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.

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.

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.

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.

Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2014-02-01

Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation. Copyright © 2013 Elsevier Inc. All rights reserved.

Efficient approach to obtain free energy gradient using QM/MM MD simulation

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

Asada, Toshio; Koseki, Shiro; The Research Institute for Molecular Electronic Devices

2015-12-31

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means ofmore » FEG and the nudged elastic band (NEB) method.« less

Infrared spectra of some acetone—magnesium adducts

NASA Astrophysics Data System (ADS)

Hisatsune, I. C.

Co-deposition of atomic magnesium with excess acetone at liquid-nitrogen temperature produces an unstable charge-transfer complex with a characteristic carbonyl infrared band at 1595 cm -1 and stable acetone adducts in which the metal atom bridges the carbonyl bond (π-complex) or coordinates to the oxygen atom (σ-complex). Infrared spectra of these complexes with (CH 3) 2CO and (CD 3) 2CO have been obtained. Corroborations for these adducts were obtained from infrared studies of acetone matrices with atomic copper and acetaldehyde matrices with atomic magnesium and with atomic copper. Infrared spectra of an acetone adduct and a dimethyl ether adduct of the Grignard reagent CH 3MgI have also been obtained. Hydrolysis of a σ-adduct gives acetone but isopropyl alcohol is obtained from hydrolysis of the π-adduct.

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.

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.

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

NASA Technical Reports Server (NTRS)

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

1993-01-01

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

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

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.

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.

Relativistic Collisions of Highly-Charged Ions

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

Ionescu, Dorin; Belkacem, Ali

1998-11-19

The physics of elementary atomic processes in relativistic collisions between highly-charged ions and atoms or other ions is briefly discussed, and some recent theoretical and experimental results in this field are summarized. They include excitation, capture, ionization, and electron-positron pair creation. The numerical solution of the two-center Dirac equation in momentum space is shown to be a powerful nonperturbative method for describing atomic processes in relativistic collisions involving heavy and highly-charged ions. By propagating negative-energy wave packets in time the evolution of the QED vacuum around heavy ions in relativistic motion is investigated. Recent results obtained from numerical calculations usingmore » massively parallel processing on the Cray-T3E supercomputer of the National Energy Research Scientific Computer Center (NERSC) at Berkeley National Laboratory are presented.« less

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-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.

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.

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.

Secondary Interstellar Oxygen in the Heliosphere: Numerical Modeling and Comparison with IBEX-Lo Data

NASA Astrophysics Data System (ADS)

Baliukin, I. I.; Izmodenov, V. V.; Möbius, E.; Alexashov, D. B.; Katushkina, O. A.; Kucharek, H.

2017-12-01

Quantitative analysis of the interstellar heavy (oxygen and neon) atom fluxes obtained by the Interstellar Boundary Explorer (IBEX) suggests the existence of the secondary interstellar oxygen component. This component is formed near the heliopause due to charge exchange of interstellar oxygen ions with hydrogen atoms, as was predicted theoretically. A detailed quantitative analysis of the fluxes of interstellar heavy atoms is only possible with a model that takes into account both the filtration of primary and the production of secondary interstellar oxygen in the boundary region of the heliosphere as well as a detailed simulation of the motion of interstellar atoms inside the heliosphere. This simulation must take into account photoionization, charge exchange with the protons of the solar wind and solar gravitational attraction. This paper presents the results of modeling interstellar oxygen and neon atoms through the heliospheric interface and inside the heliosphere based on a three-dimensional kinetic-MHD model of the solar wind interaction with the local interstellar medium and a comparison of these results with the data obtained on the IBEX spacecraft.

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.

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.

Interatomic interactions in M2(C8H4O4)2C6H12N2 (M = Zn, Cu, Co, Ni) metal-organic framework polymers: X-ray photoelectron spectroscopy, QTAIM and ELF study

NASA Astrophysics Data System (ADS)

Kozlova, S. G.; Ryzhikov, M. R.; Samsonenko, D. G.; Kalinkin, A. V.

2017-12-01

Interatomic interactions in M2(C8H4O4)2C6H12N2 (M = Co, Ni, Cu, Zn) metal-organic framework polymers have been studied with the methods of quantum chemistry and X-ray photoelectron spectroscopy. Interactions of C6H12N2 molecules and C8H4O42- anions with metal atoms are shown to be of closed-shell type. C6H12N2 molecules are positively charged, the value of the charge slightly depends on the type of the metal atoms. Msbnd M interactions are described as "intermediate interactions" with some covalence contribution which reaches maximum for the interactions between cobalt atoms. The obtained quantum-chemical data agree with those obtained from photoelectron spectroscopy measurements.

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.

The interaction of excited He, Ar and Ne metastable atoms with the CF2Cl2 molecule

NASA Astrophysics Data System (ADS)

Cherid, M.; Ben Arfa, M.; Driss Khodja, M.

2004-02-01

We studied Penning ionization of the CF2Cl2 molecule by neon and helium metastable atoms. In the case of the neon ionizing particle, we measured the electron kinetic energy as well as mass spectra; for helium metastable atoms, only the mass spectrum was recorded. We, therefore, obtained the branching ratios for the heavy charged particles produced in both interactions. In this report we will discuss the mechanism involved in the production of metastable halogen atoms in the dielectric barrier discharge further to the use of rare gases/CF2Cl2 mixtures. We show that this process needs a two-stage reaction. Ground state free halogen atoms are formed over the first stage by Penning ionization, charge transfer, dissociate excitation and ionization. Therefore, metastable halogen atoms can be produced by excitation transfer process in the second stage through interaction with metastable rare gas atoms. This paper is dedicated to Professor F M E Tuffin on the occasion of his retirement.

Application of discrete solvent reaction field model with self-consistent atomic charges and atomic polarizabilities to calculate the χ(1) and χ(2) of organic molecular crystals

NASA Astrophysics Data System (ADS)

Lu, Shih-I.

2018-01-01

We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.

Recent Development of IMP LECR3 Ion Source

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

Zhang, Z.M.; Zhao, H.W.; Li, J.Y.

2005-03-15

18GHz microwave has been fed to the LECR3 ion source to produce intense highly charged ion beams although this ion source was designed for 14.5GHz. Then 1.1 emA Ar8+ and 325 e{mu}A Ar11+ were obtained at 18GHz. During the source running for atomic physics experiment, some higher charge state ion beams such as Ar17+ and Ar18+ were detected and have been validated by atomic physics method. Furthermore, a few special gases, e.g. SiH4 and SF6, were tested on LECR3 ion source to produce required ion beams to satisfy the requirements of atomic physics experiments.

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

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.

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.

Demystifying Introductory Chemistry. Part 3: Ionization Energies, Electronegativity, Polar Bonds, and Partial Charges.

ERIC Educational Resources Information Center

Spencer, James; And Others

1996-01-01

Shows how ionization energies provide a convenient method for obtaining electronegativity values that is simpler than the conventional methods. Demonstrates how approximate atomic charges can be calculated for polar molecules and how this method of determining electronegativities may lead to deeper insights than are typically possible for the…

Reactions between NO/+/ and metal atoms using magnetically confined afterglows

NASA Technical Reports Server (NTRS)

Lo, H. H.; Clendenning, L. M.; Fite, W. L.

1977-01-01

A new method of studying thermal energy ion-neutral collision processes involving nongaseous neutral atoms is described. A long magnetic field produced by a solenoid in a vacuum chamber confines a thermal-energy plasma generated by photoionization of gas at very low pressure. As the plasma moves toward the end of the field, it is crossed by a metal atom beam. Ionic products of ion-atom reactions are trapped by the field and both the reactant and product ions move to the end of the magnetic field where they are detected by a quadrupole mass filter. The cross sections for charge transfer between NO(+) and Na, Mg, Ca, and Sr and that for rearrangement between NO(+) and Ca have been obtained. The charge-transfer reaction is found strongly dominant over the rearrangement reaction that forms metallic oxide ions.

Disordering of ultra thin WO3 films by high-energy ions

NASA Astrophysics Data System (ADS)

Matsunami, N.; Kato, M.; Sataka, M.; Okayasu, S.

2017-10-01

We have studied disordering or atomic structure modification of ultra thin WO3 films under impact of high-energy ions with non-equilibrium and equilibrium charge incidence, by means of X-ray diffraction (XRD). WO3 films were prepared by thermal oxidation of W deposited on MgO substrate. Film thickness obtained by Rutherford backscattering spectrometry (RBS) is as low as 2 nm. Smoothness of film surface was observed by atomic force microscopy. It is found that the ratio of XRD intensity degradation per 90 MeV Ni+10 ion (the incident charge is lower than the equilibrium charge) to that per 90 MeV Ni ion with the equilibrium charge depends on the film thickness. Also, film thickness dependence is observed for 100 MeV Xe+14. By comparison of the experimental result with a simple model calculation based on the assumption that the mean charge of ions along the depth follows a saturation curve with power-law approximation to the charge dependent electronic stopping power, the characteristic length attaining the equilibrium charge is obtained to be ∼7 nm for 90 MeV Ni+10 ion incidence or the electron loss cross section of ∼1016 cm2, demonstrating that disordering of ultra WO3 films has been observed and a fundamental quantity can be derived through material modification.

Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

PubMed Central

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-01-01

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca2+-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase. PMID:25730881

Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

PubMed

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-03-17

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

The earth's ring current - Present situation and future thrusts

NASA Technical Reports Server (NTRS)

Williams, D. J.

1987-01-01

Particle distributions, currents, and the ring current situation prior to the August 1984 launch of the AMPTE Charge Composition Explorer (CCE) are discussed. CCE results which demonstrate the capability of these new measurements to pursue questions of ring current sources, energization, and transport are presented. Consideration is given to various ring current generation mechanisms which have been discussed in the literature, and a two-step generation process which to a certain extent unifies the previous mechanisms is presented. The first in-situ global observations of ring current decay as obtained through the detection of energetic neutral atoms generated by charge exchange interactions between the ring current and hydrogen geocorona are discussed, as well as the possibility of using the detection of energetic neutral atoms to obtain global images of the earth's ring current.

Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex.

PubMed

Téllez S, Claudio A; Costa, Anilton C; Mondragón, M A; Ferreira, Glaucio B; Versiane, O; Rangel, J L; Lima, G Müller; Martin, A A

2016-12-05

Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Hα line shape in front of the limiter in the HT-6M tokamak

NASA Astrophysics Data System (ADS)

Wan, Baonian; Li, Jiangang; Luo, Jiarong; Xie, Jikang; Wu, Zhenwei; Zhang, Xianmei; HT-6M Group

1999-11-01

The Hα line shape in front of the limiter in the HT-6M tokamak is analysed by multi-Gaussian fitting. The energy distribution of neutral hydrogen atoms reveals that Hα radiation is contributed by Franck-Condon atoms, atoms reflected at the limiter surface and charge exchange. Multi-Gaussian fitting of the Hα spectral profile indicates contributions of 60% from reflection particles and 40% from molecule dissociation to recycling. Ion temperatures in central regions are obtained from the spectral width of charge exchange components. Dissociation of hydrogen molecules and reflection of particles at the limiter surface are dominant in edge recycling. Reduction of particle reflection at the limiter surface is important for controlling edge recycling. The measured profiles of neutral hydrogen atom density are reproduced by a particle continuity equation and a simplified one dimensional Monte Carlo simulation code.

Quantitative nanoscale electrostatics of viruses

NASA Astrophysics Data System (ADS)

Hernando-Pérez, M.; Cartagena-Rivera, A. X.; Lošdorfer Božič, A.; Carrillo, P. J. P.; San Martín, C.; Mateu, M. G.; Raman, A.; Podgornik, R.; de Pablo, P. J.

2015-10-01

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04274g

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.

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

A strategy for optical properties investigation in ABe2BO3F2 (A=K, Rb, Cs) using finite field methods

NASA Astrophysics Data System (ADS)

Mushahali, Hahaer; Mu, Baoxia; Wang, Qian; Mamat, Mamatrishat; Cao, Haibin; Yang, Guang; Jing, Qun

2018-07-01

The finite-field methods can be used to intuitively learn about the optical response and find out the atomic contributions to the birefringence and SHG tensors. In this paper, the linear and second-order nonlinear optical properties of ABe2BO3F2 family (A = K, Rb, Cs) compounds are investigated using the finite-field methods within different exchange-correlation functionals. The results show that the obtained birefringence and SHG tensors are in good agreement with the experimental values. The atomic contribution to the total birefringence was further investigated using the variation of the atomic charges, and the Born effective charges. The results show that the boron-oxygen groups give main contribution to the anisotropic birefringence.

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.

Charge Transfer in Collisions of S^4+ with He.

NASA Astrophysics Data System (ADS)

Wang, J. G.; Stancil, P. C.; Turner, A. R.; Cooper, D. L.; Schultz, D. R.; Rakovic, M. J.; Fritsch, W.; Zygelman, B.

2001-05-01

Charge transfer processes due to collisions of ground state S^4+ ions with atomic helium were investigated for energies between 0.1 meV/u and 10 MeV/u. Total and state-selective cross sections and rate coefficients were obtained utilizing the quantum-mechanical molecular-orbital close-coupling (MOCC), atomic-orbital close-coupling, classical trajectory Monte Carlo (CTMC), and continuum distorted wave methods. The MOCC calculations utilized ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained with the spin-coupled valence-bond approach. A number of variants of the CTMC approach were also explored. Previous data are limited to an earlier Landau-Zener calculation of the total rate coefficient for which our results are two orders of magnitude larger. An observed multichannel interference effect in the MOCC results will also be discussed.

Hydrodynamic flow of ions and atoms in partially ionized plasmas.

PubMed

Nemirovsky, R A; Fredkin, D R; Ron, A

2002-12-01

We have derived the hydrodynamic equations of motion for a partially ionized plasma, when the ionized component and the neutral components have different flow velocities and kinetic temperatures. Starting from the kinetic equations for a gas of ions and a gas of atoms we have considered various processes of encounters between the two species: self-collisions, interspecies collisions, ionization, recombination, and charge exchange. Our results were obtained by developing a general approach for the hydrodynamics of a gas in a binary mixture, in particular when the components drift with respect to each other. This was applied to a partially ionized plasma, when the neutral-species gas and the charged-species gas have separate velocities. We have further suggested a generalized version of the relaxation time approximation and obtained the contributions of the interspecies encounters to the transport equations.

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.

Four-dimensional ultrafast electron microscopy of phase transitions

PubMed Central

Grinolds, Michael S.; Lobastov, Vladimir A.; Weissenrieder, Jonas; Zewail, Ahmed H.

2006-01-01

Reported here is direct imaging (and diffraction) by using 4D ultrafast electron microscopy (UEM) with combined spatial and temporal resolutions. In the first phase of UEM, it was possible to obtain snapshot images by using timed, single-electron packets; each packet is free of space–charge effects. Here, we demonstrate the ability to obtain sequences of snapshots (“movies”) with atomic-scale spatial resolution and ultrashort temporal resolution. Specifically, it is shown that ultrafast metal–insulator phase transitions can be studied with these achieved spatial and temporal resolutions. The diffraction (atomic scale) and images (nanometer scale) we obtained manifest the structural phase transition with its characteristic hysteresis, and the time scale involved (100 fs) is now studied by directly monitoring coordinates of the atoms themselves. PMID:17130445

Excitation and charge transfer in low-energy hydrogen atom collisions with neutral oxygen

NASA Astrophysics Data System (ADS)

Barklem, P. S.

2018-02-01

Excitation and charge transfer in low-energy O+H collisions is studied; it is a problem of importance for modelling stellar spectra and obtaining accurate oxygen abundances in late-type stars including the Sun. The collisions have been studied theoretically using a previously presented method based on an asymptotic two-electron linear combination of atomic orbitals (LCAO) model of ionic-covalent interactions in the neutral atom-hydrogen-atom system, together with the multichannel Landau-Zener model. The method has been extended to include configurations involving excited states of hydrogen using an estimate for the two-electron transition coupling, but this extension was found to not lead to any remarkably high rates. Rate coefficients are calculated for temperatures in the range 1000-20 000 K, and charge transfer and (de)excitation processes involving the first excited S-states, 4s.5So and 4s.3So, are found to have the highest rates. Data are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/vizbin/qcat?J/A+A/610/A57. The data are also available at http://https://github.com/barklem/public-data

A model Ni-Al-Mo superalloy studied by ultraviolet pulsed-laser-assisted local-electrode atom-probe tomography.

PubMed

Tu, Yiyou; Plotnikov, Elizaveta Y; Seidman, David N

2015-04-01

This study investigates the effects of the charge-state ratio of evaporated ions on the accuracy of local-electrode atom-probe (LEAP) tomographic compositional and structural analyses, which employs a picosecond ultraviolet pulsed laser. Experimental results demonstrate that the charge-state ratio is a better indicator of the best atom-probe tomography (APT) experimental conditions compared with laser pulse energy. The thermal tails in the mass spectra decrease significantly, and the mass resolving power (m/Δm) increases by 87.5 and 185.7% at full-width half-maximum and full-width tenth-maximum, respectively, as the laser pulse energy is increased from 5 to 30 pJ/pulse. The measured composition of this alloy depends on the charge-state ratio of the evaporated ions, and the most accurate composition is obtained when Ni2+/Ni+ is in the range of 0.3-20. The γ(f.c.c.)/γ'(L12) interface is quantitatively more diffuse when determined from the measured concentration profiles for higher laser pulse energies. Conclusions of the APT compositional and structural analyses utilizing the same suitable charge-state ratio are more comparable than those collected with the same laser pulse energy.

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.

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.

Calculation of low-Z impurity pellet induced fluxes of charge exchange neutral particles escaping from magnetically confined toroidal plasmas.

PubMed

Goncharov, P R; Ozaki, T; Sudo, S; Tamura, N; Tolstikhina, I Yu; Sergeev, V Yu

2008-10-01

Measurements of energy- and time-resolved neutral hydrogen and helium fluxes from an impurity pellet ablation cloud, referred to as pellet charge exchange or PCX experiments, can be used to study local fast ion energy distributions in fusion plasmas. The estimation of the local distribution function f(i)(E) of fast ions entering the cloud requires knowledge of both the fraction F(0)(E) of incident ions exiting the cloud as neutral atoms and the attenuation factor A(E,rho) describing the loss of fast atoms in the plasma. Determination of A(E,rho), in turn, requires the total stopping cross section sigma(loss) of neutral atoms in the plasma and the Jacobian reflecting the measurement geometry and the magnetic surface shape. The obtained functions F(0)(E) and A(E,rho) enter multiplicatively into the probability density for escaping neutral particle kinetic energy. A general calculation scheme has been developed and realized as a FORTRAN code, which is to be applied for the calculation of f(i)(E) from PCX experimental results obtained with low-Z impurity pellets.

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.

2S-4S spectroscopy in hydrogen atom: The new value for the Rydberg constant and the proton charge radius

NASA Astrophysics Data System (ADS)

Kolachevsky, N.; Beyer, A.; Maisenbacher, L.; Matveev, A.; Pohl, R.; Khabarova, K.; Grinin, A.; Lamour, T.; Yost, D. C.; Haensch, T. W.; Udem, Th.

2018-02-01

The core of the "proton radius puzzle" is the discrepancy of four standard deviations between the proton root mean square charge radii (rp) determined from regular hydrogen (H), and the muonic hydrogen atom (μp). We have measured the 2S-4P transition frequency in H, utilizing a cryogenic beam of H and directly demonstrate that quantum interference of neighboring atomic resonances can lead to line shifts much larger than the proton radius discrepancy. Using an asymmetric fit function we obtain rp = 0.8335(95) fm and the Rydberg constant R∞ = 10 973 731.568 076 (96) m-1. The new value for rp is 3.3 combined standard deviations smaller than the latest CODATA value, but in good agreement with the value from μp.

Charge Transfer in Collisions of S^4+ with H.

NASA Astrophysics Data System (ADS)

Stancil, P. C.; Turner, A. R.; Cooper, D. L.; Schultz, D. R.; Rakovic, M. J.; Fritsch, W.; Zygelman, B.

2001-05-01

Charge transfer processes due to collisions of ground state S^4+ ions with atomic hydrogen were investigated for energies between 1 meV/u and 10 MeV/u using the quantum-mechanical molecular-orbital close-coupling (MOCC), atomic-orbital close-coupling, classical trajectory Monte Carlo (CTMC), and continuum distorted wave methods. The MOCC calculations utilized ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained with the spin-coupled valence-bond approach. A number of variants of the CTMC approach were explored, including different momentum and radial distributions for the initial state, as well as effective charge and quantum-defect models to determine the corresponding quantum state after capture into final partially-stripped S^3+ excited classical states. Hydrogen target isotope effects were explored and rate coefficients for temperatures between 100 and 10^6 K will be presented

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.

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

1993-01-01

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

Theoretical approach to oxygen atom degradation of silver

NASA Technical Reports Server (NTRS)

Fromhold, Albert T., Jr.; Noh, Seung; Beshears, Ronald; Whitaker, Ann F.; Little, Sally A.

1987-01-01

Based on available Rutherford backscattering spectrometry (RBS), proton induced X-ray emission (PIXE) and ellipsometry data obtained on silver specimens subjected to atomic oxygen attack in low Earth orbit STS flight 41-G, a theory was developed to model the oxygen atom degradation of silver. The diffusion of atomic oxygen in a microscopically nonuniform medium is an essential constituent of the theory. The driving force for diffusion is the macroscopic electrochemical potential gradient developed between the specimen surface exposed to the ambient and the bulk of the silver specimen. The longitudinal electric effect developed parallel to the gradient is modified by space charge of the diffusing charged species. Lateral electric fields and concentration differences also exist due to the nonuniform nature of the medium. The lateral concentration differences are found to be more important than the lateral electric fields in modifying the diffusion rate. The model was evaluated numerically. Qualitative agreement exists between the kinetics predicted by the theory and kinetic data taken in ground-based experiments utilizing a plasma asher.

Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

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

Priyanka,; Dharamvir, Keya; Sharma, Hitesh

2011-12-12

The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding siliconmore » doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.« less

Laser wavelength effect on charge transfer and excitation processes in laser-assisted collisions of Li+ + H

NASA Astrophysics Data System (ADS)

Domínguez-Gutiérrez, F. Javier; Cabrera-Trujillo, R.

2014-05-01

Total, n = 2 , and 3 charge transfer and n = 2 target excitation probabilities for collision of Li+ with ground state atomic hydrogen are calculated numerically, in the impact energy collision range 0.25-5 keV. The total wave function at the end of the dynamics of the collision is obtained by solving the time-dependent Schrödinger equation by means the finite-difference method. We use a pseudo-potential method to model the electronic structure of the Li+ ion. The n = 2 , and 3 charge transfer and n = 2 target excitation probabilities are obtained by projecting the stationary states of Lithium and Hydrogen neutral atoms to the total wave function of the collision, respectively; the stationary states of Li and H are obtained numerically. To assess the validity of our method, our numerical results have been compared with those obtained experimentally and by other theoretical methods found in the literature. We study the laser-assited collision by using a short (3 fs at FWHM) and intense (3.15 ×12 W/cm2) Gaussian laser pulse. We consider a wavelength range between 400 - 1000 nm in steps of 100 nm. Finally, we analyze the laser assisted collision by a qualitatively way with a two level approach. We acknowledge support from grant PAPIIT IN 110-714 and CONACyT (Ph.D. scholarship).

Rayleigh scattering of x-ray and γ-ray by 1s and 2s electrons in ions and neutral atoms

NASA Astrophysics Data System (ADS)

Costescu, A.; Karim, K.; Moldovan, M.; Spanulescu, S.; Stoica, C.

2011-02-01

Using the Coulomb-Green function method and considering the nonrelativistic limit for the two-photon S-matrix element, the right nonrelativistic 2s Rayleigh scattering amplitudes are obtained. Our result takes into account all multipoles, retardation and relativistic kinematics contributions, and the old dipole approximation result of Costescu [1] is retrieved as a limit case. The total photoeffect cross-section which is related to the imaginary part of the Rayleigh forward scattering amplitude through the optical theorem is also obtained. Our Coulombian formulae are used in the more realistic case of elastic scattering of photons by bound 1s and 2s electrons in ions and neutral atoms. Screening effects are considered in the independent particle approximation through the Hartree-Fock method. The effective charge Zeff is obtained by fitting the Hartree-Fock charge distribution by a Coulombian one. Good agreement (within 10%) is found when comparing the numerical predictions given by our nonrelativistic formulae with the full relativistic numerical results of Kissel [2] in the case of elastic scattering of photons by 1s and 2s electrons and Scofield [3] in the case of K-shell and 2s subshell photoionization for neutral atoms with 18 <= Z <= 92 and photon energies ω <= αZm.

The study of the plasmon modes of square atomic clusters based on the eigen-oscillation equation of charge under the free-electron gas model

NASA Astrophysics Data System (ADS)

Xue, Hong-Jie; Wu, Reng-Lai; Hu, Cheng-Xi; Zhang, Ming

2018-04-01

In atomic clusters, plasmon modes are generally gained by the resonant responses for external fields. However, these resonant methods still carry some defects: some plasmon modes may not have been found as that may not have been excited by the external fields. Recently, by employing the extended Hubbard model to describe electron systems of atomic clusters, we have presented the eigen-oscillation equation of charge to study plasmon modes. In this work, based on the free-electron gas model, we further explore the eigen-equation method. Under different external electric fields, some of the plasmon mode spectrums with obvious differences are found, which display the defects of the resonant methods. All the plasmon modes obtained by the resonant methods are predicted by the eigen-equation method. This effectively shows that the eigen-equation method is feasible and reliable in the process of finding plasmon. In addition, various kinds of plasmons are displayed by charge distributions, and the evolution features of plasmon with system parameters are gained by the energy absorption spectrum.

Charge and Exchange

NASA Technical Reports Server (NTRS)

2008-01-01

Even though comets are basically giant dirty snowballs, a few years ago they surprised astronomers by emitting X-radiation. These X-rays are not produced by multi-million degree gas (as is often the case) but rather by a process called 'charge exchange'. In this process, ionized atoms (which have lost one or more electrons) which are carried within the solar wind collide with neutral atoms in the comet's coma. The solar wind ion can collide with and capture an electron from the neutral comet atom, and in doing so some of the energy of the collision is observed in the form of X-rays. This produces a glow of X-rays on the sunward side of the comet's atmosphere. Charge exchange can occur in a variety of astrophysical settings, and cometary charge exchange provides astronomers a means to study this process up close. The image above is a pretty picture of comet 73P/Schwassmann-Wachmann 3 passing by the Ring Nebula. This image was obtained by the ultraviolet and optical telescope (UVOT) on the Swift gamma-ray burst hunter. The UVOT observations help astronomers to study the structure and chemistry of the comet, while Swift's X-ray Telescope (XRT) simultaneously monitors the charge exchange process. Comet 73P/Schwassmann-Wachmann 3 is currently in the process of breaking up, and the UVOT observations show important details of how this breakup is occurring.

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.

Level-energy-dependent mean velocities of excited tungsten atoms sputtered by krypton-ion bombardment

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

Nogami, Keisuke; Sakai, Yasuhiro; Mineta, Shota

2015-11-15

Visible emission spectra were acquired from neutral atoms sputtered by 35–60 keV Kr{sup +} ions from a polycrystalline tungsten surface. Mean velocities of excited tungsten atoms in seven different 6p states were also obtained via the dependence of photon intensities on the distance from the surface. The average velocities parallel to the surface normal varied by factors of 2–4 for atoms in the different 6p energy levels. However, they were almost independent of the incident ion kinetic energy. The 6p-level energy dependence indicated that the velocities of the excited atoms were determined by inelastic processes that involve resonant charge exchange.

Evidence of charge exchange pumping in calcium-xenon system

NASA Technical Reports Server (NTRS)

Chubb, D. L.

1973-01-01

Charge exchange between xenon ions and calcium atoms may produce an inversion between the 5s or 4d and 4p energy levels of the calcium ions. A low power flowing xenon plasma seeded with calcium was utilized to determine if charge exchange or electron collisions populate the 5s and 4d levels Ca(+). Line intensity ratios proportional to the density ratios n5s/n4p and n4d/n4p were measured. From the dependence of these intensity ratios on power input to the xenon plasma it was concluded that charge exchange pumping of the 5s and 4d levels predominates over electron collisional pumping of these levels. Also, by comparing intensity ratios obtained using argon and krypton in place of xenon with those obtained in xenon the same conclusion was made.

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

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

Fang, Li; Xiong, Hui; Kukk, Edwin

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

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.

Electron capture in collisions of S4+ with atomic hydrogen

NASA Astrophysics Data System (ADS)

Stancil, P. C.; Turner, A. R.; Cooper, D. L.; Schultz, D. R.; Rakovic, M. J.; Fritsch, W.; Zygelman, B.

2001-06-01

Charge transfer processes due to collisions of ground state S4+(3s2 1S) ions with atomic hydrogen are investigated for energies between 1 meV u-1 and 10 MeV u-1 using the quantum mechanical molecular-orbital close-coupling (MOCC), atomic-orbital close-coupling, classical trajectory Monte Carlo (CTMC) and continuum distorted wave methods. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained with the spin-coupled valence-bond approach. A number of variants of the CTMC approach were explored, including different momentum and radial distributions for the initial state, as well as effective charge and quantum-defect models to determine the corresponding quantum state after capture into final partially stripped S3+ excited classical states. Hydrogen target isotope effects are explored and rate coefficients for temperatures between 100 and 106 K are also presented.

The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

NASA Astrophysics Data System (ADS)

Tahan, Arezoo; Khojandi, Mahya; Salari, Ali Akbar

2016-01-01

The density functional theory (DFT) and Tomasi's polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G ( d, p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure's azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

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.

Light-induced charge separation across bio-inorganic interface.

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

Dimitrijevic, N. M.; Rajh, T.; De La Garza, L.

Rational design of hybrid biomolecule - nanoparticulate semiconductor conjugates enables coupling of functionality of biomolecules with the capability of semiconductors for solar energy capture, that can have potential application in energy conversion, sensing and catalysis. The particular challenge is to obtain efficient charge separation analogous to the natural photosynthesis process. The synthesis of axially anisotropic TiO{sub 2} nano-objects such as tubes, rods and bricks, as well as spherical and faceted nanoparticles has been developed in our laboratory. Depending on their size and shape, these nanostructures exhibit different domains of crystallinity, surface areas and aspect ratios. Moreover, in order to accommodatemore » for high curvature in nanoscale regime, the surfaces of TiO{sub 2} nano-objects reconstructs resulting in changes in the coordination of surface Ti atoms from octahedral (D{sub 2d}) to square pyramidal structures (C{sub 4v}). The formation of these coordinatively unsaturated Ti atoms, thus depends strongly on the size and shape of nanocrystallites and affects trapping and reactivity of photogenerated charges. We have exploited these coordinatively unsaturated Ti atoms to coupe electron-donating (such as dopamine) and electron-accepting (pyrroloquinoline quinone) conductive linkers that allow wiring of biomolecules and proteins resulting in enhanced charge separation which increases the yield of ensuing chemical transformations.« less

Population inversion calculations using near resonant charge exchange as a pumping mechanism

NASA Technical Reports Server (NTRS)

Chubb, D. L.; Rose, J. R.

1972-01-01

Near resonance charge exchange between ions of a large ionization potential gas such as helium or neon and vapors of metals such as zinc, cadmium, selenium, or tellurium has produced laser action in the metal ion gas. The possibility of obtaining population inversions in near resonant charge exchange systems (Xe-Ca, Xe-Mg, Xe-Sr, Xe-Ba, Ar-Mg, N-Ca) was investigated. The analysis is an initial value problem that utilizes rate equations for the densities of relevant levels of the laser gas (Ca, Ba, Mg, or Sr) and an electron energy equation. Electron excitation rates are calculated using the Bohr-Thomson approximation for the cross section. Approximations to experimental values of the electron ionization cross section and the ion-atom charge exchange cross section are used. Preliminary results have been obtained for the Ca-Xe system and show that it is possible to obtain gains greater than 10 to the 14th power/m with inversion times up to 8x10 to the minus 7th power second. A possible charge exchange laser system using a MPD arc plasma accelerator is also described.

X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

DOE PAGES

Fang, Li; Xiong, Hui; Kukk, Edwin; ...

2017-05-19

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Measurement of the Spatial Distribution of Ultracold Cesium Rydberg Atoms by Time-of-Flight Spectroscopy

NASA Astrophysics Data System (ADS)

Li, Jingkui; Zhang, Linjie; Zhang, Hao; Zhao, Jianming; Jia, Suotang

2015-09-01

We prepare nS (n = 49) cesium Rydberg atoms by two-photon excitation in a standard magnetooptical trap to obtain the spatial distribution of the Rydberg atoms by measuring the time-of-flight (TOF) spectra in the case of a low Rydberg density. We analyze the time evolution of the ultracold nS Rydberg atoms distribution by changing the delay time of the pulsed ionization field, defined as the duration from the moment of switching off the excitation lasers to the time of switching on the ionization field. TOF spectra of Rydberg atoms are observed as a function of the delay time and initial Rydberg atomic density. The corresponding full widths at half maximum (FWHMs) are obtained by fitting the spectra with a Gaussian profile. The FWHM decreases with increasing delay time at a relatively high Rydberg atom density (>5 × 107/cm3) because of the decreasing Coulomb interaction between released charges during their flight to the detector. The temperature of the cold atoms is deduced from the dependence of the TOF spectra on the delay time under the condition of low Rydberg atom density.

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.

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.

Collisional excitation of the highly excited hydrogen atoms in the dipole form of the semiclassical impact parameter and Born approximations

NASA Technical Reports Server (NTRS)

Omidvar, K.

1971-01-01

Expressions for the excitation cross section of the highly excited states of the hydrogenlike atoms by fast charged particles have been derived in the dipole approximation of the semiclassical impact parameter and the Born approximations, making use of a formula for the asymptotic expansion of the oscillator strength of the hydrogenlike atoms given by Menzel. When only the leading term in the asymptotic expansion is retained, the expression for the cross section becomes identical to the expression obtained by the method of the classical collision and correspondence principle given by Percival and Richards. Comparisons are made between the Bethe coefficients obtained here and the Bethe coefficients of the Born approximation for transitions where the Born calculation is available. Satisfactory agreement is obtained only for n yields n + 1 transitions, with n the principal quantum number of the excited state.

Chemical and biochemical thermodynamics: Is it time for a reunification?

PubMed

Iotti, Stefano; Raff, Lionel; Sabatini, Antonio

2017-02-01

The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for Δ r G' 0 and Δ r H' 0 can be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis has reunited the "two separate worlds" of conventional thermodynamics and transformed thermodynamics. In addition, it is also shown that the value of the conditional Gibbs energy of reaction, Δ r G', for a biochemical reaction is the same of the value of Δ r G for any chemical reaction involving pseudoisomers of the biochemical reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme.

PubMed

Asada, Toshio; Ando, Kanta; Sakurai, Koji; Koseki, Shiro; Nagaoka, Masataka

2015-10-28

An efficient approach to evaluate free energy gradients (FEGs) within the quantum mechanical/molecular mechanical (QM/MM) framework has been proposed to clarify reaction processes on the free energy surface (FES) in molecular assemblies. The method is based on response kernel approximations denoted as the charge and the atom dipole response kernel (CDRK) model that include explicitly induced atom dipoles. The CDRK model was able to reproduce polarization effects for both electrostatic interactions between QM and MM regions and internal energies in the QM region obtained by conventional QM/MM methods. In contrast to charge response kernel (CRK) models, CDRK models could be applied to various kinds of molecules, even linear or planer molecules, without using imaginary interaction sites. Use of the CDRK model enabled us to obtain FEGs on QM atoms in significantly reduced computational time. It was also clearly demonstrated that the time development of QM forces of the solvated propylene carbonate radical cation (PC˙(+)) provided reliable results for 1 ns molecular dynamics (MD) simulation, which were quantitatively in good agreement with expensive QM/MM results. Using FEG and nudged elastic band (NEB) methods, we found two optimized reaction paths on the FES for decomposition reactions to generate CO2 molecules from PC˙(+), whose reaction is known as one of the degradation mechanisms in the lithium-ion battery. Two of these reactions proceed through an identical intermediate structure whose molecular dipole moment is larger than that of the reactant to be stabilized in the solvent, which has a high relative dielectric constant. Thus, in order to prevent decomposition reactions, PC˙(+) should be modified to have a smaller dipole moment along two reaction paths.

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

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.

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.

Simultaneous measurement of triboelectrification and triboluminescence of crystalline materials

NASA Astrophysics Data System (ADS)

Collins, Adam L.; Camara, Carlos G.; Van Cleve, Eli; Putterman, Seth J.

2018-01-01

Triboelectrification has been studied for over 2500 years, yet there is still a lack of fundamental understanding as to its origin. Given its utility in areas such as xerography, powder spray painting, and energy harvesting, many devices have been made to investigate triboelectrification at many length-scales, though few seek to additionally make use of triboluminescence: the emission of electromagnetic radiation immediately following a charge separation event. As devices for measuring triboelectrification became smaller and smaller, now measuring down to the atomic scale with atomic force microscope based designs, an appreciation for the collective and multi-scale nature of triboelectrification has perhaps abated. Consider that the energy required to move a unit charge is very large compared to a van der Waals interaction, yet peeling Scotch tape (whose adhesion is derived from van der Waals forces) can provide strong enough energy-focusing to generate X-ray emission. This paper presents a device to press approximately cm-sized materials together in a vacuum, with in situ alignment. Residual surface charge, force, and position and X-ray, visible light, and RF emission are measured for single crystal samples. Charge is therefore tracked throughout the charging and discharging processes, resulting in a more complete picture of triboelectrification, with controllable and measurable environmental influence. Macroscale charging is directly measured, whilst triboluminescence, originating in atomic-scale processes, probes the microscale. The apparatus was built with the goal of obtaining an ab initio-level explanation of triboelectrification for well-defined materials, at the micro- and macro-scale, which has eluded scientists for millennia.

