Environmental contaminants are usually encountered as mixtures, and many of these mixtures yield synergistic or antagonistic effects attributable to an intracellular chemical reaction that pose a potential threat on ecological systems. However, how atomic charges of individual chemicals determine their intracellular chemical reactions, and then determine the joint effects for mixtures containing reactive toxicants, is not well understood. To address this issue, the joint effects between cyanogenic toxicants and aldehydes on Photobacterium phosphoreum were observed in the present study. Their toxicological joint effects differed from one another. This difference is inherently related to the two atomic charges of the individual chemicals: the oxygen charge of -CHO (O(aldehyde toxicant)) in aldehyde toxicants and the carbon-atom charge of a carbon chain in the cyanogenic toxicant (C(cyanogenic toxicant)). Based on these two atomic charges, the following QSAR (quantitative structure-activity relationship) model was proposed: When (O(aldehyde toxicant) -C(cyanogenic toxicant) )> -0.125, the joint effect of equitoxic binary mixtures at median inhibition (TU, the sum of toxic units) can be calculated as TU = 1.00 ± 0.20; when (O(aldehyde toxicant) -C(cyanogenic toxicant) ) ≤ -0.125, the joint effect can be calculated using TU = - 27.6 x O (aldehyde toxicant) - 5.22 x C (cyanogenic toxicant) - 6.97 (n = 40, r = 0.887, SE = 0.195, F = 140, p < 0.001, q(2) (Loo) = 0.748; SE is the standard error of the regression, F is the F test statistic). The result provides insight into the relationship between the atomic charges and the joint effects for mixtures containing cyanogenic toxicants and aldehydes. This demonstrates that the essence of the joint effects resulting from intracellular chemical reactions depends on the atomic charges of individual chemicals. The present study provides a possible approach for the development of a QSAR model for mixtures containing reactive toxicants based on the atomic charges. Copyright © 2011 SETAC.

Band gap modulation of graphene by metal substrate: A first principles study

NASA Astrophysics Data System (ADS)

Sahoo, Mihir Ranjan; Sahu, Sivabrata; Kushwaha, Anoop Kumar; Nayak, S. K.

2018-04-01

Due to high in-plane charge carrier mobility with high electron velocity and long spin diffusion length, graphene guarantees as a completely unique material for devices with various applications. Unaffected 2pz orbitals of carbon atoms in graphene can be highly influenced by substrates and leads to tuning in electronic properties. We report here a density functional calculation of graphene monolayer based on metallic substrate like nickel surfaces. Band-gap of graphene near K points opens due to interactions between 2pz and d-orbitals of nickel atoms and the gap modulation can be done with the increasing number of layers of substrates.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Simple Pencil-and-Paper Notation for Representing Electrical Charge States

NASA Astrophysics Data System (ADS)

Morse, Robert A.

2017-11-01

In Benjamin Franklin's one fluid theory of electrification, ordinary unelectrified matter consisted of a matrix of matter suffused with a certain amount of "electrical fluid." Electrical effects were due to an excess or deficit of electrical fluid, hence the terms positive and negative. Before the development of a modern view of the atom, diagrams showing charged objects would simply have "+" or "-" signs to indicate the charged state. As physicists we know how to interpret these diagrams and understand what they are telling us about the underlying atomic model of charging. However, novice students may not readily make the connection between the atomic model, in which a charged solid object either gains or loses electrons but does not gain or lose positive charges. Furthermore, when isolated objects become charged, the total number of electrons must be accounted for as charge is a conserved quantity. To really understand the changes that occur in charging by contact, conduction, or induction, it is useful for students to visually represent the processes in a way that emphasizes the atomicity of the processes, including the induced polarization of objects, and the requirement that charge be conserved.

Atom Probe Analysis of Ex Situ Gas-Charged Stable Hydrides.

PubMed

Haley, Daniel; Bagot, Paul A J; Moody, Michael P

2017-04-01

In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200-500 kPa (2-5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide-metal interface of a native oxide formed on vanadium. Through these experiments, we demonstrate the feasibility of ex situ hydrogen analysis for hydrides via atom probe tomography, and thus a practical route to three-dimensional imaging of hydrogen in hydrides at the atomic scale.

Bands dispersion and charge transfer in β-BeH2

NASA Astrophysics Data System (ADS)

Trivedi, D. K.; Galav, K. L.; Joshi, K. B.

2018-04-01

Predictive capabilities of ab-initio method are utilised to explore bands dispersion and charge transfer in β-BeH2. Investigations are carried out using the linear combination of atomic orbitals method at the level of density functional theory. The crystal structure and related parameters are settled by coupling total energy calculations with the Murnaghan equation of state. Electronic bands dispersion from PBE-GGA is reported. The PBE-GGA, and PBE0 hybrid functional, show that β-BeH2 is a direct gap semiconductor with 1.18 and 2.40 eV band gap. The band gap slowly decreases with pressure and beyond l00 GPa overlap of conduction and valence bands at the r point is observed. Charge transfer is studied by means of Mullikan population analysis.

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

“Glass-like” thermal conductivity gradually induced in thermoelectric Sr{sub 8}Ga{sub 16}Ge{sub 30} clathrate by off-centered guest atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christensen, Sebastian; Schmøkel, Mette Stokkebro; Borup, Kasper Andersen

The origin of the “glass-like” plateau in thermal conductivity of inorganic type I clathrates has been debated for more than a decade. Here, it is demonstrated that the low temperature thermal conductivity of Sr{sub 8}Ga{sub 16}Ge{sub 30} can be controlled by the synthesis method: A flux-grown sample has a “glass-like” plateau in thermal conductivity at low temperature, while a zone-melted sample instead has a crystalline peak. A combination of flux-growth and zone-melting produces an intermediate thermal conductivity. In a comprehensive study of three single crystal samples, it is shown by neutron diffraction that the transition from crystalline peak to “glass-like”more » plateau is related to an increase in Sr guest atom off-centering distance from 0.24 Å to 0.43 Å. By modifying ab initio calculated force constants for the guest atom to an isotropic model, we reproduce both measured heat capacity and inelastic neutron scattering data. The transition from peak to plateau in the thermal conductivity can be modeled by a combined increase of Rayleigh and disorder scattering. Measurement of heat capacity refutes simple models for tunneling of Sr between off-center sites. Furthermore, the electronic properties of the same samples are characterized by Hall carrier density, Seebeck coefficient, and resistivity. The present comprehensive analysis excludes tunneling and charge carrier scattering as dominant contributors to the “glass-like” plateau. The increased guest atom off-centering distance controlled by synthesis provides a possible microscopic mechanism for reducing the low temperature thermal conductivity of clathrates.« less

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

PubMed

Yang, Yang; Yu, Haibo; York, Darrin; Cui, Qiang; Elstner, Marcus

2007-10-25

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.

Geometries and properties of bimetallic phosphido-bridged complex Cp(CO) 2W(μ-PPh 2)W(CO) 5 and Cp(CO) 3W(μ-PPh 2)W(CO) 5

NASA Astrophysics Data System (ADS)

Wang, Fang; Yang, Hongmei; Yang, Zuoyin; Zhang, Jingchang; Cao, Weiliang

2007-01-01

Complete geometry optimizations were carried out by HF and DFT methods to study the molecular structure of binuclear transition-metal compounds (Cp(CO) 3W(μ-PPh 2)W(CO) 5) (I) and (Cp(CO) 2W(μ-PPh 2)W(CO) 5) (II). A comparison of the experimental data and calculated structural parameters demonstrates that the most accurate geometry parameters are predicted by the MPW1PW91/LANL2DZ among the three DFT methods. Topological properties of molecular charge distributions were analyzed with the theory of atoms in molecules. (3, -1) critical points, namely bond critical point, were found between the two tungsten atoms, and between W1 and C10 in complex II, which confirms the existence of the metal-metal bond and a semi-bridging CO between the two tungsten atoms. The result provided a theoretical guidance of detailed study on the binuclear phosphido-bridged complex containing transition metal-metal bond, which could be useful in the further study of the heterobimetallic phosphido-bridged complexes.

Compact, accurate description of diagnostic neutral beam propagation and attenuation in a high temperature plasma for charge exchange recombination spectroscopy analysis.

PubMed

Bespamyatnov, Igor O; Rowan, William L; Granetz, Robert S

2008-10-01

Charge exchange recombination spectroscopy on Alcator C-Mod relies on the use of the diagnostic neutral beam injector as a source of neutral particles which penetrate deep into the plasma. It employs the emission resulting from the interaction of the beam atoms with fully ionized impurity ions. To interpret the emission from a given point in the plasma as the density of emitting impurity ions, the density of beam atoms must be known. Here, an analysis of beam propagation is described which yields the beam density profile throughout the beam trajectory from the neutral beam injector to the core of the plasma. The analysis includes the effects of beam formation, attenuation in the neutral gas surrounding the plasma, and attenuation in the plasma. In the course of this work, a numerical simulation and an analytical approximation for beam divergence are developed. The description is made sufficiently compact to yield accurate results in a time consistent with between-shot analysis.

Plentiful magnetic moments in oxygen deficient SrTiO 3

DOE PAGES

Ganesh, Panchapakesan; Lopez-Bezanilla, Alejandro; Littlewood, Peter B.

2015-10-06

In this research, correlated band theory is employed to investigate the magnetic and electronic properties of different arrangements of oxygen di- and tri-vacancy clusters in SrTiO 3. Hole and electron doping of oxygen deficient SrTiO 3 yields various degrees of magnetization as a result of the interaction between localized magnetic moments at the defect sites. Different kinds of Ti atomic orbital hybridization are described as a function of the doping level and defect geometry. We find that magnetism in SrTiO 3–δ is sensitive to the arrangement of neighbouring vacancy sites, charge carrier density, and vacancy-vacancy interaction. Permanent magnetic moments inmore » the absence of vacancy doping electrons are observed. Our description of the charged clusters of oxygen vacancies widens the previous descriptions of mono- and multi-vacancies and points out the importance of the controlled formation at the atomic level of defects for the realization of transition metal oxide based devices with a desirable magnetic performance.« less

MUSIC for localization of thunderstorm cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosher, J.C.; Lewis, P.S.; Rynne, T.M.

1993-12-31

Lightning represents an event detectable optically, electrically, and acoustically, and several systems are already in place to monitor such activity. Unfortunately, such detection of lightning can occur too late, since operations need to be protected in advance of the first lightning strike. Additionally, the bolt itself can traverse several kilometers before striking the ground, leaving a large region of uncertainty as to the center of the storm and its possible strike regions. NASA Kennedy Space Center has in place an array of electric field mills that monitor the (effectively) DC electric field. Prior to the first lightning strike, the surfacemore » electric fields rise as the storm generator within a thundercloud begins charging. Extending methods we developed for an analogous source localization problem in mangnetoencephalography, we present Cramer-Rao lower bounds and MUSIC scans for fitting a point-charge source model to the electric field mill data. Such techniques can allow for the identification and localization of charge centers in cloud structures.« less

DFT computational analysis of piracetam

NASA Astrophysics Data System (ADS)

Rajesh, P.; Gunasekaran, S.; Seshadri, S.; Gnanasambandan, T.

2014-11-01

Density functional theory calculation with B3LYP using 6-31G(d,p) and 6-31++G(d,p) basis set have been used to determine ground state molecular geometries. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of piracetam is calculated using B3LYP/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO/NLMO analysis. The calculation of first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. Molecular electrostatic potential (MEP) at a point in the space around a molecule gives an indication of the net electrostatic effect produced at that point by the total charge distribution of the molecule. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charge is also calculated. Because of vibrational analysis, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-Vis spectra and electronic absorption properties are explained and illustrated from the frontier molecular orbitals.

A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids

PubMed Central

Boschitsch, Alexander H.; Fenley, Marcia O.

2011-01-01

An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent – analytical solutions are available for this case, thus allowing rigorous assessment of the solution accuracy; (ii) a pair of low dielectric charged spheres embedded in a ionic solvent to compute electrostatic interaction free energies as a function of the distance between sphere centers; (iii) surface potentials of proteins, nucleic acids and their larger-scale assemblies such as ribosomes; and (iv) electrostatic solvation free energies and their salt sensitivities – obtained with both linear and nonlinear Poisson-Boltzmann equation – for a large set of proteins. These latter results along with timings can serve as benchmarks for comparing the performance of different PBE solvers. PMID:21984876

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins

PubMed Central

Dadarlat, Voichita M.; Post, Carol Beth

2016-01-01

In this paper we use the results from all atom MD simulations of proteins and peptides to assess individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the “unfolded state”) and charged amino acids in globular proteins (the “folded state”). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO−) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while NH3+ groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously. PMID:18303881

Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

NASA Astrophysics Data System (ADS)

Gross, Leo

The fuctionalization of tips by atomic manipulation dramatically increased the resolution of atomic force microscopy (AFM). The combination of high-resolution AFM with atomic manipulation now offers the unprecedented possibility to custom-design individual molecules by making and breaking bonds with the tip of the microscope and directly characterizing the products on the atomic scale. We recently applied this technique to generate and study reaction intermediates and to investigate chemical reactions trigged by atomic manipulation. We formed diradicals by dissociating halogen atoms and then reversibly triggered ring-opening and -closing reactions via atomic manipulation, allowing us to switch and control the molecule's reactivity, magnetic and optical properties. Additional information about charge states and charge distributions can be obtained by Kelvin probe force spectroscopy. On multilayer insulating films we investigated single-electron attachment, detachment and transfer between individual molecules. EU ERC AMSEL (682144), EU project PAMS (610446).

Discovery of S···C≡N Intramolecular Bonding in a Thiophenylcyanoacrylate-Based Dye: Realizing Charge Transfer Pathways and Dye···TiO 2 Anchoring Characteristics for Dye-Sensitized Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cole, Jacqueline M.; Blood-Forsythe, Martin A.; Lin, Tze-Chia

Donor-pi-acceptor dyes containing thiophenyl pi-conjugated units and cyanoacrylate acceptor groups are among the best-performing organic chromophores used in dye-sensitized solar cell (DSC) applications. Yet, the molecular origins of their high photovoltaic output have remained unclear until now. This synchrotron-based X-ray diffraction study elucidates these origins for the high-performance thiophenylcyanoacrylate-based dye MK-2 (7.7% DSC device efficiency) and its molecular building block, MK-44. The crystal structures of MK-2 and MK-44 are both determined, while a high-resolution charge-density mapping of the smaller molecule was also possible, enabling the nature of its bonding to be detailed. A strong S center dot center dot centermore » dot C equivalent to N intramolecular interaction is discovered, which bears a bond critical point, thus proving that this interaction should be formally classified as a chemical bond. A topological analysis of the pi-conjugated portion of MK-44 shows that this S center dot center dot center dot C equivalent to N bonding underpins the highly efficient intramolecular charge transfer(ICT) in thiophenylcyanoacrylate dyes. This manifests as two bipartite ICT pathways bearing carboxylate and nitrile end points. In turn, these pathways dictate a preferred COO/CN anchoring mode for the dye as it adsorbs onto TiO2 surfaces, to form the dye TiO2 interface that constitutes the DSC working electrode. These results corroborate a recent proposal that all cyanoacrylate groups anchor onto TiO2 in this COO/CN binding configuration. Conformational analysis of the MK-44 and MK-2 crystal structures reveals that this S center dot center dot center dot C equivalent to N bonding will persist in MK-2. Accordingly, this newly discovered bond affords a rational explanation for the attractive photovoltaic properties of,MK-2. More generally, this study provides the first unequivocal evidence for an S center dot center dot center dot C equivalent to N interaction, confirming previous speculative assignments of such interactions in other compounds.« less

Charge injection and transport in a single organic monolayer island

NASA Astrophysics Data System (ADS)

Vuillaume, Dominique

2005-03-01

We report how electrons and holes, that are locally injected in a single organic monolayer island (where organic monolayers are made from sublimated oligomers (pentacene and other oligoacenes), or made from chemisorption in solution (self-assembled monolayers) of pi-conjugated moieties), stay localized or are able to delocalize over the island as a function of the molecular conformation (order vs. disorder) of this island. Charge carriers were locally injected by the apex of an atomic force microscope tip, and the resulting two-dimensional distribution and concentration of injected charges were measured by electrical force microscopy (EFM) experiments. We show that in crystalline monolayer islands, both electrons and holes can be equally injected, at a similar charge concentration for symmetric injection bias conditions, and that both charge carriers are delocalized over the whole island. On the contrary, charges injected into a more disordered monolayer stay localized at their injection point. These different results are discussed in relation with the electrical performances of molecular devices made from these monolayers (OFET, SAMFET). These results provide insight into the electronic properties, at the nanometer scale, of these molecular devices.

How to harvest solar energy with the photosynthetic reaction center

NASA Astrophysics Data System (ADS)

Balaeff, Alexander; Reyes, Justin

Photosynthetic reaction center (PRC) is a protein complex that performs a key step in photosynthesis: the electron-hole separation driven by photon absorbtion. The PRC has a great promise for applications in solar energy harvesting and photosensing. Such applications, however, are hampered by the difficulty in extracting the photogenerated electric charge from the PRC. To that end, it was proposed to attach the PRC to a molecular wire through which the charge could be collected. In order to find the attachment point for the wire that would maximize the rate of charge outflow from the PRC, we performed a computational study of the PRC from the R. virdis bacterium. An ensemble of PRC structures generated by a molecular dynamics simulation was used to calculate the rate of charge transport from the site of initial charge separation to several trial sites on the protein surface. The Pathways model was used to calculate the charge transfer rate in each step of the network of heme co-factors through which the charge transport was presumed to proceed. A simple kinetic model was then used to determine the overall rate of the multistep charge transport. The calculations revealed several candidate sites for the molecular wire attachment, recommended for experimental verification.

Proton-hydrogen collisions for Rydberg n,l-changing transitions in the early Universe

NASA Astrophysics Data System (ADS)

Vrinceanu, Daniel

2013-05-01

Cosmic Microwave Background (CMB) is a vestige radiation generated during the Recombination era, some 390,000 years after the Big Bang, when the Universe had become transparent for the first time. Initial observations of CMB made by the Wilkinson Microwave Anisotropy Probe (WMAP) led to determining the age of the Universe. The mechanisms that drove the recombination have been discovered by using modeling of the primordial plasma and seeking agreement with the observations. The new Plank Surveyor Instrument launched in 2009 is expected to produce data about the recombination era of an unprecedented accuracy, that require including better information regarding the basic atomic physics processes into the present models. In this talk, I will review the results for various Rydberg atom - charge particle collisions and establish their relative importance during the stages of recombination era, with respect to each other and to radiative processes. Energy changing and angular momentum changing collisions with electrons and ions are considered. This work has been supported by NSF through grants to the Institute for Theoretical Atomic and Molecular Physics at Harvard Smithsonian Center for Astrophysics and to the Center for Research on Complex Networks at Texas Southern University.

Seventeen-Coordinate Actinide Helium Complexes.

PubMed

Kaltsoyannis, Nikolas

2017-06-12

The geometries and electronic structures of molecular ions featuring He atoms complexed to actinide cations are explored computationally using density functional and coupled cluster theories. A new record coordination number is established, as AcHe 17 3+ , ThHe 17 4+ , and PaHe 17 4+ are all found to be true geometric minima, with the He atoms clearly located in the first shell around the actinide. Analysis of AcHe n 3+ (n=1-17) using the quantum theory of atoms in molecules (QTAIM) confirms these systems as having closed shell, charge-induced dipole bonding. Excellent correlations (R 2 >0.95) are found between QTAIM metrics (bond critical point electron densities and delocalization indices) and the average Ac-He distances, and also with the incremental He binding energies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan

2012-02-07

The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated withmore » the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.« less

A New Instrument Design for Imaging Low Energy Neutral Atoms

NASA Technical Reports Server (NTRS)

Keller, John W.; Collier, Michael R.; Chornay, Dennis; Rozmarynowski, Paul; Getty, Stephanie; Cooper, John F.; Smith, Billy

2007-01-01

The MidSTAR-2 satellite, to be built at the US Naval Academy as a follow-on to the successful MidSTAR-1 satellite (http://web.ew.usna.edu/midstar/), will launch in 2011 and carry three Goddard Space Flight Center (GSFC) experiments developed under Goddard's Internal Research and Development (IRAD) program. One of these GSFC instruments, the Miniature Imager for Neutral Ionospheric atoms and Magnetospheric Electrons (MINI-ME) builds on the heritage of the Goddard-developed Low-Energy Neutral Atom (LENA) imager launched on the IMAGE spacecraft in 2000. MINI-ME features a Venetian-blind conversion surface assembly that improves both light rejection and conversion efficiency in a smaller and lighter package than LENA making this an highly effective instrument for viewing solar wind charge exchange with terrestrial and planetary exospheres. We will describe the MINI-ME prototyping effort and its science targets.

DFT investigation on the electronic structure of Faujasite

NASA Astrophysics Data System (ADS)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

2013-11-01

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

Scanning Tunneling Spectroscopy of Potassium on Graphene

NASA Astrophysics Data System (ADS)

Cormode, Daniel; Leroy, Brian; Yankowitz, Matthew

2012-02-01

We investigate the effect of charged impurities on the electronic properties of large single crystal CVD grown graphene using scanning tunneling microscopy. Mono- and multilayer crystals were prepared by transferring graphene from copper onto exfoliated boron nitride flakes on 300 nm SiO2 substrates. The boron nitride provides an ultra flat surface for the graphene. Potassium atoms are controllably deposited on the graphene at low temperature by heating a nearby getter source. Scanning tunneling spectroscopy and transport measurements were performed in ultra high vacuum at 4.5 K. Transport measurements demonstrate the shifting of the Dirac point as the samples are doped, while STM measurements demonstrate the size, arrangement and local electronic influence of the potassium atoms.

Proximity effects in cold gases of multiply charged atoms (Review)

NASA Astrophysics Data System (ADS)

Chikina, I.; Shikin, V.

2016-07-01

Possible proximity effects in gases of cold, multiply charged atoms are discussed. Here we deal with rarefied gases with densities nd of multiply charged (Z ≫ 1) atoms at low temperatures in the well-known Thomas-Fermi (TF) approximation, which can be used to evaluate the statistical properties of single atoms. In order to retain the advantages of the TF formalism, which is successful for symmetric problems, the external boundary conditions accounting for the finiteness of the density of atoms (donors), nd ≠ 0, are also symmetrized (using a spherical Wigner-Seitz cell) and formulated in a standard way that conserves the total charge within the cell. The model shows that at zero temperature in a rarefied gas of multiply charged atoms there is an effective long-range interaction Eproxi(nd), the sign of which depends on the properties of the outer shells of individual atoms. The long-range character of the interaction Eproxi is evaluated by comparing it with the properties of the well-known London dispersive attraction ELond(nd) < 0, which is regarded as a long-range interaction in gases. For the noble gases argon, krypton, and xenon Eproxi>0 and for the alkali and alkaline-earth elements Eproxi < 0. At finite temperatures, TF statistics manifests a new, anomalously large proximity effect, which reflects the tendency of electrons localized at Coulomb centers to escape into the continuum spectrum. The properties of thermal decay are interesting in themselves as they determine the important phenomenon of dissociation of neutral complexes into charged fragments. This phenomenon appears consistently in the TF theory through the temperature dependence of the different versions of Eproxi. The anomaly in the thermal proximity effect shows up in the following way: for T ≠ 0 there is no equilibrium solution of TS statistics for single multiply charged atoms in a vacuum when the effect is present. Instability is suppressed in a Wigner-Seitz model under the assumption that there are no electron fluxes through the outer boundary R3 ∝ n-1d of a Wigner-Seitz cell. Eproxi corresponds to the definition of the correlation energy in a gas of interacting particles. This review is written so as to enable comparison of the results of the TF formalism with the standard assumptions of the correlation theory for classical plasmas. The classic example from work on weak solutions (including charged solutions)—the use of semi-impermeable membranes for studies of osmotic pressure—is highly appropriate for problems involving Eproxi. Here we are speaking of one or more sharp boundaries formed by the ionic component of a many-particle problem. These may be a metal-vacuum boundary in a standard Casimir cell in a study of the vacuum properties in the 2l gap between conducting media of different kinds or different layered systems (quantum wells) in semiconductors, etc. As the mobile part of the equilibrium near a sharp boundary, electrons can (should) escape beyond the confines of the ion core into a gap 2l with a probability that depends, among other factors, on the properties of Eproxi for the electron cloud inside the conducting walls of the Casimir cell (quantum well). The analog of the Casimir sandwich in semiconductors is the widely used multilayer heterostructures referred to as quantum wells of width 2l with sides made of suitable doped materials, which ensure statistical equilibrium exchange of electrons between the layers of the multilayer structure. The thermal component of the proximity effects in semiconducting quantum wells provides an idea of many features of the dissociation process in doped semiconductors. In particular, a positive Eproxi > 0 (relative to the bottom of the conduction band) indicates that TF donors with a finite density nd ≠ 0 form a degenerate, semiconducting state in the semiconductor. At zero temperature, there is a finite density of free carriers which increases with a power-law dependence on T.

Mixed addenda polyoxometalate "solutions" for stationary energy storage.

PubMed

Pratt, Harry D; Anderson, Travis M

2013-11-28

A series of redox flow batteries utilizing mixed addenda (vanadium and tungsten), phosphorus-based polyoxometalates (A-α-PV3W9O40(6-), B-α-PV3W9O40(6-), and P2V3W15O62(9-)) were prepared and tested. Cyclic voltammetry and bulk electrolysis experiments on the Keggin compounds (A-α-PV3W9O40(6-) and B-α-PV3W9O40(6-)) established that the vanadium centers of these compounds could be used as the positive electrode (PV(IV)3W(VI)9O40(9-)/PV(V)3W(VI)9O40(6-)), and the tungsten centers could be used as the negative electrode (PV(IV)3W(VI)9O40(9-)/PV(IV)3W(V)3W(VI)6O40(12-)) since these electrochemical processes are separated by about 1 V. The results showed that A-α-PV3W9O40(6-) (where A indicates adjacent, corner-sharing vanadium atoms) had coulombic efficiencies (charge in divided by charge out) above 80%, while the coulombic efficiency of B-α-PV3W9O40(6-) (where B indicates adjacent edge-sharing vanadium atoms) fluctuated between 50% and 70% during cycling. The electrochemical yield, a measurement of the actual charge or discharge observed in comparison with the theoretical charge, was between 40% and 50% for A-α-PV3W9O40(6-), and (31)P NMR showed small amounts of PV2W10O40(5-) and PVW11O40(4-) formed with cycling. The electrochemical yield for B-α-PV3W9O40(6-) decreased from 90% to around 60% due to precipitation of the compound on the electrode, but there were no decomposition products detected in the solution by (31)P NMR, and infrared data on the electrode suggested that the cluster remained intact. Testing of P2V3W15O62(9-) (Wells-Dawson structure) suggested higher charge density clusters were not as suitable as the Keggin structures for a redox flow battery due to the poor stability and inaccessibility of the highly reduced materials.

Ionization equilibrium at the transition from valence-band to acceptor-band migration of holes in boron-doped diamond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poklonski, N. A., E-mail: poklonski@bsu.by; Vyrko, S. A.; Poklonskaya, O. N.

A quasi-classical model of ionization equilibrium in the p-type diamond between hydrogen-like acceptors (boron atoms which substitute carbon atoms in the crystal lattice) and holes in the valence band (v-band) is proposed. The model is applicable on the insulator side of the insulator–metal concentration phase transition (Mott transition) in p-Dia:B crystals. The densities of the spatial distributions of impurity atoms (acceptors and donors) and of holes in the crystal are considered to be Poissonian, and the fluctuations of their electrostatic potential energy are considered to be Gaussian. The model accounts for the decrease in thermal ionization energy of boron atomsmore » with increasing concentration, as well as for electrostatic fluctuations due to the Coulomb interaction limited to two nearest point charges (impurity ions and holes). The mobility edge of holes in the v-band is assumed to be equal to the sum of the threshold energy for diffusion percolation and the exchange energy of the holes. On the basis of the virial theorem, the temperature T{sub j} is determined, in the vicinity of which the dc band-like conductivity of holes in the v-band is approximately equal to the hopping conductivity of holes via the boron atoms. For compensation ratio (hydrogen-like donor to acceptor concentration ratio) K ≈ 0.15 and temperature T{sub j}, the concentration of “free” holes in the v-band and their jumping (turbulent) drift mobility are calculated. Dependence of the differential energy of thermal ionization of boron atoms (at the temperature 3T{sub j}/2) as a function of their concentration N is calculated. The estimates of the extrapolated into the temperature region close to T{sub j} hopping drift mobility of holes hopping from the boron atoms in the charge states (0) to the boron atoms in the charge states (−1) are given. Calculations based on the model show good agreement with electrical conductivity and Hall effect measurements for p-type diamond with boron atom concentrations in the range from 3 × 10{sup 17} to 3 × 10{sup 20 }cm{sup −3}, i.e., up to the Mott transition. The model uses no fitting parameters.« less

Carbon-, sulfur-, and phosphorus-based charge transfer reactions in inductively coupled plasma-atomic emission spectrometry

NASA Astrophysics Data System (ADS)

Grindlay, Guillermo; Gras, Luis; Mora, Juan; de Loos-Vollebregt, Margaretha T. C.

2016-01-01

In this work, the influence of carbon-, sulfur-, and phosphorus-based charge transfer reactions on the emission signal of 34 elements (Ag, Al, As, Au, B, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, Ga, Hg, I, In, Ir, K, Li, Mg, Mn, Na, Ni, P, Pb, Pd, Pt, S, Sb, Se, Sr, Te, and Zn) in axially viewed inductively coupled plasma-atomic emission spectrometry has been investigated. To this end, atomic and ionic emission signals for diluted glycerol, sulfuric acid, and phosphoric acid solutions were registered and results were compared to those obtained for a 1% w w- 1 nitric acid solution. Experimental results show that the emission intensities of As, Se, and Te atomic lines are enhanced by charge transfer from carbon, sulfur, and phosphorus ions. Iodine and P atomic emission is enhanced by carbon- and sulfur-based charge transfer whereas the Hg atomic emission signal is enhanced only by carbon. Though signal enhancement due to charge transfer reactions is also expected for ionic emission lines of the above-mentioned elements, no experimental evidence has been found with the exception of Hg ionic lines operating carbon solutions. The effect of carbon, sulfur, and phosphorus charge transfer reactions on atomic emission depends on (i) wavelength characteristics. In general, signal enhancement is more pronounced for electronic transitions involving the highest upper energy levels; (ii) plasma experimental conditions. The use of robust conditions (i.e. high r.f. power and lower nebulizer gas flow rates) improves carbon, sulfur, and phosphorus ionization in the plasma and, hence, signal enhancement; and (iii) the presence of other concomitants (e.g. K or Ca). Easily ionizable elements reduce ionization in the plasma and consequently reduce signal enhancement due to charge transfer reactions.

The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Zhen; Voth, Gregory A., E-mail: gavoth@uchicago.edu

It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operatormore » are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippov, A. V., E-mail: fav@triniti.ru

The interaction of two charged point macroparticles located in Wigner–Seitz cells of simple cubic (SC), body-centered cubic (BCC), or face-centered cubic (FCC) lattices in an equilibrium plasma has been studied within the Debye approximation or, more specifically, based on the linearized Poisson–Boltzmann model. The shape of the outer boundary is shown to exert a strong influence on the pattern of electrostatic interaction between the two macroparticles, which transforms from repulsion at small interparticle distances to attraction as the interparticle distance approaches half the length of the computational cell. The macroparticle pair interaction potential in an equilibrium plasma is shown tomore » be nevertheless the Debye one and purely repulsive for likely charged macroparticles.« less

Basic Electricity. Part 2.

ERIC Educational Resources Information Center

Kilmer, Donald C.

This guide, the second (part 2) in a set of four guides, is designed for the student interested in a vocation in electrical work, and includes two units: Unit IV--Electrical Theory, covering thirteen lessons (matter, the atom, electrical charges in the atom, rules of electric charges, electricity, atoms in an electrical conductor, electrical…

FAST TRACK COMMUNICATION: Electronic structure of a graphene/hexagonal-BN heterostructure grown on Ru(0001) by chemical vapor deposition and atomic layer deposition: extrinsically doped graphene

NASA Astrophysics Data System (ADS)

Bjelkevig, Cameron; Mi, Zhou; Xiao, Jie; Dowben, P. A.; Wang, Lu; Mei, Wai-Ning; Kelber, Jeffry A.

2010-08-01

A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling microscopy/spectroscopy. The unoccupied σ*(Γ1 +) band dispersion yields an effective mass of 0.05 me for graphene in the graphene/h-BN(0001) heterostructure, in spite of strong perturbations to the graphene conduction band edge placement.

Phonon-induced topological transition to a type-II Weyl semimetal

DOE PAGES

Wang, Lin-Lin; Jo, Na Hyun; Wu, Yun; ...

