Neutron total cross-section of hydrogenous and deuterated 1- and 2-propanol and n-butanol measured using the VESUVIO spectrometer

NASA Astrophysics Data System (ADS)

Rodríguez Palomino, L. A.; Dawidowski, J.; Márquez Damián, J. I.; Cuello, G. J.; Romanelli, G.; Krzystyniak, M.

2017-10-01

This work presents the total cross sections of a set of normal and deuterated alcohols (hydrogenous 1- and 2-propanol and n-butanol, 1-propanol(OD) and fully deuterated 2-propanol and n-butanol), measured at spectrometer VESUVIO (ISIS spallation neutron source, United Kingdom). Granada's Synthetic Model was applied to describe those systems and a satisfactory agreement with the measured total cross section was achieved in the range of energies from 10-3 to 100 eV. The input parameters of the model were determined from the essential features of the vibrational spectra of the atoms that compose the systems, which were studied using Molecular Dynamics.

A laser application to nuclear astrophysics

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

Barbui, M.; Hagel, K.; Schmidt, K.

2014-05-09

In the last decade, the availability in high-intensity laser beams capable of producing plasmas with ion energies large enough to induce nuclear reactions has opened new research paths in nuclear physics. We studied the reactions {sup 3}He(d,p){sup 4}He and d(d,n){sup 3}He at temperatures of few keV in a plasma, generated by the interaction of intense ultrafast laser pulses with molecular deuterium or deuterated-methane clusters mixed with {sup 3}He atoms. The yield of 14.7 MeV protons from the {sup 3}He(d,p){sup 4}He reaction was used to extract the astrophysical S factor. Results of the experiment performed at the Center for High Energymore » Density Science at The University of Texas at Austin will be presented.« less

Deuteration Effect on the Nh/nd Stretch Band of the Jet-Cooled 7-AZAINDOLE and its Tautomeric Dimers: Relation to the Ground-State Double Proton-Transfer Reaction

NASA Astrophysics Data System (ADS)

Ishikawa, Haruki; Nakano, Takumi; Takashima, Tsukiko; Yabuguchi, Hiroki; Fuke, Kiyokazu

2013-06-01

In order to investigate the deuteration effect on the vibrational dynamics of the NH and/or ND stretch excited levels of the 7-azaindole (7-AI) normal dimer and its tautomeric dimer, we have carried out infrared spectroscopy of three isotopic species for each dimers; undeuterated one (NH-NH) and one or two hydrogen atom(s) of the NH groups is deuterated ones (NH-ND and ND-ND, respectively). It is found that the ND stretch band profiles of the NH-ND and ND-ND tautomeric dimers are very similar with each other. This result is very distinct from the result of the comparison of the NH stretch band profiles of the NH-NH and NH-ND dimers in our previous study. For a further discussion, we have examined the deuteration effect in the case of the 7-AI normal dimer. It is found that the NH stretch band profiles of the NH-NH and the NH-ND dimers and also the ND stretch band profiles of the NH-ND and the ND-ND dimers exhibit similar patterns, respectively. These facts indicates that the vibrational relaxation from the NH/ND stretch level of the normal dimer basically proceed within a monomer unit. The large deuteration effect of the NH stretch band profile observed previously is found to be characteristic of the tautomeric dimer. This behavior is related to a large anharmonicity of the potential energy surface originating from an existence of the double-proton transfer reaction barrier. H. Ishikawa, H. Yabuguchi, Y. Yamada, A. Fujihara, K. Fuke, J. Phys. Chem. A 114, 3199 (2010).

Refined energetic ordering for sulphate-water (n = 3-6) clusters using high-level electronic structure calculations

NASA Astrophysics Data System (ADS)

Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Epifanovsky, Evgeny; Head-Gordon, Martin

2012-10-01

This work reports refinements of the energetic ordering of the known low-energy structures of sulphate-water clusters ? (n = 3-6) using high-level electronic structure methods. Coupled cluster singles and doubles with perturbative triples (CCSD(T)) is used in combination with an estimate of basis set effects up to the complete basis set limit using second-order Møller-Plesset theory. Harmonic zero-point energy (ZPE), included at the B3LYP/6-311 + + G(3df,3pd) level, was found to have a significant effect on the energetic ordering. In fact, we show that the energetic ordering is a result of a delicate balance between the electronic and vibrational energies. Limitations of the ZPE calculations, both due to electronic structure errors, and use of the harmonic approximation, probably constitute the largest remaining errors. Due to the often small energy differences between cluster isomers, and the significant role of ZPE, deuteration can alter the relative energies of low-lying structures, and, when it is applied in conjunction with calculated harmonic ZPEs, even alters the global minimum for n = 5. Experiments on deuterated clusters, as well as more sophisticated vibrational calculations, may therefore be quite interesting.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

High-level expression and deuteration of sperm whale myoglobin: A study of its solvent structure by X-ray and neutron diffraction methods

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

Shu, F.; Ramakrishnan, V.; Schoenborn, B.P.

1994-12-31

Neutron diffraction has become one of the best ways to study light atoms, such as hydrogens. Hydrogen however has a negative coherent scattering factor, and a large incoherent scattering factor, while deuterium has virtually no incoherent scattering, but a large positive coherent scattering factor. Beside causing high background due to its incoherent scattering, the negative coherent scattering of hydrogen tends to cancel out the positive contribution from other atoms in a neutron density map. Therefore a fully deuterated sample will yield better diffraction data with stronger density in the hydrogen position. On this basis, a sperm whale myoglobin gene modifiedmore » to include part of the A cII protein gene has been cloned into the T7 expression system. Milligram amounts of fully deuterated holo-myoglobin have been obtained and used for crystallization. The synthetic sperm whale myoglobin crystallized in P2{sub 1} space group isomorphous with the native protein crystal. A complete X-ray diffraction dataset at 1.5{Angstrom} has been collected. This X-ray dataset, and a neutron data set collected previously on a protonated carbon-monoxymyoglobin crystal have been used for solvent structure studies. Both X-ray and neutron data have shown that there are ordered hydration layers around the protein surface. Solvent shell analysis on the neutron data further has shown that the first hydration layer behaves differently around polar and apolar regions of the protein surface. Finally, the structure of per-deuterated myoglobin has been refined using all reflections to a R factor of 17%.« less

Infrared absorption spectra of partially deuterated methoxy radicals CH2DO and CHD2O isolated in solid para-hydrogen.

PubMed

Haupa, Karolina A; Johnson, Britta A; Sibert, Edwin L; Lee, Yuan-Pern

2017-10-21

The investigation of partially deuterated methoxy radicals is important because the symmetry lowering from C 3v to C s provides new insights into the couplings between rovibronic states via Jahn-Teller and spin-orbit interactions. The vibrational spectrum of the partially deuterated methoxy radical CH 2 DO in a matrix of p-H 2 has been recorded. This species was prepared by irradiating a p-H 2 matrix containing deuterated d 1 -nitritomethane (CH 2 DONO) at 3.3 K with laser light at 355 nm. The identification of the radical is based on the photochemical behavior of the precursor and comparison of observed vibrational wavenumbers and infrared (IR) intensities with those predicted from a refined quartic, curvilinear, internal coordinate force field calculated with the coupled-cluster singles and doubles with perturbative triples/cc-pVTZ method. CH 2 DO reacts with H 2 with a rate coefficient (3.5 ± 1.0) × 10 -3 s -1 . Predominantly c-CHDOH and a negligibly small amount of t-CHDOH were produced. This stereoselectivity results from the reaction H + C s -CH 2 DOH, which was demonstrated by an additional experiment on irradiation of a CH 2 DOH/Cl 2 /p-H 2 matrix with ultraviolet and IR light to induce the H + CH 2 DOH reaction; only c-CHDOH was observed from this experiment. Even though the energies of transition states and products for the formation of c-CHDOH and t-CHDOH differ by only ∼10 cm -1 , the selective formation of c-CHDOH can be explained by tunneling of the hydrogen atom via an optimal tunneling path. Similarly, the vibronic spectrum for the partially deuterated specie d 2 -methoxy radical (CHD 2 O) was obtained upon irradiation of d 2 -nitritomethane (CHD 2 ONO) at 355 nm. Lines associated with the fundamental vibrational modes were observed and assigned; line positions agree with theoretically predicted vibrational wavenumbers. CHD 2 O reacts with H 2 with a rate coefficient (6.0 ± 1.4) × 10 -3 s -1 ; CD 2 OH was produced as a major product because the barrier for the formation of CHDOH from H + CHD 2 OH is greater by ∼400 cm -1 . Rate coefficients of the decays of CH 3 O, CH 2 DO, CHD 2 O, and CD 3 O and their corresponding potential energy surfaces are compared.

Infrared absorption spectra of partially deuterated methoxy radicals CH2DO and CHD2O isolated in solid para-hydrogen

NASA Astrophysics Data System (ADS)

Haupa, Karolina A.; Johnson, Britta A.; Sibert, Edwin L.; Lee, Yuan-Pern

2017-10-01

The investigation of partially deuterated methoxy radicals is important because the symmetry lowering from C3v to Cs provides new insights into the couplings between rovibronic states via Jahn-Teller and spin-orbit interactions. The vibrational spectrum of the partially deuterated methoxy radical CH2DO in a matrix of p-H2 has been recorded. This species was prepared by irradiating a p-H2 matrix containing deuterated d1-nitritomethane (CH2DONO) at 3.3 K with laser light at 355 nm. The identification of the radical is based on the photochemical behavior of the precursor and comparison of observed vibrational wavenumbers and infrared (IR) intensities with those predicted from a refined quartic, curvilinear, internal coordinate force field calculated with the coupled-cluster singles and doubles with perturbative triples/cc-pVTZ method. CH2DO reacts with H2 with a rate coefficient (3.5 ± 1.0) × 10-3 s-1. Predominantly c-CHDOH and a negligibly small amount of t-CHDOH were produced. This stereoselectivity results from the reaction H + Cs-CH2DOH, which was demonstrated by an additional experiment on irradiation of a CH2DOH/Cl2/p-H2 matrix with ultraviolet and IR light to induce the H + CH2DOH reaction; only c-CHDOH was observed from this experiment. Even though the energies of transition states and products for the formation of c-CHDOH and t-CHDOH differ by only ˜10 cm-1, the selective formation of c-CHDOH can be explained by tunneling of the hydrogen atom via an optimal tunneling path. Similarly, the vibronic spectrum for the partially deuterated specie d2-methoxy radical (CHD2O) was obtained upon irradiation of d2-nitritomethane (CHD2ONO) at 355 nm. Lines associated with the fundamental vibrational modes were observed and assigned; line positions agree with theoretically predicted vibrational wavenumbers. CHD2O reacts with H2 with a rate coefficient (6.0 ± 1.4) × 10-3 s-1; CD2OH was produced as a major product because the barrier for the formation of CHDOH from H + CHD2OH is greater by ˜400 cm-1. Rate coefficients of the decays of CH3O, CH2DO, CHD2O, and CD3O and their corresponding potential energy surfaces are compared.

Spectroscopic study on deuterated benzenes. II. High-resolution laser spectroscopy and rotational structure in the S{sub 1} state

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

Kunishige, Sachi; Katori, Toshiharu; Baba, Masaaki, E-mail: baba@kuchem.kyoto-u.ac.jp

High-resolution spectra of the S{sub 1}←S{sub 0} transition in jet-cooled deuterated benzenes were observed using pulse dye amplification of single-mode laser light and mass-selective resonance enhanced multiphoton ionization (REMPI) detection. The vibrational and rotational structures were accurately analyzed for the vibronic levels in the S{sub 1} state. The degenerate 6{sup 1} levels of C{sub 6}H{sub 6} or C{sub 6}D{sub 6} are split into 6a{sup 1} and 6b{sup 1} in many of deuterated benzenes. The rigid-rotor rotational constants were assessed and found to be slightly different between 6a and 6b because of different mean molecular structures. Their rotational levels are significantlymore » shifted by Coriolis interactions. It was found that the Coriolis parameter proportionally changed with the number of substituted D atoms.« less

A diffuse reflectance infrared Fourier transform spectroscopic study of adsorbed hydrazines

NASA Technical Reports Server (NTRS)

Davis, Dennis D.; Kilduff, Jan E.; Koontz, Steven L.

1988-01-01

Diffuse reflectance spectroscopy of fuel hydrazines adsorbed on silica, silica-alumina and alimina surfaces indicates that the primary surface-hydrazine interaction is hydrogen bonding. Hydrazine, on adsorption to a deuterated silica surface, undergoes a rapid H/D exchange with deuterated surface silanol (Si-OD) groups. Adsorption equilibria are rapidly established at room temperature. Monomethylhydrazine and unsymmetrical dimethylhydrazine are similarly adsorbed. On adsorption, the C-H stretching and methyl deformation modes of the methylhydrazines are shifted to higher frequencies by 10 to 20 cm(-1). These shifts are postulated to be due to changes in the lone-pair electro-density on the adjacent nitrogen atom and an electronegativity effect.

Synthetic use of the primary kinetic isotope effect in hydrogen atom transfer 2: generation of captodatively stabilised radicals.

PubMed

Wood, Mark E; Bissiriou, Sabine; Lowe, Christopher; Windeatt, Kim M

2013-04-28

Using C-3 di-deuterated morpholin-2-ones bearing N-2-iodobenzyl and N-3-bromobut-3-enyl radical generating groups, only products derived from the more stabilised C-3, rather than the less stabilised C-5 translocated radicals, were formed after intramolecular 1,5-hydrogen atom transfer, suggesting that any kinetic isotope effect present was not sufficient to offset captodative stabilisation.

Part 2. Mechanistic aspects of the reduction of S-alkyl-thionocarbonates in the presence of triethylborane and air

PubMed Central

Allais, Florent; Boivin, Jean; Nguyen, Van Tai

2007-01-01

Experiments conducted with deuterated compounds demonstrated that during the reduction of S-alkylxanthates with triethylborane, the hydrogen atom transferred has several competing origins. Hydrogen abstraction from water (or an alcohol) is the most favourable route. PMID:18076755

Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR.

PubMed

Vasa, Suresh Kumar; Rovó, Petra; Giller, Karin; Becker, Stefan; Linser, Rasmus

2016-03-28

Interactions within proteins, with their surrounding, and with other molecules are mediated mostly by hydrogen atoms. In fully protonated, inhomogeneous, or larger proteins, however, aliphatic proton shifts tend to show little dispersion despite fast Magic-Angle Spinning. 3D correlations dispersing aliphatic proton shifts by their better resolved amide N/H shifts can alleviate this problem. Using inverse second-order cross-polarization (iSOCP), we here introduce dedicated and improved means to sensitively link site-specific chemical shift information from aliphatic protons with a backbone amide resolution. Thus, even in cases where protein deuteration is impossible, this approach may enable access to various aspects of protein functions that are reported on by protons.

Reactions of solvated electrons initiated by sodium atom ionization at the vacuum-liquid interface.

PubMed

Alexander, William A; Wiens, Justin P; Minton, Timothy K; Nathanson, Gilbert M

2012-03-02

Solvated electrons are powerful reagents in the liquid phase that break chemical bonds and thereby create additional reactive species, including hydrogen atoms. We explored the distinct chemistry that ensues when electrons are liberated near the liquid surface rather than within the bulk. Specifically, we detected the products resulting from exposure of liquid glycerol to a beam of sodium atoms. The Na atoms ionized in the surface region, generating electrons that reacted with deuterated glycerol, C(3)D(5)(OD)(3), to produce D atoms, D(2), D(2)O, and glycerol fragments. Surprisingly, 43 ± 4% of the D atoms traversed the interfacial region and desorbed into vacuum before attacking C-D bonds to produce D(2).

RATE CONSTANTS FOR THE REACTIONS OF OH RADICALS AND CL ATOMS WITH DI-N-PROPYL ETHER AND DI-N-BUTYL ETHER AND THEIR DEUTERATED ANALOGS. (R825252)

EPA Science Inventory

Using relative rate methods, rate constants for the gas-phase reactions of OH radicals and Cl atoms with di-n-propyl ether, di-n-propyl ether-d₁₄, di-n-butyl ether and di-n-butyl ether-d₁₈ have been measured at 296 ? 2 K and atmos...

Tracing the atomic nitrogen abundance in star-forming regions with ammonia deuteration

NASA Astrophysics Data System (ADS)

Furuya, Kenji; Persson, Magnus V.

2018-06-01

Partitioning of elemental nitrogen in star-forming regions is not well constrained. Most nitrogen is expected to be partitioned among atomic nitrogen (N I), molecular nitrogen (N_2), and icy N-bearing molecules, such as NH_3 and N_2. N I is not directly observable in the cold gas. In this paper, we propose an indirect way to constrain the amount of N I in the cold gas of star-forming clouds, via deuteration in ammonia ice, the [ND2H/NH2D]/[NH2D/NH3] ratio. Using gas-ice astrochemical simulations, we show that if atomic nitrogen remains as the primary reservoir of nitrogen during cold ice formation stages, the [ND2H/NH2D]/[NH2D/NH3] ratio is close to the statistical value of 1/3 and lower than unity, whereas if atomic nitrogen is largely converted into N-bearing molecules, the ratio should be larger than unity. Observability of ammonia isotopologues in the inner hot regions around low-mass protostars, where ammonia ice has sublimated, is also discussed. We conclude that the [ND2H/NH2D]/[NH2D/NH3] ratio can be quantified using a combination of Very Large Array and Atacama Large Millimeter/submillimeter Array observations with reasonable integration times, at least towards IRAS 16293-2422, where high molecular column densities are expected.

Neutron scattering of residual hydrogen in 1,4-dioxane d 8 liquid: Understanding measurements with molecular dynamics simulations

DOE PAGES

Liu, Hongjun; Herwig, Kenneth W.; Kidder, Michelle K.; ...

2016-06-08

That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies betweenmore » simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen–deuterium pair, and complementary interference from the deuterium–deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. As a result, we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be performed to either understand measurements or calibrate/validate molecular dynamics models.« less

Results from the MARBLE Campaign on the National Ignition Facility: Implosion of Foam-Filled Capsules for Studying Thermonuclear Burn in the Presence of Heterogeneous Mix

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Douglas, M. R.; Cardenas, T.; Devolder, B. G.; Fincke, J. R.; Gunderson, M. A.; Haines, B. M.; Hamilton, C. E.; Kim, Y. H.; Lee, M. N.; Oertel, J. A.; Olson, R. E.; Randolph, R. B.; Shah, R. C.; Smidt, J. M.

2016-10-01

The MARBLE campaign on NIF investigates the effect of heterogeneous mix on thermonuclear burn for comparison to a probability distribution function (PDF) burn model. MARBLE utilizes plastic capsules filled with deuterated plastic foam and tritium gas. The ratio of DT to DD neutron yield is indicative of the degree to which the foam and the gas atomically mix. Platform development experiments have been performed to understand the behavior of the foam and of the gas separately using two types of capsule. The first uses partially deuterated foam and hydrogen gas fill to understand the burn in the foam. The second uses undeuterated foam and deuterium gas fill to understand the dynamics of the gas. Experiments using deuterated foam and tritium gas are planned. Results of these experiments, and the implications for our understanding of thermonuclear burn in heterogeneously mixed separated reactant experiments will be discussed. This work is supported by US DOE/NNSA, performed at LANL, operated by LANS LLC under contract DE-AC52-06NA25396.

Glass transition in ferroic glass K x (ND4)1-x D2PO4: a complete x-ray diffraction line shape analysis

NASA Astrophysics Data System (ADS)

Ranjan Choudhury, Rajul; Chitra, R.; Jayakrishnan, V. B.

2016-03-01

Quenching of dynamic disorder in glassy systems is termed as the glass transition. Ferroic glasses belong to the class of paracrystalline materials having crystallographic order in-between that of a perfect crystal and amorphous material, a classic example of ferroic glass is the solid solution of ferroelectric deuterated potassium dihydrogen phosphate and antiferroelectric deuterated ammonium dihydrogen phosphate. Lowering temperature of this ferroic glass can lead to a glass transition to a quenched disordered state. The subtle atomic rearrangement that takes place at such a glass transition can be revealed by careful examination of the temperature induced changes occurring in the x-ray powder diffraction (XRD) patterns of these materials. Hence we report here results of a complete diffraction line shape analysis of the XRD patterns recorded at different temperatures from deuterated mixed crystals DK x A1-x DP with mixing concentration x ranging as 0 < x < 1. Changes observed in diffraction peak shapes have been explained on the basis of structural rearrangements induced by changing O-D-O hydrogen bond dynamics in these paracrystals.

Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

NASA Astrophysics Data System (ADS)

Lindner, Robert; Lou, Xinghua; Reinstein, Jochen; Shoeman, Robert L.; Hamprecht, Fred A.; Winkler, Andreas

2014-06-01

Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation.

PubMed

Lindner, Robert; Lou, Xinghua; Reinstein, Jochen; Shoeman, Robert L; Hamprecht, Fred A; Winkler, Andreas

2014-06-01

Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Hydrogenation at low temperatures does not always lead to saturation: the case of HNCO

NASA Astrophysics Data System (ADS)

Noble, J. A.; Theule, P.; Congiu, E.; Dulieu, F.; Bonnin, M.; Bassas, A.; Duvernay, F.; Danger, G.; Chiavassa, T.

2015-04-01

Context. It is generally agreed that hydrogenation reactions dominate chemistry on grain surfaces in cold, dense molecular cores, saturating the molecules present in ice mantles. Aims: We present a study of the low temperature reactivity of solid phase isocyanic acid (HNCO) with hydrogen atoms, with the aim of elucidating its reaction network. Methods: Fourier transform infrared spectroscopy and mass spectrometry were employed to follow the evolution of pure HNCO ice during bombardment with H atoms. Both multilayer and monolayer regimes were investigated. Results: The hydrogenation of HNCO does not produce detectable amounts of formamide (NH2CHO) as the major product. Experiments using deuterium reveal that deuteration of solid HNCO occurs rapidly, probably via cyclic reaction paths regenerating HNCO. Chemical desorption during these reaction cycles leads to loss of HNCO from the surface. Conclusions: It is unlikely that significant quantities of NH2CHO form from HNCO. In dense regions, however, deuteration of HNCO will occur. HNCO and DNCO will be introduced into the gas phase, even at low temperatures, as a result of chemical desorption.

Highly efficient D2 generation by dehydrogenation of formic acid in D2O through H+/D+ exchange on an iridium catalyst: application to the synthesis of deuterated compounds by transfer deuterogenation.

PubMed

Wang, Wan-Hui; Hull, Jonathan F; Muckerman, James T; Fujita, Etsuko; Hirose, Takuji; Himeda, Yuichiro

2012-07-23

Deuterated compounds have received increasing attention in both academia and industrial fields. However, preparations of these compounds are limited for both economic and practical reasons. Herein, convenient generation of deuterium gas (D(2)) and the preparation of deuterated compounds on a laboratory scale are demonstrated by using a half-sandwich iridium complex with 4,4'-dihydroxy-2,2'-bipyridine. The "umpolung" (i.e., reversal of polarity) of a hydrogen atom of water was achieved in consecutive reactions, that is, a cationic H(+)/D(+) exchange reaction and anionic hydride or deuteride transfer, under mild conditions. Selective D(2) evolution (purity up to 89 %) was achieved by using HCO(2)H as an electron source and D(2)O as a deuterium source; a rhodium analogue provided HD gas (98 %) under similar conditions. Furthermore, pressurized D(2) (98 %) without CO gas was generated by using DCO(2)D in D(2)O in a glass autoclave. Transfer deuterogenation of ketones gave α-deuterated alcohols with almost quantitative yields and high deuterium content by using HCO(2)H in D(2)O. Mechanistic studies show that the H(+)/D(+) exchange reaction in the iridium hydride complex was much faster than β-elimination and hydride (deuteride) transfer. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters

NASA Astrophysics Data System (ADS)

Neustetter, Michael; Mahmoodi-Darian, Masoomeh; Denifl, Stephan

2017-05-01

Mass spectroscopic investigations on tetrahydrofuran (THF, C4H8O), a common model molecule of the DNA-backbone, have been carried out. We irradiated isolated THF and (hydrated) THF clusters with low energy electrons (electron energy 70 eV) in order to study electron ionization and ionic fragmentation. For elucidation of fragmentation pathways, deuterated TDF (C4D8O) was investigated as well. One major observation is that the cluster environment shows overall a protective behavior on THF. However, also new fragmentation channels open in the cluster. In this context, we were able to solve a discrepancy in the literature about the fragment ion peak at mass 55 u in the electron ionization mass spectrum of THF. We ascribe this ion yield to the fragmentation of ionized THF clusters.

Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

USGS Publications Warehouse

Rawn, C.J.; Rondinone, A.J.; Chakoumakos, B.C.; Circone, S.; Stern, L.A.; Kirby, S.H.; Ishii, Y.

2003-01-01

Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters.

From the tunneling dimer to the onset of microsolvation: Infrared spectroscopy of allyl radical water aggregates in helium nanodroplets

NASA Astrophysics Data System (ADS)

Leicht, Daniel; Kaufmann, Matin; Pal, Nitish; Schwaab, Gerhard; Havenith, Martina

2017-03-01

The infrared spectrum of allyl:water clusters embedded in helium nanodroplets was recorded. Allyl radicals were produced by flash vacuum pyrolysis and trapped in helium droplets. Deuterated water was added to the doped droplets, and the infrared spectrum of the radical water aggregates was recorded in the frequency range 2570-2820 cm-1. Several absorption bands are observed and assigned to 1:1 and 1:2 allyl:D2O clusters, based on pressure dependent measurements and accompanying quantum chemical calculations. The analysis of the 1:1 cluster spectrum revealed a tunneling splitting as well as a combination band. For the 1:2 cluster, we observe a water dimer-like motif that is bound by one π-hydrogen bond to the allyl radical.

Laboratory Measurements for Deuterated Astrochemistry

NASA Astrophysics Data System (ADS)

Hillenbrand, Pierre-Michel; Bowen, Kyle Patrick; Miller, Kenneth A.; De Ruette, Nathalie; Urbain, Xavier; Savin, Daniel Wolf

2017-06-01

Deuterated molecules are powerful probes of the cold interstellar medium (ISM). Observations of D-bearing molecules are used to infer the chemistry of the ISM and to trace out physical conditions such as density, ionization fraction, and thermal history. The chemistry of the cold ISM results from a complicated interplay between gas-phase processes, reactions on dust grain surfaces, and chemistry occurring both in and on the icy mantles of dust grains. Our focus here is on an improved understanding of the relevant deuterated gas-phase chemistry. At the low temperatures and densities typical of the cold ISM, much of this chemistry is driven by binary ion-neutral reactions, which are typically barrierless and exoergic (as compared to neutral-neutral reactions which often have significant activation energies).One of the biggest challenges in generating a reliable deuterated gas-phase astrochemical network is the uncertainty of the necessary rate coefficients. The vast majority of available chemical kinetic data are for fully hydrogenated species. For those D-bearing reactions where no laboratory data are available, two approaches have been adopted for converting the fully hydrogenated data into partial- and fully-deuterated species. The first approach simply “clones” the H-bearing reactions into D-bearing reactions and assumes that the rate coefficients are the same. The second approach uses a simple mass scaling relationship based on the Langevin formalism.We have initiated a series of laboratory measurements aimed at resolving this issue. For this we use our novel dual-source, merged fast-beams apparatus, which enables us to study reactions of neutral atoms and charged molecules. Using co-propagating beams enables us to achieve collision energies corresponding to temperatures as low as 25 K, limited only by the divergences of the two beams. Recently we have measured the reaction C + H2+(D2+) forming CH+(CD+) + H(D). We are now studying D + H3+(D2H+) forming H2D+(D3+) + H. Here we report on these results and discuss their astrochemical implications.