Thomson scattering in the average-atom approximation.

PubMed

Johnson, W R; Nilsen, J; Cheng, K T

2012-09-01

The average-atom model is applied to study Thomson scattering of x-rays from warm dense matter with emphasis on scattering by bound electrons. Parameters needed to evaluate the dynamic structure function (chemical potential, average ionic charge, free electron density, bound and continuum wave functions, and occupation numbers) are obtained from the average-atom model. The resulting analysis provides a relatively simple diagnostic for use in connection with x-ray scattering measurements. Applications are given to dense hydrogen, beryllium, aluminum, and titanium plasmas. In the case of titanium, bound states are predicted to modify the spectrum significantly.

Elimination of Spurious Fractional Charges in Dissociating Molecules by Correcting the Shape of Approximate Kohn-Sham Potentials.

PubMed

Komsa, Darya N; Staroverov, Viktor N

2016-11-08

Standard density-functional approximations often incorrectly predict that heteronuclear diatomic molecules dissociate into fractionally charged atoms. We demonstrate that these spurious charges can be eliminated by adapting the shape-correction method for Kohn-Sham potentials that was originally introduced to improve Rydberg excitation energies [ Phys. Rev. Lett. 2012 , 108 , 253005 ]. Specifically, we show that if a suitably determined fraction of electron charge is added to or removed from a frontier Kohn-Sham orbital level, the approximate Kohn-Sham potential of a stretched molecule self-corrects by developing a semblance of step structure; if this potential is used to obtain the electron density of the neutral molecule, charge delocalization is blocked and spurious fractional charges disappear beyond a certain internuclear distance.

Quantitative nanoscale electrostatics of viruses.

PubMed

Hernando-Pérez, M; Cartagena-Rivera, A X; Lošdorfer Božič, A; Carrillo, P J P; San Martín, C; Mateu, M G; Raman, A; Podgornik, R; de Pablo, P J

2015-11-07

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.

Charge transfer in single and multiple scattering events at metal surfaces: a wavepacket study of the Na(+)/Cu(100) system.

PubMed

Sindona, A; Pisarra, M; Maletta, S; Riccardi, P; Falcone, G

2010-12-01

Resonant neutralization of hyperthermal energy Na(+) ions impinging on Cu(100) surfaces is studied, focusing on two specific collision events: one in which the projectile is reflected off the surface, the other in which the incident atom penetrates the outer surface layers initiating a series of scattering processes, within the target, and coming out together with a single surface atom. A semi-empirical model potential is adopted that embeds: (i) the electronic structure of the sample, (ii) the central field of the projectile, and (iii) the contribution of the Cu atom ejected in multiple scattering events. The evolution of the ionization orbital of the scattered atom is simulated, backwards in time, using a wavepacket propagation algorithm. The output of the approach is the neutralization probability, obtained by projecting the time-reversed valence wavefunction of the projectile onto the initially filled conduction band states. The results are in agreement with available data from the literature (Keller et al 1995 Phys. Rev. Lett. 75 1654) indicating that the motion of surface atoms, exiting the targets with kinetic energies of the order of a few electronvolts, plays a significant role in the final charge state of projectiles.

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.

Spectroscopy of muonic atoms and the proton radius puzzle

NASA Astrophysics Data System (ADS)

Antognini, Aldo

2017-09-01

We have measured several 2 S -2 P transitions in muonic hydrogen (μp), muonic deuterium (μd) and muonic helium ions (μ3He, μ4He). From muonic hydrogen we extracted a proton charge radius 20 times more precise than obtained from electron-proton scattering and hydrogen high-precision laser spectroscopy but at a variance of 7 σ from these values. This discrepancy is nowadays referred to as the proton radius puzzle. New insight has been recently provided by the first determination of the deuteron charge radius from laser spectroscopy of μd. The status of the proton charge radius puzzle including the new insights obtained by μd spectroscopy will be discussed. Work supported by the Swiss National Science Foundation SNF-200021-165854 and the ERC CoG. #725039.

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.

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.

Charge Exchange X-Ray Emission due to Highly Charged Ion Collisions with H, He, and H2: Line Ratios for Heliospheric and Interstellar Applications

NASA Astrophysics Data System (ADS)

Cumbee, R. S.; Mullen, P. D.; Lyons, D.; Shelton, R. L.; Fogle, M.; Schultz, D. R.; Stancil, P. C.

2018-01-01

The fundamental collisional process of charge exchange (CX) has been established as a primary source of X-ray emission from the heliosphere, planetary exospheres, and supernova remnants. In this process, X-ray emission results from the capture of an electron by a highly charged ion from a neutral atom or molecule, to form a highly excited, high-charge state ion. As the captured electron cascades down to the lowest energy level, photons are emitted, including X-rays. To provide reliable CX-induced X-ray spectral models to realistically simulate these environments, line ratios and spectra are computed using theoretical CX cross sections obtained with the multi-channel Landau-Zener, atomic-orbital close-coupling, molecular-orbital close-coupling, and classical trajectory Monte Carlo methods for various collisional velocities relevant to astrophysics. X-ray spectra were computed for collisions of bare and H-like C to Al ions with H, He, and H2 with results compared to available experimental data. Using these line ratios, XSPEC models of CX emission in the northeast rim of the Cygnus Loop supernova remnant and the heliosphere are shown as examples with ion velocity dependence.

Charge injection in thin dielectric layers by atomic force microscopy: influence of geometry and material work function of the AFM tip on the injection process

NASA Astrophysics Data System (ADS)

Villeneuve-Faure, C.; Makasheva, K.; Boudou, L.; Teyssedre, G.

2016-06-01

Charge injection and retention in thin dielectric layers remain critical issues for the reliability of many electronic devices because of their association with a large number of failure mechanisms. To overcome this drawback, a deep understanding of the mechanisms leading to charge injection close to the injection area is needed. Even though the charge injection is extensively studied and reported in the literature to characterize the charge storage capability of dielectric materials, questions about charge injection mechanisms when using atomic force microscopy (AFM) remain open. In this paper, a thorough study of charge injection by using AFM in thin plasma-processed amorphous silicon oxynitride layers with properties close to that of thermal silica layers is presented. The study considers the impact of applied voltage polarity, work function of the AFM tip coating and tip curvature radius. A simple theoretical model was developed and used to analyze the obtained experimental results. The electric field distribution is computed as a function of tip geometry. The obtained experimental results highlight that after injection in the dielectric layer the charge lateral spreading is mainly controlled by the radial electric field component independently of the carrier polarity. The injected charge density is influenced by the nature of electrode metal coating (work function) and its geometry (tip curvature radius). The electron injection is mainly ruled by the Schottky injection barrier through the field electron emission mechanism enhanced by thermionic electron emission. The hole injection mechanism seems to differ from the electron one depending on the work function of the metal coating. Based on the performed analysis, it is suggested that for hole injection by AFM, pinning of the metal Fermi level with the metal-induced gap states in the studied silicon oxynitride layers starts playing a role in the injection mechanisms.

Predicting p Ka values from EEM atomic charges

PubMed Central

2013-01-01

The acid dissociation constant p Ka is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p Ka prediction. We have evaluated the p Ka prediction capabilities of QSPR models based on empirical atomic charges calculated by the Electronegativity Equalization Method (EEM). Specifically, we collected 18 EEM parameter sets created for 8 different quantum mechanical (QM) charge calculation schemes. Afterwards, we prepared a training set of 74 substituted phenols. Additionally, for each molecule we generated its dissociated form by removing the phenolic hydrogen. For all the molecules in the training set, we then calculated EEM charges using the 18 parameter sets, and the QM charges using the 8 above mentioned charge calculation schemes. For each type of QM and EEM charges, we created one QSPR model employing charges from the non-dissociated molecules (three descriptor QSPR models), and one QSPR model based on charges from both dissociated and non-dissociated molecules (QSPR models with five descriptors). Afterwards, we calculated the quality criteria and evaluated all the QSPR models obtained. We found that QSPR models employing the EEM charges proved as a good approach for the prediction of p Ka (63% of these models had R2 > 0.9, while the best had R2 = 0.924). As expected, QM QSPR models provided more accurate p Ka predictions than the EEM QSPR models but the differences were not significant. Furthermore, a big advantage of the EEM QSPR models is that their descriptors (i.e., EEM atomic charges) can be calculated markedly faster than the QM charge descriptors. Moreover, we found that the EEM QSPR models are not so strongly influenced by the selection of the charge calculation approach as the QM QSPR models. The robustness of the EEM QSPR models was subsequently confirmed by cross-validation. The applicability of EEM QSPR models for other chemical classes was illustrated by a case study focused on carboxylic acids. In summary, EEM QSPR models constitute a fast and accurate p Ka prediction approach that can be used in virtual screening. PMID:23574978

Microscopic origin of the charge transfer in single crystals based on thiophene derivatives: A combined NEXAFS and density functional theory approach

NASA Astrophysics Data System (ADS)

Chernenkaya, A.; Morherr, A.; Backes, S.; Popp, W.; Witt, S.; Kozina, X.; Nepijko, S. A.; Bolte, M.; Medjanik, K.; Öhrwall, G.; Krellner, C.; Baumgarten, M.; Elmers, H. J.; Schönhense, G.; Jeschke, H. O.; Valentí, R.

2016-07-01

We have investigated the charge transfer mechanism in single crystals of DTBDT-TCNQ and DTBDT-F4TCNQ (where DTBDT is dithieno[2,3-d;2',3'-d'] benzo[1,2-b;4,5-b']dithiophene) using a combination of near-edge X-ray absorption spectroscopy (NEXAFS) and density functional theory calculations (DFT) including final state effects beyond the sudden state approximation. In particular, we find that a description that considers the partial screening of the electron-hole Coulomb correlation on a static level as well as the rearrangement of electronic density shows excellent agreement with experiment and allows to uncover the details of the charge transfer mechanism in DTBDT-TCNQ and DTBDT-F4 TCNQ, as well as a reinterpretation of previous NEXAFS data on pure TCNQ. Finally, we further show that almost the same quality of agreement between theoretical results and experiment is obtained by the much faster Z+1/2 approximation, where the core hole effects are simulated by replacing N or F with atomic number Z with the neighboring atom with atomic number Z+1/2.

Direct Probing of Polarization Charge at Nanoscale Level

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

Kwon, Owoong; Seol, Daehee; Lee, Dongkyu

Ferroelectric materials possess spontaneous polarization that can be used for multiple applications. Owing to a long-term development of reducing the sizes of devices, the preparation of ferroelectric materials and devices is entering the nanometer-scale regime. In order to evaluate the ferroelectricity, there is a need to investigate the polarization charge at the nanoscale. Nonetheless, it is generally accepted that the detection of polarization charges using a conventional conductive atomic force microscopy (CAFM) without a top electrode is not feasible because the nanometer-scale radius of an atomic force microscopy (AFM) tip yields a very low signal-to-noise ratio. But, the detection ismore » unrelated to the radius of an AFM tip and, in fact, a matter of the switched area. In this work, the direct probing of the polarization charge at the nanoscale is demonstrated using the positive-up-negative-down method based on the conventional CAFM approach without additional corrections or circuits to reduce the parasitic capacitance. The polarization charge densities of 73.7 and 119.0 µC cm -2 are successfully probed in ferroelectric nanocapacitors and thin films, respectively. The results we obtained show the feasibility of the evaluation of polarization charge at the nanoscale and provide a new guideline for evaluating the ferroelectricity at the nanoscale.« less

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.

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.

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.

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Nanoscale Charge-Balancing Mechanism in Alkali-Substituted Calcium-Silicate-Hydrate Gels.

PubMed

Özçelik, V Ongun; White, Claire E

2016-12-15

Alkali-activated materials and related alternative cementitious systems are sustainable technologies that have the potential to substantially lower the CO 2 emissions associated with the construction industry. However, these systems have augmented chemical compositions as compared to ordinary Portland cement (OPC), which may impact the evolution of the hydrate phases. In particular, calcium-silicate-hydrate (C-S-H) gel, the main hydrate phase in OPC, is likely to be altered at the atomic scale due to changes in the bulk chemical composition, specifically via the addition of alkalis (i.e., Na or K) and aluminum. Here, via density functional theory calculations, we reveal the presence of a charge balancing mechanism at the molecular level in C-S-H gel (as modeled using crystalline 14 Å tobermorite) when alkalis and aluminum atoms are introduced into the structure. 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 substitutional and charge balancing effects on the structures is assessed by analyzing the formation energies, local bonding environments, diffusion barriers and mechanical properties. The results of this computational study provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental atomic level mechanisms that play a crucial role in these complex disordered materials.

Point-to-plane and plane-to-plane electrostatic charge injection atomization for insulating liquids

NASA Astrophysics Data System (ADS)

Malkawi, Ghazi

An electrostatic charge injection atomizer was fabricated and used to introduce and study the electrostatic charge injection atomization methods for highly viscous vegetable oils and high conductivity low viscosity aviation fuel, JP8. The total, spray and leakage currents and spray breakup characteristics for these liquids were investigated and compared with Diesel fuel data. Jet breakup and spray atomization mechanism showed differences for vegetable oils and lower viscosity hydrocarbon fuels. For vegetable oils, a bending/spinning instability phenomenon was observed similar to the phenomenon found in liquid jets of high viscosity polymer solutions. The spray tip lengths and cone angles were presented qualitatively and quantitatively and correlated with the appropriate empirical formulas. The different stages of the breakup mechanisms for such oils, as a function of specific charges and flow rates, were discussed. In order to make this method of atomization more suitable for practical use in high flow rate applications, a blunt face electrode (plane-to-plane) was used as the charge emitter in place of a single pointed electrode (point-to-plane). This allowed the use of a multi-orifice emitter that maintained a specific charge with the flow rate increase which could not be achieved with the needle electrode. The effect of the nozzle geometry, liquid physical properties and applied bulk flow on the spray charge, total charge, maximum critical spray specific charge and electrical efficiency compared with the needle point-to-plane atomizer results was presented. Our investigation revealed that the electrical efficiency of the atomizer is dominated by the charge forced convection rate rather than charge transport by ion motilities and liquid motion by the electric field. As a result of the electric coulomb forces between the electrified jets, the multi-orifice atomizer provided a unique means of dispersing the fuel in a hollow cone with wide angles making the new method suitable for variety of combustion applications.

Electron capture in collisions of N^+ with H and H^+ with N

NASA Astrophysics Data System (ADS)

Lin, C. Y.; Stancil, P. C.; Gu, J. P.; Buenker, R. J.; Kimura, M.

2004-05-01

Charge transfer processes due to collisions of N^+ with atomic hydrogen and H^+ with atomic nitrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potential curves and nonadiabatic radial and rotational coupling matrix elements obtained with the multireference single- and double-excitation configuration interaction approach. Total and state-selective cross sections for the energy range 0.1-500 eV/u will be presented and compared with existing experimental and theoretical data.

Total photoionization cross sections of atomic oxygen from threshold to 44.3 A

NASA Technical Reports Server (NTRS)

Angel, G. C.; Samson, James A. R.

1988-01-01

Synchrotron radiation was used to obtain the relative photoionization cross section of atomic oxygen for the production of singly charged ions over the 44.3-910.5-A wavelength range. Measurement of the contribution of multiple ionization to the cross sections has made possible the determination of total photoionization cross sections below 250 A. The series of autoionizing resonances leading to the 4P state of the oxygen ion has been observed using an ionization-type experimental procedure for the first time.

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.

Tunable charge donation and spin polarization of metal adsorbates on graphene using an applied electric field

NASA Astrophysics Data System (ADS)

Parq, Jae-Hyeon; Yu, Jaejun; Kwon, Young-Kyun; Kim, Gunn

2010-11-01

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 the microscopic physics of the metal-atom-induced 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.

Synthesis, crystal growth, characterization and theoretical studies of 4-aminobenzophenonium picrate

NASA Astrophysics Data System (ADS)

Aditya Prasad, A.; Muthu, K.; Rajasekar, M.; Meenatchi, V.; Meenakshisundaram, S. P.

2015-01-01

Single crystals of 4-aminobenzophenonium picrate (4ABPP) were grown by slow evaporation of a mixed solvent system methanol-acetone (1:1,v/v) containing equimolar quantities of picric acid and 4-aminobenzophenone. The proton and carbon signals are confirmed by nuclear magnetic resonance spectroscopy. The various functional groups present in the molecule are identified by FT-IR analysis. Optimized geometry, first-order molecular hyperpolarizability (β), polarizability (α), bond length, bond angles and excited state energy from theoretical UV were derived by Hartree-Fock calculations. The complete assignment of the vibrational modes for 4-aminobenzophenonium picrate was performed by the scaled quantum mechanics force field (SQMFF) methodology using potential energy distribution. Natural bond orbital (NBO) calculations were employed to study the stabilities arising from charge delocalization and intermolecular interactions of 4ABPP. The atomic charge distributions of the various atoms present in 4ABPP are obtained by Mulliken charge population analysis. The as-grown crystal is further characterized by thermal and optical absorbance studies.

Unexpectedly large charge radii of neutron-rich calcium isotopes

DOE PAGES

Garcia Ruiz, R. F.; Bissell, M. L.; Blaum, K.; ...

2016-02-08

Here, despite being a complex many-body system, the atomic nucleus exhibits simple structures for certain ‘magic’ numbers of protons and neutrons. The calcium chain in particular is both unique and puzzling: evidence of doubly magic features are known in 40,48Ca, and recently suggested in two radioactive isotopes, 52,54Ca. Although many properties of experimentally known calcium isotopes have been successfully described by nuclear theory, it is still a challenge to predict the evolution of their charge radii. Here we present the first measurements of the charge radii of 49,51,52Ca, obtained from laser spectroscopy experiments at ISOLDE, CERN. The experimental results aremore » complemented by state-of-the-art theoretical calculations. The large and unexpected increase of the size of the neutron-rich calcium isotopes beyond N = 28 challenges the doubly magic nature of 52Ca and opens new intriguing questions on the evolution of nuclear sizes away from stability, which are of importance for our understanding of neutron-rich atomic nuclei.« less

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

2010-12-01

Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

Possible impact of multi-electron loss events on the average beam charge state in an HIF target chamber and a neutral beam approach

NASA Astrophysics Data System (ADS)

Grisham, L. R.

2001-05-01

Experiments were carried out during the early 1980s to assess the obtainable atomic neutralization of energetic beams of negative ions ranging from lithium to silicon. The experiments found (Grisham et al. Rev. Sci. Instrum. 53 (1982) 281; Princeton Plasma Physics Laboratory Report PPPL-1857, 1981) that, for higher atomic number elements than lithium, it appeared that a substantial fraction of the time more than one electron was being lost in a single collision. This result was inferred from the existence of more than one ionization state in the product beam for even the thinnest line densities at which any electron removal took place. Because of accelerator limitations, these experiments were limited to maximum energies of 7 MeV. However, based upon these results, it is possible that multi-electron loss events may also play a significant role in determining the average ion charge state of the much higher Z and more energetic beams traversing the medium in an heavy ion fusion chamber. This could result in the beam charge state being considerably higher than previously anticipated, and might require designers to consider harder vacuum ballistic focusing approaches, or the development of additional space charge neutralization schemes. This paper discusses the measurements that gave rise for these concerns, as well as a description of further measurements that are proposed to be carried out for atomic numbers and energies per amu which would be closer to those required for heavy ion fusion drivers. With a very low current beam of a massive, but low charge state energetic ion, the charge state distribution emerging from a target gas cell could be measured as a function of line density and medium composition. Varying the line density would allow one to simulate the charge state evolution of the beam as a function of distance into the target chamber. This paper also briefly discusses a possible alternative driver approach using photodetachment-neutralized atomic beams, which could reduce plasma complications far from the target, but which would impose more stringent limitations upon chamber pressure and repetition rate.

Global and Local Partitioning of the Charge Transferred in the Parr-Pearson Model.

PubMed

Orozco-Valencia, Angel Ulises; Gázquez, José L; Vela, Alberto

2017-05-25

Through a simple proposal, the charge transfer obtained from the cornerstone theory of Parr and Pearson is partitioned, for each reactant, in two channels: an electrophilic, through which the species accepts electrons, and the other, a nucleophilic, where the species donates electrons. It is shown that this global model allows us to determine unambiguously the charge-transfer mechanism prevailing in a given reaction. The partitioning is extended to include local effects through the Fukui functions of the reactants. This local model is applied to several emblematic reactions in organic and inorganic chemistry, and we show that besides improving the correlations obtained with the global model it provides valuable information concerning the atoms in the reactants playing the most important roles in the reaction and thus improving our understanding of the reaction under study.

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.

Kinetic equations for cylindrically symmetric plasmas including atomic coherence and Coulomb potential effects

NASA Astrophysics Data System (ADS)

Csanak, G.; Fontes, C. J.; Kilcrease, D. P.; Hakel, P.; Inal, M. K.

2017-05-01

The rate equations used to model plasma kinetics and spectroscopy are typically obtained from intuitive considerations. A few years ago, the authors (Csanak et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 215701) have shown that the population-alignment collisional-radiative (CR) model and the magnetic sublevel to magnetic sublevel rate-equation scheme can be obtained from the Fano-Ben-Reuven quantum impact approximation (QIA). Here we provide a formal derivation of the rate-equation schemes for modeling hydrogenic plasmas and highly charged ionic plasmas with cylindrical symmetry using the QIA under certain approximations. In the case of hydrogenic plasmas the ‘accidental degeneracy’ (if present) leads to some coherences among the excited states of the atom (or ion) that have to be taken into account when constructing the rate equations. In the case of highly charged plasmas the Coulomb potential can be taken into account (as suggested originally by Baranger) in defining the ‘bath particles’, which leads to a derivation of the kinetic equations where no singularity occurs. For the case of spherically symmetric plasmas, this method also provides a derivation of the standard CR equations that have been implemented in many codes to successfully model the kinetics and spectra of highly charged ions.

Nanoscale charge transfer and diffusion at the MoS2/SiO2 interface by atomic force microscopy: contact injection versus triboelectrification.

PubMed

Xu, Rui; Ye, Shili; Xu, Kunqi; Lei, Le; Hussain, Sabir; Zheng, Zhiyue; Pang, Fei; Xing, Shuya; Liu, Xinmeng; Ji, Wei; Cheng, Zhihai

2018-08-31

Understanding the process of charge generation, transfer, and diffusion between two-dimensional (2D) materials and their supporting substrates is very important for potential applications of 2D materials. Compared with the systematic studies of triboelectric charging in a bulk sample, a fundamental understanding of the triboelectrification of the 2D material/insulator system is rather limited. Here, the charge transfer and diffusion of both the SiO 2 surface and MoS 2 /SiO 2 interface through contact electrification and frictional electrification are investigated systematically in situ by scanning Kelvin probe microscopy and dual-harmonic electrostatic force microscopy. Different from the simple static charge transfer between SiO 2 and the PtSi alloy atomic force microscope (AFM) tip, the charge transfer between the tip and the MoS 2 /SiO 2 system is complicated. Triboelectric charges, generated by contact or frictional electrification with the AFM tip, are trapped at the MoS 2 /SiO 2 interface and act as floating gates. The local charge discharge processes can be obtained by monitoring the surface potential. The charge decay time (τ) of the MoS 2 /SiO 2 interface is one (or two) orders of magnitude larger than the decay time τ of the SiO 2 surface. This work facilitates an understanding of the triboelectric and de-electrification of the interface between 2D materials and substrates. In addition to the charge transfer and diffusion, we demonstrate the nanopatterns of surface and interfacial charges, which have great potential for the application of self-assembly of charged nanostructures.

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…

Magnetic properties of the synthetically charged neutral bosons

NASA Astrophysics Data System (ADS)

Hassan, Ahmed S.; Abbas, Abbas H.; El-Sherbini, Tharwat M.; Seif, Walaa M.

2018-07-01

In this paper, we conclude that BEC of synthetically charged bosons is possible and leads to several new and interesting phenomena. Thermal and magnetic properties of the system are investigated. The temperature dependence of the magnetic parameters, including the magnetization, magnetic susceptibility and the heat capacity at constant synthetic magnetic field are calculated. These properties are investigated for finite atoms number and synthetic magnetic field strength. We show that those properties, in particular Bose- Einstein transition temperature, depends upon the strength of the synthetic magnetic field. A diffuse condensation of the synthetically charged bosons appears for changing the synthetic field. The obtained results provide important magnetic properties.

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 ...

A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

NASA Astrophysics Data System (ADS)

Danel, J.-F.; Kazandjian, L.

2018-06-01

It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

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

Torii, Hajime, E-mail: torii.hajime@shizuoka.ac.jp

The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper showsmore » how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.« less

Testing the Concept of Hypervalency: Charge Density Analysis of K[subscript 2]SO[subscript 4

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

Schmøkel, Mette S.; Cenedese, Simone; Overgaard, Jacob

2012-10-25

One of the most basic concepts in chemical bonding theory is the octet rule, which was introduced by Lewis in 1916, but later challenged by Pauling to explain the bonding of third-row elements. In the third row, the central atom was assumed to exceed the octet by employing d orbitals in double bonding leading to hypervalency. Ever since, polyoxoanions such as SO{sub 4}{sup 2-}, PO{sub 4}{sup 3-}, and ClO{sub 4}{sup -} have been paradigmatic examples for the concept of hypervalency in which the double bonds resonate among the oxygen atoms. Here, we examine S-O bonding by investigating the charge densitymore » of the sulfate group, SO{sub 4}{sup 2-}, within a crystalline environment based both on experimental and theoretical methods. K{sub 2}SO{sup 4} is a high symmetry inorganic solid, where the crystals are strongly affected by extinction effects. Therefore, high quality, very low temperature single crystal X-ray diffraction data were collected using a small crystal (30 {micro}m) and a high-energy (30 keV) synchrotron beam. The experimental charge density was determined by multipole modeling, whereas a theoretical density was obtained from periodic ab initio DFT calculations. The chemical bonding was jointly analyzed within the framework of the Quantum Theory of Atoms In Molecules only using quantities derived from an experimental observable (the charge density). The combined evidence suggests a bonding situation where the S-O interactions can be characterized as highly polarized, covalent bonds, with the 'single bond' description significantly prevailing over the 'double bond' picture. Thus, the study rules out the hypervalent description of the sulfur atom in the sulfate group.« 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.

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

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.

A nebula of gases from Io surrounding Jupiter.

PubMed

Krimigis, Stamatios M; Mitchell, Donald G; Hamilton, Douglas C; Dandouras, Jannis; Armstrong, Thomas P; Bolton, Scott J; Cheng, Andrew F; Gloeckler, George; Hsieh, K C; Keath, Edwin P; Krupp, Norbert; Lagg, Andreas; Lanzerotti, Louis J; Livi, Stefano; Mauk, Barry H; McEntire, Richard W; Roelof, Edmond C; Wilken, Berend; Williams, Donald J

2002-02-28

Several planetary missions have reported the presence of substantial numbers of energetic ions and electrons surrounding Jupiter; relativistic electrons are observable up to several astronomical units (au) from the planet. A population of energetic (>30[?]keV) neutral particles also has been reported, but the instrumentation was not able to determine the mass or charge state of the particles, which were subsequently labelled energetic neutral atoms. Although images showing the presence of the trace element sodium were obtained, the source and identity of the neutral atoms---and their overall significance relative to the loss of charged particles from Jupiter's magnetosphere---were unknown. Here we report the discovery by the Cassini spacecraft of a fast (>103[?]km[?]s-1) and hot magnetospheric neutral wind extending more than 0.5[?]au from Jupiter, and the presence of energetic neutral atoms (both hot and cold) that have been accelerated by the electric field in the solar wind. We suggest that these atoms originate in volcanic gases from Io, undergo significant evolution through various electromagnetic interactions, escape Jupiter's magnetosphere and then populate the environment around the planet. Thus a 'nebula' is created that extends outwards over hundreds of jovian radii.

Long-range interactions between metastable rare gases atoms

NASA Astrophysics Data System (ADS)

Vrinceanu, D.; Marinescu, M.; Flannery, M. R.

1998-10-01

Knowledge of the long-range interaction between atoms and molecules is of fundamental importance for low-energy and low-temperature collisions. The electronic interaction between the charge distributions of two metastable rare gases atoms can be expanded in inverse powers of R, the internuclear distance. The coefficients C_6, C_8, and C_10 of, respectively, the R-6, R-8, and R-10 terms are calculated by integrating the products of the dynamic electric polarizabilities of the individual atoms at imaginary frequencies, which are in turn obtained by solving a system of coupled inhomogeneous differential equations. The triplet state spectrum of the rare gases atoms is described by precise l-dependent one-electron model potentials. Numerical results for the C_6, C_8, and C_10 dispersion coefficients for homonuclear and heteronuclear metastable rare gases diatoms are presented.

Long-range interactions between metastable rare gases atoms

NASA Astrophysics Data System (ADS)

Vrinceanu, D.; Marinescu, M.; Flannery, M. R.

1998-05-01

Knowledge of the long-range interaction between atoms and molecules is of fundamental importance for low-energy and low-temperature collisions. The electronic interaction between the charge distributions of two metastable rare gases atoms can be expanded in inverse powers of R, the internuclear distance. The coefficients C_6, C_8, and C_10 of, respectively, the R-6, R-8, and R-10 terms are calculated by integrating the products of the dynamic electric polarizabilities of the individual atoms at imaginary frequencies, which are in turn obtained by solving a system of coupled inhomogeneous differential equations. The triplet state spectrum of the rare gases atoms is described by precise l-dependent one-electron model potentials. Numerical results for the C_6, C_8, and C_10 dispersion coefficients for homonuclear and heteronuclear metastable rare gases diatoms are presented.

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.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

Spontaneous magnetization and anomalous Hall effect in an emergent Dice lattice

PubMed Central

Dutta, Omjyoti; Przysiężna, Anna; Zakrzewski, Jakub

2015-01-01

Ultracold atoms in optical lattices serve as a tool to model different physical phenomena appearing originally in condensed matter. To study magnetic phenomena one needs to engineer synthetic fields as atoms are neutral. Appropriately shaped optical potentials force atoms to mimic charged particles moving in a given field. We present the realization of artificial gauge fields for the observation of anomalous Hall effect. Two species of attractively interacting ultracold fermions are considered to be trapped in a shaken two dimensional triangular lattice. A combination of interaction induced tunneling and shaking can result in an emergent Dice lattice. In such a lattice the staggered synthetic magnetic flux appears and it can be controlled with external parameters. The obtained synthetic fields are non-Abelian. Depending on the tuning of the staggered flux we can obtain either anomalous Hall effect or its quantized version. Our results are reminiscent of Anomalous Hall conductivity in spin-orbit coupled ferromagnets. PMID:26057635

Vecksler-Macmillan phase stability for neutral atoms accelerated by a laser beam

NASA Astrophysics Data System (ADS)

Mel'nikov, I. V.; Haus, J. W.; Kazansky, P. G.

2003-05-01

We use a Fokker-Planck equation to study the phenomenon of accelerating a neutral atom bunch by a chirped optical beam. This method enables us to obtain a semi-analytical solution to the problem in which a wide range of parameters can be studied. In addition it provides a simple physical interpretation where the problem is reduced to an analogous problem of charged particles accelerators, that is, the Vecksler-Macmillan principle of phase stability. A possible experimental scenario is suggested, which uses a photonic crystal fiber as the guiding medium.

Evidence for strong Breit interaction in dielectronic recombination of highly charged heavy ions.

PubMed

Nakamura, Nobuyuki; Kavanagh, Anthony P; Watanabe, Hirofumi; Sakaue, Hiroyuki A; Li, Yueming; Kato, Daiji; Currell, Fred J; Ohtani, Shunsuke

2008-02-22

Resonant strengths have been measured for dielectronic recombination of Li-like iodine, holmium, and bismuth using an electron beam ion trap. By observing the atomic number dependence of the state-resolved resonant strength, clear experimental evidence has been obtained that the importance of the generalized Breit interaction (GBI) effect on dielectronic recombination increases as the atomic number increases. In particular, it has been shown that the GBI effect is exceptionally strong for the recombination through the resonant state [1s2s(2)2p(1/2)](1).

The Definition Study for Implementation of the IMAP Mission

NASA Technical Reports Server (NTRS)

Frank, L. A.

1997-01-01

The Small Explorer Mission in intended to provide the first global visualization of Earth's inner magnetosphere. IMAP promises to greatly advance our knowledge of the global distributions and dynamics of near-Earth radiation environment by obtaining first simultaneous images of the plasmasphere at extreme ultraviolet wavelengths, of the extraterrestrial ring current and the earthward portions of the plasma sheet as seen in their emissions of neutral atoms from charge exchange of plasma hot ions with geocoronal hydrogen atoms, and of the aurora in its far-ultraviolet emissions.

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.

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.

Single charge exchange between hydrogen-like projectiles and hydrogen atom: the post version of the BDW-4B approximation

NASA Astrophysics Data System (ADS)

Azizan, Sh; Shojaei, F.; Fathi, R.

2016-04-01

The post version of the four-body Born distorted wave method (BDW-4B) is applied to calculate the total cross section for single electron exchange in the collision of hydrogen-like projectiles with hydrogen atom. The post form of transition amplitude is obtained in terms of two-dimensional real integrals which can be computed numerically. This second-order theory which satisfies the correct boundary conditions is used for the collision of {{H}}, {{H}}{{{e}}}+, {{L}}{{{i}}}2+, {{{B}}}4+, {{{C}}}5+ with hydrogen atoms at intermediate and high impact energies. The validity of our results is assessed in comparison with available experimental data and other theories.

XUV and x-ray elastic scattering of attosecond electromagnetic pulses on atoms

NASA Astrophysics Data System (ADS)

Rosmej, F. B.; Astapenko, V. A.; Lisitsa, V. S.

2017-12-01

Elastic scattering of electromagnetic pulses on atoms in XUV and soft x-ray ranges is considered for ultra-short pulses. The inclusion of the retardation term, non-dipole interaction and an efficient scattering tensor approximation allowed studying the scattering probability in dependence of the pulse duration for different carrier frequencies. Numerical calculations carried out for Mg, Al and Fe atoms demonstrate that the scattering probability is a highly nonlinear function of the pulse duration and has extrema for pulse carrier frequencies in the vicinity of the resonance-like features of the polarization charge spectrum. Closed expressions for the non-dipole correction and the angular dependence of the scattered radiation are obtained.

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.

Electron capture in collisions of N+ with H and H+ with N

NASA Astrophysics Data System (ADS)

Lin, C. Y.; Stancil, P. C.; Gu, J. P.; Buenker, R. J.; Kimura, M.

2005-06-01

Charge-transfer processes due to collisions of N+ with atomic hydrogen and H+ with atomic nitrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial and rotational couplings obtained with the multireference single- and double-excitation configuration interaction approach. Total and state-selective cross sections for the energy range 0.1meV/u-1keV/u are presented and compared with existing experimental and theoretical data. A large number of low-energy resonances are obtained for exoergic channels and near thresholds of endoergic channels. Rate coefficients are also obtained and comparison to previous calculations suggests nonadiabatic effects dominate for temperatures greater than 20 000 K, but that the spin-orbit interaction plays a major role for lower temperatures.

Last results of DIRAC experiment on study hadronic hydrogen-like atoms at PS CERN

NASA Astrophysics Data System (ADS)

Afanasyev, Leonid

2016-04-01

Results on study the hydrogen-like atoms consisting of charged pions and Kaons are presented. The first measurement of K+ π and Kπ+ atoms lifetime was fulfilled basing on identification of 178 ± 49 Kπ pairs from the atom breakup. The measured lifetime is τ = (2.5-1.8+3.0) fs. This value is dictated by properties of the strong πK-interaction at low energy, namely S-wave πK scattering length. The first experimental value of the isospin-odd combination of S-wave πK scattering length was obtained | a0- | =1/3 |a/2 -a3/2 | = (0.11-0.04+0.09) Mπ-1 (ai for isospin I). A dedicated experiment with π+ π atoms allows further study of these already observed atoms. The preliminary results on observation of the long-lived (metastable) states of π+ π atoms are presented. The observation of long-lived states opens the possibility to measure the energy difference between ns and np states - the Lamb shift.

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

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

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

Isomeric organic semiconductors containing fused-thiophene cores: molecular packing and charge transport.

PubMed

Dang, Dongfeng; Zhou, Pei; Wu, Yong; Xu, Yanzi; Zhi, Ying; Zhu, Weiguo

2018-05-16

Isomeric TF1 and TF2 with highly fused thiophene cores were designed and synthesized here, in which a highly planar molecular structure was obtained for TF1 with the face-to-face sulfur atoms in the lateral region and a twisted molecular backbone was observed for TF2 with the back-to-back sulfur atoms. It is worth noting that different intermolecular interactions dominated in TF1 and TF2 caused by their isomeric thiophene cores, in which strong π-π stacking was achieved for TF1, whereas sulphur-involved nonbonding intermolecular interactions dominated in TF2, leading to the different fluorescence behaviors and also the altered liquid crystalline phases. Finally, typical P-type charge transport behaviors were achieved in both TF1- and TF2-based solution-processed OFETs. Also owing to the much ordered molecular packing in TF1, a higher charge carrier mobility of 3.7 × 10-3 cm2 V-1 s-1 was achieved for TF1-based OFETs compared to TF2-based OFETs.