2017-04-11

Given the importance of crystal symmetry for the emergence of topological quantum states, we have studied here, as exemplified in NbNiTe 2, the interplay of crystal symmetry, atomic displacements (lattice vibration), band degeneracy, and band topology. For the NbNiTe 2 structure in space-group 53 (Pmna)$-$ having an inversion center arising from two glide planes and one mirror plane with a two-fold rotation and screw axis$-$a full gap opening exists between two band manifolds near the Fermi energy. Upon atomic displacements by optical phonons, the symmetry lowers to space-group 28 (Pma2), eliminating one glide plane along c, the associated rotation andmore » screw axis, and the inversion center. As a result, 20 Weyl points emerge, including four type-IIWeyl points in the Γ-X direction at the boundary between a pair of adjacent electron and hole bands. Thus, optical phonons may offer control of the transition to a Weyl fermion state.« less

Quantum State Transmission in a Superconducting Charge Qubit-Atom Hybrid

PubMed Central

Yu, Deshui; Valado, María Martínez; Hufnagel, Christoph; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2016-01-01

Hybrids consisting of macroscopic superconducting circuits and microscopic components, such as atoms and spins, have the potential of transmitting an arbitrary state between different quantum species, leading to the prospective of high-speed operation and long-time storage of quantum information. Here we propose a novel hybrid structure, where a neutral-atom qubit directly interfaces with a superconducting charge qubit, to implement the qubit-state transmission. The highly-excited Rydberg atom located inside the gate capacitor strongly affects the behavior of Cooper pairs in the box while the atom in the ground state hardly interferes with the superconducting device. In addition, the DC Stark shift of the atomic states significantly depends on the charge-qubit states. By means of the standard spectroscopic techniques and sweeping the gate voltage bias, we show how to transfer an arbitrary quantum state from the superconducting device to the atom and vice versa. PMID:27922087

Interactions of small platinum clusters with the TiC(001) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Jianjun; Li, Shasha; Chu, Xingli

2015-11-14

Density functional theory calculations are used to elucidate the interactions of small platinum clusters (Pt{sub n}, n = 1–5) with the TiC(001) surface. The results are analyzed in terms of geometric, energetic, and electronic properties. It is found that a single Pt atom prefers to be adsorbed at the C-top site, while a Pt{sub 2} cluster prefers dimerization and a Pt{sub 3} cluster forms a linear structure on the TiC(001). As for the Pt{sub 4} cluster, the three-dimensional distorted tetrahedral structure and the two-dimensional square structure almost have equal stability. In contrast with the two-dimensional isolated Pt{sub 5} cluster, the adsorbed Pt{submore » 5} cluster prefers a three-dimensional structure on TiC(001). Substantial charge transfer takes place from TiC(001) surface to the adsorbed Pt{sub n} clusters, resulting in the negatively charged Pt{sub n} clusters. At last, the d-band centers of the absorbed Pt atoms and their implications in the catalytic activity are discussed.« less

Investigation of exotic stable calcium carbides using theory and experiment

DOE PAGES

Li, Yan-Ling; Wang, Sheng-Nan; Oganov, Artem R.; ...

2015-05-11

It is well known that pressure causes profound changes in the properties of atoms and chemical bonding, leading to the formation of many unusual materials. Here we systematically explore all stable calcium carbides at pressures from ambient to 100 GPa using variable-composition evolutionary structure predictions. We find that Ca 5C 2, Ca 2C, Ca 3C 2, CaC, Ca 2C 3, and CaC 2 have stability fields on the phase diagram. Among these, Ca2C and Ca2C3 are successfully synthesized for the first time via high-pressure experiments with excellent structural correspondence to theoretical predictions. Of particular significance are the base-centered monoclinic phasemore » (space group C 2/m) of Ca 2C, a quasi-two-dimensional metal with layers of negatively charged calcium atoms, and the primitive monoclinic phase (space group P21/c) of CaC with zigzag C 4 groups. Interestingly, strong interstitial charge localization is found in the structure of R-3m-Ca 5C 2 with semimetallic behaviour.« less

Linear free energy study of ring-substituted aniline ozonation for developing treatment of aniline-based pesticide wastes.

PubMed

Pierpoint, A C; Hapeman, C J; Torrents, A

2001-08-01

The relative rate constants for the reaction of ozone were determined for several substituted anilines in aqueous solutions at pH 6.5 and 1.5. At pH 6.5, with the exception of m- and p-nitroaniline, the rate constants obey Hammett's equation: log(k(X)/k(H)) = rho sigma. The departure of m- and p-nitroaniline may be explained by direct conjugation of the reaction center. The commonly used sigma(p)(-) value of 1.27, which extends the range of applicability of the Hammett equation, was insufficient to account for the conjugation effects on ozonation of p-nitroaniline; rho = -1.48 (R = 0.973). Use of amine group atomic charge determinations significantly improved correlations: (k(X)/k(H)) = 48.7 delta - 18.2 (R = 0.996). A linear plot of Hammett constants versus relative rate data at pH 1.5 showed poor correlation: rho = 0.72 (R = 0.572). Poor correlation was similarly observed for amine group atomic charge determinations, suggesting varied reaction mechanisms.

A molecular dynamics simulation study of irradiation induced defects in gold nanowire

NASA Astrophysics Data System (ADS)

Liu, Wenqiang; Chen, Piheng; Qiu, Ruizhi; Khan, Maaz; Liu, Jie; Hou, Mingdong; Duan, Jinglai

2017-08-01

Displacement cascade in gold nanowires was studied using molecular dynamics computer simulations. Primary knock-on atoms (PKAs) with different kinetic energies were initiated either at the surface or at the center of the nanowires. We found three kinds of defects that were induced by the cascade, including point defects, stacking faults and crater at the surface. The starting points of PKAs influence the number of residual point defects, and this consequently affect the boundary of anti-radiation window which was proposed by calculation of diffusion of point defects to the free surface of nanowires. Formation of stacking faults that expanded the whole cross-section of gold nanowires was observed when the PKA's kinetic energy was higher than 5 keV. Increasing the PKA's kinetic energy up to more than 10 keV may lead to the formation of crater at the surface of nanowires due to microexplosion of hot atoms. At this energy, PKAs started from the center of nanowires can also result in the creation of crater because length of cascade region is comparable to diameter of nanowires. Both the two factors, namely initial positions of PKAs as well as the craters induced by higher energy irradiation, would influence the ability of radiation resistance of metal nanowires.

A Review on Resistive Switching in High-k Dielectrics: A Nanoscale Point of View Using Conductive Atomic Force Microscope

PubMed Central

Lanza, Mario

2014-01-01

Metal-Insulator-Metal (MIM) structures have raised as the most promising configuration for next generation information storage, leading to great performance and fabrication-friendly Resistive Random Access Memories (RRAM). In these cells, the memory concept is no more based on the charge storage, but on tuning the electrical resistance of the insulating layer by applying electrical stresses to reach a high resistive state (HRS or “0”) and a low resistive state (LRS or “1”), which makes the memory point. Some high-k dielectrics show this unusual property and in the last years high-k based RRAM have been extensively analyzed, especially at the device level. However, as resistance switching (in the most promising cells) is a local phenomenon that takes place in areas of ~100 nm2, the use of characterization tools with high lateral spatial resolution is necessary. In this paper the status of resistive switching in high-k materials is reviewed from a nanoscale point of view by means of conductive atomic force microscope analyses. PMID:28788561

Electrical conductivity and phase diagram of binary alloys. 21: The system palladium-chromium

NASA Technical Reports Server (NTRS)

Grube, G.; Knabe, R.

1985-01-01

Pd-Cr alloys were investigated by thermal analysis, hardness measurements, X-ray analysis, microscopic examination of etched pieces, and temperature-resistance curves of the solid alloys. Only one compound, Pd2Cr3, m, 1389 deg, is formed. It possesses a cubic face centered lattice and forms with excess Pd a series of solid solutions with a minimum m.p. at 45 atoms% Pd. Hardness maximum appears at the Pd2Cr3 point. Pd2Cr3 forms no solid solutions with Cr but eutectic point appears at 25 atoms% Pd, m. 1320 deg. The sp. resistance of pure Cr in an atom of H, indicates no allotropic forms. Cr2O3 is solid in molten Cr. Pure Cr melts at 1890 plus or minus 10 deg but Cr contg. Cr2O3 starts to melt at 1770 to 1790 deg.

Enhanced water purification: a single atom makes a difference.

PubMed

Stewart, Tom A; Trudell, Daniel E; Alam, Todd M; Ohlin, C André; Lawler, Christian; Casey, William H; Jett, Stephen; Nyman, May

2009-07-15

The aluminum Keggin polycation (Al13) has been identified as an effective specie for neutralization and coagulation of anionic contaminants in water. In this study, we compare efficacy of the aluminum Keggin-ion to the analogues containing a single Ga-atom or single Ge-atom (GaAl12 and GeAl12, respectively) substituted into the center of the polycation in water-treatment studies. We investigated removal of bacteriophage (model viruses), Cryptosporidium, dissolved organic carbon (DOC), and turbidity. In every study, the order of contaminant removal efficacy trends GaAl12 > Al13 > GeAl12. By ESI MS (electrospray ionization mass spectrometry), we noted the GaAl12 deprotonates least of the three aluminum polycations, and thus probably carries the highest charge, and also optimal contaminant-neutralization ability. The ESI MS studies of the aluminum polycation solutions, as well as solid-state characterization of their resulting precipitates both reveal some conversion of Al13 to larger polycations, Al30 for instance. The GaAl12 does not show any evidence for this alteration that is responsible for poor shelf life of commercial prehydrolyzed aluminum coagulants such as polyaluminum chloride. Based on these studies, we conclude that substitution of a single Ga-atom in the center of the aluminum Keggin polycation produces an optimal water-treatment product due to enhanced shelf life and efficacy in neutralization of anionic contaminants.

Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

NASA Astrophysics Data System (ADS)

Blum, Volker

This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

Inductive electronegativity scale. Iterative calculation of inductive partial charges.

PubMed

Cherkasov, Artem

2003-01-01

A number of novel QSAR descriptors have been introduced on the basis of the previously elaborated models for steric and inductive effects. The developed "inductive" parameters include absolute and effective electronegativity, atomic partial charges, and local and global chemical hardness and softness. Being based on traditional inductive and steric substituent constants these 3D descriptors provide a valuable insight into intramolecular steric and electronic interactions and can find broad application in structure-activity studies. Possible interpretation of physical meaning of the inductive descriptors has been suggested by considering a neutral molecule as an electrical capacitor formed by charged atomic spheres. This approximation relates inductive chemical softness and hardness of bound atom(s) with the total area of the facings of electrical capacitor formed by the atom(s) and the rest of the molecule. The derived full electronegativity equalization scheme allows iterative calculation of inductive partial charges on the basis of atomic electronegativities, covalent radii, and intramolecular distances. A range of inductive descriptors has been computed for a variety of organic compounds. The calculated inductive charges in the studied molecules have been validated by experimental C-1s Electron Core Binding Energies and molecular dipole moments. Several semiempirical chemical rules, such as equalized electronegativity's arithmetic mean, principle of maximum hardness, and principle of hardness borrowing could be explicitly illustrated in the framework of the developed approach.

Martian Atmospheric Pressure Static Charge Elimination Tool

NASA Technical Reports Server (NTRS)

Johansen, Michael R.

2014-01-01

A Martian pressure static charge elimination tool is currently in development in the Electrostatics and Surface Physics Laboratory (ESPL) at NASA's Kennedy Space Center. In standard Earth atmosphere conditions, static charge can be neutralized from an insulating surface using air ionizers. These air ionizers generate ions through corona breakdown. The Martian atmosphere is 7 Torr of mostly carbon dioxide, which makes it inherently difficult to use similar methods as those used for standard atmosphere static elimination tools. An initial prototype has been developed to show feasibility of static charge elimination at low pressure, using corona discharge. A needle point and thin wire loop are used as the corona generating electrodes. A photo of the test apparatus is shown below. Positive and negative high voltage pulses are sent to the needle point. This creates positive and negative ions that can be used for static charge neutralization. In a preliminary test, a floating metal plate was charged to approximately 600 volts under Martian atmospheric conditions. The static elimination tool was enabled and the voltage on the metal plate dropped rapidly to -100 volts. This test data is displayed below. Optimization is necessary to improve the electrostatic balance of the static elimination tool.

The structure of K3C60 and the mechanism of superconductivity.

PubMed Central

Pauling, L

1991-01-01

Analysis of the interatomic distances in the superconducting substance K3C60 indicates that each of the K atoms in tetrahedral interstices between C60 spheres accepts three electrons from C60, thus becoming quadricovalent; its four bonds resonate among the 24 adjacent carbon atoms to give a strong framework in which the negative charges are localized on these K atoms. The electric current is carried by the motion of positive charges (holes) through the network of C60 spheres and the K atoms in octahedral holes. Superconductivity is favored by the localization of the negative charges on the tetrahedral K atoms and their noninvolvement in valence-bond resonance, decreasing the rate of mutual extinction of electrons and holes. PMID:11607222

Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

PubMed

Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

2006-03-02

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.

Energetic Nitrogen Ions within the Inner Magnetosphere of Saturn

NASA Astrophysics Data System (ADS)

Sittler, E. C.; Johnson, R. E.; Richardson, J. D.; Jurac, S.; Moore, M.; Cooper, J. F.; Mauk, B. H.; Smith, H. T.; Michael, M.; Paranicus, C.; Armstrong, T. P.; Tsurutani, B.; Connerney, J. E. P.

2003-05-01

Titan's interaction with Saturn's magnetosphere will result in the energetic ejection of atomic nitrogen atoms into Saturn's magnetosphere due to dissociation of N2 by electrons, ions, and UV photons. The ejection of N atoms into Saturn's magnetosphere will form a nitrogen torus around Saturn with mean density of about 4 atoms/cm3 with source strength of 4.5x1025 atoms/sec. These nitrogen atoms are ionized by photoionization, electron impact ionization and charge exchange reactions producing an N+ torus of 1-4 keV suprathermal ions centered on Titan's orbital position. We will show Voyager plasma observations that demonstrate presence of a suprathermal ion component within Saturn's outer magnetosphere. The Voyager LECP data also reported the presence of inward diffusing energetic ions from the outer magnetosphere of Saturn, which could have an N+ contribution. If so, when one conserves the first and second adiabatic invariant the N+ ions will have energies in excess of 100 keV at Dione's L shell and greater than 400 keV at Enceladus' L shell. Energetic charged particle radial diffusion coefficients are also used to constrain the model results. But, one must also consider the solar wind as another important source of keV ions, in the form of protons and alpha particles, for Saturn's outer magnetosphere. Initial estimates indicate that a solar wind source could dominate in the outer magnetosphere, but various required parameters for this estimate are highly uncertain and will have to await Cassini results for confirmation. We show that satellite sweeping and charged particle precipitation within the middle and outer magnetosphere will tend to enrich N+ ions relative to protons within Saturn's inner magnetosphere as they diffuse radially inward for radial diffusion coefficients that do not violate observations. Charge exchange reactions within the inner magnetosphere can be an important loss mechanism for O+ ions, but to a lesser degree for N+ ions. Initial LECP results using composition data at energies greater than 200 keV/nucl., showed that heavy ions within Saturn's inner magnetosphere dominated over protons, but that contrary to original suggestions that these ions were O+ , we now argue that they are instead N+ ions. With energetic N+ ions bombarding the icy satellite surfaces chemical reactions can occur at the end of the ion tracks and produce nitrogen oxides or other nitrogen containing molecules such that the radiology within the icy surfaces is driven by the impacting energetic nitrogen ions. These can accumulate over the lifetime of the Saturn system.

Evidence for side-chain π-delocalization in a planar substituted benzene: an experimental and theoretical charge density study on 2,5-dimethoxybenzaldehyde thiosemicarbazone.

PubMed

Farrugia, Louis J; Khalaji, Aliakbar Dehno

2011-11-17

The charge density in 2,5-dimethoxybenzaldehyde thiosemicarbazone (1) has been studied experimentally using Mo-K(α) X-ray diffraction at 100 K, and by theory using DFT calculations at the B3LYP/6-311++G(2d,2p) level. The quantum theory of atoms in molecules (QTAIM) was used to investigate the extent of π-delocalization in the thioamide side-chain, which is virtually coplanar with the benzene ring. The experimental and theoretical ellipticity profiles along the bond paths were in excellent agreement, and showed that some of the formal single bonds in the side-chain have significant π-bond character. This view was supported by the magnitudes of the topological bond orders and by the delocalization indices δ(Ω(A), Ω(B)). An orbital decomposition of δ(Ω(A), Ω(B)) demonstrated that there was significant π-character in all the interchain non-H chemical bonds. On the other hand, the source function referenced at the interchain bond critical points could not provide any evidence for π-delocalization, showing instead only limited σ-delocalization between nearest neighbors. Overall, the topological evidence and the atomic graphs of the oxygen atoms did not provide convincing evidence for π-delocalization involving the methoxy substituents.

Crystallographic perturbations to valence charge density and hydrogen-surface interactions

NASA Astrophysics Data System (ADS)

Ciston, James W.

The subject of surfaces has been the epicenter of numerous studies in recent years, particularly with respect to applications in catalysis, thin films, and self-assembly of nanostructures where the surface-to-volume ratio is large. Understanding how the atomic structure of materials differs at surfaces where the atoms are far less constrained can yield fundamental insight into these interesting nanoscale phenomena. Quantum surface crystallography takes this one step further in an attempt to experimentally measure the structure of the electrons themselves, which is of greater importance than atomic positions in determining material properties. We report a procedure for obtaining a much better initial parameterization of the charge density than what is possible from a neutral atom model. This procedure involves the parameterization of a bulk charge density model in terms of simple variables such as bond lengths, which can then be transferred to the problem of interest, for instance a surface. Parameterization is accomplished through the fitting of Density Functional Theory calculations of a variety of crystal distortions to a bond-centered pseudoatom (BCPA) model. This parameterized model can then be applied to surfaces or for other problems where an initial higher-order model is needed without the addition of any extra fitted parameters. Through the use of the BCPA model, we report a three-dimensional charge density refinement from x-ray diffraction intensities of the Si (001) 2x1H surface. By properly accounting for the covalent bonding effects in the silicon structure, we were able to stably refine the positions of hydrogen atoms at this surface in three dimensions, which had never before been accomplished for any surface. In addition, we found experimentally an increased, slightly localized bond density of approximately 0.31 electrons between each Si atom pair at the surface. Both the atomic positions and the charge density were found to be in remarkably good agreement with density functional theory (DFT) calculations. The BCPA model was also applied to an experimental refinement of the local charge density at the Si (111) 7x7 surface utilizing a combination of x-ray and high energy electron diffraction. By perturbing about the bond-centered pseudoatom model, we found experimentally that the adatoms were in an anti-bonding state with the atoms directly below. We were also able to experimentally refine a charge transfer of 0.26+/-0.04 e- from each adatom site to the underlying layers. This was the first statistically significant refinement of site-specific bonding information at any surface utilizing x-ray diffraction data. Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction. To further investigate the usefulness of this technique, we performed a systematic study of the effect of precession angle on the mineral andalusite where the semiangle was varied from 6.5 to 32 mrad in five discrete steps. We have shown that the intensities of kinematically forbidden reflections decayed exponentially as the precession semiangle (ϕ) was increased. Additionally, we have determined that charge density effects were best observed at moderately low angles (6.5-13 mrad) even though PED patterns became more kinematical in nature as the precession angle was increased further. We have also shown that the amount of interpretable information provided by direct methods phase inversion of the diffraction data increases monotonically but non-systematically as ϕ increases. We report an experimental and theoretical analysis of the ✓3x✓3-R30° and 2x2 reconstructions on the MgO (111) surface combining transmission electron microscopy, x-ray photoelectron spectroscopy, and reasonably accurate density functional calculations using the meta-GGA functional TPSS. We have not only conclusively solved the atomic structures of these reconstructions, but have developed a kinetic model for an evolutionary pathway between structures driven entirely by exchange of water molecules between the surface and the environment that does not require the cations to move when the structure transforms. This is the first time an experimentally and theoretically supported kinetic model has described not only all of the structures in a series on a single oxide surface, but also describes why none of the structures pass through the thermodynamically most stable configuration. Lastly, we have investigated the observability of valence bonding effects in aberration-corrected high resolution electron microscopy (HREM) images along the [010] projection of the mineral Forsterite (Mg2SiO 4). Direct observability of bonding effects would be both faster and less ambiguous than the refinement of similar features against diffraction data. Through analysis of simulated high resolution electron microscopy images, we have determined that bonding effects should be observable at levels approaching 20% of the total contrast. Initial experimental results for this material system have also been presented.

Analytic treatment of charge cloud overlaps: an improvement of the tomographic atom probe efficiency

NASA Astrophysics Data System (ADS)

Bas, P.; Bostel, A.; Grancher, G.; Deconihout, B.; Blavette, D.

1996-03-01

Although reliable position and composition data are obtained with the Tomographic Atom Probe, the procedure of position calculation by charge centroiding fails when the detector receives two or more ions with close spaced positions and the same mass-to-charge ratio. As the charge clouds of the ions overlap, they form a unique charge pattern on the multianode detector. Only one atom is represented and its position is biased. In order to estimate real positions, we have developed a correction method. The spatial distribution of charges inside a cloud issued from one impact is modelled by a Gaussian law. The particular properties of the Gaussian enable the calculation of exact positions of the two impacts of the overlapped charge patterns and charges of corresponding clouds. The calculation may be generalized for more than two overlapped clouds. The method was tested on a plane-by-plane analysis of a fully ordered Cu 3Au alloy performed on a (100) pole.

Towards a unified description of the charge transport mechanisms in conductive atomic force microscopy studies of semiconducting polymers.

PubMed

Moerman, D; Sebaihi, N; Kaviyil, S E; Leclère, P; Lazzaroni, R; Douhéret, O

2014-09-21

In this work, conductive atomic force microscopy (C-AFM) is used to study the local electrical properties in thin films of self-organized fibrillate poly(3-hexylthiophene) (P3HT), as a reference polymer semiconductor. Depending on the geometrical confinement in the transport channel, the C-AFM current is shown to be governed either by the charge transport in the film or by the carrier injection at the tip-sample contact, leading to either bulk or local electrical characterization of the semiconducting polymer, respectively. Local I-V profiles allow discrimination of the different dominating electrical mechanisms, i.e., resistive in the transport regime and space charge limited current (SCLC) in the local regime. A modified Mott-Gurney law is analytically derived for the contact regime, taking into account the point-probe geometry of the contact and the radial injection of carriers. Within the SCLC regime, the probed depth is shown to remain below 12 nm with a lateral electrical resolution below 5 nm. This confirms that high resolution is reached in those C-AFM measurements, which therefore allows for the analysis of single organic semiconducting nanostructures. The carrier density and mobility in the volume probed under the tip under steady-state conditions are also determined in the SCLC regime.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

Atomic Charge Parameters for the Finite Difference Poisson-Boltzmann Method Using Electronegativity Neutralization.

PubMed

Yang, Qingyi; Sharp, Kim A

2006-07-01

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.

High performance SONOS flash memory with in-situ silicon nanocrystals embedded in silicon nitride charge trapping layer

NASA Astrophysics Data System (ADS)

Lim, Jae-Gab; Yang, Seung-Dong; Yun, Ho-Jin; Jung, Jun-Kyo; Park, Jung-Hyun; Lim, Chan; Cho, Gyu-seok; Park, Seong-gye; Huh, Chul; Lee, Hi-Deok; Lee, Ga-Won

2018-02-01

In this paper, SONOS-type flash memory device with highly improved charge-trapping efficiency is suggested by using silicon nanocrystals (Si-NCs) embedded in silicon nitride (SiNX) charge trapping layer. The Si-NCs were in-situ grown by PECVD without additional post annealing process. The fabricated device shows high program/erase speed and retention property which is suitable for multi-level cell (MLC) application. Excellent performance and reliability for MLC are demonstrated with large memory window of ∼8.5 V and superior retention characteristics of 7% charge loss for 10 years. High resolution transmission electron microscopy image confirms the Si-NC formation and the size is around 1-2 nm which can be verified again in X-ray photoelectron spectroscopy (XPS) where pure Si bonds increase. Besides, XPS analysis implies that more nitrogen atoms make stable bonds at the regular lattice point. Photoluminescence spectra results also illustrate that Si-NCs formation in SiNx is an effective method to form deep trap states.

Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

PubMed

Zhang, Changzhe; Bu, Yuxiang

2016-09-14

Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Quantification of surface charge density and its effect on boundary slip.

PubMed

Jing, Dalei; Bhushan, Bharat

2013-06-11

Reduction of fluid drag is important in the micro-/nanofluidic systems. Surface charge and boundary slip can affect the fluid drag, and surface charge is also believed to affect boundary slip. The quantification of surface charge and boundary slip at a solid-liquid interface has been widely studied, but there is a lack of understanding of the effect of surface charge on boundary slip. In this paper, the surface charge density of borosilicate glass and octadecyltrichlorosilane (OTS) surfaces immersed in saline solutions with two ionic concentrations and deionized (DI) water with different pH values and electric field values is quantified by fitting experimental atomic force microscopy (AFM) electrostatic force data using a theoretical model relating the surface charge density and electrostatic force. Results show that pH and electric field can affect the surface charge density of glass and OTS surfaces immersed in saline solutions and DI water. The mechanisms of the effect of pH and electric field on the surface charge density are discussed. The slip length of the OTS surface immersed in saline solutions with two ionic concentrations and DI water with different pH values and electric field values is measured, and their effects on the slip length are analyzed from the point of surface charge. Results show that a larger absolute value of surface charge density leads to a smaller slip length for the OTS surface.

Electrostatic atomization--Experiment, theory and industrial applications

NASA Astrophysics Data System (ADS)

Okuda, H.; Kelly, Arnold J.

1996-05-01

Experimental and theoretical research has been initiated at the Princeton Plasma Physics Laboratory on the electrostatic atomization process in collaboration with Charged Injection Corporation. The goal of this collaboration is to set up a comprehensive research and development program on the electrostatic atomization at the Princeton Plasma Physics Laboratory so that both institutions can benefit from the collaboration. Experimental, theoretical and numerical simulation approaches are used for this purpose. An experiment consisting of a capillary sprayer combined with a quadrupole mass filter and a charge detector was installed at the Electrostatic Atomization Laboratory to study fundamental properties of the charged droplets such as the distribution of charges with respect to the droplet radius. In addition, a numerical simulation model is used to study interaction of beam electrons with atmospheric pressure water vapor, supporting an effort to develop an electrostatic water mist fire-fighting nozzle.

The formation of excited atoms during charge exchange between hydrogen ions and alkali atoms. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Nieman, R. A.

1971-01-01

The charge exchange cross sections for protons and various alkali atoms are calculated using the classical approximation of Gryzinski. It is assumed that the hydrogen atoms resulting from charge exchange exist in all possible excited states. Charge transfer collisions between protons and potassium as well as protons and sodium atoms are studied. The energy range investigated is between 4 and 30 keV. The theoretical calculations of the capture cross section and the cross section for the creation of metastable 2S hydrogen are compared to experimental values. Good quantitative agreement is found for the capture cross section but only qualitative agreement for the metastable cross section. Analysis of the Lyman alpha window in molecular oxygen suggests that measured values of the metastable cross section may be in error. Thick alkali target data are also presented. This allows the determination of the total electron loss cross section. Finally, some work was done with H2(+).

An improved limit on the charge of antihydrogen from stochastic acceleration.

PubMed

Ahmadi, M; Baquero-Ruiz, M; Bertsche, W; Butler, E; Capra, A; Carruth, C; Cesar, C L; Charlton, M; Charman, A E; Eriksson, S; Evans, L T; Evetts, N; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayden, M E; Isaac, C A; Ishida, A; Jones, S A; Jonsell, S; Kurchaninov, L; Madsen, N; Maxwell, D; McKenna, J T K; Menary, S; Michan, J M; Momose, T; Munich, J J; Nolan, P; Olchanski, K; Olin, A; Povilus, A; Pusa, P; Rasmussen, C Ø; Robicheaux, F; Sacramento, R L; Sameed, M; Sarid, E; Silveira, D M; So, C; Tharp, T D; Thompson, R I; van der Werf, D P; Wurtele, J S; Zhmoginov, A I

2016-01-21

Antimatter continues to intrigue physicists because of its apparent absence in the observable Universe. Current theory requires that matter and antimatter appeared in equal quantities after the Big Bang, but the Standard Model of particle physics offers no quantitative explanation for the apparent disappearance of half the Universe. It has recently become possible to study trapped atoms of antihydrogen to search for possible, as yet unobserved, differences in the physical behaviour of matter and antimatter. Here we consider the charge neutrality of the antihydrogen atom. By applying stochastic acceleration to trapped antihydrogen atoms, we determine an experimental bound on the antihydrogen charge, Qe, of |Q| < 0.71 parts per billion (one standard deviation), in which e is the elementary charge. This bound is a factor of 20 less than that determined from the best previous measurement of the antihydrogen charge. The electrical charge of atoms and molecules of normal matter is known to be no greater than about 10(-21)e for a diverse range of species including H2, He and SF6. Charge-parity-time symmetry and quantum anomaly cancellation demand that the charge of antihydrogen be similarly small. Thus, our measurement constitutes an improved limit and a test of fundamental aspects of the Standard Model. If we assume charge superposition and use the best measured value of the antiproton charge, then we can place a new limit on the positron charge anomaly (the relative difference between the positron and elementary charge) of about one part per billion (one standard deviation), a 25-fold reduction compared to the current best measurement.

Microcircuit Device Reliability. Digital Evaluation and Failure Analysis Data. Parts 1 and 2, Summer 1980

DTIC Science & Technology

1980-01-01

l1i Research Institute (IITRI). RAC is charged with the collection , analysis and dis- semination of reliabil;,y information pertaining to parts used...RCM) is also operating under the auspices of the RAC and serves as the focal point for the collection and analysis of all reliability-related in...the Rome Air Development Center (RADC), and operated at RADC hy lI Research Institute (IITR I). RAC is charged with the collection , analysis and dis

Metal-ligand bond directionality in the M2-NH3 complexes (M = Cu, Ag and Au)

NASA Astrophysics Data System (ADS)

Eskandari, K.; Ebadinejad, F.

2018-05-01

The metal-ligand bonds in the M2-NH3 complexes (M = Au, Ag and Cu) are directional and the M-M-N angles tend to be linear. Natural energy decomposition analysis (NEDA) and localised molecular orbital energy decomposition analysis (LMOEDA) approaches indicate that the metal-ligand bonds in these complexes are mainly electrostatic in nature, however, the electrostatic is not the cause of the linearity of M-M-N arrangements. Instead, NEDA shows that the charge transfer and core repulsion are mainly responsible for the directionality of these bonds. In the LMOEDA point of view, the repulsion term is the main reason for the linearity of these complexes. Interacting quantum atoms (IQA) analysis shows that inter-atomic and inter-fragment interactions favour the nonlinear arrangements; however, these terms are compensated by the atomic self-energies, which stabilise the linear structure.

Shannon entropies and Fisher information of K-shell electrons of neutral atoms

NASA Astrophysics Data System (ADS)

Sekh, Golam Ali; Saha, Aparna; Talukdar, Benoy

2018-02-01

We represent the two K-shell electrons of neutral atoms by Hylleraas-type wave function which fulfils the exact behavior at the electron-electron and electron-nucleus coalescence points and, derive a simple method to construct expressions for single-particle position- and momentum-space charge densities, ρ (r) and γ (p) respectively. We make use of the results for ρ (r) and γ (p) to critically examine the effect of correlation on bare (uncorrelated) values of Shannon information entropies (S) and of Fisher information (F) for the K-shell electrons of atoms from helium to neon. Due to inter-electronic repulsion the values of the uncorrelated Shannon position-space entropies are augmented while those of the momentum-space entropies are reduced. The corresponding Fisher information are found to exhibit opposite behavior in respect of this. Attempts are made to provide some plausible explanation for the observed response of S and F to electronic correlation.

Rutherford's Nuclear Model

NASA Astrophysics Data System (ADS)

Heibron, John

2011-04-01

Rutherford's nuclear model originally was a theory of scattering that represented both the incoming alpha particles and their targets as point charges. The assumption that the apha particle, which Rutherford knew to be a doubly ionized helium atom, was a bare nucleus, and the associated assumption that the electronic structure of the atom played no significant role in large-angle scattering, had immediate and profound consequences well beyond the special problem for which Rutherford introduced them. The group around him in Manchester in 1911/12, which included Niels Bohr, Charles Darwin, Georg von Hevesy, and Henry Moseley, worked out some of these consequences. Their elucidation of radioactivity, isotopy, atomic number, and quantization marked an epoch in microphysics. Rutherford's nuclear model was exemplary not only for its fertility and picturability, but also for its radical simplicity. The lecturer will not undertake to answer the baffling question why such simple models work.

AtomDB Progress Report: Atomic data and new models for X-ray spectroscopy.

NASA Astrophysics Data System (ADS)

Smith, Randall K.; Foster, Adam; Brickhouse, Nancy S.; Stancil, Phillip C.; Cumbee, Renata; Mullen, Patrick Dean; AtomDB Team

2018-06-01

The AtomDB project collects atomic data from both theoretical and observational/experimental sources, providing both a convenient interface (http://www.atomdb.org/Webguide/webguide.php) as well as providing input to spectral models for many types of astrophysical X-ray plasmas. We have released several updates to AtomDB in response to the Hitomi data, including new data for the Fe K complex, and have expanded the range of models available in AtomDB to include the Kronos charge exchange models from Mullen at al. (2016, ApJS, 224, 2). Combined with the previous AtomDB charge exchange model (http://www.atomdb.org/CX/), these data enable a velocity-dependent model for X-ray and EUV charge exchange spectra. We also present a new Kappa-distribution spectral model, enabling plasmas with non-Maxwellian electron distributions to be modeled with AtomDB. Tools are provided within pyAtomDB to explore and exploit these new plasma models. This presentation will review these enhancements and describe plans for the new few years of database and code development in preparation for XARM, Athena, and (hopefully) Arcus.

Exciton-phonon cooperative mechanism of the triple-q charge-density-wave and antiferroelectric electron polarization in TiSe2

NASA Astrophysics Data System (ADS)

Kaneko, Tatsuya; Ohta, Yukinori; Yunoki, Seiji

2018-04-01

We investigate the microscopic mechanisms of the charge-density-wave (CDW) formation in a monolayer TiSe2 using a realistic multiorbital d -p model with electron-phonon coupling and intersite Coulomb (excitonic) interactions. First, we estimate the tight-binding bands of Ti 3 d and Se 4 p orbitals in the monolayer TiSe2 on the basis of the first-principles band-structure calculations. We thereby show orbital textures of the undistorted band structure near the Fermi level. Next, we derive the electron-phonon coupling using the tight-binding approximation and show that the softening occurs in the transverse phonon mode at the M point of the Brillouin zone. The stability of the triple-q CDW state is thus examined to show that the transverse phonon modes at the M1, M2, and M3 points are frozen simultaneously. Then, we introduce the intersite Coulomb interactions between the nearest-neighbor Ti and Se atoms that lead to the excitonic instability between the valence Se 4 p and conduction Ti 3 d bands. Treating the intersite Coulomb interactions in the mean-field approximation, we show that the electron-phonon and excitonic interactions cooperatively stabilize the triple-q CDW state in TiSe2. We also calculate a single-particle spectrum in the CDW state and reproduce the band folding spectra observed in photoemission spectroscopies. Finally, to clarify the nature of the CDW state, we examine the electronic charge density distribution and show that the CDW state in TiSe2 is of a bond type and induces a vortexlike antiferroelectric polarization in the kagome network of Ti atoms.

On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2.