Hydrogenation and Deuteration of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} on Cold Grains: A Clue to the Formation Mechanism of C{sub 2}H{sub 6} with Astronomical Interest

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

Kobayashi, Hitomi; Kawakita, Hideyo; Hidaka, Hiroshi

We quantitatively investigated the hydrogen addition reactions of acetylene (C{sub 2}H{sub 2}) and ethylene (C{sub 2}H{sub 4}) on amorphous solid water (ASW) at 10 and 20 K relevant to the formation of ethane (C{sub 2}H{sub 6}) on interstellar icy grains. We found that the ASW surface enhances the reaction rates for C{sub 2}H{sub 2} and C{sub 2}H{sub 4} by approximately a factor of 2 compared to those on the pure-solid C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 10 K, probably due to an increase in the sticking coefficient and adsorption energy of the H atoms on ASW. In contrastmore » to the previous proposal that the hydrogenation rate of C{sub 2}H{sub 4} is orders of magnitude larger than that of C{sub 2}H{sub 2}, the present results show that the difference in hydrogenation rates of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} is only within a factor of 3 on both the surfaces of pure solids and ASW. In addition, we found the small kinetic isotope effect for hydrogenation/deuteration of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 10 K, despite the requirement of quantum tunneling. At 20 K, the reaction rate of deuteration becomes even larger than that of hydrogenation. These unusual isotope effects might originate from a slightly larger number density of D atoms than H atoms on ASW at 20 K. The hydrogenation of C{sub 2}H{sub 2} is four times faster than CO hydrogenation and can produce C{sub 2}H{sub 6} efficiently through C{sub 2}H{sub 4} even in the environment of a dark molecular cloud.« less

Results from MARBLE DT Experiments on the National Ignition Facility: Implosion of Foam-Filled Capsules for Studying Thermonuclear Burn in the Presence of Heterogeneous Mix

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Douglas, M. R.; Cardenas, T.; Cooley, J. H.; Gunderson, M. A.; Haines, B. M.; Hamilton, C. E.; Kim, Y.; Lee, M. N.; Oertel, J. A.; Olson, R. E.; Randolph, R. B.; Shah, R. C.; Smidt, J. M.

2017-10-01

The MARBLE campaign on NIF investigates the effect of heterogeneous mix on thermonuclear burn for comparison to a probability distribution function (PDF) burn model. MARBLE utilizes plastic capsules filled with deuterated plastic foam and tritium gas. The ratio of DT to DD neutron yield is indicative of the degree to which the foam and the gas atomically mix. Platform development experiments have been performed to understand the behavior of the foam and of the gas separately using two types of capsule. The first experiments using deuterated foam and tritium gas have been performed. Results of these experiments, and the implications for our understanding of thermonuclear burn in heterogeneously mixed separated reactant experiments will be discussed. This work is supported by US DOE/NNSA, performed at LANL, operated by LANS LLC under contract DE-AC52-06NA25396.

Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules

PubMed Central

Su, Jielong; Raghuwanshi, Vikram S.; Raverty, Warwick; Garvey, Christopher J.; Holden, Peter J.; Gillon, Marie; Holt, Stephen A.; Tabor, Rico; Batchelor, Warren; Garnier, Gil

2016-01-01

Novel thin and smooth deuterated cellulose films were synthesised to visualize adsorbed bio-macromolecules using contrast variation neutron reflectivity (NR) measurements. Incorporation of varying degrees of deuteration into cellulose was achieved by growing Gluconacetobacter xylinus in deuterated glycerol as carbon source dissolved in growth media containing D2O. The derivative of deuterated cellulose was prepared by trimethylsilylation(TMS) in ionic liquid(1-butyl-3-methylimidazolium chloride). The TMS derivative was dissolved in toluene for thin film preparation by spin-coating. The resulting film was regenerated into deuterated cellulose by exposure to acidic vapour. A common enzyme, horseradish peroxidase (HRP), was adsorbed from solution onto the deuterated cellulose films and visualized by NR. The scattering length density contrast of the deuterated cellulose enabled accurate visualization and quantification of the adsorbed HRP, which would have been impossible to achieve with non-deuterated cellulose. The procedure described enables preparing deuterated cellulose films that allows differentiation of cellulose and non-deuterated bio-macromolecules using NR. PMID:27796332

OT1_dlis_2: Ammonia as a Tracer of the Earliest Stages of Star Formation

NASA Astrophysics Data System (ADS)

Lis, D.

2010-07-01

Stars form in molecular cloud cores, cold and dense regions enshrouded by dust. The initiation of this process is among the least understood steps of star formation. Highresolution heterodyne spectroscopy provides invaluable information about the physical conditions (density, temperature), kinematics (infall, outflows), and chemistry of these regions. Classical molecular tracers, such CO, CS, and many other abundant gasphase species, have been shown to freeze out onto dust grain mantles in prestellar cores. However, Nbearing species, in particular ammonia, are much less affected by depletion and are observed to stay in the gas phase at densities in excess of 1e6 cm3. The molecular freezeout has important consequences for the chemistry of dense gas. In particular, the depletion of abundant gasphase species with heavy atoms drives up abundances of deuterated H3+ isotopologues, which in turn results in spectacular deuteration levels of molecules that do remain in the gas phase. Consequently, lines of deuterated Nbearing species, in particular the fundamental lines of ammonia isotopologues, having very high critical densities, are optimum tracers of innermost regions of dense cores. We propose to study the morphology, density structure and kinematics of cold and dense cloud cores, by mapping the spatial distribution of ammonia isotopologues in isolated dense prestellar cores using Herschel/HIFI. These observations provide optimum probes of the onset of star formation, as well as the physical processes that control gasgrain interaction, freezeout, mantle ejection and deuteration. The sensitive, highresolution spectra acquired within this program will be analyzed using sophisticated radiative transfer models and compared with outputs of stateoftheart 3D MHD simulations and chemical models developed by the members of our team.

OT2_dlis_3: Ammonia as a Tracer of the Earliest Stages of Star Formation

NASA Astrophysics Data System (ADS)

Lis, D.

2011-09-01

Stars form in molecular cloud cores, cold and dense regions enshrouded by dust. The initiation of this process is among the least understood steps of star formation. High!resolution heterodyne spectroscopy provides invaluable information about the physical conditions (density, temperature), kinematics (infall, outflows), and chemistry of these regions. Classical molecular tracers, such CO, CS, and many other abundant gas!phase species, have been shown to freeze out onto dust grain mantles in pre!stellar cores. However, N!bearing species, in particular ammonia, are much less affected by depletion and are observed to stay in the gas phase at densities in excess of 1e6 cm!3. The molecular freeze!out has important consequences for the chemistry of dense gas. In particular, the depletion of abundant gas!phase species with heavy atoms drives up abundances of deuterated H3+ isotopologues, which in turn results in spectacular deuteration levels of molecules that do remain in the gas phase. Consequently, lines of deuterated N!bearing species, in particular the fundamental lines of ammonia isotopologues, having very high critical densities, are optimum tracers of innermost regions of dense cores. We propose to study the morphology, density structure and kinematics of cold and dense cloud cores, by mapping the spatial distribution of ammonia isotopologues in isolated dense pre!stellar cores using Herschel/HIFI. These observations provide optimum probes of the onset of star formation, as well as the physical processes that control gas!grain interaction, freeze!out, mantle ejection and deuteration. The sensitive, high!resolution spectra acquired within this program will be analyzed using sophisticated radiative transfer models and compared with outputs of state!of!the!art 3D MHD simulations and chemical models developed by the members of our team.

Laboratory measurements of H-D substitution rates in solid methanol-dn (n=0-2) at 10 K

NASA Astrophysics Data System (ADS)

Nagaoka, Akihiro; Watanabe, Naoki; Kouchi, Akira

The deuterium fractionation of interstellar methanol is investigated experimentally using the ASURA (Apparatus for SUrface Reactions in Astrophysics) system. Recent observations toward the low-mass protostars IRAS16293 found the very high D/H ratios in formaldehyde and methanol up to 0.2 and 0.4, respectively (Loinard et al. 2000; Parise et al. 2004; Aikawa et al. 2005). To date, several models have been proposed to explain D-fractionation mechanism. Pure gas-phase models are difficult to reproduce the D-fractionation, particularly, for multideuterated species, while the results of some gas-grain models can achieve the observed fractionation levels fairly well (Stantcheva & Herbst 2003). However, the gas-grain models require many assumptions regarding the grain surface reactions. Then, the experiments on the surface reaction have been highly desirable. In this context, we performed the experiments on the formation of deuterated formaldehyde and methanol on cold (10 K) interstellar grain analogues and revealed that a key route for the D-fractionation is not successive addition of H and D to CO as previously considered (e.g., Charnley, Tielens, & Rodgers 1997) but H-D substitution in solid CH3OH on icy grains (Nagaoka, Watanabe, & Kouchi 2005). We report the results of further experiments on the deuteration of CH3OH using a cold (30 K) atomic D beam. The relative rates of H-D substitution reactions; CH3OH → CH2DOH, CH2DOH → CHD2OH, CHD2OH → CD3OH, were measured. Experiments were performed using the ASURA system described previously (Watanabe et al. 2004; Nagaoka, Watanabe, & Kouchi 2005). The experimental procedure is as follows. An aluminum substrate was placed in the centre of an ultra-high vacuum chamber (10-10 Torr) and cooled to 10 K by a helium refrigerator. The solid samples of normal and deuterated methanol (CH3OH, CH2DOH, CHD2OH) were vapor-deposited on the substrate. The D atoms produced by dissociation of D2 molecules by microwave discharge were irradiated to samples. D atoms were cooled to 30 K in the atomic source chamber before irradiation. During the irradiation with D atoms, we measured the variations of chemical composition of the samples, in-situ, with FT-IR. From the attenuation curves of parent molecules upon the irradiation with cold D atoms, we determined the relative rates of H-D substitution reactions (k1, k2, k3) of solid methanol;

Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction

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

Soorkia, Satchin; Taatjes, Craig A.; Osborn, David L.

The reaction of the ground state methylidyne radical CH (X2Pi) with pyrrole (C4H5N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 90 oC (363 K), at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr3) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C5H5N) is identified as the product of the reaction and resolved from 79Br atoms, and themore » result is consistent with CH addition to pyrrole followed by Helimination. The Photoionization Efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C5H4DN and identified as deuterated pyridine (dpyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as in gas-phase combustion processes, are discussed.« less

The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra

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

Vasilatou, K.; Michaud, J. M.; Baykusheva, D.

2014-08-14

The cyclopropene radical cation (c-C{sub 3}H{sub 4}{sup +}) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X{sup ~+} {sup 2}B{sub 2} ground electronic state of c-C{sub 3}H{sub 4}{sup +} at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra ofmore » deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C{sub 2v}-symmetric R{sub 0} structure for the ground electronic state of c-C{sub 3}H{sub 4}{sup +}. Two vibrational modes of c-C{sub 3}H{sub 4}{sup +} are found to have vibrational wave numbers below 300 cm{sup −1}, which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to the CH{sub 2} torsional mode (ν{sub 8}{sup +}, A{sub 2} symmetry) and of the second-lowest-frequency mode (≈210 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to a mode combining a CH out-of-plane with a CH{sub 2} rocking motion (ν{sub 15}{sup +}, B{sub 2} symmetry). The potential energy along the CH{sub 2} torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.« less

Structure of Aqueous Trehalose Solution by Neutron Diffraction and Structural Modeling.

PubMed

Olsson, Christoffer; Jansson, Helén; Youngs, Tristan; Swenson, Jan

2016-12-15

The molecular structure of an aqueous solution of the disaccharide trehalose (C 12 H 22 O 11 ) has been studied by neutron diffraction and empirical potential structure refinement modeling. Six different isotope compositions with 33 wt % trehalose (corresponding to 38 water molecules per trehalose molecule) were measured to ensure that water-water, trehalose-water, and trehalose-trehalose correlations were accurately determined. In fact, this is the first neutron diffraction study of an aqueous trehalose solution in which also the nonexchangeable hydrogen atoms in trehalose are deuterated. With this approach, it was possible to determine that (1) there is a substantial hydrogen bonding between trehalose and water (∼11 hydrogen bonds per trehalose molecule), which is in contrast to previous neutron diffraction studies, and (2) there is no tendency of clustering of trehalose, in contrast to what is generally observed by molecular dynamics simulations and experimentally found for other disaccharides. Thus, the results give the structural picture that trehalose prefers to interact with water and participate in a hydrogen-bonded network. This strong network character of the solution might be one of the key reasons for its extraordinary stabilization effect on biological materials.

A compact and accurate semi-global potential energy surface for malonaldehyde from constrained least squares regression

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

Mizukami, Wataru, E-mail: wataru.mizukami@bristol.ac.uk; Tew, David P., E-mail: david.tew@bristol.ac.uk; Habershon, Scott, E-mail: S.Habershon@warwick.ac.uk

2014-10-14

We present a new approach to semi-global potential energy surface fitting that uses the least absolute shrinkage and selection operator (LASSO) constrained least squares procedure to exploit an extremely flexible form for the potential function, while at the same time controlling the risk of overfitting and avoiding the introduction of unphysical features such as divergences or high-frequency oscillations. Drawing from a massively redundant set of overlapping distributed multi-dimensional Gaussian functions of inter-atomic separations we build a compact full-dimensional surface for malonaldehyde, fit to explicitly correlated coupled cluster CCSD(T)(F12*) energies with a root mean square deviations accuracy of 0.3%–0.5% up tomore » 25 000 cm{sup −1} above equilibrium. Importance-sampled diffusion Monte Carlo calculations predict zero point energies for malonaldehyde and its deuterated isotopologue of 14 715.4(2) and 13 997.9(2) cm{sup −1} and hydrogen transfer tunnelling splittings of 21.0(4) and 3.2(4) cm{sup −1}, respectively, which are in excellent agreement with the experimental values of 21.583 and 2.915(4) cm{sup −1}.« less

Estimation of Koc values for deuterated benzene, toluene, and ethylbenzene, and application to ground water contamination studies.

PubMed

Poulson, S R; Drever, J I; Colberg, P J

1997-11-01

Sorption partition coefficients between water and organic carbon (Koc) for deuterated benzene, toluene, and ethylbenzene have been estimated by measuring values of the octanol-water partition coefficient (Kow) and HPLC retention factors (k1), which correlate closely to values of Koc. Measured values of log Kow for non-deuterated and deuterated toluene are 2.77 (+/- 0.02) and 2.78 (+/- 0.04), respectively, indicating that within experimental error, log Koc for deuterated and non-deuterated toluene are the same. The HPLC method provides greater precision, and yields values of delta log Koc (= log Koc [deuterated]-log Koc [non-deuterated]) of -0.021 (+/- 0.001) for benzene, -0.028 (+/- 0.002) for toluene, and -0.035 (+/- 0.003) for ethylbenzene. The small values of delta log Koc demonstrates that deuterated compounds are excellent tracers for the hydrologic behavior of ground water contaminants.

Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.

PubMed

Claesen, Jürgen; Burzykowski, Tomasz

2017-09-01

Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017. © 2016 Wiley Periodicals, Inc.

Development of a polar direct drive platform for mix and burn experiments on the National Ignition Facility

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Kyrala, G. A.; Krasheninnikova, N. S.; Bradley, P. A.; Cobble, J. A.; Tregillis, I. L.; Obrey, K. A. D.; Baumgaertel, J. A.; Hsu, S. C.; Shah, R. C.; Hakel, P.; Kline, J. L.; Schmitt, M. J.; Kanzleiter, R. J.; Batha, S. H.; Wallace, R. J.; Bhandarkar, S.; Fitzsimmons, P.; Hoppe, M.; Nikroo, A.; McKenty, P.

2016-03-01

Capsules driven with polar drive [1, 2] on the National Ignition Facility [3] are being used [4] to study mix in convergent geometry. In preparation for experiments that will utilize deuterated plastic shells with a pure tritium fill, hydrogen-filled capsules with copper- doped deuterated layers have been imploded on NIF to provide spectroscopic and nuclear measurements of capsule performance. Experiments have shown that the mix region, when composed of shell material doped with about 1% copper (by atom), reaches temperatures of about 2 keV, while undoped mixed regions reach about 3 keV. Based on the yield from these implosions, we estimate the thickness of CD that mixed into the gas as between about 0.25 and 0.43 μm of the inner capsule surface, corresponding to about 5 to 9 μg of material. Using 5 atm of tritium as the fill gas should result in over 1013 DT neutrons being produced, which is sufficient for neutron imaging [5].

Stability chart of small mixed 4He-3He clusters

NASA Astrophysics Data System (ADS)

Guardiola, R.; Navarro, J.

2003-11-01

A stability chart of mixed 4He and 3He clusters has been obtained by means of the diffusion Monte Carlo method, using both the Aziz HFD-B and the Tang-Toennies-Yiu atom-atom interaction. The investigated clusters contain up to eight 4He atoms and up to 20 3He atoms. One single 4He binds 20 3He atoms, and two 4He bind 1, 2, 8, and more than 14 3He atoms. All clusters with three or more 4He atoms are bound, although the combinations 4He33He9,10,11 and 4He34He9 are metastable. Clusters with 2, 8, and 20 3He atoms are particularly stable and define magic 3He numbers.

Platinum clusters with precise numbers of atoms for preparative-scale catalysis.

PubMed

Imaoka, Takane; Akanuma, Yuki; Haruta, Naoki; Tsuchiya, Shogo; Ishihara, Kentaro; Okayasu, Takeshi; Chun, Wang-Jae; Takahashi, Masaki; Yamamoto, Kimihisa

2017-09-25

Subnanometer noble metal clusters have enormous potential, mainly for catalytic applications. Because a difference of only one atom may cause significant changes in their reactivity, a preparation method with atomic-level precision is essential. Although such a precision with enough scalability has been achieved by gas-phase synthesis, large-scale preparation is still at the frontier, hampering practical applications. We now show the atom-precise and fully scalable synthesis of platinum clusters on a milligram scale from tiara-like platinum complexes with various ring numbers (n = 5-13). Low-temperature calcination of the complexes on a carbon support under hydrogen stream affords monodispersed platinum clusters, whose atomicity is equivalent to that of the precursor complex. One of the clusters (Pt 10 ) exhibits high catalytic activity in the hydrogenation of styrene compared to that of the other clusters. This method opens an avenue for the application of these clusters to preparative-scale catalysis.The catalytic activity of a noble metal nanocluster is tied to its atomicity. Here, the authors report an atom-precise, fully scalable synthesis of platinum clusters from molecular ring precursors, and show that a variation of only one atom can dramatically change a cluster's reactivity.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE PAGES

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-24

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

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

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

The effect of deuteration on the structure of bacterial cellulose

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

Bali, Garima; Foston, Marcus; O'Neill, Hugh Michael

2013-01-01

ABSTRACT In vivo generated deuterated bacterial cellulose, cultivated from 100% deuterated glycerol in D2O medium, was analyzed for deuterium incorporation by ionic liquid dissolution and 2H and 1H nuclear magnetic resonance (NMR). A solution NMR method of the dissolved cellulose was used to determine that this bacterial cellulose had 85 % deuterium incorporation. Acetylation and 1H and 2H NMR of deuterated bacterial cellulose indicated near equal deuteration at all sites of the glucopyranosyl ring except C-6 which was partly deuterated. Despite the high level of deuterium incorporation there were no significant differences in the molecular and morphological properties were observedmore » for the deuterated and protio bacterial cellulose samples. The highly deuterated bacterial cellulose presented here can be used as a model substrate for studying cellulose biopolymer properties via future small angle neutron scattering (SANS) studies.« less

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

Deuterium enrichment of polycyclic aromatic hydrocarbons by photochemically induced exchange with deuterium-rich cosmic ices

NASA Technical Reports Server (NTRS)

Sandford, S. A.; Bernstein, M. P.; Allamandola, L. J.; Gillette, J. S.; Zare, R. N.

2000-01-01

The polycyclic aromatic hydrocarbon (PAH) coronene (C24H12) frozen in D2O ice in a ratio of less than 1 part in 500 rapidly exchanges its hydrogen atoms with the deuterium in the ice at interstellar temperatures and pressures when exposed to ultraviolet radiation. Exchange occurs via three different chemical processes: D atom addition, D atom exchange at oxidized edge sites, and D atom exchange at aromatic edge sites. Observed exchange rates for coronene (C24H12)-D2O and d12-coronene (C24D12)-H2O isotopic substitution experiments show that PAHs in interstellar ices could easily attain the D/H levels observed in meteorites. These results may have important consequences for the abundance of deuterium observed in aromatic materials in the interstellar medium and in meteorites. These exchange mechanisms produce deuteration in characteristic molecular locations on the PAHs that may distinguish them from previously postulated processes for D enrichment of PAHs.

Reaction of atomic hydrogen with formic acid.

PubMed

Cao, Qian; Berski, Slawomir; Latajka, Zdzislaw; Räsänen, Markku; Khriachtchev, Leonid

2014-04-07

We study the reaction of atomic hydrogen with formic acid and characterize the radical products using IR spectroscopy in a Kr matrix and quantum chemical calculations. The reaction first leads to the formation of an intermediate radical trans-H2COOH, which converts to the more stable radical trans-cis-HC(OH)2via hydrogen atom tunneling on a timescale of hours at 4.3 K. These open-shell species are observed for the first time as well as a reaction between atomic hydrogen and formic acid. The structural assignment is aided by extensive deuteration experiments and ab initio calculations at the UMP2 and UCCSD(T) levels of theory. The simplest geminal diol radical trans-cis-HC(OH)2 identified in the present work as the final product of the reaction should be very reactive, and further reaction channels are of particular interest. These reactions and species may constitute new channels for the initiation and propagation of more complex organic species in the interstellar clouds.

Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

PubMed

Sugimoto, Yoshiaki; Yurtsever, Ayhan; Hirayama, Naoki; Abe, Masayuki; Morita, Seizo

2014-07-11

Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

Structures of 38-atom gold-platinum nanoalloy clusters

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

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations.

PubMed

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J

2018-04-28

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s -1 ) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

NASA Astrophysics Data System (ADS)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-01

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s-1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Deuteration as a Means to Tune Crystallinity of Conducting Polymers

DOE PAGES

Jakowski, Jacek; Huang, Jingsong; Garashchuk, Sophya; ...

2017-08-25

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied in this paper experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of themore » dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton–proton and deuteron–deuteron motions but not of the proton–deuteron motion. Thus and finally, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.« less

Deuteration as a Means to Tune Crystallinity of Conducting Polymers

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

Jakowski, Jacek; Huang, Jingsong; Garashchuk, Sophya

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied in this paper experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of themore » dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton–proton and deuteron–deuteron motions but not of the proton–deuteron motion. Thus and finally, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.« less

Phosphonic Acids on an Atomically Defined Oxide Surface: The Binding Motif Changes with Surface Coverage.

PubMed

Schuschke, Christian; Schwarz, Matthias; Hohner, Chantal; Silva, Thais N; Fromm, Lukas; Döpper, Tibor; Görling, Andreas; Libuda, Jörg

2018-04-19

We have studied the anchoring mechanism of a phosphonic acid on an atomically defined oxide surface. Using time-resolved infrared reflection absorption spectroscopy, we investigated the reaction of deuterated phenylphosphonic acid (DPPA, C 6 H 5 PO 3 D 2 ) with an atomically defined Co 3 O 4 (111) surface in situ during film growth by physical vapor deposition. We show that the binding motif of the phosphonate anchor group changes as a function of coverage. At low coverage, DPPA binds in the form of a chelating tridentate phosphonate, while a transition to a chelating bidentate occurs close to monolayer saturation coverage. However, the coverage-dependent change in the binding motif is not associated with a major change of the molecular orientation, suggesting that the rigid phosphonate linker always maintains the DPPA in a strongly tilted orientation irrespective of the surface coverage.

Reaction rates and kinetic isotope effects of H{sub 2} + OH → H{sub 2}O + H

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

Meisner, Jan; Kästner, Johannes, E-mail: kaestner@theochem.uni-stuttgart.de

2016-05-07

We calculated reaction rate constants including atom tunneling of the reaction of dihydrogen with the hydroxy radical down to a temperature of 50 K. Instanton theory and canonical variational theory with microcanonical optimized multidimensional tunneling were applied using a fitted potential energy surface [J. Chen et al., J. Chem. Phys. 138, 154301 (2013)]. All possible protium/deuterium isotopologues were considered. Atom tunneling increases at about 250 K (200 K for deuterium transfer). Even at 50 K the rate constants of all isotopologues remain in the interval 4 ⋅ 10{sup −20} to 4 ⋅ 10{sup −17} cm{sup 3} s{sup −1}, demonstrating thatmore » even deuterated versions of the title reaction are possibly relevant to astrochemical processes in molecular clouds. The transferred hydrogen atom dominates the kinetic isotope effect at all temperatures.« less

Laboratory Measurements for H3+ Deuteration Reactions

NASA Astrophysics Data System (ADS)

Bowen, Kyle; Hillenbrand, Pierre-Michel; Urbain, Xavier; Savin, Daniel Wolf

2018-06-01

Deuterated molecules are important chemical tracers of protostellar cores. At the ~106 cm-3 particle densities and ~20 K temperatures typical for protostellar cores, most molecules freeze onto dust grains. A notable exception is H3+ and its isotopologues. These become important carriers of positive charge in the gas, can couple to any ambient magnetic field, and can thereby alter the cloud dynamics. Knowing the total abundance of H3+ and its isotopologues is important for studying the evolution of protostellar cores. However, H3+ and D3+ have no dipole moment. They lack a pure rotational spectrum and are not observable at protostellar core temperatures. Fortunately H2D+ and D2H+ have dipole moments and a pure rotational spectrum that can be excited in protostellar cores. Observations of these two molecules, combined with astrochemical models, provide information about the total abundance of H3+ and all its isotopologues. The inferred abundances, though, rely on accurate astrochemical data for the deuteration of H3+ and its isotopologues.Here we present laboratory measurements of the rate coefficients for three important deuterating reactions, namely D + H3+/H2D+/D2H+ → H + H2D+/ D2H+/D3+. Astrochemical models currently rely on rate coefficients from classical (Langevin) or semi-classical methods for these reactions, as fully quantum-mechanical calculations are beyond current computational capabilities. Laboratory studies are the most tractable means of providing the needed data. For our studies we used our novel dual-source, merged fast-beams apparatus, which enables us to study reactions of neutral atoms and molecular ions. Co-propagating beams allow us to measure experimental rate coefficients as a function of collision energy. We extract cross section data from these results, which we then convolve with a Maxwell-Boltzmann distribution to generate thermal rate coefficients. Here we present our results for these three reactions and discuss some implications.

Cryptic microtextures and geological histories of K-rich alkali feldspars revealed by charge contrast imaging

NASA Astrophysics Data System (ADS)

Flude, Stephanie; Lee, Martin R.; Sherlock, Sarah C.; Kelley, Simon P.