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.

Atomistic and molecular effects in electric double layers at high surface charges

DOE PAGES

Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

2015-06-16

Here, the Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities providedmore » by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.« less

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

Precipitation of energetic neutral atoms and induced non-thermal escape fluxes from the Martian atmosphere

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

Lewkow, N. R.; Kharchenko, V.

2014-08-01

The precipitation of energetic neutral atoms, produced through charge exchange collisions between solar wind ions and thermal atmospheric gases, is investigated for the Martian atmosphere. Connections between parameters of precipitating fast ions and resulting escape fluxes, altitude-dependent energy distributions of fast atoms and their coefficients of reflection from the Mars atmosphere, are established using accurate cross sections in Monte Carlo (MC) simulations. Distributions of secondary hot (SH) atoms and molecules, induced by precipitating particles, have been obtained and applied for computations of the non-thermal escape fluxes. A new collisional database on accurate energy-angular-dependent cross sections, required for description of themore » energy-momentum transfer in collisions of precipitating particles and production of non-thermal atmospheric atoms and molecules, is reported with analytic fitting equations. Three-dimensional MC simulations with accurate energy-angular-dependent cross sections have been carried out to track large ensembles of energetic atoms in a time-dependent manner as they propagate into the Martian atmosphere and transfer their energy to the ambient atoms and molecules. Results of the MC simulations on the energy-deposition altitude profiles, reflection coefficients, and time-dependent atmospheric heating, obtained for the isotropic hard sphere and anisotropic quantum cross sections, are compared. Atmospheric heating rates, thermalization depths, altitude profiles of production rates, energy distributions of SH atoms and molecules, and induced escape fluxes have been determined.« less

Debye screening and a Thomas - Fermi model of a dyonic atom in a two potential theory of electromagnetism

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

Wolf, C.

1993-02-01

We study the screening of a central Abelian dyon by a surrounding dyon cloud in a two potential theory of electromagnetism. A generalized formula for the Debye screening length is obtained and a Thomas - Fermi Model for a charged cloud surrounding a central Dyonic Core is studied. 20 refs.

Determining the charged fractions of 218Po and 214Pb using an environmental gamma-ray and Rn detector.

PubMed

Maiello, M L; Harley, N H

1989-07-01

The rate of 218Po and 214Pb atoms collected electrostatically inside an environmental gamma-ray and 222Rn detector (EGARD) was measured. These measurements were used to directly infer the charged fraction of 218Po and to calculate the charged fraction of 214Pb. Thirty-two percent of the 218Po was collected electrostatically using approximately -1500 V on a 2.54 cm diameter Mylar covered disc inside a vented A1 EGARD of 1 L volume. About 91% of the 214Pb is collected electrostatically under the same conditions. The measurements were performed in a calibrated 222Rn test chamber at the Environmental Measurements Laboratory (EML) using the Thomas alpha-counting method with 222Rn concentrations averaging about 4300 Bq m-3. The atomic collection rates were used with other measured quantities to calculate the thermoluminescent dosimeter (TLD) signal acquired from EGARD for exposure to 1 Bq m-3 of 222Rn. The calculations account for 222Rn progeny collection using a Teflon electret and alpha and beta detection using TLDs inside EGARD. The measured quantities include the energies of 218Po and 214Po alpha-particles degraded by passage through the 25 microns thick electret. The TLD responses to these alpha- and beta-particles with an average energy approaching that obtained from the combined spectra of 214Pb and 214Bi were also measured. The calculated calibration factor is within 30% of the value obtained by exposing EGARD to a known concentration of 222Rn. This result supports our charged fraction estimates for 218Po and 214Pb.

Charge transfer of O3+ ions with atomic hydrogen

NASA Astrophysics Data System (ADS)

Wang, J. G.; Stancil, P. C.; Turner, A. R.; Cooper, D. L.

2003-01-01

Charge transfer processes due to collisions of ground state O3+(2s22p 2P) ions with atomic hydrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial and rotational coupling matrix elements obtained with the spin-coupled valence-bond approach. Total and state-selective cross sections and rate coefficients are presented. Comparison with existing experimental and theoretical data shows our results to be in better agreement with the measurements than the previous calculations, although problems with some of the state-selective measurements are noted. Our calculations demonstrate that rotational coupling is not important for the total cross section, but for state-selective cross sections, its relevance increases with energy. For the ratios of triplet to singlet cross sections, significant departures from a statistical value are found, generally in harmony with experiment.

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.

HM{sup +}–RG complexes (M = group 2 metal; RG = rare gas): Physical vs. chemical interactions

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

Harris, Joe P.; Dodson, Hannah; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2015-04-21

Previous work on the HM{sup +}–He complexes (M = Be–Ra) has been extended to the cases of the heavier rare gas atoms, HM{sup +}–RG (RG = Ne–Rn). Optimized geometries and harmonic vibrational frequencies have been calculated using MP2 theory and quadruple-ζ quality basis sets. Dissociation energies for the loss of the rare gas atom have been calculated at these optimized geometries using coupled cluster with single and double excitations and perturbative triples, CCSD(T)theory, extrapolating interaction energies to the basis set limit. Comparisons are made between the present data and the previously obtained helium results, as well as to those ofmore » the bare HM{sup +} molecules; furthermore, comparisons are made to the related M{sup +}–RG and M{sup 2+}–RG complexes. Partial atomic charge analyses have also been undertaken, and these used to test a simple charge-induced dipole model. Molecular orbital diagrams are presented together with contour plots of the natural orbitals from the quadratic configuration with single and double excitations (QCISD) density. The conclusion is that the majority of these complexes are physically bound, with very little sharing of electron density; however, for M = Be, and to a lesser extent M = Mg, some evidence for chemical effects is seen in HM{sup +}–RG complexes involving RG atoms with the higher atomic numbers.« less

Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

PubMed

Matta, Chérif F; Bader, Richard F W

2003-08-15

This article presents a study of the molecular charge distributions of the genetically encoded amino acids (AA), one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules (QTAIM) that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the AA. The use of the atomic properties in obtaining an understanding of the biological functions of the AA, whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the AA side chains of particular importance is the charge separation index (CSI), a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The CSI values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the CSI, which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the AAs. The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of AAs and from cyclohexane to water upon interchanging 190 pairs of AAs, were modeled using only three calculated parameters (representing electrostatic and volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 approximately 0.9) were obtained between DeltaCSI upon mutation and each of the two terms DeltaDeltaH and TDeltaDeltaS taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield DeltaDeltaG, the quadratic terms nearly cancel, and the result is a simple linear fit between DeltaDeltaG and DeltaCSI with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a DeltaCSI term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the AA triplet genetic codon is given concrete expression in a classification of the side chains in terms of their CSI values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in mRNA possess side-chain CSI < or = 2.8 (with the exception of Cys), whereas all those with CSI > 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the "stereochemical code" proposed as the determinant in the folding process. Copyright 2003 Wiley-Liss, Inc.

Intermediate coupled superconductivity in yttrium intermetallics

NASA Astrophysics Data System (ADS)

Sharma, Ramesh; Ahmed, Gulzar; Sharma, Yamini

2017-09-01

Non-magnetic YIn3, LaIn3 and LuIn3 with a superconducting transition temperature Tc of 0.78, 0.71 and 0.24 K were investigated for superconductivity. Similarly, rare-earth compound LaSn3 has been reported to exhibit superconductivity around 6.25 K, whereas the non-magnetic YSn3 is a superconductor with Tc of 7 K. The substitution of 13th group In-atoms by 14th group Sn-atoms is seen to enhance Tc by nearly one order, although the lattice parameters increase by ∼1.0% in YSn3 compared to YIn3 compound. It is observed from the ground state properties that the slight difference in the energy band structures of YIn3, YIn2Sn and YSn3 gives rise to various complex Fermi surfaces which are multiply connected and exhibit vast differences. The Fermi level lies on a sharp peak in YSn3 which has a higher density of states N(EF), whereas Fermi level lies on the shoulder of a sharp peak in YIn3. The electron localization function (ELF) and difference charge density maps clearly illustrate the difference in the nature of bonding; the Ysbnd Sn bonds are clearly more ionic (due to larger bond length) than Ysbnd In bonds. These results are consistent with the Bader charges which show loss of charges from Y-atoms and a gain of charges by In/Sn atoms. The dynamical properties also clearly illustrate the difference in the nature of bonds in YX3 intermetallics. A softening of the lowermost acoustic modes is observed in YIn3, whereas all the modes in YSn3 are observed to have positive frequencies which imply its greater stability. Since λel-ph < 1, both YIn3 and YSn3 compounds exhibit type I superconductivity according to BCS theory. However, the smaller N(EF) obtained from the density of states (DOS); the electron-phonon coupling constant λel-ph obtained from the temperature dependent specific heat as well as the instability in phonon modes due to stronger Ysbnd In and Insbnd In bonds in YIn3 may be the cause of lower Tc and filamentary nature of superconductivity. Insertion of Sn-atom in the YIn3 lattice further consolidates the superconducting nature due to increase in N(EF) and γ (electronic component of specific heat), along with lowering of the frequency of imaginary modes from 5.6 THz to 1.5-0.6 THz. Thus Tc is directly related to the valence electron concentration and ternary YIn2Sn may exhibit intermediate superconducting transition temperature.

Synthesis, spectroscopic investigations (FT-IR, NMR, UV-Vis, and TD-DFT), and molecular docking of (E)-1-(benzo[d][1, 3]dioxol-6-yl)-3-(6-methoxynaphthalen-2-yl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Therasa Alphonsa, A.; Loganathan, C.; Athavan Alias Anand, S.; Kabilan, S.

2017-02-01

The compound (E)-1-(benzo [d] [1, 3] dioxol-6-yl)-3-(6-methoxy naphthalen-2-yl) prop-2-en-1-one (AKN) was synthesized and characterized by FT-IR, NMR, and UV-Vis spectrometer. The optimized molecular geometry, bond lengths, bond angles, atomic charges, harmonic vibrational wave numbers and intensities of vibrational bonds of the title compound have been investigated by Time dependent- Density Functional Theory (TD-DFT) using a standard B3LYP method with 6-31 G (d, p) basis set available in the Gaussian 09W package. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-independent atomic orbital method (GIAO). Experimental excitation energies of the molecules were matched with the theoretically calculated energies. The atomic charge distributions of the various atoms present in the AKN were obtained by Mulliken charge population analysis. The Molecular Electrostatic Potential (MEP) analysis reveals the sites for electrophilic attack and nucleophilic reactions in the molecule. The difference between the observed and scaled frequencies was small. The HOMO to LUMO transition implies an electron density transfer. The intramolecular contacts have been interpreted using Natural Bond Orbital (NBO) analysis. The calculation results were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. To provide information about the interactions between human cytochrome protein and the novel compound theoretically, docking studies were carried out using Schrödinger software.

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.

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…

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

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

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

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

Heterogeneous Single-Atom Catalyst for Visible-Light-Driven High-Turnover CO2 Reduction: The Role of Electron Transfer.

PubMed

Gao, Chao; Chen, Shuangming; Wang, Ying; Wang, Jiawen; Zheng, Xusheng; Zhu, Junfa; Song, Li; Zhang, Wenkai; Xiong, Yujie

2018-03-01

Visible-light-driven conversion of CO 2 into chemical fuels is an intriguing approach to address the energy and environmental challenges. In principle, light harvesting and catalytic reactions can be both optimized by combining the merits of homogeneous and heterogeneous photocatalysts; however, the efficiency of charge transfer between light absorbers and catalytic sites is often too low to limit the overall photocatalytic performance. In this communication, it is reported that the single-atom Co sites coordinated on the partially oxidized graphene nanosheets can serve as a highly active and durable heterogeneous catalyst for CO 2 conversion, wherein the graphene bridges homogeneous light absorbers with single-atom catalytic sites for the efficient transfer of photoexcited electrons. As a result, the turnover number for CO production reaches a high value of 678 with an unprecedented turnover frequency of 3.77 min -1 , superior to those obtained with the state-of-the-art heterogeneous photocatalysts. This work provides fresh insights into the design of catalytic sites toward photocatalytic CO 2 conversion from the angle of single-atom catalysis and highlights the role of charge kinetics in bridging the gap between heterogeneous and homogeneous photocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic scale imaging of magnetic circular dichroism by achromatic electron microscopy.

PubMed

Wang, Zechao; Tavabi, Amir H; Jin, Lei; Rusz, Ján; Tyutyunnikov, Dmitry; Jiang, Hanbo; Moritomo, Yutaka; Mayer, Joachim; Dunin-Borkowski, Rafal E; Yu, Rong; Zhu, Jing; Zhong, Xiaoyan

2018-03-01

In order to obtain a fundamental understanding of the interplay between charge, spin, orbital and lattice degrees of freedom in magnetic materials and to predict and control their physical properties 1-3 , experimental techniques are required that are capable of accessing local magnetic information with atomic-scale spatial resolution. Here, we show that a combination of electron energy-loss magnetic chiral dichroism 4 and chromatic-aberration-corrected transmission electron microscopy, which reduces the focal spread of inelastically scattered electrons by orders of magnitude when compared with the use of spherical aberration correction alone, can achieve atomic-scale imaging of magnetic circular dichroism and provide element-selective orbital and spin magnetic moments atomic plane by atomic plane. This unique capability, which we demonstrate for Sr 2 FeMoO 6 , opens the door to local atomic-level studies of spin configurations in a multitude of materials that exhibit different types of magnetic coupling, thereby contributing to a detailed understanding of the physical origins of magnetic properties of materials at the highest spatial resolution.

Plane wave density functional molecular dynamics study of exothermic reactions of Al/CuO thermites

NASA Astrophysics Data System (ADS)

Oloriegbe, Suleiman; Sewell, Thomas; Chen, Zhen; Jiang, Shan; Gan, Yong

2014-03-01

Exothermic reactions between nanosize aluminum (Al) and copper oxide (CuO) structures are of current interest because of their high reaction enthalpy and energy density which exceed those of traditional monomolecular energetic compounds such as TNT, RDX, and HMX. In this work, molecular dynamics simulations with forces obtained from plane wave density functional theory are used to investigate the atomic-scale and electronic processes that occur during the fast thermite reactions between Al and CuO nanostructures under adiabatic conditions. Aluminum surfaces in contact with O-exposed and Cu-exposed CuO surfaces are studied. Starting from initial temperature T = 800 K, we have observed: faster chemical reaction at the oxygen-rich interface during the initial 0.5 ps, linear temperature rise, and fast oxygen diffusion into the Al region with the rate 1.87 X 10-3 cm2/s. The density-derived electrostatic and chemical method is used to evaluate the net atomic charges and charge transfer during the important redox processes. High charge density around the oxygen-exposed interface may be responsible for the faster initial reactions at that interface. The overall reaction rate, determined using the time evolution of Cu-O charge orbital overlap population, is approximately first order.

Background of the completed research; relevances to solar physics

NASA Technical Reports Server (NTRS)

Sellin, I. A.

1973-01-01

Research activities reported consider the atomic structures of highly stripped heavy ions and their modes of formation and destruction in collisions. The lifetime of the metastable 2 3p1 state of the two electron ion F-7(+) was determined by measuring the radiative decay of an excited helium-like fluorine beam, Metastable state quenching measurements were performed on a helium-like ion to obtain the 1 1S0 to 2 3p2 transition probability. Exponential exchange state dependence of X-ray production cross sections was studied in heavy target atoms during collisions with light charged particles.

Comment on "Impurity spectra of graphene under electric and magnetic fields"

NASA Astrophysics Data System (ADS)

Van Pottelberge, R.; Zarenia, M.; Peeters, F. M.

2018-05-01

In a recent paper [Phys. Rev. B 89, 155403 (2014), 10.1103/PhysRevB.89.155403], the authors investigated the spectrum of a Coulomb impurity in graphene in the presence of magnetic and electric fields using the coupled series expansion approach. In the first part of their paper, they investigated how Coulomb impurity states collapse in the presence of a perpendicular magnetic field. We argue that the obtained spectrum does not give information about the atomic collapse and that their interpretation of the spectrum regarding atomic collapse is not correct. We also argue that the obtained results are only valid up to the dimensionless charge |α |=0.5 and, to obtain correct results for α >0.5 , a proper regularization of the Coulomb interaction is required. Here we present the correct numerical results for the spectrum for arbitrary values of α .

Near Hartree-Fock quality GTO basis sets for the second-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry

1987-01-01

Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

Electrostatic energy and screened charge interaction near the surface of metals with different Fermi surface shape

NASA Astrophysics Data System (ADS)

Gabovich, A. M.; Il'chenko, L. G.; Pashitskii, E. A.; Romanov, Yu. A.

1980-04-01

Using the Poisson equation Green function for a self-consistent field in a spatially inhomogeneous system, expressions for the electrostatic energy and screened charge interaction near the surface of a semi-infinite metal and a thin quantizing film are derived. It is shown that the decrease law and Friedel oscillation amplitude of adsorbed atom indirect interaction are determined by the electron spectrum character and the Fermi surface shape. The results obtained enable us to explain, in particular, the submonolayer adsorbed film structure on the W and Mo surfaces.

Characteristics of the optical radiation from Kaufman thrusters

NASA Technical Reports Server (NTRS)

Milder, N. L.; Sovey, J. S.

1971-01-01

The optical radiation from plasma discharges of electron-bombardment mercury-ion thrusters was investigated. Spectrographic measurements indicated that the discharge was composed primarily of mercury atoms and singly charged ions. Excitation spectra of doubly charged mercury ions was measured to obtain the fraction of such ions in the discharge. Accomplishments of spectroscopic measurements of a hollow cathode thruster included the identification of two diagnostic lines in the mercury spectrum and the interpretation of the spectral amplitudes in terms of a superposition of primary and Maxwellian electron distributions. Potential application of optical techniques to thruster control applications was also suggested by the measurements.

Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

PubMed

Wang, Jui-Chih; Lin, Jung-Hsin; Chen, Chung-Ming; Perryman, Alex L; Olson, Arthur J

2011-10-24

Ordinary least-squares (OLS) regression has been used widely for constructing the scoring functions for protein-ligand interactions. However, OLS is very sensitive to the existence of outliers, and models constructed using it are easily affected by the outliers or even the choice of the data set. On the other hand, determination of atomic charges is regarded as of central importance, because the electrostatic interaction is known to be a key contributing factor for biomolecular association. In the development of the AutoDock4 scoring function, only OLS was conducted, and the simple Gasteiger method was adopted. It is therefore of considerable interest to see whether more rigorous charge models could improve the statistical performance of the AutoDock4 scoring function. In this study, we have employed two well-established quantum chemical approaches, namely the restrained electrostatic potential (RESP) and the Austin-model 1-bond charge correction (AM1-BCC) methods, to obtain atomic partial charges, and we have compared how different charge models affect the performance of AutoDock4 scoring functions. In combination with robust regression analysis and outlier exclusion, our new protein-ligand free energy regression model with AM1-BCC charges for ligands and Amber99SB charges for proteins achieve lowest root-mean-squared error of 1.637 kcal/mol for the training set of 147 complexes and 2.176 kcal/mol for the external test set of 1427 complexes. The assessment for binding pose prediction with the 100 external decoy sets indicates very high success rate of 87% with the criteria of predicted root-mean-squared deviation of less than 2 Å. The success rates and statistical performance of our robust scoring functions are only weakly class-dependent (hydrophobic, hydrophilic, or mixed).

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.

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

Dust Particle Dynamics in The Presence of Highly Magnetized Plasmas

NASA Astrophysics Data System (ADS)

Lynch, Brian; Konopka, Uwe; Thomas, Edward; Merlino, Robert; Rosenberg, Marlene

2016-10-01

Complex plasmas are four component plasmas that contain, in addition to the usual electrons, ions, and neutral atoms, macroscopic electrically charged (nanometer to micrometer) sized ``dust'' particles. These macroscopic particles typically obtain a net negative charge due to the higher mobility of electrons compared to that of ions. Because the electrons, ions, and dust particles are charged, their dynamics may be significantly modified by the presence of electric and magnetic fields. Possible consequences of this modification may be the charging rate and the equilibrium charge. For example, in the presence of a strong horizontal magnetic field (B >1 Tesla), it may be possible to observe dust particle gx B deflection and, from that deflection, determine the dust grain charge. In this poster, we present recent data from performing multiple particle dropping experiments to characterize the g x B deflection in the Magnetized Dusty Plasma Experiment (MDPX). This work is supported by funding from the U. S. Department of Energy Grant Number DE - SC0010485 and the NASA/Jet Propulsion Laboratory, JPL-1543114.

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

Absolute atomic hydrogen densities in a radio frequency discharge measured by two-photon laser induced fluorescence imaging

NASA Astrophysics Data System (ADS)

Chérigier, L.; Czarnetzki, U.; Luggenhölscher, D.; Schulz-von der Gathen, V.; Döbele, H. F.

1999-01-01

Absolute atomic hydrogen densities were measured in the gaseous electronics conference reference cell parallel plate reactor by Doppler-free two-photon absorption laser induced fluorescence spectroscopy (TALIF) at λ=205 nm. The capacitively coupled radio frequency discharge was operated at 13.56 MHz in pure hydrogen under various input power and pressure conditions. The Doppler-free excitation technique with an unfocused laser beam together with imaging the fluorescence radiation by an intensified charge coupled device camera allows instantaneous spatial resolution along the radial direction. Absolute density calibration is obtained with the aid of a flow tube reactor and titration with NO2. The influence of spatial intensity inhomogenities along the laser beam and subsequent fluorescence are corrected by TALIF in xenon. A full mapping of the absolute density distribution between the electrodes was obtained. The detection limit for atomic hydrogen amounts to about 2×1018 m-3. The dissociation degree is of the order of a few percent.

Final Results from the Jefferson Lab Qweak Experiment

NASA Astrophysics Data System (ADS)

Smith, Gregory

2017-09-01

The Qweak collaboration has unblinded our final result. We briefly describe the e-> p elastic scattering experiment used to extract the asymmetries measured in the two distinct running periods which constituted the experiment. The precision obtained on the final combined asymmetry is +/- 9.3 ppb. Some of the backgrounds and corrections applied in the experiment will be explained and quantified. We then provide the results of several methods we have used to extract consistent values of the proton's weak charge QWp from our asymmetry measurements. We also present results for the strange and axial form factors obtained from a fit to existing parity-violating electron scattering data. In conjunction with existing atomic parity violation results on 133Cs we extract the vector weak quark couplings C1u and C1d. The latter are combined to obtain the neutron's weak charge. From the proton's weak charge we obtain a result for sin2θW at the energy scale of our experiment, a sensitive SM test of the running of sin2θW . We also show the mass reach for new beyond-the-Standard-Model physics obtained from our determination of the proton's weak charge and its uncertainty, and discuss sensitivity to specific models. This work was supported by the U.S. Department of Energy, Office of Science, under Contract DE-AC05-06OR23177, the Natural Sciences and Engineering Research Council of Canada (NSERC), and the National Science Foundation (NSF).

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.

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.

Accelerated procedure to solve kinetic equation for neutral atoms in a hot plasma

NASA Astrophysics Data System (ADS)

Tokar, Mikhail Z.

2017-12-01

The recombination of plasma charged components, electrons and ions of hydrogen isotopes, on the wall of a fusion reactor is a source of neutral molecules and atoms, recycling back into the plasma volume. Here neutral species participate, in particular, in charge-exchange (c-x) collisions with the plasma ions and, as a result, atoms of high energies with chaotically directed velocities are generated. Some fraction of these hot atoms hit the wall. Statistical Monte Carlo methods normally used to model c-x atoms are too time consuming for reasonably small level of accident errors and extensive parameter studies are problematic. By applying pass method to evaluate integrals from functions, including the ion velocity distribution, an iteration approach to solve one-dimensional kinetic equation [1], being alternative to Monte Carlo procedure, has been tremendously accelerated, at least by a factor of 30-50 [2]. Here this approach is developed further to solve the 2-D kinetic equation, applied to model the transport of c-x atoms in the vicinity of an opening in the wall, e.g., the entrance of the duct guiding to a diagnostic installation. This is necessary to determine firmly the energy spectrum of c-x atoms penetrating into the duct and to assess the erosion of the installation there. The results of kinetic modeling are compared with those obtained with the diffusion description for c-x atoms, being strictly relevant under plasma conditions of low temperature and high density, where the mean free path length between c-x collisions is much smaller than that till the atom ionization by electrons. It is demonstrated that the previous calculations [3], done with the diffusion approximation for c-x atoms, overestimate the erosion rate of Mo mirrors in a reactor by a factor of 3 compared to the result of the present kinetic study.

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.

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

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.

Understanding the interrelationship between the synthesis of urea and gluconeogenesis by formulating an overall balanced equation.

PubMed

Ipata, Piero L; Pesi, Rossana

2017-06-01

It is well known that a strong metabolic interrelationship exists between ureagenesis and gluconeogenesis. In this paper, we present a detailed, overall equation, describing a possible metabolic link between ureagenesis and gluconeogenesis. We adopted a guided approach in which we strongly suggest that students, when faced with the problem of obtaining the overall equation of a metabolic pathway, carefully account for all atoms and charges of the single reactions, as well as the cellular localizations of the substrates, and the related transport systems. If this suggestion is always taken into account, a balanced, overall equation of a metabolic pathway will be obtained, which strongly facilitates the discussion of its physiological role. Unfortunately, textbooks often report unbalanced overall equations of metabolic pathways, including ureagenesis and gluconeogenesis. Most likely the reason is that metabolism and enzymology have been neglected for about three decades, owing to the remarkable advances of molecular biology and molecular genetics. In this paper, we strongly suggest that students, when faced with the problem of obtaining the overall reaction of a metabolic pathway, carefully control if the single reactions are properly balanced for atoms and charges. Following this suggestion, we were able to obtain an overall equation describing the metabolic interrelationship between ureagenesis and gluconeogenesis, in which urea and glucose are the final products. The aim is to better rationalize this topic and to convince students and teachers that metabolism is an important and rewarding chapter of human physiology. Copyright © 2017 the American Physiological Society.

Surface conversion techniques for low energy neutral atom imagers

NASA Technical Reports Server (NTRS)

Quinn, J. M.

1995-01-01

This investigation has focused on development of key technology elements for low energy neutral atom imaging. More specifically, we have investigated the conversion of low energy neutral atoms to negatively charged ions upon reflection from specially prepared surfaces. This 'surface conversion' technique appears to offer a unique capability of detecting, and thus imaging, neutral atoms at energies of 0.01 - 1 keV with high enough efficiencies to make practical its application to low energy neutral atom imaging in space. Such imaging offers the opportunity to obtain the first instantaneous global maps of macroscopic plasma features and their temporal variation. Through previous in situ plasma measurements, we have a statistical picture of large scale morphology and local measurements of dynamic processes. However, with in situ techniques it is impossible to characterize or understand many of the global plasma transport and energization processes. A series of global plasma images would greatly advance our understanding of these processes and would provide the context for interpreting previous and future in situ measurements. Fast neutral atoms, created from ions that are neutralized in collisions with exospheric neutrals, offer the means for remotely imaging plasma populations. Energy and mass analysis of these neutrals provides critical information about the source plasma distribution. The flux of neutral atoms available for imaging depends upon a convolution of the ambient plasma distribution with the charge exchange cross section for the background neutral population. Some of the highest signals are at relatively low energies (well below 1 keV). This energy range also includes some of the most important plasma populations to be imaged, for example the base of the cleft ion fountain.

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.

Energy-transfer processes in neon-hydrogen mixtures excited by electron beams

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

Morozov, A.; Kruecken, R.; Ulrich, A.

2005-12-15

Energy- and charge-transfer processes in neon-hydrogen mixtures (500-1400 hPa neon and 0.001-3 hPa hydrogen partial pressures) excited by a pulsed low-energy ({approx}10 keV) electron beam were investigated using time-resolved spectroscopy. Time spectra of the hydrogen Lyman-{alpha} line, neon excimer emission (second continuum), and neon atomic lines (3p-3s transitions) were recorded. The time-integrated intensity of the Lyman-{alpha} emission was measured for the same range of gas mixtures. It is shown that direct energy transfer from Ne{sub 2}* excimers and neon atoms in the four lowest excited states as well as recombination of H{sub 3}{sup +} ions are the main channels populatingmore » atomic hydrogen in the n=2 state. A rate constant of (4.2{+-}1.4)x10{sup -11} cm{sup 3} s{sup -1} was obtained for the charge transfer from Ne{sub 2}{sup +} ions to molecular hydrogen. A lower limit for the depopulation rate constant of Ne{sub 2}* excimers by molecular hydrogen (combination of energy transfer and ionization) was found to be 1.0x10{sup -10} cm{sup 3} s{sup -1}.« less

The Response of the Ionospheric Cusp to the Solar Wind Through Two Perspectives: Low Energy Charged Particle In-Situ Measurements and Low-Energy Neutral Atom Imaging

NASA Technical Reports Server (NTRS)

Coffey, V. N.; Moore, T. E.; Chandler, M. O.; Giles, B. L.; Craven, P. D.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) mission provides a new perspective on the study of the response of the magnetosphere/ionosphere system to changing solar wind conditions, particularly the variability of ion outflow. Learning to interpret this new type of data becomes an essential step in the process of melding these results with the wealth of in-situ charged particle observations obtained over the past 25 years. In order to understand how the in-situ data correspond to and contrast with IMAGE results we will perform a conjunctive study of event data from two instruments to shed light on the coupling of the solar wind and ionosphere from these different perspectives. We will use the Low Energy Neutral Atom instrument (LENA) which images energetic neutral atom emissions from upward flowing ionospheric ions and the Thermal Ion Dynamics Instrument (TIDE) on the Polar satellite which measures in-situ ion outflow from 0.3-300 eV. Our primary goal will be to understand how comparing the imaging and in-situ perspectives can aid in the analysis of both data sets.

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.

The effect of the charge exchange source on the velocity and 'temperature' distributions and their anisotropies in the earth's exosphere

NASA Technical Reports Server (NTRS)

Hodges, R. R., Jr.; Rohrbaugh, R. P.; Tinsley, B. A.

1981-01-01

The velocity distribution of atomic hydrogen in the earth's exosphere is calculated as a function of altitude and direction taking into account both the classic exobase source and the higher-altitude plasmaspheric charge exchange source. Calculations are performed on the basis of a Monte Carlo technique in which random ballistic trajectories of individual atoms are traced through a three-dimensional grid of audit zones, at which relative concentrations and momentum or energy fluxes are obtained. In the case of the classical exobase source alone, the slope of the velocity distribution is constant only for the upward radial velocity component and increases dramatically with altitude for the incoming radial and transverse velocity components, resulting in a temperature decrease. The charge exchange source, which produces the satellite hydrogen component and the hot ballistic and escape components of the exosphere, is found to enhance the wings of the velocity distributions, however this effect is not sufficient to overcome the temperature decreases at altitudes above one earth radius. The resulting global model of the hydrogen exosphere may be used as a realistic basis for radiative transfer calculations.

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

Ab Initio Study of Aluminium Impurity and Interstitial-Substitutional Complexes in Ge Using a Hybrid Functional (HSE)

NASA Astrophysics Data System (ADS)

Igumbor, E.; Mapasha, R. E.; Meyer, W. E.

2017-07-01

The results of an ab initio modelling of aluminium substitutional impurity ({\\hbox {Al}}_Ge), aluminium interstitial in Ge [{\\hbox {I}}_Al for the tetrahedral (T) and hexagonal (H) configurations] and aluminium interstitial-substitutional pairs in Ge ({\\hbox {I}}_Al{\\hbox {Al}}_Ge) are presented. For all calculations, the hybrid functional of Heyd, Scuseria, and Ernzerhof in the framework of density functional theory was used. Defects formation energies, charge state transition levels and minimum energy configurations of the {\\hbox {Al}}_Ge, {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge were obtained for -2, -1, 0, +1 and +2 charge states. The calculated formation energy shows that for the neutral charge state, the {\\hbox {I}}_Al is energetically more favourable in the T than the H configuration. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge forms with formation energies of -2.37 eV and -2.32 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge is energetically more favourable when the interstitial atom is at the T site with a binding energy of 0.8 eV. The {\\hbox {I}}_Al in the T configuration, induced a deep donor (+2/+1) level at EV+0.23 eV and the {\\hbox {Al}}_Ge induced a single acceptor level (0/-1) at EV+0.14 eV in the band gap of Ge. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge induced double-donor levels are at E_V+0.06 and E_V+0.12 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge exhibit properties of charge state-controlled metastability.

Hollow atoms below, above, and at surface

NASA Astrophysics Data System (ADS)

Briand, Jean Pierre

1993-12-01

It is now quite obvious that, in most cases, when a highly charged ion approaches, or penetrates a surface, many electrons are captured in excited states of the projectile. The nature of the hollow atoms formed depends on the velocity of the ion, and whether or not capture has occurred above, below, or at the surface. I would like in this talk to discuss the nature, namely the electronic configuration of the hollow atoms formed in various circumstances. In the first two sections I shall summarize recent results, some of them are already published, or have been presented in other conferences. Section I will be devoted to the study of hollow atoms formed inside the surface, section II to those formed far from the surface. In a third section I will present some new results, obtained at very low velocities, on hollow atoms at surface. These results have been obtained through a large international collaboration: J.P. DESCLAUX, CEN, Grenoble; B. d'ETAT, G. GIARDINO, L. de BILLY, S. BARDIN, LPAN-Université P&M Curie, Paris; D. SCHNEIDER, M. BRIERE, M. CLARK, D. KNAPP, V. DECAUX, LLNL, Livermore-Californie; R. ALI, N. RENARD, M. STOCKLI, P. RICHARD, KSU, Manhattan-Kansas; A. BRENAC, G. LAMBOLLEY, AIM, Grenoble; J. FAURE, Laboratoire National Saturne, Saclay.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

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.

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

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.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

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.

HEAVY ION LINEAR ACCELERATOR

DOEpatents

Van Atta, C.M.; Beringer, R.; Smith, L.

1959-01-01

A linear accelerator of heavy ions is described. The basic contributions of the invention consist of a method and apparatus for obtaining high energy particles of an element with an increased charge-to-mass ratio. The method comprises the steps of ionizing the atoms of an element, accelerating the resultant ions to an energy substantially equal to one Mev per nucleon, stripping orbital electrons from the accelerated ions by passing the ions through a curtain of elemental vapor disposed transversely of the path of the ions to provide a second charge-to-mass ratio, and finally accelerating the resultant stripped ions to a final energy of at least ten Mev per nucleon.

Ultrafast absorption of intense x rays by nitrogen molecules

NASA Astrophysics Data System (ADS)

Buth, Christian; Liu, Ji-Cai; Chen, Mau Hsiung; Cryan, James P.; Fang, Li; Glownia, James M.; Hoener, Matthias; Coffee, Ryan N.; Berrah, Nora

2012-06-01

We devise a theoretical description for the response of nitrogen molecules (N2) to ultrashort and intense x rays from the free electron laser Linac Coherent Light Source (LCLS). We set out from a rate-equation description for the x-ray absorption by a nitrogen atom. The equations are formulated using all one-x-ray-photon absorption cross sections and the Auger and radiative decay widths of multiply-ionized nitrogen atoms. Cross sections are obtained with a one-electron theory and decay widths are determined from ab initio computations using the Dirac-Hartree-Slater (DHS) method. We also calculate all binding and transition energies of nitrogen atoms in all charge states with the DHS method as the difference of two self-consistent field (SCF) calculations (ΔSCF method). To describe the interaction with N2, a detailed investigation of intense x-ray-induced ionization and molecular fragmentation are carried out. As a figure of merit, we calculate ion yields and the average charge state measured in recent experiments at the LCLS. We use a series of phenomenological models of increasing sophistication to unravel the mechanisms of the interaction of x rays with N2: a single atom, a symmetric-sharing model, and a fragmentation-matrix model are developed. The role of the formation and decay of single and double core holes, the metastable states of N_2^{2+}, and molecular fragmentation are explained.

Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review

PubMed Central

Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

2014-01-01

Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

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

Garcia Ruiz, R. F.; Bissell, M. L.; Blaum, K.

Here, despite being a complex many-body system, the atomic nucleus exhibits simple structures for certain ‘magic’ numbers of protons and neutrons. The calcium chain in particular is both unique and puzzling: evidence of doubly magic features are known in 40,48Ca, and recently suggested in two radioactive isotopes, 52,54Ca. Although many properties of experimentally known calcium isotopes have been successfully described by nuclear theory, it is still a challenge to predict the evolution of their charge radii. Here we present the first measurements of the charge radii of 49,51,52Ca, obtained from laser spectroscopy experiments at ISOLDE, CERN. The experimental results aremore » complemented by state-of-the-art theoretical calculations. The large and unexpected increase of the size of the neutron-rich calcium isotopes beyond N = 28 challenges the doubly magic nature of 52Ca and opens new intriguing questions on the evolution of nuclear sizes away from stability, which are of importance for our understanding of neutron-rich atomic nuclei.« less

Liquid Adsorption of Organic Compounds on Hematite α-Fe2O3 Using ReaxFF.