PubMed

Terlan, Bürgehan; Akselrud, Lev; Baranov, Alexey I; Borrmann, Horst; Grin, Yuri

2015-12-01

Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B-B interactions and the polar covalent B-M interactions. The resembling features of the crystal structures are well reflected by the respective B-B interatomic distances as well as by ρ(r) values at the B-B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B-B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

Dynamics behavior of lithium in graphite lattice: MD calculation approach

NASA Astrophysics Data System (ADS)

Shimizu, A.; Tachikawa, H.

2000-12-01

In order to investigate the diffusion process of Li atom in graphite, molecular dynamics simulation was achieved on the basis of molecular mechanics 2 (MM2) method using four layers cluster model one of which is composed of C150H30 with terminating hydrogen atoms. According to the simulations at 500 K, Li atom stabilizes initially around the center of mass, gets out of the graphite layers after 3.0 ps through diffusion, which is different from the movement of Li+ ion captured by the dangling bonds of the edge carbon atoms. The diffusion process of Li atom is found to be composed of following four steps in series: (1) vibration around the stabilization point; (2) bulk diffusion; (3) vibration under influence of the dangling bonds of edge carbon atoms; and (4) escape from the graphite layers. The diffusivity for step (3) is smaller than that for step (2).

The role of charge transfer in the oxidation state change of Ce atoms in the TM13-CeO2(111) systems (TM = Pd, Ag, Pt, Au): a DFT + U investigation.

PubMed

Tereshchuk, Polina; Freire, Rafael L H; Ungureanu, Crina G; Seminovski, Yohanna; Kiejna, Adam; Da Silva, Juarez L F

2015-05-28

Despite extensive studies of transition metal (TM) clusters supported on ceria (CeO2), fundamental issues such as the role of the TM atoms in the change in the oxidation state of Ce atoms are still not well understood. In this work, we report a theoretical investigation based on static and ab initio molecular dynamics density functional theory calculations of the interaction of 13-atom TM clusters (TM = Pd, Ag, Pt, Au) with the unreduced CeO2(111) surface represented by a large surface unit cell and employing Hubbard corrections for the strong on-site Coulomb correlation in the Ce f-electrons. We found that the TM13 clusters form pyramidal-like structures on CeO2(111) in the lowest energy configurations with the following stacking sequence, TM/TM4/TM8/CeO2(111), while TM13 adopts two-dimensional structures at high energy structures. TM13 induces a change in the oxidation state of few Ce atoms (3 of 16) located in the topmost Ce layer from Ce(IV) (itinerant Ce f-states) to Ce(III) (localized Ce f-states). There is a charge flow from the TM atoms to the CeO2(111) surface, which can be explained by the electronegativity difference between the TM (Pd, Ag, Pt, Au) and O atoms, however, the charge is not uniformly distributed on the topmost O layer due to the pressure induced by the TM13 clusters on the underlying O ions, which yields a decrease in the ionic charge of the O ions located below the cluster and an increase in the remaining O ions. Due to the charge flow mainly from the TM8-layer to the topmost O-layer, the charge cannot flow from the Ce(IV) atoms to the O atoms with the same magnitude as in the clean CeO2(111) surface. Consequently, the effective cationic charge decreases mainly for the Ce atoms that have a bond with the O atoms not located below the cluster, and hence, those Ce atoms change their oxidation state from IV to III. This increases the size of the Ce(III) compared with the Ce(IV) cations, which builds-in a strain within the topmost Ce layer, and hence, also affecting the location of the Ce(III) cations and the structure of the TM13 clusters.

Band-bending induced by charged defects and edges of atomically thin transition metal dichalcogenide films

NASA Astrophysics Data System (ADS)

Le Quang, T.; Nogajewski, K.; Potemski, M.; Dau, M. T.; Jamet, M.; Mallet, P.; Veuillen, J.-Y.

2018-07-01

We report scanning tunneling microscopy/spectroscopy (STM/STS) investigations of the band-bending in the vicinity of charged point defects and edges of monolayer MoSe2 and mono- and trilayer WSe2 films deposited on graphitized silicon carbide substrates. By tracing the spatial evolution of the structures of the STS spectra, we evaluate the magnitude and the extent of the band-bending to be equal to few hundreds milielectronvolts and several nanometres, respectively. With the aid of a simple electrostatic model, we show that the spatial variation of the Coulomb potential close to the film edges can be well reproduced by taking into account the metallic screening by graphene. Additionally, the analysis of our data for trilayer WSe2 provides reasonable estimations of its dielectric constant () and of the magnitude of the charge trapped at the defect site (Q  =  +e).

Responsivity calibration of the LoWEUS spectrometer

DOE PAGES

Lepson, J. K.; Beiersdorfer, P.; Kaita, R.; ...

2016-09-02

We performed an in situ calibration of the relative responsivity function of the Long-Wavelength Extreme Ultraviolet Spectrometer (LoWEUS), while operating on the Lithium Tokamak Experiment (LTX) at Princeton Plasma Physics Laboratory. The calibration was accomplished by measuring oxygen lines, which are typically present in LTX plasmas. The measured spectral line intensities of each oxygen charge state were then compared to the calculated emission strengths given in the CHIANTI atomic database. Normalizing the strongest line in each charge state to the CHIANTI predictions, we obtained the differences between the measured and predicted values for the relative strengths of the other linesmore » of a given charge state. We find that a 3rd degree polynomial function provides a good fit to the data points. Lastly, our measurements show that the responsivity between about 120 and 300 Å varies by factor of ~30.« less

Relativistic electron diffraction at the UCLA Pegasus photoinjector laboratory.

PubMed

Musumeci, P; Moody, J T; Scoby, C M

2008-10-01

Electron diffraction holds the promise to yield real-time resolution of atomic motion in an easily accessible environment like a university laboratory at a fraction of the cost of fourth-generation X-ray sources. Currently the limit in time-resolution for conventional electron diffraction is set by how short an electron pulse can be made. A very promising solution to maintain the highest possible beam intensity without excessive pulse broadening from space charge effects is to increase the electron energy to the MeV level where relativistic effects significantly reduce the space charge forces. Rf photoinjectors can in principle deliver up to 10(7)-10(8) electrons packed in bunches of approximately 100-fs length, allowing an unprecedented time resolution and enabling the study of irreversible phenomena by single-shot diffraction patterns. The use of rf photoinjectors as sources for ultrafast electron diffraction has been recently at the center of various theoretical and experimental studies. The UCLA Pegasus laboratory, commissioned in early 2007 as an advanced photoinjector facility, is the only operating system in the country, which has recently demonstrated electron diffraction using a relativistic beam from an rf photoinjector. Due to the use of a state-of-the-art ultrashort photoinjector driver laser system, the beam has been measured to be sub-100-fs long, at least a factor of 5 better than what measured in previous relativistic electron diffraction setups. Moreover, diffraction patterns from various metal targets (titanium and aluminum) have been obtained using the Pegasus beam. One of the main laboratory goals in the near future is to fully develop the rf photoinjector-based ultrafast electron diffraction technique with particular attention to the optimization of the working point of the photoinjector in a low-charge ultrashort pulse regime, and to the development of suitable beam diagnostics.

Point-Defect Nature of the Ultraviolet Absorption Band in AlN

NASA Astrophysics Data System (ADS)

Alden, D.; Harris, J. S.; Bryan, Z.; Baker, J. N.; Reddy, P.; Mita, S.; Callsen, G.; Hoffmann, A.; Irving, D. L.; Collazo, R.; Sitar, Z.

2018-05-01

We present an approach where point defects and defect complexes are identified using power-dependent photoluminescence excitation spectroscopy, impurity data from SIMS, and density-functional-theory (DFT)-based calculations accounting for the total charge balance in the crystal. Employing the capabilities of such an experimental computational approach, in this work, the ultraviolet-C absorption band at 4.7 eV, as well as the 2.7- and 3.9-eV luminescence bands in AlN single crystals grown via physical vapor transport (PVT) are studied in detail. Photoluminescence excitation spectroscopy measurements demonstrate the relationship between the defect luminescent bands centered at 3.9 and 2.7 eV to the commonly observed absorption band centered at 4.7 eV. Accordingly, the thermodynamic transition energy for the absorption band at 4.7 eV and the luminescence band at 3.9 eV is estimated at 4.2 eV, in agreement with the thermodynamic transition energy for the CN- point defect. Finally, the 2.7-eV PL band is the result of a donor-acceptor pair transition between the VN and CN point defects since nitrogen vacancies are predicted to be present in the crystal in concentrations similar to carbon-employing charge-balance-constrained DFT calculations. Power-dependent photoluminescence measurements reveal the presence of the deep donor state with a thermodynamic transition energy of 5.0 eV, which we hypothesize to be nitrogen vacancies in agreement with predictions based on theory. The charge state, concentration, and type of impurities in the crystal are calculated considering a fixed amount of impurities and using a DFT-based defect solver, which considers their respective formation energies and the total charge balance in the crystal. The presented results show that nitrogen vacancies are the most likely candidate for the deep donor state involved in the donor-acceptor pair transition with peak emission at 2.7 eV for the conditions relevant to PVT growth.

Energetics of halogen impurities in thorium dioxide

NASA Astrophysics Data System (ADS)

Kuganathan, Navaratnarajah; Ghosh, Partha S.; Arya, Ashok K.; Dey, Gautam K.; Grimes, Robin W.

2017-11-01

Defect energies for halogen impurity atoms (Cl, Br and I) in thoria are calculated using the generalized gradient approximation and projector augmented plane wave potentials under the framework of density functional theory. The energy to place a halogen atom at a pre-existing lattice site is the incorporation energy. Seven sites are considered: octahedral interstitial, O vacancy, Th vacancy, Th-O di-vacancy cluster (DV) and the three O-Th-O tri-vacancy cluster (NTV) configurations. For point defects and vacancy clusters, neutral and all possible defect charge states up to full formal charge are considered. The most favourable incorporation site for Cl is the singly charged positive oxygen vacancy while for Br and I it is the NTV1 cluster. By considering the energy to form the defect sites, solution energies are generated. These show that in both ThO2-x and ThO2 the most favourable solution equilibrium site for halides is the single positively charged oxygen vacancy (although in ThO2, I demonstrates the same solubility in the NTV1 and DV clusters). Solution energies are much lower in ThO2-x than in ThO2 indicating that stoichiometry is a significant factor in determining solubility. In ThO2, all three halogens are highly insoluble and in ThO2-x Br and I remain insoluble. Although ½Cl2 is soluble in ThO2-x alternative phases such as ZrCl4 exist which are of lower energy.

Atomic partial charges on CH{sub 3}NH{sub 3}PbI{sub 3} from first-principles electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madjet, Mohamed E., E-mail: mmadjet@qf.org.qa; El-Mellouhi, Fedwa; Carignano, Marcelo A.

We calculated the partial charges in methylammonium (MA) lead-iodide perovskite CH{sub 3}NH{sub 3}PbI{sub 3} in its different crystalline phases using different first-principles electronic charge partitioning approaches, including the Bader, ChelpG, and density-derived electrostatic and chemical (DDEC) schemes. Among the three charge partitioning methods, the DDEC approach provides chemically intuitive and reliable atomic charges for this material, which consists of a mixture of transition metals, halide ions, and organic molecules. The DDEC charges are also found to be robust against the use of hybrid functionals and/or upon inclusion of spin–orbit coupling or dispersive interactions. We calculated explicitly the atomic charges withmore » a special focus on the dipole moment of the MA molecules within the perovskite structure. The value of the dipole moment of the MA is reduced with respect to the isolated molecule due to charge redistribution involving the inorganic cage. DDEC charges and dipole moment of the organic part remain nearly unchanged upon its rotation within the octahedral cavities. Our findings will be of both fundamental and practical importance, as the accurate and consistent determination of the atomic charges is important in order to understand the average equilibrium distribution of the electrons and to help in the development of force fields for larger scale atomistic simulations to describe static, dynamic, and thermodynamic properties of the material.« less

Defects in oxide surfaces studied by atomic force and scanning tunneling microscopy

PubMed Central

König, Thomas; Simon, Georg H; Heinke, Lars; Lichtenstein, Leonid

2011-01-01

Summary Surfaces of thin oxide films were investigated by means of a dual mode NC-AFM/STM. Apart from imaging the surface termination by NC-AFM with atomic resolution, point defects in magnesium oxide on Ag(001) and line defects in aluminum oxide on NiAl(110), respectively, were thoroughly studied. The contact potential was determined by Kelvin probe force microscopy (KPFM) and the electronic structure by scanning tunneling spectroscopy (STS). On magnesium oxide, different color centers, i.e., F0, F+, F2+ and divacancies, have different effects on the contact potential. These differences enabled classification and unambiguous differentiation by KPFM. True atomic resolution shows the topography at line defects in aluminum oxide. At these domain boundaries, STS and KPFM verify F2+-like centers, which have been predicted by density functional theory calculations. Thus, by determining the contact potential and the electronic structure with a spatial resolution in the nanometer range, NC-AFM and STM can be successfully applied on thin oxide films beyond imaging the topography of the surface atoms. PMID:21977410

First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

NASA Astrophysics Data System (ADS)

Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

2015-07-01

We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

DFT computational analysis of piracetam.

PubMed

Rajesh, P; Gunasekaran, S; Seshadri, S; Gnanasambandan, T

2014-11-11

Density functional theory calculation with B3LYP using 6-31G(d,p) and 6-31++G(d,p) basis set have been used to determine ground state molecular geometries. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of piracetam is calculated using B3LYP/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO/NLMO analysis. The calculation of first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. Molecular electrostatic potential (MEP) at a point in the space around a molecule gives an indication of the net electrostatic effect produced at that point by the total charge distribution of the molecule. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charge is also calculated. Because of vibrational analysis, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-Vis spectra and electronic absorption properties are explained and illustrated from the frontier molecular orbitals. Copyright © 2014 Elsevier B.V. All rights reserved.

Calculation of the spin-polarized electronic structure of an interstitial iron impurity in silicon

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, H.; Zunger, Alex

1985-06-01

We apply our self-consistent, all-electron, spin-polarized Green's-function method within an impurity-centered, dynamic basis set to study the interstitial iron impurity in silicon. We use two different formulations of the interelectron interactions: the local-spin-density (LSD) formalism and the self-interaction-corrected (SIC) local-spin-density (SIC-LSD) formalism. We find that the SIC-LSD approach is needed to obtain the correct high-spin ground state of Si:Fe+. We propose a quantitative explanation to the observed donor ionization energy and the high-spin ground states for Si:Fe+ within the SIC-LSD approach. For both Si:Fe0 and Si:Fe+, this approach leads to a hyperfine field, contact spin density, and ionization energy in better agreement with experiments than the simple LSD approach. The apparent dichotomy between the covalently delocalized nature of Si:Fe as suggested on the one hand by its reduced hyperfine field (relative to the free atom) and extended spin density and by the occurrence of two closely spaced, stable charge states (within 0.4 eV) and on the other hand by the atomically localized picture (suggested, for example, by the stability of a high-spin, ground-state configuration) is resolved. We find a large reduction in the hyperfine field and contact spin density due to the covalent hybridization between the impurity 3d orbitals and the tails of the delocalized sp3 hybrid orbitals of the surrounding silicon atoms. Using the calculated results, we discuss (i) the underlying mechanism for the stability and plurality of charged states, (ii) the covalent reduction in the hyperfine field, (iii) the remarkable constancy of the impurity Mössbauer isomer shift for different charged states, (iv) comparison with the multiple charged states in ionic crystals, and (v) some related speculation about the mechanism of (Fe2+/Fe3+) oxidation-reduction ionizations in heme proteins and electron-transporting biological systems.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; Giese, Timothy J.; York, Darrin M.

2015-12-01

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

Comparison between field mill and corona point instrumentation at Kennedy Space Center - Use of these data with a model to determine cloudbase electric fields

NASA Technical Reports Server (NTRS)

Markson, R.; Anderson, B.; Govaert, J.; Fairall, C. W.

1989-01-01

A novel coronal current-determining instrument is being used at NASA-KSC which overcomes previous difficulties with wind sensitivity and a voltage-threshold 'deadband'. The mounting of the corona needle at an elevated location reduces coronal and electrode layer space-charge influences on electric fields, rendering the measurement of space charge density possible. In conjunction with a space-charge compensation model, these features allow a more realistic estimation of cloud base electric fields and the potential for lightning strike than has previously been possible with ground-based sensors.

Cooling of trapped ions by resonant charge exchange

NASA Astrophysics Data System (ADS)

Dutta, Sourav; Rangwala, S. A.

2018-04-01

The two most widely used ion cooling methods are laser cooling and sympathetic cooling by elastic collisions (ECs). Here, we demonstrate another method of cooling ions that is based on resonant charge exchange (RCE) between the trapped ion and the ultracold parent atom. Specifically, trapped C s+ ions are cooled by collisions with cotrapped, ultracold Cs atoms and, separately, by collisions with cotrapped, ultracold Rb atoms. We observe that the cooling of C s+ ions by Cs atoms is more efficient than the cooling of C s+ ions by Rb atoms. This signals the presence of a cooling mechanism apart from the elastic ion-atom collision channel for the Cs-C s+ case, which is cooling by RCE. The efficiency of cooling by RCE is experimentally determined and the per-collision cooling is found to be two orders of magnitude higher than cooling by EC. The result provides the experimental basis for future studies on charge transport by electron hopping in atom-ion hybrid systems.

Simulations to Predict the Phase Behavior and Structure of Multipolar Colloidal Particles

NASA Astrophysics Data System (ADS)

Rutkowski, David Matthew

Colloidal particles with anisotropic charge distributions can assemble into a number of interesting structures including chains, lattices and micelles that could be useful in biotechnology, optics and electronics. The goal of this work is to understand how the properties of the colloidal particles, such as their charge distribution or shape, affect the selfassembly and phase behavior of collections of such particles. The specific aim of this work is to understand how the separation between a pair of oppositely signed charges affects the phase behavior and structure of assemblies of colloidal particles. To examine these particles, we have used both discontinuous molecular dynamics (DMD) and Monte Carlo (MC) simulation techniques. In our first study of colloidal particles with finite charge separation, we simulate systems of 2-D colloidal rods with four possible charge separations. Our simulations show that the charge separation does indeed have a large effect on the phase behavior as can be seen in the phase diagrams we construct for these four systems in the area fraction-reduced temperature plane. The phase diagrams delineate the boundaries between isotropic fluid, string-fluid and percolated fluid for all systems considered. In particular, we find that coarse gel-like structures tend to form at large charge separations while denser aggregates form at small charge separations, suggesting a route to forming low volume gels by focusing on systems with large charge separations. Next we examine systems of circular particles with four embedded charges of alternating sign fixed to a triangular lattice. This system is found to form a limit periodic structure, a theoretical structure with an infinite number of phase transitions, under specific conditions. The limit-periodic structure only forms when the rotation of the particles in the system is restricted to increments of pi/3. When the rotation is restricted to increments of th/6 or the rotation is continuous, related structures form including a striped phase and a phase with nematic order. Neither the distance from the point charges to the center of the particle nor the angle between the charges influences whether the system forms a limit-periodic structure, suggesting that point quadrupoles may also be able to form limit-periodic structures. Results from these simulations will likely aid in the quest to find an experimental realization of a limit-periodic structure. Next we examine the effect of charge separation on the self-assembly of systems of 2-D colloidal particles with off-center extended dipoles. We simulate systems with both small and large charge separations for a set of displacements of the dipole from the particle center. Upon cooling, these particles self-assemble into closed, cyclic structures at large displacements including dimers, triangular shapes and square shapes, and chain-like structures at small displacements. At extremely low temperatures, the cyclic structures form interesting lattices with particles of similar chirality grouped together. Results from this work could aid in the experimental construction of open lattice-like structures that could find use in photonic applications. Finally, we present work in collaboration with Drs. Bhuvnesh Bharti and Orlin Velev in which we investigate how the surface coverage affects the self-assembly of systems of Janus particles coated with both an iron oxide and fatty acid chain layer. We model these particles by decorating a sphere with evenly dispersed points that interact with points on other spheres through square-well interactions. The interactions are designed to mimic specific coverage values for the iron oxide/fatty acid chain layer. Structures similar to those found in experiment form readily in the simulations. The number of clusters formed as a function of surface coverage agrees well with experiment. The aggregation behavior of these novel particles can therefore, be described by a relatively simple model.

DFT investigation on the electronic structure of Faujasite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian

2013-11-13

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed formore » describing atomic charge distribution in the chosen systems.« less

Laboratory Studies of Thermal Energy Charge Transfer of Silicon and Iron Ions in Astrophysical Plasmas

NASA Technical Reports Server (NTRS)

Kwong, Victor H. S.

1997-01-01

The laser ablation/ion storage facility at the UNLV Physics Department is dedicated to the study of atomic processes in low temperature plasmas. Our current program is directed to the study of charge transfer of multiply charged ions and neutrals that are of importance to astrophysics at energies less than 1 eV (about 10(exp 4) K). Specifically, we measure the charge transfer rate coefficient of ions such as N(2+), Si(3+), Si(3+), with helium and Fe(2+) with molecular and atomic hydrogen. All these ions are found in a variety of astrophysical plasmas. Their electron transfer reactions with neutral atoms can affect the ionization equilibrium of the plasma.

Measuring protein isoelectric points by AFM-based force spectroscopy using trace amounts of sample

NASA Astrophysics Data System (ADS)

Guo, Shifeng; Zhu, Xiaoying; Jańczewski, Dominik; Lee, Serina Siew Chen; He, Tao; Teo, Serena Lay Ming; Vancso, G. Julius

2016-09-01

Protein charge at various pH and isoelectric point (pI) values is important in understanding protein function. However, often only trace amounts of unknown proteins are available and pI measurements cannot be obtained using conventional methods. Here, we show a method based on the atomic force microscope (AFM) to determine pI using minute quantities of proteins. The protein of interest is immobilized on AFM colloidal probes and the adhesion force of the protein is measured against a positively and a negatively charged substrate made by layer-by-layer deposition of polyelectrolytes. From the AFM force-distance curves, pI values with an estimated accuracy of ±0.25 were obtained for bovine serum albumin, myoglobin, fibrinogen and ribonuclease A over a range of 4.7-9.8. Using this method, we show that the pI of the ‘footprint’ of the temporary adhesive proteins secreted by the barnacle cyprid larvae of Amphibalanus amphitrite is in the range 9.6-9.7.

Proton Radii of 4,6,8He Isotopes from High-Precision Nucleon-Nucleon Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caurier, E; Navratil, P

2005-11-16

Recently, precision laser spectroscopy on {sup 6}He atoms determined accurately the isotope shift between {sup 4}He and {sup 6}He and, consequently, the charge radius of {sup 6}He. A similar experiment for {sup 8}He is under way. We have performed large-scale ab initio calculations for {sup 4,6,8}He isotopes using high-precision nucleon-nucleon (NN) interactions within the no-core shell model (NCSM) approach. With the CD-Bonn 2000 NN potential we found point-proton root-mean-square (rms) radii of {sup 4}He and {sup 6}He 1.45(1) fm and 1.89(4), respectively, in agreement with experiment and predict the {sup 8}He point proton rms radius to be 1.88(6) fm. Atmore » the same time, our calculations show that the recently developed nonlocal INOY NN potential gives binding energies closer to experiment, but underestimates the charge radii.« less

C library for topological study of the electronic charge density.

PubMed

Vega, David; Aray, Yosslen; Rodríguez, Jesús

2012-12-05

The topological study of the electronic charge density is useful to obtain information about the kinds of bonds (ionic or covalent) and the atom charges on a molecule or crystal. For this study, it is necessary to calculate, at every space point, the electronic density and its electronic density derivatives values up to second order. In this work, a grid-based method for these calculations is described. The library, implemented for three dimensions, is based on a multidimensional Lagrange interpolation in a regular grid; by differentiating the resulting polynomial, the gradient vector, the Hessian matrix and the Laplacian formulas were obtained for every space point. More complex functions such as the Newton-Raphson method (to find the critical points, where the gradient is null) and the Cash-Karp Runge-Kutta method (used to make the gradient paths) were programmed. As in some crystals, the unit cell has angles different from 90°, the described library includes linear transformations to correct the gradient and Hessian when the grid is distorted (inclined). Functions were also developed to handle grid containing files (grd from DMol® program, CUBE from Gaussian® program and CHGCAR from VASP® program). Each one of these files contains the data for a molecular or crystal electronic property (such as charge density, spin density, electrostatic potential, and others) in a three-dimensional (3D) grid. The library can be adapted to make the topological study in any regular 3D grid by modifying the code of these functions. Copyright © 2012 Wiley Periodicals, Inc.

Density functional study of H2O molecule adsorption on α-U(001) surface.

PubMed

Huang, Shanqisong; Zeng, Xiu-Lin; Zhao, Feng-Qi; Ju, Xuehai

2016-04-01

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H2O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H2O molecular dissociate reaction. The long-bridge site is the most favorable site of H2O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H2O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H2O is -1.994 to -2.215 eV on U(001) surface, while the dissociating energy decreases to -3.351 to -3.394 eV with two hydrogen atoms dissociating from H2O. These phenomena also indicate that the Oads can promote the dehydrogenation of H2O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.

Positive and negative contribution to birefringence in a family of carbonates: A Born effective charges analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jing, Qun; Yang, Guang; Hou, Juan

It is an important topic to investigate the birefringence and reveal the contribution from ions to birefringence because it plays an important role in nonlinear optical materials. In this paper, the birefringence of carbonates with coplanar CO{sub 3} groups were investigated using the first-principles method. The results show that the lead carbonates exhibit relative large birefringence. After detailed investigate the electronic structures, and Born effective charges, the authors find out that anisotropic electron distribution in the CO{sub 3} groups and Pb atoms give positive contribution, while the negative contribution was found from fluorine atoms, meanwhile the Ca, Mg, and Cdmore » atoms give very small contribution to birefringence. - Graphical abstract: Using the DFT and Born effective charges, the birefringence and the contribution of ions were investigated, the positive and negative contribution was found from Pb and F ions, respectively. - Highlights: • Optical properties and Born effective charges of carbonates are investigated. • Lead carbonates exhibit relative large birefringence. • Coplanar CO{sub 3} groups and Pb atoms give positive contribution. • F atoms give negative contribution. • Ca, Mg, and Cd atoms give very small contribution.« less

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

A facility to produce an energetic, ground state atomic oxygen beam for the simulation of the Low-Earth Orbit environment

NASA Technical Reports Server (NTRS)

Ketsdever, Andrew D.; Weaver, David P.; Muntz, E. P.

1994-01-01

Because of the continuing commitment to activity in low-Earth orbit (LEO), a facility is under development to produce energetic atmospheric species, particularly atomic oxygen, with energies ranging from 5 to 80 eV. This relatively high flux facility incorporates an ion engine to produce the corresponding specie ion which is charge exchanged to produce a neutral atomic beam. Ion fluxes of around 10(exp 15) sec(exp -1) with energies of 20-70 eV have been achieved. A geometrically augmented inertially tethered charge exchanger (GAITCE) was designed to provide a large column depth of charge exchange gas while reducing the gas load to the low pressure portion of the atomic beam facility. This is accomplished using opposed containment jets which act as collisional barriers to the escape of the dense gas region formed between the jets. Leak rate gains to the pumping system on the order of 10 were achieved for moderate jet mass flows. This system provides an attractive means for the charge exchange of atomic ions with a variety of gases to produce energetic atomic beams.

Quantum theory of atoms in molecules/charge-charge flux-dipole flux models for fundamental vibrational intensity changes on H-bond formation of water and hydrogen fluoride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silva, Arnaldo F.; Richter, Wagner E.; Bruns, Roy E., E-mail: bruns@iqm.unicamp.br

The Quantum Theory of Atoms In Molecules/Charge-Charge Flux-Dipole Flux (QTAIM/CCFDF) model has been used to investigate the electronic structure variations associated with intensity changes on dimerization for the vibrations of the water and hydrogen fluoride dimers as well as in the water-hydrogen fluoride complex. QCISD/cc-pVTZ wave functions applied in the QTAIM/CCFDF model accurately provide the fundamental band intensities of water and its dimer predicting symmetric and antisymmetric stretching intensity increases for the donor unit of 159 and 47 km mol{sup −1} on H-bond formation compared with the experimental values of 141 and 53 km mol{sup −1}. The symmetric stretching ofmore » the proton donor water in the dimer has intensity contributions parallel and perpendicular to its C{sub 2v} axis. The largest calculated increase of 107 km mol{sup −1} is perpendicular to this axis and owes to equilibrium atomic charge displacements on vibration. Charge flux decreases occurring parallel and perpendicular to this axis result in 42 and 40 km mol{sup −1} total intensity increases for the symmetric and antisymmetric stretches, respectively. These decreases in charge flux result in intensity enhancements because of the interaction contributions to the intensities between charge flux and the other quantities. Even though dipole flux contributions are much smaller than the charge and charge flux ones in both monomer and dimer water they are important for calculating the total intensity values for their stretching vibrations since the charge-charge flux interaction term cancels the charge and charge flux contributions. The QTAIM/CCFDF hydrogen-bonded stretching intensity strengthening of 321 km mol{sup −1} on HF dimerization and 592 km mol{sup −1} on HF:H{sub 2}O complexation can essentially be explained by charge, charge flux and their interaction cross term. Atomic contributions to the intensities are also calculated. The bridge hydrogen atomic contributions alone explain 145, 237, and 574 km mol{sup −1} of the H-bond stretching intensity enhancements for the water and HF dimers and their heterodimer compared with total increments of 149, 321, and 592 km mol{sup −1}, respectively.« less

Retrieval of ion distributions in RC from TWINS ENA images by CT technique

NASA Astrophysics Data System (ADS)

Ma, S.; Yan, W.; Xu, L.; Goldstein, J.; McComas, D. J.

2010-12-01

The Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission is the first constellation to employ imagers on two separate spacecraft to measure energetic neutral atoms (ENA) produced by charge exchange between ring current energetic ions and cold exospheric neutral atoms. By applying the 3-D volumetric pixel (voxel) computed tomography (CT) inversion method to TWINS images, parent ion populations in the ring current (RC) and auroral regions are retrieved from their ENA signals. This methodology is implemented for data obtained during the main phase of a moderate geomagnetic storm on 11 October 2008. For this storm the two TWINS satellites were located in nearly the same meridian plane at vantage points widely separated in magnetic local time, and both more than 5 RE geocentric distance from the Earth. In the retrieval process, the energetic ion fluxes to be retrieved are assumed being isotropic with respect to pitch angle. The ENA data used in this study are differential fluxes averaged over 12 sweeps (corresponding to an interval of 16 min.) at different energy levels ranging throughout the full 1--100 keV energy range of TWINS. The ENA signals have two main components: (1) a low-latitude/ high-altitude signal from trapped RC ions and (2) a low-altitude signal from precipitating ions in the auroral/subauroral ionosphere. In the retrieved ion distributions, the main part of the RC component is located around midnight toward dawn sector with L from 3 to 7 or farther, while the subauroral low-altitude component is mainly at pre-midnight. It seems that the dominant energy of the RC ions for this storm is at the lowest energy level of 1-2 keV, with another important energy band centered about 44 keV. The low-altitude component is consistent with in situ observations by DMSP/SSJ4. The result of this study demonstrates that with satellite constellations such as TWINS, using all-sky ENA imagers deployed at multiple vantage points, 3-D distribution of RC ion intensity may be reconstructed via the CT technique. Acknowledgement: This work is supported by NSFC (Grant No. 40674078).

Femtosecond excited state studies of the two-center three-electron bond driven twisted internal charge transfer dynamics in 1,8-bis(dimethylamino)naphthalene.

PubMed

Balkowski, Grzegorz; Szemik-Hojniak, Anna; van Stokkum, Ivo H M; Zhang, Hong; Buma, Wybren J

2005-04-28

Femtosecond fluorescence upconversion and transient absorption experiments have been performed to monitor the photoinduced electronic, geometry, and solvent relaxation dynamics of 1,8-bis(dimethylamino)naphthalene dissolved in methylcyclohexane or n-hexane, n-dodecane, dichloromethane, and acetonitrile. The data have been analyzed by using a sequential global analysis method that gives rise to species associated difference spectra. The spectral features in these spectra and their dynamic behavior enable us to associate them with specific processes occurring in the molecule. The experiments show that the internal charge-transfer lpi* state is populated after internal conversion from the 1La state. In the lpi state the molecule is concluded to be subject to a large-amplitude motion, thereby confirming our previous predictions that internal charge transfer in this state is accompanied by the formation of a two-center three-electron bond between the two nitrogen atoms. Solvent relaxation and vibrational cooling in the lpi* state cannot be separated in polar solvents, but in apolar solvents a distinct vibrational cooling process in the lpi* state is discerned. The spectral and dynamic characteristics of the final species created in the experiments are shown to correspond well with what has been determined before for the relaxed emissive lpi state.

Charge transfer in ultracold gases via Feshbach resonances

NASA Astrophysics Data System (ADS)

Gacesa, Marko; Côté, Robin

2017-06-01

We investigate the prospects of using magnetic Feshbach resonance to control charge exchange in ultracold collisions of heteroisotopic combinations of atoms and ions of the same element. The proposed treatment, readily applicable to alkali or alkaline-earth metals, is illustrated on cold collisions of +9Be and 10Be. Feshbach resonances are characterized by quantum scattering calculations in a coupled-channel formalism that includes non-Born-Oppenheimer terms originating from the nuclear kinetic operator. Near a resonance predicted at 322 G, we find the charge exchange rate coefficient to rise from practically zero to values greater than 10-12cm3 /s. Our results suggest controllable charge exchange processes between different isotopes of suitable atom-ion pairs, with potential applications to quantum systems engineered to study charge diffusion in trapped cold atom-ion mixtures and emulate many-body physics.

Ultrafast Photoinduced Electron Transfer in a π-Conjugated Oligomer/Porphyrin Complex.