2012-06-01

Charge contrast imaging in the scanning electron microscope can provide new insights into the scale and composition of alkali feldspar microtextures, and such information helps considerably with the interpretation of their geological histories and results of argon isotope thermochronological analyses. The effectiveness of this technique has been illustrated using potassium-rich alkali feldspars from the Dartmoor granite (UK). These feldspars contain strain-controlled lamellar crypto- and microperthites that are cross-cut by strain-free deuteric microperthites. The constituent albite- and orthoclase-rich phases of both microperthite generations can be readily distinguished by atomic number contrast imaging. The charge contrast results additionally show that sub-micrometre-sized albite `platelets' are commonplace between coarser exsolution lamellae and occur together to make cryptoperthites. Furthermore, charge contrast imaging reveals that the orthoclase-rich feldspar is an intergrowth of two phases, one that is featureless with uniform contrast and another that occurs as cross-cutting veins and grains with the {110} adularia habit. Transmission electron microscopy shows that the featureless feldspar is tweed orthoclase, whereas the veins and euhedral grains are composed of irregular microcline that has formed from orthoclase by `unzipping' during deuteric or hydrothermal alteration. The charge contrast imaging results are especially important in demonstrating that deuteric perthites are far more abundant in alkali feldspars than would be concluded from investigations using conventional microscopy techniques. The unexpected presence of such a high volume of replacement products has significant implications for understanding the origins and geological histories of crustal rocks and the use of alkali feldspars in geo- and thermochronology. Whilst the precise properties of feldspars that generate contrast remain unclear, the similarity between charge contrast images and corresponding cathodoluminescence images of deuteric microperthites indicates that trace element chemistry and possibly also elastic strain within the crystal play a major role.

Methods for the synthesis of deuterated vinyl pyridine monomers

DOEpatents

Hong, Kunlun; Yang, Jun; Bonnesen, Peter V

2014-02-25

Methods for synthesizing deuterated vinylpyridine compounds of the Formula (1), wherein the method includes: (i) deuterating an acyl pyridine of the Formula (2) in the presence of a metal catalyst and D.sub.2O, wherein the metal catalyst is active for hydrogen exchange in water, to produce a deuterated acyl compound of Formula (3); (ii) reducing the compound of Formula (3) with a deuterated reducing agent to convert the acyl group to an alcohol group, and (iii) dehydrating the compound produced in step (ii) with a dehydrating agent to afford the vinylpyridine compound of Formula (1). The resulting deuterated vinylpyridine compounds are also described.

Methods for the synthesis of deuterated vinyl pyridine monomers

DOEpatents

Hong, Kunlun; Yang, Jun; Bonnesen, Peter V

2015-01-13

Methods for synthesizing deuterated vinylpyridine compounds of the Formula (1), wherein the method includes: (i) deuterating an acyl pyridine of the Formula (2) in the presence of a metal catalyst and D.sub.2O, wherein the metal catalyst is active for hydrogen exchange in water, to produce a deuterated acyl compound of Formula (3); (ii) reducing the compound of Formula (3) with a deuterated reducing agent to convert the acyl group to an alcohol group, and (iii) dehydrating the compound produced in step (ii) with a dehydrating agent to afford the vinylpyridine compound of Formula (1). The resulting deuterated vinylpyridine compounds are also described.

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Melting of size-selected gallium clusters with 60-183 atoms.

PubMed

Pyfer, Katheryne L; Kafader, Jared O; Yalamanchali, Anirudh; Jarrold, Martin F

2014-07-10

Heat capacities have been measured as a function of temperature for size-selected gallium cluster cations with between 60 and 183 atoms. Almost all clusters studied show a single peak in the heat capacity that is attributed to a melting transition. The peaks can be fit by a two-state model incorporating only fully solid-like and fully liquid-like species, and hence no partially melted intermediates. The exceptions are Ga90(+), which does not show a peak, and Ga80(+) and Ga81(+), which show two peaks. For the clusters with two peaks, the lower temperature peak is attributed to a structural transition. The melting temperatures for clusters with less than 50 atoms have previously been shown to be hundreds of degrees above the bulk melting point. For clusters with more than 60 atoms the melting temperatures decrease, approaching the bulk value (303 K) at around 95 atoms, and then show several small upward excursions with increasing cluster size. A plot of the latent heat against the entropy change for melting reveals two groups of clusters: the latent heats and entropy changes for clusters with less than 94 atoms are distinct from those for clusters with more than 93 atoms. This observation suggests that a significant change in the nature of the bonding or the structure of the clusters occurs at 93-94 atoms. Even though the melting temperatures are close to the bulk value for the larger clusters studied here, the latent heats and entropies of melting are still far from the bulk values.

Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

PubMed

Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

2016-02-18

Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

Application of chirally-deuterated (S)-D-(6-2H1)glucose to conformational studies

USDA-ARS?s Scientific Manuscript database

Deuterated sugars are widely used to elucidate mechanisms of biosynthesis and of chemical reactions, and to confirm assignments of complex NMR or mass spectra. To date, however, there are few reported syntheses for regio and stereospecifically deuterated pyranoses. Chirally-deuterated (S)-D-(6-**2...

Hund’s rule in superatoms with transition metal impurities

PubMed Central

Medel, Victor M.; Reveles, Jose Ulises; Khanna, Shiv N.; Chauhan, Vikas; Sen, Prasenjit; Castleman, A. Welford

2011-01-01

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund’s rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMgn clusters where TM is a 3d atom. The clusters exhibit Hund’s filling, opening the pathway to superatoms with magnetic shells. PMID:21646542

Hund's rule in superatoms with transition metal impurities.

PubMed

Medel, Victor M; Reveles, Jose Ulises; Khanna, Shiv N; Chauhan, Vikas; Sen, Prasenjit; Castleman, A Welford

2011-06-21

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund's rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMg(n) clusters where TM is a 3d atom. The clusters exhibit Hund's filling, opening the pathway to superatoms with magnetic shells.

The Oxidation Stability of Deuterated Esters.

DTIC Science & Technology

1983-01-01

UNCLASSIFIED FIG I1/8 NL ELL W 1328 jW 11111.25 . 1= W2. MICROCOP ROL6TO ES HR N. T 0A1 NU tAU 0 T NDfD GC-TR483-1 82 THE OXIDATION STABILITY OF DEUTERATED... Compounds .... 23 3.2.3 Differentiation of the Synergistic Effect of Alkali Metal Compounds from the Deuteration Effect ....... 27 3.2.4 Conclusion... Compounds ................ 25 4 Oxidation-Corrosion Tests: Comparison of Deuterated and Non-Deuterated Basestocks with Herc in presence of Ag + Al + Ti + Fe

Photoionization of rare gas clusters

NASA Astrophysics Data System (ADS)

Zhang, Huaizhen

This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the angular distribution parameter values of the two-spin-orbit components from Ar 2p clusters are slightly different. When comparing the beta values for Ar between atoms and clusters, we found different results between Ar 3s atoms and clusters, and between Ar 3p atoms and clusters. Argon cluster resonance from surface and bulk were also measured. Furthermore, the angular distribution parameters of Ar cluster photoelectrons and Ar atom photoelectrons in the 3s → np ionization region were obtained.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Central Doping of a Foreign Atom into the Silver Cluster for Catalytic Conversion of CO2 toward C-C Bond Formation.

PubMed

Liu, Yuanyuan; Chai, Xiaoqi; Cai, Xiao; Chen, Mingyang; Jin, Rongchao; Ding, Weiping; Zhu, Yan

2018-06-19

Clusters with an exact number of atoms are of particular research interest in catalysis. Their catalytic behaviors can be potentially altered with the addition or removal of a single atom. Herein we explore the effects of the single-foreign-atom (Au, Pd and Pt) doping into the core of an Ag cluster with 25-atoms on the catalytic properties, where the foreign atom is protected by 24 Ag atoms (i.e., Au@Ag24, Pd@Ag24, and Pt@Ag24). The central doping of a single atom into the Ag25 cluster is found to have a substantial influence on the catalytic performance in the carboxylation reaction of CO2 with terminal alkyne through C-C bond formation to produce propiolic acid. Our studies reveal that the catalytic properties of the cluster catalysts can be dramatically changed with the subtle alteration by a single atom away from the active sites. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple valence superatoms.

PubMed

Reveles, J U; Khanna, S N; Roach, P J; Castleman, A W

2006-12-05

We recently demonstrated that, in gas phase clusters containing aluminum and iodine atoms, an Al(13) cluster behaves like a halogen atom, whereas an Al(14) cluster exhibits properties analogous to an alkaline earth atom. These observations, together with our findings that Al(13)(-) is inert like a rare gas atom, have reinforced the idea that chosen clusters can exhibit chemical behaviors reminiscent of atoms in the periodic table, offering the exciting prospect of a new dimension of the periodic table formed by cluster elements, called superatoms. As the behavior of clusters can be controlled by size and composition, the superatoms offer the potential to create unique compounds with tailored properties. In this article, we provide evidence of an additional class of superatoms, namely Al(7)(-), that exhibit multiple valences, like some of the elements in the periodic table, and hence have the potential to form stable compounds when combined with other atoms. These findings support the contention that there should be no limitation in finding clusters, which mimic virtually all members of the periodic table.

Meta-atom cluster acoustic metamaterial with broadband negative effective mass density

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

Chen, Huaijun; Zhai, Shilong; Ding, Changlin

2014-02-07

We design a resonant meta-atom cluster, via which a two-dimensional (2D) acoustic metamaterial (AM) with broadband negative effective mass density from 1560 Hz to 5580 Hz is fabricated. Experimental results confirm that there is only weak interaction among the meta-atoms in the cluster. And then the meta-atoms in the cluster independently resonate, resulting in the cluster becoming equivalent to a broadband resonance unit. Extracted effective refractive indices from reflection and transmission measurements of the 2D AM appear to be negative from 1500 Hz to 5480 Hz. The broadband negative refraction has also been demonstrated by our further experiments. We expectmore » that this meta-atom cluster AM will significantly contribute to the design of broadband negative effective mass density AM.« less

Intramolecular hydrogen bonding in N-salicylideneaniline: FT-IR spectrum and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Moosavi-Tekyeh, Zainab; Dastani, Najmeh

2015-12-01

FT-IR and FT-Raman spectra of N-salicylideneaniline (SAn) and its deuterated analogue (D-SAn) are recorded, and the theoretical calculations are performed on their molecular structures and vibrational frequencies. The same calculations are performed for SAn in different solutions using the polarizable conductor continuum model (CPCM) method. Comparisons between the spectra obtained and the corresponding theoretical calculations are used to assign the vibrational frequencies for these compounds. The spectral behavior of SAn upon deuteration is also used to distinguish the positions of OH vibrational frequencies. The hydrogen bond strength of SAn is investigated by applying the atoms-in-molecules (AIM) theory, natural bond orbital (NBO) analysis, and geometry calculations. The harmonic vibrational frequencies of SAn are calculated at B3LYP and X3LYP levels of theory using 6-31G*, 6-311G**, and 6-311++G** basis sets. The AIM results support a medium hydrogen bonding in SAn. The observed νOH/νOD and γOH/γOD for SAn appear at 2940/2122 and 830/589 cm-1, respectively.

Supramolecular hydrogen-bonding network in 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate crystal

NASA Astrophysics Data System (ADS)

Perpétuo, Genivaldo J.; Gonçalves, Rafael S.; Janczak, Jan

2015-09-01

The single crystals of 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate were grown using a solution growth technique. The compound crystallises in the centrosymmetric P21/c space group of the monoclinic system. The conformation of the 1-(diaminomethylene)thiouron-1-ium cation is not strictly planar, but twisted. Both arms of the cation are oppositely rotated by 8.5(1)° around the Csbnd N bonds involving the central N atom. The arrangement of oppositely charged components, i.e. 1-(diaminomethylene)thiouron-1-ium cations and 4-hydroxybenzenesulfonate anions in the crystal is mainly determined by ionic and hydrogen-bonding interactions forming supramolecular network. The possible hydrogen-bonding interactions between cation and anion units were analysed on the basis of molecular orbital calculations. The obtained deuterated analogue crystallises similar as H-compound in the monoclinic system (P21/c) with quite similar lattice parameters. The compound was also characterised by the FT-IR and Raman spectroscopies. The characteristic bands of the functional and skeletal groups of the protiated and deuterated analogue of 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate are discussed.

Helium behavior in oxide dispersion strengthened (ODS) steel: Insights from ab initio modeling

NASA Astrophysics Data System (ADS)

Sun, Dan; Li, Ruihuan; Ding, Jianhua; Huang, Shaosong; Zhang, Pengbo; Lu, Zheng; Zhao, Jijun

2018-02-01

Using first-principles calculations, we systemically investigate the energetics and stability behavior of helium (He) atoms and small Hen (n = 2-4) clusters inside oxide dispersion strengthened (ODS) steel, as well as the incorporation of large amount of He atoms inside Y2O3 crystal. From the energetic point of view, He atom inside Y2O3 cluster is most stable, followed by the interstitial sites at the α-Fe/Y2O3 interface, and the tetrahedral interstitial sites inside α-Fe region. We further consider Hen (n = 2-4) clusters at the tetrahedral interstitial site surrounded by four Y atoms, which is the most stable site in the ODS steel model. The incorporation energies of all these Hen clusters are lower than that of single He atom in α-Fe, while the binding energy between two He atoms is relatively small. With insertion of 15 He atoms into 80-atom unit cell of Y2O3 crystal, the incorporation energy of He atoms is still lower than that of He4 cluster in α-Fe crystal. These theoretical results suggest that He atoms tend to aggregate inside Y2O3 clusters or at the α-Fe/Y2O3 interface, which is beneficial to prevent the He embrittlement in ODS steels.

Change of Energy of the Cubic Subnanocluster of Iron Under Influence of Interstitial and Substitutional Atoms.

PubMed

Nedolya, Anatoliy V; Bondarenko, Natalya V

2016-12-01

Energy change of an iron face-centred cubic subnanocluster was evaluated using molecular mechanics method depending on the position of a carbon interstitial atom and substitutional atoms of nickel. Calculations of all possible positions of impurity atoms show that the energy change of the system are discrete and at certain positions of the atoms are close to continuous.In terms of energy, when all impurity atoms are on the same edge of an atomic cluster, their positions are more advantageous. The presence of nickel atoms on the edge of a cubic cluster resulted in decrease of potential barrier for a carbon atom and decrease in energy in the whole cluster. A similar drift of a carbon atom from central octahedral interstitial site to the surface in the direction <011> occurred under the influence of surface factors.Such configuration corresponds to decreasing symmetry and increasing the number of possible energy states of a subnanocluster, and it corresponds to the condition of spontaneous crystallization process in an isolated system.Taking into account accidental positions of the nickel atom in the iron cluster, such behaviour of the carbon atom can explain the mechanism of growth of a new phase and formation of new clusters in the presence of other kind of atoms because of surface influence.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

PubMed

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

2017-05-01

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

Effect of in Vivo Deuteration on Structure of Switchgrass Lignin

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

Meng, Xianzhi; Evans, Barbara R.; Yoo, Chang Geun

Biomass deuteration is an effective engineering method that can be used to provide key insights into understanding of biomass recalcitrance and the complex biomass conversion process. In this study, production of deuterated switchgrass was accomplished by growing the plants in 50% D 2O under hydroponic conditions in a perfusion chamber. Cellulolytic enzyme lignin was isolated from deuterated switchgrass, characterized by Fourier transform infrared (FTIR), gel permeation chromatography (GPC), and nuclear magnetic resonance (NMR) and compared with its protiated control sample to determine the effect of in vivo deuteration on the chemical structure of lignin. FTIR results showed that D 2Omore » can be taken up by the roots and transported to the leaves, and deuterium was subsequently incorporated into hydroxyl and alkyl groups in the plant and its lignin through photosynthesis. According to GPC results, deuterated lignin had slightly higher molecular weight, presumably due to isotope effects. 31P and heteronuclear single quantum coherence (HSQC) NMR results revealed that lignin in the deuterated biomass preserved its native physicochemical characteristics. Finally, the conserved characteristics of the deuterated lignin show its great potential applications for structural and dynamic studies of lignocellulose by techniques such as neutron scattering.« less

Effect of in Vivo Deuteration on Structure of Switchgrass Lignin

DOE PAGES

Meng, Xianzhi; Evans, Barbara R.; Yoo, Chang Geun; ...

2017-07-27

Biomass deuteration is an effective engineering method that can be used to provide key insights into understanding of biomass recalcitrance and the complex biomass conversion process. In this study, production of deuterated switchgrass was accomplished by growing the plants in 50% D 2O under hydroponic conditions in a perfusion chamber. Cellulolytic enzyme lignin was isolated from deuterated switchgrass, characterized by Fourier transform infrared (FTIR), gel permeation chromatography (GPC), and nuclear magnetic resonance (NMR) and compared with its protiated control sample to determine the effect of in vivo deuteration on the chemical structure of lignin. FTIR results showed that D 2Omore » can be taken up by the roots and transported to the leaves, and deuterium was subsequently incorporated into hydroxyl and alkyl groups in the plant and its lignin through photosynthesis. According to GPC results, deuterated lignin had slightly higher molecular weight, presumably due to isotope effects. 31P and heteronuclear single quantum coherence (HSQC) NMR results revealed that lignin in the deuterated biomass preserved its native physicochemical characteristics. Finally, the conserved characteristics of the deuterated lignin show its great potential applications for structural and dynamic studies of lignocellulose by techniques such as neutron scattering.« less

The study of structures and properties of PdnHm(n=1-10, m=1,2) clusters by density functional theory

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Chen, Guo-Xiang; Zhang, Jian-Min; Wu, Hua

2018-04-01

The geometrical evolution, local relative stability, magnetism and charge transfer characteristics of PdnHm(n = 1-10, m = 1,2) have been systematically calculated by using density functional theory. The studied results show that the most stable geometries of PdnH and PdnH2 (n = 1-10) can be got by doping one or two H atoms on the sides of Pdn clusters except Pd6H and Pd6H2. It is found that doping one or two H atoms on Pdn clusters cannot change the basic framework of Pdn. The analysis of stability shows that Pd2H, Pd4H, Pd7H, Pd2H2, Pd4H2 and Pd7H2 clusters have higher local relative stability than neighboring clusters. The analysis of magnetic properties demonstrates that absorption of hydrogen atoms decreases the average atomic magnetic moments compared with pure Pdn clusters. More charges transfer from H atoms to Pd atoms for Pd6H and Pd6H2 clusters, demonstrating the adsorption of hydrogen atoms change from side adsorption to surface adsorption.

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

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

Atomic dynamics and the problem of the structural stability of free clusters of solidified inert gases

NASA Astrophysics Data System (ADS)

Verkhovtseva, É. T.; Gospodarev, I. A.; Grishaev, A. V.; Kovalenko, S. I.; Solnyshkin, D. D.; Syrkin, E. S.; Feodos'ev, S. B.

2003-05-01

The dependence of the rms amplitudes of atoms in free clusters of solidified inert gases on the cluster size is investigated theoretically and experimentally. Free clusters are produced by homogeneous nucleation in an adiabatically expanding supersonic stream. Electron diffraction is used to measure the rms amplitudes of the atoms; the Jacobi-matrix method is used for theoretical calculations. A series of distinguishing features of the atomic dynamics of microclusters was found. This was necessary to determine the character of the formation and the stability conditions of the crystal structure. It wass shown that for clusters consisting of less than N˜103 atoms, as the cluster size decreases, the rms amplitudes grow much more rapidly than expected from the increase in the specific contribution of the surface. It is also established that an fcc structure of a free cluster, as a rule, contains twinning defects (nuclei of an hcp phase). One reason for the appearance of such defects is the so-called vertex instability (anomalously large oscillation amplitudes) of the atoms in coordination spheres.

Exploring molecular complexity with ALMA (EMoCA): Deuterated complex organic molecules in Sagittarius B2(N2)

NASA Astrophysics Data System (ADS)

Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

2016-03-01

Context. Deuteration is a powerful tracer of the history of the cold prestellar phase in star-forming regions. Apart from methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in regions forming high-mass stars. Aims: Our goal is to detect deuterated complex organic molecules toward the high mass star-forming region Sagittarius B2 (Sgr B2) and derive the level of deuteration for these molecules. Methods: We use a complete 3-mm spectral line survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA) to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We constructed population diagrams and integrated intensity maps to fit rotational temperatures and emission sizes for each molecule. Column densities are derived by modeling the full spectrum under the assumption of local thermodynamic equilibrium. We compare the results to predictions of two astrochemical models that treat the deuteration process. Results: We report the detection of CH2DCN toward Sgr B2(N2) with a deuteration level of 0.4%, and tentative detections of CH2DOH, CH2DCH2CN, the chiral molecule CH3CHDCN, and DC3N with levels in the range 0.05%-0.12%. A stringent deuteration upper limit is obtained for CH3OD (<0.07%). Upper limits in the range 0.5-1.8% are derived for the three deuterated isotopologues of vinyl cyanide, the four deuterated species of ethanol, and CH2DOCHO. Ethyl cyanide is less deuterated than methyl cyanide by at least a factor five. The [CH2DOH]/[CH3OD] abundance ratio is higher than 1.8. It may still be consistent with the value obtained in Orion KL. Except for methyl cyanide, the measured deuteration levels lie at least a factor four below the predictions of current astrochemical models. The deuteration levels in Sgr B2(N2) are also lower than in Orion KL by a factor of a few up to a factor ten. Conclusions: The discrepancy between the deuteration levels of Sgr B2(N2) and the predictions of chemical models, and the difference between Sgr B2(N2) and Orion KL may both be due to the higher kinetic temperatures that characterize the Galactic center region compared to nearby clouds. Alternatively, they may result from a lower overall abundance of deuterium itself in the Galactic center region by up to a factor ten.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Many particle spectroscopy of atoms, molecules, clusters and surfaces: international conference MPS-2016

NASA Astrophysics Data System (ADS)

Grum-Grzhimailo, Alexei N.; Popov, Yuri V.; Gryzlova, Elena V.; Solov'yov, Andrey V.

2017-07-01

The conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces (MPS-2016) brought together near to a hundred scientists in the field of electronic, photonic, atomic and molecular collisions, and spectroscopy from around the world. We deliver an Editorial of a topical issue presenting original research results from some of the participants on both experimental and theoretical studies involving many particle spectroscopy of atoms, molecules, clusters and surfaces. Contribution to the Topical Issue "Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces", edited by A.N. Grum-Grzhimailo, E.V. Gryzlova, Yu.V. Popov, and A.V. Solov'yov.

Observation of a barium xenon exciplex within a large argon cluster.

PubMed

Briant, M; Gaveau, M-A; Mestdagh, J-M

2010-07-21

Spectroscopic measurements provide fluorescence and excitation spectra of a single barium atom codeposited with xenon atoms on argon clusters of average size approximately 2000. The spectra are studied as a function of the number of xenon atoms per cluster. The excitation spectrum with approximately 10 xenon atoms per cluster is qualitatively similar to that observed when no xenon atom is present on the cluster. It consists of two bands located on each side of the 6s6p (1)P-6s(2) (1)S resonance line of the free barium. In contrast, the fluorescence spectrum differs qualitatively since a barium-xenon exciplex is observed, which has no counterpart in xenon free clusters. In particular an emission is observed, which is redshifted by 729 cm(-1) with respect to the Ba(6s6p (1)P-6s(2) (1)S) resonance line.

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

NMR spectroscopic properties (1H at 500 MHz) of deuterated* ribonucleotide-dimers ApU*, GpC*, partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*), d(ApT*), d(GpC*) and their comparison with natural counterparts (1H-NMR window).

PubMed

Földesi, A; Nilson, F P; Glemarec, C; Gioeli, C; Chattopadhyaya, J

1993-02-01

Pure 1'#,2',3',4'#,5',5''-2H6-ribonucleoside derivatives 10-14, 1'#,2',2'',3',4'#,5',5''-2H7-2'-deoxynucleoside blocks 15-18 and their natural-abundance counterparts were used to assemble partially deuterated ribonucleotide-dimers (* indicates deuteration at 1'#,2',3',4'#,5',5''(2H6)): ApU* 21, GpC* 22 and partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*) 23, d(ApT*) 25, d(GpC*) 26 (* indicates deuteration at 1'#,2',2'',3',4'#,5',5''(2H7)) according to the procedure described by Földesi et al. (Tetrahedron, in press). These five partially deuterated oligonucleotides were subsequently compared with their corresponding natural-abundance counterparts by 500 MHz 1H-NMR spectroscopy to evaluate the actual NMR simplifications achieved in the non-deuterated part (1H-NMR window) as a result of specific deuterium incorporation. Detailed one-dimensional 1H-NMR (500 MHz), two-dimensional correlation spectra (DQF-COSY and TOCSY) and deuterium isotope effect on the chemical shifts of oligonucleotides have been presented.

Partially deuterated potassium dihydrogen phosphate optimized for ultra-broadband optical parametric amplification

NASA Astrophysics Data System (ADS)

Fujioka, K.; Fujimoto, Y.; Tsubakimoto, K.; Kawanaka, J.; Shoji, I.; Miyanaga, N.

2015-03-01

The refractive index of a potassium dihydrogen phosphate (KDP) crystal strongly depends on the deuteration fraction of the crystal. The wavelength dependence of the phase-matching angle in the near-infrared optical parametric process shows convex and concave characteristics for pure KDP and pure deuterated KDP (DKDP), respectively, when pumped by the second harmonic of Nd- or Yb-doped solid state lasers. Using these characteristics, ultra-broadband phase matching can be realized by optimization of the deuteration fraction. The refractive index of DKDP that was grown with a different deuteration fraction (known as partially deuterated KDP or pDKDP) was measured over a wide wavelength range of 0.4-1.5 μm by the minimum deviation method. The wavelength dispersions of the measured refractive indices were fitted using a modified Sellmeier equation, and the deuteration fraction dependence was analyzed using the Lorentz-Lorenz equation. The wavelength-dependent phase-matching angle for an arbitrary deuteration fraction was then calculated for optical parametric amplification with pumping at a wavelength of 526.5 nm. The results revealed that a refractive index database with precision of more than 2 × 10-5 was necessary for exact evaluation of the phase-matching condition. An ultra-broad gain bandwidth of up to 490 nm will be feasible when using the 68% pDKDP crystal.

Probing the Structural, Electronic, and Magnetic Properties of Ag n V (n = 1-12) Clusters.

PubMed

Xiong, Ran; Die, Dong; Xiao, Lu; Xu, Yong-Gen; Shen, Xu-Ying

2017-12-16

The structural, electronic, and magnetic properties of Ag n V (n = 1-12) clusters have been studied using density functional theory and CALYPSO structure searching method. Geometry optimizations manifest that a vanadium atom in low-energy Ag n V clusters favors the most highly coordinated location. The substitution of one V atom for an Ag atom in Ag n + 1 (n ≥ 5) cluster modifies the lowest energy structure of the host cluster. The infrared spectra, Raman spectra, and photoelectron spectra of Ag n V (n = 1-12) clusters are simulated and can be used to determine the most stable structure in the future. The relative stability, dissociation channel, and chemical activity of the ground states are analyzed through atomic averaged binding energy, dissociation energy, and energy gap. It is found that V atom can improve the stability of the host cluster, Ag 2 excepted. The most possible dissociation channels are Ag n V = Ag + Ag n - 1 V for n = 1 and 4-12 and Ag n V = Ag 2  + Ag n - 2 V for n = 2 and 3. The energy gap of Ag n V cluster with odd n is much smaller than that of Ag n + 1 cluster. Analyses of magnetic property indicate that the total magnetic moment of Ag n V cluster mostly comes from V atom and varies from 1 to 5 μ B . The charge transfer between V and Ag atoms should be responsible for the change of magnetic moment.