PubMed

Chia, Chung-Lim; Avendaño, Carlos; Siperstein, Flor R; Filip, Sorin

2017-10-24

ReaxFF-based molecular dynamics simulations are used in this work to study the effect of the polarity of adsorbed molecules in the liquid phase on the structure and polarization of hematite (α-Fe 2 O 3 ). We compared the adsorption of organic molecules with different polarities on a rigid hematite surface and on a flexible and polarizable surface. We show that the displacements of surface atoms and surface polarization in a flexible hematite model are proportional to the adsorbed molecule's polarity. The increase in electrostatic interactions resulting from charge transfer in the outermost solid atoms in a flexible hematite model results in better-defined adsorbed layers that are less ordered than those obtained assuming a rigid solid. These results suggest that care must be taken when parametrizing empirical transferable force fields because the calculated charges on a solid slab in vacuum may not be representative of a real system, especially when the solid is in contact with a polar liquid.

Characterizing Plasmonic Excitations of Quasi-2D Chains

NASA Astrophysics Data System (ADS)

Townsend, Emily; Bryant, Garnett

A quantum description of the optical response of nanostructures and other atomic-scale systems is desirable for modeling systems that use plasmons for quantum information transfer, or coherent transport and interference of quantum states, as well as systems small enough for electron tunneling or quantum confinement to affect the electronic states of the system. Such a quantum description is complicated by the fact that collective and single-particle excitations can have similar energies and thus will mix. We seek to better understand the excitations of nanosystems to identify which characteristics of the excitations are most relevant to modeling their behavior. In this work we use a quasi 2-dimensional linear atomic chain as a model system, and exact diagonalization of the many-body Hamiltonian to obtain its excitations. We compare this to previous work in 1-d chains which used a combination of criteria involving a many-body state's transfer dipole moment, balance, transfer charge, dynamical response, and induced-charge distribution to identify which excitations are plasmonic in character.

EXPERIMENTAL MEASUREMENT AND INTERPRETATION OF VOLT-AMPERE CURVES

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

Gingrich, J.E.; Warner, C.; Weeks, C.C.

1962-07-01

Cylindrical and parallel-plane cesium vapor thermionic converters were used for obtaining volt-ampere curves for systematic variations of emitter, collector, and cesium reservoir temperatures, with electrode spacings ranging from a few to many mean free paths, and with space charge conditions varying from electron-rich to ion-rich. The resulting curves exhibit much variety. The saturation currents agree well with the data of Houston and Aamodt for the space charge neutralized, few-mean-free-path cases. Apparent'' saturation currents for space charge limited cases were observed and were always less than the currents predicted by Houston and Aamodt. Several discontinuities in slope were observed in themore » reverse current portion of the curves and these have tentatively been identified with volume ionization of atoms in both the ground and excited states. Similar processes may be important for obtaining the ignited mode. The methods used to measure static and dynamic volt-ampere curves are described. The use of a controlled-current load has yielded a negative resistance'' region in the curves which show the ignited mode. The curves obtained with poor current control do not show this phenomenon. Extinction is considered from the standpoint of Kaufmann' s criterion for stability. (auth)« less

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.

Progress towards measuring the Rydberg Constant Using Circular Rydberg Atoms in an Intensity-Modulated Optical Lattice

NASA Astrophysics Data System (ADS)

Ramos, Andira; Moore, Kaitlin; Raithel, Georg

2015-05-01

Recent significant disagreement with the previously established size of the proton demonstrates a need to reconsider the current value of the Rydberg constant, the effects of the nuclear charge distribution and QED in hydrogen-like atoms. An experiment is in progress to obtain a measurement of the Rydberg constant by studying circular Rydberg atoms, which exhibit very small QED shifts and electron wavefunctions which do not overlap with the nucleus. Cold Rydberg atoms are trapped using a ponderomotive potential. To drive the transitions, a novel type of spectroscopy is used which utilizes an optical-lattice field that is intensity-modulated at the frequencies of atomic transitions. The method is free of typical spectroscopic selection rules and has been shown to drive transitions up to fifth order. Combined with optical Rydberg-atom trapping, the method enables the measurement of narrow, sub-THz transitions between long-lived circular Rydberg levels. Energy shifts affecting this precision measurement will also be discussed. This work is suported by NSF, NIST and NASA grants.

Simulation of Energetic Neutral Atom Images at Venus

NASA Astrophysics Data System (ADS)

Gunell, H.; Holmström, M.; Biernat, H. K.; Erkaev, N. V.; Lammer, H.; Lichtenegger, H.; Penz, T.

2003-12-01

We present simulated images of energetic neutral atoms (ENAs) produced in charge exchange collisions between solar wind protons and neutral atoms in the exosphere of Venus. The plasma flow around Venus is modelled by a semi-analytical MHD simulation that includes mass-loading (Biernat et al., J. Geophys. Res., vol. 104, 12617--12626, 1999; Biernat,et al., Adv. Space Res., 28, 2001). These results are compared with the results that are obtained when the Spreiter-Stahara flow model (Spreiter and Stahara, Adv Space Res., 14, 5--19, 1994) is used. The ENA images are calculated by combining the proton bulk flow and temperature results of the MHD model with a model of the neutral atmosphere using the energy dependent cross sections for the charge exchange collisions. The ENA production rate is integrated along lines of sight to a virtual instrument, thus simulating what could be measured by a space-craft-carried ENA instrument. The images are found to be dominated by two local maxima. One produced by charge exchange collisions in the solar wind, upstream of the bow shock, and the other close to the dayside ionopause. The main contribution to the ENA flux observed in the ENA images stems from a region of space between the ionopause and the bow shock on the dayside of the planet. The simulated ENA fluxes at Venus are lower than those obtained in similar simulations of ENA images at Mars (Holmström et al., J. Geophys. Res., 107, 1277, doi: 10.1029/2001JA000325, 2002). The reason for the lower ENA flux at Venus is thought to be the smaller extent of Venus' exosphere. The steeper falloff of the neutral gas density with altitude in the exosphere of Venus is caused by Venus' mass, which is 7.5 times greater than the mass of Mars. The dependence of the ENA flux on the altitude of the ionopause is studied numerically, and it is found that the ENA flux decreases as the ionopause altitude is increased.

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.

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.

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.

Charge migration and charge transfer in molecular systems

PubMed Central

Wörner, Hans Jakob; Arrell, Christopher A.; Banerji, Natalie; Cannizzo, Andrea; Chergui, Majed; Das, Akshaya K.; Hamm, Peter; Keller, Ursula; Kraus, Peter M.; Liberatore, Elisa; Lopez-Tarifa, Pablo; Lucchini, Matteo; Meuwly, Markus; Milne, Chris; Moser, Jacques-E.; Rothlisberger, Ursula; Smolentsev, Grigory; Teuscher, Joël; van Bokhoven, Jeroen A.; Wenger, Oliver

2017-01-01

The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review. PMID:29333473

QSTR of the toxicity of some organophosphorus compounds by using the quantum chemical and topological descriptors.

PubMed

Senior, Samir A; Madbouly, Magdy D; El massry, Abdel-Moneim

2011-09-01

Quantum chemical and topological descriptors of some organophosphorus compounds (OP) were correlated with their toxicity LD(50) as a dermal. The quantum chemical parameters were obtained using B3LYP/LANL2DZdp-ECP optimization. Using linear regression analysis, equations were derived to calculate the theoretical LD(50) of the studied compounds. The inclusion of quantum parameters, having both charge indices and topological indices, affects the toxicity of the studied compounds resulting in high correlation coefficient factors for the obtained equations. Two of the new four firstly supposed descriptors give higher correlation coefficients namely the Heteroatom Corrected Extended Connectivity Randic index ((1)X(HCEC)) and the Density Randic index ((1)X(Den)). The obtained linear equations were applied to predict the toxicity of some related structures. It was found that the sulfur atoms in these compounds must be replaced by oxygen atoms to achieve improved toxicity. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Development of a united-atom force field for 1-ethyl-3-methylimidazolium tetracyanoborate ionic liquid

NASA Astrophysics Data System (ADS)

Koller, Thomas; Ramos, Javier; Garrido, Nuno M.; Fröba, Andreas P.; Economou, Ioannis G.

2012-06-01

Three united-atom (UA) force fields are presented for the ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, abbreviated as [EMIM]+[B(CN)4]-. The atomistic charges were calculated based on the restrained electrostatic potential (RESP) of the isolated ions (abbreviated as force field 1, FF-1) and the ensemble averaged RESP (EA-RESP) method from the most stable ion pair configurations obtained by MP2/6-31G*+ calculations (abbreviated as FF-2 and FF-3). Non-electrostatic parameters for both ions were taken from the literature and Lennard-Jones parameters for the [B(CN)4]- anion were fitted in two different ways to reproduce the experimental liquid density. Molecular dynamics (MD) simulations were performed over a wide temperature range to identify the effect of the electrostatic and non-electrostatic potential on the liquid density and on transport properties such as self-diffusion coefficient and viscosity. Predicted liquid densities for the three parameter sets deviate less than 0.5% from experimental data. The molecular mobility with FF-2 and FF-3 using reduced charge sets is appreciably faster than that obtained with FF-1. FF-3 presents a refined non-electrostatic potential that leads to a notable improvement in both transport properties when compared to experimental data.

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.

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.

Photostop of iodine atoms from electrically oriented ICl molecules

NASA Astrophysics Data System (ADS)

Bao, Da-Xiao; Deng, Lian-Zhong; Xu, Liang; Yin, Jian-Ping

2015-11-01

The dynamics of photostopping iodine atoms from electrically oriented ICl molecules was numerically studied based on their orientational probability distribution functions. Velocity distributions of the iodine atoms and their production rates were investigated for orienting electrical fields of various intensities. For the ICl precursor beams with an initial rotational temperature of ∼ 1 K, the production of the iodine atoms near zero speed will be improved by about ∼ 5 times when an orienting electrical field of ∼ 200 kV/cm is present. A production rate of ∼ 0.5‰ is obtained for photostopped iodine atoms with speeds less than 10 m/s, which are suitable for magnetic trapping. The electrical orientation of ICl precursors and magnetic trapping of photostopped iodine atoms in situ can be conveniently realized with a pair of charged ring magnets. With the maximal value of the trapping field being ∼ 0.28 T, the largest trapping speed is ∼ 7.0 m/s for the iodine atom. Project supported by the National Natural Science Foundation of China (Grant Nos. 11034002, 61205198, and 11274114) and the National Key Basic Research and Development Program of China (Grant No. 2011CB921602).

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.

Partially Oxidized SnS2 Atomic Layers Achieving Efficient Visible-Light-Driven CO2 Reduction.

PubMed

Jiao, Xingchen; Li, Xiaodong; Jin, Xiuyu; Sun, Yongfu; Xu, Jiaqi; Liang, Liang; Ju, Huanxin; Zhu, Junfa; Pan, Yang; Yan, Wensheng; Lin, Yue; Xie, Yi

2017-12-13

Unraveling the role of surface oxide on affecting its native metal disulfide's CO 2 photoreduction remains a grand challenge. Herein, we initially construct metal disulfide atomic layers and hence deliberately create oxidized domains on their surfaces. As an example, SnS 2 atomic layers with different oxidation degrees are successfully synthesized. In situ Fourier transform infrared spectroscopy spectra disclose the COOH* radical is the main intermediate, whereas density-functional-theory calculations reveal the COOH* formation is the rate-limiting step. The locally oxidized domains could serve as the highly catalytically active sites, which not only benefit for charge-carrier separation kinetics, verified by surface photovoltage spectra, but also result in electron localization on Sn atoms near the O atoms, thus lowering the activation energy barrier through stabilizing the COOH* intermediates. As a result, the mildly oxidized SnS 2 atomic layers exhibit the carbon monoxide formation rate of 12.28 μmol g -1 h -1 , roughly 2.3 and 2.6 times higher than those of the poorly oxidized SnS 2 atomic layers and the SnS 2 atomic layers under visible-light illumination. This work uncovers atomic-level insights into the correlation between oxidized sulfides and CO 2 reduction property, paving a new way for obtaining high-efficiency CO 2 photoreduction performances.

Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

PubMed

Álvarez-Barcia, Sonia; Kästner, Johannes

2017-06-01

Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

"Doping" pentacene with sp(2)-phosphorus atoms: towards high performance ambipolar semiconductors.

PubMed

Long, Guankui; Yang, Xuan; Chen, Wangqiao; Zhang, Mingtao; Zhao, Yang; Chen, Yongsheng; Zhang, Qichun

2016-01-28

Recent research progress in black phosphorus sheets strongly encourages us to employ pentacene as a parent system to systematically investigate how the "doping" of sp(2)-phosphorus atoms onto the backbone of pentacene influences its optical and charge transport properties. Our theoretical investigations proved that increasing the contribution of the pz atomic orbital of the sp(2)-phosphorus to the frontier molecular orbital of phosphapentacenes could significantly decrease both hole and electron reorganization energies and dramatically red-shift the absorption of pentacene. The record smallest hole and electron reorganization energies of 69.80 and 95.74 meV for heteropentacene derivatives were obtained. These results suggest that phosphapentacenes (or phosphaacenes) could be potential promising candidates to achieve both higher and balanced mobilities in organic field effect transistors and realize a better power conversion efficiency in organic photovoltaics.

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.

Energetic ion bombardment of Ag surfaces by C60+ and Ga+ projectiles.

PubMed

Sun, Shixin; Szakal, Christopher; Winograd, Nicholas; Wucher, Andreas

2005-10-01

The ion bombardment-induced release of particles from a metal surface is investigated using energetic fullerene cluster ions as projectiles. The total sputter yield as well as partial yields of neutral and charged monomers and clusters leaving the surface are measured and compared with corresponding data obtained with atomic projectile ions of similar impact kinetic energy. It is found that all yields are enhanced by about one order of magnitude under bombardment with the C60+ cluster projectiles compared with Ga+ ions. In contrast, the electronic excitation processes determining the secondary ion formation probability are unaffected. The kinetic energy spectra of sputtered particles exhibit characteristic differences which reflect the largely different nature of the sputtering process for both types of projectiles. In particular, it is found that under C60+ impact (1) the energy spectrum of sputtered atoms peaks at significantly lower kinetic energies than for Ga+ bombardment and (2) the velocity spectra of monomers and dimers are virtually identical, a finding which is in pronounced contrast to all published data obtained for atomic projectiles. The experimental findings are in reasonable agreement with recent molecular dynamics simulations.

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.

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.

Energetic Neutral Atom Spectra in the 0.2-3.0 keV from a Residual Source Across the Sky Obtained by the Neutral Particle Detector on board Venus Express

NASA Astrophysics Data System (ADS)

Brandt, Pontus; Roelof, Edmond; Wurz, Peter; Decker, Robert; Barabash, Stas; Bazell, David; Sotirelis, Thomas

We have surveyed the sky for residual energetic neutral atom (ENA) signals in the energy range of 0.2-3.0 keV [Brandt et al., AIP Proceedings, 2009]. Approximately three years of data obtained by the Neutral Particle Detector (NPD) on board Venus Express (VEX) from May 2006 through August 2009 have been analyzed. After applying strict viewing criteria to minimize all known signals and subtracting the UV background from the Milky Way, we find a residual energy spectral shape with a ledge/bump at around 0.5 keV and a break in the spectral slope at about 1.0 keV, reiminiscent of the spectral shape obtained in reverse shocks. The ledge/bump at about 0.5 keV appears consistent with twice the plasma flow velocity obtained by the V1 measurements in the inner HS. When the ENA spectrum is divided by the energy dependent charge exchange cross section its slope above 1 keV has a spectral power-law index of 1.5, with some variations across the sky. In order to better understand the spectral shape over an extended energy range we compare the spectra obtained by VEX/NPD with the ones reported by the Interstellar Boundary Explorer (IBEX) [Funsten et al., Science, 2009], by the Ion Neutral Camera (INCA) on board Cassini [Krimigis et al., Science, 2009]and with those measured in-situ in the inner heliosheath (HS) by the Low-Energy Charged Particle (LECP) instrument (>40 keV) on board Voyager-1 (V1).

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Sherrill, C. David

2014-07-01

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

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

Parrish, Robert M.; Sherrill, C. David, E-mail: sherrill@gatech.edu

2014-07-28

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work throughmore » the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.« less

A method for determining poloidal rotation from poloidal asymmetry in toroidal rotation (invited)

DOE PAGES

Chrystal, Chrystal; Burrell, Keith H.; Grierson, Brian A.; ...

2014-08-08

A new diagnostic has been developed on DIII-D that determines the impurity poloidal rotation from the poloidal asymmetry in the toroidal angular rotation velocity. This asymmetry is measured with recently added tangential charge exchange viewchords on the high-field side of the tokamak midplane. Measurements are made on co- and counter-current neutral beams, allowing the charge exchange cross section effect to be measured and eliminating the need for atomic physics calculations. The diagnostic implementation on DIII-D restricts the measurement range to the core (r/a < 0.6) where, relative to measurements made with the vertical charge exchange system, the spatial resolution ismore » improved. Furthermore, significant physics results have been obtained with this new diagnostic; for example, poloidal rotation measurements that significantly exceed neoclassical predictions.« less

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.

Nanoscale Multigate TiN Metal Nanocrystal Memory Using High-k Blocking Dielectric and High-Work-Function Gate Electrode Integrated on Silcon-on-Insulator Substrate

NASA Astrophysics Data System (ADS)

Lu, Chi-Pei; Luo, Cheng-Kei; Tsui, Bing-Yue; Lin, Cha-Hsin; Tzeng, Pei-Jer; Wang, Ching-Chiun; Tsai, Ming-Jinn

2009-04-01

In this study, a charge-trapping-layer-engineered nanoscale n-channel trigate TiN nanocrystal nonvolatile memory was successfully fabricated on silicon-on-insulator (SOI) wafer. An Al2O3 high-k blocking dielectric layer and a P+ polycrystalline silicon gate electrode were used to obtain low operation voltage and suppress the back-side injection effect, respectively. TiN nanocrystals were formed by annealing TiN/Al2O3 nanolaminates deposited by an atomic layer deposition system. The memory characteristics of various samples with different TiN wetting layer thicknesses, post-deposition annealing times, and blocking oxide thicknesses were also investigated. The sample with a thicker wetting layer exhibited a much larger memory window than other samples owing to its larger nanocrystal size. Good retention with a mere 12% charge loss for up to 10 years and high endurance were also obtained. Furthermore, gate disturbance and read disturbance were measured with very small charge migrations after a 103 s stressing bias.

Impact of new clock technologies on the stability and accuracy of the International Atomic Time TAI.

NASA Astrophysics Data System (ADS)

Thomas, C.

1997-05-01

The BIPM Time Section is in charge of the generation of the reference time scales TAI and UTC. Both time scales are obtained in deferred-time by combining the data front a number of atomic clocks spread worldwide. The accuracy of TAI is estimated by the departure between the duration of the TAI scale interval and the SI second as produced on the rotating geoid by primary frequency standards. It is now possible to estimate TAI accuracy through the combination of results obtained from six different primary standards: LPTF-FO1, PTB CS1, PTB CS2, PTB CS3, NIST-7, and SU MCsR 102, all corrected for the black-body radiation shift. This led to a mean departure of the TAI scale interval of +2.0×10-14s over 1995, known with a relative uncertainty of 0.5×10-14(1σ).

Nuclear charge radii: density functional theory meets Bayesian neural networks

NASA Astrophysics Data System (ADS)

Utama, R.; Chen, Wei-Chia; Piekarewicz, J.

2016-11-01

The distribution of electric charge in atomic nuclei is fundamental to our understanding of the complex nuclear dynamics and a quintessential observable to validate nuclear structure models. The aim of this study is to explore a novel approach that combines sophisticated models of nuclear structure with Bayesian neural networks (BNN) to generate predictions for the charge radii of thousands of nuclei throughout the nuclear chart. A class of relativistic energy density functionals is used to provide robust predictions for nuclear charge radii. In turn, these predictions are refined through Bayesian learning for a neural network that is trained using residuals between theoretical predictions and the experimental data. Although predictions obtained with density functional theory provide a fairly good description of experiment, our results show significant improvement (better than 40%) after BNN refinement. Moreover, these improved results for nuclear charge radii are supplemented with theoretical error bars. We have successfully demonstrated the ability of the BNN approach to significantly increase the accuracy of nuclear models in the predictions of nuclear charge radii. However, as many before us, we failed to uncover the underlying physics behind the intriguing behavior of charge radii along the calcium isotopic chain.

Structural, vibrational, and quasiparticle properties of the Peierls semiconductor BaBiO3 : A hybrid functional and self-consistent GW+vertex-corrections study

NASA Astrophysics Data System (ADS)

Franchini, C.; Sanna, A.; Marsman, M.; Kresse, G.

2010-02-01

BaBiO3 is characterized by a charge disproportionation with half of the Bi atoms possessing a valence 3+ and half a valence 5+ . Because of self-interaction errors, local- and semilocal-density functionals fail to describe the charge disproportionation quantitatively, yielding a too small structural distortion and no band gap. Using hybrid functionals, we obtain a satisfactory description of the structural, electronic, optical, and vibrational properties of BaBiO3 . The results obtained using GW (Green’s function G and screened Coulomb potential W) based schemes on top of hybrid functionals, including fully self-consistent GW calculations with vertex corrections in the dielectric screening, qualitatively confirm the Heyd-Scuseria-Ernzerhof picture but a systematic overestimation of the band gap by about 0.4 eV is observed.

Dielectric and vibrational properties of amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2004-09-01

We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.

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

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.

Extended Fenske-Hall LCAO MO calculations of core-level shifts in solid P compounds

NASA Astrophysics Data System (ADS)

Franke, R.; Chassé, T.; Reinhold, J.; Streubel, P.; Szargan, R.

1997-08-01

Extended Fenske-Hall LCAO-MO ΔSCF calculations on solids modelled as H-pseudoatom saturated clusters are reported. The computational results verify the experimentally obtained initial-state (effective atomic charges, Madelung potential) and relaxation-energy contributions to the XPS phosphorus core-level binding energy shifts measured in Na 3PO 3S, Na 3PO 4, Na 2PO 3F and NH 4PF 6 in reference to red phosphorus. It is shown that the different initial-state contributions observed in the studied phosphates are determined by local and nonlocal terms while the relaxation-energy contributions are mainly dependent on the nature of the nearest neighbors of the phosphorus atom.

Pressure dependence of electron density distribution and d-p-π hybridization in titanate perovskite ferroelectrics

NASA Astrophysics Data System (ADS)

Yamanaka, Takamitsu; Nakamoto, Yuki; Ahart, Muhtar; Mao, Ho-kwang

2018-04-01

Electron density distributions of PbTi O3 , BaTi O3 , and SrTi O3 were determined by synchrotron x-ray powder diffraction up to 55 GPa at 300 K and ab initio quantum chemical molecular orbital (MO) calculations, together with a combination of maximum entropy method calculations. The intensity profiles of Bragg peaks reveal split atoms in both ferroelectric PbTi O3 and BaTi O3 , reflecting the two possible positions occupied by the Ti atom. The experimentally obtained atomic structure factor was used for the determination of the deformation in electron density and the d-p-π hybridization between dx z (and dy z) of Ti and px (and py) of O in the Ti-O bond. Ab initio MO calculations proved the change of the molecular orbital coupling and of Mulliken charges with a structure transformation. The Mulliken charge of Ti in the Ti O6 octahedron increased in the ionicity with increasing pressure in the cubic phase. The bonding nature is changed with a decrease in the hybridization of the Ti-O bond and the localization of the electron density with increasing pressure. The hybridization decreases with pressure and disappears in the cubic paraelectric phase, which has a much more localized electron density distribution.

Ultraflat Au nanoplates as a new building block for molecular electronics.

PubMed

Jeong, Wooseok; Lee, Miyeon; Lee, Hyunsoo; Lee, Hyoban; Kim, Bongsoo; Park, Jeong Young

2016-05-27

We demonstrate the charge transport properties of a self-assembled organic monolayer on Au nanoplates with conductive probe atomic force microscopy (CP-AFM). Atomically flat Au nanoplates, a few hundred micrometers on each side, that have only (111) surfaces, were synthesized using the chemical vapor transport method; these nanoplates were employed as the substrates for hexadecanethiol (HDT) self-assembled monolayers (SAMs). Atomic-scale high-resolution images show (√3 x √3) R30° molecular periodicity, indicating a well-ordered structure of the HDT on the Au nanoplates. We observed reduced friction and adhesion forces on the HDT SAMs on Au nanoplates, compared with Si substrates, which is consistent with the lubricating nature of HDT SAMs. The electrical properties, such as I-V characteristics and current as a function of load, were measured using CP-AFM. We obtained a tunneling decay constant (β) of 0.57 Å(-1), including through-bond (βtb = 0.99 Å(-1)) and through-space (βts = 1.36 Å(-1)) decay constants for the two-pathway model. This indicates that the charge transport properties of HDT SAMs on Au nanoplates are consistent with those on a Au (111) film, suggesting that SAMs on nanoplates can provide a new building block for molecular electronics.

Multivariate statistical characterization of charged and uncharged domain walls in multiferroic hexagonal YMnO3 single crystal visualized by a spherical aberration-corrected STEM.

PubMed

Matsumoto, Takao; Ishikawa, Ryo; Tohei, Tetsuya; Kimura, Hideo; Yao, Qiwen; Zhao, Hongyang; Wang, Xiaolin; Chen, Dapeng; Cheng, Zhenxiang; Shibata, Naoya; Ikuhara, Yuichi

2013-10-09

A state-of-the-art spherical aberration-corrected STEM was fully utilized to directly visualize the multiferroic domain structure in a hexagonal YMnO3 single crystal at atomic scale. With the aid of multivariate statistical analysis (MSA), we obtained unbiased and quantitative maps of ferroelectric domain structures with atomic resolution. Such a statistical image analysis of the transition region between opposite polarizations has confirmed atomically sharp transitions of ferroelectric polarization both in antiparallel (uncharged) and tail-to-tail 180° (charged) domain boundaries. Through the analysis, a correlated subatomic image shift of Mn-O layers with that of Y layers, exhibiting a double-arc shape of reversed curvatures, have been elucidated. The amount of image shift in Mn-O layers along the c-axis is statistically significant as small as 0.016 nm, roughly one-third of the evident image shift of 0.048 nm in Y layers. Interestingly, a careful analysis has shown that such a subatomic image shift in Mn-O layers vanishes at the tail-to-tail 180° domain boundaries. Furthermore, taking advantage of the annular bright field (ABF) imaging technique combined with MSA, the tilting of MnO5 bipyramids, the very core mechanism of multiferroicity of the material, is evaluated.

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.

Boron Nitride Nanoporous Membranes with High Surface Charge by Atomic Layer Deposition.

PubMed

Weber, Matthieu; Koonkaew, Boonprakrong; Balme, Sebastien; Utke, Ivo; Picaud, Fabien; Iatsunskyi, Igor; Coy, Emerson; Miele, Philippe; Bechelany, Mikhael

2017-05-17

In this work, we report the design and the fine-tuning of boron nitride single nanopore and nanoporous membranes by atomic layer deposition (ALD). First, we developed an ALD process based on the use of BBr 3 and NH 3 as precursors in order to synthesize BN thin films. The deposited films were characterized in terms of thickness, composition, and microstructure. Next, we used the newly developed process to grow BN films on anodic aluminum oxide nanoporous templates, demonstrating the conformality benefit of BN prepared by ALD, and its scalability for the manufacturing of membranes. For the first time, the ALD process was then used to tune the diameter of fabricated single transmembrane nanopores by adjusting the BN thickness and to enable studies of the fundamental aspects of ionic transport on a single nanopore. At pH = 7, we estimated a surface charge density of 0.16 C·m -2 without slip and 0.07 C·m -2 considering a reasonable slip length of 3 nm. Molecular dynamics simulations performed with experimental conditions confirmed the conductivities and the sign of surface charges measured. The high ion transport results obtained and the ability to fine-tune nanoporous membranes by such a scalable method pave the way toward applications such as ionic separation, energy harvesting, and ultrafiltration devices.

Passivation mechanism of thermal atomic layer-deposited Al2O3 films on silicon at different annealing temperatures.

PubMed

Zhao, Yan; Zhou, Chunlan; Zhang, Xiang; Zhang, Peng; Dou, Yanan; Wang, Wenjing; Cao, Xingzhong; Wang, Baoyi; Tang, Yehua; Zhou, Su

2013-03-02

Thermal atomic layer-deposited (ALD) aluminum oxide (Al2O3) acquires high negative fixed charge density (Qf) and sufficiently low interface trap density after annealing, which enables excellent surface passivation for crystalline silicon. Qf can be controlled by varying the annealing temperatures. In this study, the effect of the annealing temperature of thermal ALD Al2O3 films on p-type Czochralski silicon wafers was investigated. Corona charging measurements revealed that the Qf obtained at 300°C did not significantly affect passivation. The interface-trapping density markedly increased at high annealing temperature (>600°C) and degraded the surface passivation even at a high Qf. Negatively charged or neutral vacancies were found in the samples annealed at 300°C, 500°C, and 750°C using positron annihilation techniques. The Al defect density in the bulk film and the vacancy density near the SiOx/Si interface region decreased with increased temperature. Measurement results of Qf proved that the Al vacancy of the bulk film may not be related to Qf. The defect density in the SiOx region affected the chemical passivation, but other factors may dominantly influence chemical passivation at 750°C.

Passivation mechanism of thermal atomic layer-deposited Al2O3 films on silicon at different annealing temperatures

PubMed Central

2013-01-01

Thermal atomic layer-deposited (ALD) aluminum oxide (Al2O3) acquires high negative fixed charge density (Qf) and sufficiently low interface trap density after annealing, which enables excellent surface passivation for crystalline silicon. Qf can be controlled by varying the annealing temperatures. In this study, the effect of the annealing temperature of thermal ALD Al2O3 films on p-type Czochralski silicon wafers was investigated. Corona charging measurements revealed that the Qf obtained at 300°C did not significantly affect passivation. The interface-trapping density markedly increased at high annealing temperature (>600°C) and degraded the surface passivation even at a high Qf. Negatively charged or neutral vacancies were found in the samples annealed at 300°C, 500°C, and 750°C using positron annihilation techniques. The Al defect density in the bulk film and the vacancy density near the SiOx/Si interface region decreased with increased temperature. Measurement results of Qf proved that the Al vacancy of the bulk film may not be related to Qf. The defect density in the SiOx region affected the chemical passivation, but other factors may dominantly influence chemical passivation at 750°C. PMID:23452508

The Helium Warm Breeze in IBEX Observations As a Result of Charge-exchange Collisions in the Outer Heliosheath

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

Bzowski, Maciej; Kubiak, Marzena A.; Czechowski, Andrzej

2017-08-10

We simulated the signal due to neutral He atoms, observed by the Interstellar Boundary Explorer ( IBEX ), assuming that charge-exchange collisions between neutral He atoms and He{sup +} ions operate everywhere between the heliopause and a distant source region in the local interstellar cloud, where the neutral and charged components are in thermal equilibrium. We simulated several test cases of the plasma flow within the outer heliosheath (OHS) and investigated the signal generation for plasma flows both in the absence and in the presence of the interstellar magnetic field (ISMF). We found that a signal in the portion ofmore » IBEX data identified as being due to the Warm Breeze (WB) does not arise when a homogeneous plasma flow in front of the heliopause is assumed, but it appears immediately when any reasonable disturbance in its flow due to the presence of the heliosphere is assumed. We obtained a good qualitative agreement between the data selected for comparison and the simulations for a model flow with the velocity vector of the unperturbed gas and the direction and intensity of magnetic field adopted from recent determinations. We conclude that direct-sampling observations of neutral He atoms at 1 au from the Sun are a sensitive tool for investigating the flow of interstellar matter in the OHS, that the WB is indeed the secondary population of interstellar helium, which was hypothesized earlier, and that the WB signal is consistent with the heliosphere distorted from axial symmetry by the ISMF.« less

Band alignment of atomic layer deposited MgO/Zn0.8Al0.2O heterointerface determined by charge corrected X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Yan, Baojun; Liu, Shulin; Yang, Yuzhen; Heng, Yuekun

2016-05-01

Pure magnesium (MgO) and zinc oxide doped with aluminum oxide (Zn0.8Al0.2O) were prepared via atomic layer deposition. We have studied the structure and band gap of bulk Zn0.8Al0.2O material by X-ray diffractometer (XRD) and Tauc method, and the band offsets and alignment of atomic layer deposited MgO/Zn0.8Al0.2O heterointerface were investigated systematically using X-ray photoelectron spectroscopy (XPS) in this study. Different methodologies, such as neutralizing electron gun, the use of C 1s peak recalibration and zero charging method, were applied to recover the actual position of the core levels in insulator materials which were easily influenced by differential charging phenomena. Schematic band alignment diagram, valence band offset (ΔEV) and conduction band offset (ΔEC) for the interface of the MgO/Zn0.8Al0.2O heterostructure have been constructed. An accurate value of ΔEV = 0.72 ± 0.11 eV was obtained from various combinations of core levels of heterojunction with varied MgO thickness. Given the experimental band gaps of 7.83 eV for MgO and 5.29 eV for Zn0.8Al0.2O, a type-II heterojunction with a ΔEC of 3.26 ± 0.11 eV was found. Band offsets and alignment studies of these heterojunctions are important for gaining deep consideration to the design of various optoelectronic devices based on such heterointerface.

Electron spectroscopy for chemical analysis: Sample analysis

NASA Technical Reports Server (NTRS)

Carter, W. B.

1989-01-01

Exposure conditions in atomic oxygen (ESCA) was performed on an SSL-100/206 Small Spot Spectrometer. All data were taken with the use of a low voltage electron flood gun and a charge neutralization screen to minimize charging effects on the data. The X-ray spot size and electron flood gun voltage used are recorded on the individual spectra as are the instrumental resolutions. Two types of spectra were obtained for each specimen: (1) general surveys, and (2) high resolution spectra. The two types of data reduction performed are: (1) semiquantitative compositional analysis, and (2) peak fitting. The materials analyzed are: (1) kapton 4, 5, and 6, (2) HDPE 19, 20, and 21, and (3) PVDF 4, 5, and 6.

A novel double-focusing time-of-flight mass spectrometer for absolute recoil ion cross sections measurements

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

Sigaud, L., E-mail: lsigaud@if.uff.br; Jesus, V. L. B. de; Ferreira, Natalia

In this work, the inclusion of an Einzel-like lens inside the time-of-flight drift tube of a standard mass spectrometer coupled to a gas cell—to study ionization of atoms and molecules by electron impact—is described. Both this lens and a conical collimator are responsible for further focalization of the ions and charged molecular fragments inside the spectrometer, allowing a much better resolution at the time-of-flight spectra, leading to a separation of a single mass-to-charge unit up to 100 a.m.u. The procedure to obtain the overall absolute efficiency of the spectrometer and micro-channel plate detector is also discussed.

A novel double-focusing time-of-flight mass spectrometer for absolute recoil ion cross sections measurements.

PubMed

Sigaud, L; de Jesus, V L B; Ferreira, Natalia; Montenegro, E C

2016-08-01

In this work, the inclusion of an Einzel-like lens inside the time-of-flight drift tube of a standard mass spectrometer coupled to a gas cell-to study ionization of atoms and molecules by electron impact-is described. Both this lens and a conical collimator are responsible for further focalization of the ions and charged molecular fragments inside the spectrometer, allowing a much better resolution at the time-of-flight spectra, leading to a separation of a single mass-to-charge unit up to 100 a.m.u. The procedure to obtain the overall absolute efficiency of the spectrometer and micro-channel plate detector is also discussed.

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.

Low-temperature SiON films deposited by plasma-enhanced atomic layer deposition method using activated silicon precursor

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

Suh, Sungin; Kim, Jun-Rae; Kim, Seongkyung

2016-01-15

It has not been an easy task to deposit SiN at low temperature by conventional plasma-enhanced atomic layer deposition (PE-ALD) since Si organic precursors generally have high activation energy for adsorption of the Si atoms on the Si-N networks. In this work, in order to achieve successful deposition of SiN film at low temperature, the plasma processing steps in the PE-ALD have been modified for easier activation of Si precursors. In this modification, the efficiency of chemisorption of Si precursor has been improved by additional plasma steps after purging of the Si precursor. As the result, the SiN films preparedmore » by the modified PE-ALD processes demonstrated higher purity of Si and N atoms with unwanted impurities such as C and O having below 10 at. % and Si-rich films could be formed consequently. Also, a very high step coverage ratio of 97% was obtained. Furthermore, the process-optimized SiN film showed a permissible charge-trapping capability with a wide memory window of 3.1 V when a capacitor structure was fabricated and measured with an insertion of the SiN film as the charge-trap layer. The modified PE-ALD process using the activated Si precursor would be one of the most practical and promising solutions for SiN deposition with lower thermal budget and higher cost-effectiveness.« less

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

Distinct Optoelectronic Signatures for Charge Transfer and Energy Transfer in Quantum Dot-MoS 2 Hybrid Photodetectors Revealed by Photocurrent Imaging Microscopy

DOE PAGES

Li, Mingxing; Chen, Jia-Shiang; Routh, Prahlad K.; ...