PubMed

Aly, Shawkat M; Goswami, Subhadip; Alsulami, Qana A; Schanze, Kirk S; Mohammed, Omar F

2014-10-02

Controlling charge transfer (CT), charge separation (CS), and charge recombination (CR) at the donor-acceptor interface is extremely important to optimize the conversion efficiency in solar cell devices. In general, ultrafast CT and slow CR are desirable for optimal device performance. In this Letter, the ultrafast excited-state CT between platinum oligomer (DPP-Pt(acac)) as a new electron donor and porphyrin as an electron acceptor is monitored for the first time using femtosecond (fs) transient absorption (TA) spectroscopy with broad-band capability and 120 fs temporal resolution. Turning the CT on/off has been shown to be possible either by switching from an organometallic oligomer to a metal-free oligomer or by controlling the charge density on the nitrogen atom of the porphyrin meso unit. Our time-resolved data show that the CT and CS between DPP-Pt(acac) and cationic porphyrin are ultrafast (approximately 1.5 ps), and the CR is slow (ns time scale), as inferred from the formation and the decay of the cationic and anionic species. We also found that the metallic center in the DPP-Pt(acac) oligomer and the positive charge on the porphyrin are the keys to switching on/off the ultrafast CT process.

Local Fitting of the Kohn-Sham Density in a Gaussian and Plane Waves Scheme for Large-Scale Density Functional Theory Simulations.

PubMed

Golze, Dorothea; Iannuzzi, Marcella; Hutter, Jürg

2017-05-09

A local resolution-of-the-identity (LRI) approach is introduced in combination with the Gaussian and plane waves (GPW) scheme to enable large-scale Kohn-Sham density functional theory calculations. In GPW, the computational bottleneck is typically the description of the total charge density on real-space grids. Introducing the LRI approximation, the linear scaling of the GPW approach with respect to system size is retained, while the prefactor for the grid operations is reduced. The density fitting is an O(N) scaling process implemented by approximating the atomic pair densities by an expansion in one-center fit functions. The computational cost for the grid-based operations becomes negligible in LRIGPW. The self-consistent field iteration is up to 30 times faster for periodic systems dependent on the symmetry of the simulation cell and on the density of grid points. However, due to the overhead introduced by the local density fitting, single point calculations and complete molecular dynamics steps, including the calculation of the forces, are effectively accelerated by up to a factor of ∼10. The accuracy of LRIGPW is assessed for different systems and properties, showing that total energies, reaction energies, intramolecular and intermolecular structure parameters are well reproduced. LRIGPW yields also high quality results for extended condensed phase systems such as liquid water, ice XV, and molecular crystals.

Molecular Building Block-Based Electronic Charges for High-Throughput Screening of Metal-Organic Frameworks for Adsorption Applications.

PubMed

Argueta, Edwin; Shaji, Jeena; Gopalan, Arun; Liao, Peilin; Snurr, Randall Q; Gómez-Gualdrón, Diego A

2018-01-09

Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms. HTS-compatible methods to assign charges to MOF atoms need to accurately reproduce electrostatic potentials (ESPs) and be computationally affordable, but current methods present an unsatisfactory trade-off between computational cost and accuracy. We illustrate a method to assign charges to MOF atoms based on ab initio calculations on MOF molecular building blocks. A library of building blocks with built-in charges is thus created and used by an automated MOF construction code to create hundreds of MOFs with charges "inherited" from the constituent building blocks. The molecular building block-based (MBBB) charges are similar to REPEAT charges-which are charges that reproduce ESPs obtained from ab initio calculations on crystallographic unit cells of nanoporous crystals-and thus similar predictions of adsorption loadings, heats of adsorption, and Henry's constants are obtained with either method. The presented results indicate that the MBBB method to assign charges to MOF atoms is suitable for use in computational high-throughput screening of MOFs for applications that involve adsorption of molecules such as carbon dioxide.

Tight-binding molecular-dynamics study of point defects in GaAs

NASA Astrophysics Data System (ADS)

Seong, Hyangsuk; Lewis, Laurent J.

1995-08-01

Tight-binding molecular-dynamics simulations at 0 K have been performed in order to study the effect of defects (vacancies and antisites) in different states of charge on the electronic and structural properties of GaAs. Relaxations are fully included in the model, and for each defect we calculate the local atomic structure, the volume change upon relaxing, the formation energy (including chemical potential contributions), and the ionization levels. We find Ga vacancies to relax by an amount which is independent of the state of charge, consistent with positron lifetime measurements. Our calculations also predict Ga vacancies to exhibit a negative-U effect, and to assume a triply negative charge state for most values of the electron chemical potential. The relaxation of As vacancies, on the contrary, depends sensitively on the state of charge. The model confirms the two experimentally observed ionization levels for this defect, just below the conduction-band minimum. Likewise, Ga antisites exhibit large relaxations. In fact, in the neutral state, relaxation is so large that it leads to a ``broken-bond'' configuration, in excellent accord with the first-principles calculations of Zhang and Chadi [Phys. Rev. Lett. 64, 1789 (1990)]. This system also exhibits a negative-U effect, for values of the electron chemical potential near midgap. For As antisites, we find only a weak relaxation, independent of the charge. The model predicts the neutral state of the defect to be the ground state for values of the electron chemical potential near and above midgap, which supports the view that the EL2 defect is a neutral As antisite. Upon comparing the formation energies of the various defects we finally find that, for all values of the atomic chemical potentials, antisites are most likely to occur than vacancies.

Generalized charge-screening in relativistic Thomas–Fermi model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akbari-Moghanjoughi, M.

In this paper, we study the charge shielding within the relativistic Thomas-Fermi model for a wide range of electron number-densities and the atomic-number of screened ions. A generalized energy-density relation is obtained using the force-balance equation and taking into account the Chandrasekhar's relativistic electron degeneracy pressure. By numerically solving a second-order nonlinear differential equation, the Thomas-Fermi screening length is investigated, and the results are compared for three distinct regimes of the solid-density, warm-dense-matter, and white-dwarfs (WDs). It is revealed that our nonlinear screening theory is compatible with the exponentially decaying Thomas-Fermi-type shielding predicted by the linear response theory. Moreover, themore » variation of relative Thomas-Fermi screening length shows that extremely dense quantum electron fluids are relatively poor charge shielders. Calculation of the total number of screening electrons around a nucleus shows that there is a position of maximum number of screening localized electrons around the screened nucleus, which moves closer to the point-like nucleus by increase in the plasma number density but is unaffected due to increase in the atomic-number value. It is discovered that the total number of screening electrons, (N{sub s}∝r{sub TF}{sup 3}/r{sub d}{sup 3} where r{sub TF} and r{sub d} are the Thomas-Fermi and interparticle distance, respectively) has a distinct limit for extremely dense plasmas such as WD-cores and neutron star crusts, which is unique for all given values of the atomic-number. This is equal to saying that in an ultrarelativistic degeneracy limit of electron-ion plasma, the screening length couples with the system dimensionality and the plasma becomes spherically self-similar. Current analysis can provide useful information on the effects of relativistic correction to the charge screening for a wide range of plasma density, such as the inertial-confined plasmas and compact stellar objects.« less

Charge Versus Energy Transfer in Atomically Thin Graphene-Transition Metal Dichalcogenide van der Waals Heterostructures

NASA Astrophysics Data System (ADS)

Froehlicher, Guillaume; Lorchat, Etienne; Berciaud, Stéphane

2018-01-01

Made from stacks of two-dimensional materials, van der Waals heterostructures exhibit unique light-matter interactions and are promising for novel optoelectronic devices. The performance of such devices is governed by near-field coupling through, e.g., interlayer charge and/or energy transfer. New concepts and experimental methodologies are needed to properly describe two-dimensional heterointerfaces. Here, we report an original study of interlayer charge and energy transfer in atomically thin metal-semiconductor [i.e., graphene-transition metal dichalcogenide (TMD, here molybdenum diselenide, MoSe2 )] heterostructures using a combination of microphotoluminescence and Raman scattering spectroscopies. The photoluminescence intensity in graphene /MoSe2 is quenched by more than 2 orders of magnitude and rises linearly with the incident photon flux, demonstrating a drastically shortened (about 1 ps) room-temperature MoSe2 exciton lifetime. Key complementary insights are provided from a comprehensive analysis of the graphene and MoSe2 Raman modes, which reveals net photoinduced electron transfer from MoSe2 to graphene and hole accumulation in MoSe2 . Remarkably, the steady-state Fermi energy of graphene saturates at 290 ±15 meV above the Dirac point. This reproducible behavior is observed both in ambient air and in vacuum and is discussed in terms of intrinsic factors (i.e., band offsets) and environmental effects. In this saturation regime, balanced photoinduced flows of electrons and holes may transfer to graphene, a mechanism that effectively leads to energy transfer. Using a broad range of incident photon fluxes and diverse environmental conditions, we find that the presence of net photoinduced charge transfer has no measurable impact on the near-unity photoluminescence quenching efficiency in graphene /MoSe2 . This absence of correlation strongly suggests that energy transfer to graphene (either in the form of electron exchange or dipole-dipole interaction) is the dominant interlayer coupling mechanism between atomically thin TMDs and graphene.

Effect of plasma-induced surface charging on catalytic processes: application to CO2 activation

NASA Astrophysics Data System (ADS)

Bal, Kristof M.; Huygh, Stijn; Bogaerts, Annemie; Neyts, Erik C.

2018-02-01

Understanding the nature and effect of the multitude of plasma-surface interactions in plasma catalysis is a crucial requirement for further process development and improvement. A particularly intriguing and rather unique property of a plasma-catalytic setup is the ability of the plasma to modify the electronic structure, and hence chemical properties, of the catalyst through charging, i.e. the absorption of excess electrons. In this work, we develop a quantum chemical model based on density functional theory to study excess negative surface charges in a heterogeneous catalyst exposed to a plasma. This method is specifically applied to investigate plasma-catalytic CO2 activation on supported M/Al2O3 (M = Ti, Ni, Cu) single atom catalysts. We find that (1) the presence of a negative surface charge dramatically improves the reductive power of the catalyst, strongly promoting the splitting of CO2 to CO and oxygen, and (2) the relative activity of the investigated transition metals is also changed upon charging, suggesting that controlled surface charging is a powerful additional parameter to tune catalyst activity and selectivity. These results strongly point to plasma-induced surface charging of the catalyst as an important factor contributing to the plasma-catalyst synergistic effects frequently reported for plasma catalysis.

Quasi-four-body treatment of charge transfer in the collision of protons with atomic helium: I. Thomas related mechanisms

NASA Astrophysics Data System (ADS)

Safarzade, Zohre; Fathi, Reza; Shojaei Akbarabadi, Farideh; Bolorizadeh, Mohammad A.

2018-04-01

The scattering of a completely bare ion by atoms larger than hydrogen is at least a four-body interaction, and the charge transfer channel involves a two-step process. Amongst the two-step interactions of the high-velocity single charge transfer in an anion-atom collision, there is one whose amplitude demonstrates a peak in the angular distribution of the cross sections. This peak, the so-called Thomas peak, was predicted by Thomas in a two-step interaction, classically, which could also be described through three-body quantum mechanical models. This work discusses a four-body quantum treatment of the charge transfer in ion-atom collisions, where two-step interactions illustrating a Thomas peak are emphasized. In addition, the Pauli exclusion principle is taken into account for the initial and final states as well as the operators. It will be demonstrated that there is a momentum condition for each two-step interaction to occur in a single charge transfer channel, where new classical interactions lead to the Thomas mechanism.

Structural investigations in helium charged titanium films using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Wan, Chubin; Zhou, Xiaosong; Wang, Yuting; Li, Shina; Ju, Xin; Peng, Shuming

2014-01-01

The crystal structure and local atomic arrangements surrounding Ti atoms were determined for He-charged hexagonal close-packed (hcp) Ti films and measured at glancing angles by synchrotron radiation X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively. The charged specimens were prepared by direct current magnetron sputtering with a He/Ar mixture. He atoms with a relatively medium concentration (He/Ti atomic ratio as high as 17 at.%) were incorporated evenly in the deposited films. XRD results showed the changes in the peak intensities in Ti films with different He contents. EXAFS Fourier Transform analysis indicated that the average Ti-Ti distance decreased significantly, and proved the existence of phase transition.

An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water.

PubMed

Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O

2014-07-28

Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

Trauma systems and the costs of trauma care.

PubMed Central

Goldfarb, M G; Bazzoli, G J; Coffey, R M

1996-01-01

OBJECTIVE. This study examines the cost of providing trauma services in trauma centers organized by publicly administered trauma systems, compared to hospitals not part of a formal trauma system. DATA SOURCES AND STUDY SETTING. Secondary administrative discharge abstracts for a national sample of severely injured trauma patients in 44 trauma centers and 60 matched control hospitals for the year 1987 were used. STUDY DESIGN. Retrospective univariate and multivariate analyses were conducted to examine the impact of formal trauma systems and trauma center designation on the costs of treating trauma patients. Key dependent variables included length of stay, charge per day per patient, and charge per hospital stay. Key impact variables were type of trauma system and level of trauma designation. Control variables included patient, hospital, and community characteristics. DATA COLLECTION/EXTRACTION METHODS. Data were selected for hospitals based on (1) a large national hospital discharge database, the Hospital Cost and Utilization Project, 1980-1987 (HCUP-2) and (2) a special survey of trauma systems and trauma designation undertaken by the Hospital Research and Educational Trust of the American Hospital Association. PRINCIPAL FINDINGS. The results show that publicly designated Level I trauma centers, which are the focal point of most trauma systems, have the highest charge per case, the highest average charge per day, and similar or longer average lengths of stay than other hospitals. These findings persist after controlling for patient injury and health status, and for demographic characteristics and hospital and community characteristics. CONCLUSIONS. Prior research shows that severely injured trauma patients have greater chances of survival when treated in specialized trauma centers. However, findings here should be of concern to the many states developing trauma systems since the high costs of Level I centers support limiting the number of centers designated at this level and/or reconsidering the requirements placed on these centers. PMID:8617611

Probes for dark matter physics

NASA Astrophysics Data System (ADS)

Khlopov, Maxim Yu.

The existence of cosmological dark matter is in the bedrock of the modern cosmology. The dark matter is assumed to be nonbaryonic and consists of new stable particles. Weakly Interacting Massive Particle (WIMP) miracle appeals to search for neutral stable weakly interacting particles in underground experiments by their nuclear recoil and at colliders by missing energy and momentum, which they carry out. However, the lack of WIMP effects in their direct underground searches and at colliders can appeal to other forms of dark matter candidates. These candidates may be weakly interacting slim particles, superweakly interacting particles, or composite dark matter, in which new particles are bound. Their existence should lead to cosmological effects that can find probes in the astrophysical data. However, if composite dark matter contains stable electrically charged leptons and quarks bound by ordinary Coulomb interaction in elusive dark atoms, these charged constituents of dark atoms can be the subject of direct experimental test at the colliders. The models, predicting stable particles with charge ‑ 2 without stable particles with charges + 1 and ‑ 1 can avoid severe constraints on anomalous isotopes of light elements and provide solution for the puzzles of dark matter searches. In such models, the excessive ‑ 2 charged particles are bound with primordial helium in O-helium atoms, maintaining specific nuclear-interacting form of the dark matter. The successful development of composite dark matter scenarios appeals for experimental search for doubly charged constituents of dark atoms, making experimental search for exotic stable double charged particles experimentum crucis for dark atoms of composite dark matter.

Iron(III)-oxo centers on TiO{sub 2} for visible light photocatalysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Libera, J. A.; Elam, J. W.; Sather, N. F.

Isolated iron(III)-oxo clusters were synthesized onto TiO{sub 2} using atomic layer deposition. The Fe{sub x}O{sub y}/TiO{sub 2} nanocomposites have unique properties that enable not only absorption of visible light, but efficient photocatalysis as demonstrated by methylene blue degradation. The localization of photogenerated electrons in core TiO{sub 2} nanocrystallites upon visible light excitation demonstrates coupling of conduction bands of mixed oxides. The redox properties of photogenerated charges in nanocomposites were studied using in situ electron paramagnetic resonance spectroscopy.

Electric-field control of conductance in metal quantum point contacts by electric-double-layer gating

NASA Astrophysics Data System (ADS)

Shibata, K.; Yoshida, K.; Daiguji, K.; Sato, H.; , T., Ii; Hirakawa, K.

2017-10-01

An electric-field control of quantized conductance in metal (gold) quantum point contacts (QPCs) is demonstrated by adopting a liquid-gated electric-double-layer (EDL) transistor geometry. Atomic-scale gold QPCs were fabricated by applying the feedback-controlled electrical break junction method to the gold nanojunction. The electric conductance in gold QPCs shows quantized conductance plateaus and step-wise increase/decrease by the conductance quantum, G0 = 2e2/h, as EDL-gate voltage is swept, demonstrating a modulation of the conductance of gold QPCs by EDL gating. The electric-field control of conductance in metal QPCs may open a way for their application to local charge sensing at room temperature.

Impact of local electrostatic field rearrangement on field ionization

NASA Astrophysics Data System (ADS)

Katnagallu, Shyam; Dagan, Michal; Parviainen, Stefan; Nematollahi, Ali; Grabowski, Blazej; Bagot, Paul A. J.; Rolland, Nicolas; Neugebauer, Jörg; Raabe, Dierk; Vurpillot, François; Moody, Michael P.; Gault, Baptiste

2018-03-01

Field ion microscopy allows for direct imaging of surfaces with true atomic resolution. The high charge density distribution on the surface generates an intense electric field that can induce ionization of gas atoms. We investigate the dynamic nature of the charge and the consequent electrostatic field redistribution following the departure of atoms initially constituting the surface in the form of an ion, a process known as field evaporation. We report on a new algorithm for image processing and tracking of individual atoms on the specimen surface enabling quantitative assessment of shifts in the imaged atomic positions. By combining experimental investigations with molecular dynamics simulations, which include the full electric charge, we confirm that change is directly associated with the rearrangement of the electrostatic field that modifies the imaging gas ionization zone. We derive important considerations for future developments of data reconstruction in 3D field ion microscopy, in particular for precise quantification of lattice strains and characterization of crystalline defects at the atomic scale.

Energy & mass-charge distribution peculiarities of ion emitted from penning source

NASA Astrophysics Data System (ADS)

Mamedov, N. V.; Kolodko, D. V.; Sorokin, I. A.; Kanshin, I. A.; Sinelnikov, D. N.

2017-05-01

The optimization of hydrogen Penning sources used, in particular, in plasma chemical processing of materials and DLC deposition, is still very important. Investigations of mass-charge composition of these ion source emitted beams are particular relevant for miniature linear accelerators (neutron flux generators) nowadays. The Penning ion source energy and mass-charge ion distributions are presented. The relation between the discharge current abrupt jumps with increasing plasma density in the discharge center and increasing potential whipping (up to 50% of the anode voltage) is shown. Also the energy spectra in the discharge different modes as the pressure and anode potential functions are presented. It has been revealed that the atomic hydrogen ion concentration is about 5-10%, and it weakly depends on the pressure and the discharge current (in the investigated range from 1 to 10 mTorr and from 50 to 1000 μA) and increases with the anode voltage (up 1 to 3,5 kV).

50 Years of the Radiological Research Accelerator Facility (RARAF)

PubMed Central

Marino, Stephen A.

2017-01-01

The Radiological Research Accelerator Facility (RARAF) is in its 50th year of operation. It was commissioned on April 1, 1967 as a collaboration between the Radiological Research Laboratory (RRL) of Columbia University, and members of the Medical Research Center of Brookhaven National Laboratory (BNL). It was initially funded as a user facility for radiobiology and radiological physics, concentrating on monoenergetic neutrons. Facilities for irradiation with MeV light charged particles were developed in the mid-1970s. In 1980 the facility was relocated to the Nevis Laboratories of Columbia University. RARAF now has seven beam lines, each having a dedicated irradiation facility: monoenergetic neutrons, charged particle track segments, two charged particle microbeams (one electrostatically focused to <1 μm, one magnetically focused), a 4.5 keV soft X-ray microbeam, a neutron microbeam, and a facility that produces a neutron spectrum similar to that of the atomic bomb dropped at Hiroshima. Biology facilities are available on site within close proximity to the irradiation facilities, making the RARAF very user friendly. PMID:28140790

Comparison of direct and flow integration based charge density population analyses.

PubMed

Francisco, E; Martín Pendas, A; Blanco, M A; Costales, A

2007-12-06

Different exhaustive and fuzzy partitions of the molecular electron density (rho) into atomic densities (rho(A)) are used to compute the atomic charges (Q(A)) of a representative set of molecules. The Q(A)'s derived from a direct integration of rho(A) are compared to those obtained from integrating the deformation density rho(def) = rho - rho(0) within each atomic domain. Our analysis shows that the latter methods tend to give Q(A)'s similar to those of the (arbitrary) reference atomic densities rho(A)(0) used in the definition of the promolecular density, rho(0) = SigmaArho(A)(0). Moreover, we show that the basis set independence of these charges is a sign not of their intrinsic quality, as commonly stated, but of the practical insensitivity on the basis set of the atomic domains that are employed in this type of methods.

Hyperspherical close-coupling calculations for charge-transfer cross sections in He2++H(1s) collisions at low energies

NASA Astrophysics Data System (ADS)

Liu, Chien-Nan; Le, Anh-Thu; Morishita, Toru; Esry, B. D.; Lin, C. D.

2003-05-01

A theory for ion-atom collisions at low energies based on the hyperspherical close-coupling (HSCC) method is presented. In hyperspherical coordinates the wave function is expanded in analogy to the Born-Oppenheimer approximation where the adiabatic channel functions are calculated with B-spline basis functions while the coupled hyperradial equations are solved by a combination of R-matrix propagation and the slow/smooth variable discretization method. The HSCC method is applied to calculate charge-transfer cross sections for He2++H(1s)→He+(n=2)+H+ reactions at center-of-mass energies from 10 eV to 4 keV. The results are shown to be in general good agreement with calculations based on the molecular orbital (MO) expansion method where electron translation factors (ETF’s) or switching functions have been incorporated in each MO. However, discrepancies were found at very low energies. It is shown that the HSCC method can be used to study low-energy ion-atom collisions without the need to introduce the ad hoc ETF’s, and the results are free from ambiguities associated with the traditional MO expansion approach.

The 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid nanodroplets on solid surfaces and in electric field: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Dong, Dengpan; Vatamanu, Jenel P.; Wei, Xiaoyu; Bedrov, Dmitry

2018-05-01

Atomistic molecular dynamics simulations were conducted to study the wetting states of 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid (IL) nanodroplets on surfaces with different strengths of van der Waals (VDW) interactions and in the presence of an electric field. By adjusting the depth of Lennard-Jones potential, the van der Waals interaction between the solid surface and ionic liquid was systematically varied. The shape of the droplets was analyzed to extract the corresponding contact angle utilized to characterize wetting states of the nanodroplets. The explored range of surface-IL interactions allowed contact angles ranging from complete IL spreading on the surface to poor wettability. The effect of the external electrical field was explored by adding point charges to the surface atoms. Systems with two charge densities (±0.002 e/atom and ±0.004 e/atom) that correspond to 1.36 V/nm and 2.72 V/nm electric fields were investigated. Asymmetrical wetting states were observed for both cases. At 1.36 V/nm electric field, contributions of IL-surface VDW interactions and Coulombic interactions to the wetting state were competitive. At 2.72 V/nm field, electrostatic interactions dominate the interaction between the nanodroplet and surface, leading to enhanced wettability on all surfaces.

Influence of annealing atmosphere on formation of electrically-active defects in rutile TiO2

NASA Astrophysics Data System (ADS)

Zimmermann, C.; Bonkerud, J.; Herklotz, F.; Sky, T. N.; Hupfer, A.; Monakhov, E.; Svensson, B. G.; Vines, L.

2018-04-01

Electronic states in the upper part of the bandgap of reduced and/or hydrogenated n-type rutile TiO2 single crystals have been studied by means of thermal admittance and deep-level transient spectroscopy measurements. The studies were performed at sample temperatures between 28 and 300 K. The results reveal limited charge carrier freeze-out even at 28 K and evidence the existence of dominant shallow donors with ionization energies below 25 meV. Interstitial atomic hydrogen is considered to be a major contributor to these shallow donors, substantiated by infrared absorption measurements. Three defect energy levels with positions of about 70 meV, 95 meV, and 120 meV below the conduction band edge occur in all the studied samples, irrespective of the sample production batch and the post-growth heat treatment used. The origin of these levels is discussed in terms of electron polarons, intrinsic point defects, and/or common residual impurities, where especially interstitial titanium atoms, oxygen vacancies, and complexes involving Al atoms appear as likely candidates. In contrast, no common deep-level defect, exhibiting a charge state transition in the 200-700 meV range below the conduction band edge, is found in different samples. This may possibly indicate a strong influence on deep-level defects by the post-growth heat treatments employed.

Polarization Bremsstrahlung: what is it and why haven't we seen it?

NASA Astrophysics Data System (ADS)

Quarles, C. A.

1997-10-01

Normal bremsstrahlung (NB) is the radiation by a charged particle when deflected in the Coulomb field of a target atom. This process has been studied in some detail since identification of the continuous x-ray spectrum early in this century. Since the early 1980's it has been possible, mainly due to the work of R. H. Pratt and co-workers, to obtain good theoretical predictions for NB for a wide range of incident electron energies and target atomic numbers. In the early 1980's, a second, distinct and competing process which has come to be called polarization bremsstrahlung (PB) was proposed by M. Ya. Amusia and others. PB is the radiation by a polarizable target due to the changing dipole moment induced by the passing charged projectile. It was argued that in some cases, especially for photon energies near the target atom absorption edges, PB would dominate over NB. Only recently, however, with the calculations of A. Korol and his co-workers has it been possible to consider what PB may look like over the whole range of the photon spectrum observed in a typical bremsstrahlung experiment. This paper will discuss, from the point of view of an experimentalist, what is involved in looking for the PB effect, why perhaps it has not been convincingly detected in bremsstrahlung experiments to date, and what the prospects are for its future observation.

Guide to Federal Funding, Financing, and Technical Assistance for Plug-in Electric Vehicles and Charging Stations

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

The U.S. Department of Energy and the U.S. Department of Transportation have published a guide to highlight examples of federal support and technical assistance for plug-in electric vehicles (PEVs) and charging stations. The guide provides a description of each opportunity and a point of contact to assist those interested in advancing PEV technology. The Department of Energy’s Alternative Fuels Data Center provides a comprehensive database of federal and state programs that support plug-in electric vehicles and infrastructure.

Binding affinity and adhesion force of organophosphate hydrolase enzyme with soil particles related to the isoelectric point of the enzyme.

PubMed

Islam, Shah Md Asraful; Yeasmin, Shabina; Islam, Md Saiful; Islam, Md Shariful

2017-07-01

The binding affinity of organophosphate hydrolase enzyme (OphB) with soil particles in relation to the isoelectric point (pI) was studied. Immobilization of OphB with soil particles was observed by confocal microscopy, Fourier transform infrared spectroscopy (FT-IR), and Atomic force microscopy (AFM). The calculated pI of OphB enzyme was increased from 8.69 to 8.89, 9.04 and 9.16 by the single, double and triple mutant of OphB enzyme, respectively through the replacement of negatively charged aspartate with positively charged histidine. Practically, the binding affinity was increased to 5.30%, 11.50%, and 16.80% for single, double and triple mutants, respectively. In contrast, enzyme activity of OphB did not change by the mutation of the enzyme. On the other hand, adhesion forces were gradually increased for wild type OphB enzyme (90 pN) to 96, 100 and 104 pN for single, double and triple mutants of OphB enzyme, respectively. There was an increasing trend of binding affinity and adhesion force by the increase of isoelectric point (pI) of OphB enzyme. Copyright © 2017 Elsevier Inc. All rights reserved.

Machine Learning of ABO3 Crystalline Compounds

NASA Astrophysics Data System (ADS)

Gubernatis, J. E.; Balachandran, P. V.; Lookman, T.

We apply two advanced machine learning methods to a database of experimentally known ABO3 materials to predict the existence of possible new perovskite materials and possible new cubic perovskites. Constructing a list of 625 possible new materials from charge conserving combinations of A and B atoms in known stable ABO3 materials, we predict about 440 new perovskites. These new perovskites are predicted most likely to occur when the A and B atoms are a lanthanide or actinide, when the A atom is a alkali, alkali earth, or late transition metal, and a when the B atom is a p-block atom. These results are in basic agreement with the recent materials discovery by substitution analysis of Hautier et al. who data-mined the entire ICSD data base to develop the probability that in any crystal structure atom X could be substituted for by atom Y. The results of our analysis has several points of disagreement with a recent high throughput DFT study of ABO3 crystalline compounds by Emery et al. who predict few, if any, new perovskites whose A and B atoms are both a lanthanide. They also predict far more new cubic perovskites than we do: We predict few, if any, with a high degree of probability. This work was supported by the LDRD DR program of the Los Alamos National Laboratory.

Characterization of the surface charge distribution on kaolinite particles using high resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kumar, Naveen; Zhao, Cunlu; Klaassen, Aram; van den Ende, Dirk; Mugele, Frieder; Siretanu, Igor

2016-02-01

Most solid surfaces, in particular clay minerals and rock surfaces, acquire a surface charge upon exposure to an aqueous environment due to adsorption and/or desorption of ionic species. Macroscopic techniques such as titration and electrokinetic measurements are commonly used to determine the surface charge and ζ -potential of these surfaces. However, because of the macroscopic averaging character these techniques cannot do justice to the role of local heterogeneities on the surfaces. In this work, we use dynamic atomic force microscopy (AFM) to determine the distribution of surface charge on the two (gibbsite-like and silica-like) basal planes of kaolinite nanoparticles immersed in aqueous electrolyte with a lateral resolution of approximately 30 nm. The surface charge density is extracted from force-distance curves using DLVO theory in combination with surface complexation modeling. While the gibbsite-like and the silica-like facet display on average positive and negative surface charge values as expected, our measurements reveal lateral variations of more than a factor of two on seemingly atomically smooth terraces, even if high resolution AFM images clearly reveal the atomic lattice on the surface. These results suggest that simple surface complexation models of clays that attribute a unique surface chemistry and hence homogeneous surface charge densities to basal planes may miss important aspects of real clay surfaces.

Effect of Atomic Oxygen Exposure on Surface Resistivity Change of Spacecraft Insulator Material

NASA Astrophysics Data System (ADS)

Mundari, Noor Danish Ahrar; Khan, Arifur Rahman; Chiga, Masaru; Okumura, Teppei; Masui, Hirokazu; Iwata, Minoru; Toyoda, Kazuhiro; Cho, Mengu

Spacecraft surface charging can lead to arcing and a loss of electricity generation capability in solar panels or even loss of a satellite. The charging problem may be further aggravated by atomic oxygen (AO) exposure in Low Earth orbits, which modifies the surface of materials like polyimide, Teflon, anti-reflective coatings, cover glass etc, used on satellite surfaces, affecting materials properties, such as resistivity, secondary electron emissivity and photo emission, which govern the charging behavior. These properties are crucial input parameters for spacecraft charging analysis. To study the AO exposure effect on charging governing properties, an atomic oxygen exposure facility based on laser detonation of oxygen was built. The facility produces AO with a peak velocity value around 10-12km/s and a higher flux than that existing in orbit. After exposing the polyimide test material to the equivalent of 10 years of AO fluence at an altitude of 700-800 km, surface charging properties like surface resistivity and volume resistivity were measured. The measurement was performed in a vacuum using the charge storage decay method at room temperature, which is considered the most appropriate for measuring resistivity for space applications. The results show that the surface resistivity increases and the volume resistivity remains almost the same for the AO exposure fluence of 5.4×1018 atoms cm-2.

Complex Stoichiometry reordering of PTCDA on Ag(111) upon K Intercalation

NASA Astrophysics Data System (ADS)

Brivio, G. P.; Baby, A.; Zwick, C.; Gruenewald, M.; Forker, R.; Fritz, T.; Fratesi, G.; Hofmann, O. T.; Zojer, E.

Alkali metal atoms are a simple yet efficient n-type dopant of organic semiconductors. However, the molecular crystal structures need be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into PTCDA monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low temperature scanning tunneling microscopy (STM), scanning tunneling hydrogen microscopy (STHM), and low-energy electron diffraction (LEED) as a function of the stoichiometry and by density functional theory (DFT) calculations. Large stable monolayer domains are found for x=2,4. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Angstrom precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend on the mutual alignment between donor atoms and acceptor molecules.

Measurements of atomic splittings in atomic hydrogen and the proton charge radius

NASA Astrophysics Data System (ADS)

Hessels, E. A.

2016-09-01

The proton charge radius can be determined from precise measurements of atomic hydrogen spectroscopy. A review of the relevant measurements will be given, including an update on our measurement of the n=2 Lamb shift. The values obtained from hydrogen will be compared to those obtained from muonic hydrogen and from electron-proton elastic scattering measurements. This work is funded by NSERC, CRC and CFI.

KSC-03pd0361

NASA Image and Video Library

2003-02-12

KENNEDY SPACE CENTER, FLA. - Retired Navy Admiral Harold W. Gehman Jr. (center), chairman of the Columbia Accident Investigation Board, visits the Thermal Protection System shop and is briefed by Martin Wilson (pointing), the shop manager. Gehman and other members of the board are visiting sites at KSC to become familiar with the Shuttle launch process. The independent board is charged with determining what caused the destruction of the Space Shuttle Columbia and the loss of its seven-member crew on Feb. 1 during reentry.

Ion-induced particle desorption in time-of-flight medium energy ion scattering

NASA Astrophysics Data System (ADS)

Lohmann, S.; Primetzhofer, D.

2018-05-01

Secondary ions emitted from solids upon ion impact are studied in a time-of-flight medium energy ion scattering (ToF-MEIS) set-up. In order to investigate characteristics of the emission processes and to evaluate the potential for surface and thin film analysis, experiments employing TiN and Al samples were conducted. The ejected ions exhibit a low initial kinetic energy of a few eV, thus, requiring a sufficiently high acceleration voltage for detection. Molecular and atomic ions of different charge states originating both from surface contaminations and the sample material are found, and relative yields of several species were determined. Experimental evidence that points towards a predominantly electronic sputtering process is presented. For emitted Ti target atoms an additional nuclear sputtering component is suggested.