Site-specific polarizabilities as descriptors of metallic behavior in atomic clusters

NASA Astrophysics Data System (ADS)

Jackson, Koblar; Jellinek, Julius

The electric dipole polarizability of a cluster is a measure of its response to an applied electric field. The site specific polarizability method decomposes the total cluster polarizability into contributions from individual atoms and also allows it to be partitioned into charge transfer and electric dipole contributions. By systematically examining the trends in these quantities for several types of metal atom clusters over a wide range of cluster sizes, we find common characteristics that uniquely link the behavior of the clusters to that of the corresponding bulk metals for clusters as small as 10 atoms. We discuss these trends and compare and contrast them with results for non-metal clusters. This work was supported by the Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, U.S. Department of Energy under Grant SC0001330 (KAJ) and Contract No. DE-AC02-06CH11357 (JJ).

Synthesis of deuterium-labelled analogues of NLRP3 inflammasome inhibitor MCC950.

PubMed

Salla, Manohar; Butler, Mark S; Massey, Nicholas L; Reid, Janet C; Cooper, Matthew A; Robertson, Avril A B

2018-02-15

This study describes the syntheses of di, tetra and hexa deuterated analogues of the NOD-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome inhibitor MCC950. In di and tetra deuterated analogues, deuteriums were incorporated into the 1,2,3,5,6,7-hexahydro-s-indacene moiety, whereas in the hexa deuterated MCC950 deuteriums were incorporated into the 2-(furan-3-yl)propan-2-ol moiety. The di deuterated MCC950 analogue was synthesised from 4-amino-3,5,6,7-tetrahydro-s-indacen-1(2H)-one 5. Tetra deuterated analogues were synthesised in 10 chemical steps starting with 5-bromo-2,3-dihydro-1H-inden-1-one 9, whereas the hexa deuterated analogue was synthesised in four chemical steps starting with ethyl-3-furoate 24. All of the compounds exhibited similar activity to MCC950 (IC 50  = 8 nM). These deuterated analogues are useful as internal standards in LC-MS analyses of biological samples from in vivo studies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

Dielectric properties of ferroelectric betaine phosphite crystals with a high degree of deuteration

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Yurko, E. I.; Svinarev, F. B.; Pankova, G. A.

2015-12-01

The dielectric properties of deuterated betaine phosphite crystals with a high degree of deuteration in the region of the antiferrodistorsive (at T = T c1) and ferroelectric (at T = T c2) phase transitions have been investigated. The temperature behavior of the dielectric permittivity of betaine phosphite and deuterated betaine phosphite has been described within the framework of the Landau thermodynamic model taking into account the biquadratic coupling between the polar order parameter of the ferroelectric transition and the nonpolar order parameter of the antiferrodistorsive phase transition. It has been shown that an increase in the degree of deuteration leads to a decrease in the coupling between the order parameters. An increase in the temperature of the ferroelectric phase transition due to the deuteration of betaine phosphite is caused by an increase in the dielectric permittivity in the symmetric phase above the temperature of the antiferrodistorsive phase transition.

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

Kira, M., E-mail: mackillo.kira@physik.uni-marburg.de

Atomic Bose–Einstein condensates (BECs) can be viewed as macroscopic objects where atoms form correlated atom clusters to all orders. Therefore, the presence of a BEC makes the direct use of the cluster-expansion approach–lucrative e.g. in semiconductor quantum optics–inefficient when solving the many-body kinetics of a strongly interacting Bose. An excitation picture is introduced with a nonunitary transformation that describes the system in terms of atom clusters within the normal component alone. The nontrivial properties of this transformation are systematically studied, which yields a cluster-expansion friendly formalism for a strongly interacting Bose gas. Its connections and corrections to the standard Hartree–Fock–Bogoliubov approachmore » are discussed and the role of the order parameter and the Bogoliubov excitations are identified. The resulting interaction effects are shown to visibly modify number fluctuations of the BEC. Even when the BEC has a nearly perfect second-order coherence, the BEC number fluctuations can still resolve interaction-generated non-Poissonian fluctuations. - Highlights: • Excitation picture expresses interacting Bose gas with few atom clusters. • Semiconductor and BEC many-body investigations are connected with cluster expansion. • Quantum statistics of BEC is identified in terms of atom clusters. • BEC number fluctuations show extreme sensitivity to many-body correlations. • Cluster-expansion friendly framework is established for an interacting Bose gas.« less

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

DYNAMIC DEUTERIUM ENRICHMENT IN COMETARY WATER VIA ELEY–RIDEAL REACTIONS

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

Yao, Yunxi; Giapis, Konstantinos P., E-mail: giapis@cheme.caltech.edu

2017-01-20

The deuterium-to-hydrogen ratio (D/H) in water found in the coma of Jupiter family comet (JFC) 67P/Churyumov–Gerasimenko was reported to be (5.3 ± 0.7) × 10{sup −4}, the highest among comets and three times the value for other JFCs with an ocean-like ratio. This discrepancy suggests the diverse origins of JFCs and clouds the issue of the origin of Earth’s oceanic water. Here we demonstrate that Eley–Rideal reactions between accelerated water ions and deuterated cometary surface analogs can lead to instantaneous deuterium enrichment in water scattered from the surface. The reaction proceeds with H{sub 2}O{sup +} abstracting adsorbed D atoms, formingmore » an excited H{sub 2}DO* state, which dissociates subsequently to produce energetic HDO. Hydronium ions are also produced readily by the abstraction of H atoms, consistent with H{sub 3}O{sup +} detection and abundance in various comets. Experiments with water isotopologs and kinematic analysis on deuterated platinum surfaces confirmed the dynamic abstraction mechanism. The instantaneous fractionation process is independent of the surface temperature and may operate on the surface of cometary nuclei or dust grains, composed of deuterium-rich silicates and carbonaceous chondrites. The requisite energetic water ions have been detected in the coma of 67P in two populations. This dynamic fractionation process may temporarily increase the water D/H ratio, especially as the comet gets closer to the Sun. The magnitude of the effect depends on the water ion energy-flux and the deuterium content of the exposed cometary surfaces.« less

Structural molecular biology: Recent results from neutron diffraction

NASA Astrophysics Data System (ADS)

Timmins, Peter A.

1995-02-01

Neutron diffraction is of importance in structural biology at several different levels of resolution. In most cases the unique possibility arising from deuterium labelling or contrast variation is of fundamental importance in providing information complementary to that which can be obtained from X-ray diffraction. At high resolution, neutron crystallography of proteins allows the location of hydrogen atoms in the molecule or of the hydration water, both of which may be central to biological activity. A major difficulty in this field has been the poor signal-to-noise ratio of the data arising not only from relatively low beam intensities and small crystals but, most importantly from the incoherent background due to hydrogen atoms in the sample. Modern methods of molecular biology now offer ways of producing fully deuterated proteins by cloning in bacteria grown on fully deuterated media. At a slightly lower resolution, there are a number of systems which may be ordered in one or two dimensions. This is the case in the purple membrane where neutron diffraction with deuterium labelling has complemented high resolution electron diffraction. Finally there is a class of very large macromolecular systems which can be crystallised and have been studied by X-ray diffraction but in which part of the structure is locally disordered and usually has insufficient contrast to be seen with X-rays. In this case the use of H 2O/D 2O contrast variation allows these components to be located. Examples of this are the nucleic acid in virus structures and detergent bound to membrane proteins.

Facile Rearrangement of 3-Oxoalkyl Radicals is Evident in Low-Temperature Gas-Phase Oxidation of Ketones

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

Scheer, Adam M.; Welz, Oliver; Sasaki, Darryl Y.

The pulsed photolytic chlorine-initiated oxidation of methyl-tert-butyl ketone (MTbuK), di-tert-butyl ketone (DTbuK), and a series of partially deuterated diethyl ketones (DEK) is studied in the gas phase at 8 Torr and 550–650 K. Products are monitored as a function of reaction time, mass, and photoionization energy using multiplexed photoionization mass spectrometry with tunable synchrotron ionizing radiation. The results establish that the primary 3-oxoalkyl radicals of those ketones, formed by abstraction of a hydrogen atom from the carbon atom in γ-position relative to the carbonyl oxygen, undergo a rapid rearrangement resulting in an effective 1,2-acyl group migration, similar to that inmore » a Dowd–Beckwith ring expansion. Without this rearrangement, peroxy radicals derived from MTbuK and DTbuK cannot undergo HO2 elimination to yield a closed-shell unsaturated hydrocarbon coproduct. However, not only are these coproducts observed, but they represent the dominant oxidation channels of these ketones under the conditions of this study. For MTbuK and DTbuK, the rearrangement yields a more stable tertiary radical, which provides the thermodynamic driving force for this reaction. Even in the absence of such a driving force in the oxidation of partially deuterated DEK, the 1,2-acyl group migration is observed. Quantum chemical (CBS-QB3) calculations show the barrier for gas-phase rearrangement to be on the order of 10 kcal mol–1. The MTbuK oxidation experiments also show several minor channels, including β-scission of the initial radicals and cyclic ether formation.« less

Ce(x)O(y)⁻ (x = 2-3) + D₂O reactions: stoichiometric cluster formation from deuteroxide decomposition and anti-Arrhenius behavior.

PubMed

Felton, Jeremy A; Ray, Manisha; Waller, Sarah E; Kafader, Jared O; Jarrold, Caroline Chick

2014-10-30

Reactions between small cerium oxide cluster anions and deuterated water were monitored as a function of both water concentration and temperature in order to determine the temperature dependence of the rate constants. Sequential oxidation reactions of the Ce(x)O(y)⁻ (x = 2, 3) suboxide cluster anions were found to exhibit anti-Arrhenius behavior, with activation energies ranging from 0 to -18 kJ mol⁻¹. Direct oxidation of species up to y = x was observed, after which, -OD abstraction and D₂O addition reactions were observed. However, the stoichiometric Ce₂O₄⁻ and Ce₃O₆⁻ cluster anions also emerge in reactions between D₂O and the respective precursors, Ce₂O₃D⁻ and Ce₃O₅D₂⁻. Ce₂O₄⁻ and Ce₃O₆⁻ product intensities diminish relative to deuteroxide complex intensities with increasing temperature. The kinetics of these reactions are compared to the kinetics of the previously studied Mo(x)O(y)⁻ and W(x)O(y)⁻ reactions with water, and the possible implications for the reaction mechanisms are discussed.

Infrared Spectroscopy of Deuterated Compounds.

ERIC Educational Resources Information Center

MacCarthy, Patrick

1985-01-01

Background information, procedures used, and typical results obtained are provided for an experiment (based on the potassium bromide pressed-pellet method) involving the infrared spectroscopy of deuterated compounds. Deuteration refers to deuterium-hydrogen exchange at active hydrogen sites in the molecule. (JN)

Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

PubMed

Manzoor, Dar; Pal, Sourav

2015-06-18

Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

Does Each Atom Count in the Reactivity of Vanadia Nanoclusters?

PubMed

Zhang, Mei-Qi; Zhao, Yan-Xia; Liu, Qing-Yu; Li, Xiao-Na; He, Sheng-Gui

2017-01-11

Vanadium oxide cluster anions (V 2 O 5 ) n V x O y - (n = 1-31; x = 0, 1; and x + y ≤ 5) with different oxygen deficiencies (Δ = 2y-1-5x = 0, ± 1, and ±2) have been prepared by laser ablation and reacted to abstract hydrogen atoms from alkane molecules (n-butane) in a fast flow reactor. When the cluster size n is less than 25, the Δ = 1 series [(V 2 O 5 ) n O - clusters] that can contain atomic oxygen radical anions (O •- ) generally have much higher reactivity than the other four cluster series (Δ = -2, -1, 0, and 2), indicating that each atom counts in the hydrogen-atom abstraction (HAA) reactivity. Unexpectedly, all of the five cluster series have similar HAA reactivity when the cluster size is greater than 25. The critical dimension of vanadia particles separating the cluster behavior (each atom counts) from the bulk behavior (each atom contributes a little part) is thus about 1.6 nm (∼V 50 O 125 ). The strong electron-phonon coupling of the vanadia particles has been proposed to create the O •- radicals (V 5+ = O 2- + heat → V 4+ -O •- ) for the n > 25 clusters with Δ = -2, -1, 0, and 2. Such a mechanism is supported by a comparative study with the scandium system [(Sc 2 O 3 ) n Sc x O y - (n = 1-29; x = 0, 1; and x + y ≤ 4)] for which the Δ = 1 series [(Sc 2 O 3 ) n O - clusters] always have much higher HAA reactivity than the other cluster series.

Composition formulas of binary eutectics

PubMed Central

Ma, Y. P.; Dong, D. D.; Dong, C.; Luo, L. J.; Wang, Q.; Qiang, J. B.; Wang, Y. M.

2015-01-01

The present paper addresses the long-standing composition puzzle of eutectic points by introducing a new structural tool for the description of short-range-order structural unit, the cluster-plus-glue-atom model. In this model, any structure is dissociated into a 1st-neighbor cluster and a few glue atoms between the clusters, expressed by a cluster formula [cluster]gluex. This model is applied here to establish the structural model for eutectic liquids, assuming that a eutectic liquid consist of two subunits issued from the relevant eutectic phases, each being expressed by the cluster formula for ideal metallic glasses, i.e., [cluster](glue atom)1 or 3. A structural unit is then composed of two clusters from the relevant eutectic phases plus 2, 4, or 6 glue atoms. Such a dual cluster formulism is well validated in all boron-containing (except those located by the extreme phase diagram ends) and in some commonly-encountered binary eutectics, within accuracies below 1 at.%. The dual cluster formulas vary extensively and are rarely identical even for eutectics of close compositions. They are generally formed with two distinctly different cluster types, with special cluster matching rules such as cuboctahedron plus capped trigonal prism and rhombidodecahedron plus octahedral antiprism. PMID:26658618

Geometric, electronic, and bonding properties of AuNM (N = 1-7, M = Ni, Pd, Pt) clusters.

PubMed

Yuan, D W; Wang, Yang; Zeng, Zhi

2005-03-15

Employing first-principles methods, based on density functional theory, we report the ground state geometric and electronic structures of gold clusters doped with platinum group atoms, Au(N)M (N = 1-7, M = Ni, Pd, Pt). The stability and electronic properties of Ni-doped gold clusters are similar to that of pure gold clusters with an enhancement of bond strength. Due to the strong d-d or s-d interplay between impurities and gold atoms originating in the relativistic effects and unique properties of dopant delocalized s-electrons in Pd- and Pt-doped gold clusters, the dopant atoms markedly change the geometric and electronic properties of gold clusters, and stronger bond energies are found in Pt-doped clusters. The Mulliken populations analysis of impurities and detailed decompositions of bond energies as well as a variety of density of states of the most stable dopant gold clusters are given to understand the different effects of individual dopant atom on bonding and electronic properties of dopant gold clusters. From the electronic properties of dopant gold clusters, the different chemical reactivity toward O(2), CO, or NO molecule is predicted in transition metal-doped gold clusters compared to pure gold clusters.

Structural and electronic properties of Aun-xPtx (n = 2-14; x ⩽ n) clusters: The density functional theory investigation

NASA Astrophysics Data System (ADS)

Yuan, H. K.; Kuang, A. L.; Tian, C. L.; Chen, H.

2014-03-01

The structural evolutions and electronic properties of bimetallic Aun-xPtx (n = 2-14; x ⩽ n) clusters are investigated by using the density functional theory (DFT) with the generalized gradient approximation (GGA). The monatomic doping Aun-1Pt clusters are emphasized and compared with the corresponding pristine Aun clusters. The results reveal that the planar configurations are favored for both Aun-1Pt and Aun clusters with size up to n = 13, and the former often employ the substitution patterns based on the structures of the latter. The most stable clusters are Au6 and Au6Pt, which adopt regular planar triangle (D3h) and hexagon-ring (D6h) structures and can be regarded as the preferential building units in designing large clusters. For Pt-rich bimetallic clusters, their structures can be obtained from the substitution of Pt atoms by Au atoms from the Ptn structures, where Pt atoms assemble together and occupy the center yet Au atoms prefer the apex positions showing a segregation effect. With respect to pristine Au clusters, AunPt clusters exhibit somewhat weaker and less pronounced odd-even oscillations in the highest occupied and lowest unoccupied molecular-orbital gaps (HOMO-LUMO gap), electron affinity (EA), and ionization potential (IP) due to the partially released electron pairing effect. The analyses of electronic structure indicate that Pt atoms in AuPt clusters would delocalize their one 6s and one 5d electrons to contribute the electronic shell closure. The sp-d hybridizations as well as the d-d interactions between the host Au and dopant Pt atoms result in the enhanced stabilities of AuPt clusters.

Experimental study of fusion neutron and proton yields produced by petawatt-laser-irradiated D₂-³He or CD₄-³He clustering gases.

PubMed

Bang, W; Barbui, M; Bonasera, A; Quevedo, H J; Dyer, G; Bernstein, A C; Hagel, K; Schmidt, K; Gaul, E; Donovan, M E; Consoli, F; De Angelis, R; Andreoli, P; Barbarino, M; Kimura, S; Mazzocco, M; Natowitz, J B; Ditmire, T

2013-09-01

We report on experiments in which the Texas Petawatt laser irradiated a mixture of deuterium or deuterated methane clusters and helium-3 gas, generating three types of nuclear fusion reactions: D(d,^{3}He)n, D(d,t)p, and ^{3}He(d,p)^{4}He. We measured the yields of fusion neutrons and protons from these reactions and found them to agree with yields based on a simple cylindrical plasma model using known cross sections and measured plasma parameters. Within our measurement errors, the fusion products were isotropically distributed. Plasma temperatures, important for the cross sections, were determined by two independent methods: (1) deuterium ion time of flight and (2) utilizing the ratio of neutron yield to proton yield from D(d,^{3}He)n and ^{3}He(d,p)^{4}He reactions, respectively. This experiment produced the highest ion temperature ever achieved with laser-irradiated deuterium clusters.

Deuterated drugs; where are we now?

PubMed Central

Timmins, Graham S

2015-01-01

Introduction Deuterated versions of existing drugs can exhibit improved pharmacokinetic or toxicological properties due the stronger deuterium-carbon bond modifying their metabolism. There is great interest in the current state of development of this approach. Areas Covered This review covers recent US patent applications and prosecutions in this area, that are based upon beneficial modifications in metabolism of deuterated versions of existing drugs. The current state of 35 U.S.C. §103 ‘obviousness’ rejections, are emphasized as is the development of strategies to overcome such rejections. Current trials and market considerations are also discussed. Expert Opinion Deuterated drugs collectively are worth at least a billion dollars. It would seem that the likelihood of obviousness rejections is increasing in this area. However, careful elucidation of metabolic outcomes from deuteration that would not be anticipated from the prior art, and are instead unexpected and unobvious, has enabled allowance. Showing drug deuteration alters pharmacokinetics by mechanisms not currently part of the prior art surrounding, deuterated drugs has also been successful. Development of these and other strategies, combined with developing the extensive base of issued patents will enable the field to remain commercially attractive for some time. PMID:25069517

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Relaxation channels of multi-photon excited xenon clusters

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

Serdobintsev, P. Yu.; Melnikov, A. S.; Department of Physics, St. Petersburg State University, Saint Petersburg 198904

2015-09-21

The relaxation processes of the xenon clusters subjected to multi-photon excitation by laser radiation with quantum energies significantly lower than the thresholds of excitation of atoms and ionization of clusters were studied. Results obtained by means of the photoelectron spectroscopy method showed that desorption processes of excited atoms play a significant role in the decay of two-photon excited xenon clusters. A number of excited states of xenon atoms formed during this process were discovered and identified.

Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms

NASA Astrophysics Data System (ADS)

Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan

2017-10-01

The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.

[The use of the deuterated internal standard for morphine quantitation for the purpose of doping control by gas chromatography with mass-selective detection].

PubMed

Savel'eva, N B; Bykovskaia, N Iu; Dikunets, M A; Bolotov, S L; Rodchenkov, G M

2010-01-01

The objective of this study was to demonstrate the possibility to use deuterated compounds as internal standards for the quantitative analysis of morphine by gas chromatography with mass-selective detection for the purpose of doping control. The paper is focused on the problems associated with the use of deuterated morphine-D3 as the internal standard. Quantitative characteristics of the calibration dependence thus documented are presented along with uncertainty values obtained in the measurements with the use of deuterated morphine-D6. An approach to the assessment of method bias associated with the application of morphine-D6 as the deuterated internal standard is described.

Hydrogen isotope exchanges between water and methanol in interstellar ices

NASA Astrophysics Data System (ADS)

Faure, A.; Faure, M.; Theulé, P.; Quirico, E.; Schmitt, B.

2015-12-01

The deuterium fractionation of gas-phase molecules in hot cores is believed to reflect the composition of interstellar ices. The deuteration of methanol is a major puzzle, however, because the isotopologue ratio [CH2DOH]/[CH3OD], which is predicted to be equal to 3 by standard grain chemistry models, is much larger (~20) in low-mass hot corinos and significantly lower (~1) in high-mass hot cores. This dichotomy in methanol deuteration between low-mass and massive protostars is currently not understood. In this study, we report a simplified rate equation model of the deuterium chemistry occurring in the icy mantles of interstellar grains. We apply this model to the chemistry of hot corinos and hot cores, with IRAS 16293-2422 and the Orion KL Compact Ridge as prototypes, respectively. The chemistry is based on a statistical initial deuteration at low temperature followed by a warm-up phase during which thermal hydrogen/deuterium (H/D) exchanges occur between water and methanol. The exchange kinetics is incorporated using laboratory data. The [CH2DOH]/[CH3OD] ratio is found to scale inversely with the D/H ratio of water, owing to the H/D exchange equilibrium between the hydroxyl (-OH) functional groups of methanol and water. Our model is able to reproduce the observed [CH2DOH]/[CH3OD] ratios provided that the primitive fractionation of water ice [HDO]/[H2O] is ~2% in IRAS 16293-2422 and ~0.6% in Orion KL. We conclude that the molecular D/H ratios measured in hot cores may not be representative of the original mantles because molecules with exchangeable deuterium atoms can equilibrate with water ice during the warm-up phase.

International Journal of Quantum Chemistry. Quantum Chemistry Symposium Number 26: Proceedings of the International Symposium on Atomic, Molecular, and Condensed Matter Theory and Computational Methods Held in St. Augustine, Florida on 14-21 March 1992

DTIC Science & Technology

1993-02-01

Spectrum The vibrational IR spectra of formaldeh.de and its deuterated species have been measured by a number of groups and analyzed in several studies ... studies [23-28]. The order of the frontier (r) orbitals, a textbook example for simple group theory arguments, is determined by the high symmetry (Dy...simplexes will give a structure with octahedral symmetr\\ since the subgroup of the Coxeter group which leaves one component of a four -vector invariant

Study of water diffusion on single-supported bilayer lipid membranes by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Bai, M.; Miskowiec, A.; Hansen, F. Y.; Taub, H.; Jenkins, T.; Tyagi, M.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.; Wang, S.-K.

2012-05-01

High-energy-resolution quasielastic neutron scattering has been used to elucidate the diffusion of water molecules in proximity to single bilayer lipid membranes supported on a silicon substrate. By varying sample temperature, level of hydration, and deuteration, we identify three different types of diffusive water motion: bulk-like, confined, and bound. The motion of bulk-like and confined water molecules is fast compared to those bound to the lipid head groups (7-10 H2O molecules per lipid), which move on the same nanosecond time scale as H atoms within the lipid molecules.

Qualitative and quantitative analysis of mixtures of compounds containing both hydrogen and deuterium

NASA Technical Reports Server (NTRS)

Crespi, H. L.; Harkness, L.; Katz, J. J.; Norman, G.; Saur, W.

1969-01-01

Method allows qualitative and quantitative analysis of mixtures of partially deuterated compounds. Nuclear magnetic resonance spectroscopy determines location and amount of deuterium in organic compounds but not fully deuterated compounds. Mass spectroscopy can detect fully deuterated species but not the location.

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.

Atomic cluster collisions

NASA Astrophysics Data System (ADS)

Korol, Andrey V.; Solov'yov, Andrey

2013-01-01

Atomic cluster collisions are a field of rapidly emerging research interest by both experimentalists and theorists. The international symposium on atomic cluster collisions (ISSAC) is the premier forum to present cutting-edge research in this field. It was established in 2003 and the most recent conference was held in Berlin, Germany in July of 2011. This Topical Issue presents original research results from some of the participants, who attended this conference. This issues specifically focuses on two research areas, namely Clusters and Fullerenes in External Fields and Nanoscale Insights in Radiation Biodamage.

Interaction of intense laser pulses with hydrogen atomic clusters

NASA Astrophysics Data System (ADS)

Du, Hong-Chuan; Wang, Hui-Qiao; Liu, Zuo-Ye; Sun, Shao-Hua; Li, Lu; Ma, Ling-Ling; Hu, Bi-Tao

2010-03-01

The interaction between intense femtosecond laser pulses and hydrogen atomic clusters is studied by a simplified Coulomb explosion model. The dependences of average proton kinetic energy on cluster size, pulse duration, laser intensity and wavelength are studied respectively. The calculated results indicate that the irradiation of a femtosecond laser of longer wavelength on hydrogen atomic clusters may be a simple, economical way to produce highly kinetic hydrogen ions. The phenomenon suggests that the irradiation of femtosecond laser of longer wavelength on deuterium atomic clusters may be easier than that of shorter wavelength to drive nuclear fusion reactions. The product of the laser intensity and the squared laser wavelength needed to make proton energy saturated as a function of the squared cluster radius is also investigated. The proton energy distribution calculated is also shown and compared with the experimental data. Our results are in agreement with the experimental results fairly well.

The stability of vacancy clusters and their effect on helium behaviors in 3C-SiC

NASA Astrophysics Data System (ADS)

Sun, Jingjing; Li, B. S.; You, Yu-Wei; Hou, Jie; Xu, Yichun; Liu, C. S.; Fang, Q. F.; Wang, Z. G.

2018-05-01

We have carried out systematical ab initio calculations to study the stability of vacancy clusters and their effect on helium behaviors in 3C-SiC. It is found that the formation energies of vacancy clusters containing only carbon vacancies are the lowest although the vacancies are not closest to each other, while the binding energies of vacancy clusters composed of both silicon and carbon vacancies in the closest neighbors to each other are the highest. Vacancy clusters can provide with free space for helium atoms to aggregate, while interstitial sites are not favorable for helium atoms to accumulate. The binding energies of vacancy clusters with helium atoms increase almost linearly with the ratio of helium to vacancy, n/m. The binding strength of vacancy cluster having the participation of the silicon vacancy with helium is relatively stronger than that without silicon vacancy. The vacancy clusters with more vacancies can trap helium atoms more tightly. With the presence of vacancy clusters in the material, the diffusivity of helium will be significantly reduced. Moreover, the three-dimension electron density is calculated to analyze the interplay of vacancy clusters with helium.

Electronic levels and charge distribution near the interface of nickel

NASA Technical Reports Server (NTRS)

Waber, J. T.