2018-05-17

Atomically thin transition metal dichalcogenides (TMDCs) have intriguing nanoscale properties like high charge mobility, photosensitivity, layer-thickness-dependent bandgap, and mechanical flexibility, which are all appealing for the development of next generation optoelectronic, catalytic, and sensory devices. Their atomically thin thickness, however, renders TMDCs poor absorptivity. For this study, bilayer MoS 2 is combined with core-only CdSe QDs and core/shell CdSe/ZnS QDs to obtain hybrids with increased light harvesting and exhibiting interfacial charge transfer (CT) and nonradiative energy transfer (NET), respectively. Field-effect transistors based on these hybrids and their responses to varying laser power and applied gate voltage are investigated with scanningmore » photocurrent microscopy (SPCM) in view of their potential utilization in light harvesting and photodetector applications. CdSe–MoS 2 hybrids are found to exhibit encouraging properties for photodetectors, like high responsivity and fast on/off response under low light exposure while CdSe/ZnS–MoS 2 hybrids show enhanced charge carrier generation with increased light exposure, thus suitable for photovoltaics. While distinguishing optically between CT and NET in QD–TMDCs is nontrivial, it is found that they can be differentiated by SPCM as these two processes exhibit distinctive light-intensity dependencies: CT causes a photogating effect, decreasing the photocurrent response with increasing light power while NET increases the photocurrent response with increasing light power, opposite to CT case.« less

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.

Distinct Optoelectronic Signatures for Charge Transfer and Energy Transfer in Quantum Dot-MoS 2 Hybrid Photodetectors Revealed by Photocurrent Imaging Microscopy

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

Li, Mingxing; Chen, Jia-Shiang; Routh, Prahlad K.

Atomically thin transition metal dichalcogenides (TMDCs) have intriguing nanoscale properties like high charge mobility, photosensitivity, layer-thickness-dependent bandgap, and mechanical flexibility, which are all appealing for the development of next generation optoelectronic, catalytic, and sensory devices. Their atomically thin thickness, however, renders TMDCs poor absorptivity. For this study, bilayer MoS 2 is combined with core-only CdSe QDs and core/shell CdSe/ZnS QDs to obtain hybrids with increased light harvesting and exhibiting interfacial charge transfer (CT) and nonradiative energy transfer (NET), respectively. Field-effect transistors based on these hybrids and their responses to varying laser power and applied gate voltage are investigated with scanningmore » photocurrent microscopy (SPCM) in view of their potential utilization in light harvesting and photodetector applications. CdSe–MoS 2 hybrids are found to exhibit encouraging properties for photodetectors, like high responsivity and fast on/off response under low light exposure while CdSe/ZnS–MoS 2 hybrids show enhanced charge carrier generation with increased light exposure, thus suitable for photovoltaics. While distinguishing optically between CT and NET in QD–TMDCs is nontrivial, it is found that they can be differentiated by SPCM as these two processes exhibit distinctive light-intensity dependencies: CT causes a photogating effect, decreasing the photocurrent response with increasing light power while NET increases the photocurrent response with increasing light power, opposite to CT case.« 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)

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.).

Towards All-Inorganic Transport Layers for Wide-Band-Gap Formamidinium Lead Bromide-Based Planar Photovoltaics

DOE PAGES

Subbiah, Anand S.; Mahuli, Neha; Agarwal, Sumanshu; ...

2017-07-21

Hybrid perovskite photovoltaic devices heavily rely on the use of organic (rather than inorganic) charge-transport layers on top of a perovskite absorber layer because of difficulties in depositing inorganic materials on top of these fragile absorber layers. However, in comparison to the unstable and expensive organic transport materials, inorganic charge-transport layers provide improved charge transport and stability to the device architecture. Here, we report photovoltaic devices using all-inorganic transport layers in a planar p-i-n junction device configuration using formamidinium lead tribromide (FAPbBr 3) as an absorber. Efficient planar devices are obtained through atomic layer deposition of nickel oxide and sputteredmore » zinc oxide as hole- and electron-transport materials, respectively. Using only inorganic charge-transport layers resulted in planar FAPbBr 3 devices with a power conversion efficiency of 6.75% at an open-circuit voltage of 1.23 V. In conclusion, the transition of planar FAPbBr 3 devices making from all-organic towards all-inorganic charge-transport layers is studied in detail.« less

Towards All-Inorganic Transport Layers for Wide-Band-Gap Formamidinium Lead Bromide-Based Planar Photovoltaics

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

Subbiah, Anand S.; Mahuli, Neha; Agarwal, Sumanshu

Hybrid perovskite photovoltaic devices heavily rely on the use of organic (rather than inorganic) charge-transport layers on top of a perovskite absorber layer because of difficulties in depositing inorganic materials on top of these fragile absorber layers. However, in comparison to the unstable and expensive organic transport materials, inorganic charge-transport layers provide improved charge transport and stability to the device architecture. Here, we report photovoltaic devices using all-inorganic transport layers in a planar p-i-n junction device configuration using formamidinium lead tribromide (FAPbBr 3) as an absorber. Efficient planar devices are obtained through atomic layer deposition of nickel oxide and sputteredmore » zinc oxide as hole- and electron-transport materials, respectively. Using only inorganic charge-transport layers resulted in planar FAPbBr 3 devices with a power conversion efficiency of 6.75% at an open-circuit voltage of 1.23 V. In conclusion, the transition of planar FAPbBr 3 devices making from all-organic towards all-inorganic charge-transport layers is studied in detail.« less

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.

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.

Investigation of tunneling current and local contact potential difference on the TiO2(110) surface by AFM/KPFM at 78 K.

PubMed

Wen, Huan Fei; Li, Yan Jun; Arima, Eiji; Naitoh, Yoshitaka; Sugawara, Yasuhiro; Xu, Rui; Cheng, Zhi Hai

2017-03-10

We propose a new multi-image method for obtaining the frequency shift, tunneling current and local contact potential difference (LCPD) on a TiO 2 (110) surface with atomic resolution. The tunneling current image reveals rarely observed surface oxygen atoms contrary to the conventional results. We analyze how the surface and subsurface defects affect the distribution of the LCPD. In addition, the subsurface defects are observed clearly in the tunneling current image, in contrast to a topographic image. To clarify the origin of the atomic contrast, we perform site-dependent spectroscopy as a function of the tip-sample distance. The multi-image method is expected to be widely used to investigate the charge transfer phenomena between the nanoparticles and surface sites, and it is useful for elucidating the mechanisms of catalytic reactions.

Precision Muonium Spectroscopy

NASA Astrophysics Data System (ADS)

Jungmann, Klaus P.

2016-09-01

The muonium atom is the purely leptonic bound state of a positive muon and an electron. It has a lifetime of 2.2 µs. The absence of any known internal structure provides for precision experiments to test fundamental physics theories and to determine accurate values of fundamental constants. In particular ground state hyperfine structure transitions can be measured by microwave spectroscopy to deliver the muon magnetic moment. The frequency of the 1s-2s transition in the hydrogen-like atom can be determined with laser spectroscopy to obtain the muon mass. With such measurements fundamental physical interactions, in particular quantum electrodynamics, can also be tested at highest precision. The results are important input parameters for experiments on the muon magnetic anomaly. The simplicity of the atom enables further precise experiments, such as a search for muonium-antimuonium conversion for testing charged lepton number conservation and searches for possible antigravity of muons and dark matter.

Ground-state energies and highest occupied eigenvalues of atoms in exchange-only density-functional theory

NASA Astrophysics Data System (ADS)

Li, Yan; Harbola, Manoj K.; Krieger, J. B.; Sahni, Viraht

1989-11-01

The exchange-correlation potential of the Kohn-Sham density-functional theory has recently been interpreted as the work required to move an electron against the electric field of its Fermi-Coulomb hole charge distribution. In this paper we present self-consistent results for ground-state total energies and highest occupied eigenvalues of closed subshell atoms as obtained by this formalism in the exchange-only approximation. The total energies, which are an upper bound, lie within 50 ppm of Hartree-Fock theory for atoms heavier than Be. The highest occupied eigenvalues, as a consequence of this interpretation, approximate well the experimental ionization potentials. In addition, the self-consistently calculated exchange potentials are very close to those of Talman and co-workers [J. D. Talman and W. F. Shadwick, Phys. Rev. A 14, 36 (1976); K. Aashamar, T. M. Luke, and J. D. Talman, At. Data Nucl. Data Tables 22, 443 (1978)].

Cyclic steady states in diffusion-induced plasticity with applications to lithium-ion batteries

NASA Astrophysics Data System (ADS)

Peigney, Michaël

2018-02-01

Electrode materials in lithium-ion batteries offer an example of medium in which stress and plastic flow are generated by the diffusion of guest atoms. In such a medium, deformation and diffusion are strongly coupled processes. For designing electrodes with improved lifetime and electro-mechanical efficiency, it is crucial to understand how plasticity and diffusion evolve over consecutive charging-recharging cycles. With such questions in mind, this paper provides general results for the large-time behavior of media coupling plasticity with diffusion when submitted to cyclic chemo-mechanical loadings. Under suitable assumptions, we show that the stress, the plastic strain rate, the chemical potential and the flux of guest atoms converge to a cyclic steady state which is largely independent of the initial state. A special emphasis is laid on the special case of elastic shakedown, which corresponds to the situation where the plastic strain stops evolving after a sufficiently large number of cycles. Elastic shakedown is expected to be beneficial for the fatigue behavior and - in the case of lithium-ion batteries - for the electro-chemical efficiency. We provide a characterization of the chemo-mechanical loadings for which elastic shakedown occurs. Building on that characterization, we suggest a general method for designing structures in such fashion that they operate in the elastic shakedown regime, whatever the initial state is. An attractive feature of the proposed method is that incremental analysis of the fully coupled plasticity-diffusion problem is avoided. The results obtained are applied to the model problem of a battery electrode cylinder particle under cyclic charging. Closed-form expressions are obtained for the set of charging rates and charging amplitudes for which elastic shakedown occurs, as well as for the corresponding cyclic steady states of stress, lithium concentration and chemical potential. Some results for a spherical particle are also presented.

Ab initio study of charge transfer in B2+ low-energy collisions with atomic hydrogen

NASA Astrophysics Data System (ADS)

Turner, A. R.; Cooper, D. L.; Wang, J. G.; Stancil, P. C.

2003-07-01

Charge transfer processes due to collisions of ground state B2+(2s 2S) ions with atomic hydrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial and rotational coupling matrix elements obtained with the spin-coupled valence-bond approach. Total and state-selective cross sections and rate coefficients are presented. Comparison with the existing experiments shows our results to be in good agreement. When E<80 eV/u, the differences between the current total MOCC cross sections with and without rotational coupling are small (<3%). Rotational coupling becomes more important with increasing energy: for collision energies E>400 eV/u, inclusion of rotational coupling increases the total cross section by 50% 80%, improving the agreement between the current calculations and experiments. For state-selective cross sections, rotational coupling induces mixing between different symmetries; however, its effect, especially at low collision energies, is not as important as had been suggested in previous work.

A comparison of neutron and gamma damage effects on silica glass in a nuclear reactor radiation environment

NASA Astrophysics Data System (ADS)

Holcomb, David E.; Miller, Don W.

1993-08-01

A study of the relative damage effects of neutrons and gamma rays on silica glass in a nuclear reactor radiation environment is reported. The neutron and gamma energy spectra of the Ohio State University Research Reactor beam port #1 were applied to silica glass to obtain primary knock-on charged particle energy spectra. The resultant charged particle spectra were then applied to the polyatomic forms of the Lindhard et al. integrodifferential equation for damage energy and the Parkin and Coulter integrodifferential equation for net atomic displacement. The results show that near a nuclear reactor core the vast majority of the dose to silica is due to gamma rays (factor of roughly 40) and that neutrons cause much more displacement damage than gamma rays (35 times the oxygen displacement rate and 500 times the silicon displacement rate). However, pure silica core optical fibers irradiated in a nuclear reactor's mixed neutron/gamma environment exhibit little difference in transmission loss on an equal dose basis compared to fibers irradiated in a gamma only environment, indicating that atomic displacement is not a significant damage mechanism.

Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis.

PubMed

Ivanov, Yuri D; Pleshakova, Tatyana; Malsagova, Krystina; Kozlov, Andrey; Kaysheva, Anna; Kopylov, Arthur; Izotov, Alexander; Andreeva, Elena; Kanashenko, Sergey; Usanov, Sergey; Archakov, Alexander

2014-10-01

An approach combining atomic force microscopy (AFM) fishing and mass spectrometry (MS) analysis to detect proteins at ultra-low concentrations is proposed. Fishing out protein molecules onto a highly oriented pyrolytic graphite surface coated with polytetrafluoroethylene film was carried out with and without application of an external electric field. After that they were visualized by AFM and identified by MS. It was found that injection of solution leads to charge generation in the solution, and an electric potential within the measuring cell is induced. It was demonstrated that without an external electric field in the rapid injection input of diluted protein solution the fishing is efficient, as opposed to slow fluid input. The high sensitivity of this method was demonstrated by detection of human serum albumin and human cytochrome b5 in 10(-17) -10(-18) m water solutions. It was shown that an external negative voltage applied to highly oriented pyrolytic graphite hinders the protein fishing. The efficiency of fishing with an external positive voltage was similar to that obtained without applying any voltage. © 2014 FEBS.

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.

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.

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.

Visualization of the evolution of charged droplet formation and jet transition in electrostatic atomization

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

Huo, Yuanping, E-mail: huoyuanping@gmail.com; Wang, Junfeng, E-mail: wangjunfeng@ujs.edu.cn; Zuo, Ziwen

2015-11-15

A detailed experimental study on the evolution of charged droplet formation and jet transition from a capillary is reported. By means of high-speed microscopy, special attention has been paid to the dynamics of the liquid thread and satellite droplets in the dripping mode, and a method for calculating the surface charge on the satellite droplet is proposed. Jet transition behavior based on the electric Bond number has been visualized, droplet sizes and velocities are measured to obtain the ejection characteristic of the spray plume, and the charge and hydrodynamic relaxation are linked to give explanations for ejection dynamics with differentmore » properties. The results show that the relative length is very sensitive to the hydrodynamic relaxation time. The magnitude of the electric field strength dominates the behavior of coalescence and noncoalescence, with the charge relationship between the satellite droplet and the main droplet being clear for every noncoalescence movement. Ejection mode transitions mainly depend on the magnitude of the electric Bond number, and the meniscus dynamics is determined by the ratio of the charge relaxation time to the hydrodynamic relaxation time.« less

Upgrade of the TITAN EBIT High Voltage Operation

NASA Astrophysics Data System (ADS)

Foster, Matt; Titan Collaboration

2016-09-01

TRIUMF's Ion Trap for Atomic and Nuclear science (TITAN) is a setup dedicated to highly precise mass measurements of short-lived isotopes down to 10ms. TITAN's Electron Beam Ion Trap (EBIT) is a charge breeder integrated into the setup to perform in-trap decay spectroscopy of highly charged ions and increase the precision of mass measurements. In its previous configuration TITAN's EBIT could not fulfil its maximum design specification due to high voltage safety restrictions, limiting its obtainable charge states. A recently completed upgrade of the high voltage operation that will allow the EBIT to fulfil its design specification and achieve higher charge states for heavier species is undergoing preliminary tests with stable beam. Simulations were performed to optimise the injection and extraction efficiency at high voltage and initial tests have involved using a Ge detector to identify x-rays produced by charge breeding stable ions. Future work comprises exploring electron capture rates of Ne-, He- and H-like charge states of 64Cu and higher masses, which were not previously accessible. The function of the EBIT within the TITAN setup, the work carried out on the upgrade thus far and its scope for future work will be presented.

Ionic Adsorption and Desorption of CNT Nanoropes

PubMed Central

Shang, Jun-Jun; Yang, Qing-Sheng; Yan, Xiao-Hui; He, Xiao-Qiao; Liew, Kim-Meow

2016-01-01

A nanorope is comprised of several carbon nanotubes (CNTs) with different chiralities. A molecular dynamic model is built to investigate the ionic adsorption and desorption of the CNT nanoropes. The charge distribution on the nanorope is obtained by using a modified gradient method based on classical electrostatic theory. The electrostatic interactions among charged carbon atoms are calculated by using the Coulomb law. It was found here that the charged nanorope can adsorb heavy metal ions, and the adsorption and desorption can be realized by controlling the strength of applied electric field. The distance between the ions and the nanorope as well as the amount of ions have an effect on the adsorption capacity of the nanorope. The desorption process takes less time than that of adsorption. The study indicates that the CNT nanorope can be used as a core element of devices for sewage treatment. PMID:28335306

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

Ionic Adsorption and Desorption of CNT Nanoropes.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Yan, Xiao-Hui; He, Xiao-Qiao; Liew, Kim-Meow

2016-09-28

A nanorope is comprised of several carbon nanotubes (CNTs) with different chiralities. A molecular dynamic model is built to investigate the ionic adsorption and desorption of the CNT nanoropes. The charge distribution on the nanorope is obtained by using a modified gradient method based on classical electrostatic theory. The electrostatic interactions among charged carbon atoms are calculated by using the Coulomb law. It was found here that the charged nanorope can adsorb heavy metal ions, and the adsorption and desorption can be realized by controlling the strength of applied electric field. The distance between the ions and the nanorope as well as the amount of ions have an effect on the adsorption capacity of the nanorope. The desorption process takes less time than that of adsorption. The study indicates that the CNT nanorope can be used as a core element of devices for sewage treatment.

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

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.

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

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.

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.

Dissociative adsorption of water on Au/MgO/Ag(001) from first principles calculations

NASA Astrophysics Data System (ADS)

Nevalaita, J.; Häkkinen, H.; Honkala, K.

2015-10-01

The molecular and dissociative adsorption of water on a Ag-supported 1 ML, 2 ML and 3 ML-a six atomic layer-thick MgO films with a single Au adatom is investigated using density functional theory calculations. The obtained results are compared to a bulk MgO(001) surface with an Au atom. On thin films the negatively charged Au strengthens the binding of the polar water molecule due to the attractive Au-H interaction. The adsorption energy trends of OH and H with respect to the film thickness depend on an adsorption site. In the case OH or H binds atop Au on MgO/Ag(001), the adsorption becomes more exothermic with the increasing film thickness, while the reverse trend is seen when the adsorption takes place on bare MgO/Ag(001). This behavior can be explained by different bonding mechanisms identified with the Bader analysis. Interestingly, we find that the rumpling of the MgO film and the MgO-Ag interface distance correlate with the charge transfer over the thin film and the interface charge, respectively. Moreover, we employ a modified Born-Haber-cycle to analyze the effect of film thickness to the adsorption energy of isolated Au and OH species on MgO/Ag(001). The analysis shows that the attractive Coulomb interaction between the negatively charged adsorbate and the positive MgO-Ag-interface does not completely account for the weaker binding with increasing film thickness. The redox energy associated with the charge transfer from the interface to the adsorbate is more exothermic with the increasing film thickness and partly compensates the decrease in the attractive Coulomb interaction.

Gamma and proton irradiation effects and thermal stability of electrical characteristics of metal-oxide-silicon capacitors with atomic layer deposited Al 2O 3 dielectric

DOE PAGES

J. M. Rafi; Lynn, D.; Pellegrini, G.; ...

2015-12-11

The radiation hardness and thermal stability of the electrical characteristics of atomic layer deposited Al 2O 3 layers to be used as passivation films for silicon radiation detectors with slim edges are investigated. To directly measure the interface charge and to evaluate its change with the ionizing dose, metal-oxide-silicon (MOS) capacitors implementing differently processed Al 2O 3 layers were fabricated on p-type silicon substrates. Qualitatively similar results are obtained for degradation of capacitance–voltage and current–voltage characteristics under gamma and proton irradiations up to equivalent doses of 30 Mrad and 21.07 Mrad, respectively. While similar negative charge densities are initially extractedmore » for all non-irradiated capacitors, superior radiation hardness is obtained for MOS structures with alumina layers grown with H 2O instead of O 3 as oxidant precursor. Competing effects between radiation-induced positive charge trapping and hydrogen release from the H 2O-grown Al 2O 3 layers may explain their higher radiation resistance. Finally, irradiated and non-irradiated MOS capacitors with differently processed Al 2O 3 layers have been subjected to thermal treatments in air at temperatures ranging between 100 °C and 200 °C and the thermal stability of their electrical characteristics has been evaluated. Partial recovery of the gamma-induced degradation has been noticed for O 3-grown MOS structures. Lastly, this can be explained by a trapped holes emission process, for which an activation energy of 1.38 ± 0.15 eV has been extracted.« less

Electron shakeoff following the β+ decay of +19Ne and +35Ar trapped ions

NASA Astrophysics Data System (ADS)

Fabian, X.; Fléchard, X.; Pons, B.; Liénard, E.; Ban, G.; Breitenfeldt, M.; Couratin, C.; Delahaye, P.; Durand, D.; Finlay, P.; Guillon, B.; Lemière, Y.; Mauger, F.; Méry, A.; Naviliat-Cuncic, O.; Porobic, T.; Quéméner, G.; Severijns, N.; Thomas, J.-C.

2018-02-01

The electron shakeoff of 19F and 35Cl atoms resulting from the β+ decay of +19Ne and +35Ar ions has been investigated using a Paul trap coupled to a time of flight recoil-ion spectrometer. The charge-state distributions of the recoiling daughter nuclei were compared to theoretical calculations based on the sudden approximation and accounting for subsequent Auger processes. The excellent agreement obtained for 35Cl is not reproduced in 19F. The shortcoming is attributed to the inaccuracy of the independent particle model employed to calculate the primary shakeoff probabilities in systems with rather low atomic numbers. This calls for more elaborate calculations, including explicitly the electron-electron correlations.

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.

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.

Charge Separation and Exciton Dynamics at Polymer/ZnO Interface from First-Principles Simulations.

PubMed

Wu, Guangfen; Li, Zi; Zhang, Xu; Lu, Gang

2014-08-07

Charge separation and exciton dynamics play a crucial role in determining the performance of excitonic photovoltaics. Using time-dependent density functional theory with a range-separated exchange-correlation functional as well as nonadiabatic ab initio molecular dynamics, we have studied the formation and dynamics of charge-transfer (CT) excitons at polymer/ZnO interface. The interfacial atomic structure, exciton density of states and conversions between exciton species are examined from first-principles. The exciton dynamics exhibits both adiabatic and nonadiabatic characters. While the adiabatic transitions are facilitated by C═C vibrations along the polymer (P3HT) backbone, the nonadiabatic transitions are realized by exciton hopping between the excited states. We find that the localized ZnO surface states lead to localized low-energy CT states and poor charge separation. In contrast, the surface states of crystalline C60 are indistinguishable from the bulk states, resulting in delocalized CT states and efficient charge separation in polymer/fullerene (P3HT/PCBM) heterojunctions. The hot CT states are found to cool down in an ultrafast time scale and may not play a major role in charge separation of P3HT/ZnO. Finally we suggest that the dimensions of nanostructured acceptors can be tuned to obtain both efficient charge separation and high open circuit voltages.

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.

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.

Tuning optical properties of magic number cluster (SiO2)4O2H4 by substitutional bonding with gold atoms.

PubMed

Cai, Xiulong; Zhang, Peng; Ma, Liuxue; Zhang, Wenxian; Ning, Xijing; Zhao, Li; Zhuang, Jun

2009-04-30

By bonding gold atoms to the magic number cluster (SiO(2))(4)O(2)H(4), two groups of Au-adsorbed shell-like clusters Au(n)(SiO(2))(4)O(2)H(4-n) (n = 1-4) and Au(n)(SiO(2))(4)O(2) (n = 5-8) were obtained, and their spectral properties were studied. The ground-state structures of these clusters were optimized by density functional theory, and the results show that in despite of the different numbers and types of the adsorbed Au atoms, the cluster core (SiO(2))(4)O(2) of T(d) point-group symmetry keeps almost unchanged. The absorption spectra were obtained by time-dependent density functional theory. From one group to the other, an extension of absorption wavelength from the UV-visible to the NIR region was observed, and in each group the absorption strengths vary linearly with the number of Au atoms. These features indicate their advantages for exploring novel materials with easily controlled tunable optical properties. Furthermore, due to the weak electronic charge transfer between the Au atoms, the clusters containing Au(2) dimers, especially Au(8)(SiO(2))(4)O(2), absorb strongly NIR light at 900 approximately 1200 nm. Such strong absorption suggests potential applications of these shell-like clusters in tumor cells thermal therapy, like the gold-coated silica nanoshells with larger sizes.

Local Electric Field Facilitates High-Performance Li-Ion Batteries.

PubMed

Liu, Youwen; Zhou, Tengfei; Zheng, Yang; He, Zhihai; Xiao, Chong; Pang, Wei Kong; Tong, Wei; Zou, Youming; Pan, Bicai; Guo, Zaiping; Xie, Yi

2017-08-22

By scrutinizing the energy storage process in Li-ion batteries, tuning Li-ion migration behavior by atomic level tailoring will unlock great potential for pursuing higher electrochemical performance. Vacancy, which can effectively modulate the electrical ordering on the nanoscale, even in tiny concentrations, will provide tempting opportunities for manipulating Li-ion migratory behavior. Herein, taking CuGeO 3 as a model, oxygen vacancies obtained by reducing the thickness dimension down to the atomic scale are introduced in this work. As the Li-ion storage progresses, the imbalanced charge distribution emerging around the oxygen vacancies could induce a local built-in electric field, which will accelerate the ions' migration rate by Coulomb forces and thus have benefits for high-rate performance. Furthermore, the thus-obtained CuGeO 3 ultrathin nanosheets (CGOUNs)/graphene van der Waals heterojunctions are used as anodes in Li-ion batteries, which deliver a reversible specific capacity of 1295 mAh g -1 at 100 mA g -1 , with improved rate capability and cycling performance compared to their bulk counterpart. Our findings build a clear connection between the atomic/defect/electronic structure and intrinsic properties for designing high-efficiency electrode materials.

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

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

Analytical modeling of relative luminescence efficiency of Al2O3:C optically stimulated luminescence detectors exposed to high-energy heavy charged particles.

PubMed

Sawakuchi, Gabriel O; Yukihara, Eduardo G

2012-01-21

The objective of this work is to test analytical models to calculate the luminescence efficiency of Al(2)O(3):C optically stimulated luminescence detectors (OSLDs) exposed to heavy charged particles with energies relevant to space dosimetry and particle therapy. We used the track structure model to obtain an analytical expression for the relative luminescence efficiency based on the average radial dose distribution produced by the heavy charged particle. We compared the relative luminescence efficiency calculated using seven different radial dose distribution models, including a modified model introduced in this work, with experimental data. The results obtained using the modified radial dose distribution function agreed within 20% with experimental data from Al(2)O(3):C OSLDs relative luminescence efficiency for particles with atomic number ranging from 1 to 54 and linear energy transfer in water from 0.2 up to 1368 keV µm(-1). In spite of the significant improvement over other radial dose distribution models, understanding of the underlying physical processes associated with these radial dose distribution models remain elusive and may represent a limitation of the track structure model.

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.

The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

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

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca

2014-01-01

Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of themore » simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.« less

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

Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile

NASA Astrophysics Data System (ADS)

Premkumar, S.; Jawahar, A.; Mathavan, T.; Kumara Dhas, M.; Milton Franklin Benial, A.

2015-03-01

The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908 × 10-30 issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π → π∗ transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature.

Conformational Properties, Spectroscopy and Structure of ISATIN-(WATER)_{n=1-3} Clusters

NASA Astrophysics Data System (ADS)

Singh, Milind K.; Upadhya, D. M.; Singh, Vipin B.

2009-06-01

The structure, stability and vibrational characteristics of Isatin-(Water)_n clusters with n=1=3 have been investigated using second order Moller-Plesset (MP2) perturbation tehory and Density Functional Theory (with B3LYP) methods employing the basis set 6-31+G(d). The vertical excitation energies for these complexes have been also computed using the time-dependent density functional theory. The three stable conformational isomers, each for Isatin-(Water)_1 and Isatin-(Water)_2 clusters were obtained. It is shown that in the most stable isomer of Isatin-(Water)_1 cluster hydrogen bond between amide hydrogen and oxygen of water is found stronger as compared to the H-bond in Indole-(Water)_1 cluster. For a particular position of complexation of water, between the carbonyl oxygen's, results an unusual increase in the dipole moment due to an electronic charge displacement from the N atom to the C atom of the neighboring carbonyl bond. This causes a large separation between the effective charges forming the dipole. The complexes involving this position of water are expected to show a small charge transfer character. The experimentally observed electronic absorption peaks are reasonably reproduced by the TD-DFT calculations and it is found that the longest wavelength absorption peak of isatin at 406 nm is significantly red shifted after addition of a water molecule.

Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Zhou, Yu; Liang, Qin; Chen, Da-Fu; Guo, Rui; Lai, Rong-Cai

2016-10-01

In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)-H2O/CH3CH2OH and apigenin (II)-H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin-H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X-H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4-O5···H, C9-O4···H and C13-O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

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.

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.

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.

Electron- and Photon-stimulated Desorption of Alkali Atoms from Lunar Sample and a Model Mineral Surface

NASA Technical Reports Server (NTRS)

Yakshinskiy, B. V.; Madey, T. E.

2003-01-01

We report recent results on an investigation of source mechanisms for the origin of alkali atoms in the tenuous planetary atmospheres, with focus on non-thermal processes (photon stimulated desorption (PSD), electron stimulated desorption (ESD), and ion sputtering). Whereas alkaline earth oxides (MgO, CaO) are far more abundant in lunar samples than alkali oxides (Na2O, K2O), the atmosphere of the Moon contains easily measurable concentrations of Na and K, while Ca and Mg are undetected there; traces of Ca have recently been seen in the Moon's atmosphere (10-3 of Na). The experiments have included ESD, PSD and ion sputtering of alkali atoms from model mineral surface (amorphous SiO2) and from a lunar basalt sample obtained from NASA. The comparison is made between ESD and PSD efficiency of monovalent alkalis (Na, K) and divalent alkaline earths (Ba, Ca).The ultrahigh vacuum measurement scheme for ESD and PSD of Na atoms includes a highly sensitive alkali metal detector based on surface ionization, and a time-of-flight technique. For PSD measurements, a mercury arc light source (filtered and chopped) is used. We find that bombardment of the alkali covered surfaces by ultraviolet photons or by low energy electrons (E>4 eV) causes desorption of hot alkali atoms. This results are consistent with the model developed to explain our previous measurements of sodium desorption from a silica surface and from water ice: electron- or photon-induced charge transfer from the substrate to the ionic adsorbate causes formation of a neutral alkali atom in a repulsive configuration, from which desorption occurs. The two-electron charge transfer to cause desorption of divalent alkaline eath ions is a less likely process.The data support the suggestion that PSD by UV solar photons is a dominant source process for alkalis in the tenuous lunar atmosphere.

Determination of the tip temperature in laser assisted atom-probe tomography using charge state distributions

NASA Astrophysics Data System (ADS)

Marquis, Emmanuelle A.; Gault, Baptiste

2008-10-01

The method suggested by Kellogg [J. Appl. Phys. 52, 5320 (1981)] to estimate the temperature of a field emitter under laser pulsing irradiation is reconsidered in the case of a W-Re alloy. It is shown that the temperature obtained using this method is not the absolute temperature, but, if properly calibrated, a value that could be considered as a good approximation of the average temperature reached by the tip when illuminated by picosecond laser pulses.

Elucidating Complex Surface Reconstructions with Atomic-Resolution Scanning Tunneling Microscopy: Au(100)-Aqueous Electrochemical Interface

DTIC Science & Technology

1992-05-01

that unusually high-quality STM data of this type 5-7can be obtained at ordered gold -aqueous interfaces. Reconstruction is seen 2 to be triggered on...all three low-index gold surfaces by altering the potential to values corresponding to small (10-15 pC cm-2 ) negative surface electronic 5-7 charges...connections. The former was platinum and the latter was a freshly electrooxidized gold wire. All electrode potentials quoted here, however, are

Formation of neutral and charged gold carbonyls on highly facetted gold nanostructures

NASA Astrophysics Data System (ADS)

Chau, Thoi-Dai; Visart de Bocarmé, Thierry; Kruse, Norbert; Wang, Richard L. C.; Kreuzer, Hans Jürgen

2003-12-01

We show that gold mono- and di-carbonyls are formed on gold field emitter tips during interaction with carbon monoxide gas at room temperature and in the presence of high electrostatic fields. The experiments are done in a time-of-flight atom probe to obtain mass spectra. The yield of monocarbonyl cations is about twice that of di-carbonyl ions. Density functional theory calculations are reported that explain the field stabilization of adsorbed carbonyls and the desorption yield of their cations.

Influence of inelastic Rydberg atom-atom collisional process on kinetic and optical properties of low-temperature laboratory and astrophysical plasmas

NASA Astrophysics Data System (ADS)

Klyucharev, A. N.; Bezuglov, N. N.; Mihajlov, A. A.; Ignjatović, Lj M.

2010-11-01

Elementary processes in plasma phenomena traditionally attract physicist's attention. The channel of charged-particle formation in Rydberg atom-atom thermal and sub-thermal collisions (the low temperature plasmas conditions) leads to creation of the molecular ions - associative ionization (AI). atomic ions - Penning-like ionization (PI) and the pair of the negative and positive ions. In our universe the chemical composition of the primordial gas consists mainly of Hydrogen and Helium (H, H-, H+, H2, He,He+). Hydrogen-like alkali-metal Lithium (Li, Li+,Li-) and combinations (HeH+, LiH-, LiH+). There is a wide range of plasma parameters in which the Rydberg atoms of the elements mentioned above make the dominant contribution to ionization and that process may be regarded as a prototype of the elementary process of light excitation energy transformation into electric one. The latest stochastic version of chemi-ionisation (AI+PI) on Rydberg atom-atom collisions extends the treatment of the "dipole resonant" model by taking into account redistribution of population over a range of Rydberg states prior to ionization. This redistribution is modelled as diffusion within the frame of stochastic dynamic of the Rydberg electron in the Rydberg energy spectrum. This may lead to anomalies of Rydberg atom spectra. Another result obtained in recent time is understanding that experimental results on chemi-ionization relate to the group of mixed Rydberg atom closed to the primary selected one. The Rydberg atoms ionisation theory today makes a valuable contribution in the deterministic and stochastic approaches correlation in atomic physic.

Scanning Probe Microscopy of Organic Solar Cells

NASA Astrophysics Data System (ADS)

Reid, Obadiah G.

Nanostructured composites of organic semiconductors are a promising class of materials for the manufacture of low-cost solar cells. Understanding how the nanoscale morphology of these materials affects their efficiency as solar energy harvesters is crucial to their eventual potential for large-scale deployment for primary power generation. In this thesis we describe the use of optoelectronic scanning-probe based microscopy methods to study this efficiency-structure relationship with nanoscale resolution. In particular, our objective is to make spatially resolved measurements of each step in the power conversion process from photons to an electric current, including charge generation, transport, and recombination processes, and correlate them with local device structure. We have achieved two aims in this work: first, to develop and apply novel electrically sensitive scanning probe microscopy experiments to study the optoelectronic materials and processes discussed above; and second, to deepen our understanding of the physics underpinning our experimental techniques. In the first case, we have applied conductive-, and photoconductive atomic force (cAFM & pcAFM) microscopy to measure both local photocurrent collection and dark charge transport properties in a variety of model and novel organic solar cell composites, including polymer/fullerene blends, and polymer-nanowire/fullerene blends, finding that local heterogeneity is the rule, and that improvements in the uniformity of specific beneficial nanostructures could lead to large increases in efficiency. We have used scanning Kelvin probe microscopy (SKPM) and time resolved-electrostatic force microscopy (trEFM) to characterize all-polymer blends, quantifying their sensitivity to photochemical degradation and the subsequent formation of local charge traps. We find that while trEFM provides a sensitive measure of local quantum efficiency, SKPM is generally unsuited to measurements of efficiency, less sensitive than trEFM, and of greater utility in identifying local changes in steady-state charge density that can be associated with charge trapping. In the second case, we have developed a new understanding of charge transport between a sharp AFM tip and planar substrates applicable to conductive and photoconductive atomic force microscopy, and shown that hole-only transport characteristics can be easily obtained including quantitative values of the charge carrier mobility. Finally, we have shown that intensity-dependent photoconductive atomic force microscopy measurements can be used to infer the 3D structure of organic photovoltaic materials, and gained new insight into the influence vertical composition of the these devices can have on their open-circuit voltage and its intensity dependence.

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.

Relativistic calculations of atomic properties

NASA Astrophysics Data System (ADS)

Kaur, Jasmeet; Sahoo, B. K.; Arora, Bindiya

2017-04-01

Singly charged ions are engaging candidates in many areas of Physics. They are especially important in astrophysics for evaluating the radiative properties of stellar objects, in optical frequency standards and for fundamental physics studies such as searches for permanent electric dipole moments and atomic parity violation. Interpretation of these experiments often requires a knowledge of their transition wavelengths and electric dipole amplitudes. In this work, we discuss the calculation of various properties of alkaline earth ions. The relativistic all-order SD method in which all single and double excitations of the Dirac-Fock wave function are included, is used to calculate these atomic properties. We use this method for evaluation of electric dipole matrix elements of alkaline earth ions. Combination of these matrix elements with experimental energies allow to obtain the polarizabilities of ground and excited states of ions. We discuss the applications of estimated polarizabiities as a function of imaginary frequencies in the calculations of long-range atom-ion interactions. We have also located the magic wavelengths for nS1 / 2 - nD3 / 2 , 5 / 2 transitions of alkaline earth ions. These calculated properties will be highly valuable to atomic and astrophysics community. UGC-BSR Grant No. F.7-273/2009/BSR.