Crystal structure of (1-eth­oxy­ethyl­idene)di­methyl­aza­nium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2015-01-01

In the cation of the title salt, C6H14NO+·C24H20B−, the C—N bond lengths are 1.297 (2), 1.464 (2) and 1.468 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.309 (2) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H⋯π inter­actions between the iminium H atoms and the phenyl C atoms of the anion are present. The phenyl rings form aromatic pockets, in which the iminium ions are embedded. PMID:26870564

Effects of Ion Atomic Number on Single-Event Gate Rupture (SEGR) Susceptibility of Power MOSFETs

NASA Technical Reports Server (NTRS)

Lauenstein, Jean-Marie; Goldsman, Neil; Liu, Sandra; Titus, Jeffrey L.; Ladbury, Raymond L.; Kim, Hak S.; Phan, Anthony M.; LaBel, Kenneth A.; Zafrani, Max; Sherman, Phillip

2012-01-01

The relative importance of heavy-ion interaction with the oxide, charge ionized in the epilayer, and charge ionized in the drain substrate, on the bias for SEGR failure in vertical power MOSFETs is experimentally investigated. The results indicate that both the charge ionized in the epilayer and the ion atomic number are important parameters of SEGR failure. Implications on SEGR hardness assurance are discussed.

Partial Ionic Character beyond the Pauling Paradigm: Metal Nanoparticles

DOE PAGES

Duanmu, Kaining; Truhlar, Donald G.

2014-11-12

A canonical perspective on the chemical bond is the Pauling paradigm: a bond in a molecule containing only identical atoms has no ionic character. However, we show that homonuclear silver clusters have very uneven charge distributions (for example, the C 2v structure of Ag 4 has a larger dipole moment than formaldehyde or acetone), and we show how to predict the charge distribution from coordination numbers and Hirshfeld charges. The new charge model is validated against Kohn–Sham calculations of dipole moments with four approximations for the exchange–correlation functional. We report Kohn–Sham studies of the binding energies of CO on silvermore » monomer and silver clusters containing 2–18 atoms. We also find that an accurate charge model is essential for understanding the site dependence of binding. In particular we find that atoms with more positive charges tend to have higher binding energies, which can be used for guidance in catalyst modeling and design. Furthermore, the nonuniform charge distribution of silver clusters predisposes the site preference of binding of carbon monoxide, and we conclude that nonuniform charge distributions are an important property for understanding binding of metal nanoparticles in general.« less

Excited State Atom-Ion Charge-Exchange

NASA Astrophysics Data System (ADS)

Li, Ming; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana

2017-04-01

We theoretically investigate the exothermic charge-exchange reaction between an excited atom and a ground-state positive ion. In particular, we focus on MOT-excited Ca*(4s4p 1P) atoms colliding with ground-state Yb+ ions, which are under active study by the experimental group of E. Hudson at UCLA. Collisions between an excited atom and an ion are guided by two major contributions to the long-range interaction potentials, the induction C4 /R4 and charge-quadrupole C3 /R3 potentials, and their coupling by the electron-exchange interaction. Our model of these forces leads to close-coupling equations for multiple reaction channels. We find several avoided crossings between the potentials that couple to the nearby asymptotic limits of Yb*+Ca+, some of which can possibly provide large charge exchange rate coefficients above 10-10 cm3 / s. We acknowledge support from the US Army Research Office, MURI Grants W911NF-14-1-0378 and the US National Science Foundation, Grant PHY-1619788.

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

PubMed

Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

2013-10-28

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

Current at Metal-Organic Interfaces

NASA Astrophysics Data System (ADS)

Kern, Klaus

2012-02-01

Charge transport through atomic and molecular constrictions greatly affects the operation and performance of organic electronic devices. Much of our understanding of the charge injection and extraction processes in these systems relays on our knowledge of the electronic structure at the metal-organic interface. Despite significant experimental and theoretical advances in studying charge transport in nanoscale junctions, a microscopic understanding at the single atom/molecule level is missing. In the present talk I will present our recent results to probe directly the nanocontact between single molecules and a metal electrode using scanning probe microscopy and spectroscopy. The experiments provide unprecedented microscopic details of single molecule and atom junctions and open new avenues to study quantum critical and many body phenomena at the atomic scale. Implications for energy conversion devices and carbon based nanoelectronics will also be discussed.

Effect of incorporation of nitrogen atoms in Al2O3 gate dielectric of wide-bandgap-semiconductor MOSFET on gate leakage current and negative fixed charge

NASA Astrophysics Data System (ADS)

Kojima, Eiji; Chokawa, Kenta; Shirakawa, Hiroki; Araidai, Masaaki; Hosoi, Takuji; Watanabe, Heiji; Shiraishi, Kenji

2018-06-01

We performed first-principle calculations to investigate the effect of incorporation of N atoms into Al2O3 gate dielectrics. Our calculations show that the defect levels generated by VO in Al2O3 are the origin of the stress-induced gate leakage current and that VOVAl complexes in Al2O3 cause negative fixed charge. We revealed that the incorporation of N atoms into Al2O3 eliminates the VO defect levels, reducing the stress-induced gate leakage current. Moreover, this suppresses the formation of negatively charged VOVAl complexes. Therefore, AlON can reduce both stress-induced gate leakage current and negative fixed charge in wide-bandgap-semiconductor MOSFETs.

Molecular aspects of the Eu3+/Eu2+ redox reaction at the interface between a molten salt and a metallic electrode

NASA Astrophysics Data System (ADS)

Pounds, Michael A.; Salanne, Mathieu; Madden, Paul A.

2015-09-01

We perform molecular dynamics simulations of a system consisting of Eu3+ and Eu2+ species dissolved in a high-temperature KCl electrolyte between two metallic electrodes. The interaction potential includes ion polarisation effects, and a constant electric potential is maintained within the electrodes by allowing the atomic charges to fluctuate in response to the environment. This setup allows us to study the electrochemical Eu3+/Eu2+ reaction in the framework of Marcus theory. Numerous studies have pointed to the highly structured nature of ionic liquids and molten salts close to solid surfaces which is not accounted for in the conventional mean-field description of this interface that underpins the theories of electrochemical reaction rates. Here we examine the influence on the kinetics of the charge-transfer event of the electrical potential across the electrode-electrolyte interface and on the effect of the presence of charged surface on the coordination structure and energetics of the ions in the region important for the charge-transfer event.

Effect of Thermospheric Neutral Density upon Inner Trapped-belt Proton Flux

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, M. A. K.; Diaz, Abel B.

2007-01-01

We wish to point out that a secular change in the Earth's atmospheric neutral density alters charged-particle lifetime in the inner trapped radiation belts, in addition to the changes recently reported as produced by greenhouse gases. Heretofore, changes in neutral density have been of interest primarily because of their effect on the orbital drag of satellites. We extend this to include the orbital lifetime of charged particles in the lower radiation belts. It is known that the charged-belt population is coupled to the neutral density of the atmosphere through changes induced by solar activity, an effect produced by multiple scattering off neutral and ionized atoms along with ionization loss in the thermosphere where charged and neutral populations interact. It will be shown here that trapped-belt flux J is bivariant in energy E and thermospheric neutral density , as J(E,rho). One can conclude that proton lifetimes in these belts are also directly affected by secular changes in the neutral species populating the Earth s thermosphere. This result is a consequence of an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present.

Intrinsic electron traps in atomic-layer deposited HfO{sub 2} insulators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cerbu, F.; Madia, O.; Afanas'ev, V. V.

2016-05-30

Analysis of photodepopulation of electron traps in HfO{sub 2} films grown by atomic layer deposition is shown to provide the trap energy distribution across the entire oxide bandgap. The presence is revealed of two kinds of deep electron traps energetically distributed at around E{sub t} ≈ 2.0 eV and E{sub t} ≈ 3.0 eV below the oxide conduction band. Comparison of the trapped electron energy distributions in HfO{sub 2} layers prepared using different precursors or subjected to thermal treatment suggests that these centers are intrinsic in origin. However, the common assumption that these would implicate O vacancies cannot explain the charging behaviormore » of HfO{sub 2}, suggesting that alternative defect models should be considered.« less

Alternative Fuels Data Center: Electric Vehicle Charging Stations

Science.gov Websites

Electric Vehicle Charging Stations to someone by E-mail Share Alternative Fuels Data Center : Electric Vehicle Charging Stations on Facebook Tweet about Alternative Fuels Data Center: Electric Vehicle Charging Stations on Twitter Bookmark Alternative Fuels Data Center: Electric Vehicle Charging Stations on

How can we make stable linear monoatomic chains? Gold-cesium binary subnanowires as an example of a charge-transfer-driven approach to alloying.

PubMed

Choi, Young Cheol; Lee, Han Myoung; Kim, Woo Youn; Kwon, S K; Nautiyal, Tashi; Cheng, Da-Yong; Vishwanathan, K; Kim, Kwang S

2007-02-16

On the basis of first-principles calculations of clusters and one dimensional infinitely long subnanowires of the binary systems, we find that alkali-noble metal alloy wires show better linearity and stability than either pure alkali metal or noble metal wires. The enhanced alternating charge buildup on atoms by charge transfer helps the atoms line up straight. The cesium doped gold wires showing significant charge transfer from cesium to gold can be stabilized as linear or circular monoatomic chains.

Two-electron states of a group-V donor in silicon from atomistic full configuration interactions

NASA Astrophysics Data System (ADS)

Tankasala, Archana; Salfi, Joseph; Bocquel, Juanita; Voisin, Benoit; Usman, Muhammad; Klimeck, Gerhard; Simmons, Michelle Y.; Hollenberg, Lloyd C. L.; Rogge, Sven; Rahman, Rajib

2018-05-01

Two-electron states bound to donors in silicon are important for both two-qubit gates and spin readout. We present a full configuration interaction technique in the atomistic tight-binding basis to capture multielectron exchange and correlation effects taking into account the full band structure of silicon and the atomic-scale granularity of a nanoscale device. Excited s -like states of A1 symmetry are found to strongly influence the charging energy of a negative donor center. We apply the technique on subsurface dopants subjected to gate electric fields and show that bound triplet states appear in the spectrum as a result of decreased charging energy. The exchange energy, obtained for the two-electron states in various confinement regimes, may enable engineering electrical control of spins in donor-dot hybrid qubits.

Metallic ions in the equatorial ionosphere

NASA Technical Reports Server (NTRS)

Aikin, A. C.; Goldberg, R. A.

1972-01-01

Four positive ion composition measurements of the equatorial E region made at Thumba, India, are presented. During the day, the major ions between 90 and 125 km are NO(+) and O2(+). A metallic ion layer centered at 92 km is observed, and found to contain Mg(+), Fe(+), Ca(+), K(+), Al(+), and Na(+) ions. The layer is explained in terms of a similarly shaped latitude distribution of neutral atoms which are photoionized and charge-exchanged with NO(+) and O2(+). Three body reactions form molecular metallic ions which are rapidly lost by dissociative ion-electron recombination. Nighttime observations show downward drifting of the metallic ion layer caused by equatorial dynamo effects. These ions react and form neutral metals which exchange charges with NO(+) and O2(+) to produce an observed depletion of those ions within the metallic ion region.

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

PubMed Central

Mei, Ye; Simmonett, Andrew C.; Pickard, Frank C.; DiStasio, Robert A.; Brooks, Bernard R.; Shao, Yihan

2015-01-01

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in 8 small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development; (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles. PMID:25945749

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

DOE PAGES

Mei, Ye; Simmonett, Andrew C.; Pickard, IV, Frank C.; ...

2015-05-06

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed in this study using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Lowdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to computemore » the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. In conclusion, the overall results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.« less

Study of photon emission by electron capture during solar nuclei acceleration, 1: Temperature-dependent cross section for charge changing processes

NASA Technical Reports Server (NTRS)

Perez-Peraza, J.; Alvarez, M.; Laville, A.; Gallegos, A.

1985-01-01

The study of charge changing cross sections of fast ions colliding with matter provides the fundamental basis for the analysis of the charge states produced in such interactions. Given the high degree of complexity of the phenomena, there is no theoretical treatment able to give a comprehensive description. In fact, the involved processes are very dependent on the basic parameters of the projectile, such as velocity charge state, and atomic number, and on the target parameters, the physical state (molecular, atomic or ionized matter) and density. The target velocity, may have also incidence on the process, through the temperature of the traversed medium. In addition, multiple electron transfer in single collisions intrincates more the phenomena. Though, in simplified cases, such as protons moving through atomic hydrogen, considerable agreement has been obtained between theory and experiments However, in general the available theoretical approaches have only limited validity in restricted regions of the basic parameters. Since most measurements of charge changing cross sections are performed in atomic matter at ambient temperature, models are commonly based on the assumption of targets at rest, however at Astrophysical scales, temperature displays a wide range in atomic and ionized matter. Therefore, due to the lack of experimental data , an attempt is made here to quantify temperature dependent cross sections on basis to somewhat arbitrary, but physically reasonable assumptions.

Revisiting the Bohr Atom 100 Years Later

NASA Astrophysics Data System (ADS)

Wall, Ernst

2013-03-01

We use a novel electron model wherein the electron is modeled as a point charge behaving as a trapped photon revolving in a Compton wavelength orbit at light speed. The revolving point charge gives rise to spiraling Compton wavelets around the electron, which give rise to de Broglie waves. When applied to the Bohr model, the orbital radius of the electron scales to the first Bohr orbit's radius via the fine structure constant. The orbiting electron's orbital velocity, Vb, scales to that of the electron's charge's internal velocity (the velocity of light, c) via the fine structure constant. The Compton wavelets, if they reflect off the nucleus, have a round trip time just long enough to allow the electron to move one of its diameters in distance in the first Bohr orbit. The ratio of the electron's rotational frequency, fe, to its rotational frequency in the Bohr orbit fb, is fe/fb = 1/α2, which is also the number of electron rotations in single orbit. If we scale the electron's rotational energy (h*fe) to that of the orbit using this, the orbital energy value (h*fb) would be 27.2114 eV. However, the virial theorem reduces it to 13.6057, the ground state energy of the first Bohr orbit. Ref: www.tachyonmodel.com.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Fast Atom Ionization in Strong Electromagnetic Radiation

NASA Astrophysics Data System (ADS)

Apostol, M.

2018-05-01

The Goeppert-Mayer and Kramers-Henneberger transformations are examined for bound charges placed in electromagnetic radiation in the non-relativistic approximation. The consistent inclusion of the interaction with the radiation field provides the time evolution of the wavefunction with both structural interaction (which ensures the bound state) and electromagnetic interaction. It is shown that in a short time after switching on the high-intensity radiation the bound charges are set free. In these conditions, a statistical criterion is used to estimate the rate of atom ionization. The results correspond to a sudden application of the electromagnetic interaction, in contrast with the well-known ionization probability obtained by quasi-classical tunneling through classically unavailable non-stationary states, or other equivalent methods, where the interaction is introduced adiabatically. For low-intensity radiation the charges oscillate and emit higher-order harmonics, the charge configuration is re-arranged and the process is resumed. Tunneling ionization may appear in these circumstances. Extension of the approach to other applications involving radiation-induced charge emission from bound states is discussed, like ionization of molecules, atomic clusters or proton emission from atomic nuclei. Also, results for a static electric field are included.

Charge renormalization at the large-D limit for N-electron atoms and weakly bound systems

NASA Astrophysics Data System (ADS)

Kais, S.; Bleil, R.

1995-05-01

We develop a systematic way to determine an effective nuclear charge ZRD such that the Hartree-Fock results will be significantly closer to the exact energies by utilizing the analytically known large-D limit energies. This method yields an expansion for the effective nuclear charge in powers of (1/D), which we have evaluated to the first order. This first order approximation to the desired effective nuclear charge has been applied to two-electron atoms with Z=2-20, and weakly bound systems such as H-. The errors for the two-electron atoms when compared with exact results were reduced from ˜0.2% for Z=2 to ˜0.002% for large Z. Although usual Hartree-Fock calculations for H- show this to be unstable, our results reduce the percent error of the Hartree-Fock energy from 7.6% to 1.86% and predicts the anion to be stable. For N-electron atoms (N=3-18, Z=3-28), using only the zeroth order approximation for the effective charge significantly reduces the error of Hartree-Fock calculations and recovers more than 80% of the correlation energy.

Heat transport through atomic contacts.

PubMed

Mosso, Nico; Drechsler, Ute; Menges, Fabian; Nirmalraj, Peter; Karg, Siegfried; Riel, Heike; Gotsmann, Bernd

2017-05-01

Heat transport and dissipation at the nanoscale severely limit the scaling of high-performance electronic devices and circuits. Metallic atomic junctions serve as model systems to probe electrical and thermal transport down to the atomic level as well as quantum effects that occur in one-dimensional (1D) systems. Whereas charge transport in atomic junctions has been studied intensively in the past two decades, heat transport remains poorly characterized because it requires the combination of a high sensitivity to small heat fluxes and the formation of stable atomic contacts. Here we report heat-transfer measurements through atomic junctions and analyse the thermal conductance of single-atom gold contacts at room temperature. Simultaneous measurements of charge and heat transport reveal the proportionality of electrical and thermal conductance, quantized with the respective conductance quanta. This constitutes a verification of the Wiedemann-Franz law at the atomic scale.

CALCOM: a software for calculating the center of mass of proteins.

PubMed

Costantini, Susan; Paladino, Antonella; Facchiano, Angelo M

2008-02-09

The center of mass of a protein is an artificial point useful for detecting important and simple features of proteins structure, shape and association.CALCOM is a software which calculates the center of mass of a protein, starting from PDB protein structure files. In the case of protein complexes and of protein-small ligand complexes, the position of protein residues or of ligand atoms respect to each protein subunit can be evaluated, as well as the distance among the center of mass of the protein subunits, in order to compare different conformations and evaluate the relative motion of subunits. THE SERVICE IS AVAILABLE AT THE URL: http://bioinformatica.isa.cnr.it/CALCOM/.

Switched capacitor charge pump used for low-distortion imaging in atomic force microscope.

PubMed

Zhang, Jie; Zhang, Lian Sheng; Feng, Zhi Hua

2015-01-01

The switched capacitor charge pump (SCCP) is an effective method of linearizing charges on piezoelectric actuators and therefore constitute a significant approach to nano-positioning. In this work, it was for the first time implemented in an atomic force microscope for low-distortion imaging. Experimental results showed that the image quality was improved evidently under the SCCP drive compared with that under traditional linear voltage drive. © Wiley Periodicals, Inc.

Forms of adsorption and transition states of oxidation of carbon monoxide by molecular oxygen and dissociation of nitrogen monooxide, catalyzed by monovalent copper

NASA Astrophysics Data System (ADS)

Ermakov, A. I.; Mashutin, V. Y.; Vishnjakov, A. V.

With the help of the results of semiempirical (parametric method 3) and ab initio (second-order Møller-Plesset [MP2] unrestricted Hartree-Fock [UHF] 6-31G**, unrestricted density functional theory [UDFT] 6-31G** Becke's three-parameter exchange functional and the gradient-corrected functional of Lee, Yang, and Paar [B3LYP] and UDFT LANL2DZ B3LYP) quantum-chemical calculations has been studied the complexation CO and NO with molecular hydroxide of copper(I). The influence of charge defects has been simulated by the calculations of anionic, neutral, and cationic systems. It is shown that CO and NO are mainly coordinated by nonoxygen atom on an atom of copper(I) hydroxide as one- and two-center forms. These forms are suitable for appearance of prereactionary complexes of catalytic oxidation CO by molecular oxygen and decomposition NO into atoms of nitrogen and oxygen. The corresponding prereactionary complexes for systems with participation of copper(II) hydroxide and copper(III) hydroxide are not revealed. The calculations predict inhibiting impact of copper(II) and copper(III) of the observed reactions. Computed stability of complexes CO and NO with copper(I) hydroxide and activation energy of catalytic conversion of monooxides essentially depend on an excessive charge of the system. Introduction of electron-donating additives into copper(I) hydroxide promotes rise of catalytic activity of copper(I) compound.

Polar rotor scattering as atomic-level origin of low mobility and thermal conductivity of perovskite CH3NH3PbI3

PubMed Central

Li, Bing; Kawakita, Yukinobu; Liu, Yucheng; Wang, Mingchao; Matsuura, Masato; Shibata, Kaoru; Ohira-Kawamura, Seiko; Yamada, Takeshi; Lin, Shangchao; Nakajima, Kenji; Liu, Shengzhong (Frank)

2017-01-01

Perovskite CH3NH3PbI3 exhibits outstanding photovoltaic performances, but the understanding of the atomic motions remains inadequate even though they take a fundamental role in transport properties. Here, we present a complete atomic dynamic picture consisting of molecular jumping rotational modes and phonons, which is established by carrying out high-resolution time-of-flight quasi-elastic and inelastic neutron scattering measurements in a wide energy window ranging from 0.0036 to 54 meV on a large single crystal sample, respectively. The ultrafast orientational disorder of molecular dipoles, activated at ∼165 K, acts as an additional scattering source for optical phonons as well as for charge carriers. It is revealed that acoustic phonons dominate the thermal transport, rather than optical phonons due to sub-picosecond lifetimes. These microscopic insights provide a solid standing point, on which perovskite solar cells can be understood more accurately and their performances are perhaps further optimized. PMID:28665407

Evolution from Rydberg gas to ultracold plasma in a supersonic atomic beam of Xe

NASA Astrophysics Data System (ADS)

Hung, J.; Sadeghi, H.; Schulz-Weiling, M.; Grant, E. R.

2014-08-01

A Rydberg gas of xenon, entrained in a supersonic atomic beam, evolves slowly to form an ultracold plasma. In the early stages of this evolution, when the free-electron density is low, Rydberg atoms undergo long-range \\ell -mixing collisions, yielding states of high orbital angular momentum. The development of high-\\ell states promotes dipole-dipole interactions that help to drive Penning ionization. The electron density increases until it reaches the threshold for avalanche. Ninety μs after the production of a Rydberg gas with the initial state, {{n}_{0}}{{\\ell }_{0}}=42d, a 432 V cm-1 electrostatic pulse fails to separate charge in the excited volume, an effect which is ascribed to screening by free electrons. Photoexcitation cross sections, observed rates of \\ell -mixing, and a coupled-rate-equation model simulating the onset of the electron-impact avalanche point consistently to an initial Rydberg gas density of 5\\times {{10}^{8}}\\;c{{m}^{-3}}.

Symmetry and novelty in the electronic and geometric structure of nanoalloys:. the case of Ag27Cu7

NASA Astrophysics Data System (ADS)

Ortigoza, M. Alcántara; Rahman, T. S.

2008-04-01

Nanoparticles of bimetallic alloys have been shown to possess composition dependent characteristics which distinguish themselves from the corresponding bulk alloys. Taking the 34-atom nanoalloy of Ag and Cu (Ag27Cu7), we show using first principles electronic structure calculations that this core-shell alloy indeed has perfect D5h symmetry and consists of only 6 non-equivalent (2 Cu and 4 Ag) atoms. Analysis of the interatomic bond lengths and detailed electronic structure further reveal that the Cu atoms play a major role in controlling the characteristics of the nanoalloy. The higher cohesive energy, together with shorter bond length for Cu, compared to Ag, conspire to produce a hierarchy in the relative strengths of the Ag - Cu, Ag - Ag, and Cu - Cu bonds and corresponding interatomic bond lengths, point to the uniqueness in the characteristics of this nanoalloy. Charge density plots of Ag27Cu7 provide further insights into the relative strengths of the various interatomic bonds.

Crystal chemistry and temperature behavior of the natural hydrous borate colemanite, a mineral commodity of boron

NASA Astrophysics Data System (ADS)

Lotti, Paolo; Gatta, G. Diego; Demitri, Nicola; Guastella, Giorgio; Rizzato, Silvia; Ortenzi, Marco Aldo; Magrini, Fabrizio; Comboni, Davide; Guastoni, Alessandro; Fernandez-Diaz, Maria Teresa

2018-05-01

Colemanite, CaB3O4(OH)3ṡH2O, is the most common hydrous Ca-borate, as well as a major mineral commodity of boron. In this study, we report a thorough chemical analysis and the low-temperature behavior of a natural sample of colemanite by means of a multi-methodological approach. From the chemical point of view, the investigated sample resulted to be relatively pure, its composition being very close to the ideal one, with only a minor substitution of Sr2+ for Ca2+. At about 270.5 K, a displacive phase transition from the centrosymmetric P21/ a to the acentric P21 space group occurs. On the basis of in situ single-crystal synchrotron X-ray (down to 104 K) and neutron diffraction (at 20 K) data, the hydrogen-bonding configuration of both the polymorphs and the structural modifications at the atomic scale at varying temperatures are described. The asymmetric distribution of ionic charges along the [010] axis, allowed by the loss of the inversion center, is likely responsible for the reported ferroelectric behavior of colemanite below the phase transition temperature.

Spectroscopic analysis of the powdery complex chitosan-iodine

NASA Astrophysics Data System (ADS)

Gegel, Natalia O.; Babicheva, Tatyana S.; Belyakova, Olga A.; Lugovitskaya, Tatyana N.; Shipovskaya, Anna B.

2018-04-01

A chitosan-iodine complex was obtained by modification of polymer powder in the vapor of an iodine-containing sorbate and studied by electron and IR spectroscopy, optical rotation dispersion. It was found that the electronic spectra of an aqueous solution of the modified chitosan (the source one and that stored for a year) showed intense absorption bands of triiodide and iodate ions, and also polyiodide ions, bound to the macromolecule by exciton bonding with charge transfer. Analysis of the IR spectra shows destruction of the network of intramolecular and intermolecular hydrogen bonds in the iodinated chitosan powder in comparison with the source polymer and the formation of a new chemical substance. E.g., the absorption band of deformation vibrations of the hydroxyl group disappears in the modified sample, and that of the protonated amino group shifts toward shorter wavelengths. The intensity of the stretching vibration band of the glucopyranose ring atoms significantly reduces. Heating of the modified sample at a temperature below the thermal degradation point of the polymer leads to stabilization of the chitosan-iodine complex. Based on our studies, the hydroxyl and amino groups of the aminopolysaccharide have been recognized as the centers of retention of polyiodide chains in the chitosan matrix.

Theoretical study of negatively charged Fe(-)-(H2O)(n ≤ 6) clusters.

PubMed

Castro, Miguel

2012-06-14

Interactions of a singly negatively charged iron atom with water molecules, Fe(-)-(H(2)O)(n≤6), in the gas phase were studied by means of density functional theory. All-electron calculations were performed using the B3LYP functional and the 6-311++G(2d,2p) basis set for the Fe, O, and H atoms. In the lowest total energy states of Fe(-)-(H(2)O)(n), the metal-hydrogen bonding is stronger than the metal-oxygen one, producing low-symmetry structures because the water molecules are directly attached to the metal by basically one of their hydrogen atoms, whereas the other ones are involved in a network of hydrogen bonds, which together with the Fe(δ-)-H(δ+) bonding accounts for the nascent hydration of the Fe(-) anion. For Fe(-)-(H(2)O)(3≤n), three-, four-, five-, and six-membered rings of water molecules are bonded to the metal, which is located at the surface of the cluster in such a way as to reduce the repulsion with the oxygen atoms. Nevertheless, internal isomers appear also, lying less than 3 or 5 kcal/mol for n = 2-3 or n = 4-6. These results are in contrast with those of classical TM(+)-(H(2)O)(n) complexes, where the direct TM(+)-O bonding usually produces high symmetry structures with the metal defining the center of the complex. They show also that the Fe(-) anions, as the TM(+) ions, have great capability for the adsorption of water molecules, forming Fe(-)-(H(2)O)(n) structures stabilized by Fe(δ-)-H(δ+) and H-bond interactions.

Multi-level modeling of total ionizing dose in a-silicon dioxide: First principles to circuits

NASA Astrophysics Data System (ADS)

Nicklaw, Christopher J.

Oxygen vacancies have long been known to be the dominant intrinsic defect in amorphous SiO2. They exist, in concentrations dependent on processing conditions, as neutral defects in thermal oxides without usually causing any significant deleterious effects, with some spatial and energy distribution. During irradiation they can capture holes and become positively charged E '-centers, contributing to device degradation. Over the years, a considerable database has been amassed on the dynamics of E' -centers in bulk SiO2 films, and near the interface under different irradiation and annealing conditions. Theoretical calculations so far have revealed the basic properties of prototype oxygen vacancies, primarily as they behave in either a crystalline quartz environment, or in small clusters that serve as a substitute for a real amorphous structure. To date at least three categories of E'-centers, existing at or above room temperature, have been observed in SiO2. The unifying feature is an unpaired electron on a threefold coordinated silicon atom, having the form O3 ≡ Si·. Feigl et al. identified the E'1 -center in crystalline quartz as a trapped hole on an oxygen vacancy, which causes an asymmetrical relaxation, resulting in a paramagnetic center. The unpaired electron in the E'1 -center is localized on the three-fold coordinated Si atoms, while the hole is localized on the other Si atom. Results from an ab initio statistical simulation examination of the behaviors of oxygen vacancies, within amorphous structures, identify a new form of the E'-center, the E'g5 and help in the understanding of the underlying physical mechanisms involved in switched-bias annealing, and electron paramagnetic resonance (EPR) studies. The results also suggest a common border trap, induced by trapped holes in SiO2, is a hole trapped at an oxygen vacancy defect, which can be compensated by an electron, as originally proposed by Lelis and co-workers at Harry Diamond Laboratories. This dissertation provides new insights into the basic mechanisms of a-SiO2 defects, and provides a link between basic mechanisms and Electronic Design Automation (EDA) tools, providing an enhanced design flow for radiation-resistant electronics.

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

PubMed

Udier-Blagović, Marina; Morales De Tirado, Patricia; Pearlman, Shoshannah A; Jorgensen, William L

2004-08-01

Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. Copyright 2004 Wiley Periodicals, Inc.

Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers.

PubMed

Lazaridis, Themis; Leveritt, John M; PeBenito, Leo

2014-09-01

The energetic cost of burying charged groups in the hydrophobic core of lipid bilayers has been controversial, with simulations giving higher estimates than certain experiments. Implicit membrane approaches are usually deemed too simplistic for this problem. Here we challenge this view. The free energy of transfer of amino acid side chains from water to the membrane center predicted by IMM1 is reasonably close to all-atom free energy calculations. The shape of the free energy profile, however, for the charged side chains needs to be modified to reflect the all-atom simulation findings (IMM1-LF). Membrane thinning is treated by combining simulations at different membrane widths with an estimate of membrane deformation free energy from elasticity theory. This approach is first tested on the voltage sensor and the isolated S4 helix of potassium channels. The voltage sensor is stably inserted in a transmembrane orientation for both the original and the modified model. The transmembrane orientation of the isolated S4 helix is unstable in the original model, but a stable local minimum in IMM1-LF, slightly higher in energy than the interfacial orientation. Peptide translocation is addressed by mapping the effective energy of the peptide as a function of vertical position and tilt angle, which allows identification of minimum energy pathways and transition states. The barriers computed for the S4 helix and other experimentally studied peptides are low enough for an observable rate. Thus, computational results and experimental studies on the membrane burial of peptide charged groups appear to be consistent. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014 Elsevier B.V. All rights reserved.

Electronic structure at transition metal phthalocyanine-transition metal oxide interfaces: Cobalt phthalocyanine on epitaxial MnO films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glaser, Mathias; Peisert, Heiko, E-mail: heiko.peisert@uni-tuebingen.de; Adler, Hilmar

2015-03-14

The electronic structure of the interface between cobalt phthalocyanine (CoPc) and epitaxially grown manganese oxide (MnO) thin films is studied by means of photoemission (PES) and X-ray absorption spectroscopy (XAS). Our results reveal a flat-lying adsorption geometry of the molecules on the oxide surface which allows a maximal interaction between the π-system and the substrate. A charge transfer from MnO, in particular, to the central metal atom of CoPc is observed by both PES and XAS. The change of the shape of N-K XAS spectra at the interface points, however, to the involvement of the Pc macrocycle in the chargemore » transfer process. As a consequence of the charge transfer, energetic shifts of MnO related core levels were observed, which are discussed in terms of a Fermi level shift in the semiconducting MnO films due to interface charge redistribution.« less

Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganesh, P.; Kim, Jeongnim; Park, Changwon

2014-11-03

In highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Moreover, the highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based onmore » point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. Our results demonstrate that the lithium carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.« less

Stabilizing Rabi oscillation of a charge qubit via the atomic clock technique

NASA Astrophysics Data System (ADS)

Yu, Deshui; Landra, Alessandro; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2018-02-01

We propose a superconducting circuit-atom hybrid, where the Rabi oscillation of single excess Cooper pair in the island is stabilized via the common atomic clock technique. The noise in the superconducting circuit is mapped onto the voltage source which biases the Cooper-pair box via an inductor and a gate capacitor. The fast fluctuations of the gate charge are significantly suppressed by an inductor-capacitor resonator, leading to a long-relaxation-time Rabi oscillation. More importantly, the residual low-frequency fluctuations are further reduced by using the general feedback-control method, in which the voltage bias is stabilized via continuously measuring the dc-Stark-shift-induced atomic Ramsey signal. The stability and coherence time of the resulting charge-qubit Rabi oscillation are both enhanced. The principal structure of this Cooper-pair-box oscillator is studied in detail.

Ewald Electrostatics for Mixtures of Point and Continuous Line Charges.

PubMed

Antila, Hanne S; Tassel, Paul R Van; Sammalkorpi, Maria

2015-10-15

Many charged macro- or supramolecular systems, such as DNA, are approximately rod-shaped and, to the lowest order, may be treated as continuous line charges. However, the standard method used to calculate electrostatics in molecular simulation, the Ewald summation, is designed to treat systems of point charges. We extend the Ewald concept to a hybrid system containing both point charges and continuous line charges. We find the calculated force between a point charge and (i) a continuous line charge and (ii) a discrete line charge consisting of uniformly spaced point charges to be numerically equivalent when the separation greatly exceeds the discretization length. At shorter separations, discretization induces deviations in the force and energy, and point charge-point charge correlation effects. Because significant computational savings are also possible, the continuous line charge Ewald method presented here offers the possibility of accurate and efficient electrostatic calculations.

Coaxial anode improves sensitivity of gas radiation counters

NASA Technical Reports Server (NTRS)

Kraushaar, W. L.

1974-01-01

Anode wire itself is enclosed by three segments. Two on ends are rejector segments, and middle one is primary charge-detecting segment. Anode wire is made from tungsten and is surrounded by enamel insulation. Enamel is covered by segments of vapor-deposited gold. At one point in center segment, gold layer makes direct contact with anode wire.