1982-01-01

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

Energetic proton generation from intense Coulomb explosion of large-size ethane clusters

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

Li Song; Zhou Zili; Tian Ye

An experimental investigation is performed on the interaction of intense femtosecond laser pulses at the intensity of 6 Multiplication-Sign 10{sup 17} W/cm{sup 2} (55 fs, 160 mJ at 800 nm) with ethane cluster (C{sub 2}H{sub 6}){sub N} jets prepared under the backing pressure of 30 bars at room temperature (298 K). The experiment results indicate the generation of energetic protons, whose average and maximum kinetic energies are 12.2 and 138.1 keV, respectively, by Coulomb explosion of (C{sub 2}H{sub 6}){sub N} clusters. (C{sub 2}H{sub 6}){sub N} clusters of 5 nm in radius are generated in the experiment, which are 1.7 timesmore » larger than that of (CH{sub 4}){sub N} clusters prepared in the same conditions. Empirical estimation suggests that (C{sub 2}H{sub 6}){sub N} clusters with radius of about 9.6 nm can be prepared at 80-bars backing pressure at 308 K. While (C{sub 2}H{sub 6}){sub N} clusters of so large size are irradiated by sufficiently intense laser pulses, the average energy of protons will be increased up to 50 keV. It is inferred that such large-size deuterated ethane clusters (C{sub 2}D{sub 6}){sub N} will favor more efficient neutron generation due to the significant increase of the D-D nuclear reaction cross section in laser-driven cluster nuclear fusion.« less

Point defect induced segregation of alloying solutes in α-Fe

NASA Astrophysics Data System (ADS)

You, Yu-Wei; Zhang, Yange; Li, Xiangyan; Xu, Yichun; Liu, C. S.; Chen, J. L.; Luo, G.-N.

2016-10-01

Segregation of alloying solute toward clusters and precipitates can result in hardening and embrittlement of ferritic and ferritic/martensitic steels in aging nuclear power plants. Thus, it is essential to study the segregation of solute in α-Fe. In this study, the segregation of eight kinds of alloying solutes (Al, Si, P, S, Ga, Ge, As, Se) in defect-free system and at vacancy, divacancy, and self-interstitial atom in α-Fe has been systematically studied by first-principles calculations. We find that it is energetically favorable for multiple solute S or Se atoms to segregate in defect-free system to form solute clusters, whereas it is very difficult for the other solute atoms to form the similar clusters. With the presence of vacancy and divacancy, the segregation of all the solutes are significantly promoted to form vacancy-solute and divacancy-solute clusters. The divacancy-solute cluster is more stable than the vacancy-solute cluster. The most-stable self-interstitial atom 〈110〉 dumbbell is also found to tightly bind with multiple solute atoms. The 〈110〉-S is even more stable than divacancy-S cluster. Meanwhile, the law of mass action is employed to predict the concentration evolution of vacancy-Si, vacancy-P, and vacancy-S clusters versus temperature and vacancy concentration.

About the atomic structures of icosahedral quasicrystals

NASA Astrophysics Data System (ADS)

Quiquandon, Marianne; Gratias, Denis

2014-01-01

This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

Self-organized formation of quantum dots of a material on a substrate

DOEpatents

Zhang, Zhenyu; Wendelken, John F.; Chang, Ming-Che; Pai, Woei Wu

2001-01-01

Systems and methods are described for fabricating arrays of quantum dots. A method for making a quantum dot device, includes: forming clusters of atoms on a substrate; and charging the clusters of atoms such that the clusters of atoms repel one another. The systems and methods provide advantages because the quantum dots can be ordered with regard to spacing and/or size.

Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

Electrodeposition of Isolated Platinum Atoms and Clusters on Bismuth-Characterization and Electrocatalysis.

PubMed

Zhou, Min; Dick, Jeffrey E; Bard, Allen J

2017-12-06

We describe a method for the electrodeposition of an isolated single Pt atom or small cluster, up to 9 atoms, on a bismuth ultramicroelectrode (UME). This deposition was immediately followed by electrochemical characterization via the hydrogen evolution reaction (HER) that occurs readily on the electrodeposited Pt but not on Bi. The observed voltammetric current plateau, even for a single atom, which behaves as an electrode, allows the estimation of deposit size. Pt was plated from solutions of femtomolar PtCl 6 2- , which allowed precise control of the arrival of ions and thus the plating rate on the Bi UME, to one ion every few seconds. This allowed the atom-by-atom fabrication of isolated platinum deposits, ranging from single atoms to 9-atom clusters. The limiting currents in voltammetry gave the size and number of atoms of the clusters. Given the stochasticity of the plating process, we show that the number of atoms plated over a given time (10 and 20 s) follows a Poisson distribution. Taking the potential at a certain current density as a measure of the relative rate of the HER, we found that the potential shifted positively as the size increased, with single atoms showing the largest overpotentials compared to bulk Pt.

Probing the structural and electronic properties of cationic rubidium-gold clusters: [AunRb]+ (n = 1-10)

NASA Astrophysics Data System (ADS)

Zhao, Ya-Ru; Zhang, Hai-Rong; Qian, Yu; Duan, Xu-Chao; Hu, Yan-Fei

2016-03-01

Density functional theory has been applied to study the geometric structures, relative stabilities, and electronic properties of cationic [AunRb]+ and Aun + 1+ (n = 1-10) clusters. For the lowest energy structures of [AunRb]+ clusters, the planar to three-dimensional transformation is found to occur at cluster size n = 4 and the Rb atoms prefer being located at the most highly coordinated position. The trends of the averaged atomic binding energies, fragmentation energies, second-order difference of energies, and energy gaps show pronounced even-odd alternations. It indicated that the clusters containing odd number of atoms maintain greater stability than the clusters in the vicinity. In particular, the [Au6Rb]+ clusters are the most stable isomer for [AunRb]+ clusters in the region of n = 1-10. The charges in [AunRb]+ clusters transfer from the Rb atoms to Aun host. Density of states revealed that the Au-5d, Au-5p, and Rb-4p orbitals hardly participated in bonding. In addition, it is found that the most favourable channel of the [AunRb]+ clusters is Rb+ cation ejection. The electronic localisation function (ELF) analysis of the [AunRb]+ clusters shown that strong interactions are not revealed in this study.

Interaction of scandium and titanium atoms with a carbon surface containing five- and seven-membered rings

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

Krasnov, P. O., E-mail: kpo1980@gmail.com; Eliseeva, N. S.; Kuzubov, A. A., E-mail: alex_xx@rambler.ru

2012-01-15

The use of carbon nanotubes coated by atoms of transition metals to store molecular hydrogen is associated with the problem of the aggregation of these atoms, which leads to the formation of metal clusters. The quantum-chemical simulation of cluster models of the carbon surface of a graphene type with scandium and titanium atoms has been performed. It has been shown that the presence of five- and seven-membered rings, in addition to six-membered rings, in these structures makes it possible to strongly suppress the processes of the migration of metal atoms over the surface, preventing their clustering.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

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

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

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

Hurtubise, R.J.

Interaction models were developed for moisture effects on room-temperature fluorescence (RTF) and room-temperature phosphorescence (RTP) of compounds adsorbed on filter paper. The models described both dynamic and matrix quenching and also related the Young modulus of filter paper to quenching of phosphor on moist filter paper. Photophysical parameters for lumiphors in solution and on solid matrices were compared. Results showed that for some compounds, solid-matrix luminescence has greater analytical potential than solution luminescence. Also, the solid-matrix systems into one of two categories depending on how the intersystem crossing rate constants change with temperature. The first study was carried out onmore » effects of heavy atom on solid-matrix luminescence. With some heavy atoms, maximum solid-matrix phosphorescence quantum yield was obtained at room temperature, and there was no need to use low temperature to obtain a strong phosphorescence signal. By studying solid-matrix luminescence properties of phosphors adsorbed on sodium acetate and deuterated sodium acetate, an interaction model was developed for p-aminobenzoic acid anion adsorbed on sodium acetate. It was shown that the energy-gap law was applicable to solid-matrix luminescence. Also, deuterated phenanthrene and undeuterated phenanthrene were used to study nonradiative transition of excited triplet state of adsorbed phosphors. Heat capacities of several solid matrices were obtained vs temperature and related to vibrational coupling of solid matrix with phosphor. Photophysical study was performed on the hydrolysis products of benzo(a)pyrene-DNA adducts. Also, an analytical method was developed for tetrols in human lung fractions. Work was initiated on the formation of room temperature glasses with glucose and trehalose. Also, work has begun for the development of an oxygen sensor by measuring the RTP quenching of triphenylene on filter paper.« less

Theoretical study of the kinetics of reactions of the monohalogenated methanes with atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-04-01

Ab initio calculations at the G2 level were used in a theoretical description of the kinetics and mechanism of the hydrogen abstraction reactions from fluoro-, chloro- and bromomethane by chlorine atoms. The profiles of the potential energy surfaces show that mechanism of the reactions under investigation is complex and consists of two - in the case of CH3F+Cl - and of three elementary steps for CH3Cl+Cl and CH3Br+Cl. The heights of the energy barrier related to the H-abstraction are of 8-10 kJ mol(-1), the lowest value corresponds to CH3Cl+Cl and the highest one to CH3F+Cl. The rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The kinetic equations derived in this study[Formula: see text]and[Formula: see text]allow a description of the kinetics of the reactions under investigation in the temperature range of 200-3000 K. The kinetics of reactions of the entirely deuterated reactants were also included in the kinetic analysis. Results of ab initio calculations show that D-abstraction process is related with the energy barrier of 5 kJ mol(-1) higher than the H-abstraction from the corresponding non-deuterated reactant molecule. The derived analytical equations for the reactions, CD3X+Cl, CH2X+HCl and CD2X+DCl (X = F, Cl and Br) are a substantial supplement of the kinetic data necessary for the description and modeling of the processes of importance in the atmospheric chemistry.

Method for the production of atomic ion species from plasma ion sources

DOEpatents

Spence, David; Lykke, Keith

1998-01-01

A technique to enhance the yield of atomic ion species (H.sup.+, D.sup.+, O.sup.+, N.sup.+, etc.) from plasma ion sources. The technique involves the addition of catalyzing agents to the ion discharge. Effective catalysts include H.sub.2 O, D.sub.2 O, O.sub.2, and SF.sub.6, among others, with the most effective being water (H.sub.2 O) and deuterated water (D.sub.2 O). This technique has been developed at Argonne National Laboratory, where microwave generated plasmas have produced ion beams comprised of close to 100% purity protons (H.sup.+) and close to 100% purity deuterons (D.sup.+). The technique also increases the total yield of protons and deuterons by converting unwanted ion species, namely, H.sub.2.sup.+,H.sub.3.sup.+ and D.sub.2.sup.+, D.sub.3.sup.+, into the desired ion species, H.sup.+ and D.sup.+, respectively.

Periodic disorder along ramie cellulose microfibrils.

PubMed

Nishiyama, Yoshiharu; Kim, Ung-Jin; Kim, Dae-Young; Katsumata, Kyoko S; May, Roland P; Langan, Paul

2003-01-01

Small angle neutron scattering studies have been carried out on cellulose fibers from ramie and Populus maximowicii (cotton wood). Labile hydrogen atoms were replaced by deuterium atoms, in water-accessible disordered regions of the fibers, to increase the neutron scattering contrast between the disordered and crystalline regions. A meridional Bragg reflection, corresponding to a longitudinal periodicity of 150 nm, was observed when scattering collected from hydrogenated and deuterated dry ramie fibers was subtracted. No Bragg reflection was observed with the cotton wood fibers, probably because of lower orientation of the microfibrils in the cell wall. The ramie fibers were then subjected to electron microscopy, acid hydrolysis, gel permeation chromatography, and viscosity studies. The leveling off degree of polymerization (LODP) of the hydrolyzed samples matched exactly the periodicity observed in the diffraction studies. The weight loss related to the LODP was only about 1.5%, and thus, the microfibrils can be considered to have 4-5 disordered residues every 300 residues.

Method for the production of atomic ion species from plasma ion sources

DOEpatents

Spence, D.; Lykke, K.

1998-08-04

A technique to enhance the yield of atomic ion species (H{sup +}, D{sup +}, O{sup +}, N{sup +}, etc.) from plasma ion sources. The technique involves the addition of catalyzing agents to the ion discharge. Effective catalysts include H{sub 2}O, D{sub 2}O, O{sub 2}, and SF{sub 6}, among others, with the most effective being water (H{sub 2}O) and deuterated water (D{sub 2}O). This technique has been developed at Argonne National Laboratory, where microwave generated plasmas have produced ion beams comprised of close to 100% purity protons (H{sup +}) and close to 100% purity deuterons (D{sup +}). The technique also increases the total yield of protons and deuterons by converting unwanted ion species, namely, H{sub 2}{sup +}, H{sub 3}{sup +} and D{sub 2}{sup +}, D{sub 3}{sup +}, into the desired ion species, H{sup +} and D{sup +}, respectively. 4 figs.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework.

PubMed

Kim, In Soo; Li, Zhanyong; Zheng, Jian; Platero-Prats, Ana E; Mavrandonakis, Andreas; Pellizzeri, Steven; Ferrandon, Magali; Vjunov, Aleksei; Gallington, Leighanne C; Webber, Thomas E; Vermeulen, Nicolaas A; Penn, R Lee; Getman, Rachel B; Cramer, Christopher J; Chapman, Karena W; Camaioni, Donald M; Fulton, John L; Lercher, Johannes A; Farha, Omar K; Hupp, Joseph T; Martinson, Alex B F

2018-01-22

Single atoms and few-atom clusters of platinum are uniformly installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 °C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and X-ray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novel catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Wang, Lin -Lin; Johnson, Duane D.; Tringides, Michael C.

Density functional theory is used to study structural energetics of Pb vacancy cluster formation on C 60/Pb/Si(111) to explain the unusually fast and error-free transformations between the “Devil's Staircase” (DS) phases on the Pb/Si(111) wetting layer at low temperature (~110K). The formation energies of vacancy clusters are calculated in C 60/Pb/Si(111) as Pb atoms are progressively ejected from the initial dense Pb wetting layer. Vacancy clusters larger than five Pb atoms are found to be stable with seven being the most stable, while vacancy clusters smaller than five are highly unstable, which agrees well with the observed ejection rate ofmore » ~5 Pb atoms per C 60. Furthermore, the high energy cost (~0.8 eV) for the small vacancy clusters to form indicates convincingly that the unusually fast transformation observed experimentally between the DS phases, upon C 60 adsorption at low temperature, cannot be the result of single-atom random walk diffusion but of correlated multi-atom processes.« less

Use of deuterated water as a conservative artificial ground water tracer

USGS Publications Warehouse

Becker, M.W.; Coplen, T.B.

2001-01-01

Conservative tracers are necessary to obtain groundwater transport velocities at the field scale. Deuterated water is an effective tracer for this purpose due to its similarity to water, chemical stability, non-reactivity, ease of handling and sampling, relatively neutral buoyancy, and reasonable price. Reliable detection limits of 0.1 mg deuterium/L may be obtained in field tests. A field example is presented in which deuterated water, bromide, and pentafluorobenzoic acid are used as groundwater tracers. Deuterated water appeared to be transported conservatively, producing almost identical breakthrough curves as that of other soluble tracers. ?? Springer-Verlag 2001.

Ligand-protected gold clusters: the structure, synthesis and applications

NASA Astrophysics Data System (ADS)

Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

2015-11-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

Catalysis applications of size-selected cluster deposition

DOE PAGES

Vajda, Stefan; White, Michael G.

2015-10-23

In this Perspective, we review recent studies of size-selected cluster deposition for catalysis applications performed at the U.S. DOE National Laboratories, with emphasis on work at Argonne National Laboratory (ANL) and Brookhaven National Laboratory (BNL). The focus is on the preparation of model supported catalysts in which the number of atoms in the deposited clusters is precisely controlled using a combination of gas-phase cluster ion sources, mass spectrometry, and soft-landing techniques. This approach is particularly effective for investigations of small nanoclusters, 0.5-2 nm (<200 atoms), where the rapid evolution of the atomic and electronic structure makes it essential to havemore » precise control over cluster size. Cluster deposition allows for independent control of cluster size, coverage, and stoichiometry (e.g., the metal-to-oxygen ratio in an oxide cluster) and can be used to deposit on any substrate without constraints of nucleation and growth. Examples are presented for metal, metal oxide, and metal sulfide cluster deposition on a variety of supports (metals, oxides, carbon/diamond) where the reactivity, cluster-support electronic interactions, and cluster stability and morphology are investigated. Both UHV and in situ/operando studies are presented that also make use of surface-sensitive X-ray characterization tools from synchrotron radiation facilities. Novel applications of cluster deposition to electrochemistry and batteries are also presented. This review also highlights the application of modern ab initio electronic structure calculations (density functional theory), which can essentially model the exact experimental system used in the laboratory (i.e., cluster and support) to provide insight on atomic and electronic structure, reaction energetics, and mechanisms. As amply demonstrated in this review, the powerful combination of atomically precise cluster deposition and theory is able to address fundamental aspects of size-effects, cluster-support interactions, and reaction mechanisms of cluster materials that are central to how catalysts function. Lastly, the insight gained from such studies can be used to further the development of novel nanostructured catalysts with high activity and selectivity.« less

LIF excitation spectra for S 0 → S 1 transition of deuterated anthranilic acid COOD, ND 2 in supersonic-jet expansion

NASA Astrophysics Data System (ADS)

Kolek, Przemysław; Leśniewski, Sebastian; Andrzejak, Marcin; Góra, Maciej; Cias, Pawel; Weģrzynowicz, Adam; Najbar, Jan

2010-12-01

Laser induced fluorescence (LIF) excitation spectrum for the S 0 → S 1 transition of anthranilic acid molecules deuterated in the substituent groups (COOD, ND 2) was investigated. Analysis of the LIF spectrum allowed for the assignment of the six most prominent fundamental in-plane modes of frequencies up to ca. 850 cm. The experimental results show good correlation with the frequency changes upon deuteration computed with CIS (CI-Singles) and TD-DFT for the S 1 state. Deuteration induced red-shifts of the identified fundamental bands are used for examination of the alternative assignments proposed in earlier studies. Potential energy distributions (PED) and overlaps of the in-plane normal modes with frequencies below 850 cm indicate that the correspondence of the respective vibrations of the deuterated and non-deuterated molecule is very good. A blue-shift of the 00 transition due to the isotopic substitution, is equal to 47 cm. This relatively large value is caused primarily by a significant decrease of the N-H stretching frequency associated with the increase of strength of the intramolecular hydrogen bond upon the electronic excitation. The deuteration shift of the 00 band was interpreted in terms of the differences of the zero point energy (ZPE) between the S 0 and S 1 electronic states, computed with DFT and TD-DFT methods, respectively.

Endohedral beryllium atoms in germanium clusters with eight and fewer vertices: how small can a cluster be and still encapsulate a central atom?

PubMed

Uţă, M M; King, R B

2012-05-31

Structures of the beryllium-centered germanium clusters Be@Ge(n)(z) (n = 8, 7, 6; z = -4, -2, 0, +2) have been investigated by density functional theory to provide some insight regarding the smallest metal cluster that can encapsulate an interstitial atom. The lowest energy structures of the eight-vertex Be@Ge(8)(z) clusters (z = -4, -2, 0, +2) all have the Be atom at the center of a closed polyhedron, namely, a D(4d) square antiprism for Be@Ge(8)(4-), a D(2d) bisdisphenoid for Be@Ge(8)(2-), an ideal O(h) cube for Be@Ge(8), and a C(2v) distorted cube for Be@Ge(8)(2+). The Be-centered cubic structures predicted for Be@Ge(8) and Be@Ge(8)(2+) differ from the previously predicted lowest energy structures for the isoelectronic Ge(8)(2-) and Ge(8). This appears to be related to the larger internal volume of the cube relative to other closed eight-vertex polyhedra. The lowest energy structures for the smaller seven- and six-vertex clusters Be@Ge(n)(z) (n = 7, 6; z = -4, -2, 0, +2) no longer have the Be atom at the center of a closed Ge(n) polyhedron. Instead, either the Ge(n) polyhedron has opened up to provide a larger volume for the Be atom or the Be atom has migrated to the surface of the polyhedron. However, higher energy structures are found in which the Be atom is located at the center of a Ge(n) (n = 7, 6) polyhedron. Examples of such structures are a centered C(2v) capped trigonal prismatic structure for Be@Ge(7)(2-), a centered D(5h) pentagonal bipyramidal structure for Be@Ge(7), a centered D(3h) trigonal prismatic structure for Be@Ge(6)(4-), and a centered octahedral structure for Be@Ge(6). Cluster buildup reactions of the type Be@Ge(n)(z) + Ge(2) → Be@Ge(n+2)(z) (n = 6, 8; z = -4, -2, 0, +2) are all predicted to be highly exothermic. This suggests that interstitial clusters having an endohedral atom inside a bare post transition element polyhedron with eight or fewer vertices are less than the optimum size. This is consistent with the experimental observation of several types of 10-vertex polyhedral bare post transition element clusters with interstitial atoms but the failure to observe such clusters with external polyhedra having eight or fewer vertices.

High Intensity Femtosecond XUV Pulse Interactions with Atomic Clusters: Final Report

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

Ditmire, Todd

We propose to expand our recent studies on the interactions of intense extreme ultraviolet (XUV) femtosecond pulses with atomic and molecular clusters. The work described follows directly from work performed under BES support for the past grant period. During this period we upgraded the THOR laser at UT Austin by replacing the regenerative amplifier with optical parametric amplification (OPA) using BBO crystals. This increased the contrast of the laser, the total laser energy to ~1.2 J , and decreased the pulse width to below 30 fs. We built a new all reflective XUV harmonic beam line into expanded lab space. This enabled an increase influence by a factor ofmore » 25 and an increase in the intensity by a factor of 50. The goal of the program proposed in this renewal is to extend this class of experiments to available higher XUV intensity and a greater range of wavelengths. In particular we plan to perform experiments to confirm our hypothesis about the origin of the high charge states in these exploding clusters, an effect which we ascribe to plasma continuum lowering (ionization potential depression) in a cluster nano-­plasma. To do this we will perform experiments in which XUV pulses of carefully chosen wavelength irradiate clusters composed of only low-Z atoms and clusters with a mixture of this low-­Z atom with higher Z atoms. The latter clusters will exhibit higher electron densities and will serve to lower the ionization potential further than in the clusters composed only of low Z atoms. This should have a significant effect on the charge states produced in the exploding cluster. We will also explore the transition of explosions in these XUV irradiated clusters from hydrodynamic expansion to Coulomb explosion. The work proposed here will explore clusters of a wider range of constituents, including clusters from solids. Experiments on clusters from solids will be enabled by development we performed during the past grant period in which we constructed and tested a cluster generator based on the Laser Ablation of Microparticles (LAM) method.« less

Addition of a thallium vertex to empty and centered nine-atom deltahedral zintl ions of germanium and tin.

PubMed

Rios, Daniel; Gillett-Kunnath, Miriam M; Taylor, Jacob D; Oliver, Allen G; Sevov, Slavi C

2011-03-21

Nickel atoms were inserted into nine-atom deltahedral Zintl ions of E(9)(4-) (E = Ge, Sn) via reactions with Ni(cod)(2) (cod = cyclooctadiene), and [Ni@Sn(9)](3-) was structurally characterized. Both the empty and the Ni-centered clusters react with TlCp (Cp = cyclopentadienyl anion) and add a thallium vertex to form the deltahedral ten-atom closo-species [E(9)Tl](3-) and [Ni@E(9)Tl](3-), respectively. The structures of [Ge(9)Tl](3-) and [Ni@Sn(9)Tl](3-) showed that, as expected, the geometry of the ten-atom clusters is that of a bicapped square antiprism where the Tl-atom occupies one of the two capping vertices. This illustrates that centering a nine-atom cluster with a nickel atom does not change its reactivity toward TlCp. All compounds were characterized by electrospray mass spectrometry.

First-principles melting of gallium clusters down to nine atoms: structural and electronic contributions to melting.

PubMed

Steenbergen, Krista G; Gaston, Nicola

2013-10-07

First-principles Born-Oppenheimer molecular dynamics simulations of small gallium clusters, including parallel tempering, probe the distinction between cluster and molecule in the size range of 7-12 atoms. In contrast to the larger sizes, dynamic measures of structural change at finite temperature demonstrate that Ga7 and Ga8 do not melt, suggesting a size limit to melting in gallium exists at 9 atoms. Analysis of electronic structure further supports this size limit, additionally demonstrating that a covalent nature cannot be identified for clusters larger than the gallium dimer. Ga9, Ga10 and Ga11 melt at greater-than-bulk temperatures, with no evident covalent character. As Ga12 represents the first small gallium cluster to melt at a lower-than-bulk temperature, we examine the structural properties of each cluster at finite temperature in order to probe both the origins of greater-than-bulk melting, as well as the significant differences in melting temperatures induced by a single atom addition. Size-sensitive melting temperatures can be explained by both energetic and entropic differences between the solid and liquid phases for each cluster. We show that the lower-than-bulk melting temperature of the 12-atom cluster can be attributed to persistent pair bonding, reminiscent of the pairing observed in α-gallium. This result supports the attribution of greater-than-bulk melting in gallium clusters to the anomalously low melting temperature of the bulk, due to its dimeric structure.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Effects of biradical deuteration on the performance of DNP: Towards better performing polarizing agents

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

Perras, Frédéric A.; Reinig, Regina R.; Slowing, Igor I.

2015-11-20

We study the effects of the deuteration of biradical polarizing agents on the efficiency of dynamic nuclear polarization (DNP) via the cross-effect. To this end, we synthesized a series of bTbK and TOTAPol biradicals with systematically increased deuterium substitution. The deuteration increases the radicals' relaxation time, thus contributing to a higher saturation factor and larger DNP enhancement, and reduces the pool of protons within the so-called spin diffusion barrier. Notably, we report that full or partial deuteration leads to improved DNP enhancement factors in standard samples, but also slows down the build-up of hyperpolarization. Improvements in DNP enhancements factors ofmore » up to 70% and time savings of up to 38% are obtained upon full deuteration. As a result, it is foreseen that this approach may be applied to other DNP polarizing agents thus enabling further sensitivity improvements.« less

Neutron interrogation systems using pyroelectric crystals and methods of preparation thereof

DOEpatents

Tang, Vincent; Meyer, Glenn A.; Falabella, Steven; Guethlein, Gary; Rusnak, Brian; Sampayan, Stephen; Spadaccini, Christopher M.; Wang, Li-Fang; Harris, John; Morse, Jeff

2017-08-01

According to one embodiment, an apparatus includes a pyroelectric crystal, a deuterated or tritiated target, an ion source, and a common support coupled to the pyroelectric crystal, the deuterated or tritiated target, and the ion source. In another embodiment, a method includes producing a voltage of negative polarity on a surface of a deuterated or tritiated target in response to a temperature change of a pyroelectric crystal, pulsing a deuterium ion source to produce a deuterium ion beam, accelerating the deuterium ion beam to the deuterated or tritiated target to produce a neutron beam, and directing the ion beam onto the deuterated or tritiated target to make neutrons using a voltage of the pyroelectric crystal and/or an HGI surrounding the pyroelectric crystal. The directionality of the neutron beam is controlled by changing the accelerating voltage of the system. Other apparatuses and methods are presented as well.

Melting phenomena: effect of composition for 55-atom Ag-Pd bimetallic clusters.

PubMed

Cheng, Daojian; Wang, Wenchuan; Huang, Shiping

2008-05-14

Understanding the composition effect on the melting processes of bimetallic clusters is important for their applications. Here, we report the relationship between the melting point and the metal composition for the 55-atom icosahedral Ag-Pd bimetallic clusters by canonical Monte Carlo simulations, using the second-moment approximation of the tight-binding potentials (TB-SMA) for the metal-metal interactions. Abnormal melting phenomena for the systems of interest are found. Our simulation results reveal that the dependence of the melting point on the composition is not a monotonic change, but experiences three different stages. The melting temperatures of the Ag-Pd bimetallic clusters increase monotonically with the concentration of the Ag atoms first. Then, they reach a plateau presenting almost a constant value. Finally, they decrease sharply at a specific composition. The main reason for this change can be explained in terms of the relative stability of the Ag-Pd bimetallic clusters at different compositions. The results suggest that the more stable the cluster, the higher the melting point for the 55-atom icosahedral Ag-Pd bimetallic clusters at different compositions.