Chemical scissors cut phosphorene and their novel electronic properties

NASA Astrophysics Data System (ADS)

Peng, Xihong; Wei, Qun

2015-03-01

Phosphorene, a recently fabricated two-dimensional puckered honeycomb structure of black phosphorus, showed promising properties for applications in nano-electronics. In this work, we report a chemical scissors effect on phosphorene, using first principles density-functional methods. It was found that chemical species, such as H, OH, F, and Cl, can act as scissors to cut phosphorene. Phosphorus nanochains and nanoribbons can be obtained using such chemical scissors. The scissors effect results from the strong bonding between the chemical species and phosphorus atoms. Other species such as O, S and Se fail to cut phosphorene due to their weak bonding with phosphorus. The electronic structures of the produced P-chains reveal that the hydrogenated P-chain is an insulator; however, the pristine P-chain is a one-dimensional Dirac material, in which the charge carriers are massless fermions travelling at an effective speed of light approximately 8x105 m/s. The obtained zigzag phosphorene nanoribbons show either metallic or semiconducting behaviors, depending on the treatment of the edge phosphorus atoms.

Chemical scissors cut phosphorene nanostructures

NASA Astrophysics Data System (ADS)

Peng, Xihong; Wei, Qun

2014-12-01

Phosphorene, a recently fabricated two-dimensional puckered honeycomb structure of phosphorus, showed promising properties for applications in nano-electronics. In this work, we report a chemical scissors effect on phosphorene, using first-principles method. It was found that chemical species, such as H, OH, F, and Cl, can act as scissors to cut phosphorene. Phosphorus nanochains and nanoribbons can be obtained. The scissors effect results from the strong bonding between the chemical species and phosphorus atoms. Other species such as O, S and Se fail to cut phosphorene nanostructures due to their weak bonding with phosphorus. The electronic structures of the produced P-chains reveal that the hydrogenated chain is an insulator while the pristine chain is a one-dimensional Dirac material, in which the charge carriers are massless fermions travelling at an effective speed of light ˜8 × 105 m s-1. The obtained zigzag phosphorene nanoribbons show either metallic or semiconducting behaviors, depending on the treatment of the edge phosphorus atoms.

Coherent electron emission from O2 in collisions with fast electrons

NASA Astrophysics Data System (ADS)

Chowdhury, Madhusree Roy; Stia, Carlos R.; Tachino, Carmen A.; Fojón, Omar A.; Rivarola, Roberto D.; Tribedi, Lokesh C.

2017-08-01

Absolute double differential cross sections (DDCS) of secondary electrons emitted in ionization of O2 by fast electrons have been measured for different emission angles. Theoretical calculations of atomic DDCS were obtained using the first Born approximation with an asymptotic charge of Z T = 1. The measured molecular DDCS were divided by twice the theoretical atomic DDCS to detect the presence of interference effects which was the aim of the experiment. The experimental to theoretical DDCS ratios showed clear signature of first order interference oscillation for all emission angles. The ratios were fitted by a first order Cohen-Fano type model. The variation of the oscillation amplitudes as a function of the electron emission angle showed a parabolic behaviour which goes through a minimum at 90°. The single differential and total ionization cross sections have also been deduced, besides the KLL Auger cross sections. In order to make a comparative study, we have discussed these results along with our recent experimental data obtained for N2 molecule.

A novel series of thiosemicarbazone drugs: From synthesis to structure

NASA Astrophysics Data System (ADS)

Ebrahimi, Hossein Pasha; Hadi, Jabbar S.; Alsalim, Tahseen A.; Ghali, Thaer S.; Bolandnazar, Zeinab

2015-02-01

A new series of thiosemicarbazones (TSCs) and their 1,3,4-thiadiazolines (TDZs) containing acetamide group have been synthesized from thiosemicarbazide compounds by the reaction of TSCs with cyclic ketones as well as aromatic aldehydes. The structures of newly synthesized 1,3,4-thiadiazole derivatives obtained by heterocyclization of the TSCs with acetic anhydride were experimentally characterized by spectral methods using IR, 1H NMR, 13C NMR and mass spectroscopic methods. Furthermore, the structural, thermodynamic, and electronic properties of the studied compounds were also studied theoretically by performing Density Functional Theory (DFT) to access reliable results to the experimental values. The molecular geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and Mulliken atomic charges of the studied compounds have been calculated at the B3LYP method and standard 6-31+G(d,p) basis set starting from optimized geometry. The theoretical 13C chemical shift results were also calculated using the gauge independent atomic orbital (GIAO) approach and their respective linear correlations were obtained.

Change in the frequency and intensity of the spectral lines of a hydrogen-like atom in the field of a point charge

NASA Astrophysics Data System (ADS)

Ovsyannikov, V. D.; Kamenskii, A. A.

2002-03-01

The changes in the wave functions and the energies of a hydrogen-like atom in the static field of a structureless charged particle are calculated in the asymptotic approximation. The corrections to the energy of states, as well as to the dipole matrix elements of radiative transitions caused by the interaction of the atom with the point charge at long range are calculated using the perturbation theory and the Sturm series for a reduced Coulomb Green’s function in parabolic coordinates. The analytical expressions are derived and tables of numerical values of the coefficients of asymptotic series that determine the corrections to the matrix elements and the intensities of transitions of the Lyman and Balmer series are presented.

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.

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

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.

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.

Atomic structure calculations for F-like tungsten

NASA Astrophysics Data System (ADS)

Sunny, Aggarwal

2014-09-01

Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

Electromechanical response of amorphous LaAlO{sub 3} thin film probed by scanning probe microscopies

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

Borowiak, Alexis S.; Baboux, Nicolas; Albertini, David

The electromechanical response of a 3 nm thick amorphous LaAlO{sub 3} layer obtained by molecular beam epitaxy has been studied using scanning probe microscopies. Although this kind of sample is not ferroelectric due to its amorphous nature, the resulting images are identical to what is generally obtained on truly ferroelectric samples probed by piezoresponse force microscopy: domains of apparently opposite polarisation are detected, and perfect, square shaped hysteresis loops are recorded. Moreover, written patterns are stable within 72 h. We discuss in the general case the possible origins of this behaviour in terms of charge injection, ionic conduction and motion ofmore » oxygen vacancies. In the case presented in this paper, since the writing process has been conducted with applied voltages lower than the injection threshold measured by conductive atomic force Microscopy, allowing to withdraw the hypothesis of charge injection in the sample, we propose that a bistable distribution of oxygen vacancies is responsible for this contrast.« less

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.

Charge transfer and ionization in collisions of Si3+ with H from low to high energy

NASA Astrophysics Data System (ADS)

Wang, J. G.; He, B.; Ning, Y.; Liu, C. L.; Yan, J.; Stancil, P. C.; Schultz, D. R.

2006-11-01

Charge transfer processes due to collisions of ground state Si3+(3sS1) ions with atomic hydrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) and classical-trajectory Monte Carlo (CTMC) methods. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained from Herrero [J. Phys. B 29, 5583 (1996)] which were calculated with a full configuration-interaction method. Total and state-selective single-electron capture cross sections are obtained for collision energies from 0.01eV/u to 1MeV/u . Total and state-selective rate coefficients are also presented for temperatures from 2×103K to 107K . Comparison with existing data reveals that the total CTMC cross sections are in good agreement with the experimental measurements at the higher considered energies and that previous Landau-Zener calculations underestimate the total rate coefficients by a factor of up to two. The CTMC calculations of target ionization are presented for high energies.

CMOS active pixel sensors response to low energy light ions

NASA Astrophysics Data System (ADS)

Spiriti, E.; Finck, Ch.; Baudot, J.; Divay, C.; Juliani, D.; Labalme, M.; Rousseau, M.; Salvador, S.; Vanstalle, M.; Agodi, C.; Cuttone, G.; De Napoli, M.; Romano, F.

2017-12-01

Recently CMOS active pixel sensors have been used in Hadrontherapy ions fragmentation cross section measurements. Their main goal is to reconstruct tracks generated by the non interacting primary ions or by the produced fragments. In this framework the sensors, unexpectedly, demonstrated the possibility to obtain also some informations that could contribute to the ion type identification. The present analysis shows a clear dependency in charge and number of pixels per cluster (pixels with a collected amount of charge above a given threshold) with both fragment atomic number Z and energy loss in the sensor. This information, in the FIRST (F ragmentation of I ons R elevant for S pace and T herapy) experiment, has been used in the overall particle identification analysis algorithm. The aim of this paper is to present the data analysis and the obtained results. An empirical model was developed, in this paper, that reproduce the cluster size as function of the deposited energy in the sensor.

Electron capture by U(91+) and U(92+) and ionization of U(90+) and U(91+)

NASA Technical Reports Server (NTRS)

Gould, H.; Greiner, D.; Lindstrom, P.; Symons, T. J. M.; Crawford, H.

1984-01-01

U(92+)/U(91+) and U(91+)/U(90+) electron-capture and ionization cross sections and equilibrium charge-state distributions are measured experimentally in mylar, Cu and Ta of varying thickness. Relativistic U(68+) ions at 437 or 962 MeV/nucleon are produced by a heavy-ion linear accelerator and synchrotron in tandem and passed through the target material into a magnetic specrometer and position-sensitive proportional counter for evaluation of charge states. The results are presented graphically and discussed. At 962 MeV/nucleon, beams containing 85 percent bare U(92+) nuclei are obtained using 150-mg/sq cm Cu or 85-mg/sq cm Ta; at 437 MeV/nucleon, 50 percent bare U(92+) nuclei are obtained with 90-mg/sq cm Cu. The techniques decribed can be applied to produce beams of bare U nuclei for acceleration to ultrarelativistic speeds or beams of few-electron U for atomic-physics experiments on quantum electrodynamics.

Electromechanical response of amorphous LaAlO3 thin film probed by scanning probe microscopies

NASA Astrophysics Data System (ADS)

Borowiak, Alexis S.; Baboux, Nicolas; Albertini, David; Vilquin, Bertrand; Saint Girons, Guillaume; Pelloquin, Sylvain; Gautier, Brice

2014-07-01

The electromechanical response of a 3 nm thick amorphous LaAlO3 layer obtained by molecular beam epitaxy has been studied using scanning probe microscopies. Although this kind of sample is not ferroelectric due to its amorphous nature, the resulting images are identical to what is generally obtained on truly ferroelectric samples probed by piezoresponse force microscopy: domains of apparently opposite polarisation are detected, and perfect, square shaped hysteresis loops are recorded. Moreover, written patterns are stable within 72 h. We discuss in the general case the possible origins of this behaviour in terms of charge injection, ionic conduction and motion of oxygen vacancies. In the case presented in this paper, since the writing process has been conducted with applied voltages lower than the injection threshold measured by conductive atomic force Microscopy, allowing to withdraw the hypothesis of charge injection in the sample, we propose that a bistable distribution of oxygen vacancies is responsible for this contrast.

ptchg: A FORTRAN program for point-charge calculations of electric field gradients (EFGs)

NASA Astrophysics Data System (ADS)

Spearing, Dane R.

1994-05-01

ptchg, a FORTRAN program, has been developed to calculate electric field gradients (EFG) around an atomic site in crystalline solids using the point-charge direct-lattice summation method. It uses output from the crystal structure generation program Atoms as its input. As an application of ptchg, a point-charge calculation of the EFG quadrupolar parameters around the oxygen site in SiO 2 cristobalite is demonstrated. Although point-charge calculations of electric field gradients generally are limited to ionic compounds, the computed quadrupolar parameters around the oxygen site in SiO 2 cristobalite, a highly covalent material, are in good agreement with the experimentally determined values from nuclear magnetic resonance (NMR) spectroscopy.

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

Electrostatic atomization: Effect of electrode materials on electrostatic atomizer performance

NASA Astrophysics Data System (ADS)

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

2016-11-01

Electrostatic atomization was studied experimentally with a pointed electrode in a converging nozzle. Experiments were carried out on poorly conductive canola oil where it was observed that electrode material may affect charge transfer. This points at the possible faradaic reactions that can occur at the surfaces of the electrodes. The supply voltage is applied to the sharp electrode and the grounded nozzle body constitutes the counter-electrode. The charge transfer is controlled by the electrochemical reactions on both the electrodes. The electrical performance study of the atomizer issuing a charged oil jet was conducted using three different nozzle body materials - brass, copper and stainless steel. Also, two sharp electrode materials - brass and stainless steel - were tested. The experimental results revealed that both the nozzle body material, as well as the sharp electrode material affected the spray and leak currents. Moreover, the effect of the sharp electrode material is quite significant. This research is supported by NSF Grant 1505276.

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.

Residue-Specific α-Helix Propensities from Molecular Simulation

PubMed Central

Best, Robert B.; de Sancho, David; Mittal, Jeetain

2012-01-01

Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w and Amber ff99SB∗. Encouragingly, we find that the overall helix propensity of many residues is captured well by both energy functions, with Amber ff99SB∗ being more accurate. Nonetheless, there are some residues that deviate considerably from experiment, which can be attributed to two aspects of the energy function: i), variations of the charge model used to determine the atomic partial charges, with residues whose backbone charges differ most from alanine tending to have the largest error; ii), side-chain torsion potentials, as illustrated by the effect of modifications to the torsion angles of I, L, D, N. We find that constrained refitting of residue charges for charged residues in Amber ff99SB∗ significantly improves their helix propensity. The resulting parameters should more faithfully reproduce helix propensities in simulations of protein folding and disordered proteins. PMID:22455930

A new analysis of charge transfer and polarization for ligand-metal bonding - Model studies of Al4CO and Al4NH3

NASA Technical Reports Server (NTRS)

Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr.

1984-01-01

The nature of the bonding of CO and NH3 ligands to Al is analyzed, and the intra-unit charge polarization and inter-unit donation for the interaction of ligands with metals are studied. The consequences of metal-to-ligand and ligand-to-metal charge transfer are separately considered by performing a constrained space orbital variation (CSOV) with the electrons of the metal member of the complex in the field of frozen ligand. The electrons of the metal atoms are then frozen in the relaxed distribution given by the CSOV SCF wave function and the ligand electrons are allowed to relax. Quantitative measures of the importance of inter-unit charge transfers and intra-unit polarization are obtained using results of SCF studies of Al4CO and Al4NH3 clusters chosen to simulate the adsorption of the ligands at an on-top side of the Al(111) surface. The electrostatic attraction of the effective dipole moments of the metal and ligand units makes an important contribution to the bond.

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

Nuclear Quantum Effects in H+ and OH- Diffusion Along Confined Water Wires from Ab Initio Path Integral Molecular Dyanmics

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David

Diffusion of H+ and OH- along water wires provides an efficient mechanism for charge transport that is exploited by biological systems and shows promise in technological applications. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we consider H+ and OH- in finite water wires using density functional theory. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition of the charge. We employ thermostated ring polymer molecular dynamics and extract a ``universal'' diffusion coefficient from simulations with different wire sizes by considering Langevin dynamics on the potential of mean force of the charged species. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate O-O distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire, presumably making them more robust to environment fluctuations.

Ionic strength independence of charge distributions in solvation of biomolecules

NASA Astrophysics Data System (ADS)

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

2014-12-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

Experimental and theoretical charge density studies at subatomic resolution.

PubMed

Fischer, A; Tiana, D; Scherer, W; Batke, K; Eickerling, G; Svendsen, H; Bindzus, N; Iversen, B B

2011-11-17

Analysis of accurate experimental and theoretical structure factors of diamond and silicon reveals that the contraction of the core shell due to covalent bond formation causes significant perturbations of the total charge density that cannot be ignored in precise charge density studies. We outline that the nature and origin of core contraction/expansion and core polarization phenomena can be analyzed by experimental studies employing an extended Hansen-Coppens multipolar model. Omission or insufficient treatment of these subatomic charge density phenomena might yield erroneous thermal displacement parameters and high residual densities in multipolar refinements. Our detailed studies therefore suggest that the refinement of contraction/expansion and population parameters of all atomic shells is essential to the precise reconstruction of electron density distributions by a multipolar model. Furthermore, our results imply that also the polarization of the inner shells needs to be adopted, especially in cases where second row or even heavier elements are involved in covalent bonding. These theoretical studies are supported by direct multipolar refinements of X-ray powder diffraction data of diamond obtained from a third-generation synchrotron-radiation source (SPring-8, BL02B2).

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.

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.

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.

Predictions of nuclear charge radii

NASA Astrophysics Data System (ADS)

Bao, M.; Lu, Y.; Zhao, Y. M.; Arima, A.

2016-12-01

The nuclear charge radius is a fundamental property of an atomic nucleus. In this article we study the predictive power of empirical relations for experimental nuclear charge radii of neighboring nuclei and predict the unknown charge radii of 1085 nuclei based on the experimental CR2013 database within an uncertainty of 0.03 fm.

Solar Wind Charge Exchange Studies Of Highly Charged Ions On Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Draganić, I. N.; Seely, D. G.; McCammon, D.; Havener, C. C.

2011-06-01

Accurate studies of low-energy charge exchange (CX) are critical to understanding underlying soft X-ray radiation processes in the interaction of highly charged ions from the solar wind with the neutral atoms and molecules in the heliosphere, cometary comas, planetary atmospheres, interstellar winds, etc.. Particularly important are the CX cross sections for bare, H-like, and He-like ions of C, N, O and Ne, which are the dominant charge states for these heavier elements in the solar wind. Absolute total cross sections for single electron capture by H-like ions of C, N, O and fully-stripped O ions from atomic hydrogen have been measured in an expanded range of relative collision energies (5 eV/u-20 keV/u) and compared to previous H-oven measurements. The present measurements are performed using a merged-beams technique with intense highly charged ion beams extracted from a 14.5 GHz ECR ion source installed on a high voltage platform at the Oak Ridge National Laboratory. For the collision energy range of 0.3 keV/u-3.3 keV/u, which corresponds to typical ion velocities in the solar wind, the new measurements are in good agreement with previous H-oven measurements. The experimental results are discussed in detail and compared with theoretical calculations where available.

ON THE GEOMETRY OF THE IBEX RIBBON

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

Sylla, Adama; Fichtner, Horst

2015-10-01

The Energetic Neutral Atom (ENA) full-sky maps obtained with the Interstellar Boundary Explorer (IBEX) show an unexpected bright narrow band of increased intensity. This so-called ENA ribbon results from charge exchange of interstellar neutral atoms with protons in the outer heliosphere or beyond. Among other hypotheses it has been argued that this ribbon may be related to a neutral density enhancement, or H-wave, in the local interstellar medium. Here we quantitatively demonstrate, on the basis of an analytical model of the principal large-scale heliospheric structure, that this scenario for the ribbon formation leads to results that are fully consistent withmore » the observed location of the ribbon in the full-sky maps at all energies detected with high-energy sensor IBEX-Hi.« less

Photovoltaic Effect in an Electrically Tunable van der Waals Heterojunction

PubMed Central

2014-01-01

Semiconductor heterostructures form the cornerstone of many electronic and optoelectronic devices and are traditionally fabricated using epitaxial growth techniques. More recently, heterostructures have also been obtained by vertical stacking of two-dimensional crystals, such as graphene and related two-dimensional materials. These layered designer materials are held together by van der Waals forces and contain atomically sharp interfaces. Here, we report on a type-II van der Waals heterojunction made of molybdenum disulfide and tungsten diselenide monolayers. The junction is electrically tunable, and under appropriate gate bias an atomically thin diode is realized. Upon optical illumination, charge transfer occurs across the planar interface and the device exhibits a photovoltaic effect. Advances in large-scale production of two-dimensional crystals could thus lead to a new photovoltaic solar technology. PMID:25057817

Charge exchange cross sections in slow collisions of Si3+ with Hydrogen atom

NASA Astrophysics Data System (ADS)

Joseph, Dwayne; Quashie, Edwin; Saha, Bidhan

2011-05-01

In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. Work supported by NSF CREST project (grant #0630370).

Probing the Importance of Charge Flux in Force Field Modeling.

PubMed

Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

2017-08-08

We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

PubMed Central

Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

2008-01-01

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

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

NASA Technical Reports Server (NTRS)

Kwong, Victor H. S.

1996-01-01

Charge transfer at electron-volt energies between multiply charged atomic ions and neutral atoms and molecules is of considerable importance in astrophysics, plasma physics, and in particular, fusion plasmas. In the year covered by this report, several major tasks were completed. These include: (1) the re-calibration of the ion gauge to measure the absolute particle densities of H2, He, N2, and CO for our current measurements; (2) the analysis of data for charge transfer reactions of N(exp 2 plus) ion and He, H2, N2, and CO; (3) measurement and data analysis of the charge transfer reaction of (Fe(exp 2 plus) ion and H2; (4) charge transfer measurement of Fe(exp 2 plus) ion and H2; and (5) redesign and modification of the ion detection and data acquisition system for the low energy beam facility (reflection time of flight mass spectrometer) dedicated to the study of state select charge transfer.

Charge density wave modulation and gap measurements in CeTe 3

DOE PAGES

Ralevic, U.; Lazarevic, N.; Baum, A.; ...

2016-10-14

Here, we present a study of charge density wave (CDW) ordering in CeTe 3 at room temperature using a scanning tunneling microscope and Raman spectroscopy. Two characteristic CDW ordering wave vectors obtained from the Fourier analysis are assessed to be |c* – q|=4.19nm –1 and |q|=10.26nm –1 where |c*|=2π/c is the reciprocal lattice vector. The scanning tunneling spectroscopy measurements, along with inelastic light (Raman) scattering measurements, show a CDW gap Δ max of approximately 0.37 eV. In addition to the CDW modulation, we observe an organization of the Te sheet atoms in an array of alternating V- and N-shaped groupsmore » along the CDW modulation, as predicted in the literature.« less

Photo ion spectrometer

DOEpatents

Gruen, D.M.; Young, C.E.; Pellin, M.J.

1989-12-26

A charged particle spectrometer is described 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. 12 figs.

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

Bonthuis, Douwe Jan, E-mail: douwe.bonthuis@physics.ox.ac.uk; Mamatkulov, Shavkat I.; Netz, Roland R.

We optimize force fields for H{sub 3}O{sup +} and OH{sup −} that reproduce the experimental solvation free energies and the activities of H{sub 3}O{sup +} Cl{sup −} and Na{sup +} OH{sup −} 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 H{sub 3}O{sup +} force field is 0.8 ± 0.1|e|—significantly higher than the value typically used for nonpolarizable water models and H{sub 3}O{sup +} force fields. In contrast,more » the optimal partial charge on the hydrogen atom of OH{sup −} turns out to be zero. Standard combination rules can be used for H{sub 3}O{sup +} Cl{sup −} solutions, while for Na{sup +} OH{sup −} 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.« less

Excitation and charge transfer in low-energy hydrogen atom collisions with neutral iron

NASA Astrophysics Data System (ADS)

Barklem, P. S.

2018-05-01

Data for inelastic processes due to hydrogen atom collisions with iron are needed for accurate modelling of the iron spectrum in late-type stars. Excitation and charge transfer in low-energy Fe+H collisions is studied theoretically using a previously presented method based on an asymptotic two-electron linear combination of atomic orbitals model of ionic-covalent interactions in the neutral atom-hydrogen-atom system, together with the multi-channel Landau-Zener model. An extensive calculation including 166 covalent states and 25 ionic states is presented and rate coefficients are calculated for temperatures in the range 1000-20 000 K. The largest rates are found for charge transfer processes to and from two clusters of states around 6.3 and 6.6 eV excitation, corresponding in both cases to active 4d and 5p electrons undergoing transfer. Excitation and de-excitation processes among these two sets of states are also significant. Full Tables and rate coefficient data are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/612/A90

Spatially resolving density-dependent screening around a single charged atom in graphene

NASA Astrophysics Data System (ADS)

Wong, Dillon; Corsetti, Fabiano; Wang, Yang; Brar, Victor W.; Tsai, Hsin-Zon; Wu, Qiong; Kawakami, Roland K.; Zettl, Alex; Mostofi, Arash A.; Lischner, Johannes; Crommie, Michael F.

2017-05-01

Electrons in two-dimensional graphene sheets behave as interacting chiral Dirac fermions and have unique screening properties due to their symmetry and reduced dimensionality. By using a combination of scanning tunneling spectroscopy measurements and theoretical modeling we have characterized how graphene's massless charge carriers screen individual charged calcium atoms. A backgated graphene device configuration has allowed us to directly visualize how the screening length for this system can be tuned with carrier density. Our results provide insight into electron-impurity and electron-electron interactions in a relativistic setting with important consequences for other graphene-based electronic devices.

Apport de la microscopie a effet tunnel a la caracterisation d'interfaces molecule-metal a fort transfert de charge

NASA Astrophysics Data System (ADS)

Bedwani, Stephane

To assess the importance of charge-transfer on the interface properties, we studied the interaction of the tetracyanoethylene (TCNE) molecule with various copper surfaces. TCNE, a highly electrophilic molecule, appears as an ideal candidate to study the influence of high charge-transfer on the electronic and structural properties of molecule-surface interfaces. Indeed, various TCNE-transition metal complexes exhibit magnetism at room temperature, which is in agreement with a very significant change of the residual charge on the TCNE molecule. The adsorption of TCNE molecules on Cu(100) and Cu(111) surfaces was studied by scanning tunneling microscopy (STM) and by density functional theory (DFT) calculations with a local density approximation (LDA). DFT-LDA calculations were performed to determine the geometric and electronic structure of the studied interfaces. Mulliken analysis was used to evaluate the partial net charge on the adsorbed species. The density of states (DOS) diagrams provided informations on the nature of the frontier orbitals involved in the charge-transfer at molecule-metal interfaces. To validate the theoretical observations, a comparative study was conducted between our simulated STM images and experimental STM images provided by our collaborators. The theoretical STM images were obtained with the SPAGS-STM software using the Landauer-Buttiker formalism with a semi-empirical Hamiltonian based on the extended Huckel theory (EHT) and parameterized using DFT calculations. During the development of the SPAGS-STM software, we have created a discretization module allowing rapid generation of STM images. This module is based on an adaptive Delaunay meshing scheme to minimize the amount of tunneling current to be computed. The general idea consists into refining the mesh, and therefore the calculations, near large contrast zones rather than over the entire image. The adapted mesh provides an STM image resolution equivalent to that obtained with a conventional Cartesian grid but with a significantly smaller number of calculated pixels. This module is independent of the solver used to compute the tunneling current and can be transposed to different imaging techniques. Our work on the adsorption of TCNE molecules on Cu(100) surfaces revealed that the molecules assemble into a 1D chain, thereby buckling excessively a few Cu atoms from the surface. The large deformations observed at the molecule-metal interface show that the Cu atoms close to the TCNE nitrile groups assist the molecular assembly and show a distinct behavior compared with other Cu atoms. A strong charge-transfer is observed at the interface leading to an almost complete occupation of the state ascribed to the lowest unoccupied molecular orbital (LUMO) of TCNE in gas phase. In addition, a back-donation of charge from the molecule to the metal via the states associated with the highest occupied molecular orbitals (HOMO) of TCNE in gas phase may be seen. The magnitude of the charge-transfer between a TCNE molecule and Cu atoms is of the same order on the Cu(111) surface but causes much less buckling than that on the Cu(100) surface. However, experimental STM images of single TCNE molecules adsorbed on Cu(111) surfaces reveal a surprising electronic multistability. In addition, scanning tunneling spectroscopy (STS) reveals that one of these states has a magnetic nature and shows a Kondo resonance. STM simulations identified the source of two non-magnetic states. DFT-LDA calculations were able to ascribe the magnetic state to the partial occupation of a state corresponding to the LUMO+2 of TCNE. Moreover, the calculations showed that additional molecular deformations to those of TCNE in adsorbed phase, such the elongation of the C=C central bond and the bend of nitrile groups toward the surface, favor this charge-transfer to the LUMO+2. This suggested the presence of a Kondo state through the vibrational excitation of the stretching mode of the C=C central bond. The main results of this thesis led to the conclusion that strong charge-transfer between adsorbed molecules on a metallic surface may induce significant buckling of the surface. This surface reconstruction mechanism that involves a bidirectional charge-transfer between the species results into a partial net charge over the molecule. This mechanism is involved in the supramolecular self-assembly process that appears similar to a coordination network. Moreover, the adsorbed molecule presents some important geometric distortions that alter its electronic structure. Additional distortions on the adsorbed molecule induced by some molecular vibration modes seem to explain a stable magnetic state that can be switch on or off by an electrical impulse. (Abstract shortened by UMI.)

Positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Olenga, Antoine; Weiss, A. H.

2013-03-01

The process by which oxide layers are formed on metal surfaces is still not well understood. In this work we present the results of theoretical studies of positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface. An ab-initio investigation of stability and associated electronic properties of different adsorption phases of oxygen on Cu(110) has been performed on the basis of density functional theory and using DMOl3 code. The changes in the positron work function and the surface dipole moment when oxygen atoms occupy on-surface and sub-surface sites have been attributed to charge redistribution within the first two layers, buckling effects within each layer and interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, elemental content, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidized transition metal surfaces using positron annihilation induced Auger electron spectroscopy. This work was supported in part by the National Science Foundation Grant DMR-0907679.

Fabrication of an SPR Sensor Surface with Antifouling Properties for Highly Sensitive Detection of 2,4,6-Trinitrotoluene Using Surface-Initiated Atom Transfer Polymerization

PubMed Central

Yatabe, Rui; Onodera, Takeshi; Toko, Kiyoshi

2013-01-01

In this study, we modified a surface plasmon resonance immunosensor chip with a polymer using surface-initiated atom transfer polymerization (SI-ATRP) for the highly sensitive detection of 2,4,6-trinitrotoluene (TNT). To immobilize a TNT analogue on the polymer, mono-2-(methacryloyloxy)ethylsuccinate (MES), which has a carboxyl group, was used in this study. However, the anti-TNT antibody may adsorb non-specifically on the polymer surface by an electrostatic interaction because MES is negatively charged. Therefore, a mixed monomer with MES and diethylaminoethylmethacrylate (DEAEM), which has a tertiary amino group and is positively charged, was prepared to obtain electroneutrality for suppressing the nonspecific adsorption. The detection of TNT was performed by inhibition assay using the polymer surface. To ensure high sensitivity to TNT, the affinity between the surface and the antibody was optimized by controlling the density of the initiator for ATRP by mixing two types of self-assembled monolayer reagents. As a result, a limit of detection of 5.7 pg/mL (ppt) for TNT was achieved using the optimized surface. PMID:23877126

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

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

Ghosh, H.N.; Pal, H.; Sapre, A.V.

Photoexcitation of complexes between fullerence C[sub 60] and organic amines in benzene solutions is known to result in charge separation (CS) and subsequent charge recombination (CR) reactions, which lead to varying yields of fullerence triplet formation. Picosecond flash photolysis studies are carried out on C[sub 60]-diphenylamine (DPA), C[sub 60]-triethylamine (TEA), C[sub 60]-diazabicyclooctane (DABCO), and C[sub 60]-triphenylamine (TPA) systems to find out mechanistic details of the triplet formation on CR by inducing heavy atom and polarity effects by using suitable solvents. It is found that in the case of C[sub 60]-DPA, C[sub 60]-TEA, and C[sub 60]-DABCO systems proton transfer from themore » amine cation to the C[sub 60] anion in the ion pair state dominates, leading to poor triplet yields, which improve in heavy atom containing solvents. In TPA, proton transfer is not possible and hence fullerene triplet yields are high. Increase of solvent polarity for this system results in decreased C[sub 60] triplet yields with a consequent increase in the ion dissociation yield. A suitable reaction scheme is proposed to explain the results obtained. 34 refs., 5 figs., 2 tabs.« less

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

Roles of additives and surface control in slurry atomization

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

Tsai, S.C.

1990-01-01

This report focuses on the effects of interparticle forces on the rheology and airblast atomization of micronized coal water slurry (CWS). We found that the CWS flow behavior index is determined by the relative importance of the interparticle van der Waals attraction and the interparticle electrostatic repulsion. The former intensifies as the Hamaker constant increases and the interparticle distance reduces while the latter increases as the particle surface charge density increases. The interparticle attraction causes particle aggregation, which breaks down at high shear rates, and thus leads to slurry pseudoplastic behavior. In contrast, the interparticle repulsion prevents particle aggregation andmore » thus leads to Newtonian behavior. Both atomized at low atomizing air pressures (less than 270 kPa) using twin-fluid jet atomizers of various distributor designs. We found that the atomized drop sizes of micronized coal water slurries substantially decrease as the atomizing air pressure exceeds a threshold value. The effects of coal volume fraction, coal particle surface charge, liquid composition and liquid viscosity on slurry atomization can be accounted for by their effects on slurry rheology. 26 refs.« less

Kinetic theory of weakly ionized dilute gas of hydrogen-like atoms of the first principles of quantum statistics and dispersion laws of eigenwaves

NASA Astrophysics Data System (ADS)

Slyusarenko, Yurii V.; Sliusarenko, Oleksii Yu.

2017-11-01

We develop a microscopic approach to the construction of the kinetic theory of dilute weakly ionized gas of hydrogen-like atoms. The approach is based on the statements of the second quantization method in the presence of bound states of particles. The basis of the derivation of kinetic equations is the method of reduced description of relaxation processes. Within the framework of the proposed approach, a system of common kinetic equations for the Wigner distribution functions of free oppositely charged fermions of two kinds (electrons and cores) and their bound states—hydrogen-like atoms— is obtained. Kinetic equations are used to study the spectra of elementary excitations in the system when all its components are non-degenerate. It is shown that in such a system, in addition to the typical plasma waves, there are longitudinal waves of matter polarization and the transverse ones with a behavior characteristic of plasmon polaritons. The expressions for the dependence of the frequencies and Landau damping coefficients on the wave vector for all branches of the oscillations discovered are obtained. Numerical evaluation of the elementary perturbation parameters in the system on an example of a weakly ionized dilute gas of the 23Na atoms using the D2-line characteristics of the natrium atom is given. We note the possibility of using the results of the developed theory to describe the properties of a Bose condensate of photons in the diluted weakly ionized gas of hydrogen-like atoms.

Understanding the impact of the central atom on the ionic liquid behavior: phosphonium vs ammonium cations.

PubMed

Carvalho, Pedro J; Ventura, Sónia P M; Batista, Marta L S; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A P

2014-02-14

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

Understanding the impact of the central atom on the ionic liquid behavior: Phosphonium vs ammonium cations

NASA Astrophysics Data System (ADS)

Carvalho, Pedro J.; Ventura, Sónia P. M.; Batista, Marta L. S.; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A. P.

2014-02-01

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

PubMed Central

2016-01-01

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

Thermal stability of atomic layer deposition Al2O3 film on HgCdTe

NASA Astrophysics Data System (ADS)

Zhang, P.; Sun, C. H.; Zhang, Y.; Chen, X.; He, K.; Chen, Y. Y.; Ye, Z. H.

2015-06-01

Thermal stability of Atomic Layer Deposition Al2O3 film on HgCdTe was investigated by Al2O3 film post-deposition annealing treatment and Metal-Insulator-Semiconductor device low-temperature baking treatment. The effectiveness of Al2O3 film was evaluated by measuring the minority carrier lifetime and capacitance versus voltage characteristics. After annealing treatment, the minority carrier lifetime of the HgCdTe sample presented a slight decrease. Furthermore, the fixed charge density and the slow charge density decreased significantly in the annealed MIS device. After baking treatment, the fixed charge density and the slow charge density of the unannealed and annealed MIS devices decreased and increased, respectively.

Synthesis, spectroscopic characterization, DFT studies and antifungal activity of (E)-4-amino-5-[N'-(2-nitro-benzylidene)-hydrazino]-2,4-dihydro-[1,2,4]triazole-3-thione

NASA Astrophysics Data System (ADS)

Joshi, Rachana; Pandey, Nidhi; Yadav, Swatantra Kumar; Tilak, Ragini; Mishra, Hirdyesh; Pokharia, Sandeep

2018-07-01

The hydrazino Schiff base (E)-4-amino-5-[N'-(2-nitro-benzylidene)-hydrazino]-2,4-dihydro-[1,2,4]triazole-3-thione was synthesized and structurally characterized by elemental analysis, FT-IR, Raman, 1H and 13C-NMR and UV-Vis studies. A density functional theory (DFT) based electronic structure calculations were accomplished at B3LYP/6-311++G(d,p) level of theory. A comparative analysis of calculated vibrational frequencies with experimental vibrational frequencies was carried out and significant bands were assigned. The results indicate a good correlation (R2 = 0.9974) between experimental and theoretical IR frequencies. The experimental 1H and 13C-NMR resonance signals were also compared to the calculated values. The theoretical UV-Vis spectral studies were carried out using time dependent-DFT method in gas phase and IEFPCM model in solvent field calculation. The geometrical parameters were calculated in the gas phase. Atomic charges at selected atoms were calculated by Mulliken population analysis (MPA), Hirshfeld population analysis (HPA) and Natural population analysis (NPA) schemes. The molecular electrostatic potential (MEP) map was calculated to assign reactive site on the surface of the molecule. The conceptual-DFT based global and local reactivity descriptors were calculated to obtain an insight into the reactivity behaviour. The frontier molecular orbital analysis was carried out to study the charge transfer within the molecule. The detailed natural bond orbital (NBO) analysis was performed to obtain an insight into the intramolecular conjugative electronic interactions. The titled compound was screened for in vitro antifungal activity against four fungal strains and the results obtained are explained through in silico molecular docking studies.

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.