A statistical model of a metallic inclusion in semiconducting media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shikin, V. B., E-mail: shikin@issp.ac.ru

The properties of an isolated multicharged atom embedded into a semiconducting medium are discussed. The analysis generalizes the results of the known Thomas–Fermi theory for a multicharged (Z ≫ 1) atom in vacuum when it is immersed into an electron–hole gas of finite temperature. The Thomas–Fermi–Debye (TFD) atom problem is directly related to the properties of donors in low-doped semiconductors and is alternative in its conclusions to the ideal scenario of dissociation of donors. In the existing ideal statistics, an individual donor under infinitely low doping is completely ionized (a charged center does not hold its neutralizing counter-ions). A Thomas–Fermi–Debyemore » atom (briefly, a TFD donor) remains a neutral formation that holds its screening “coat” even for infinitely low doping level, i.e., in the region of n{sub d}λ{sub 0}{sup 3} ≪ 1, where n{sub d} is the concentration of the doping impurity and λ{sub 0} is the Debye length with the parameters of intrinsic semiconductor. Various observed consequences in the behavior of a TFD donor are discussed that allow one to judge the reality of the implications of the TFD donor model.« less

Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

PubMed

Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.

STM studies of an atomic-scale gate electrode formed by a single charged vacancy in GaAs

NASA Astrophysics Data System (ADS)

Lee, Donghun; Daughton, David; Gupta, Jay

2009-03-01

Electric-field control of spin-spin interactions at the atomic level is desirable for the realization of spintronics and spin-based quantum computation. Here we demonstrate the realization of an atomic-scale gate electrode formed by a single charged vacancy on the GaAs(110) surface[1]. We can position these vacancies with atomic precision using the tip of a home-built, low temperature STM. Tunneling spectroscopy of single Mn acceptors is used to quantify the electrostatic field as a function of distance from the vacancy. Single Mn acceptors are formed by substituting Mn adatoms for Ga atoms in the first layer of the p-GaAs(110) surface[2]. Depending on the distance, the in-gap resonance of single Mn acceptors can shift as much as 200meV. Our data indicate that the electrostatic field decays according to a screened Coulomb potential. The charge state of the vacancy can be switched to neutral, as evidenced by the Mn resonance returning to its unperturbed position. Reversible control of the local electric field as well as charged states of defects in semiconductors can open new insights such as realizing an atomic-scale gate control and studying spin-spin interactions in semiconductors. http://www.physics.ohio-state.edu/sim jgupta [1] D. Lee and J.A. Gupta (in preparation) [2] D. Kitchen et al., Nature 442, 436-439 (2006)

Positive column of a glow discharge in neon with charged dust grains (a review)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polyakov, D. N., E-mail: cryolab@ihed.ras.ru; Shumova, V. V.; Vasilyak, L. M.

The effect of charged micron-size dust grains (microparticles) on the electric parameters of the positive column of a low-pressure dc glow discharge in neon has been studied experimentally and numerically. Numerical analysis is carried out in the diffusion-drift approximation with allowance for the interaction of dust grains with metastable neon atoms. In a discharge with a dust grain cloud, the longitudinal electric field increases. As the number density of dust grains in an axisymmetric cylindrical dust cloud rises, the growth of the electric field saturates. It is shown that the contribution of metastable atoms to ionization is higher in amore » discharge with dust grains, in spite of the quenching of metastable atoms on dust grains. The processes of charging of dust grains and the dust cloud are considered. As the number density of dust grains rises, their charge decreases, while the space charge of the dust cloud increases. The results obtained can be used in plasma technologies involving microparticles.« less

A unified formulation of dichroic signals using the Borrmann effect and twisted photon beams.

PubMed

Collins, Stephen P; Lovesey, Stephen W

2018-05-21

Dichroic X-ray signals derived from the Borrmann effect and a twisted photon beam with topological charge l = 1 are formulated with an effective wavevector. The unification applies for non-magnetic and magnetic materials. Electronic degrees of freedom associated with an ion are encapsulated in multipoles previously used to interpret conventional dichroism and Bragg diffraction enhanced by an atomic resonance. A dichroic signal exploiting the Borrmann effect with a linearly polarized beam presents charge-like multipoles that include a hexadecapole. A difference between dichroic signals obtained with a twisted beam carrying spin polarization (circular polarization) and opposite winding numbers presents charge-like atomic multipoles, whereas a twisted beam carrying linear polarization alone presents magnetic (time-odd) multipoles. Charge-like multipoles include a quadrupole, and magnetic multipoles include a dipole and an octupole. We discuss the practicalities and relative merits of spectroscopy exploiting the two remarkably closely-related processes. Signals using beams with topological charges l ≥ 2 present additional atomic multipoles.

Charge-free method of forming nanostructures on a substrate

DOEpatents

Hoffbauer; Mark , Akhadov; Elshan

2010-07-20

A charge-free method of forming a nanostructure at low temperatures on a substrate. A substrate that is reactive with one of atomic oxygen and nitrogen is provided. A flux of neutral atoms of least one of oxygen and nitrogen is generated within a laser-sustained-discharge plasma source and a collimated beam of energetic neutral atoms and molecules is directed from the plasma source onto a surface of the substrate to form the nanostructure. The energetic neutral atoms and molecules in the beam have an average kinetic energy in a range from about 1 eV to about 5 eV.

GW/Bethe-Salpeter calculations for charged and model systems from real-space DFT

NASA Astrophysics Data System (ADS)

Strubbe, David A.

GW and Bethe-Salpeter (GW/BSE) calculations use mean-field input from density-functional theory (DFT) calculations to compute excited states of a condensed-matter system. Many parts of a GW/BSE calculation are efficiently performed in a plane-wave basis, and extensive effort has gone into optimizing and parallelizing plane-wave GW/BSE codes for large-scale computations. Most straightforwardly, plane-wave DFT can be used as a starting point, but real-space DFT is also an attractive starting point: it is systematically convergeable like plane waves, can take advantage of efficient domain parallelization for large systems, and is well suited physically for finite and especially charged systems. The flexibility of a real-space grid also allows convenient calculations on non-atomic model systems. I will discuss the interfacing of a real-space (TD)DFT code (Octopus, www.tddft.org/programs/octopus) with a plane-wave GW/BSE code (BerkeleyGW, www.berkeleygw.org), consider performance issues and accuracy, and present some applications to simple and paradigmatic systems that illuminate fundamental properties of these approximations in many-body perturbation theory.

Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy

PubMed Central

2017-01-01

High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl2 concentration. Using DLVO theory with charge regulation, we determine from the measured force–distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca2+ ion adsorption, while Cl– adsorption at higher CaCl2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl– ions will co-adsorb, thereby changing the observed ordered surface structure. PMID:29140711

Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy.

PubMed

Kumar, N; Andersson, M P; van den Ende, D; Mugele, F; Siretanu, I

2017-12-19

High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl 2 concentration. Using DLVO theory with charge regulation, we determine from the measured force-distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl 2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl 2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca 2+ ion adsorption, while Cl - adsorption at higher CaCl 2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca 2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl - ions will co-adsorb, thereby changing the observed ordered surface structure.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

Computing the binding affinity of Zn2+ in human carbonic anhydrase II on the basis of all-atom molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Wambo, Thierry; Rodriguez, Roberto

Human carbonic anhydrase II (hCAII) is a metalloenzyme with a Zinc cation at its binding site. The presence of the Zinc turns the protein into an efficient enzyme which catalyzes the reversible hydration of carbon dioxide into bicarbonate anion. Available X-ray structures of the apo-hCAII and holo-hCAII show no significant differences in the overall structure of these proteins. What difference, if any, is there between the structures of the hydrated apo-hCAII and holo? How can we use computer simulation to efficiently compute the binding affinity of Zinc to hCAII? We will present a scheme developed to compute the binding affinity of Zinc cation to hCAII on the basis of all-atom molecular dynamics simulation where Zinc is represented as a point charge and the CHARMM36 force field is used for running the dynamics of the system. Our computed binding affinity of the cation to hCAII is in good agreement with experiment, within the margin of error, while a look at the dynamics of the binding site suggests that in the absence of the Zinc, there is a re-organization of the nearby histidine residues which adopt a new distinct configuration. The authors are thankful for the NIH support through Grants GM084834 and GM060655. They also acknowledge the Texas Advanced Computing Center at the University of Texas at Austin for the supercomputing time. They thank Dr Liao Chen for his comments.

On the validity of the amphoteric-defect model in gallium arsenide and a criterion for Fermi-level pinning by defects

NASA Astrophysics Data System (ADS)

Chen, C.-H.; Tan, T. Y.

1995-10-01

Using the theoretically calculated point-defect total-energy values of Baraff and Schlüter in GaAs, an amphoteric-defect model has been proposed by Walukiewicz to explain a large number of experimental results. The suggested amphoteric-defect system consists of two point-defect species capable of transforming into each other: the doubly negatively charged Ga vacancy V {Ga/2-} and the triply positively charged defect complex (ASGa+ V As)3+, with AsGa being the antisite defect of an As atom occupying a Ga site and V As being an As vacancy. When present in sufficiently high concentrations, the amphoteric defect system V {Ga/2-}/(AsGa+ V As)3+ is supposed to be able to pin the GaAs Fermi level at approximately the E v +0.6 eV level position, which requires that the net free energy of the V Ga/(AsGa+ V As) defect system to be minimum at the same Fermi-level position. We have carried out a quantitative study of the net energy of this defect system in accordance with the individual point-defect total-energy results of Baraff and Schlüter, and found that the minimum net defect-system-energy position is located at about the E v +1.2 eV level position instead of the needed E v +0.6 eV position. Therefore, the validity of the amphoteric-defect model is in doubt. We have proposed a simple criterion for determining the Fermi-level pinning position in the deeper part of the GaAs band gap due to two oppositely charged point-defect species, which should be useful in the future.

Evolution of Triplet Paramagnetic Centers in Diamonds Obtained by Sintering of Detonation Nanodiamonds at High Pressure and Temperature

NASA Astrophysics Data System (ADS)

Osipov, V. Yu.; Shames, A. I.; Efimov, N. N.; Shakhov, F. M.; Kidalov, S. V.; Minin, V. V.; Vul', A. Ya.

2018-04-01

The electron paramagnetic resonance (EPR) spectra of triplet centers in detonation nanodiamonds (DNDs) and diamond single crystals of submicrometer size, synthesized from those DNDs at high pressures and temperatures, are studied. In the EPR spectra of DNDs, signals from negatively charged nitrogen- vacancy centers (NV)/sup(-) with a g factor of g 1 = 4.24 and multivacancies with g 2 = 4.00 are observed. The signals from (NV)/sup(-) centers disappear in the spectra of diamond single crystals, and a quintet signal with g = 4.00 is detected at the position of the signal from multivacancies. Analysis of the shape and position of the quintet' lines showed that this ESR signal is due to the pairs of nitrogen substitution centers in diamond, separated from each other by distances not exceeding 0.7 nm, between which a strong exchange interaction takes place. A comparison of the experimental data and the simulation results allows determining the spin-Hamiltonian parameters of the exchange-coupled pairs of paramagnetic impurity nitrogen atoms.

Use of scanning near-field optical microscope with an aperture probe for detection of luminescent nanodiamonds

NASA Astrophysics Data System (ADS)

Shershulin, V. A.; Samoylenko, S. R.; Shenderova, O. A.; Konov, V. I.; Vlasov, I. I.

2017-02-01

The suitability of scanning near-field optical microscopy (SNOM) to image photoluminescent diamond nanoparticles with nanoscale resolution is demonstrated. Isolated diamond nanocrystals with an average size of 100 nm, containing negatively charged nitrogen-vacancy (NV-) centers, were chosen as tested material. The NV- luminescence was stimulated by continuous 532 nm laser light. Sizes of analyzed crystallites were monitored by an atomic force microscope. The lateral resolution of the order of 100 nm was reached in SNOM imaging of diamond nanoparticles using 150 nm square aperture of the probe.

Coupled-cluster treatment of molecular strong-field ionization

NASA Astrophysics Data System (ADS)

Jagau, Thomas-C.

2018-05-01

Ionization rates and Stark shifts of H2, CO, O2, H2O, and CH4 in static electric fields have been computed with coupled-cluster methods in a basis set of atom-centered Gaussian functions with a complex-scaled exponent. Consideration of electron correlation is found to be of great importance even for a qualitatively correct description of the dependence of ionization rates and Stark shifts on the strength and orientation of the external field. The analysis of the second moments of the molecular charge distribution suggests a simple criterion for distinguishing tunnel and barrier suppression ionization in polyatomic molecules.

Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network.

PubMed

Golmohammadi, Hassan

2009-11-30

A quantitative structure-property relationship (QSPR) study was performed to develop models those relate the structure of 141 organic compounds to their octanol-water partition coefficients (log P(o/w)). A genetic algorithm was applied as a variable selection tool. Modeling of log P(o/w) of these compounds as a function of theoretically derived descriptors was established by multiple linear regression (MLR), partial least squares (PLS), and artificial neural network (ANN). The best selected descriptors that appear in the models are: atomic charge weighted partial positively charged surface area (PPSA-3), fractional atomic charge weighted partial positive surface area (FPSA-3), minimum atomic partial charge (Qmin), molecular volume (MV), total dipole moment of molecule (mu), maximum antibonding contribution of a molecule orbital in the molecule (MAC), and maximum free valency of a C atom in the molecule (MFV). The result obtained showed the ability of developed artificial neural network to prediction of partition coefficients of organic compounds. Also, the results revealed the superiority of ANN over the MLR and PLS models. Copyright 2009 Wiley Periodicals, Inc.

Hough transform method for track finding in center drift chamber

NASA Astrophysics Data System (ADS)

Azmi, K. A. Mohammad Kamal; Wan Abdullah, W. A. T.; Ibrahim, Zainol Abidin

2016-01-01

Hough transform is a global tracking method used which had been expected to be faster approach for tracking the circular pattern of electron moving in Center Drift Chamber (CDC), by transforming the point of hit into a circular curve. This paper present the implementation of hough transform method for the reconstruction of tracks in Center Drift Chamber (CDC) which have been generated by random number in C language programming. Result from implementation of this method shows higher peak of circle parameter value (xc,yc,rc) that indicate the similarity value of the parameter needed for circular track in CDC for charged particles in the region of CDC.

Deciphering the "chemical" nature of the exotic isotopes of hydrogen by the MC-QTAIM analysis: the positively charged muon and the muonic helium as new members of the periodic table.

PubMed

Goli, Mohammad; Shahbazian, Shant

2014-04-14

This report is a primarily survey on the chemical nature of some exotic species containing the positively charged muon and the muonic helium, i.e., the negatively charged muon plus helium nucleus, as exotic isotopes of hydrogen, using the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis, employing ab initio non-Born-Oppenhiemer wavefunctions. Accordingly, the "atoms in molecules" analysis performed on various asymmetric exotic isotopomers of the hydrogen molecule, recently detected experimentally [Science, 2011, 331, 448], demonstrates that both the exotic isotopes are capable of forming atoms in molecules and retaining the identity of hydrogen atoms. Various derived properties of atomic basins containing the muonic helium cast no doubt that apart from its short life time, it is a heavier isotope of hydrogen while the properties of basins containing the positively charged muon are more remote from those of the orthodox hydrogen basins, capable of appreciable donation of electrons as well as large charge polarization. However, with some tolerance, they may also be categorized as hydrogen basins though with a smaller electronegativity. All in all, the present study also clearly demonstrates that the MC-QTAIM analysis is an efficient approach to decipher the chemical nature of species containing exotic constituents, which are difficult to elucidate by experimental and/or alternative theoretical schemes.

The Ring of Gyges: Anonymity and Technological Advance’s Effect on the Deterrence of Nonstate Actors in 2035

DTIC Science & Technology

2012-10-01

Technical Information Center, 1972), 723–24. A case in point is the Manhattan Project undertaken by the United States to produce the first atomic weapon. A...capital and operations costs from 1942 through 1945. Costs adjusted using a base year of 1944 (the year of highest Manhattan Project expenditures). 39

Alternative Fuels Data Center: Electric Vehicle Charging Station Locations

Science.gov Websites

Electric Vehicle Charging Station Locations to someone by E-mail Share Alternative Fuels Data Center: Electric Vehicle Charging Station Locations on Facebook Tweet about Alternative Fuels Data Center : Electric Vehicle Charging Station Locations on Twitter Bookmark Alternative Fuels Data Center: Electric

Alternative Fuels Data Center: Minneapolis Makes EV-Charging History Record

Science.gov Websites

Minneapolis Makes EV-Charging History Record to someone by E-mail Share Alternative Fuels Data Center: Minneapolis Makes EV-Charging History Record on Facebook Tweet about Alternative Fuels Data Center: Minneapolis Makes EV-Charging History Record on Twitter Bookmark Alternative Fuels Data Center

Quantum Theory of Atoms in Molecules Charge-Charge Transfer-Dipolar Polarization Classification of Infrared Intensities.

PubMed

Duarte, Leonardo J; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E

2017-10-26

Fundamental infrared vibrational transition intensities of gas-phase molecules are sensitive probes of changes in electronic structure accompanying small molecular distortions. Models containing charge, charge transfer, and dipolar polarization effects are necessary for a successful classification of the C-H, C-F, and C-Cl stretching and bending intensities. C-H stretching and in-plane bending vibrations involving sp 3 carbon atoms have small equilibrium charge contributions and are accurately modeled by the charge transfer-counterpolarization contribution and its interaction with equilibrium charge movement. Large C-F and C═O stretching intensities have dominant equilibrium charge movement contributions compared to their charge transfer-dipolar polarization ones and are accurately estimated by equilibrium charge and the interaction contribution. The C-F and C-Cl bending modes have charge and charge transfer-dipolar polarization contribution sums that are of similar size but opposite sign to their interaction values resulting in small intensities. Experimental in-plane C-H bends have small average intensities of 12.6 ± 10.4 km mol -1 owing to negligible charge contributions and charge transfer-counterpolarization cancellations, whereas their average out-of-plane experimental intensities are much larger, 65.7 ± 20.0 km mol -1 , as charge transfer is zero and only dipolar polarization takes place. The C-F bending intensities have large charge contributions but very small intensities. Their average experimental out-of-plane intensity of 9.9 ± 12.6 km mol -1 arises from the cancellation of large charge contributions by dipolar polarization contributions. The experimental average in-plane C-F bending intensity, 5.8 ± 7.3 km mol -1 , is also small owing to charge and charge transfer-counterpolarization sums being canceled by their interaction contributions. Models containing only atomic charges and their fluxes are incapable of describing electronic structure changes for simple molecular distortions that are of interest in classifying infrared intensities. One can expect dipolar polarization effects to also be important for larger distortions of chemical interest.

Origin of Transitions between Metallic and Insulating States in Simple Metals

DOE PAGES

Naumov, Ivan I.; Hemley, Russell J.

2015-04-17

Unifying principles that underlie recently discovered transitions between metallic and insulating states in elemental solids under pressure are developed. Using group theory arguments and first principles calculations, we show that the electronic properties of the phases involved in these transitions are controlled by symmetry principles not previously recognized. The valence bands in these systems are described by simple and composite band representations constructed from localized Wannier functions centered on points unoccupied by atoms, and which are not necessarily all symmetrical. The character of the Wannier functions is closely related to the degree of s-p(-d) hybridization and reflects multi-center chemical bondingmore » in these insulating states. The conditions under which an insulating state is allowed for structures having an integer number of atoms per primitive unit cell as well as re-entrant (i.e., metal-insulator-metal) transition sequences are detailed, resulting in predictions of novel behavior such as phases having three-dimensional Dirac-like points. The general principles developed are tested and applied to the alkali and alkaline earth metals, including elements where high-pressure insulating phases have been identified or reported (e.g., Li, Na, and Ca).« less

Semiconductor color-center structure and excitation spectra: Equation-of-motion coupled-cluster description of vacancy and transition-metal defect photoluminescence

NASA Astrophysics Data System (ADS)

Lutz, Jesse J.; Duan, Xiaofeng F.; Burggraf, Larry W.

2018-03-01

Valence excitation spectra are computed for deep-center silicon-vacancy defects in 3C, 4H, and 6H silicon carbide (SiC), and comparisons are made with literature photoluminescence measurements. Optimizations of nuclear geometries surrounding the defect centers are performed within a Gaussian basis-set framework using many-body perturbation theory or density functional theory (DFT) methods, with computational expenses minimized by a QM/MM technique called SIMOMM. Vertical excitation energies are subsequently obtained by applying excitation-energy, electron-attached, and ionized equation-of-motion coupled-cluster (EOMCC) methods, where appropriate, as well as time-dependent (TD) DFT, to small models including only a few atoms adjacent to the defect center. We consider the relative quality of various EOMCC and TD-DFT methods for (i) energy-ordering potential ground states differing incrementally in charge and multiplicity, (ii) accurately reproducing experimentally measured photoluminescence peaks, and (iii) energy-ordering defects of different types occurring within a given polytype. The extensibility of this approach to transition-metal defects is also tested by applying it to silicon-substituted chromium defects in SiC and comparing with measurements. It is demonstrated that, when used in conjunction with SIMOMM-optimized geometries, EOMCC-based methods can provide a reliable prediction of the ground-state charge and multiplicity, while also giving a quantitative description of the photoluminescence spectra, accurate to within 0.1 eV of measurement for all cases considered.

Theoretical studies of the nucleophilic substitution of halides and amine at a sulfonyl center.

PubMed

Sung, Dae Dong; Kim, Tae Joon; Lee, Ikchoon

2009-06-25

Gas-phase nucleophilic substitution reactions, F(-) + CH(3)SO(2)F, Cl(-) + CH(3)SO(2)Cl, Cl(-) + CH(3)SO(2)F, and NH(3) + CH(3)SO(2)Cl, have been investigated at the B3LYP/6-311+G** and MP2/6-31+G* levels of theory. A very shallow well for the reaction intermediate in a triple-well potential energy surface (PES) was observed for the identity fluoride exchange, but double well PESs were obtained for the other three reactions with three different PES profiles. NBO analyses of the transition states showed substantial charge transfer interactions in all cases which provided a much larger amount of stabilization energy compared with the corresponding species at the carbon center of methyl halides. This difference is primarily caused by the strong electropositive nature of the sulfur center. The F-S-F axial linkage in the distorted TBP type intermediate in the identity fluoride exchange reaction exhibited a weak three-center, four-electron omega-bonding, which is considered to provide stability of the intermediate. All the reactant (RC) and product complexes (PC) have Cs symmetry. The symmetry plane bisects angles HCH (of methyl group), OSO (of sulfonyl group), and HNH (of ammonia). Vicinal charge transfer interactions between the two out-of-plane C-H, S-O, and N-H bonds provide extra stabilization to the ion-dipole complexes together with H-bond formation of in-plane H atom with the nucleophile and/or leaving group.

Theory of the stopping power of fast multicharged ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yudin, G.L.

1991-12-01

The processes of Coulomb excitation and ionization of atoms by a fast charged particle moving along a classical trajectory are studied. The target electrons are described by the Dirac equation, while the field of the incident particle is described by the Lienard-Wiechert potential. The theory is formulated in the form most convenient for investigation of various characteristics of semiclassical atomic collisions. The theory of sudden perturbations, which is valid at high enough velocities for a high projectile charge, is employed to obtain probabilities and cross sections of the Coulomb excitation and ionization of atomic hydrogen by fast multiply charged ions.more » Based on the semiclassical sudden Born approximation, the ionization cross section and the average electronic energy loss of a fast ion in a single collision with an atom are investigated over a wide specific energy range from 500 keV/amu to 50 MeV/amu.« less

Symmetric Resonance Charge Exchange Cross Section Based on Impact Parameter Treatment

NASA Technical Reports Server (NTRS)

Omidvar, Kazem; Murphy, Kendrah; Atlas, Robert (Technical Monitor)

2002-01-01

Using a two-state impact parameter approximation, a calculation has been carried out to obtain symmetric resonance charge transfer cross sections between nine ions and their parent atoms or molecules. Calculation is based on a two-dimensional numerical integration. The method is mostly suited for hydrogenic and some closed shell atoms. Good agreement has been obtained with the results of laboratory measurements for the ion-atom pairs H+-H, He+-He, and Ar+-Ar. Several approximations in a similar published calculation have been eliminated.

A Water Geochemistry Study of Indian Wells Valley, Inyo and Kern Counties, California. Supplement. Isotope Geochemistry and Appendix H.

DTIC Science & Technology

1990-09-01

accuracy by Carl F. Austin, NWC; James Moore, California Energy Co.; and Robert 0. Fournier, Unites States Geological Survey. Approved by Under authority...protons, electrons , and neutrons. The electrical charge of protons is positive, and that of electrons is negative. Neutrons have no electrical charge...The number of protons determines what element an atom is and gives it its atomic number. In a neutral or nonionized atom the number of electrons

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Particle confinement by a radially polarized laser Bessel beam

NASA Astrophysics Data System (ADS)

Laredo, Gilad; Kimura, Wayne D.; Schächter, Levi

2017-03-01

The stable trajectory of a charged particle in an external guiding field is an essential condition for its acceleration or for forcing it to generate radiation. Examples of possible guiding devices include a solenoidal magnetic field or permanent periodic magnet in klystrons, a wiggler in free-electron lasers, the lattice of any accelerator, and finally the crystal lattice for the case of channeling radiation. We demonstrate that the trajectory of a point-charge in a radially polarized laser Bessel beam may be stable similarly to the case of a positron that bounces back and forth in the potential well generated by two adjacent atomic planes. While in the case of channeling radiation, the transverse motion is controlled by a harmonic oscillator equation, for a Bessel beam the transverse motion is controlled by the Mathieu equation. Some characteristics of the motion are presented.

Orbital occupancy evolution across spin- and charge-ordering transitions in YBaFe2O5

NASA Astrophysics Data System (ADS)

Lindén, J.; Lindroos, F.; Karen, P.

2017-08-01

Thermal evolution of the Fe2+-Fe3+ valence mixing in YBaFe2O5 is investigated using Mössbauer spectroscopy. In this high-spin double-cell perovskite, the d6 and d5 Fe states differ by the single minority-spin electron which then controls all the spin- and charge-ordering transitions. Orbital occupancies can be extracted from the spectra in terms of the dxz , dz2 and either dx2-y2 (Main Article) or dxy (Supplement) populations of this electron upon conserving its angular momentum. At low temperatures, the minority-spin electrons fill up the ordered dxz orbitals of Fe2+, in agreement with the considerable orthorhombic distortion of the structure. Heating through the Verwey transition supplies 93% of the mixing entropy, at which point the predominantly mixing electron occupies mainly the dx2-y2 /dxy orbitals weakly bonding the two Fe atoms that face each other across the bases of their coordination pyramids. This might stabilize a weak coulombic checkerboard order suggested by McQueeney et alii in Phys. Rev. B 87(2013)045127. When the remaining 7% of entropy is supplied at a subsequent transition, the mixing electron couples the two Fe atoms predominantly via their dz2 orbitals. The valence mixing concerns more than 95% of the Fe atoms present in the crystalline solid; the rest is semi-quantitatively interpreted as domain walls and antiphase boundaries formed upon cooling through the Néel and Verwey-transition temperatures, respectively.

Density functional study of structural and electronic properties of bimetallic silver-gold clusters: Comparison with pure gold and silver clusters

NASA Astrophysics Data System (ADS)

Bonacic-Koutecky, Vlasta; Burda, Jaroslav; Mitric, Roland; Ge, Maofa; Zampella, Giuseppe; Fantucci, Piercarlo

2002-08-01

Bimetallic silver-gold clusters offer an excellent opportunity to study changes in metallic versus "ionic" properties involving charge transfer as a function of the size and the composition, particularly when compared to pure silver and gold clusters. We have determined structures, ionization potentials, and vertical detachment energies for neutral and charged bimetallic AgmAun 3[less-than-or-equal](m+n)[less-than-or-equal]5 clusters. Calculated VDE values compare well with available experimental data. In the stable structures of these clusters Au atoms assume positions which favor the charge transfer from Ag atoms. Heteronuclear bonding is usually preferred to homonuclear bonding in clusters with equal numbers of hetero atoms. In fact, stable structures of neutral Ag2Au2, Ag3Au3, and Ag4Au4 clusters are characterized by the maximum number of hetero bonds and peripheral positions of Au atoms. Bimetallic tetramer as well as hexamer are planar and have common structural properties with corresponding one-component systems, while Ag4Au4 and Ag8 have 3D forms in contrast to Au8 which assumes planar structure. At the density functional level of theory we have shown that this is due to participation of d electrons in bonding of pure Aun clusters while s electrons dominate bonding in pure Agm as well as in bimetallic clusters. In fact, Aun clusters remain planar for larger sizes than Agm and AgnAun clusters. Segregation between two components in bimetallic systems is not favorable, as shown in the example of Ag5Au5 cluster. We have found that the structures of bimetallic clusters with 20 atoms Ag10Au10 and Ag12Au8 are characterized by negatively charged Au subunits embedded in Ag environment. In the latter case, the shape of Au8 is related to a pentagonal bipyramid capped by one atom and contains three exposed negatively charged Au atoms. They might be suitable for activating reactions relevant to catalysis. According to our findings the charge transfer in bimetallic clusters is responsible for formation of negatively charged gold subunits which are expected to be reactive, a situation similar to that of gold clusters supported on metal oxides.

Sea quarks contribution to the nucleon magnetic moment and charge radius at the physical point

NASA Astrophysics Data System (ADS)

Sufian, Raza Sabbir; Yang, Yi-Bo; Liang, Jian; Draper, Terrence; Liu, Keh-Fei; χ QCD Collaboration

2017-12-01

We report a comprehensive analysis of the light and strange disconnected-sea quarks contribution to the nucleon magnetic moment, charge radius, and the electric and magnetic form factors. The lattice QCD calculation includes ensembles across several lattice volumes and lattice spacings with one of the ensembles at the physical pion mass. We adopt a model-independent extrapolation of the nucleon magnetic moment and the charge radius. We have performed a simultaneous chiral, infinite volume, and continuum extrapolation in a global fit to calculate results in the continuum limit. We find that the combined light and strange disconnected-sea quarks contribution to the nucleon magnetic moment is μM(DI )=-0.022 (11 )(09 ) μN and to the nucleon mean square charge radius is ⟨r2⟩E(DI ) =-0.019 (05 )(05 ) fm2 which is about 1 /3 of the difference between the ⟨rp2⟩E of electron-proton scattering and that of a muonic atom and so cannot be ignored in obtaining the proton charge radius in the lattice QCD calculation. The most important outcome of this lattice QCD calculation is that while the combined light-sea and strange quarks contribution to the nucleon magnetic moment is small at about 1%, a negative 2.5(9)% contribution to the proton mean square charge radius and a relatively larger positive 16.3(6.1)% contribution to the neutron mean square charge radius come from the sea quarks in the nucleon. For the first time, by performing global fits, we also give predictions of the light and strange disconnected-sea quarks contributions to the nucleon electric and magnetic form factors at the physical point and in the continuum and infinite volume limits in the momentum transfer range of 0 ≤Q2≤0.5 GeV2 .

Atomic study on the ordered structure in Al melts induced by liquid/substrate interface with Ti solute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, H. L.; Han, Y. F., E-mail: yfhan@sjtu.edu.cn, E-mail: bdsun@sjtu.edu.cn; Zhou, W.

2015-01-26

Atomic ordering in Al melts induced by liquid/substrate interface with Ti solute was investigated by ab initio molecular dynamics simulations and in-situ synchrotron X-ray diffraction. It is predicted that deformed nanoscale ordering Al layers with a rhombohedral-centered hexagonal structure (R3{sup ¯}m space group) instead of the intrinsic fcc structure (Fm3{sup ¯}m space group) form on substrate at temperature above Al liquids. With Al atoms stacking away from the interface, the ordering structure reaches a critical thickness, which inhibits the consecutive stacking of Al atoms on substrates. The locally stacking reconstruction induced by Ti atom relieves the accumulated elastic strain energymore » in ordered Al layers, facilitating fully heterogeneous nucleation on substrate beyond the deformed ordering Al layer around the melting point. The roles of liquid/substrate interface with Ti solute in the physical behavior of heterogeneous nucleation on substrate were discussed.« less

Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides

NASA Astrophysics Data System (ADS)

Moss, Christopher L.; Chung, Thomas W.; Wyer, Jean A.; Nielsen, Steen Brøndsted; Hvelplund, Preben; Tureček, František

2011-04-01

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H2PO4 radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Studies of flerovium and element 115 homologs with macrocyclic extractants

NASA Astrophysics Data System (ADS)

Despotopulos, John Dustin

Study of the chemistry of the heaviest elements, Z ? 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Crown ethers show high selectivity for metal ions based on their size compared to the negatively charged cavity of the ether. Extraction by crown ethers occur based on electrostatic ion-dipole interactions between the negatively charged ring atoms (oxygen, sulfur, etc.) and the positively charged metal cations. Extraction chromatography resins produced by Eichrom Technologies, specifically the Pb resin based on di-t-byutlcyclohexano-18-crown-6, were chosen as a starting point for these studies. Simple chemical systems based solely on HCl matrices were explored to determine the extent of extraction for Pb, Sn and Hg on the resin. The kinetics and mechanism of extraction were also explored to determine suitability for a Fl chemical experiment. Systems based on KI/HCl and KI/HNO3 were explored for Bi and Sb. In both cases suitable separations, with high separation factors, were performed with vacuum flow columns containing the Pb-resin. Unfortunately the kinetics of uptake for Hg are far too slow on the traditional crown-ether to perform a Fl experiment and obtain whether or not Fl has true Hg-like character or not. However, the kinetics of Pb and Sn are more than sufficient for a Fl experiment to differentiate between Pb- or Sn-like character. To assess this kinetic issue a novel macrocyclic extractant based on sulfur donors was synthesized. Hexathia-18-crown-6, the sulfur analog of 18-crown-6, was synthesized based with by a template reaction using high dilution techniques. The replacement of oxygen ring atoms with sulfur should give the extractant a softer character, which should allow for far greater affinity toward soft metals such as Hg and Pb. From HCl matrices hexathia-18-crown-6 showed far greater kinetics and affinity for Hg than the Pb-resin; however, no affinity for Pb or Sn was seen. This presumably is due to the fact the charge density of sulfur crown ethers does not point to the center of the ring, and future synthesis of a substituted sulfur crown ether which forces the charge density to mimic that of the traditional crown ether should enable extraction of Pb and Sn to a greater extent than with the Pb-resin. Initial studies show promise for the separation of Bi and Sb from HCl matrices using hexathia-18-crown-6. Other macrocyclic extractants, including 2,2,2-cryptand, calix[6]arene and tetrathia-12-crown-4, were also investigated for comparison to the crown ethers. It was noted that these extractants are inferior compared to the crown and thiacrown ethers for extraction of Fl and element 115 homologs. A potential chemical system for Fl was established based on the Eichrom Pb resin, and insight to an improved system based on thiacrown ethers is presented.