Correlation between the resistivity and the atomic clusters in liquid Cu-Sn alloys

NASA Astrophysics Data System (ADS)

Jia, Peng; Zhang, Jinyang; Hu, Xun; Li, Cancan; Zhao, Degang; Teng, XinYing; Yang, Cheng

2018-05-01

The liquid structure of CuxSn100-x (x = 0, 10, 20, 33, 40, 50, 60, 75, 80 and 100) alloys with atom percentage were investigated with resistivity and viscosity methods. It can be found from the resistivity data that the liquid Cu75Sn25 and Cu80Sn20 alloys had a negative temperature coefficient of resistivity (TCR), and liquid Cu75Sn25 alloy had a minimum value of -9.24 μΩ cm K-1. While the rest of liquid Cu-Sn alloys had a positive TCR. The results indicated that the Cu75Sn25 atomic clusters existed in Cu-Sn alloys. In addition, the method of calculating the percentage of Cu75Sn25 atomic clusters was established on the basis of resistivity theory and the law of conservation of mass. The Cu75Sn25 alloy had a maximum volume of the atomic clusters and a highest activation energy. The results further proved the existence of Cu75Sn25 atomic clusters. Furthermore, the correlation between the liquid structure and the resistivity was established. These results provide a useful reference for the investigation of liquid structure via the sensitive physical properties to the liquid structure.

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Autoionization following nanoplasma formation in atomic and molecular clusters

NASA Astrophysics Data System (ADS)

Schütte, Bernd; Lahl, Jan; Oelze, Tim; Krikunova, Maria; Vrakking, Marc J. J.; Rouzée, Arnaud

2016-05-01

Nanoplasmas resulting from the ionization of nano-scale particles by intense laser pulses are typically described by quasiclassical models, where electron emission is understood to take place via thermal processes. Recently, we discovered that, following the interaction of intense near-infrared (NIR) laser pulses with molecular oxygen clusters, electron emission from nanoplasmas can also occur from atomic bound states via autoionization [Schütte et al., Phys. Rev. Lett. 114, 123002 (2015)]. Here we extend these studies and demonstrate that the formation and decay of doubly-excited atoms and ions is a very common phenomenon in nanoplasmas. We report on the observation of autoionization involving spin-orbit excited states in molecular oxygen and carbon dioxide clusters as well as in atomic krypton and xenon clusters ionized by intense NIR pulses, for which we find clear bound-state signatures in the electron kinetic energy spectra. By applying terahertz (THz) streaking, we show that the observed autoionization processes take place on a picosecond to nanosecond timescale after the interaction of the NIR laser pulse with the clusters. Contribution to the Topical Issue "Atomic Cluster Collisions (7th International Symposium)", edited by Gerardo Delgado Barrio, Andrey Solov'Yov, Pablo Villarreal, Rita Prosmiti.

Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.

PubMed

Mannix, Andrew J; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D; Alducin, Diego; Myers, Benjamin D; Liu, Xiaolong; Fisher, Brandon L; Santiago, Ulises; Guest, Jeffrey R; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R; Hersam, Mark C; Guisinger, Nathan P

2015-12-18

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. Copyright © 2015, American Association for the Advancement of Science.

Evaluation of Solute Clusters Associated with Bake-Hardening Response in Isothermal Aged Al-Mg-Si Alloys Using a Three-Dimensional Atom Probe

NASA Astrophysics Data System (ADS)

Aruga, Yasuhiro; Kozuka, Masaya; Takaki, Yasuo; Sato, Tatsuo

2014-12-01

Temporal changes in the number density, size distribution, and chemical composition of clusters formed during natural aging at room temperature and pre-aging at 363 K (90 °C) in an Al-0.62Mg-0.93Si (mass pct) alloy were evaluated using atom probe tomography. More than 10 million atoms were examined in the cluster analysis, in which about 1000 clusters were obtained for each material after various aging treatments. The statistically proven records show that both number density and the average radius of clusters in pre-aged materials are larger than in naturally aged materials. It was revealed that the fraction of clusters with a low Mg/Si ratio after natural aging for a short time is higher than with other aging treatments, regardless of cluster size. This indicates that Si-rich clusters form more easily after short-period natural aging, and that Mg atoms can diffuse into the clusters or possibly form another type of Mg-Si cluster after prolonged natural aging. The formation of large clusters with a uniform Mg/Si ratio is encouraged by pre-aging. It can be concluded that an increase of small clusters with various Mg/Si ratios does not promote the bake-hardening (BH) response, whereas large clusters with a uniform Mg/Si ratio play an important role in hardening during the BH treatment at 443 K (170 °C).

Growth of Ni nanoclusters on irradiated graphene: a molecular dynamics study.

PubMed

Valencia, F J; Hernandez-Vazquez, E E; Bringa, E M; Moran-Lopez, J L; Rogan, J; Gonzalez, R I; Munoz, F

2018-04-23

We studied the soft landing of Ni atoms on a previously damaged graphene sheet by means of molecular dynamics simulations. We found a monotonic decrease of the cluster frequency as a function of its size, but few big clusters comprise an appreciable fraction of the total number of Ni atoms. The aggregation of Ni atoms is also modeled by means of a simple phenomenological model. The results are in clear contrast with the case of hard or energetic landing of metal atoms, where there is a tendency to form mono-disperse metal clusters. This behavior is attributed to the high diffusion of unattached Ni atoms, together with vacancies acting as capture centers. The findings of this work show that a simple study of the energetics of the system is not enough in the soft landing regime, where it is unavoidable to also consider the growth process of metal clusters.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, James F.; Furuya, Frederic R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

The interaction between atomic displacement cascades and tilt symmetrical grain boundaries in α-zirconium

NASA Astrophysics Data System (ADS)

Kapustin, P.; Svetukhin, V.; Tikhonchev, M.

2017-06-01

The atomic displacement cascade simulations near symmetric tilt grain boundaries (GBs) in hexagonal close packed-Zirconium were considered in this paper. Further defect structure analysis was conducted. Four symmetrical tilt GBs -∑14?, ∑14? with the axis of rotation [0 0 0 1] and ∑32?, ∑32? with the axis of rotation ? - were considered. The molecular dynamics method was used for atomic displacement cascades' simulation. A tendency of the point defects produced in the cascade to accumulate near the GB plane, which was an obstacle to the spread of the cascade, was discovered. The results of the point defects' clustering produced in the cascade were obtained. The clusters of both types were represented mainly by single point defects. At the same time, vacancies formed clusters of a large size (more than 20 vacancies per cluster), while self-interstitial atom clusters were small-sized.

Sequential desorption energy of hydrogen from nickel clusters

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

Deepika,; Kumar, Rakesh, E-mail: rakesh@iitrpr.ac.in; R, Kamal Raj.

2015-06-24

We report reversible Hydrogen adsorption on Nickel clusters, which act as a catalyst for solid state storage of Hydrogen on a substrate. First-principles technique is employed to investigate the maximum number of chemically adsorbed Hydrogen molecules on Nickel cluster. We observe a maximum of four Hydrogen molecules adsorbed per Nickel atom, but the average Hydrogen molecules adsorbed per Nickel atom decrease with cluster size. The dissociative chemisorption energy per Hydrogen molecule and sequential desorption energy per Hydrogen atom on Nickel cluster is found to decrease with number of adsorbed Hydrogen molecules, which on optimization may help in economical storage andmore » regeneration of Hydrogen as a clean energy carrier.« less

Endo-Fullerene and Doped Diamond Nanocrystallite Based Models of Qubits for Solid-State Quantum Computers

NASA Technical Reports Server (NTRS)

Park, Seongjun; Srivastava, Deepak; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

Models of encapsulated 1/2 nuclear spin H-1 and P-31 atoms in fullerene and diamond nanocrystallite, respectively, are proposed and examined with ab-initio local density functional method for possible applications as single quantum bits (qubits) in solid-state quantum computers. A H-1 atom encapsulated in a fully deuterated fullerene, C(sub 20)D(sub 20), forms the first model system and ab-initio calculation shows that H-1 atom is stable in atomic state at the center of the fullerene with a barrier of about 1 eV to escape. A P-31 atom positioned at the center of a diamond nanocrystallite is the second model system, and 3 1P atom is found to be stable at the substitutional site relative to interstitial sites by 15 eV, Vacancy formation energy is 6 eV in diamond so that substitutional P-31 atom will be stable against diffusion during the formation mechanisms within the nanocrystallite. The coupling between the nuclear spin and weakly bound (valance) donor electron coupling in both systems is found to be suitable for single qubit applications, where as the spatial distributions of (valance) donor electron wave functions are found to be preferentially spread along certain lattice directions facilitating two or more qubit applications. The feasibility of the fabrication pathways for both model solid-state qubit systems within practical quantum computers is discussed with in the context of our proposed solid-state qubits.

Terahertz Spectroscopy and Global Analysis of the Rotational Spectrum of Bis-Deuterated Amidogen Radical Nd_{2}

NASA Astrophysics Data System (ADS)

Melosso, Mattia; Degli Esposti, Claudia; Tamassia, Filippo; Canè, Elisabetta; Dore, Luca

2017-11-01

The deuteration mechanism of molecules in the interstellar medium (ISM) is still being debated. Observations of deuterium-bearing species in several astronomical sources represent a powerful tool to improve our understanding of the interstellar chemistry. In this scenario, the doubly-deuterated form of the amidogen radical could be a target of detection in space.

Effects of deuteration of the methyl and phenyl hydrogens on the rotational spectrum of anisole-water

NASA Astrophysics Data System (ADS)

Giuliano, Barbara M.; Melandri, Sonia; Caminati, Walther

2017-07-01

The role of non-covalent interactions in determining the structure of the 1:1 anisole-water molecular complex has been investigated by the analysis of the rotational spectra of the complex formed by the C6H5OCD3 and C6D5OCH3 deuterated species of anisole recorded with pulsed jet Fourier transform microwave spectroscopy. The deuteration of the methyl and phenyl hydrogens does not affect the structure and the internal dynamics of the complex, differently from the deuteration of the water moiety, which leads to large isotopic effects (Giuliano et al., 2005).

Effects of deuteration on the metabolism of halogenated anesthetics in the rat

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

McCarty, L.P.; Malek, R.S.; Larsen, E.R.

1979-08-01

The authors studied the effects of substituting deuterium for hydrogen in several volatile anesthetics on their metabolism in the Fischer rat. Substitution of deuterium in the ethyl portion of methoxyflurane increased the metabolic production of fluoride ion by 19 percent when administered at a concentration of 0.05%. Total replacement of hydrogen by deuterium resulted in a 29% decrease in the amount of fluoride produced, while deuteration of only the methoxyl group produced a 33% decrease in fluoride produced. Deuteration of halothane resulted in a 15 or 26% decrease in serum bromide at 0.75% or 1.0%, respectively. Deuteration in the ethylmore » portions of enflurane and two experimental agents, CF2HOCF2CFBrH and CF2HOCF2CCl2H resulted in 65, 76, and 29% decreases in urinary fluoride, respectively. Anesthesia with deuterated chloroform at a concentration of 0.36% produced a 35% decrease in serum glutamic pyruvic transaminase (SGPT). It is concluded that deuteration of volatile anesthetics changes their metabolism, in most cases producing decreases in metabolism. This effect may lessen the organ toxicity believed to occur with some of these anesthetics.« less

The astrochemistry of H+3

NASA Astrophysics Data System (ADS)

Herbst, E.

2000-09-01

The reactions of the molecular ion H3+ are pivotal to the chemistry of dense interstellar clouds. Produced by the cosmic-ray ionizati on of molecular hydrogen, H3+ reacts with a variety of a toms and molecules to produce species that are precursors to many of the detect ed molecules in dense clouds. For example, the reaction of H3+ with atomic O leads, eventually, to the production of water, while the re action with HD leads to the production of a wide variety of deuterated isotopom ers. In this article, the chemistry of H3+ and the produc ts derived from it are discussed in the larger context of interstellar chemistr y.

Structural, electronic, and magnetic properties of Y(n)O (n=2-14) clusters: Density functional study.

PubMed

Yang, Zhi; Xiong, Shi-Jie

2008-09-28

The geometries stability, electronic properties, and magnetism of Y(n)O clusters up to n=14 are systematically studied with density functional theory. In the lowest-energy structures of Y(n)O clusters, the equilibrium site of the oxygen atom gradually moves from an outer site of the cluster, via a surface site, and finally, to an interior site as the number of the Y atoms increases from 2 to 14. Starting from n=12, the O atom falls into the center of the cluster with the Y atoms forming the outer frame. The results show that clusters with n=2, 4, 8, and 12 are more stable than their respective neighbors, and that the total magnetic moments of Y(n)O clusters are all quite small except Y(12)O cluster. The lowest-energy structure of Y(12)O cluster is a perfect icosahedron with a large magnetic moment 6mu(B). In addition, we find that the total magnetic moments are quenched for n=2, 6, and 8 due to the closed-shell electronic configuration. The calculated ionization potentials and electron affinities are in good agreement with the experimental results, which imply that the present theoretical treatments are satisfactory.

Barrierless growth of precursor-free, ultrafast laser-fragmented noble metal nanoparticles by colloidal atom clusters - A kinetic in situ study.

PubMed

Jendrzej, Sandra; Gökce, Bilal; Amendola, Vincenzo; Barcikowski, Stephan

2016-02-01

Unintended post-synthesis growth of noble metal colloids caused by excess amounts of reactants or highly reactive atom clusters represents a fundamental problem in colloidal chemistry, affecting product stability or purity. Hence, quantified kinetics could allow defining nanoparticle size determination in dependence of the time. Here, we investigate in situ the growth kinetics of ps pulsed laser-fragmented platinum nanoparticles in presence of naked atom clusters in water without any influence of reducing agents or surfactants. The nanoparticle growth is investigated for platinum covering a time scale of minutes to 50days after nanoparticle generation, it is also supplemented by results obtained from gold and palladium. Since a minimum atom cluster concentration is exceeded, a significant growth is determined by time resolved UV/Vis spectroscopy, analytical disc centrifugation, zeta potential measurement and transmission electron microscopy. We suggest a decrease of atom cluster concentration over time, since nanoparticles grow at the expense of atom clusters. The growth mechanism during early phase (<1day) of laser-synthesized colloid is kinetically modeled by rapid barrierless coalescence. The prolonged slow nanoparticle growth is kinetically modeled by a combination of coalescence and Lifshitz-Slyozov-Wagner kinetic for Ostwald ripening, validated experimentally by the temperature dependence of Pt nanoparticle size and growth quenching by Iodide anions. Copyright © 2015. Published by Elsevier Inc.

Deuterated-xylene (xylene-d10; EJ301D): A new, improved deuterated liquid scintillator for neutron energy measurements without time-of-flight

NASA Astrophysics Data System (ADS)

Becchetti, F. D.; Raymond, R. S.; Torres-Isea, R. O.; Di Fulvio, A.; Clarke, S. D.; Pozzi, S. A.; Febbraro, M.

2016-06-01

In conjunction with Eljen Technology, Inc. (Sweetwater,TX) we have designed, constructed, and evaluated a 3 in. ×3 in. deuterated-xylene organic liquid scintillator (C8D10; EJ301D) as a fast neutron detector. Similar to deuterated benzene (C6D6; NE230, BC537, and EJ315) this scintillator can provide good pulse-shape discrimination between neutrons and gamma rays, has good timing characteristics, and can provide a light spectrum with peaks corresponding to discrete neutron energy groups up to ca. 20 MeV. Unlike benzene-based detectors, deuterated xylene is less volatile, less toxic, is not known to be carcinogenic, has a higher flashpoint, and hence is much safer for many applications. In addition EJ301D can provide slightly more light output and better PSD than deuterated-benzene scintillators. We show that, as with deuterated-benzene scintillators, the light-response spectra can be unfolded to provide useable neutron energy spectra without need for time-of-flight (ToF). An array of these detectors arranged at many angles close to a reaction target can be much more effective (×10 to ×100 or more) than an array of long-path ToF detectors which must utilize a narrowly-bunched and pulse-selected beam. As we demonstrate using a small Van de Graaff accelerator, measurements can thus be performed when a bunched and pulse-selected beam (as needed for time-of-flight) is not available.

C 60 -induced Devil's Staircase transformation on a Pb/Si(111) wetting layer

DOE PAGES

Wang, Lin -Lin; Johnson, Duane D.; Tringides, Michael C.

2015-12-03

Density functional theory is used to study structural energetics of Pb vacancy cluster formation on C 60/Pb/Si(111) to explain the unusually fast and error-free transformations between the “Devil's Staircase” (DS) phases on the Pb/Si(111) wetting layer at low temperature (~110K). The formation energies of vacancy clusters are calculated in C 60/Pb/Si(111) as Pb atoms are progressively ejected from the initial dense Pb wetting layer. Vacancy clusters larger than five Pb atoms are found to be stable with seven being the most stable, while vacancy clusters smaller than five are highly unstable, which agrees well with the observed ejection rate ofmore » ~5 Pb atoms per C 60. Furthermore, the high energy cost (~0.8 eV) for the small vacancy clusters to form indicates convincingly that the unusually fast transformation observed experimentally between the DS phases, upon C 60 adsorption at low temperature, cannot be the result of single-atom random walk diffusion but of correlated multi-atom processes.« less

Theoretical studies on structural, magnetic, and spintronic characteristics of sandwiched Eu(n)COT(n+1) (n = 1-4) clusters.

PubMed

Zhang, Xiuyun; Ng, Man-Fai; Wang, Yanbiao; Wang, Jinlan; Yang, Shuo-Wang

2009-09-22

Europium (Eu)-cyclootetatrene (COT = C(8)H(8)) multidecker clusters (Eu(n)COT(n+1), n = 1-4) are studied by relativistic density functional theory calculations. These clusters are found to be thermodynamically stable with freely rotatable COT rings, and their total magnetic moments (MMs) increase linearly along with the number of Eu atoms. Each Eu atom contributes about 7 mu(B) to the cluster. Meanwhile, the internal COT rings have little MM contribution while the external COT rings have about 1 mu(B) MM aligned in opposite direction to that of the Eu atoms. The total MM of the Eu(n)COT(n+1) clusters can thus be generalized as 7n - 2 mu(B) where n is the number of Eu atoms. Besides, the ground states of these clusters are ferromagnetic and energetically competitive with the antiferromagnetic states, meaning that their spin states are very unstable, especially for larger clusters. More importantly, we uncover an interesting bonding characteristic of these clusters in which the interior ionic structure is capped by two hybrid covalent-ionic terminals. We suggest that such a characteristic makes the Eu(n)COT(n+1) clusters extremely stable. Finally, we reveal that for the positively charged clusters, the hybrid covalent-ionic terminals will tip further toward the interior part of the clusters to form deeper covalent-ionic caps. In contrast, the negatively charged clusters turn to pure ionic structures.

Carbonyl reduction in the biosynthesis of a male sex pheromone secreted by the grape borer Xylotrechus pyrrhoderus.

PubMed

Iwabuchi, Kikuo; Arakawa, Maki; Kiyota, Ryutaro; Hoshino, Keita; Ando, Tetsu

2014-10-01

Males of the cerambycid beetle Xylotrechus pyrrhoderus release a mixture of (S)-2-hydroxy-3-octanone [(S)-1] and (2S,3S)-2,3-octanediol [(2S,3S)-2] as a sex pheromone that attracts conspecific females. The chemical structures of these pheromone components include a common motif and are assumed to be biosynthetically related. Here, we show that deuterated (S)-1, applied on the cuticle of a pronotal pheromone gland, was converted into (2S,3S)-2, that included deuterium atoms, but a reverse conversion did not take place. These results reveal a carbonyl reductase to be active in the pheromone gland, and that the ketol is a biosynthetic precursor of the diol. Males did not produce (R)-1; however, deuterated (R)-1 was converted into (2R,3R)-2, indicating an attack of the enzyme from the opposite side of the hydroxyl group at the 2-position. Furthermore, to understand the substrate specificity of the enzyme, racemates of 2-hydroxy-3-hexanone and 2-hydroxy-3-decanone were synthesized and applied to the gland. Their conversion into the corresponding diols suggests that the enzyme reduces the carbonyl group at the 3-position, regardless of the chain length.

THERMAL TRANSITIONS IN NORMAL AND DEUTERATED RAT-TAIL TENDON, HUMAN SKIN, AND TUNA-FISH SKIN

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

Rigby, B.J.

1962-07-30

The transition temperature and shrinkage temperature of collogens were determined in normal and deuterated rat-tail tendon, human skin, and tuna-fish skin. Increases were observed in the deuterated samples. Results, obtained with solid collagen, are compared with those obtained with collagen in solution. It is concluded that hydrogen bonds are involved in both reactions. (C.H.)

Helium cluster isolation spectroscopy

NASA Astrophysics Data System (ADS)

Higgins, John Paul

Clusters of helium, each containing ~103- 104 atoms, are produced in a molecular beam and are doped with alkali metal atoms (Li, Na, and K) and large organic molecules. Electronic spectroscopy in the visible and UV regions of the spectrum is carried out on the dopant species. Since large helium clusters are liquid and attain an equilibrium internal temperature of 0.4 K, they interact weakly with atoms or molecules absorbed on their surface or resident inside the cluster. The spectra that are obtained are characterized by small frequency shifts from the positions of the gas phase transitions, narrow lines, and cold vibrational temperatures. Alkali atoms aggregate on the helium cluster surface to form dimers and trimers. The spectra of singlet alkali dimers exhibit the presence of elementary excitations in the superfluid helium cluster matrix. It is found that preparation of the alkali molecules on the surface of helium clusters leads to the preferential formation of high-spin, van der Waals bound, triplet dimers and quartet trimers. Four bound-bound and two bound-free transitions are observed in the triplet manifold of the alkali dimers. The quartet trimers serve as an ideal system for the study of a simple unimolecular reaction in the cold helium cluster environment. Analysis of the lowest quartet state provides valuable insight into three-body forces in a van der Waals trimer. The wide range of atomic and molecular systems studied in this thesis constitutes a preliminary step in the development of helium cluster isolation spectroscopy, a hybrid technique combining the advantages of high resolution spectroscopy with the synthetic, low temperature environment of matrices.

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

Protein dynamics as seen by (quasi) elastic neutron scattering.

PubMed

Magazù, S; Mezei, F; Falus, P; Farago, B; Mamontov, E; Russina, M; Migliardo, F

2017-01-01

Elastic and quasielastic neutron scattering studies proved to be efficient probes of the atomic mean square displacement (MSD), a fundamental parameter for the characterization of the motion of individual atoms in proteins and its evolution with temperature and compositional environment. We present a technical overview of the different types of experimental situations and the information quasi-elastic neutron scattering approaches can make available. In particular, MSD can crucially depend on the time scale over which the averaging (building of the "mean") takes place, being defined by the instrumental resolution. Due to their high neutron scattering cross section, hydrogen atoms can be particularly sensitively observed with little interference by the other atoms in the sample. A few examples, including new data, are presented for illustration. The incoherent character of neutron scattering on hydrogen atoms restricts the information obtained to the self-correlations in the motion of individual atoms, simplifying at the same time the data analysis. On the other hand, the (often overlooked) exploration of the averaging time dependent character of MSD is crucial for unambiguous interpretation and can provide a wealth of information on micro- and nanoscale atomic motion in proteins. By properly exploiting the broad range capabilities of (quasi)elastic neutron scattering techniques to deliver time dependent characterization of atomic displacements, they offer a sensitive, direct and simple to interpret approach to exploration of the functional activity of hydrogen atoms in proteins. Partial deuteration can add most valuable selectivity by groups of hydrogen atoms. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo". Copyright © 2016 Elsevier B.V. All rights reserved.

A CROSSED MOLECULAR BEAM, LOW-TEMPERATURE KINETICS, AND THEORETICAL INVESTIGATION OF THE REACTION OF THE CYANO RADICAL (CN) WITH 1,3-BUTADIENE (C{sub 4}H{sub 6}). A ROUTE TO COMPLEX NITROGEN-BEARING MOLECULES IN LOW-TEMPERATURE EXTRATERRESTRIAL ENVIRONMENTS

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

Morales, Sebastien B.; Bennett, Christopher J.; Le Picard, Sebastien D.

2011-11-20

We present a joint crossed molecular beam and kinetics investigation combined with electronic structure and statistical calculations on the reaction of the ground-state cyano radical, CN(X {sup 2}{Sigma}{sup +}), with the 1,3-butadiene molecule, H{sub 2}CCHCHCH{sub 2}(X {sup 1} A{sub g}), and its partially deuterated counterparts, H{sub 2}CCDCDCH{sub 2}(X {sup 1} A{sub g}) and D{sub 2}CCHCHCD{sub 2}(X {sup 1} A{sub g}). The crossed beam studies indicate that the reaction proceeds via a long-lived C{sub 5}H{sub 6}N complex, yielding C{sub 5}H{sub 5}N isomer(s) plus atomic hydrogen under single collision conditions as the nascent product(s). Experiments with the partially deuterated 1,3-butadienes indicate thatmore » the atomic hydrogen loss originates from one of the terminal carbon atoms of 1,3-butadiene. A combination of the experimental data with electronic structure calculations suggests that the thermodynamically less favorable 1-cyano-1,3-butadiene isomer represents the dominant reaction product; possible minor contributions of less than a few percent from the aromatic pyridine molecule might be feasible. Low-temperature kinetics studies demonstrate that the overall reaction is very fast from room temperature down to 23 K with rate coefficients close to the gas kinetic limit. This finding, combined with theoretical calculations, indicates that the reaction proceeds on an entrance barrier-less potential energy surface (PES). This combined experimental and theoretical approach represents an important step toward a systematic understanding of the formation of complex, nitrogen-bearing molecules-here on the C{sub 5}H{sub 6}N PES-in low-temperature extraterrestrial environments. These results are compared to the reaction dynamics of D1-ethynyl radicals (C{sub 2}D; X {sup 2}{Sigma}{sup +}) with 1,3-butadiene accessing the isoelectronic C{sub 6}H{sub 7} surface as tackled earlier in our laboratories.« less

Effect of charge and composition on the structural fluxionality and stability of nine atom tin-bismuth Zintl analogues.

PubMed

Gupta, Ujjwal; Reber, Arthur C; Clayborne, Penee A; Melko, Joshua J; Khanna, Shiv N; Castleman, A W

2008-12-01

Synergistic studies of bismuth doped tin clusters combining photoelectron spectra with first principles theoretical investigations establish that highly charged Zintl ions, observed in the condensed phase, can be stabilized as isolated gas phase clusters through atomic substitution that preserves the overall electron count but reduces the net charge and thereby avoids instability because of coulomb repulsion. Mass spectrometry studies reveal that Sn(8)Bi(-), Sn(7)Bi(2)(-), and Sn(6)Bi(3)(-) exhibit higher abundances than neighboring species, and photoelectron spectroscopy show that all of these heteroatomic gas phase Zintl analogues (GPZAs) have high adiabatic electron detachment energies. Sn(6)Bi(3)(-) is found to be a particularly stable cluster, having a large highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap. Theoretical calculations demonstrate that the Sn(6)Bi(3)(-) cluster is isoelectronic with the well know Sn(9)(-4) Zintl ion; however, the fluxionality reported for Sn(9)(-4) is suppressed by substituting Sn atoms with Bi atoms. Thus, while the electronic stability of the clusters is dominated by electron count, the size and position of the atoms affects the dynamics of the cluster as well. Substitution with Bi enlarges the cage compared with Sn(9)(-4) making it favorable for endohedral doping, findings which suggest that these cages may find use for building blocks of cluster assembled materials.