Hydrophilic crosslinked-polymeric surface capable of effective suppression of protein adsorption

NASA Astrophysics Data System (ADS)

Kamon, Yuri; Inoue, Naoko; Mihara, Erika; Kitayama, Yukiya; Ooya, Tooru; Takeuchi, Toshifumi

2016-08-01

We investigated the nonspecific adsorption of proteins towards three hydrophilic crosslinked-polymeric thin layers prepared by surface-initiated atom transfer radical polymerization using N,N‧-methylenebisacrylamide, 2-(methacryloyloxy)ethyl-[N-(2-methacryloyloxy)ethyl]phosphorylcholine (MMPC), or 6,6‧-diacryloyl-trehalose crosslinkers. Protein binding experiments were performed by surface plasmon resonance with six proteins of different pI values including α-lactalbumin, bovine serum albumin (BSA), myoglobin, ribonuclease A, cytochrome C, and lysozyme in buffer solution at pH 7.4. All of the obtained crosslinked-polymeric thin layers showed low nonspecific adsorption of negatively charged proteins at pH 7.4 such as α-lactalbumin, BSA, and myoglobin. Nonspecific adsorption of positively charged proteins including ribonuclease A, cytochrome C, and lysozyme was the lowest for poly(MMPC). These results suggest poly(MMPC) can effectively reduce nonspecific adsorption of a wide range of proteins that are negatively or positively charged at pH 7.4. MMPC is a promising crosslinker for a wide range of polymeric materials requiring low nonspecific protein binding.

Electronic Structure Calculations of Ammonia Adsorption on Graphene and Graphene Oxide with Epoxide and Hydroxyl Groups

NASA Astrophysics Data System (ADS)

Nancy Anna Anasthasiya, A.; Khaneja, Mamta; Jeyaprakash, B. G.

2017-10-01

Ammonia adsorption on graphene (G) and graphene oxide (GO) was investigated through density functional theory calculations. In the GO system, the obtained binding energy, band gap, charge transfer and electronic structure revealed that the epoxide (GO-O) and hydroxyl groups (GO-OH) in GO enhance the NH3 adsorption, which leads to the chemisorption of NH3 on GO. The dissociation of NH3 to NH2 and formation of OH was also observed when the O and H atoms were separated at 0.985 Å, 1.019 Å, 1.035 Å, and 1.044 Å for various GO systems. The maximum charge transfer value was found to be 0.054 |e| with the binding energy of 1.143 eV for GO with a single epoxide (GO-1O) group. The charge transfer from NH3 to G or GO and the bond formation in this study agree with the reported experimental results.

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

Effects of Charge Transfer on the Adsorption of CO on Small Molybdenum-Doped Platinum Clusters.

PubMed

Ferrari, Piero; Vanbuel, Jan; Tam, Nguyen Minh; Nguyen, Minh Tho; Gewinner, Sandy; Schöllkopf, Wieland; Fielicke, André; Janssens, Ewald

2017-03-23

The interaction of carbon monoxide with platinum alloy nanoparticles is an important problem in the context of fuel cell catalysis. In this work, molybdenum-doped platinum clusters have been studied in the gas phase to obtain a better understanding of the fundamental nature of the Pt-CO interaction in the presence of a dopant atom. For this purpose, Pt n + and MoPt n-1 + (n=3-7) clusters were studied by combined mass spectrometry and density functional theory calculations, making it possible to investigate the effects of molybdenum doping on the reactivity of platinum clusters with CO. In addition, IR photodissociation spectroscopy was used to measure the stretching frequency of CO molecules adsorbed on Pt n + and MoPt n-1 + (n=3-14), allowing an investigation of dopant-induced charge redistribution within the clusters. This electronic charge transfer is correlated with the observed changes in reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Grafting iminodiacetic acid on silica nanoparticles for facilitated refolding of like-charged protein and its metal-chelate affinity purification.

PubMed

Liu, Hu; Dong, Xiaoyan; Sun, Yan

2016-01-15

A series of highly charged nanoscale chelators were fabricated by grafting of poly(glycidyl methacrylate-iminodiacetic acid) (pGI) chains with iminodiacetic acid (IDA) chelating group on silica nanoparticles (SNPs) via atom transfer radical polymerization (ATRP). The nanoscale chelators, denoted as SNPs-pGI, possessed a nickel ion chelating capacity as high as 2800 μmol/g, 50 times higher than the IDA-modified Sepharose FF (IDA-Sepharose) resin reported in literature and offered a high affinity binding capacity for hexahistidine-tagged enhanced green fluorescence protein (6 × His-EGFP) after nickel ion loading. More importantly, the anionic SNPs-pGI of high charge densities displayed much better performance than IDA-Sepharose in facilitating the refolding of like-charged 6 × His-EGFP from inclusion bodies (IBs). For example, for 0.2mg/mL 6 × His-EGFP IB refolding, addition of 6.2 μL/mL SNPs-pGI with the highest charge density led to a refolding yield of 90%, over 43% higher than that obtained with 460 μL/mL IDA-Sepharose. It is notable that the much higher efficiency of the nanoscale chelator was obtained with a chelator consumption corresponding to only 1.4% of IDA-Sepharose. Moreover, the highly charged SNPs-pGI could efficiently facilitate the refolding of 6 × His-EGFP at higher IB concentrations (0.4 and 0.8 mg/mL). After refolding, nickel ions addition led to the recovery of the refolded 6 × His-EGFP with high yield (80%), purity (96%) and enrichment ratio (1.8). All the results suggest that the SNPs-pGI of high charge densities were promising for cost-effective recovery of His-tagged proteins expressed as IBs with the integrative like-charge facilitated refolding and metal-chelate affinity purification strategy. Copyright © 2015 Elsevier B.V. All rights reserved.

Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

PubMed

Rudenko, A; Inhester, L; Hanasaki, K; Li, X; Robatjazi, S J; Erk, B; Boll, R; Toyota, K; Hao, Y; Vendrell, O; Bomme, C; Savelyev, E; Rudek, B; Foucar, L; Southworth, S H; Lehmann, C S; Kraessig, B; Marchenko, T; Simon, M; Ueda, K; Ferguson, K R; Bucher, M; Gorkhover, T; Carron, S; Alonso-Mori, R; Koglin, J E; Correa, J; Williams, G J; Boutet, S; Young, L; Bostedt, C; Son, S-K; Santra, R; Rolles, D

2017-06-01

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.

Femtosecond response of polyatomic molecules to ultra-intense hard X-rays

DOE PAGES

Rudenko, A.; Inhester, L.; Hanasaki, K.; ...

2017-05-31

We report x-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecularmore » system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects—an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure—the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Fnally, our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.« less

Femtosecond response of polyatomic molecules to ultra-intense hard X-rays

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

Rudenko, A.; Inhester, L.; Hanasaki, K.

We report x-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecularmore » system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects—an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure—the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Fnally, our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.« less

Ultrafast molecular processes mapped by femtosecond x-ray diffraction

NASA Astrophysics Data System (ADS)

Elsaesser, Thomas

2012-02-01

X-ray diffraction with a femtosecond time resolution allows for mapping photoinduced structural dynamics on the length scale of a chemical bond and in the time domain of atomic and molecular motion. In a pump-probe approach, a femtosecond excitation pulse induces structural changes which are probed by diffracting a femtosecond hard x-ray pulse from the excited sample. The transient angular positions and intensities of diffraction peaks give insight into the momentary atomic or molecular positions and into the distribution of electronic charge density. The simultaneous measurement of changes on different diffraction peaks is essential for determining atom positions and charge density maps with high accuracy. Recent progress in the generation of ultrashort hard x-ray pulses (Cu Kα, wavelength λ=0.154 nm) in laser-driven plasma sources has led to the implementation of the powder diffraction and the rotating crystal method with a time resolution of 100 fs. In this contribution, we report new results from powder diffraction studies of molecular materials. A first series of experiments gives evidence of a so far unknown concerted transfer of electrons and protons in ammonium sulfate [(NH4)2SO4], a centrosymmetric structure. Charge transfer from the sulfate groups results in the sub-100 fs generation of a confined electron channel along the c-axis of the unit cell which is stabilized by transferring protons from the adjacent ammonium groups into the channel. Time-dependent charge density maps display a periodic modulation of the channel's charge density by low-frequency lattice motions with a concerted electron and proton motion between the channel and the initial proton binding site. A second study addresses atomic rearrangements and charge dislocations in the non-centrosymmetric potassium dihydrogen phosphate [KH2PO4, KDP]. Photoexcitation generates coherent low-frequency motions along the LO and TO phonon coordinates, leaving the average atomic positions unchanged. The time-dependent maps of electron density demonstrate a concomitant oscillatory relocation of electronic charge with a spatial amplitude of the order of a chemical bond length, two orders of magnitude larger than the vibrational amplitudes. The coherent phonon motions drive the charge relocation, similar to a soft mode driven phase transition between the ferro- and paraelectric phase of KDP.

Fabrication of polyamide thin-film nanocomposite membranes with enhanced surface charge for nitrate ion removal from water resources.

PubMed

Ghaee, A; Zerafat, M M; Askari, P; Sabbaghi, S; Sadatnia, B

2017-03-01

Exclusion due to membrane surface charge is considered as one of the main separation mechanisms occurring in charged membranes, which can be varied through various approaches to affect membrane rejection performance. In this study, thin-film composite (TFC) polyamide (PA) membranes were fabricated via interfacial polymerization of m-phenylenediamine (m-PDA) and 2,4-diaminobenzene sulfonic acid with trimesoyl chloride (TMC) on a polysulfone sub-layer. The ability of the prepared membrane to remove nitrate ions from water resources has been investigated. In order to improve membrane permeability, zeolite-PA thin film nanocomposite (TFN) membranes were fabricated by incorporating natural zeolite nanoparticles obtained through ball milling of an Iranian natural zeolite powder in the interfacial polymerization process. The size, morphology and specific surface area of the as-obtained nanozeolite were characterized using particle size analysis, FE-SEM and BET. The functional groups, morphology and surface charge of the membrane were characterized using ATR-FTIR, SEM and zeta potential analyses. Also, field-emission scanning electron microscopy (FE-SEM) and energy dispersive X-ray spectroscopy (EDS) were used to determine the distribution of nanozeolite in TFN membranes. The influence of zeolite addition to surface roughness was accessed by atomic force microscopy. The performance of TFC and TFN membranes was evaluated in terms of pure water flux and nitrate rejection. The results showed that in case of sulfonated diamine, nitrate ions rejection was enhanced from 63% to 85% which could be attributed to surface charge enhancement. TFN permeability was almost doubled by the addition of nanozeolite.

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.

Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB)

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

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Bannwarth, Christoph

2016-08-07

The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the wellmore » established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H–Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first benchmarked for vertical excitation energies of open- and closed-shell systems in comparison to other semi-empirical methods and applied to exemplary problems in electronic spectroscopy. As side products of the development, a robust and efficient valence electron TB method for the accurate determination of atomic charges as well as a more accurate calculation scheme of dipole rotatory strengths within the Tamm-Dancoff approximation is proposed.« less

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

PubMed

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

Validation of the role of bulk charging of hydrogen in the corrosion fatigue cracking of a low alloy steel

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

Griffiths, A.J.; Hutchings, R.B.; Turnbull, A.

1993-09-01

The enhanced corrosion fatigue crack growth rates of low alloy steels cathodically protected in marine environments results from absorbed hydrogen atoms. Hydrogen atoms are generated at the crack tip, crack walls and the external surface of the specimen (bulk charging). In previous work, Turnbull and Saenz de Santa Maria developed a model to predict the rate of generation of hydrogen atoms at the tips of fatigue cracks for steels cathodically polarized in marine environments. The main prediction from this work was that the external surface of the specimen can be the dominant source of hydrogen atoms at potentials more negativemore » than about [minus]900 mV (SCE), at a cyclic frequency of 0.1 Hz and a stress ratio of 0.5. The relative importance of bulk charging depends on the specific test conditions and is influenced by the applied potential, bulk chemistry, cyclic frequency, specimen thickness, temperature and use of coatings. Since laboratory test times are usually short in relation to the time required for hydrogen transport measured crack growth rates may be lower than those occurring in practice, for which there is sufficient time for full hydrogen charging. The purpose of this study is to verify experimentally the importance of bulk charging. Since the sensitivity of cracking to variations in hydrogen concentration will be material dependent a high strength steel was selected in this initial study because of its sensitivity to hydrogen. This will enable validation of the basic premise that bulk charging can be important, prior to more extensive studies using lower strength alloys.« less

Detection of subsurface core-level shifts in Si 2p core-level photoemission from Si(111)-(1x1):As

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

Paggel, J.J.; Hasselblatt, M.; Horn, K.

1997-04-01

The (7 x 7) reconstruction of the Si(111) surface arises from a lowering energy through the reduction of the number of dangling bonds. This reconstruction can be removed by the adsorption of atoms such as hydrogen which saturate the dangling bonds, or by the incorporation of atoms, such as arsenic which, because of the additional electron it possesses, can form three bonds and a nonreactive lone pair orbital from the remaining two electrons. Core and valence level photoemission and ion scattering data have shown that the As atoms replace the top silicon atoms. Previous core level spectra were interpreted inmore » terms of a bulk and a single surface doublet. The authors present results demonstrate that the core level spectrum contains two more lines. The authors assign these to subsurface silicon layers which also experience changes in the charge distribution when a silicon atom is replaced by an arsenic atom. Subsurface core level shifts are not unexpected since the modifications of the electronic structure and/or of photohole screening are likely to decay into the bulk and not just to affect the top-most substrate atoms. The detection of subsurface components suggests that the adsorption of arsenic leads to charge flow also in the second double layer of the Si(111) surface. In view of the difference in atomic radius between As and Si, it was suggested that the (1 x 1): As surface is strained. The presence of charge rearrangement up to the second double layer implies that the atomic coordinates also exhibit deviations from their ideal Si(111) counterparts, which might be detected through a LEED I/V or photoelectron diffraction analysis.« less

In silico prediction of nematic transition temperature for liquid crystals using quantitative structure-property relationship approaches.

PubMed

Fatemi, Mohammad Hossein; Ghorbanzad'e, Mehdi

2009-11-01

Quantitative structure-property relationship models for the prediction of the nematic transition temperature (T (N)) were developed by using multilinear regression analysis and a feedforward artificial neural network (ANN). A collection of 42 thermotropic liquid crystals was chosen as the data set. The data set was divided into three sets: for training, and an internal and external test set. Training and internal test sets were used for ANN model development, and the external test set was used for evaluation of the predictive power of the model. In order to build the models, a set of six descriptors were selected by the best multilinear regression procedure of the CODESSA program. These descriptors were: atomic charge weighted partial negatively charged surface area, relative negative charged surface area, polarity parameter/square distance, minimum most negative atomic partial charge, molecular volume, and the A component of moment of inertia, which encode geometrical and electronic characteristics of molecules. These descriptors were used as inputs to ANN. The optimized ANN model had 6:6:1 topology. The standard errors in the calculation of T (N) for the training, internal, and external test sets using the ANN model were 1.012, 4.910, and 4.070, respectively. To further evaluate the ANN model, a crossvalidation test was performed, which produced the statistic Q (2) = 0.9796 and standard deviation of 2.67 based on predicted residual sum of square. Also, the diversity test was performed to ensure the model's stability and prove its predictive capability. The obtained results reveal the suitability of ANN for the prediction of T (N) for liquid crystals using molecular structural descriptors.

Dielectric properties of proteins from simulations: tools and techniques

NASA Astrophysics Data System (ADS)

Simonson, Thomas; Perahia, David

1995-09-01

Tools and techniques to analyze the dielectric properties of proteins are described. Microscopic dielectric properties are determined by a susceptibility tensor of order 3 n, where n is the number of protein atoms. For perturbing charges not too close to the protein, the dielectric relaxation free energy is directly related to the dipole-dipole correlation matrix of the unperturbed protein, or equivalently to the covariance matrix of its atomic displacements. These are straightforward to obtain from existing molecular dynamics packages such as CHARMM or X- PLOR. Macroscopic dielectric properties can be derived from the dipolar fluctuations of the protein, by idealizing the protein as one or more spherical media. The dipolar fluctuations are again directly related to the covariance matrix of the atomic displacements. An interesting consequence is that the quasiharmonic approximation, which by definition exactly reproduces this covariance matrix, gives the protein dielectric constant exactly. Finally a technique is reviewed to obtain normal or quasinormal modes of vibration of symmetric protein assemblies. Using elementary group theory, and eliminating the high-frequency modes of vibration of each monomer, the limiting step in terms of memory and computation is finding the normal modes of a single monomer, with the other monomers held fixed. This technique was used to study the dielectric properties of the Tobacco Mosaic Virus protein disk.

Estimation of Enthalpy of Formation of Liquid Transition Metal Alloys: A Modified Prescription Based on Macroscopic Atom Model of Cohesion

NASA Astrophysics Data System (ADS)

Raju, Subramanian; Saibaba, Saroja

2016-09-01

The enthalpy of formation Δo H f is an important thermodynamic quantity, which sheds significant light on fundamental cohesive and structural characteristics of an alloy. However, being a difficult one to determine accurately through experiments, simple estimation procedures are often desirable. In the present study, a modified prescription for estimating Δo H f L of liquid transition metal alloys is outlined, based on the Macroscopic Atom Model of cohesion. This prescription relies on self-consistent estimation of liquid-specific model parameters, namely electronegativity ( ϕ L) and bonding electron density ( n b L ). Such unique identification is made through the use of well-established relationships connecting surface tension, compressibility, and molar volume of a metallic liquid with bonding charge density. The electronegativity is obtained through a consistent linear scaling procedure. The preliminary set of values for ϕ L and n b L , together with other auxiliary model parameters, is subsequently optimized to obtain a good numerical agreement between calculated and experimental values of Δo H f L for sixty liquid transition metal alloys. It is found that, with few exceptions, the use of liquid-specific model parameters in Macroscopic Atom Model yields a physically consistent methodology for reliable estimation of mixing enthalpies of liquid alloys.

Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile.

PubMed

Premkumar, S; Jawahar, A; Mathavan, T; Kumara Dhas, M; Milton Franklin Benial, A

2015-03-05

The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908×10(-30) issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π→π(∗) transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Warm Breeze due to Charge Exchange Collisions Between Neutral He Atoms and He+ Ions in the Outer Heliosheath.

NASA Astrophysics Data System (ADS)

Kubiak, M. A.; Bzowski, M.; Czechowski, A.; Grygorczuk, J.

2017-12-01

We simulated the signal due to neutral He atoms, observed by Interstellar Boundary Explorer (IBEX), assuming that charge exchange collisions between neutral He atoms and He+ ions operate everywhere between the heliopause and a distant source region in the local interstellar cloud (LIC). We chose the limiting distance of calculations at 5000 AU, where the neutral and charged components are in thermal equilibrium. From that distance we integrated the signal for test particles that we know they reach the IBEX detector, calculating for each particle the balance of losses and gains in the LIC, the ionization losses inside the HP, and the distribution function at 5000 AU. The resulting statistical weights were integrated over speed, inflow direction, collimator transmission, observation times, and IBEX spin angle bins to simulate the count rate actually observed by IBEX. We simulated several test cases of the plasma flow within the outer heliosheath and investigated the signal generation for plasma flows both in the presence and in the absence of the interstellar magnetic field. We found that a signal in the portion of IBEX data identified as due to the Warm Breeze does not arise when a homogeneous plasma flow in front of the heliopause is assumed. However, it appears immediately when any reasonable disturbance in the plasma flow due to the presence of the heliosphere is assumed. We obtained a good qualitative agreement between the data and the simulations for a model flow with the velocity vector of the unperturbed gas and the direction and intensity of magnetic field adopted from recent determinations. We conclude that direct-sampling observations of neutral He atoms at 1 AU from the Sun are a sensitive tool for investigating the flow of interstellar matter in the outer heliosheath; the Warm Breeze is indeed the secondary population of interstellar helium, as it was hypothesized earlier; the WB signal is consistent with that predicted by comet-like models of the heliosphere with a distortion from axial symmetry by the interstellar magnetic field of 3 microgauss, directed close to the Ribbon direction.

Ligand field splittings in core level transitions for transition metal (TM) oxides: Tanabe-Sugano diagrams and (TM) dangling bonds in vacated O-atom defects

NASA Astrophysics Data System (ADS)

Lucovsky, Gerry; Wu, Kun; Pappas, Brian; Whitten, Jerry

2013-04-01

Defect states in the forbidden band-gap below the conduction band edge are active as electron traps in nano-grain high-) transition metal (TM) oxides with thickness >0.3 nm, e.g., ZrO2 and HfO2. These oxides have received considerable attention as gate-dielectrics in complementary metal oxide semiconductor (CMOS) devices, and more recently are emerging as candidates for charge storage and memory devices. To provide a theoretical basis for device functionality, ab-initio many-electron theory is combined with X-ray absorption spectroscopy (XAS) to study O K edge and TM core level transitions. These studies identify ligand field splittings (ΔLF) for defect state features,. When compared with those obtained from O-atom and TM-atom core spectroscopic transitions, this provides direct information about defect state sun-nm bonding arrangements. comparisons are made for (i) elemental TiO2 and Ti2O3 with different formal ionic charges, Ti4+ and Ti3+ and for (ii) Magneli Phase alloys, TinO2n-1, n is an integer 9>=n>3, and (TiO2)x(HfO2)1-x alloys. The alloys display multi-valent behavior from (i) different ionic-charge states, (ii} local bond-strain, and (iii) metallic hopping transport. The intrinsic bonding defects in TM oxides are identified as pairs of singly occupied dangling bonds. For 6-fold coordinated Ti-oxides defect excited states in 2nd derivative O K pre-edge spectra are essentially the same as single Ti-atom d2 transitions in Tanabe-Sugano (T-S) diagrams. O-vacated site defects in 8-fold coordinated ZrO2 and HfO2 are described by d8 T-S diagrams. T-S defect state ordering and splittings are functions of the coordination and symmetry of vacated site bordering TM atoms. ΔLF values from the analysis of T-S diagrams indicate medium range order (MRO) extending to 3rd and 4th nearest-neighbor (NN) TM-atoms. Values are different for 6-fold Ti, and 8-fold ZrO2 and HfO2, and scale inversely with differences in respective formal ionic radii. O-vacated site bonding defects in TM nano-grain oxides are qualitatively similar to vacant-site defects in non-crystalline SiO2 and GeO2 for ulta-thin films, < 0.2 nm thick, and yield similar performance in MOSCAPs on Ge substrates heralding applications in aggressively-scale CMOS devices.

Orbital-Dependent-Functionals within Density Functional Theory: Methodology and Applications

NASA Astrophysics Data System (ADS)

Makmal, Adi

I have designed and implemented a new numerical scheme for solving Kohn-Sham (KS) equations for diatomic systems, together with a full solution of the OEP equation. The equations are solved on a real-space prolate spheroidal coordinate grid, such that all the system's electrons are taken into account. The OEP equation is solved via the S-iteration scheme. This newly developed software package is called DARSEC (DiAtomic Real-Space Electronic structure Calculations). It involves no approximation except for the one inherent in the XC functional. Thus it is especially suitable for examining new functionals of any kind, and ODFs in particular. It is also an ideal tool for assessing the validity of commonly used approximations, for the same reasons. One case for which this uniqueness of DARSEC was exploited in this thesis is the examination of the validity of the pseudopotential approximation for KS gaps that are calculated with EXX OEP (xOEP). Before this study, use of the pseudopotential approximation in such calculations was called into question. I have shown that KS gaps obtained with pseudopotentials that have been constructed in a manner consistent with the exact-exchange functional agree with the all-electron results (i.e. without the pseudopotential approximation), for the cases studied. This confirmed the reliability of the pseudopotential approximation for ODFs such as EXX. Explicit density-dependent XC functionals traditionally fail to obtain atomization-energy as well as charge-dissociation curves that are, at least qualitatively, correct for diatomic systems. On the other hand, Hartree-Fock (HF) theory encounters no such problem. Hence, an additional goal of this research was to study the performances of the EXX functional (being the DFT counterpart of HF) in describing binding energies and charge dissociations for stretched diatomic molecules. Moreover, I wanted to investigate the special features of the resulting single and local EXX KS potential, as opposed to the non-local orbital specific HF potentials. I asked the following questions: Is it at all possible to obtain correct binding energy curves and charge dissociation curves with the local exact-exchange KS potential? What are the main features of such a local KS potential? And how are they related to the spatial shapes of the KS orbitals? To answer these questions, I calculated the electronic structures of highly stretched H2, HF and LiF molecules with EXX, using the Krieger, Li, and Iafrate (KLI) scheme. All calculations were done with DARSEC, whose coordinate system is highly suitable for calculating such stretched diatomic molecules. By examining several electronic configurations in a systematic manner, low energy ones were identified, and qualitatively correct binding-energy curves were obtained. For the LiF molecule a qualitatively correct charge separation curve was also achieved. Once the local EXX KLI potential was obtained for highly stretched diatomic systems, I could study its properties. Specifically, I have identified and demonstrated the following features: (a) The location and size of a constant shift in the potential and its relation to orbital spatial shapes; (b) The dependence of the shift's position on the inter-atomic separation length; (c) The existence of multiple constant shifts of the same kind; (d) The relation between the eigenvalues of the highly stretched diatomic system and the corresponding eigenvalues of the separated atoms - and how this relation is correlated with the asymptotic shift of the local potential. Understanding this unique combination of features sheds light on the mechanism with which the EXX potential enforces the correct charge dissociation. Last, a study on a novel ODF was initiated. The new ODF, suggested by Stephan Kummel, has a local function that mixes a fraction of EXX with a complementary fraction of exchange of the homogenous electronic gas (LDA), where a different fraction is assigned for each point in space. To derive the corresponding potential, the functional derivative of the new energy expression with respect to the KS orbitals was analytically derived. The new energy and potential expressions were implemented into DARSEC, and preliminary examinations were carried out. (Abstract shortened by UMI.)

Theoretical study for heterojunction surface of NEA GaN photocathode dispensed with Cs activation

NASA Astrophysics Data System (ADS)

Xia, Sihao; Liu, Lei; Wang, Honggang; Wang, Meishan; Kong, Yike

2016-09-01

For the disadvantages of conventional negative electron affinity (NEA) GaN photocathodes activated by Cs or Cs/O, new-type NEA GaN photocathodes with heterojunction surface dispensed with Cs activation are investigated based on first-principle study with density functional theory. Through the growth of an ultrathin n-type GaN cap layer on p-type GaN emission layer, a p-n heterojunction is formed on the surface. According to the calculation results, it is found that Si atoms tend to replace Ga atoms to result in an n-type doped cap layer which contributes to the decreasing of work function. After the growth of n-type GaN cap layer, the atom structure near the p-type emission layer is changed while that away from the surface has no obvious variations. By analyzing the E-Mulliken charge distribution of emission surface with and without cap layer, it is found that the positive charge of Ga and Mg atoms in the emission layer decrease caused by the cap layer, while the negative charge of N atom increases. The conduction band moves downwards after the growth of cap layer. Si atom produces donor levels around the valence band maximum. The absorption coefficient of GaN emission layer decreases and the reflectivity increases caused by n-type GaN cap layer.

Total Born approximation cross sections for single electron loss by atoms and ions colliding with atoms

NASA Technical Reports Server (NTRS)

Rule, D. W.

1977-01-01

The first born approximation (FBA) is applied to the calculation of single electron loss cross sections for various ions and atoms containing from one to seven electrons. Screened hydrogenic wave functions were used for the states of the electron ejected from the projectile, and Hartree-Fock elastic and incoherent scattering factors were used to describe the target. The effect of the target atom on the scaling of projectile ionization cross sections with respect to the projectile nuclear charge was explored in the case of hydrogen-like ions. Scaling of the cross section with respect to the target nuclear charge for electron loss by Fe (+25) in collision with neutral atoms ranging from H to Fe is also examined. These results were compared to those of the binary encounter approximation and to the FBA for the case of ionization by completely stripped target ions.

A spectral study of a radio-frequency plasma-generated flux of atomic oxygen

NASA Technical Reports Server (NTRS)

Batten, Carmen E.; Brown, Kenneth G.; Lewis, Beverley W.

1994-01-01

The active environment of a radio-frequency (RF) plasma generator, with and without low-pressure oxygen, has been characterized through the identification of emission lines in the spectral region from 250 to 900 nm. The environment is shown to be dependent on the partial pressure of oxygen and the power applied to the RF generator. Atomic oxygen has been found in significant amounts as well as atomic hydrogen and the molecular oxygen species O2((sup 1)Sigma). The only charged species observed was the singly charged molecular ion O2(+). With a polymer specimen in the plasma chamber, carbon monoxide was also observed. The significance of these observations with respect to previous studies using this type of generator to stimulate material degradation in space is discussed. The possibility of using these generators as atomic oxygen sources in the development of oxygen atom fluorescence sensors is explored.

HZETRN: Description of a free-space ion and nucleon transport and shielding computer program

NASA Technical Reports Server (NTRS)

Wilson, John W.; Badavi, Francis F.; Cucinotta, Francis A.; Shinn, Judy L.; Badhwar, Gautam D.; Silberberg, R.; Tsao, C. H.; Townsend, Lawrence W.; Tripathi, Ram K.

1995-01-01

The high-charge-and energy (HZE) transport computer program HZETRN is developed to address the problems of free-space radiation transport and shielding. The HZETRN program is intended specifically for the design engineer who is interested in obtaining fast and accurate dosimetric information for the design and construction of space modules and devices. The program is based on a one-dimensional space-marching formulation of the Boltzmann transport equation with a straight-ahead approximation. The effect of the long-range Coulomb force and electron interaction is treated as a continuous slowing-down process. Atomic (electronic) stopping power coefficients with energies above a few A MeV are calculated by using Bethe's theory including Bragg's rule, Ziegler's shell corrections, and effective charge. Nuclear absorption cross sections are obtained from fits to quantum calculations and total cross sections are obtained with a Ramsauer formalism. Nuclear fragmentation cross sections are calculated with a semiempirical abrasion-ablation fragmentation model. The relation of the final computer code to the Boltzmann equation is discussed in the context of simplifying assumptions. A detailed description of the flow of the computer code, input requirements, sample output, and compatibility requirements for non-VAX platforms are provided.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Hydrogen rearrangements in the fragmentation of anthracene by low-energy electron impact

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Dunne, Melissa; Gradziel, Marcin L.

2018-02-01

We have measured mass spectra for positive ions produced by low-energy electron impact on anthracene using a reflectron time-of-flight mass spectrometer. The electron impact energy has been varied from 0 to 100 eV in steps of 0.5 eV. Ion yield curves of most of the fragment ions have been determined by fitting groups of adjacent peaks in the mass spectra with sequences of normalized Gaussians. Appearance energies for all these ions have been determined, and we report the first direct measurement of the triple ionization energy of anthracene at 45.5±0.5 eV. The groups of fragments containing 8-13 carbon atoms provide evidence for hydrogen rearrangements during the fragmentation, involving retention or loss of one or two additional hydrogen atoms. Groups of fragments with 6 and 7 carbon atoms clearly show the presence of doubly-charged fragments. The smaller fragments with 1-4 carbon atoms all show broadened peaks, and these fragments may be partly or mostly due to energetic charge-separation fragmentations of doubly-charged anthracene.

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.

A Variational Monte Carlo Approach to Atomic Structure

ERIC Educational Resources Information Center

Davis, Stephen L.

2007-01-01

The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

PubMed

Cohen, A; Niv, M Y; Gerber, R B

2001-01-01

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.

Turbomolecular Pumps for Holding Gases in Open Containers

NASA Technical Reports Server (NTRS)

Keller, John W.; Lorenz, John E.

2010-01-01

Proposed special-purpose turbomolecular pumps denoted turbotraps would be designed, along with mating open containers, to prevent the escape of relatively slowly (thermal) moving gas molecules from the containers while allowing atoms moving at much greater speeds to pass through. In the original intended applications, the containers would be electron-attachment cells, and the contained gases would be vapors of alkali metal atoms moving at thermal speeds that would be of the order of a fraction of 300 meters per second. These cells would be parts of apparatuses used to measure fluxes of neutral atoms incident at kinetic energies in the approximate range of 10 eV to 10 keV (corresponding to typical speeds of the order of 40,000 m/s and higher). The incident energetic neutral atoms would pass through the cells, wherein charge-exchange reactions with the alkali metal atoms would convert the neutral atoms to negative ions, which, in turn, could then be analyzed by use of conventional charged-particle optics.

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

NASA Astrophysics Data System (ADS)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.; Moon, Y.; Rai, K. B.; Woo, S. H.; Ahn, J. R.

2016-08-01

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalated at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.

An estimating formula for ion-atom association rates in gases

NASA Technical Reports Server (NTRS)

Chatterjee, B. K.; Johnsen, R.

1990-01-01

A simple estimating formula is derived for rate coefficients of three-body ion atom association in gases and compare its predictions to experimental data on ion association and three-body radiative charge transfer reactions of singly- and doubly-charged rare-gas ions. The formula appears to reproduce most experimental data quite well. It may be useful for estimating the rates of reactions that have not been studied in the laboratory.

Charge-state distribution of Li ions from the β decay of laser-trapped 6He atoms

NASA Astrophysics Data System (ADS)

Hong, R.; Leredde, A.; Bagdasarova, Y.; Fléchard, X.; García, A.; Knecht, A.; Müller, P.; Naviliat-Cuncic, O.; Pedersen, J.; Smith, E.; Sternberg, M.; Storm, D. Â. W.; Swanson, H. Â. E.; Wauters, F.; Zumwalt, D.

2017-11-01

The accurate determination of atomic final states following nuclear β decay plays an important role in several experiments. In particular, the charge state distributions of ions following nuclear β decay are important for determinations of the β -ν angular correlation with improved precision. Beyond the hydrogenic cases, the decay of neutral 6He presents the simplest case. Our measurement aims at providing benchmarks to test theoretical calculations. The kinematics of Lin + ions produced following the β decay of 6He within an electric field were measured using 6He atoms in the metastable (1 s 2 s ,S31) and (1 s 2 p ,P32) states confined by a magneto-optical trap. The electron shakeoff probabilities were deduced, including their dependence on ion energy. We find significant discrepancies on the fractions of Li ions in the different charge states with respect to a recent calculation.

Direct numerical simulation of leaky dielectrics with application to electrohydrodynamic atomization

NASA Astrophysics Data System (ADS)

Owkes, Mark; Desjardins, Olivier

2013-11-01

Electrohydrodynamics (EHD) have the potential to greatly enhance liquid break-up, as demonstrated in numerical simulations by Van Poppel et al. (JCP (229) 2010). In liquid-gas EHD flows, the ratio of charge mobility to charge convection timescales can be used to determine whether the charge can be assumed to exist in the bulk of the liquid or at the surface only. However, for EHD-aided fuel injection applications, these timescales are of similar magnitude and charge mobility within the fluid might need to be accounted for explicitly. In this work, a computational approach for simulating two-phase EHD flows including the charge transport equation is presented. Under certain assumptions compatible with a leaky dielectric model, charge transport simplifies to a scalar transport equation that is only defined in the liquid phase, where electric charges are present. To ensure consistency with interfacial transport, the charge equation is solved using a semi-Lagrangian geometric transport approach, similar to the method proposed by Le Chenadec and Pitsch (JCP (233) 2013). This methodology is then applied to EHD atomization of a liquid kerosene jet, and compared to results produced under the assumption of a bulk volumetric charge.

Status of Charge Exchange Cross Section Measurements for Highly Charged Ions on Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Draganic, I. N.; Havener, C. C.; Schultz, D. R.; Seely, D. G.; Schultz, P. C.

2011-05-01

Total cross sections of charge exchange (CX) for C5+, N6+, and O7+ ions on ground state atomic hydrogen are measured in an extended collision energy range of 1 - 20,000 eV/u. Absolute CX measurements are performed using an improved merged-beams technique with intense highly charged ion beams extracted from a 14.5 GHz ECR ion source mounted on a high voltage platform. In order to improve the problematic H+ signal collection for these exoergic CX collisions at low relative energies, a new double focusing electrostatic analyzer was installed. Experimental CX data are in good agreement with all previous H-oven relative measurements at higher collision energies. We compare our results with the most recent molecular orbital close-coupling (MOCC) and atomic orbital close-coupling (AOCC) theoretical calculations. Work supported by the NASA Solar & Heliospheric Physics Program NNH07ZDA001N, the Office of Fusion Energy Sciences and the Division of Chemical Sciences, Geosciences, and Biosciences, and the Office of Basic Energy Sciences of the U.S. DoE.

Laboratory Studies of Thermal Energy Charge Transfer of Multiply Charged Ions in Astrophysical Plasmas

NASA Technical Reports Server (NTRS)

Kwong, Victor H. S.

2003-01-01

The laser ablation/ion storage facility at the UNLV Physics Department has been dedicated to the study of atomic and molecular processes in low temperature plasmas. Our program focuses on the charge transfer (electron capture) of multiply charged ions and neutrals important in astrophysics. The electron transfer reactions with atoms and molecules is crucial to the ionization condition of neutral rich photoionized plasmas. With the successful deployment of the Far Ultraviolet Spectroscopic Explorer (FUSE) and the Chandra X-ray Observatory by NASA high resolution VUV and X-ray emission spectra fiom various astrophysical objects have been collected. These spectra will be analyzed to determine the source of the emission and the chemical and physical environment of the source. The proper interpretation of these spectra will require complete knowledge of all the atomic processes in these plasmas. In a neutral rich environment, charge transfer can be the dominant process. The rate coefficients need to be known accurately. We have also extended our charge transfer measurements to KeV region with a pulsed ion beam. The inclusion of this facility into our current program provides flexibility in extending the measurement to higher energies (KeV) if needed. This flexibility enables us to address issues of immediate interest to the astrophysical community as new observations are made by high resolution space based observatories.