Quantum mechanical/molecular mechanical and docking study of the novel analogues based on hybridization of common pharmacophores as potential anti-breast cancer agents

PubMed Central

Asadi, Parvin; Khodarahmi, Ghadamali; Farrokhpour, Hossein; Hassanzadeh, Farshid; Saghaei, Lotfollah

2017-01-01

In an attempt to identify some new potential leads as anti-breast cancer agents, novel hybrid compounds were designed by molecular hybridization approach. These derivatives were structurally derived from hybrid benzofuran–imidazole and quinazolinone derivatives, which had shown good cytotoxicity against the breast cancer cell line (MCF-7). Since aromatase enzyme (CYP19) is highly expressed in the MCF-7 cell line, the binding of these novel hybrid compounds to aromatase was investigated using the docking method. In this study, due to the positive charge on the imidazole ring of the designed ligands and also, the presence of heme iron in the active site of the enzyme, it was decided to optimize the ligand inside the protein to obtain more realistic atomic charges for it. Quantum mechanical/molecular mechanical (QM/MM) method was used to obtain more accurate atomic charges of ligand for docking calculations by considering the polarization effects of CYP19 on ligands. It was observed that the refitted charge improved the binding energy of the docked compounds. Also, the results showed that these novel hybrid compounds were adopted properly within the aromatase binding site, thereby suggesting that they could be potential inhibitors of aromatase. The main binding modes in these complexes were through hydrophobic and H bond interactions showing agreement with the basic physicochemical features of known anti aromatase compounds. Finally, the complex structures obtained from the docking study were used for single point QM/MM calculations to obtain more accurate electronic interaction energy, considering the electronic polarization of the ligand by its protein environment. PMID:28626481

Vibrational zero point energy for H-doped silicon

NASA Astrophysics Data System (ADS)

Karazhanov, S. Zh.; Ganchenkova, M.; Marstein, E. S.

2014-05-01

Most of the studies addressed to computations of hydrogen parameters in semiconductor systems, such as silicon, are performed at zero temperature T = 0 K and do not account for contribution of vibrational zero point energy (ZPE). For light weight atoms such as hydrogen (H), however, magnitude of this parameter might be not negligible. This Letter is devoted to clarify the importance of accounting the zero-point vibrations when analyzing hydrogen behavior in silicon and its effect on silicon electronic properties. For this, we estimate the ZPE for different locations and charge states of H in Si. We show that the main contribution to the ZPE is coming from vibrations along the Si-H bonds whereas contributions from other Si atoms apart from the direct Si-H bonds play no role. It is demonstrated that accounting the ZPE reduces the hydrogen formation energy by ˜0.17 eV meaning that neglecting ZPE at low temperatures one can underestimate hydrogen solubility by few orders of magnitude. In contrast, the effect of the ZPE on the ionization energy of H in Si is negligible. The results can have important implications for characterization of vibrational properties of Si by inelastic neutron scattering, as well as for theoretical estimations of H concentration in Si.

Nonlinear electronic stopping power of channeled slow light ions in ZnSe: Evidence of energy loss caused by formation and breaking of chemical bond

NASA Astrophysics Data System (ADS)

Li, Chang-kai; Wang, Feng; Gao, Cong-Zhang; Liao, Bin; Ouyang, Xiao-ping; Zhang, Feng-Shou

2018-07-01

Electronic stopping power of helium ions in a semiconductor material ZnSe has been investigated through non-adiabatic dynamics simulations at energies of a few keV under channeling condition. The stopping power is predicted to be proportional to velocity for the trajectory along middle axis of a 〈 1 1 0 〉 channel, as expected for the linear response theory accounts for election-hole pair creation. While for the off-center channeling trajectory, a counterintuitive of electronic stopping power versus velocity is observed. Our study, presented herein, finds a non-trivial connection between charge transfer and the force experienced by the projectile. Charge transfer can produce, throughout the collision process, additional force by continuously forming and breaking instantaneous chemical bonds between the projectile and the neighboring host atoms.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

Observing the Interstellar Neutral He Gas Flow with a Variable IBEX Pointing Strategy

NASA Astrophysics Data System (ADS)

Leonard, T.; Moebius, E.; Bzowski, M.; Fuselier, S. A.; Heirtzler, D.; Kubiak, M. A.; Kucharek, H.; Lee, M. A.; McComas, D. J.; Schwadron, N.; Wurz, P.

2015-12-01

The Interstellar Neutral (ISN) gas flow can be observed at Earth's orbit due to the motion of the solar system relative to the surrounding interstellar gas. Since He is minimally influenced by ionization and charge exchange, the ISN He flow provides a sample of the pristine interstellar environment. The Interstellar Boundary Explorer (IBEX) has observed the ISN gas flow over the past 7 years from a highly elliptical orbit around the Earth. IBEX is a Sun-pointing spinning spacecraft with energetic neutral atom (ENA) detectors observing perpendicular to the spacecraft spin axis. Due to the Earth's orbital motion around the Sun, it is necessary for IBEX to perform spin axis pointing maneuvers every few days to maintain a sunward pointed spin axis. The IBEX operations team has successfully pointed the spin axis in a variety of latitude orientations during the mission, including in the ecliptic during the 2012 and 2013 seasons, about 5 degrees below the ecliptic during the 2014 season, and recently about 5 degrees above the ecliptic during the 2015 season, as well as optimizing observations with the spin axis pointed along the Earth-Sun line. These observations include a growing number of measurements near the perihelion of the interstellar atom trajectories, which allow for an improved determination of the ISN He bulk flow longitude at Earth orbit. Combining these bulk flow measurements with an analytical model (Lee et al. 2012 ApJS, 198, 10) based upon orbital mechanics improves the knowledge of the narrow ISN parameter tube, obtained with IBEX, which couples the interstellar inflow longitude, latitude, speed, and temperature.

Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

2002-05-01

To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high-dielectric medium was solved and charges distributed near the molecular surface were indicated as leading to the apparent linearity.

Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

NASA Astrophysics Data System (ADS)

Kristyán, Sándor

1997-11-01

In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

Monte Carlo simulation of neutral-beam injection for mirror fusion reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Ronald Lee

1979-01-01

Computer simulation techniques using the Monte Carlo method have been developed for application to the modeling of neutral-beam intection into mirror-confined plasmas of interest to controlled thermonuclear research. The energetic (10 to 300 keV) neutral-beam particles interact with the target plasma (T i ~ 10 to 100 keV) through electron-atom and ion-atom collisional ionization as well as ion-atom charge-transfer (charge-exchange) collisions to give a fractional trapping of the neutral beam and a loss of charge-transfer-produced neutrals which escape to bombard the reactor first wall. Appropriate interaction cross sections for these processes are calculated for the assumed anisotropic, non-Maxwellian plasma ionmore » phase-space distributions.« less

A New Type of Atom Interferometry for Testing Fundamental Physics

NASA Astrophysics Data System (ADS)

Lorek, Dennis; Lämmerzahl, Claus; Wicht, Andreas

We present a new type of atom interferometer (AI) that provides a tool for ultra-high precision tests of fundamental physics. As an example we present how an AI based on highly charged hydrogen-like atoms is affected by gravitational waves (GW). A qualitative description of the quantum interferometric measurement principle is given, the modifications in the atomic Hamiltonian caused by the GW are presented, and the size of the resulting frequency shifts in hydrogen-like atoms is estimated. For a GW amplitude of h = 10-23 the frequency shift is of the order of 110μHz for an AI based on a 91-fold charged uranium ion. A frequency difference of this size can be resolved by current AIs in 1s.

Physics with Trapped Antihydrogen

NASA Astrophysics Data System (ADS)

Charlton, Michael

2017-04-01

For more than a decade antihydrogen atoms have been formed by mixing antiprotons and positrons held in arrangements of charged particle (Penning) traps. More recently, magnetic minimum neutral atom traps have been superimposed upon the anti-atom production region, promoting the trapping of a small quantity of the antihydrogen yield. We will review these advances, and describe some of the first physics experiments performed on anrtihydrogen including the observation of the two-photon 1S-2S transition, invesigation of the charge neutrailty of the anti-atom and studies of the ground state hyperfine splitting. We will discuss the physics motivations for undertaking these experiments and describe some near-future initiatives.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; Giese, Timothy J.

2015-12-21

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom’s local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion andmore » dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the S{sub N}2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.« less

Incorporating nuclear vibrational energies into the "atom in molecules" analysis: An analytical study

NASA Astrophysics Data System (ADS)

Gharabaghi, Masumeh; Shahbazian, Shant

2017-04-01

The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis. In this study, within the context of the MC-QTAIM, the formalism of including nuclear vibrational energy in the atomic basin energy is developed in detail and its contribution is derived analytically using the recently proposed non-adiabatic Hartree product nuclear wavefunction. It is demonstrated that within the context of this wavefunction, the quantum nuclei may be conceived pseudo-adiabatically as quantum oscillators and both isotropic harmonic and anisotropic anharmonic oscillator models are used to compute the zero-point nuclear vibrational energy contribution to the basin energies explicitly. Inspired by the results gained within the context of the MC-QTAIM analysis, a heuristic approach is proposed within the context of the QTAIM to include nuclear vibrational energy in the basin energy from the vibrational wavefunction derived adiabatically. The explicit calculation of the basin contribution of the zero-point vibrational energy using the uncoupled harmonic oscillator model leads to results consistent with those derived from the MC-QTAIM.

Incorporating nuclear vibrational energies into the "atom in molecules" analysis: An analytical study.

PubMed

Gharabaghi, Masumeh; Shahbazian, Shant

2017-04-21

The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis. In this study, within the context of the MC-QTAIM, the formalism of including nuclear vibrational energy in the atomic basin energy is developed in detail and its contribution is derived analytically using the recently proposed non-adiabatic Hartree product nuclear wavefunction. It is demonstrated that within the context of this wavefunction, the quantum nuclei may be conceived pseudo-adiabatically as quantum oscillators and both isotropic harmonic and anisotropic anharmonic oscillator models are used to compute the zero-point nuclear vibrational energy contribution to the basin energies explicitly. Inspired by the results gained within the context of the MC-QTAIM analysis, a heuristic approach is proposed within the context of the QTAIM to include nuclear vibrational energy in the basin energy from the vibrational wavefunction derived adiabatically. The explicit calculation of the basin contribution of the zero-point vibrational energy using the uncoupled harmonic oscillator model leads to results consistent with those derived from the MC-QTAIM.

Method and apparatus for electrostatically sorting biological cells

DOEpatents

Merrill, John T.

1982-01-01

An improved method of sorting biological cells in a conventional cell sorter apparatus includes generating a fluid jet containing cells to be sorted, measuring the distance between the centers of adjacent droplets in a zone thereof defined at the point where the fluid jet separates into descrete droplets, setting the distance between the center of a droplet in said separation zone and the position along said fluid jet at which the cell is optically sensed for specific characteristics to be an integral multiple of said center-to-center distance, and disabling a charger from electrically charging a specific droplet if a cell is detected by the optical sensor in a position wherein it will be in the neck area between droplets during droplet formation rather than within a predetermined distance from the droplet center.

Search for evidence of low energy protons in solar flares

NASA Technical Reports Server (NTRS)

Metcalf, Thomas R.; Wuelser, Jean-Pierre; Canfield, Richard C.; Hudson, Hugh S.

1992-01-01

We searched for linear polarization in the H alpha line using the Stokes Polarimeter at Mees Solar Observatory and present observations of a flare from NOAA active region 6659 which began at 01:30 UT on 14 Jun. 1991. Our dataset also includes H alpha spectra from the Mees charge coupled device (MCCD) imaging spectrograph as well as hard x ray observations from the Burst and Transient Source Experiment (BATSE) instrument on board the Gamma Ray Observatory (GRO). The polarimeter scanned a 40 x 40 inch field of view using 16 raster points in a 4 x 4 grid. Each scan took about 30 seconds with 2 seconds at each raster point. The polarimeter stopped 8.5 inches between raster points and each point covered a 6 inch region. This sparse sampling increased the total field of view without reducing the temporal cadence. At each raster point, an H alpha spectrum with 20 mA spectral sampling is obtained covering 2.6 A centered on H alpha line center. The preliminary conclusions from the research are presented.

Photoactivated processes in optical fibers: generation and conversion mechanisms of twofold coordinated Si and Ge atoms

NASA Astrophysics Data System (ADS)

Giacomazzi, Luigi; Martin-Samos, L.; Boukenter, A.; Ouerdane, Y.; Girard, S.; Alessi, A.; de Gironcoli, S.; Richard, N.

2017-05-01

In this work we present an extensive investigation of nanoscale physical phenomena related to oxygen-deficient centers (ODCs) in silica and Ge-doped silica by means of first-principles calculations, including nudged-elastic band, electron paramagnetic resonance parameters calculations, and many-body perturbation theory (GW and Bethe-Salpeter equation) techniques. We show that by neutralizing positively charged oxygen monovacancies we can obtain model structures of twofold Si and Ge defects of which the calculated absorption spectra and singlet-to-triplet transitions are in excellent agreement with the experimental optical absorption and photo-luminescence data. In particular we provide an exhaustive analysis of the main exciton peaks related to the presence of twofold defects including long-range correlation effects. By calculating the reaction pathways and energy barriers necessary for the interconversion, we advance a double precursory origin of the {E}α \\prime and Ge(2) centers as due to the ionization of neutral oxygen monovacancies (Si-Si and Ge-Si dimers) and as due to the ionization of twofold Si and Ge defects. Furthermore two distinct structural conversion mechanisms are found to occur between the neutral oxygen monovacancy and the twofold Si (and Ge) atom configurations. Such conversion mechanisms allow to explain the radiation induced generation of the ODC(II) centers, their photobleaching, and also their generation during the drawing of optical fibers.

Ab initio study of gold-doped zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Srivastava, Pankaj; Dhar, Subhra; Jaiswal, Neeraj K.

2014-12-01

The electronic transport properties of zigzag graphene nanoribbons (ZGNRs) through covalent functionalization of gold (Au) atoms is investigated by using non-equilibrium Green's function combined with density functional theory. It is revealed that the electronic properties of Au-doped ZGNRs vary significantly due to spin and its non-inclusion. We find that the DOS profiles of Au-adsorbed ZGNR due to spin reveal very less number of states available for conduction, whereas non-inclusion of spin results in higher DOS across the Fermi level. Edge Au-doped ribbons exhibit stable structure and are energetically more favorable than the center Au-doped ZGNRs. Though the chemical interaction at the ZGNR-Au interface modifies the Fermi level, Au-adsorbed ZGNR reveals semimetallic properties. A prominent qualitative change of the I-V curve from linear to nonlinear is observed as the Au atom shifts from center toward the edges of the ribbon. Number of peaks present near the Fermi level ensures conductance channels available for charge transport in case of Au-center-substituted ZGNR. We predict semimetallic nature of the Au-adsorbed ZGNR with a high DOS peak distributed over a narrow energy region at the Fermi level and fewer conductance channels. Our calculations for the magnetic properties predict that Au functionalization leads to semiconducting nature with different band gaps for spin up and spin down. The outcomes are compared with the experimental and theoretical results available for other materials.

Coordination Structure and Fragmentation Chemistry of the Tripositive Lanthanide-Thio-Diglycolamide Complexes.

PubMed

Chen, Xiuting; Li, Qingnuan; Gong, Yu

2017-12-14

Tripositive Ln(TMTDA) 3 3+ complexes (Ln = La-Lu except Pm, TMTDA = tetramethyl 3-thio-diglycolamide) were observed in the gas phase by electrospray ionization of LnCl 3 and TMTDA mixtures. Collision-induced dissociation (CID) was employed to investigate their fragmentation chemistry, which revealed the influence of metal center as well as ligand on the ligated complexes. Ln(TMTDA) 2 (TMTDA-45) 3+ resulting from C carbonyl -N bond cleavage of TMTDA and hydrogen transfer was the major CID product for all Ln(TMTDA) 3 3+ except Eu(TMTDA) 3 3+ , which predominantly formed charge-reducing product Eu II (TMTDA) 2 2+ via electron transfer from TMTDA to Eu 3+ . Density functional theory calculations on the structure of La(TMTDA) 3 3+ and Lu(TMTDA) 3 3+ revealed that Ln 3+ was coordinated by six O carbonyl atoms from three neutral TMTDA ligands, and both complexes possessed C 3h symmetry. The S ether atom deviating from the ligand plane was not coordinated to the metal center. On the basis of the CID results of Ln(TMTDA) 3 3+ , Ln(TMGA) 3 3+ , and Ln(TMOGA) 3 3+ , the fragmentation chemistry associated with the ligand depends on the coordination mode, while the redox chemistry of these tripositive ions is related to the nature of both metal centers and diamide ligands.

EUV emission spectra in collisions of highly charged tantalum ions with nitrogen and oxygen molecules

NASA Astrophysics Data System (ADS)

Tanuma, Hajime; Numadate, Naoki; Uchikura, Yoshiyuki; Shimada, Kento; Akutsu, Takuto; Long, Elaine; O'Sullivan, Gerry

2017-10-01

We have performed ion beam collision experiments using multiply charged tantalum ions and observed EUV (extreme ultra-violet) emission spectra in collisions of ions with molecular targets, N2 and O2. Broad UTAs (un-resolved transition arrays) from multiply charged Ta ions were observed, and the mean wavelengths of the UTAs shifted and became shorter at higher charge statea of Ta ions. These UTAs may be attributed to the 4f-5d and 4f-5g transitions. Not only the UTA emission from incident ions, but also the sharp emission lines from multiply charged fragment atomic ions were observed. Production of temporary highly charged molecular ions, their kinetic energy and fragmentation processes have been investigated with coincident detection technique. However, the observation of emission from the fragments might be for the first time. The formation mechanisms of the multiply charged fragment atomic ions from target molecules are discussed.

Tailoring Ion Charge State Distribution in Tetramethyltin Clusters under Influence of Moderate Intensity Picosecond Laser Pulse: Role of Laser Wavelength and Rate of Energy Deposition

NASA Astrophysics Data System (ADS)

Sharma, Pramod; Das, Soumitra; Vatsa, Rajesh K.

2017-07-01

Systematic manipulation of ionic-outcome in laser-cluster interaction process has been realized for studies carried out on tetramethyltin (TMT) clusters under picosecond laser conditions, determined by choice of laser wavelength and intensity. As a function of laser intensity, TMT clusters exhibit gradual enhancement in overall ionization of its cluster constituents, up to a saturation level of ionization, which was distinct for different wavelengths (266, 355, and 532 nm). Simultaneously, systematic appearance of higher multiply charged atomic ions and shift in relative abundance of multiply charged atomic ions towards higher charge state was observed, using time-of-flight mass spectrometer. At saturation level, multiply charged atomic ions up to (C2+, Sn2+) at 266 nm, (C4+, Sn4+) at 355 nm, and (C4+, Sn6+) at 532 nm were detected. In addition, at 355 nm intra-cluster ion chemistry within the ionized cluster leads to generation of molecular hydrogen ion (H2 +) and triatomic molecular hydrogen ion (H3 +). Generation of multiply charged atomic ions is ascribed to efficient coupling of laser pulse with the cluster media, facilitated by inner-ionized electrons produced within the cluster, at the leading edge of laser pulse. Role of inner-ionized electrons is authenticated by measuring kinetic energy distribution of electrons liberated upon disintegration of excessively ionized cluster, under the influence of picosecond laser pulse.

Alternative Fuels Data Center: Charging Plug-In Electric Vehicles in Public

Science.gov Websites

in Public to someone by E-mail Share Alternative Fuels Data Center: Charging Plug-In Electric Vehicles in Public on Facebook Tweet about Alternative Fuels Data Center: Charging Plug-In Electric Vehicles in Public on Twitter Bookmark Alternative Fuels Data Center: Charging Plug-In Electric Vehicles in

Catalytic behavior of ‘Pt-atomic chain encapsulated gold nanotube’: A density functional study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nigam, Sandeep, E-mail: snigam@barc.gov.in; Majumder, Chiranjib

2016-05-23

With an aim to design novel material and explore its catalytic performance towards CO oxidation, Pt atomic chain was introduced inside gold nanotube (Au-NT). Theoretical calculations at the level of first principles formalism was carried out to investigate the atomic and electronic properties of the composite. Geometrically Pt atoms prefer to align in zig-zag fashion. Significant electronic charge transfer from inside Pt atoms to the outer wall Au atoms is observed. Interaction of O{sub 2} with Au-NT wall follows by injection of additional electronic charge in the anti-bonding orbital of oxygen molecule leading to activation of the O-O bond. Furthermore » interaction of CO molecule with the activated oxygen molecule leads to spontaneous oxidation reaction and formation of CO{sub 2}.« less

Physicochemical and biological properties of self-assembled antisense/poly(amidoamine) dendrimer nanoparticles: the effect of dendrimer generation and charge ratio

PubMed Central

Nomani, Alireza; Haririan, Ismaeil; Rahimnia, Ramin; Fouladdel, Shamileh; Gazori, Tarane; Dinarvand, Rassoul; Omidi, Yadollah; Azizi, Ebrahim

2010-01-01

To gain a deeper understanding of the physicochemical phenomenon of self-assembled nanoparticles of different generations and ratios of poly (amidoamine) dendrimer (PAMAM) dendrimer and a short-stranded DNA (antisense oligonucleotide), multiple methods were used to characterize these nanoparticles including photon correlation spectroscopy (PCS); zeta potential measurement; and atomic force microscopy (AFM). PCS and AFM results revealed that, in contrast to larger molecules of DNA, smaller molecules produce more heterodisperse and large nanoparticles when they are condensed with a cationic dendrimer. AFM images also showed that such nanoparticles were spherical. The stability of the antisense content of the nanoparticles was investigated over different charge ratios using polyacrylamide gel electrophoresis. It was clear from such analyses that much more than charge neutrality point was required to obtain stable nanoparticles. For cell uptake, self-assembled nanoparticles were prepared with PAMAM G5 and 5’-FITC labeled antisense and the uptake experiment was carried out in T47D cell culture. This investigation also shows that the cytotoxicity of the nanoparticles was dependent upon the generation and charge ratio of the PAMAM dendrimer, and the antisense concentration had no significant effect on the cytotoxicity. PMID:20517481

Rates of Charged Clocks in an Electric Field.

NASA Astrophysics Data System (ADS)

Ozer, Murat

2008-04-01

The gravitational arguments leading to time dilation, redshift, and spacetime curvature are adapted to electric fields. The energy levels of two identical positively charged atoms at different potentials in a static electric field are shown to undergo blueshift. Secondly, the period of a charged simple pendulum (clock) in the electric field of a metallic sphere is shown to vary with the electric potential. The spacetime diagram for the world lines of two photons emitted and absorbed by two pendulums at different potentials at different times and the world lines of the pendulums, as in Schild's argument, is shown to be not a parallelogram in Minkowski spacetime, concluding that spacetime must be curved. A Pound-Rebka-Snider experiment in an electric field is proposed to confirm that photons undergo a frequency shift in an electric field and hence the spacetime manifold is curved. Next, Torretti's gravitational argument that spacetime around a mass distribution concentrated at a point is curved is extended to electric charge distributions to conclude that the nonuniform electric fields of such charge distributions too curve spacetime. Finally, the local equivalence of a uniform electric field times the charge to mass ratio to a uniform acceleration is shown through spacetime transformations and the electrical redshift is obtained in a uniformly accelerated frame by using this principle. These arguments lead to the conclusion that special relativistic electromagnetism is an approximation to a general relativistic multi-metric theory.

Maxwell's conjecture on three point charges with equal magnitudes

NASA Astrophysics Data System (ADS)

Tsai, Ya-Lun

2015-08-01

Maxwell's conjecture on three point charges states that the number of non-degenerate equilibrium points of the electrostatic field generated by them in R3 is at most four. We prove the conjecture in the cases when three point charges have equal magnitudes and show the number of isolated equilibrium points can only be zero, two, three, or four. Specifically, fixing positions of two positive charges in R3, we know exactly where to place the third positive charge to have two, three, or four equilibrium points. All equilibrium points are isolated and there are no other possibilities for the number of isolated equilibrium points. On the other hand, if both two of the fixed charges have negative charge values, there are always two equilibrium points except when the third positive charge lies in the line segment connecting the two negative charges. The exception cases are when the field contains only a curve of equilibrium points. In this paper, computations assisted by computer involve symbolic and exact integer computations. Therefore, all the results are proved rigorously.

First-principles study of codoping in lanthanum bromide

NASA Astrophysics Data System (ADS)

Erhart, Paul; Sadigh, Babak; Schleife, André; Åberg, Daniel

2015-04-01

Codoping of Ce-doped LaBr3 with Ba, Ca, or Sr improves the energy resolution that can be achieved by radiation detectors based on these materials. Here, we present a mechanism that rationalizes this enhancement on the basis of first-principles electronic structure calculations and point defect thermodynamics. It is shown that incorporation of Sr creates neutral VBr-SrLa complexes that can temporarily trap electrons. As a result, Auger quenching of free carriers is reduced, allowing for a more linear, albeit slower, scintillation light yield response. Experimental Stokes shifts can be related to different CeLa-SrLa-VBr triple complex configurations. Codoping with other alkaline as well as alkaline-earth metals is considered as well. Alkaline elements are found to have extremely small solubilities on the order of 0.1 ppm and below at 1000 K. Among the alkaline-earth metals the lighter dopant atoms prefer interstitial-like positions and create strong scattering centers, which has a detrimental impact on carrier mobilities. Only the heavier alkaline-earth elements (Ca, Sr, Ba) combine matching ionic radii with sufficiently high solubilities. This provides a rationale for the experimental finding that improved scintillator performance is exclusively achieved using Sr, Ca, or Ba. The present mechanism demonstrates that codoping of wide-gap materials can provide an efficient means for managing charge carrier populations under out-of-equilibrium conditions. In the present case dopants are introduced that manipulate not only the concentrations but also the electronic properties of intrinsic defects without introducing additional gap levels. This leads to the availability of shallow electron traps that can temporarily localize charge carriers, effectively deactivating carrier-carrier recombination channels. The principles of this mechanism are therefore not specific to the material considered here but can be adapted for controlling charge carrier populations and recombination in other wide-gap materials.

Mixed cerium-platinum oxides: Electronic structure of [CeO]Pt{sub n} (n = 1, 2) and [CeO{sub 2}]Pt complex anions and neutrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ray, Manisha; Kafader, Jared O.; Topolski, Josey E.

The electronic structures of several small Ce–Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt{sub 2} both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt{sub 2} complexes are therefore ionic, with electronic structures described qualitatively as [CeO{sup +2}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −}, respectively. The associated anions are described qualitatively as [CeO{sup +}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −2}, respectively. In both neutrals and anions, the most stable molecularmore » structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt{sub 2} moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO{sub 2}, which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO{sub 2}]Pt{sup −}. The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO{sub 2}]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt–O–Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt{sup −} daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.« less

Quantum dynamics of charge state in silicon field evaporation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silaeva, Elena P.; Uchida, Kazuki; Watanabe, Kazuyuki, E-mail: kazuyuki@rs.kagu.tus.ac.jp

2016-08-15

The charge state of an ion field-evaporating from a silicon-atom cluster is analyzed using time-dependent density functional theory coupled to molecular dynamics. The final charge state of the ion is shown to increase gradually with increasing external electrostatic field in agreement with the average charge state of silicon ions detected experimentally. When field evaporation is triggered by laser-induced electronic excitations the charge state also increases with increasing intensity of the laser pulse. At the evaporation threshold, the charge state of the evaporating ion does not depend on the electrostatic field due to the strong contribution of laser excitations to themore » ionization process both at low and high laser energies. A neutral silicon atom escaping the cluster due to its high initial kinetic energy is shown to be eventually ionized by external electrostatic field.« less

Antimicrobial properties of analgesic kyotorphin peptides unraveled through atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ribeiro, Marta M.B.; Franquelim, Henri G.; Torcato, Ines M.

Highlights: Black-Right-Pointing-Pointer New kyotorphin derivatives have antimicrobial properties against S. aureus. Black-Right-Pointing-Pointer Atomic force microscopy show membrane disturbing effects of KTP-NH{sub 2} and IbKTP-NH{sub 2}. Black-Right-Pointing-Pointer None of the KTP derivatives are hemolytic. Black-Right-Pointing-Pointer The minimal peptidic sequence with antimicrobial activity is Tyr-Arg, if amidated. -- Abstract: Antimicrobial peptides (AMPs) are promising candidates as alternatives to conventional antibiotics for the treatment of resistant pathogens. In the last decades, new AMPs have been found from the cleavage of intact proteins with no antibacterial activity themselves. Bovine hemoglobin hydrolysis, for instance, results in AMPs and the minimal antimicrobial peptide sequence was definedmore » as Tyr-Arg plus a positively charged amino acid residue. The Tyr-Arg dipeptide alone, known as kyotorphin (KTP), is an endogenous analgesic neuropeptide but has no antimicrobial activity itself. In previous studies new KTP derivatives combining C-terminal amidation and Ibuprofen (Ib) - KTP-NH{sub 2}, IbKTP, IbKTP-NH{sub 2} - were designed in order to improve KTP brain targeting. Those modifications succeeded in enhancing peptide-cell membrane affinity towards fluid anionic lipids and higher analgesic activity after systemic injection resulted therefrom. Here, we investigated if this affinity for anionic lipid membranes also translates into antimicrobial activity because bacteria have anionic membranes. Atomic force microscopy revealed that KTP derivatives perturbed Staphylococcus aureus membrane structure by inducing membrane blebbing, disruption and lysis. In addition, these peptides bind to red blood cells but are non-hemolytic. From the KTP derivatives tested, amidated KTP proves to be the most active antibacterial agent. The combination of analgesia and antibacterial activities with absence of toxicity is highly appealing from the clinical point of view and broadens the therapeutic potential and application of kyotorphin peptides.« less

Translocation Thermodynamics of Linear and Cyclic Nonaarginine into Model DPPC Bilayer via Coarse-Grained Molecular Dynamics Simulation: Implications of Pore Formation and Nonadditivity

PubMed Central

2015-01-01

Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg9) into a model DPPC bilayer. In the case of the Arg9 cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg9) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg9 [Huang, K.; et al. Biophys. J., 2013, 104, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg9 translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg9 translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths systematically predict lower free-energy barriers (ca. 90 kJ/mol lower) than the non pore-forming paths, again consistent with all-atom force field simulations. The current force field suggests no preference for the more compact or covalently cyclic structures upon entering the bilayer. Decomposition of the PMF into the system’s components indicates that the dominant stabilizing contribution along the pore-forming path originates from the membrane as both layers of it deformed due to the formation of pore. Furthermore, our analysis revealed that although there is significant entropic stabilization arising from the enhanced configurational entropy exposing more states as the peptide moves through the bilayer, the enthalpic loss (as predicted by the interactions of this coarse-grained model) far outweighs any former stabilization, thus leading to significant barrier to translocation. Finally, we observe reduction in the translocation free-energy barrier for a second Arg9 entering the bilayer in the presence of an initial peptide restrained at the center, again, in qualitative agreement with all-atom force fields. PMID:24506488

The great galactic centre mystery

NASA Technical Reports Server (NTRS)

Riegler, G. R.

1982-01-01

Gamma-ray observations of the center of the Galaxy show a varying positron-electron annihilation radiation emission, while at radio wavelengths a non-thermal compact source surrounded by ionized gas moving at high velocities can be seen. Line emission maps for atomic and ionized hydrogen and molecular gas suggest gas expulsion and a massive collapsed object. IR observations show that ionized gas in the central few parsecs of the Galactic center is concentrated in at least 14 small clouds. Charge-coupled device images show a pair of faint, very red sources within a few arc seconds of IRS 16 and the compact non-thermal radio source. The positron-electron annihilation line emission implies an annihilation rate of 10 to the 43rd per sec, compared with an observed luminosity at IR wavelengths of 10 to the 40 erg per sec. Some models are briefly discussed.

How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

NASA Astrophysics Data System (ADS)

Havu, Vile; Blum, Volker; Scheffler, Matthias

2007-03-01

Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Efficient acceleration of neutral atoms in laser produced plasma

DOE PAGES

Dalui, M.; Trivikram, T. M.; Colgan, James Patrick; ...

2017-06-20

Recent advances in high-intensity laser-produced plasmas have demonstrated their potential as compact charge particle accelerators. Unlike conventional accelerators, transient quasi-static charge separation acceleration fields in laser produced plasmas are highly localized and orders of magnitude larger. Manipulating these ion accelerators, to convert the fast ions to neutral atoms with little change in momentum, transform these to a bright source of MeV atoms. The emittance of the neutral atom beam would be similar to that expected for an ion beam. Since intense laser-produced plasmas have been demonstrated to produce high-brightness-low-emittance beams, it is possible to envisage generation of high-flux, low-emittance, highmore » energy neutral atom beams in length scales of less than a millimeter. Here, we show a scheme where more than 80% of the fast ions are reduced to energetic neutral atoms and demonstrate the feasibility of a high energy neutral atom accelerator that could significantly impact applications in neutral atom lithography and diagnostics.« less

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

PubMed

Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sissay, Adonay; Abanador, Paul; Mauger, François

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagatingmore » the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.« less

Enhanced laboratory sensitivity to variation of the fine-structure constant using highly charged ions.

PubMed

Berengut, J C; Dzuba, V A; Flambaum, V V

2010-09-17

We study atomic systems that are in the frequency range of optical atomic clocks and have enhanced sensitivity to potential time variation of the fine-structure constant α. The high sensitivity is due to coherent contributions from three factors: high nuclear charge Z, high ionization degree, and significant differences in the configuration composition of the states involved. Configuration crossing keeps the frequencies in the optical range despite the large ionization energies. We discuss a few promising examples that have the largest α sensitivities seen in atomic systems.

HIAF: New opportunities for atomic physics with highly charged heavy ions

NASA Astrophysics Data System (ADS)

Ma, X.; Wen, W. Q.; Zhang, S. F.; Yu, D. Y.; Cheng, R.; Yang, J.; Huang, Z. K.; Wang, H. B.; Zhu, X. L.; Cai, X.; Zhao, Y. T.; Mao, L. J.; Yang, J. C.; Zhou, X. H.; Xu, H. S.; Yuan, Y. J.; Xia, J. W.; Zhao, H. W.; Xiao, G. Q.; Zhan, W. L.