Probing cluster surface morphology by cryo spectroscopy of N2 on cationic nickel clusters

NASA Astrophysics Data System (ADS)

Dillinger, Sebastian; Mohrbach, Jennifer; Niedner-Schatteburg, Gereon

2017-11-01

We present the cryogenic (26 K) IR spectra of selected [Nin(N2)m]+ (n = 5-20, m = 1 - mmax), which strongly reveal n- and m-dependent features in the N2 stretching region, in conjunction with density functional theory modeling of some of these findings. The observed spectral features allow us to refine the kinetic classification [cf. J. Mohrbach, S. Dillinger, and G. Niedner-Schatteburg, J. Chem. Phys. 147, 184304 (2017)] and to define four classes of structure related surface adsorption behavior: Class (1) of Ni6+, Ni13+, and Ni19+ are highly symmetrical clusters with all smooth surfaces of equally coordinated Ni atoms that entertain stepwise N2 adsorption up to stoichiometric N2:Nisurface saturation. Class (2) of Ni12+ and Ni18+ are highly symmetrical clusters minus one. Their relaxed smooth surfaces reorganize by enhanced N2 uptake toward some low coordinated Ni surface atoms with double N2 occupation. Class (3) of Ni5+ and Ni7+ through Ni11+ are small clusters of rough surfaces with low coordinated Ni surface atoms, and some reveal semi-internal Ni atoms of high next-neighbor coordination. Surface reorganization upon N2 uptake turns rough into rough surface by Ni atom migration and turns octahedral based structures into pentagonal bipyramidal structures. Class (4) of Ni14+ through Ni17+ and Ni20+ are large clusters with rough and smooth surface areas. They possess smooth icosahedral surfaces with some proximate capping atom(s) on one hemisphere of the icosahedron with the other one largely unaffected.

THE DEUTERIUM ISOTOPE RATE EFFECT IN FREE RADICAL REACTIONS OF t-CARBON DEUTERATED DDT AND ITS ANALOGS

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

Dachauer, A.C.

1962-01-01

DDT and several of its analogs were synthesized with deuterium in the t- carbon position so that any chemical reaction involving this site in the molecule would then be subject to the deuterium isotope rate effect. Lithium aluminum deuteride, used as the source of the deuterium, was employed to reduce trichloromethyl p-chlorophenyl ketone, trichloromethyl p-bromophenyl ketone, and trichloromethyl p-methoxyphenyl ketone to the corresponding alcohols. The alcohols were then condensed with chlorobenzene, bromobenzene, and anisole respectively to form 1,1,1-trichloro2,2-bis(p-chloro-phenyl)ethane-2-d (d-DDT), 1,1,1-trichloro-2,2-bis (p-bromophenyl)ethane-2-d (d-DBrDT), and 1,1, 1-trichloro- 2,2-bis (p-methoxyphenyl)ethane (d-methoxychlor). The deuterated and non- deuterated insecticides were identical in physical appearance andmore » melting points. Infrared spectra showed sigrificant differences; in particular, each deuterated compound had a distinctive band at ca 10.5 mu , missing in the spectra of the non-deuterated insecticides. NMR analysis confirmed the tertiary position of the deuterium and gave proof of high isotopic purity, each insecticide being 98% deuterated in the desired site. The isotope rate effect was first studied in the reaction of DDT, methoxychlor, and their deuterated analogs with alcoholic sodium- hydroxide. The base catalyzed dehydrohalogenation showed an isotope rate effect, k/sub H//k/sub D/, of the order of 5.4 for DDT and 8 for methoxychlor. The results were considered to be of a magnitude sufficient for the isotope rate effect to be manifested in the in vivo studies. The insecticides and their deuterated analogs were tested for toxicity on houseflies. The results showed that d-DDT and d-DBrDT were more toxic than their non-deuterated counterparts by a factor of ca 1.5 while d-methoxychlor showed a toxicity equal to methoxychlor. The results are explained on the basis of the detoxication process in the insects. In vitro studies showed that DDT-dehydrochlorinase, an enzyme capable of detoxifying DDT, manifested the isotope rate effect. It appeared, therefore, that in the detoxication process, the deuterated insecticide reacted more slowly, and though the initial dose given to the insect was less than that of the non- deuterated insecticide, the amount reaching the susceptible site in the insect was the same. The data support the view that at least one mode of resistance to DDT is chemical in nature and that the tertiary carbon-hydrogen group is involved. The data also indicated that susceptible houseflies contain some mechanlsm that can detoxify DDT and that this detoxication is chemical and subject to the isotope rate effect. (P.C.H.)« less

Al7CX (X=Li-Cs) clusters: Stability and the prospect for cluster materials

NASA Astrophysics Data System (ADS)

Ashman, C.; Khanna, S. N.; Pederson, M. R.; Kortus, J.

2000-12-01

Al7C clusters, recently found to have a high-electron affinity and exceptional stability, are shown to form ionic molecules when combined with alkali-metal atoms. Our studies, based on an ab initio gradient-corrected density-functional scheme, show that Al7CX (X=Li-Cs) clusters have a very low-electron affinity and a high-ionization potential. When combined, the two- and four-atom composite clusters of Al7CLi units leave the Al7C clusters almost intact. Preliminary studies indicate that Al7CLi may be suitable to form cluster-based materials.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.; Furuya, F.R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

Temperature dependence of the Cl atom reaction with deuterated methanes.

PubMed

Sauer, Frank; Portmann, Robert W; Ravishankara, A R; Burkholder, James B

2015-05-14

Kinetic isotope effect (KIE) and reaction rate coefficients, k1-k4, for the gas-phase reaction of Cl atoms with (12)CH3D (k1), (12)CH2D2 (k2), (12)CHD3 (k3), and (12)CD4 (k4) over the temperature range 223-343 K in 630 Torr of synthetic air are reported. Rate coefficients were measured using a relative rate technique with (12)CH4 as the primary reference compound. Fourier transform infrared spectroscopy was used to monitor the methane isotopologue loss. The obtained KIE values were (12)CH3D: KIE1(T) = (1.227 ± 0.004) exp((43 ± 5)/T); (12)CH2D2: KIE2(T) = (1.14 ± 0.20) exp((191 ± 60)/T); (12)CHD3: KIE3(T) = (1.73 ± 0.34) exp((229 ± 60)/T); and (12)CD4: KIE4(T) = (1.01 ± 0.3) exp((724 ± 19)/T), where KIEx(T) = kCl+(12)CH4(T)/kx(T). The quoted uncertainties are at the 2σ (95% confidence) level and represent the precision of our data. The following Arrhenius expressions and 295 K rate coefficient values (in units of cm(3) molecule(-1) s(-1)) were derived from the above KIE using a rate coefficient of 7.3 × 10(-12) exp(-1280/T) cm(3) molecule(-1) s(-1) for the reaction of Cl with (12)CH4: k1(T) = (5.95 ± 0.70) × 10(-12) exp(-(1323 ± 50)/T), k1(295 K) = (6.7 ± 0.8) × 10(-14); k2(T) = (6.4 ± 1.3) × 10(-12) exp(-(1471 ± 60)/T), k2(295 K) = (4.4 ± 0.9) × 10(-14); k3(T) = (4.2 ± 1.0) × 10(-12) exp(-(1509 ± 60)/T), k3(295 K) = (2.53 ± 0.6) × 10(-14); and k4(T) = (7.13 ± 2.3) × 10(-12) exp(-(2000 ± 120)/T), k4(295 K) = (0.81 ± 0.26) × 10(-14). The reported uncertainties in the pre-exponential factors are 2σ and include estimated systematic errors in our measurements and the uncertainty in the reference reaction rate coefficient. The results from this study are compared with previously reported room-temperature rate coefficients for each of the deuterated methanes as well as the available temperature dependent data for the Cl atom reactions with CH3D and CD4. A two-dimensional atmospheric chemistry model was used to examine the implications of the present results to the atmospheric lifetime and vertical variation in the loss of the deuterated methane isotopologues. The relative contributions of the reactions of OH, Cl, and O((1)D) to the loss of the isotopologues in the stratosphere were also examined. The results of the calculations are described and discussed.

Highly selective deuteration of pharmaceutically relevant nitrogen-containing heterocycles: a flow chemistry approach.

PubMed

Ötvös, Sándor B; Mándity, István M; Fülöp, Ferenc

2011-08-01

A simple and efficient flow-based technique is reported for the catalytic deuteration of several model nitrogen-containing heterocyclic compounds which are important building blocks of pharmacologically active materials. A continuous flow reactor was used in combination with on-demand pressure-controlled electrolytic D(2) production. The D(2) source was D(2)O, the consumption of which was very low. The experimental set-up allows the fine-tuning of pressure, temperature, and flow rate so as to determine the optimal conditions for the deuteration reactions. The described procedure lacks most of the drawbacks of the conventional batch deuteration techniques, and additionally is highly selective and reproducible.

Metal-atom Interactions and Clustering in Organic Semiconductor Systems

NASA Astrophysics Data System (ADS)

Tomita, Yoko; Park, Tea-uk; Nakayama, Takashi

2017-07-01

The interatomic interactions and clustering of metal atoms have been studied by first-principles calculations in graphene, pentacene, and polyacetylene as representative organic systems. It is shown that long-range repulsive Coulomb interaction appears between metal atoms with small electronegativity such as Al due to their ionization on host organic molecules, inducing their scattered distribution in organic systems. On the other hand, metal atoms with large electronegativity such as Au are weakly bonded to organic molecules, easily diffuse in molecular solids, and prefer to combine with each other owing to their short-range strong metallic-bonding interaction, promoting metal cluster generation in organic systems.

Classification Order of Surface-Confined Intermixing at Epitaxial Interface

NASA Astrophysics Data System (ADS)

Michailov, M.

The self-organization phenomena at epitaxial interface hold special attention in contemporary material science. Being relevant to the fundamental physical problem of competing, long-range and short-range atomic interactions in systems with reduced dimensionality, these phenomena have found exacting academic interest. They are also of great technological importance for their ability to bring spontaneous formation of regular nanoscale surface patterns and superlattices with exotic properties. The basic phenomenon involved in this process is surface diffusion. That is the motivation behind the present study which deals with important details of diffusion scenarios that control the fine atomic structure of epitaxial interface. Consisting surface imperfections (terraces, steps, kinks, and vacancies), the interface offers variety of barriers for surface diffusion. Therefore, the adatoms and clusters need a certain critical energy to overcome the corresponding diffusion barriers. In the most general case the critical energies can be attained by variation of the system temperature. Hence, their values define temperature limits of system energy gaps associated with different diffusion scenarios. This systematization imply classification order of surface alloying: blocked, incomplete, and complete. On that background, two diffusion problems, related to the atomic-scale surface morphology, will be discussed. The first problem deals with diffusion of atomic clusters on atomically smooth interface. On flat domains, far from terraces and steps, we analyzed the impact of size, shape, and cluster/substrate lattice misfit on the diffusion behavior of atomic clusters (islands). We found that the lattice constant of small clusters depends on the number N of building atoms at 1 < N ≤ 10. In heteroepitaxy, this effect of variable lattice constant originates from the enhanced charge transfer and the strong influence of the surface potential on cluster atomic arrangement. At constant temperature, the variation of the lattice constant leads to variable misfit which affects the island migration. The cluster/substrate commensurability influences the oscillation behavior of the diffusion coefficient caused by variation in the cluster shape. We discuss the results in a physical model that implies cluster diffusion with size-dependent cluster/substrate misfit. The second problem is devoted to diffusion phenomena in the vicinity of atomic terraces on stepped or vicinal surfaces. Here, we develop a computational model that refines important details of diffusion behavior of adatoms accounting for the energy barriers at specific atomic sites (smooth domains, terraces, and steps) located on the crystal surface. The dynamic competition between energy gained by mixing and substrate strain energy results in diffusion scenario where adatoms form alloyed islands and alloyed stripes in the vicinity of terrace edges. Being in agreement with recent experimental findings, the observed effect of stripe and island alloy formation opens up a way regular surface patterns to be configured at different atomic levels on the crystal surface. The complete surface alloying of the entire interface layer is also briefly discussed with critical analysis and classification of experimental findings and simulation data.

Electronic and magnetic properties of small rhodium clusters

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

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Structural and magnetic properties of FeGen-/0 (n = 3-12) clusters: Mass-selected anion photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Deng, Xiao-Jiao; Kong, Xiang-Yu; Liang, Xiaoqing; Yang, Bin; Xu, Hong-Guang; Xu, Xi-Ling; Feng, Gang; Zheng, Wei-Jun

2017-12-01

The structural, electronic, and magnetic properties of FeGen-/0 (n = 3-12) clusters were investigated by using anion photoelectron spectroscopy in combination with density functional theory calculations. For both anionic and neutral FeGen (n = 3-12) clusters with n ≤ 7, the dominant structures are exohedral. The FeGe8-/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9 to 11. The structures of FeGe10-/0 can be viewed as two Ge atoms symmetrically capping the opening of the boat-shaped structure of FeGe8, and those of FeGe12-/0 are distorted hexagonal prisms with the Fe atom at the center. Natural population analysis shows that there is an electron transfer from the Ge atoms to the Fe atom at n = 8-12. The total magnetic moment of FeGen-/0 and local magnetic moment of the Fe atom have not been quenched.

Density functional theory study of small X-doped Mg(n) (X = Fe, Co, Ni, n = 1-9) bimetallic clusters: equilibrium structures, stabilities, electronic and magnetic properties.

PubMed

Kong, Fanjie; Hu, Yanfei

2014-03-01

The geometries, stabilities, and electronic and magnetic properties of Mg(n) X (X = Fe, Co, Ni, n = 1-9) clusters were investigated systematically within the framework of the gradient-corrected density functional theory. The results show that the Mg(n)Fe, Mg(n)Co, and Mg(n)Ni clusters have similar geometric structures and that the X atom in Mg(n)X clusters prefers to be endohedrally doped. The average atomic binding energies, fragmentation energies, second-order differences in energy, and HOMO-LUMO gaps show that Mg₄X (X = Fe, Co, Ni) clusters possess relatively high stability. Natural population analysis was performed and the results showed that the 3s and 4s electrons always transfer to the 3d and 4p orbitals in the bonding atoms, and that electrons also transfer from the Mg atoms to the doped atoms (Fe, Co, Ni). In addition, the spin magnetic moments were analyzed and compared. Several clusters, such as Mg₁,₂,₃,₄,₅,₆,₈,₉Fe, Mg₁,₂,₄,₅,₆,₈,₉Co, and Mg₁,₂,₅,₆,₇,₉Ni, present high magnetic moments (4 μ(B), 3 μ(B), and 2 μ(B), respectively).

Deuterated formaldehyde in the low-mass protostar HH212

NASA Astrophysics Data System (ADS)

Sahu, Dipen; Minh, Y. C.; Lee, Chin-Fei; Liu, Sheng-Yuan; Das, Ankan; Chakrabarti, S. K.; Sivaraman, Bhala

2018-04-01

HH212, a nearby (400 pc) object in Orion, is a class 0 protostellar system with a Keplerian disc and collimated bipolar SiO jets. Deuterated water, HDO, and a deuterated complex molecule, methanol (CH2DOH), have been reported in the source. Here, we report the HDCO (deuterated formaldehyde) line observation from Atacama Large Millimeter Array data to probe the inner region of HH212. We compare HDCO line with other molecular lines to understand the possible chemistry and physics of the source. The distribution of HDCO emission suggests that it may be associated with the base of the outflow. The emission also shows a rotation but it is not associated with the Keplerian rotation of disc or the rotating infalling envelope, rather it is associated with the outflow as previously seen in C34S. From the possible deuterium fractionation, we speculate that the gas phase formation of deuterated formaldehyde is active in the central hot region of the low-mass protostar system, HH212.

Accessibility of cellulose: Structural changes and their reversibility in aqueous media.

PubMed

Pönni, Raili; Kontturi, Eero; Vuorinen, Tapani

2013-04-02

During various processing treatments, the accessibility of cellulose in cellulosic fibers reduces, which is often interpreted as cellulose microfibril aggregation. This affects the reactivity of cellulose in further processing to novel cellulosic products such as nanocellulose. In this study, the effect of aqueous treatments at elevated temperatures and various pH on accessibility of an oxygen delignified eucalyptus kraft pulp was evaluated by using deuteration combined with Fourier-transform infrared (FT-IR) spectroscopy and water retention value (WRV) test. Acidic treatments reduced WRV and caused irreversible deuteration of the pulp. However, alkaline treatments increased WRV and caused reversible deuteration of the pulp. Both deuteration and reprotonation of the deuterated pulp followed the same slow, first-order dynamics. This led us to propose that incubation of alkaline cellulosic pulp suspensions at elevated temperatures does not only lead to reduction in accessibility but also to a dynamic interconversion between accessible and inaccessible regions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Habit control of deuterated potassium dihydrogen phosphate crystal for laser applications

NASA Astrophysics Data System (ADS)

Guzman, L. A.; Suzuki, M.; Fujimoto, Y.; Fujioka, K.

2016-03-01

In this study we investigate the habit of partially deuterated potassium dihydrogen phosphate (DKDP) crystals in the presence of Al3+ ions. We have grown single DKDP crystals in (50wt% and 80wt%) partially deuterated solutions and in solutions doped with Al3+ ions (2 ppm) by the point-seed rapid growth technique at controlled supercooling (ΔT=10°C). The growth length of each crystal face was measured and the aspect ratio was calculated. We found that crystals grown in partially deuterated solutions are similar in aspect ratio, while, crystals grown in deuterated solutions doped with Al3+ ions showed a relative change in aspect ratio, the crystal increased in size in the pyramidal direction (vertical axis direction). Crystal characteristics were also analyzed by X-ray diffraction, FTIR and Raman spectroscopy. We have speculated that the relative habit modification is due to a probably adsorption and inclusions of Al3+ ions in the prismatic section of the crystal.

Statistical analysis of atom probe data: detecting the early stages of solute clustering and/or co-segregation.

PubMed

Hyde, J M; Cerezo, A; Williams, T J

2009-04-01

Statistical analysis of atom probe data has improved dramatically in the last decade and it is now possible to determine the size, the number density and the composition of individual clusters or precipitates such as those formed in reactor pressure vessel (RPV) steels during irradiation. However, the characterisation of the onset of clustering or co-segregation is more difficult and has traditionally focused on the use of composition frequency distributions (for detecting clustering) and contingency tables (for detecting co-segregation). In this work, the authors investigate the possibility of directly examining the neighbourhood of each individual solute atom as a means of identifying the onset of solute clustering and/or co-segregation. The methodology involves comparing the mean observed composition around a particular type of solute with that expected from the overall composition of the material. The methodology has been applied to atom probe data obtained from several irradiated RPV steels. The results show that the new approach is more sensitive to fine scale clustering and co-segregation than that achievable using composition frequency distribution and contingency table analyses.

Effects of single atom doping on the ultrafast electron dynamics of M1Au24(SR)18 (M = Pd, Pt) nanoclusters

NASA Astrophysics Data System (ADS)

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y.; Nobusada, Katsuyuki; Jin, Rongchao

2016-03-01

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications. Electronic supplementary information (ESI) available: The pump dependent transient absorption spectra and the corresponding global analysis results. See DOI: 10.1039/c6nr01008c

Classical plasma dynamics of Mie-oscillations in atomic clusters

NASA Astrophysics Data System (ADS)

Kull, H.-J.; El-Khawaldeh, A.

2018-04-01

Mie plasmons are of basic importance for the absorption of laser light by atomic clusters. In this work we first review the classical Rayleigh-theory of a dielectric sphere in an external electric field and Thomson’s plum-pudding model applied to atomic clusters. Both approaches allow for elementary discussions of Mie oscillations, however, they also indicate deficiencies in describing the damping mechanisms by electrons crossing the cluster surface. Nonlinear oscillator models have been widely studied to gain an understanding of damping and absorption by outer ionization of the cluster. In the present work, we attempt to address the issue of plasmon relaxation in atomic clusters in more detail based on classical particle simulations. In particular, we wish to study the role of thermal motion on plasmon relaxation, thereby extending nonlinear models of collective single-electron motion. Our simulations are particularly adopted to the regime of classical kinetics in weakly coupled plasmas and to cluster sizes extending the Debye-screening length. It will be illustrated how surface scattering leads to the relaxation of Mie oscillations in the presence of thermal motion and of electron spill-out at the cluster surface. This work is intended to give, from a classical perspective, further insight into recent work on plasmon relaxation in quantum plasmas [1].

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.

The adsorption of Run (n = 1-4) on γ-Al2O3 Surface: A DFT study

NASA Astrophysics Data System (ADS)

Liu, Zhe; Guo, Yafei; Chen, Yu; Shen, Rong

2018-05-01

The density functional theory (DFT) was adopted to study the adsorption and growth of Run (n = 1-4) clusters on γ-Al2O3 surface, which is of great significances for the design of many important catalysts, especially for carbon dioxide methanation. It is found that both the Rusbnd Ru bond length and adsorption energy Eads of Ru clusters with the surface increase with the Run clusters increasing. The growth ability of the supported Run cluster is weaker than the gas phase Run clusters through comparing their respective growth process, which ascribes to the stabilization of γ-Al2O3 support. An interesting discovery is that the basin structure was supposed to be the most favorable adsorption geometry for Run clusters. Additionally, the distances between Ru atoms in the adsorbed clusters are longer than that in their isolated counterparts. Bader charge analysis was conducted for the most stable configurations of Run (n = 1-4) clusters on γ-Al2O3 surface as well. And the results suggest that Run (n = 1-4) clusters serve as the electron donators. The result of projected density of states (PDOS) shows that strong adsorption of Ru atom on the γ-Al2O3 surface correlates with strong interaction between d orbital of Ru atom and p orbital of Al or O atom of the Al2O3 support.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

PubMed

Li, Yejun; Tam, Nguyen Minh; Claes, Pieterjan; Woodham, Alex P; Lyon, Jonathan T; Ngan, Vu Thi; Nguyen, Minh Tho; Lievens, Peter; Fielicke, André; Janssens, Ewald

2014-09-18

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

PubMed

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

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.

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al(6)CuLi(3), the C-phase Al(37)Cu(3)Li(21)Mg(3), and GaMg(2)Zn(3).

PubMed

Pauling, L

1988-06-01

Single-grain precession x-ray diffraction photographs of Al(6)CuLi(3) have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 A, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the beta-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al(37)Cu(3)Li(21)Mg(3), and to GaMg(2)Zn(3). A theory of icosahedral quasicrystals and amorphous metals is described.

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al6CuLi3, the C-phase Al37Cu3Li21Mg3, and GaMg2Zn3

PubMed Central

Pauling, Linus

1988-01-01

Single-grain precession x-ray diffraction photographs of Al6CuLi3 have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 Å, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the β-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al37Cu3Li21Mg3, and to GaMg2Zn3. A theory of icosahedral quasicrystals and amorphous metals is described. PMID:16593929

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.

Kramers degeneracy and relaxation in vanadium, niobium and tantalum clusters

NASA Astrophysics Data System (ADS)

Diaz-Bachs, A.; Katsnelson, M. I.; Kirilyuk, A.

2018-04-01

In this work we use magnetic deflection of V, Nb, and Ta atomic clusters to measure their magnetic moments. While only a few of the clusters show weak magnetism, all odd-numbered clusters deflect due to the presence of a single unpaired electron. Surprisingly, for the majority of V and Nb clusters an atomic-like behavior is found, which is a direct indication of the absence of spin–lattice interaction. This is in agreement with Kramers degeneracy theorem for systems with a half-integer spin. This purely quantum phenomenon is surprisingly observed for large systems of more than 20 atoms, and also indicates various quantum relaxation processes, via Raman two-phonon and Orbach high-spin mechanisms. In heavier, Ta clusters, the relaxation is always present, probably due to larger masses and thus lower phonon energies, as well as increased spin–orbit coupling.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

Equilibrium geometries, electronic and magnetic properties of small AunNi- (n = 1-9) clusters

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Yang, Xiang-Dong

2014-05-01

Geometrical, electronic and magnetic properties of small AunNi- (n = 1-9) clusters have been investigated based on density functional theory (DFT) at PW91P86 level. An extensive structural search shows that the relative stable structures of AunNi- (n = 1-9) clusters adopt 2D structure for n = 1-5, 7 and 3D structure for n = 6, 8-9. And the substitution of a Ni atom for an Au atom in the Au-n+1 cluster obviously changes the structure of the host cluster. Moreover, an odd-even alternation phenomenon has been found for HOMO-LUMO energy gaps, indicating that the relative stable structures of the AunNi- clusters with odd-numbered gold atoms have a higher relative stability. Finally, the natural population analysis (NPA) and the vertical detachment energies (VDE) are studied, respectively. The theoretical values of VDE are reported for the first time to our best knowledge.

Catalysis by clusters with precise numbers of atoms

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

Tyo, Eric C.; Vajda, Stefan

2015-07-03

Clusters that contain only a small number of atoms can exhibit unique and often unexpected properties. The clusters are of particular interest in catalysis because they can act as individual active sites, and minor changes in size and composition – such as the addition or removal of a single atom – can have a substantial influence on the activity and selectivity of a reaction. Here we review recent progress in the synthesis, characterization and catalysis of well-defined sub-nanometre clusters. We examine work on size-selected supported clusters in ultra-high vacuum environments and under realistic reaction conditions, and explore the use ofmore » computational methods to provide a mechanistic understanding of their catalytic properties. We also highlight the potential of size-selected clusters to provide insights into important catalytic processes and their use in the development of novel catalytic systems.« less

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

Neutron and X-ray investigations of the Jahn–Teller switch in partially deuterated ammonium copper Tutton salt, (NH 4 ) 2 [Cu(H 2 O) 6 ](SO 4 ) 2

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

Jørgensen, Mads R. V.; Piccoli, Paula M. B.; Hathwar, Venkatesha R.

2017-01-31

The structural phase transition accompanied by a Jahn–Teller switch has been studied over a range of H/D ratios in (NH 4) 2[Cu(H 2O) 6](SO 4) 2(ACTS). In particular, single-crystal neutron diffraction investigations of crystals with deuteration in the range 50 to 82% are shown to be consistent with previous electron paramagnetic resonance (EPR) experiments exhibiting a phase boundary at 50% deuteration under ambient pressure. Polycrystalline samples show that the two phases can co-exist. In addition, single-crystal neutron and polycrystalline X-ray diffraction pressure experiments show a shift to lower pressure at 60% deuterationversusprevious measurements at 100% deuteration.

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters.

PubMed

Baumfalk, R; Nahler, N H; Buck, U

2001-01-01

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.

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

Numakura, H.

The structure and the formation mechanism of oxides during internal oxidation have attracted much attention, and extensive studies have been carried out on this subject. Recently, Jang et al. reported the results of atom-probe microanalysis of oxide particles, or solute-oxygen clusters, in an internally oxidized Cu-0.16 at.% Mg alloy. They found that the composition varies from particle to particle even in the same specimen, and reported that some clusters consist only of magnesium atoms. On the basis of the results, they suggested that the oxidation proceeds in this alloy as follows: (1) the solute atoms form clusters, (2) the clustersmore » absorb oxygen atoms to form both hypo- and hyperstoichiometric oxide particles, (3) the particles grow to form the stoichiometric oxide, MgO. They show the presence of Mg atom clusters with no oxygen association. By assuming that the analyzed area is in the unoxidized region, i.e., ahead of the oxidation front, they interpret this observation as evidence for clustering of the solute atoms prior to oxide formation. However, according to the phase diagram, such clustering is not expected in the absence of oxygen, since the solute concentration, 0.16 at.%, is far below the solubility limit at the oxidation temperature of 900[degree]C, about 3.5 at.%. In atom probe experiments, it sometimes happens that detection efficiencies for different ion species are considerably different because some experimental parameters are not chosen properly. It seems possible that the data resulted from an unusually low detection efficiency for O ions. Since their conclusion raises an important issue on the mechanism of internal oxidation, it is desirable to examine experimental conditions carefully, and to check the reproducibility of data.« less

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.