Spray Formation from a Charged Liquid Jet of a Dielectric Fluid

NASA Astrophysics Data System (ADS)

Doak, William; de Bellis, Victor; Chiarot, Paul; Microfluidics; Multiphase Flow Laboratory Team

2017-11-01

Atomization of a dielectric micro-jet is achieved via an electrohydrodynamic charge injection process. The atomizer is comprised of a grounded nozzle housing (ground electrode) and an internal probe (high voltage electrode) that is concentric with the emitting orifice. The internal probe is held at electric potentials ranging from 1-10 kV. A pressurized reservoir drives a dielectric fluid at a desired flow rate through the 100-micrometer diameter orifice. The fluid fills the cavity between the electrodes as it passes through the atomizer, impeding the transport of electrons. This process injects charge into the flowing fluid. Upon exiting the orifice, the emitted jet is highly charged and it deforms via a bending instability that is qualitatively similar to the behavior observed in the electrospinning of fibers. We observed bulging regions, or nodes, of highly charged fluid forming along the bent, rotating jet. These nodes separate into highly charged droplets that emit satellite droplets. The remaining ligaments break up due to capillarity in a process that produces additional satellites. All of the droplets possess a normal (inertial) and radial (electrically-driven) momentum component. The radial component is responsible for the formation of a conical spray envelope. Our research focuses on the jet, its break up, and the droplet dynamics of this system. This research supported by the American Chemical Society.

Charge Transfer Reactions

NASA Astrophysics Data System (ADS)

Dennerl, Konrad

2010-12-01

Charge transfer, or charge exchange, describes a process in which an ion takes one or more electrons from another atom. Investigations of this fundamental process have accompanied atomic physics from its very beginning, and have been extended to astrophysical scenarios already many decades ago. Yet one important aspect of this process, i.e. its high efficiency in generating X-rays, was only revealed in 1996, when comets were discovered as a new class of X-ray sources. This finding has opened up an entirely new field of X-ray studies, with great impact due to the richness of the underlying atomic physics, as the X-rays are not generated by hot electrons, but by ions picking up electrons from cold gas. While comets still represent the best astrophysical laboratory for investigating the physics of charge transfer, various studies have already spotted a variety of other astrophysical locations, within and beyond our solar system, where X-rays may be generated by this process. They range from planetary atmospheres, the heliosphere, the interstellar medium and stars to galaxies and clusters of galaxies, where charge transfer may even be observationally linked to dark matter. This review attempts to put the various aspects of the study of charge transfer reactions into a broader historical context, with special emphasis on X-ray astrophysics, where the discovery of cometary X-ray emission may have stimulated a novel look at our universe.

A script to highlight hydrophobicity and charge on protein surfaces

PubMed Central

Hagemans, Dominique; van Belzen, Ianthe A. E. M.; Morán Luengo, Tania; Rüdiger, Stefan G. D.

2015-01-01

The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively visualizes segments on protein surfaces that contribute to specificity in protein-protein interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a transmembrane domain. We provide YRB highlighting in form of a script that runs using the software PyMOL. PMID:26528483

Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water.

PubMed

Taleb Bendiab, W; Benomrane, B; Bounaceur, B; Dauchez, M; Krallafa, A M

2018-02-14

Theoretical investigations of a solute in liquid water at normal temperature and pressure can be performed at different levels of theory. Static quantum calculations as well as classical and ab initio molecular dynamics are used to completely explore the conformational space for large solvated molecular systems. In the classical approach, it is essential to describe all of the interactions of the solute and the solvent in detail. Water molecules are very often described as rigid bodies when the most commonly used interaction potentials, such as the SPCE and the TIP4P models, are employed. Recently, a physical model based upon a cluster of rigid water molecules with a tetrahedral architecture (AB 4 ) was proposed that describes liquid water as a mixture of both TIP4P and SPCE molecular species that occur in the proportions implied by the tetrahedral architecture (one central molecule versus four outer molecules; i.e., 20% TIP4P versus 80% SPCE molecules). In this work, theoretical spectroscopic data for a peptide strand were correlated with the structural properties of the peptide strand solvated in water, based on data calculated using different theoretical approaches and physical models. We focused on a particular peptide strand, KRFK (lysine-arginine-phenylalanine-lysine), found in the thrombospondin TSP-1, due to its interesting properties. As the activity and electronic structure of this system is strongly linked to its structure, we correlated its structure with charge-density maps obtained using different semi-empirical charge Q eq equations. The structural and thermodynamic properties obtained from classical simulations were correlated with ab initio molecular dynamics (AIMD) data. Structural changes in the peptide strand were rationalized in terms of the motions of atoms and groups of atoms. To achieve this, conformational changes were investigated using calculated infrared spectra for the peptide in the gas phase and in water solvent. The calculated AIMD infrared spectrum for the peptide was correlated with static quantum calculations of the molecular system based on a harmonic approach as well as the VDOS (vibrational density of states) spectra obtained using various classical solvent models (SPCE, TIP4P, and AB 4 ) and charge maps.

Charge Inversion by Electrostatic Complexation: Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Faraudo, Jordi; Travesset, Alex

2007-03-01

Ions near interfaces play an important role in many biological and physico-chemical processes and exhibit a fascinating diverse range of phenomena. A relevant example is charge inversion, where interfacial charges attract counterions in excess of their own nominal charge, thus leading to an inversion of the sign of the interfacial charge. In this work, we argue that in the case of amphiphilic interfaces, charge inversion can be generated by complexation, that is, electrostatic complexes containing several counterions bound to amphiphilic molecules. The formation of these complexes require the presence at the interface of groups with conformational degrees of freedom with many electronegative atoms. We illustrate this mechanism by analyzing all atomic molecular dynamics simulations of a DMPA (Dimirystoil-Phosphatidic acid) phospholipid monolayer in contact with divalent counterions. The results are found to be in agreement with recent experimental results on Langmuir monolayers. We also discuss the implications for biological systems, as Phosphatidic acid is emerging as a key signaling phospholipid.

Strong higher-order resonant contributions to x-ray line polarization in hot plasmas

NASA Astrophysics Data System (ADS)

Shah, Chintan; Amaro, Pedro; Steinbrügge, Rene; Beilmann, Christian; Bernitt, Sven; Fritzsche, Stephan; Surzhykov, Andrey; Crespo López-Urrutia, José R.; Tashenov, Stanislav

2016-06-01

We studied angular distributions of x rays emitted in resonant recombination of highly charged iron and krypton ions, resolving dielectronic, trielectronic, and quadruelectronic channels. A tunable electron beam drove these processes, inducing x rays registered by two detectors mounted along and perpendicular to the beam axis. The measured emission asymmetries comprehensively benchmarked full-order atomic calculations. We conclude that accurate polarization diagnostics of hot plasmas can only be obtained under the premise of inclusion of higher-order processes that were neglected in earlier work.

A phenomenological π-p scattering length from pionic hydrogen

NASA Astrophysics Data System (ADS)

Ericson, T. E. O.; Loiseau, B.; Wycech, S.

2004-07-01

We derive a closed, model independent, expression for the electromagnetic correction factor to a phenomenological hadronic scattering length ah extracted from a hydrogenic atom. It is obtained in a non-relativistic approach and in the limit of a short ranged hadronic interaction to terms of order α2logα using an extended charge distribution. A hadronic πN scattering length ahπ-p=0.0870(5)mπ-1 is deduced leading to a πNN coupling constant from the GMO relation gc2/(4π)=14.04(17).

Final Technical Report of Project DE-FG02-96ER14647

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

Lundeen, Stephen R.

This is the final technical report of work completed under DOE support over the period Sept. 1, 1996 until May 31, 2015. The title of the project was "Ion/Excited Atom Collision Studies with a Rydberg Target and a CO2 Laser" from 9/1/96 to 10/31/06, and "Properties of Actinide Ions from Measurements of Rydberg Ion Fine Structure" from 11/1/06 until 5/31/15. The primary technical results were a detailed experimental study of resonant charge transfer between Rydberg atoms and highly-charged ions, and unique measurements of many properties of multiply-charged Thorium ions.

Signatures of the atomic nucleus in laser-assisted single ionization of one-electron atoms

NASA Astrophysics Data System (ADS)

Ajana, Imane; Khalil, Driss; Makhoute, Abdelkader

2018-03-01

The dynamics of the electron-impact single ionization of hydrogenic targets in the presence of a laser field (e, 2e) has been studied for different residual ion charges Z = 1, 2, 3 and 4. The state of fast electron in the laser field is described by the Volkov state, while the dressed state of the ejected slow electron and atomic target is treated perturbatively to the first-order perturbation theory. We calculate the triple differential cross section in the Ehrhardt asymmetric coplanar geometry. We have compared and analyzed the triple differential cross sections from one-electron atoms by varying the charge state of the residual ion, and evaluating the interplay between the laser influence and the role of scattering from the residual ion.

Critical screening in the one- and two-electron Yukawa atoms

NASA Astrophysics Data System (ADS)

Montgomery, H. E.; Sen, K. D.; Katriel, Jacob

2018-02-01

The one- and two-electron Yukawa atoms, also referred to as the Debye-Hückel or screened Coulomb atoms, have been topics of considerable interest both for intrinsic reasons and because of their relevance to terrestrial and astrophysical plasmas. At sufficiently high screening the one-electron Yukawa atom ceases to be bound. Some calculations appeared to suggest that as the screening increases in the ground state of the two-electron Yukawa atom (in which both the one-particle attraction and the interparticle repulsion are screened) the two electrons are detached simultaneously, at the same screening constant at which the one-electron atom becomes unbound. Our results rule this scenario out, offering an alternative that is not less interesting. In particular, it is found that for Z <1 a mild amount of screening actually increases the binding energy of the second electron. At the nuclear charge Zc≈0.911028 ... , at which the bare Coulomb two-electron atom becomes unbound, and even over a range of lower nuclear charges, an appropriate amount of screening gives rise to a bound two-electron system.

Charge transfer collisions of Si^3+ with H at low energies

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Gu, J. P.; Saha, B. C.

2009-11-01

Charge transfer of positively charged ions with atomic hydrogen is important not only in magnetically confined plasmas between impurity ions and H atoms from the chamber walls influences the overall ionization balance and effects the plasma cooling but also in astrophysics, where it plays a key role in determining the properties of the observed gas. It also provides a recombination mechanism for multiply charged ions in X-ray ionized astronomical environments. We report an investigation using the molecular-orbital close-coupling (MOCC) method, both quantum mechanically and semi-classically, in the adiabatic representation. Ab initio adiabatic potentials and coupling matrix elements--radial and angular--are calculated using the MRD-CI method. Comparison of our results with other theoretical as well as experimental findings will be discussed.

Numerical quasi-linear study of the critical ionization velocity phenomenon

NASA Technical Reports Server (NTRS)

Moghaddam-Taaheri, E.; Goertz, C. K.

1993-01-01

The critical ionization velocity (CIV) for a neutral barium (Ba) gas cloud moving across the static magnetic field is studied numerically using quasi-linear equations and a parameter range which is typical for the shaped-charge Ba gas release experiments in space. For consistency the charge exchange between the background oxygen ions and neutral atoms and its reverse process, as well as the excitation of the neutral Ba atoms, are included. The numerical results indicate that when the ionization rate due to CIV becomes comparable to the charge exchange rate the energy lost to the ionization and excitation collisions by the superthermal electrons exceeds the energy gain from the waves that are excited by the ion beam. This results in a CIV yield less than the yield by the charge exchange process.

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

PubMed

Yuan, Jianmin

2002-10-01

An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density minus the first constant distribution. The volume of each kind of atom is proportional to the sum of the charges of the second electron part and of the nucleus within each atomic sphere. By this way, one can make sure that electrical neutrality is satisfied within each atomic sphere. Because the integration of the electron charge within each atom needs the size of that atom in advance, the calculation is carried out in a usual self-consistent way. The occupation numbers of electron on the orbitals of each kind of atom are determined by the Fermi-Dirac distribution with the same chemical potential for all kinds of atoms. The wave functions and the orbital energies are calculated with the Dirac-Slater equations. As examples, the electronic structures of the mixture of Au and Cd, water (H2O), and CO2 at a few temperatures and densities are presented.

Characterization of Ar/N2/H2 middle-pressure RF discharge and application of the afterglow region for nitridation of GaAs

NASA Astrophysics Data System (ADS)

Raud, J.; Jõgi, I.; Matisen, L.; Navrátil, Z.; Talviste, R.; Trunec, D.; Aarik, J.

2017-12-01

This work characterizes the production and destruction of nitrogen and hydrogen atoms in RF capacitively coupled middle-pressure discharge in argon/nitrogen/hydrogen mixtures. Input power, electron concentration, electric field strength and mean electron energy were determined on the basis of electrical measurements. Gas temperature and concentration of Ar atoms in 1s states were determined from spectral measurements. On the basis of experimentally determined plasma characteristics, main production and loss mechanisms of H and N atoms were discussed. The plasma produced radicals were applied for the nitridation and oxide reduction of gallium arsenide in the afterglow region of discharge. After plasma treatment the GaAs samples were analyzed using x-ray photoelectron spectroscopy (XPS) technique. Successful nitridation of GaAs sample was obtained in the case of Ar/5% N2 discharge. In this gas mixture the N atoms were generated via dissociative recombination of N2+ created by charge transfer from Ar+. The treatment in Ar/5% N2/1% H2 mixture resulted in the reduction of oxide signals in the XPS spectra. Negligible formation of GaN in the latter mixture was connected with reduced concentration of N atoms, which was, in turn, due to less efficient mechanism of N atom production (electron impact dissociation of N2 molecules) and additional loss channel in reaction with H2.

Relative optically stimulated luminescence and thermoluminescence efficiencies of Al2O3:C dosimeters to heavy charged particles with energies relevant to space and radiotherapy dosimetry

NASA Astrophysics Data System (ADS)

Sawakuchi, G. O.; Yukihara, E. G.; McKeever, S. W. S.; Benton, E. R.; Gaza, R.; Uchihori, Y.; Yasuda, N.; Kitamura, H.

2008-12-01

This article presents a comprehensive characterization of the thermoluminescence (TL) and optically stimulated luminescence (OSL) relative luminescence efficiencies of carbon-doped aluminum (Al2O3:C) for heavy charged particles (HCPs) with atomic numbers ranging from 1 (proton) to 54 (xenon) and energies ranging from 7 to 1000 MeV/u, and investigates the dependence of the Al2O3:C response on experimental conditions. Relative luminescence efficiency values are presented for 19 primary charge/energy combinations, plus 31 additional charge/energy combinations obtained by introducing absorbers in the primary beam. Our results show that for energies of hundreds of MeV/u the data can be described by a single curve of relative luminescence efficiency versus linear energy transfer (LET). This information is needed to compensate for the reduced OSL efficiency to high-LET particles in such applications as space dosimetry. For lower energies, the relative luminescence efficiency as function of LET cannot be described by a single curve; instead, it separates into different components corresponding to different particles. We also present data on the low-LET dose response of Al2O3:C, measured under the same experimental conditions in which the relative luminescence efficiencies to HCPs were obtained, providing information relevant to future theoretical investigations of HCP energy deposition and luminescence production in Al2O3:C.

Effect of tip polarity on Kelvin probe force microscopy images of thin insulator CaF2 films on Si(111)

NASA Astrophysics Data System (ADS)

Yurtsever, Ayhan; Sugimoto, Yoshiaki; Fukumoto, Masaki; Abe, Masayuki; Morita, Seizo

2012-08-01

We investigate thin insulating CaF2 films on a Si (111) surface using a combination of noncontact atomic force microscopy (NC-AFM) and Kelvin probe force microscopy (KPFM). Atomic-scale NC-AFM and KPFM images are obtained in different imaging modes by employing two different tip polarities. The KPFM image contrast and the distance-dependent variation of the local contact potential difference (LCPD) give rise to a tip-polarity-dependent contrast inversion. Ca2+ cations had a higher LCPD contrast than F- anions for a positively terminated tip, while the LCPD provided by a negatively charged tip gave a higher contrast for F- anions. Thus, this result implies that it is essential to determine the tip apex polarity to correctly interpret LCPD signals acquired by KPFM.

Introduction to Atomic Structure: Demonstrations and Labs.

ERIC Educational Resources Information Center

Ciparick, Joseph D.

1988-01-01

Demonstrates a variety of electrical phenomena to help explain atomic structure. Topics include: establishing electrical properties, electrochemistry, and electrostatic charges. Recommends demonstration equipment needed and an explanation of each. (MVL)

Can Electron-Rich Oxygen (O2-) Withdraw Electrons from Metal Centers? A DFT Study on Oxoanion-Caged Polyoxometalates.

PubMed

Takazaki, Aki; Eda, Kazuo; Osakai, Toshiyuki; Nakajima, Takahito

2017-10-12

The answer to the question "Can electron-rich oxygen (O 2- ) withdraw electrons from metal centers?" is seemingly simple, but how the electron population on the M atom behaves when the O-M distance changes is a matter of controversy. A case study has been conducted for Keggin-type polyoxometalate (POM) complexes, and the first-principles electronic structure calculations were carried out not only for real POM species but also for "hypothetical" ones whose heteroatom was replaced with a point charge. From the results of natural population analysis, it was proven that even an electron-rich O 2- , owing to its larger electronegativity as a neutral atom, withdraws electrons when electron redistribution occurs by the change of the bond length. In the case where O 2- coexists with a cation having a large positive charge (e.g., P 5+ (O 2- ) 4 = [PO 4 ] 3- ), the gross electron population (GEP) on the M atom seemingly increases as the O atom comes closer, but this increment in GEP is not due to the role of the O atom but due to a Coulombic effect of the positive charge located on the cation. Furthermore, it was suggested that not GEP but net electron population (NEP) should be responsible for the redox properties.

Effect of atomic-scale defects and dopants on phosphorene electronic structure and quantum transport properties

DOE PAGES

Lopez-Bezanilla, Alejandro

2016-01-20

By means of a multi-scale first-principles approach, a description of the local electronic structure of 2D and narrow phosphorene sheets with various types of modifications is presented. Firtly, a rational argument based on the geometry of the pristine and modified P network, and supported by the Wannier functions formalism is introduced to describe a hybridization model of the P atomic orbitals. Ab initio calculations show that non-isoelectronic foreign atoms form quasi-bound states at varying energy levels and create different polarization states depending on the number of valence electrons between P and the doping atom. The quantum transport properties of modifiedmore » phosphorene ribbons are further described with great accuracy. The distortions on the electronic bands induced by the external species lead to strong backscattering effects on the propagating charge carriers. Depending on the energy of the charge carrier and the type of doping, the conduction may range from the diffusive to the localized regime. Interstitial defects at vacant sites lead to homogeneous transport fingerprints across different types of doping atoms. We suggest that the relatively low values of charge mobility reported in experimental measurements may have its origin in the presence of defects.« less

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

Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

NASA Astrophysics Data System (ADS)

Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Wang, Yangang; Hupalo, Myron; McDougall, Dan; Tringides, Michael; Ho, Kaiming

2013-12-01

The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H2 molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H2 molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

Charge versus orbital-occupancy ordering in manganites

NASA Astrophysics Data System (ADS)

Luo, Weidong; Varela, Maria; Tao, Jing; Pennycook, Stephen J.; Pantelides, Sokrates T.

2006-03-01

It is generally assumed that density-functional theory (DFT) in the local-spin-density approximation (LSDA) or the generalized- gradient approximation (GGA) is not adequate to describe mixed- valence manganites. Here we report benchmark DFT/GGA calculations for the ground-state structural, electronic and magnetic properties for both undoped and doped CaMnO3 and find the results to be in excellent agreement with available data, including new atomic-resolution Z-contrast imaging and electron-energy loss spectra. More specifically, we found that the DFT results predict two inequivalent Mn atoms in both 0.33 and 0.5 electron-doped CaMnO3, in agreement with experimental evidence of Mn^+3/Mn^+4 oxidation state ordering. The inequivalent Mn atoms are marked by their distinctive orbital occupancies, dissimilar local Jahn-Teller distortion and different magnetic moments from DFT calculations. We also show that the spherically integrated charges associated with the two inequivalent Mn atoms are the same, and they are actually the same as in the Mn metal. This charge neutrality with different orbital occupancies is the result of self-consistency and atomic relaxations in the crystal. We conclude that DFT without additional correlations can account for the observed properties of oxidation-state ordering in this system. The impact of the results on other mixed-valence systems will be discussed.

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

PubMed

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

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.

Tuning Electrostatic Potentials for Imaging the Quantum Properties of Massless Dirac Fermions in Graphene

NASA Astrophysics Data System (ADS)

Wong, Dillon

Graphene, a two-dimensional (2D) honeycomb lattice of sp 2-bonded carbon atoms, is renowned for its many extraordinary properties. Not only does it have an extremely high carrier mobility, exceptional mechanical strength, and fascinating optical behavior, graphene additionally has an interesting energy-momentum relationship that is emergent from its space group symmetry. Graphene's low-energy electronic excitations consist of quasiparticles whose energies disperse linearly with wavevector and obey a 2D massless Dirac equation with a modified speed of light. This fortuitous circumstance allows for the exploration of ultra-relativistic phenomena using conventional tabletop techniques common to solid state physics and material science. Here I discuss experiments that probe these ultra-relativistic effects via application of scanning tunneling microscopy (STM) and spectroscopy (STS) to graphene field-effect transistors (FETs) in proximity with charged impurities. The first part of this dissertation focuses on the ultra-relativistic Coulomb problem. Depending on the strength of the potential, the Coulomb problem for massless Dirac particles is divided into two regimes: the subcritical and the supercritical. The subcritical regime is characterized by an electron-hole asymmetry in the local density of states (LDOS) and, unlike in nonrelativistic quantum mechanics, does not support bound states. In contrast, the supercritical regime hosts quasi-bound states that are analogous to "atomic collapse" orbits predicted to occur in atoms with nuclear charge Z > 170. By using an STM tip to directly position calcium (Ca) impurities on a graphene surface, we assembled "artificial nuclei" and observed a transition between the subcritical and supercritical regimes with increasing nuclear charge. We also investigated the screening of these charged impurities by massless Dirac fermions while varying the graphene carrier concentration with an electrostatic gate. The second part of this dissertation focuses on the ultra-relativistic harmonic oscillator. We developed a method for manipulating charged defects inside the boron nitride (BN) substrate underneath graphene to construct circular graphene p-n junctions. These p-n junctions were effectively quantum dots that electrostatically trapped graphene's relativistic charge carriers, and we imaged the interference patterns corresponding to this quantum confinement. The observed energy-level spectra in our p-n junctions closely matched a theoretical spectrum obtained by solving the 2D massless Dirac equation with a quadratic potential, allowing us to identify each observed state with principal and angular momentum quantum numbers. The results discussed here provide insight into fundamental aspects of relativistic quantum mechanics and into graphene properties pertinent to technological applications. In particular, graphene's response to electrostatic potentials determines the scope in which its charge carriers can be directed and harnessed for useful purposes. Furthermore, many of the results contained in this dissertation are expected to generalize to other Dirac materials.

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.

POx/Al2O3 stacks: Highly effective surface passivation of crystalline silicon with a large positive fixed charge

NASA Astrophysics Data System (ADS)

Black, Lachlan E.; Kessels, W. M. M. Erwin

2018-05-01

Thin-film stacks of phosphorus oxide (POx) and aluminium oxide (Al2O3) are shown to provide highly effective passivation of crystalline silicon (c-Si) surfaces. Surface recombination velocities as low as 1.7 cm s-1 and saturation current densities J0s as low as 3.3 fA cm-2 are obtained on n-type (100) c-Si surfaces passivated by 6 nm/14 nm thick POx/Al2O3 stacks deposited in an atomic layer deposition system and annealed at 450 °C. This excellent passivation can be attributed in part to an unusually large positive fixed charge density of up to 4.7 × 1012 cm-2, which makes such stacks especially suitable for passivation of n-type Si surfaces.

Multichordal charge exchange recombination spectroscopy on Doublet III (abstract)

NASA Astrophysics Data System (ADS)

Seraydarian, R. P.; Burrell, K. H.; Kahn, C.

1985-05-01

Single shot, multipoint ion temperature and plasma rotation profiles have been routinely obtained on the Doublet III tokamak for 32 consecutive time slices with 20-ms resolution. A six-chord tangentially viewing spectroscopic diagnostic has been built to look at radiation emitted by fully stripped low-Z impurity ions (He, C, O) that have undergone charge exchange recombination with hydrogen atoms from a 3-MW heating beam. The main components of the instrument are a single monochromator for wavelength dispersion, a single image intensifier tube for photon gain, and a pair of 1024-element linear photodiode arrays for detection. A special arrangement of fiber optics allows simultaneous data acquisition from all chords without the use of scanning mirrors or other moving parts. Ion temperature profiles taken under a variety of plasma conditions will be presented.

Characterization of X-ray emission from laser generated plasma

NASA Astrophysics Data System (ADS)

Cannavò, Antonino; Torrisi, Lorenzo; Ceccio, Giovanni; Cutroneo, Mariapompea; Calcagno, Lucia; Sciuto, Antonella; Mazzillo, Massimo

2018-01-01

X-ray emission from laser generated plasma was studied at low (1010 W/cm2) and high (1018 W/cm2) intensity using ns and fs laser, respectively. Plasma characteristics were controlled trough the laser parameters, the irradiation conditions and the target properties. The X-ray spectra were acquired using fast detection technique based on SiC diodes with different active regions. The X-ray yield increases with the atomic number of the target, both at low and high intensity, and a similar empirical law has been obtained. The X-ray emission mechanisms from plasma are correlated to the plasma temperature and density and to the Coulomb charge particle acceleration, due to the charge separation effects produced in the non-equilibrium plasma. Functional dependences, theoretical approaches and interpretation of possible mechanism will be presented and discussed.

Changes in the mean square charge radii and electromagnetic moments of neutron-deficient Bi isotopes

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

Barzakh, A. E., E-mail: barzakh@mail.ru; Batist, L. Kh.; Fedorov, D. V.

In-source laser spectroscopy experiments for neutron deficient bismuth isotopes at the 306.77 nm atomic transition were carried out at the IRIS (Investigation of Radioactive Isotopes on Synchrocyclotron) facility of Petersburg Nuclear Physics Institute (PNPI). New data on isotope shifts and hyperfine structure for {sup 189–198,} {sup 211}Bi isotopes and isomers were obtained. The changes in the mean-square charge radii and the magnetic moment values were deduced. Marked deviation from the nearly spherical behavior for ground states of bismuth isotopes at N < 109 is demonstrated, in contrast to the lead and thallium isotopic chains. The big isomer shift between Imore » = 1/2 (intruder) and I = 9/2 (normal) states for odd Bi isotopes (A = 193, 195, 197) was found.« less

Nanosecond pulsed electric field induced changes in cell surface charge density.

PubMed

Dutta, Diganta; Palmer, Xavier-Lewis; Asmar, Anthony; Stacey, Michael; Qian, Shizhi

2017-09-01

This study reports that the surface charge density changes in Jurkat cells with the application of single 60 nanosecond pulse electric fields, using atomic force microscopy. Using an atomic force microscope tip and Jurkat cells on silica in a 0.01M KCl ionic concentration, we were able to measure the interfacial forces, while also predicting surface charge densities of both Jurkat cell and silica surfaces. The most important finding is that the pulsing conditions varyingly reduced the cells' surface charge density. This offers a novel way in which to examine cellular effects of pulsed electric fields that may lead to the identification of unique mechanical responses. Compared to a single low field strength NsPEF (15kV/cm) application, exposure of Jurkat cells to a single high field strength NsPEF (60kV/cm) resulted in a further reduction in charge density and major morphological changes. The structural, physical, and chemical properties of biological cells immensely influence their electrostatic force; we were able to investigate this through the use of atomic force microscopy by measuring the surface forces between the AFM's tip and the Jurkat cells under different pulsing conditions as well as the interfacial forces in ionic concentrations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of krypton diffusion coefficients in uranium dioxide using atomic scale calculations

DOE PAGES

Vathonne, Emerson; Andersson, David Ragnar Anders; Freyss, Michel; ...

2016-12-16

We present a study of the diffusion of krypton in UO 2 using atomic scale calculations combined with diffusion models adapted to the system studied. The migration barriers of the elementary mechanisms for interstitial or vacancy assisted migration are calculated in the DFT + U framework using the nudged elastic band method. The attempt frequencies are obtained from the phonon modes of the defect at the initial and saddle points using empirical potential methods. The diffusion coefficients of Kr in UO 2 are then calculated by combining this data with diffusion models accounting for the concentration of vacancies and themore » interaction of vacancies with Kr atoms. We determined the preferred mechanism for Kr migration and the corresponding diffusion coefficient as a function of the oxygen chemical potential μ O or nonstoichiometry. For very hypostoichiometric (or U-rich) conditions, the most favorable mechanism is interstitial migration. For hypostoichiometric UO 2, migration is assisted by the bound Schottky defect and the charged uranium vacancy, V U 4–. Around stoichiometry, migration assisted by the charged uranium–oxygen divacancy (V UO 2–) and V U 4– is the favored mechanism. Finally, for hyperstoichiometric or O-rich conditions, the migration assisted by two V U 4– dominates. Kr migration is enhanced at higher μ O, and in this regime, the activation energy will be between 4.09 and 0.73 eV depending on nonstoichiometry. The experimental values available are in the latter interval. Since it is very probable that these values were obtained for at least slightly hyperstoichiometric samples, our activation energies are consistent with the experimental data, even if further experiments with precisely controlled stoichiometry are needed to confirm these results. Finally, the mechanisms and trends with nonstoichiometry established for Kr are similar to those found in previous studies of Xe.« less

Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy

NASA Astrophysics Data System (ADS)

Fatayer, Shadi; Schuler, Bruno; Steurer, Wolfram; Scivetti, Ivan; Repp, Jascha; Gross, Leo; Persson, Mats; Meyer, Gerhard

2018-05-01

Intermolecular single-electron transfer on electrically insulating films is a key process in molecular electronics1-4 and an important example of a redox reaction5,6. Electron-transfer rates in molecular systems depend on a few fundamental parameters, such as interadsorbate distance, temperature and, in particular, the Marcus reorganization energy7. This crucial parameter is the energy gain that results from the distortion of the equilibrium nuclear geometry in the molecule and its environment on charging8,9. The substrate, especially ionic films10, can have an important influence on the reorganization energy11,12. Reorganization energies are measured in electrochemistry13 as well as with optical14,15 and photoemission spectroscopies16,17, but not at the single-molecule limit and nor on insulating surfaces. Atomic force microscopy (AFM), with single-charge sensitivity18-22, atomic-scale spatial resolution20 and operable on insulating films, overcomes these challenges. Here, we investigate redox reactions of single naphthalocyanine (NPc) molecules on multilayered NaCl films. Employing the atomic force microscope as an ultralow current meter allows us to measure the differential conductance related to transitions between two charge states in both directions. Thereby, the reorganization energy of NPc on NaCl is determined as (0.8 ± 0.2) eV, and density functional theory (DFT) calculations provide the atomistic picture of the nuclear relaxations on charging. Our approach presents a route to perform tunnelling spectroscopy of single adsorbates on insulating substrates and provides insight into single-electron intermolecular transport.

Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling.

PubMed

Casati, Nicola; Genoni, Alessandro; Meyer, Benjamin; Krawczuk, Anna; Macchi, Piero

2017-08-01

The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casati et al. (2016). Nat. Commun. 7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the species syn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Magnetizabilities of relativistic hydrogenlike atoms in some arbitrary discrete energy eigenstates

NASA Astrophysics Data System (ADS)

Stefańska, Patrycja

2016-03-01

We present the results of numerical calculations of magnetizability (χ) of the relativistic one-electron atoms with a pointlike, spinless and motionless nuclei of charge Ze. Exploiting the analytical formula for χ recently derived by us Stefańska (2015), valid for an arbitrary discrete energy eigenstate, we have found the values of the magnetizability for the ground state and for the first and the second set of excited states (i.e.: 2s1/2, 2p1/2, 2p3/2, 3s1/2, 3p1/2, 3p3/2, 3d3/2, and 3d5/2) of the Dirac one-electron atom. The results for ions with the atomic number 1 ⩽ Z ⩽ 137 are given in 14 tables. The comparison of the numerical values of magnetizabilities for the ground state and for each state belonging to the first set of excited states of selected hydrogenlike ions, obtained with the use of two different values of the fine-structure constant, i.e.: α-1 = 137.035 999 139 (CODATA 2014) and α-1 = 137.035 999 074 (CODATA 2010), is also presented.

Dynamics of a single-atom electron pump.

PubMed

van der Heijden, J; Tettamanzi, G C; Rogge, S

2017-03-15

Single-electron pumps based on isolated impurity atoms have recently been experimentally demonstrated. In these devices the Coulomb potential of an atom creates a localised electron state with a large charging energy and considerable orbital level spacings, enabling robust charge capturing processes. In contrast to the frequently used gate-defined quantum dot pumps, which experience a strongly time-dependent potential, the confinement potential in these single-atom pumps is hardly affected by the periodic driving of the system. Here we describe the behaviour and performance of an atomic, single parameter, electron pump. This is done by considering the loading, isolating and unloading of one electron at the time, on a phosphorous atom embedded in a silicon double gate transistor. The most important feature of the atom pump is its very isolated ground state, which is populated through the fast loading of much higher lying excited states and a subsequent fast relaxation process. This leads to a substantial increase in pumping accuracy, and is opposed to the adverse role of excited states observed for quantum dot pumps due to non-adiabatic excitations. The pumping performance is investigated as a function of dopant position, revealing a pumping behaviour robust against the expected variability in atomic position.

Dynamics of a single-atom electron pump

PubMed Central

van der Heijden, J.; Tettamanzi, G. C.; Rogge, S.

2017-01-01

Single-electron pumps based on isolated impurity atoms have recently been experimentally demonstrated. In these devices the Coulomb potential of an atom creates a localised electron state with a large charging energy and considerable orbital level spacings, enabling robust charge capturing processes. In contrast to the frequently used gate-defined quantum dot pumps, which experience a strongly time-dependent potential, the confinement potential in these single-atom pumps is hardly affected by the periodic driving of the system. Here we describe the behaviour and performance of an atomic, single parameter, electron pump. This is done by considering the loading, isolating and unloading of one electron at the time, on a phosphorous atom embedded in a silicon double gate transistor. The most important feature of the atom pump is its very isolated ground state, which is populated through the fast loading of much higher lying excited states and a subsequent fast relaxation process. This leads to a substantial increase in pumping accuracy, and is opposed to the adverse role of excited states observed for quantum dot pumps due to non-adiabatic excitations. The pumping performance is investigated as a function of dopant position, revealing a pumping behaviour robust against the expected variability in atomic position. PMID:28295055

Colloquium: Laser probing of neutron-rich nuclei in light atoms

NASA Astrophysics Data System (ADS)

Lu, Z.-T.; Mueller, P.; Drake, G. W. F.; Nörtershäuser, W.; Pieper, Steven C.; Yan, Z.-C.

2013-10-01

The neutron-rich He6 and He8 isotopes exhibit an exotic nuclear structure that consists of a tightly bound He4-like core with additional neutrons orbiting at a relatively large distance, forming a halo. Recent experimental efforts have succeeded in laser trapping and cooling these short-lived, rare helium atoms and have measured the atomic isotope shifts along the He4-He6-He8 chain by performing laser spectroscopy on individual trapped atoms. Meanwhile, the few-electron atomic structure theory, including relativistic and QED corrections, has reached a comparable degree of accuracy in the calculation of the isotope shifts. In parallel efforts, also by measuring atomic isotope shifts, the nuclear charge radii of lithium and beryllium isotopes have been studied. The techniques employed were resonance ionization spectroscopy on neutral, thermal lithium atoms and collinear laser spectroscopy on beryllium ions. Combining advances in both atomic theory and laser spectroscopy, the charge radii of these light halo nuclei have now been determined for the first time independent of nuclear structure models. The results are compared with the values predicted by a number of nuclear structure calculations and are used to guide our understanding of the nuclear forces in the extremely neutron-rich environment.

A combined rocket-borne and ground-based study of the sodium layer and charged dust in the upper mesosphere

NASA Astrophysics Data System (ADS)

Plane, John M. C.; Saunders, Russell W.; Hedin, Jonas; Stegman, Jacek; Khaplanov, Misha; Gumbel, Jörg; Lynch, Kristina A.; Bracikowski, Phillip J.; Gelinas, Lynette J.; Friedrich, Martin; Blindheim, Sandra; Gausa, Michael; Williams, Bifford P.

2014-10-01

The Hotel Payload 2 rocket was launched on January 31st 2008 at 20.14 LT from the Andøya Rocket Range in northern Norway (69.31° N, 16.01° E). Measurements in the 75-105 km region of atomic O, negatively-charged dust, positive ions and electrons with a suite of instruments on the payload were complemented by lidar measurements of atomic Na and temperature from the nearby ALOMAR observatory. The payload passed within 2.58 km of the lidar at an altitude of 90 km. A series of coupled models is used to explore the observations, leading to two significant conclusions. First, the atomic Na layer and the vertical profiles of negatively-charged dust (assumed to be meteoric smoke particles), electrons and positive ions, can be modelled using a self-consistent meteoric input flux. Second, electronic structure calculations and Rice-Ramsperger-Kassel-Markus theory are used to show that even small Fe-Mg-silicates are able to attach electrons rapidly and form stable negatively-charged particles, compared with electron attachment to O2 and O3. This explains the substantial electron depletion between 80 and 90 km, where the presence of atomic O at concentrations in excess of 1010 cm-3 prevents the formation of stable negative ions.