2017-10-01

A new project, High Intensity heavy ion Accelerator Facility (HIAF), is currently being under design and construction in China. HIAF will provide beams of stable and unstable heavy ions with high energies, high intensities and high quality. An overview of new opportunities for atomic physics using highly charged ions and radioactive heavy ions at HIAF is given.

Effect of stray electric fields on cooling of center of mass motion of levitated graphite flakes

NASA Astrophysics Data System (ADS)

Nagornykh, Pavel; Coppock, Joyce; Kane, Bruce

2015-03-01

Levitation of charged multilayer graphene flakes in a quadrupole ion trap provides a unique way to study graphene in isolated conditions. Cooling of a flake in such a setup is necessary for high vacuum measurements of the flake and is achieved by using a parametric feedback scheme. We present data showing the strong dependence of the cooling of the flake's center of mass motion on the stray electric fields. We achieve this by using auxiliary electrodes to shift the position of the trap center in space. Once the point of minimum interaction between the stray fields and the particle is found (leading to cooling of the flake motion to temperatures below 20K at pressure of 10-7 Torr), we can estimate charge and mass of the flake by observing quantized discharge of the particle and measure transient dynamics of the center of mass motion by turning the cooling off and on. As an additional benefit, the behavior of the flake away from the optimum trap position can be used to quantify stray fields' effect on the particle motion by measuring its spinning orientation and frequency dependence on offset from the optimum position.

Charge transfer between O6+ and atomic hydrogen

NASA Astrophysics Data System (ADS)

Wu, Y.; Stancil, P. C.; Liebermann, H. P.; Buenker, R. J.; Schultz, D. R.; Hui, Y.

2011-05-01

The charge exchange process has been found to play a dominant role in the production of X-rays and/or EUV photons observed in cometary and planetary atmospheres and from the heliosphere. Charge transfer cross sections, especially state-selective cross sections, are necessary parameters in simulations of X-ray emission. In the present work, charge transfer due to collisions of ground state O6+(1s2 1 S) with atomic hydrogen has been investigated theoretically using the quantum-mechanical molecular-orbital close-coupling method (QMOCC). The multi-reference single- and double-excitation configuration interaction approach (MRDCI) has been applied to compute the adiabatic potential and nonadiabatic couplings, and the atomic basis sets used have been optimized with the method proposed previously to obtain precise potential data. Total and state-selective cross sections are calculated for energies between 10 meV/u and 10 keV/u. The QMOCC results are compared to available experimental and theoretical data as well as to new atomic-orbital close-coupling (AOCC) and classical trajectory Monte Carlo (CTMC) calculations. A recommended set of cross sections, based on the MOCC, AOCC, and CTMC calculations, is deduced which should aid in X-ray modeling studies.

A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules.

PubMed

Ouyang, Yongzhong; Ye, Fei; Liang, Yizeng

2009-08-07

To further extend the EEM approach to improve its accuracy, a new approach, in which the different connectivities and hybridized states are introduced to represent the different chemical environments, has been developed. The C, O and N atoms are distinguished between different hybridized states. Different states of hydrogen atoms are defined according to their different connectivities. Furthermore, the sp(2) carbons in the aromatic rings are also separated from the other sp(2) carbons. Geometries and NPA charges are calculated at the B3LYP/6-31G* level, and the effective electronegativity and hardness values could be calibrated with the help of a training set of 141 organic molecules using the Differential Evolution (DE) algorithm. The quality of the modified EEM charges is evaluated by comparison with the B3LYP/6-31G* charges calculated for a series of polypeptides, not contained in the training set. For further comparison, the atomic parameters of the original EEM without including chemical environments are recalibrated under the same conditions. It is found that the accuracy of the modified EEM method improves significantly as compared to that of the original EEM method.

Possible Charge-Exchange X-Ray Emission in the Cygnus Loop Detected with Suzaku

NASA Technical Reports Server (NTRS)

Katsuda, Satoru; Tsunemi, Hiroshi; Mori, Koji; Uchida, Hiroyuki; Kosugi, Hiroko; Kimura, Masashi; Nakajima, Hiroshi; Takakura, Satoru; Petre, Robert; Hewitt. John W.;

Photo ion spectrometer

DOEpatents

Gruen, Dieter M.; Young, Charles E.; Pellin, Michael J.

1989-01-01

A charged particle spectrometer for performing ultrasensitive quantitative analysis of selected atomic components removed from a sample. Significant improvements in performing energy and angular refocusing spectroscopy are accomplished by means of a two dimensional structure for generating predetermined electromagnetic field boundary conditions. Both resonance and non-resonance ionization of selected neutral atomic components allow accumulation of increased chemical information. A multiplexed operation between a SIMS mode and a neutral atomic component ionization mode with EARTOF analysis enables comparison of chemical information from secondary ions and neutral atomic components removed from the sample. An electronic system is described for switching high level signals, such as SIMS signals, directly to a transient recorder and through a charge amplifier to the transient recorder for a low level signal pulse counting mode, such as for a neutral atomic component ionization mode.

DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

PubMed

Pandey, Urmila; Srivastava, Mayuri; Singh, R P; Yadav, R A

2014-08-14

The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

High-Fidelity Simulations of Electrically-Charged Atomizing Diesel-Type Jets

NASA Astrophysics Data System (ADS)

Gaillard, Benoit; Owkes, Mark; van Poppel, Bret

2015-11-01

Combustion of liquid fuels accounts for over a third of the energy usage today. Improving efficiency of combustion systems is critical to meet the energy needs while limiting environmental impacts. Additionally, a shift away from traditional fossil fuels to bio-derived alternatives requires fuel injection systems that can atomize fuels with a wide range of properties. In this work, the potential benefits of electrically-charged atomization is investigated using numerical simulations. Particularly, the electrostatic forces on the hydrodynamic jet are quantified and the impact of the forces is analyzed by comparing simulations of Diesel-type jets at realistic flow conditions. The simulations are performed using a state-of-the-art numerical framework that globally conserves mass, momentum, and the electric charge density even at the gas-liquid interface where discontinuities exist.

Electronic Effects on Room-Temperature, Gas-Phase C-H Bond Activations by Cluster Oxides and Metal Carbides: The Methane Challenge.

PubMed

Schwarz, Helmut; Shaik, Sason; Li, Jilai

2017-12-06

This Perspective discusses a story of one molecule (methane), a few metal-oxide cationic clusters (MOCCs), dopants, metal-carbide cations, oriented-electric fields (OEFs), and a dizzying mechanistic landscape of methane activation! One mechanism is hydrogen atom transfer (HAT), which occurs whenever the MOCC possesses a localized oxyl radical (M-O • ). Whenever the radical is delocalized, e.g., in [MgO] n •+ the HAT barrier increases due to the penalty of radical localization. Adding a dopant (Ga 2 O 3 ) to [MgO] 2 •+ localizes the radical and HAT transpires. Whenever the radical is located on the metal centers as in [Al 2 O 2 ] •+ the mechanism crosses over to proton-coupled electron transfer (PCET), wherein the positive Al center acts as a Lewis acid that coordinates the methane molecule, while one of the bridging oxygen atoms abstracts a proton, and the negatively charged CH 3 moiety relocates to the metal fragment. We provide a diagnostic plot of barriers vs reactants' distortion energies, which allows the chemist to distinguish HAT from PCET. Thus, doping of [MgO] 2 •+ by Al 2 O 3 enables HAT and PCET to compete. Similarly, [ZnO] •+ activates methane by PCET generating many products. Adding a CH 3 CN ligand to form [(CH 3 CN)ZnO] •+ leads to a single HAT product. The CH 3 CN dipole acts as an OEF that switches off PCET. [MC] + cations (M = Au, Cu) act by different mechanisms, dictated by the M + -C bond covalence. For example, Cu + , which bonds the carbon atom mostly electrostatically, performs coupling of C to methane to yield ethylene, in a single almost barrier-free step, with an unprecedented atomic choreography catalyzed by the OEF of Cu + .

Electrostatic forces in the Poisson-Boltzmann systems

NASA Astrophysics Data System (ADS)

Xiao, Li; Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

2013-09-01

Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.

Interstitial Fe in MgO

NASA Astrophysics Data System (ADS)

Mølholt, T. E.; Mantovan, R.; Gunnlaugsson, H. P.; Svane, A.; Masenda, H.; Naidoo, D.; Bharuth-Ram, K.; Fanciulli, M.; Gislason, H. P.; Johnston, K.; Langouche, G.; Ólafsson, S.; Sielemann, R.; Weyer, G.

2014-01-01

Isolated 57Fe atoms were studied in MgO single-crystals by emission Mössbauer spectroscopy following implantation of 57Mn decaying to 57Fe. Four Mössbauer spectral components were found corresponding to different Fe lattice positions and/or charge states. Two components represent Fe atoms substituting Mg as Fe2+ and Fe3+, respectively; a third component is due to Fe in a strongly implantation-induced disturbed region. The fourth component, which is the focus of this paper, can be assigned to Fe at an interstitial site. Comparison of its measured isomer shift with ab initio calculations suggests that the interstitial Fe is located on, or close to, the face of the rock-salt MgO structure. To harmonize such an assignment with the measured near-zero quadrupole interaction a local motion process (cage motion) of the Fe has to be stipulated. The relation of such a local motion as a starting point for long range diffusion is discussed.

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

DETAIL VIEW OF UPPER TRAM TERMINAL STRUCTURE, LOOKING NORTHEAST TOWARD ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL VIEW OF UPPER TRAM TERMINAL STRUCTURE, LOOKING NORTHEAST TOWARD THE REAR OF THE STRUCTURE. THE WHEELS AT THE TOP OF THE TRAM BUCKETS RODE OFF THE STATIONARY CABLES ONTO THE TRACK SUPPORTED BY THE "C" IRONS SUSPENDED FROM THE TOP TIMBERS, CLEARLY SEEN AT THE TOP OF THE FRAME. THE ANCHOR POINTS FOR THE TWO STATIONARY CABLES ARE AT BOTTOM CENTER, JUST BELOW THE CABLE WHEEL. THE MAIN CABLE WHEEL IS IN THE DISTANCE AT CENTER LEFT. THE ORE CHUTES COMING FROM THE ORE BIN ARE AT LEFT CENTER EDGE. TRAM BUCKETS WERE CHARGED HERE. - Keane Wonder Mine, Park Route 4 (Daylight Pass Cutoff), Death Valley Junction, Inyo County, CA

Hough transform method for track finding in center drift chamber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azmi, K. A. Mohammad Kamal, E-mail: khasmidatul@siswa.um.edu.my; Wan Abdullah, W. A. T., E-mail: wat@um.edu.my; Ibrahim, Zainol Abidin

Hough transform is a global tracking method used which had been expected to be faster approach for tracking the circular pattern of electron moving in Center Drift Chamber (CDC), by transforming the point of hit into a circular curve. This paper present the implementation of hough transform method for the reconstruction of tracks in Center Drift Chamber (CDC) which have been generated by random number in C language programming. Result from implementation of this method shows higher peak of circle parameter value (xc,yc,rc) that indicate the similarity value of the parameter needed for circular track in CDC for charged particlesmore » in the region of CDC.« less

R1 in the Shaker S4 occupies the gating charge transfer center in the resting state

PubMed Central

Lin, Meng-chin A.; Hsieh, Jui-Yi; Mock, Allan F.

2011-01-01

During voltage-dependent activation in Shaker channels, four arginine residues in the S4 segment (R1–R4) cross the transmembrane electric field. It has been proposed that R1–R4 movement is facilitated by a “gating charge transfer center” comprising a phenylalanine (F290) in S2 plus two acidic residues, one each in S2 and S3. According to this proposal, R1 occupies the charge transfer center in the resting state, defined as the conformation in which S4 is maximally retracted toward the cytoplasm. However, other evidence suggests that R1 is located extracellular to the charge transfer center, near I287 in S2, in the resting state. To investigate the resting position of R1, we mutated I287 to histidine (I287H), paired it with histidine mutations of key voltage sensor residues, and determined the effect of extracellular Zn2+ on channel activity. In I287H+R1H, Zn2+ generated a slow component of activation with a maximum amplitude (Aslow,max) of ∼56%, indicating that only a fraction of voltage sensors can bind Zn2+ at a holding potential of −80 mV. Aslow,max decreased after applying either depolarizing or hyperpolarizing prepulses from −80 mV. The decline of Aslow,max after negative prepulses indicates that R1 moves inward to abolish ion binding, going beyond the point where reorientation of the I287H and R1H side chains would reestablish a binding site. These data support the proposal that R1 occupies the charge transfer center upon hyperpolarization. Consistent with this, pairing I287H with A359H in the S3–S4 loop generated a Zn2+-binding site. At saturating concentrations, Aslow,max reached 100%, indicating that Zn2+ traps the I287H+A359H voltage sensor in an absorbing conformation. Transferring I287H+A359H into a mutant background that stabilizes the resting state significantly enhanced Zn2+ binding at −80 mV. Our results strongly support the conclusion that R1 occupies the gating charge transfer center in the resting conformation. PMID:21788609

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

NASA Astrophysics Data System (ADS)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

NASA Astrophysics Data System (ADS)

Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

2015-05-01

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

Self-organized semiconductor nano-network on graphene

NASA Astrophysics Data System (ADS)

Son, Dabin; Kim, Sang Jin; Lee, Seungmin; Bae, Sukang; Kim, Tae-Wook; Kang, Jae-Wook; Lee, Sang Hyun

2017-04-01

A network structure consisting of nanomaterials with a stable structural support and charge path on a large area is desirable for various electronic and optoelectronic devices. Generally, network structures have been fabricated via two main strategies: (1) assembly of pre-grown nanostructures onto a desired substrate and (2) direct growth of nanomaterials onto a desired substrate. In this study, we utilized the surface defects of graphene to form a nano-network of ZnO via atomic layer deposition (ALD). The surface of pure and structurally perfect graphene is chemically inert. However, various types of point and line defects, including vacancies/adatoms, grain boundaries, and ripples in graphene are generated by growth, chemical or physical treatments. The defective sites enhance the chemical reactivity with foreign atoms. ZnO nanoparticles formed by ALD were predominantly deposited at the line defects and agglomerated with increasing ALD cycles. Due to the formation of the ZnO nano-network, the photocurrent between two electrodes was clearly changed under UV irradiation as a result of the charge transport between ZnO and graphene. The line patterned ZnO/graphene (ZnO/G) nano-network devices exhibit sensitivities greater than ten times those of non-patterned structures. We also confirmed the superior operation of a fabricated flexible photodetector based on the line patterned ZnO/G nano-network.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Highly efficient supercapacitor electrode with two-dimensional tungsten disulfide and reduced graphene oxide hybrid nanosheets

NASA Astrophysics Data System (ADS)

Tu, Chao-Chi; Lin, Lu-Yin; Xiao, Bing-Chang; Chen, Yu-Shiang

2016-07-01

Two-dimensional (2D) nanostructures with their high surface area and large in-plane conductivity have been regarded as promising materials for supercapacitors (SCs). Tungsten disulfide (WS2) is highly suitable for charge accumulation with its abundant active sites in the interspacing between the 2D structures and the intraspacing of each atomic layer, as well as on the tungsten centers with the charges generated by the Faradaic reactions. This study proposes the preparation of well-constructed WS2/reduced graphene oxide (RGO) nanosheets using a simple molten salt process as the electroactive material for SCs, which presents a high specific capacitance (CF) of 2508.07 F g-1 at the scan rate of 1 mV s-1, because of the synergic effect of WS2 with its large charge-accumulating sites on the 2D planes and RGO with its highly enhanced conductivity and improved connections in the WS2 networks. The excellent cycling stability of 98.6% retention after 5000 cycles charge/discharge process and the Coulombic efficiency close to 100% for the entire measurement are also achieved for the WS2/RGO-based SC electrode. The results suggest the potential for the combination of the 2D metal sulfide and carbon materials as the charge storage material to solve the energy problems and attain a sustainable society.

Amine templating effect absent in uranyl sulfates synthesized with 1,4-n-butyldiamine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jouffret, Laurent J., E-mail: ljouffret@nd.edu; Wylie, Ernest M.; Burns, Peter C.

2013-01-15

Two new uranyl sulfates, (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS2) and (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2})(SO{sub 4}){sub 2}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS3), were synthesized and their crystal structures determined. NDUS2 was obtained in highly acidic media heat-treated at 373 K and subsequently maintained at 278 K until crystals formed after two months. NDUS3 results from the degradation of NDUS2 over the course of a few days. NDUS2 and NDUS3 crystallize in the monoclinic space group P2{sub 1}/n, a=10.9075(4) A, b=10.4513(4) A, c=17.7881(7) A, {beta}=97.908(2) Degree-Sign , V=2008.52(13) A{sup 3}, Z=4, at 140 K and a=8.8570(4) A,more » b=7.3299(3) A, c=20.4260(9) A, {beta}=95.140(2) Degree-Sign , V=1320.74(10) A{sup 3}, Z=4, at 140 K, respectively. The compounds contain interlayer 1,4-n-butyldiammonium cations that charge-balance the anionic structural units. - Graphical abstract: Amine templating effect absent in uranyl sulfates synthesized with 1,4-diaminobutane, as shown by the synthesis of two new uranyl sulfates, (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS2) and (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2})(SO{sub 4}){sub 2}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS3). Highlights: Black-Right-Pointing-Pointer Two layered uranyl sulfates were synthesized. Black-Right-Pointing-Pointer Amine molecules are located in the interlayers of the compounds. Black-Right-Pointing-Pointer No templating effect of the amine was observed. Black-Right-Pointing-Pointer Amine molecules are only charge balancing cations in the structures.« less

Optimized nanoporous materials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Braun, Paul V.; Langham, Mary Elizabeth; Jacobs, Benjamin W.

2009-09-01

Nanoporous materials have maximum practical surface areas for electrical charge storage; every point in an electrode is within a few atoms of an interface at which charge can be stored. Metal-electrolyte interfaces make best use of surface area in porous materials. However, ion transport through long, narrow pores is slow. We seek to understand and optimize the tradeoff between capacity and transport. Modeling and measurements of nanoporous gold electrodes has allowed us to determine design principles, including the fact that these materials can deplete salt from the electrolyte, increasing resistance. We have developed fabrication techniques to demonstrate architectures inspired bymore » these principles that may overcome identified obstacles. A key concept is that electrodes should be as close together as possible; this is likely to involve an interpenetrating pore structure. However, this may prove extremely challenging to fabricate at the finest scales; a hierarchically porous structure can be a worthy compromise.« less

A DFT study for the structural and electronic properties of Zn m Se n nanoclusters

NASA Astrophysics Data System (ADS)

Yadav, Phool Singh; Pandey, Dheeraj Kumar

2012-09-01

An ab initio study has been performed for the stability, structural and electronic properties of 19 small zinc selenide Zn m Se n ( m + n = 2-4) nanoclusters. Out of these nanoclusters, one nanocluster is found to be unstable due to its imaginary vibrational frequency. A B3LYP-DFT/6-311G(3df) method is used in the optimization of the geometries of the nanoclusters. We have calculated the zero point energy (ZPE), which is ignored by the other workers. The binding energies (BE), HOMO-LUMO gaps and bond lengths have been obtained for all the optimized nanoclusters. For the same value of ` m' and ` n', we designate the most stable structure the one, which has maximum final binding energy (FBE) per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), dipole moments and charge on atoms have been investigated for the most stable nanoclusters. For the same value of ` m' and ` n', the nanocluster containing maximum number of Se atoms is found to be most stable.

First-Principles Study of the Electronic Structure and Bonding Properties of X8C46 and X8B6C40 (X: Li, Na, Mg, Ca) Carbon Clathrates

NASA Astrophysics Data System (ADS)

KoleŻyński, Andrzej; Szczypka, Wojciech

2016-03-01

Results from theoretical analysis of the crystal structure, electronic structure, and bonding properties of C46 and B6C40 carbon clathrates doped with selected alkali and alkaline earth metals cations (Li, Na, Mg, Ca) are presented. The ab initio calculations were performed by means of the WIEN2k package (full potential linearized augmented plane wave method (FP-LAPW) within density functional theory (DFT)) with PBESol and modified Becke-Johnson exchange-correlation potentials used in geometry optimization and electronic structure calculations, respectively. The bonding properties were analyzed by applying Bader's quantum theory of atoms in molecules formalism to the topological properties of total electron density obtained from ab initio calculations. Analysis of the results obtained (i.a. equilibrium geometry, equation of state, cohesive energy, band structure, density of states—both total and projected on to particular atoms, and topological properties of bond critical points and net charges of topological atoms) is presented in detail.

Structure, stability, and electronic properties of AlP nanocages evolved from the world's smallest caged fullerene C20: A computational study at DFT

NASA Astrophysics Data System (ADS)

Baei, Mohammad T.; Koohi, Maryam; Shariati, Minoo

2018-05-01

The stability, geometry, and electronic properties of C20 and its AlnPnC20-2n heterofullerenic derivatives where n = 1-10 are probed, at density functional theory (DFT). Vibrational frequency calculations show that exclusive of Al6P6C8 and Al10P8C2, other species are true minima. Exploring of the optimized structures demonstrates the shrinkage of Cdbnd C double bonds to compensate for the longer Csbnd Al, Csbnd P and Alsbnd P single bonds. The calculated binding energy, HOMO-LUMO gap and nucleus independent chemical shift at the cage center (NICS (0)) of Al1P1C18 shows it the most stable structure. While substituting of 1, 2, 3, 4, 6, and 7 Alsbnd P units enhances kinetic stability of the resulting heterofullerenes against electronic excitations via increasing their HOMO-LUMO gap, doping of 5, 8, 9, and 10 Alsbnd P units increases the conductivity of heterofullerenes through decreasing their band gap. Substitutional doping leads to a high point charge upon the surfaces of all derivatives, especially the highest delocalization on Al6P6C8, with range of -2.056 to -1.261 charged carbons, +1.493 to +1.586 charged aluminums, and +0.513 to +0.801 charged phosphor atoms, followed by Al4P4C12. These high charge distributions on the surfaces of the studied analogous can develop their storage capacity and henceforth characterize them worthy of investigation for hydrogen storage. Also, Al1P1C18, Al2P2C16, and Al10P10 are shown as the most aromatic and anti-aromatic nanocages with NICS (0) of -41.60, -39.82, and +22.59 ppm, respectively, compared to C20 (-19.61 ppm). The computed higher dipole moment of Al1P1C18 and Al5P5C10 (4.06 and 3.29 Debye, respectively) exhibits higher reactivity potential and greater affinity of them to more polar solvents. Thus, in both gas phase and polar solvent, Al1P1C18 structure is expected to be stabilized to a greater extent than the other species, which has been confirmed by the thermodynamic and kinetic data.

Valence atom with bohmian quantum potential: the golden ratio approach

PubMed Central

2012-01-01

Background The alternative quantum mechanical description of total energy given by Bohmian theory was merged with the concept of the golden ratio and its appearance as the Heisenberg imbalance to provide a new density-based description of the valence atomic state and reactivity charge with the aim of clarifying their features with respect to the so-called DFT ground state and critical charge, respectively. Results The results, based on the so-called double variational algorithm for chemical spaces of reactivity, are fundamental and, among other issues regarding chemical bonding, solve the existing paradox of using a cubic parabola to describe a quadratic charge dependency. Conclusions Overall, the paper provides a qualitative-quantitative explanation of chemical reactivity based on more than half of an electronic pair in bonding, and provide new, more realistic values for the so-called “universal” electronegativity and chemical hardness of atomic systems engaged in reactivity (analogous to the atoms-in-molecules framework). PMID:23146157

Density functional study of hypophosphite adsorption on Ni (1 1 1) and Cu (1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Zeng, Yue; Liu, Shubin; Ou, Lihui; Yi, Jianlong; Yu, Shanci; Wang, Huixian; Xiao, Xiaoming

2006-02-01

Surface structures and electronic properties of hypophosphite, H 2PO 2-, molecularly adsorbed on Ni(1 1 1) and Cu(1 1 1) surfaces are investigated in this work by density functional theory at B3LYP/6-31++g(d, p) level. We employ a four-metal-atom cluster as the simplified model for the surface and have fully optimized the geometry and orientation of H 2PO 2- on the metal cluster. Six stable orientations have been discovered on both Ni (1 1 1) and Cu (1 1 1) surfaces. The most stable orientation of H 2PO 2- was found to have its two oxygen atoms interact the surface with two P sbnd O bonds pointing downward. Results of the Mulliken population analysis showed that the back donation from 3d orbitals of the transition metal substrate to the unfilled 3d orbital of the phosphorus atom in H 2PO 2- and 4s orbital's acceptance of electron donation from one lone pair of the oxygen atom in H 2PO 2- play very important roles in the H 2PO 2- adsorption on the transition metals. The averaged electron configuration of Ni in Ni 4 cluster is 4s 0.634p 0.023d 9.35 and that of Cu in Cu 4 cluster is 4s 1.004p 0.033d 9.97. Because of this subtle difference of electron configuration, the adsorption energy is larger on the Ni surface than on the Cu surface. The amount of charge transfers due to above two donations is larger from H 2PO 2- to the Ni surface than to the Cu surface, leading to a more positively charged P atom in Ni nH 2PO 2- than in Cu nH 2PO 2-. These results indicate that the phosphorus atom in Ni nH 2PO 2- complex is easier to be attacked by a nucleophile such as OH - and subsequent oxidation of H 2PO 2- can take place more favorably on Ni substrate than on Cu substrate.

Alternative Fuels Data Center: Developing Infrastructure to Charge Plug-In

Science.gov Websites

Electric Vehicles Developing Infrastructure to Charge Plug-In Electric Vehicles to someone by E -mail Share Alternative Fuels Data Center: Developing Infrastructure to Charge Plug-In Electric Vehicles on Facebook Tweet about Alternative Fuels Data Center: Developing Infrastructure to Charge Plug-In

Density functional investigation of mercury and arsenic adsorption on nitrogen doped graphene decorated with palladium clusters: A promising heavy metal sensing material in farmland

NASA Astrophysics Data System (ADS)

Zhao, Chunjiang; Wu, Huarui

2017-03-01

Density functional theory calculations are carried out to study the adsorption of mercury and arsenic on Pdn (n = 1-6) supported on pyridine-like nitrogen doped graphene (PNG). Owing to the promising sensitivity in trace amounts of atoms or molecules, PNG can be acted as micro-sensor for sensing heavy metals in agriculture soils. Through the analyses of structural and electronic properties of pristine PNG and Pd atom decorated PNG, we find that the most favorable adsorption site for Pd atom is the vacancy site. The analyses of structural and electronic properties reveal that the Pd atom or clusters can enhance the reactivity for Hg and AsH3 adsorption on PNG. The adsorption ability of Hg on Pdn decorated PNG is found to be related to the d-band center (εd) of the Pdn, in which the closer εd of Pdn to the Fermi level, the higher adsorption strength for Hg on Pdn decorated PNG. Moreover, the charge transfer between Pdn and arsenic may constitute arsenic adsorption on Pdn decorated PNG. Further design of highly efficient carbon based sorbents for heavy metals removal should be focused on tailoring εd of adsorbed metals.

A physically interpretable quantum-theoretic QSAR for some carbonic anhydrase inhibitors with diverse aromatic rings, obtained by a new QSAR procedure.

PubMed

Clare, Brian W; Supuran, Claudiu T

2005-03-15

A QSAR based almost entirely on quantum theoretically calculated descriptors has been developed for a large and heterogeneous group of aromatic and heteroaromatic carbonic anhydrase inhibitors, using orbital energies, nodal angles, atomic charges, and some other intuitively appealing descriptors. Most calculations have been done at the B3LYP/6-31G* level of theory. For the first time we have treated five-membered rings by the same means that we have used for benzene rings in the past. Our flip regression technique has been expanded to encompass automatic variable selection. The statistical quality of the results, while not equal to those we have had with benzene derivatives, is very good considering the noncongeneric nature of the compounds. The most significant correlation was with charge on the atoms of the sulfonamide group, followed by the nodal orientation and the solvation energy calculated by COSMO and the charge polarization of the molecule calculated as the mean absolute Mulliken charge over all atoms.

Charge exchange collisions of slow C6 + with atomic and molecular H

NASA Astrophysics Data System (ADS)

Saha, Bidhan C.; Guevara, Nicolais L.; Sabin, John R.; Deumens, Erik; Öhrn, Yngve

2016-04-01

Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at projectile energies 0.1 < E < 10 keV/amu, using electron nuclear dynamics (END) - a semi-classical approximation which not only includes electron translation factors for avoiding spurious couplings but also employs full dynamical trajectories to treat nuclear motions. Both the total and partial cross sections are reported for the collision of C6+ ions with atomic and molecular hydrogen. A comparison with other theoretical and experimental results shows, in general good agreement except at very low energy, considered here. For H2, the one- and two-electron charge exchange cross sections are calculated and compared with other theoretical and experimental results. Small but non-negligible isotope effects are found at the lowest energy studied in the charge transfer of C6+ with H. In low energy region, it is observed that H2 has larger isotope effects than H atom due to the polarizability effect which is larger than the mass effect.

Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films

DOE PAGES

Han, Myung-Geun; Garlow, Joseph A.; Bugnet, Matthieu; ...

2016-09-02

Polar discontinuity at interfaces plays deterministic roles in charge transport, magnetism, and even superconductivity of functional oxides. To date, most polar discontinuity problems have been explored in hetero-interfaces between two dissimilar materials. Here, we show that charged domain walls (CDWs) in epitaxial thin films of ferroelectric PbZr 0.2Ti 0.8O 3 are strongly coupled to polar interfaces through the formation of ½<101>{h0l} type crystallographic shear planes (CSPs). Using atomic resolution imaging and spectroscopy we illustrate that the CSPs consist of both conservative and nonconservative segments when coupled to the CDWs, where necessary compensating charges for stabilizing the CDWs are associated withmore » vacancies at the CSPs. Lasly, the CDW/CSP coupling yields an atomically narrow domain walls, consisting of a single atomic layer of oxygen. This study shows that the CDW/CSP coupling is a fascinating venue to develop emergent material properties.« less

Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of vaporization.

PubMed

Puri, Swati; Chickos, James S; Welsh, William J

2002-01-01

Three-dimensional Quantitative Structure-Property Relationship (QSPR) models have been derived using Comparative Molecular Field Analysis (CoMFA) to correlate the vaporization enthalpies of a representative set of polychlorinated biphenyls (PCBs) at 298.15 K with their CoMFA-calculated physicochemical properties. Various alignment schemes, such as inertial, as is, and atom fit, were employed in this study. The CoMFA models were also developed using different partial charge formalisms, namely, electrostatic potential (ESP) charges and Gasteiger-Marsili (GM) charges. The most predictive model for vaporization enthalpy (Delta(vap)H(m)(298.15 K)), with atom fit alignment and Gasteiger-Marsili charges, yielded r2 values 0.852 (cross-validated) and 0.996 (conventional). The vaporization enthalpies of PCBs increased with the number of chlorine atoms and were found to be larger for the meta- and para-substituted isomers. This model was used to predict Delta(vap)H(m)(298.15 K) of the entire set of 209 PCB congeners.

Theory of spin-conserving excitation of the N-V(-) center in diamond.

PubMed

Gali, Adam; Janzén, Erik; Deák, Péter; Kresse, Georg; Kaxiras, Efthimios

2009-10-30

The negatively charged nitrogen-vacancy defect in diamond is an important atomic-scale structure that can be used as a qubit in quantum computing and as a marker in biomedical applications. Its usefulness relies on the ability to optically excite electrons between well-defined gap states, which requires a clear and detailed understanding of the relevant states and excitation processes. Here we show that by using hybrid density-functional-theory calculations in a large supercell we can reproduce the zero-phonon line and the Stokes and anti-Stokes shifts, yielding a complete picture of the spin-conserving excitation of this defect.

Adsorption of cyanogen chloride on the surface of boron nitride nanotubes for CNCl sensing

NASA Astrophysics Data System (ADS)

Movlarooy, Tayebeh; Fadradi, Mahboobeh Amiri

2018-05-01

The adsorption of CNCl gas, on the surface of boron nitride nanotubes in pure form, as well as doped with Al and Ga, based on the density functional theory (DFT) has been studied. The electron and structural properties of pristine and doped nanotubes have been investigated. By calculating the adsorption energy, the most stable positions and the equilibrium distance are obtained, and charge transferred and electronic properties have been calculated. The most stable molecule adsorption position for pure nanotube is obtained at the center of the hexagon and for doped nanotube above the impurity atom from N side.

Laboratory Measurements of Charge Transfer on Atomic Hydrogen at Thermal Energies

NASA Technical Reports Server (NTRS)

Havener, C. C.; Vane, C. R.; Krause, H. F.; Stancil, P. C.; Mroczkowski, T.; Savin, D. W.

2002-01-01

We describe our ongoing program to measure velocity dependent charge transfer (CT) cross sections for selected ions on atomic hydrogen using the ion-aloin merged-beams apparatus at Oak Ridge Natioiial Laboralory. Our focus is on those ions for which CT plays an important role in determining the ionization structure, line emis sion, and thermal structure of observed cosmic photoionized plasmas.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system

NASA Astrophysics Data System (ADS)

Kong, Fantai; Longo, Roberto C.; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-01

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO2. A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li2CoO2 and Li-deficient LiCo2O4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system.

PubMed

Kong, Fantai; Longo, Roberto C; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-29

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO 2 . A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li 2 CoO 2 and Li-deficient LiCo 2 O 4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

Improved method and apparatus for electrostatically sorting biological cells. [DOE patent application

DOEpatents

Merrill, J.T.

An improved method of sorting biological cells in a conventional cell sorter apparatus includes generating a fluid jet containing cells to be sorted, measuring the distance between the centers of adjacent droplets in a zone thereof defined at the point where the fluid jet separates into descrete droplets, setting the distance between the center of a droplet in said separation zone and the position along said fluid jet at which the cell is optically sensed for specific characteristics to be an integral multiple of said center-to-center distance, and disabling a charger from electrically charging a specific droplet if a cell is detected by the optical sensor in a position wherein it will be in the neck area between droplets during droplet formation rather than within a predetermined distance from the droplet center.