Are clusters important in understanding the mechanisms in atmospheric pressure ionization? Part 1: Reagent ion generation and chemical control of ion populations.

PubMed

Klee, Sonja; Derpmann, Valerie; Wißdorf, Walter; Klopotowski, Sebastian; Kersten, Hendrik; Brockmann, Klaus J; Benter, Thorsten; Albrecht, Sascha; Bruins, Andries P; Dousty, Faezeh; Kauppila, Tiina J; Kostiainen, Risto; O'Brien, Rob; Robb, Damon B; Syage, Jack A

2014-08-01

It is well documented since the early days of the development of atmospheric pressure ionization methods, which operate in the gas phase, that cluster ions are ubiquitous. This holds true for atmospheric pressure chemical ionization, as well as for more recent techniques, such as atmospheric pressure photoionization, direct analysis in real time, and many more. In fact, it is well established that cluster ions are the primary carriers of the net charge generated. Nevertheless, cluster ion chemistry has only been sporadically included in the numerous proposed ionization mechanisms leading to charged target analytes, which are often protonated molecules. This paper series, consisting of two parts, attempts to highlight the role of cluster ion chemistry with regard to the generation of analyte ions. In addition, the impact of the changing reaction matrix and the non-thermal collisions of ions en route from the atmospheric pressure ion source to the high vacuum analyzer region are discussed. This work addresses such issues as extent of protonation versus deuteration, the extent of analyte fragmentation, as well as highly variable ionization efficiencies, among others. In Part 1, the nature of the reagent ion generation is examined, as well as the extent of thermodynamic versus kinetic control of the resulting ion population entering the analyzer region.

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

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

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

DOE PAGES

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; ...

2015-06-26

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Structures and stability of metal-doped GenM (n = 9, 10) clusters

NASA Astrophysics Data System (ADS)

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

2015-06-01

The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Thermal O-H Bond Activation of Water as Mediated by Heteronuclear [Al2Mg2O5]•+: Evidence for Oxygen-Atom Scrambling.

PubMed

Geng, Caiyun; Li, Jilai; Weiske, Thomas; Schwarz, Helmut

2018-06-25

Mechanistic insight into the thermal O-H bond activation of water by the cubane-like, prototypical heteronuclear oxide cluster [Al 2 Mg 2 O 5 ] •+ has been derived from a combined experimental/computational study. Experiments in the highly diluted gas phase using Fourier transform ion-cyclotron resonance mass spectrometry show that hydrogen-atom abstraction from water by the cluster cation [Al 2 Mg 2 O 5 ] •+ occurs at ambient conditions accompanied by the liberation of an OH • radical. Due to a complete randomization of all oxygen atoms prior to fragmentation about 83% of the oxygen atoms of the hydroxyl radical released originate from the oxide cluster itself. The experimental findings are supported by detailed high-level quantum chemical calculations. The theoretical analysis reveals that the transfer of a formal hydrogen atom from water to the metal-oxide cation can proceed mechanistically via proton- or hydrogen-atom transfer exploiting different active sites of the cluster oxide. In addition to the unprecedented oxygen-atom scrambling, one of the more general and quite unexpected findings concerns the role of spin density at the hydrogen-acceptor oxide atom. While this feature is so crucial for [M-O] + /CH 4 couples, it is much less important in the O-H bond activation of water.

New Scenario of Dynamical Heterogeneity in Supercooled Liquid and Glassy States of 2D Monatomic System.

PubMed

Van Hoang, Vo; Teboul, Victor; Odagaki, Takashi

2015-12-24

Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.

Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Yamashita, Koichi

2001-01-01

Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

Influence of Cr doping on the stability and structure of small cobalt oxide clusters.

PubMed

Tung, Nguyen Thanh; Tam, Nguyen Minh; Nguyen, Minh Tho; Lievens, Peter; Janssens, Ewald

2014-07-28

The stability of mass-selected pure cobalt oxide and chromium doped cobalt oxide cluster cations, ConO+m and Con-1CrO+m (n = 2, 3; m = 2-6 and n = 4; m = 3-8), has been investigated using photodissociation mass spectrometry. Oxygen-rich ConO+m clusters (m ≥ n + 1 for n = 2, 4 and m ≥ n + 2 for n = 3) prefer to photodissociate via the loss of an oxygen molecule, whereas oxygen poorer clusters favor the evaporation of oxygen atoms. Substituting a single Co atom by a single Cr atom alters the dissociation behavior. All investigated Con-1 CrO+m clusters, except CoCrO+2 and CoCrO+3, prefer to decay by eliminating a neutral oxygen molecule. Co2O+2, Co4O+3, Co4O+4, and CoCrO+2 are found to be relatively difficult to dissociate and appear as fragmentation product of several larger clusters, suggesting that they are particularly stable. The geometric structures of pure and Cr doped cobalt oxide species are studied using density functional theory calculations. Dissociation energies for different evaporation channels are calculated and compared with the experimental observations. The influence of the dopant atom on the structure and the stability of the clusters is discussed.

Stereospecific deuteration of alpha-furanosyl azomycin nucleosides: a model reaction for tritium radiolabeling.

PubMed

Kumar, Piyush; Emami, Saeed; McEwan, Alexander J B; Wiebe, Leonard I

2008-06-01

Stereospecific synthesis of 1-alpha-d-(2-deuteroribofuranosyl)-2-nitroimidazole (2'-[(2)H]-alpha-AZR) is reported. This, deuteration was independent of the configuration of C-2' -OH group (arabinose or ribose) in sugar moiety of starting molecules. Slightly better yield (>37%) of the deuterated product, 6, from arabinosyl precursor in comparison to corresponding ribose precursor (29%) was obtained which may reflect better stereochemical availability of C-2' -OH in arabinose during oxidation.

Effect of D2O on growth properties and chemical structure of annual ryegrass (Lolium multiflorum)

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

Evans, Barbara R; Bali, Garima; Reeves, David T

2014-01-01

In present paper, we report the production and detailed structural analysis of deuterium-enriched rye grass (Lolium multiflorum) for neutron scattering experiments. An efficient method to produce deuterated biomass was developed by designing hydroponic perfusion chambers. In preliminary studies, the partial deuterated rye samples were grown in increasing levels of D2O to study the seed germination and the level of deuterium incorporation as a function of D2O concentration. Solution NMR method indicated 36.9 % deuterium incorporation in 50 % D2O grown annual rye samples and further significant increase in the deuterium incorporation level was observed by germinating the rye seedlings inmore » H2O and growing in 50 % D2O inside the perfusion chambers. Moreover, in an effort to compare the substrate characteristics related to enzymatic hydrolysis on deuterated and protiated version of biomass, annual rye grown in 50 % D2O was selected for detailed biomass characterization studies. The compositional analyses, degree of polymerization and cellulose crystallinity were compared with its protiated control. The cellulose molecular weight indicated slight variation with deuteration; however, hemicellulose molecular weights and cellulose crystallinity remain unaffected with the deuteration. Besides the minor differences in biomass components, the development of deuterated biomass for neutron scattering application is essential to understand the complex biomass conversion processes.« less

Generation of C3- and C2-deuterated L-lactic acid by human erythrocytes exposed to D-[1-13C]glucose, D-[2-13C]glucose and D-[6-13C]glucose in the presence of D2O.

PubMed

Malaisse, W J; Biesemans, M; Willem, R

1994-05-01

1. The generation of C2- and C3-deuterated L-lactate was monitored by 13C NMR in human erythrocytes exposed to D-[1-13C]glucose, D-[2-13C]glucose or D-[6-13C]glucose and incubated in a medium prepared in D2O. 2. The results suggested that the deuteration of the C1 of D-fructose 6-phosphate in the phosphoglucoisomerase reaction, the deuteration of the C1 of D-glyceraldehyde-3-phosphate in the sequence of reactions catalyzed by triose phosphate isomerase and aldolase and the deuteration of the C3 of pyruvate in the reaction catalyzed by pyruvate kinase were all lower than expected from equilibration with D2O. 3. Moreover, about 40% of the molecules of pyruvate generated by glycolysis apparently underwent deuteration on their C3 during interconversion of the 2-keto acid and L-alanine in the reaction catalyzed by glutamate-pyruvate transaminase. 4. The occurrence of the latter process was also documented in cells exposed to exogenous [3-13C]pyruvate. 5. This methodological approach is proposed to provide a new tool to assess in intact cells the extent of back-and-forth interconversion of selected metabolic intermediates.

Surface heating of electrons in atomic clusters irradiated by ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Krainov, V. P.; Sofronov, A. V.

2014-04-01

We consider a mechanism for electron heating in atomic clusters at the reflections of free electrons from the cluster surface. Electrons acquire energy from the external laser field during these reflections. A simple analytical expression has been obtained for acquired electron kinetic energy during the laser pulse. We find conditions when this mechanism dominates compared to the electron heating due to the well-known induced inverse bremsstrahlung at the electron-ion collisions inside clusters.

Magic Numbers in Small Iron Clusters: A First-Principles Study

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

Kim, Eunja; Mohrland, Andrew B.; Weck, Philippe F.

2014-10-03

We perform ab initio spin-polarized density functional calculations of Fen aggregates with n ≤ 17 atoms to reveal the origin of the observed magic numbers, which indicate particularly high stability of clusters with 7, 13 and 15 atoms. Our results clarify the controversy regarding the ground state geometry of clusters such as Fe5and indicate that magnetism plays an important role in determining the stability and magic numbers in small iron clusters.

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

PubMed

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

2017-08-17

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

Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations

PubMed Central

Schreiner, Wolfgang

2014-01-01

Dynamic variations in the distances between pairs of atoms are used for clustering subdomains of biomolecules. We draw on a well-known target function for clustering and first show mathematically that the assignment of atoms to clusters has to be crisp, not fuzzy, as hitherto assumed. This reduces the computational load of clustering drastically, and we demonstrate results for several biomolecules relevant in immunoinformatics. Results are evaluated regarding the number of clusters, cluster size, cluster stability, and the evolution of clusters over time. Crisp clustering lends itself as an efficient tool to locate semirigid domains in the simulation of biomolecules. Such domains seem crucial for an optimum performance of subsequent statistical analyses, aiming at detecting minute motional patterns related to antigen recognition and signal transduction. PMID:24959586

Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

PubMed

Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

2017-01-21

Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

The spatial effect of protein deuteration on nitroxide spin-label relaxation: Implications for EPR distance measurement

PubMed Central

El Mkami, Hassane; Ward, Richard; Bowman, Andrew; Owen-Hughes, Tom; Norman, David G.

2014-01-01

Pulsed electron–electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems. PMID:25310878

Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour.

PubMed

Martin, T L; Coe, C; Bagot, P A J; Morrall, P; Smith, G D W; Scott, T; Moody, M P

2016-07-12

Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour.

Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour

NASA Astrophysics Data System (ADS)

Martin, T. L.; Coe, C.; Bagot, P. A. J.; Morrall, P.; Smith, G. D. W.; Scott, T.; Moody, M. P.

2016-07-01

Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour.

Cold Collisions in a Molecular Synchrotron

NASA Astrophysics Data System (ADS)

van der Poel, Aernout P. P.; Zieger, Peter C.; van de Meerakker, Sebastiaan Y. T.; Loreau, Jérôme; van der Avoird, Ad; Bethlem, Hendrick L.

2018-01-01

We study collisions between neutral, deuterated ammonia molecules (ND3 ) stored in a 50 cm diameter synchrotron and argon atoms in copropagating supersonic beams. The advantages of using a synchrotron in collision studies are twofold: (i) By storing ammonia molecules many round-trips, the sensitivity to collisions is greatly enhanced; (ii) the collision partners move in the same direction as the stored molecules, resulting in low collision energies. We tune the collision energy in three different ways: by varying the velocity of the stored ammonia packets, by varying the temperature of the pulsed valve that releases the argon atoms, and by varying the timing between the supersonic argon beam and the stored ammonia packets. These give consistent results. We determine the relative, total, integrated cross section for ND3+Ar collisions in the energy range of 40 - 140 cm-1 , with a resolution of 5 - 10 cm-1 and an uncertainty of 7%-15%. Our measurements are in good agreement with theoretical scattering calculations.

Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour

PubMed Central

Martin, T. L.; Coe, C.; Bagot, P. A. J.; Morrall, P.; Smith, G. D. W; Scott, T.; Moody, M. P.

2016-01-01

Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour. PMID:27403638

Synthesis and pharmacokinetic property improvement of deuterated plinabulin 9

NASA Astrophysics Data System (ADS)

Zhao, Jianchun; Cheng, Hejuan; Sun, Tianwen; Wang, Shixiao; Ding, Zhongpeng; Dou, Guifang; Meng, Zhiyun; Guan, Huashi; Li, Wenbao

2017-04-01

Plinabulin, a potent microtubule-targeting agent, is derived from marine natural diketopiperazine `phenylahistin'. To develop novel plinabulin analogue that could display better pharmacokinetic properties and less side effects, deuterated plinabulin 9 was synthesized and evaluated in vitro and in vivo. In comparison with plinabulin, in vivo pharmacokinetic studies indicated that the deuterated derivative 9 could alter blood circulation behavior obviously, which was proved by increased area under the plasma concentration- time curve (AUC0-∞), reduced clearance (CL), and prolonged total body mean residence time (MRT). The derivative 9 also has higher inhibition rates against BxPC-3, Jurkat and A-431 tumor cell lines as compared with its prototype plinabulin. Therefore, the deuterated compound 9 might be developed as a potential agent for different cancer treatments.

Progress toward development of a platform for studying burn in the presence of mix on the National Ignition Facility

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Kyrala, G. A.; Bradley, P. A.; Krasheninnikova, N. S.; Cobble, J. A.; Tregillis, I. L.; Obrey, K. A. D.; Hsu, S. C.; Shah, R. C.; Hakel, P.; Kline, J. L.; Grim, G. P.; Baumgaertel, J. A.; Schmitt, M. J.; Kanzleiter, R. J.; Batha, S. H.

2013-10-01

Mix of shell material into ICF capsule fuel can degrade implosion performance through a number of mechanisms. One way is by dilution of the fusion fuel, which affects performance by an amount that is dependent on the degree of mix at the atomic level. Experiments are underway to quantify the mix of shell material into fuel using directly driven capsules on the National Ignition Facility. Deuterated plastic shells will be utilized with tritium fill so that the production of DT neutrons is indicative of mix at the atomic level. Neutron imaging will locate the burn region and spectroscopic imaging of the doped layers will reveal the location, temperature, and density of the shell material. Correlation of the two will be used to determine the degree of atomic mixing of the shell into the fuel and will be compared to models. This talk will review progress toward the development of an experimental platform to measure burn in the presence of measured mix. This work is supported by US DOE/NNSA, performed at LANL, operated by LANS LLC under contract DE-AC52-06NA25396.

The mineralogy of Ba- and Zr-rich alkaline pegmatites from Gordon Butte, Crazy Mountains (Montana, USA): comparisons between potassic and sodic agpaitic pegmatites

NASA Astrophysics Data System (ADS)

Chakhmouradian, Anton; Mitchell, Roger

2002-01-01

At Gordon Butte (Crazy Mountains, Montana), agpaitic nepheline-syenite pegmatites intrude potassic alkaline rocks (principally, malignites and nepheline microsyenites). All pegmatite veins are composed predominantly of potassium feldspar, nepheline, prismatic aegirine, barytolamprophyllite, wadeite, eudialyte, loparite-(Ce) and altered rinkite ("vudyavrite") embedded in spherulitic and fibrous aegirine. Well-differentiated veins contain "pockets" filled with calcite, fluorapatite, mangan-neptunite, Mn-Ti-enriched prismatic aegirine, calcium catapleiite, and an unidentified Ca-Ti silicate. The potassium feldspar corresponds to Ba-rich sanidine with relatively low Na contents. The nepheline contains low levels of SiO2 and elevated Fe contents. The compositions of nepheline cluster in the lower portion of the Morozewicz-Buerger convergence field, indicating low-temperature crystallization and/or chemical re-equilibration of this mineral. The association of sanidine with nearly stoichiometric nepheline is unusual for agpaitic rocks and probably reflects inhibition of Al/Si ordering in the feldspar by Ba. At least four types of clinopyroxene can be distinguished on the basis of their morphology and composition. All these types correspond to Al- and Ca-poor aegirine (typically <0.6 and 2.6 wt% Al2O3 and CaO, respectively). The overall evolutionary trend of clinopyroxene in the Gordon Butte rocks is from Fe-poor diopside to aegirine-augite in the malignites and nepheline microsyenites, and culminates with the pegmatitic aegirine. This trend is characteristic for potassic alkaline complexes and results from preferential partitioning of Fe2+ into biotite during the magmatic crystallization. Barytolamprophyllite in the pegmatites is primary (as opposed to deuteric); only a few crystals contain a core composed of lamprophyllite. The evolutionary history of the Gordon Butte pegmatites can be subdivided into primary, agpaitic, and deuteric stages. The earliest paragenesis to crystallize included accessory zircon and thorite. Sr-rich loparite also precipitated relatively early serving as a major repository for Sr, REE, and Nb. During the agpaitic stage, diverse titano- and zircono-silicates (barytolamprophyllite, eudialyte, wadeite, and rinkite, among others) consumed most of the Ba, Sr, Ti, Zr, and Nb still remaining in the melt. The final stage in the evolution of the pegmatites involved interaction of the earlier-formed mineral assemblages with deuteric fluids. In common with the Rocky Boy pegmatites, Sr-REE-Na-rich fluorapatite, Ba-Fe titanates and REE-bearing carbonates (ancylite, calcio-ancylite, and bastnäsite-parisite series) are chief products of the deuteric stage. The alteration of the primary mineral assemblages by deuteric fluids also produced muscovite-zeolite pseudomorphs after nepheline, replacement of wadeite and eudialyte by catapleiite-group minerals, re-deposition of Ba in the form of hyalophane, baotite, and benitoite, and cation leaching from rinkite, eudialyte, and loparite. The mineralogy of the pegmatites from Gordon Butte, other potassic complexes, and sodic agpaitic occurrences is compared in detail.

Signatures of a quantum diffusion limited hydrogen atom tunneling reaction.

PubMed

Balabanoff, Morgan E; Ruzi, Mahmut; Anderson, David T

2017-12-20

We are studying the details of hydrogen atom (H atom) quantum diffusion in highly enriched parahydrogen (pH 2 ) quantum solids doped with chemical species in an effort to better understand H atom transport and reactivity under these conditions. In this work we present kinetic studies of the 193 nm photo-induced chemistry of methanol (CH 3 OH) isolated in solid pH 2 . Short-term irradiation of CH 3 OH at 1.8 K readily produces CH 2 O and CO which we detect using FTIR spectroscopy. The in situ photochemistry also produces CH 3 O and H atoms which we can infer from the post-photolysis reaction kinetics that display significant CH 2 OH growth. The CH 2 OH growth kinetics indicate at least three separate tunneling reactions contribute; (i) reactions of photoproduced CH 3 O with the pH 2 host, (ii) H atom reactions with the CH 2 O photofragment, and (iii) long-range migration of H atoms and reaction with CH 3 OH. We assign the rapid CH 2 OH growth to the following CH 3 O + H 2 → CH 3 OH + H → CH 2 OH + H 2 two-step sequential tunneling mechanism by conducting analogous kinetic measurements using deuterated methanol (CD 3 OD). By performing photolysis experiments at 1.8 and 4.3 K, we show the post-photolysis reaction kinetics change qualitatively over this small temperature range. We use this qualitative change in the reaction kinetics with temperature to identify reactions that are quantum diffusion limited. While these results are specific to the conditions that exist in pH 2 quantum solids, they have direct implications on the analogous low temperature H atom tunneling reactions that occur on metal surfaces and on interstellar grains.

Size resolved infrared spectroscopy of Na(CH3OH)n (n = 4-7) clusters in the OH stretching region: unravelling the interaction of methanol clusters with a sodium atom and the emergence of the solvated electron.

PubMed

Forck, Richard M; Pradzynski, Christoph C; Wolff, Sabine; Ončák, Milan; Slavíček, Petr; Zeuch, Thomas

2012-03-07

Size resolved IR action spectra of neutral sodium doped methanol clusters have been measured using IR excitation modulated photoionisation mass spectroscopy. The Na(CH(3)OH)(n) clusters were generated in a supersonic He seeded expansion of methanol by subsequent Na doping in a pick-up cell. A combined analysis of IR action spectra, IP evolutions and harmonic predictions of IR spectra (using density functional theory) of the most stable structures revealed that for n = 4, 5 structures with an exterior Na atom showing high ionisation potentials (IPs) of ~4 eV dominate, while for n = 6, 7 clusters with lower IPs (~3.2 eV) featuring fully solvated Na atoms and solvated electrons emerge and dominate the IR action spectra. For n = 4 simulations of photoionisation spectra using an ab initio MD approach confirm the dominance of exterior structures and explain the previously reported appearance IP of 3.48 eV by small fractions of clusters with partly solvated Na atoms. Only for this cluster size a shift in the isomer composition with cluster temperature has been observed, which may be related to kinetic stabilisation of less Na solvated clusters at low temperatures. Features of slow fragmentation dynamics of cationic Na(+)(CH(3)OH)(6) clusters have been observed for the photoionisation near the adiabatic limit. This finding points to the relevance of previously proposed non-vertical photoionisation dynamics of this system.

Effects of single atom doping on the ultrafast electron dynamics of M1Au24(SR)18 (M = Pd, Pt) nanoclusters.

PubMed

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y; Nobusada, Katsuyuki; Jin, Rongchao

2016-04-07

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.

Effects of single atom doping on the ultrafast electron dynamics of M 1Au 24(SR) 18 (M = Pd, Pt) nanoclusters

DOE PAGES

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y.; ...

2016-02-29

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M 1@Au 24(SR) 18 (M = Pd, Pt; R = CH 2CH 2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M 1Au 12 core states; (2) core to shell relaxation in a few picoseconds; and (3)more » relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au 25(SR) 18 cluster. As a result, the detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.« less

Cluster size dependence of high-order harmonic generation

NASA Astrophysics Data System (ADS)

Tao, Y.; Hagmeijer, R.; Bastiaens, H. M. J.; Goh, S. J.; van der Slot, P. J. M.; Biedron, S. G.; Milton, S. V.; Boller, K.-J.

2017-08-01

We investigate high-order harmonic generation (HHG) from noble gas clusters in a supersonic gas jet. To identify the contribution of harmonic generation from clusters versus that from gas monomers, we measure the high-order harmonic output over a broad range of the total atomic number density in the jet (from 3×1016 to 3 × 1018 {{cm}}-3) at two different reservoir temperatures (303 and 363 K). For the first time in the evaluation of the harmonic yield in such measurements, the variation of the liquid mass fraction, g, versus pressure and temperature is taken into consideration, which we determine, reliably and consistently, to be below 20% within our range of experimental parameters. By comparing the measured harmonic yield from a thin jet with the calculated corresponding yield from monomers alone, we find an increased emission of the harmonics when the average cluster size is less than 3000. Using g, under the assumption that the emission from monomers and clusters add up coherently, we calculate the ratio of the average single-atom response of an atom within a cluster to that of a monomer and find an enhancement of around 100 for very small average cluster size (∼200). We do not find any dependence of the cut-off frequency on the composition of the cluster jet. This implies that HHG in clusters is based on electrons that return to their parent ions and not to neighboring ions in the cluster. To fully employ the enhanced average single-atom response found for small average cluster sizes (∼200), the nozzle producing the cluster jet must provide a large liquid mass fraction at these small cluster sizes for increasing the harmonic yield. Moreover, cluster jets may allow for quasi-phase matching, as the higher mass of clusters allows for a higher density contrast in spatially structuring the nonlinear medium.

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

Xiong, Haifeng; Lin, Sen; Goetze, Joris

CeO2 supports are unique in their ability to trap ionic Pt, providing exceptional stability for isolated single atoms of Pt. Here, we explore the reactivity and stability of single atom Pt species for the industrially important reaction of light alkane dehydrogenation. The single atom Pt/CeO2 catalysts are stable during propane dehydrogenation, but we observe no selectivity towards propene. DFT calculations show strong adsorption of the olefin produced, leading to further unwanted reactions. In contrast, when Sn is added to ceria, the single atom Pt catalyst undergoes an activation phase where it transforms into Pt-Sn clusters under reaction conditions. Formation ofmore » small Pt-Sn clusters allows the catalyst to achieve high selectivity towards propene, due to facile desorption of the product. The CeO2-supported Pt-Sn clusters are very stable, even during extended reaction at 680 °C. By adding water vapor to the feed, coke formation can almost completely be suppressed. Furthermore, the Pt-Sn clusters can be readily transformed back to the atomically dispersed species on ceria via oxidation, making Pt-Sn/CeO2 a fully regenerable catalyst.« less

BIOLOGICAL EFFECTS OF DEUTERIUM OXIDE

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

Rothstein, E.L.

1962-01-01

D/sub 2/0 was used to study the synthesis of viral nucleic acid and cellular lipids. Deuteration of bacterial and mammalian cells resulted in increascd size and an altered lipid profile. Infection of Escherichia coli with phages T5 and T7 resulted in the production of increased amounts of T7. Such increases were appearently a function of deuteration in the life cycle of the virus. Similarly, the HeLa cell, maintained in tissue culture, produced increased amounts of polio virus when cells were deuterated. (H.H.D.)

Deuterated scintillators and their application to neutron spectroscopy

NASA Astrophysics Data System (ADS)

Febbraro, M.; Lawrence, C. C.; Zhu, H.; Pierson, B.; Torres-Isea, R. O.; Becchetti, F. D.; Kolata, J. J.; Riggins, J.

2015-06-01

Deuterated scintillators have been used as a tool for neutron spectroscopy without Neutron Time-of-Flight (n-ToF) for more than 30 years. This article will provide a brief historical overview of the technique and current uses of deuterated scintillators in the UM-DSA and DESCANT arrays. Pulse-shape discrimination and spectrum unfolding with the maximum-likelihood expectation maximization algorithm will be discussed. Experimental unfolding and cross section results from measurements of (d,n), (3He,n) and (α,n) reactions are shown.

Equilibrium structure and atomic vibrations of Nin clusters

NASA Astrophysics Data System (ADS)

Borisova, Svetlana D.; Rusina, Galina G.

2017-12-01

The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

Density-functional theory study of the geometries, stabilities, and electronic properties of Au n Rb (n = 1-10) clusters: comparison with pure gold clusters

NASA Astrophysics Data System (ADS)

Hu, Yan-Fei; Jiang, Gang; Meng, Da-Qiao

2012-01-01

The density functional method with the relativistic effective core potential has been employed to investigate systematically the geometric structures, relative stabilities, growth-pattern behavior, and electronic properties of small bimetallic Au n Rb (n = 1-10) and pure gold Au n (n ≤ 11) clusters. For the geometric structures of the Au n Rb (n = 1-10) clusters, the dominant growth pattern is for a Rb-substituted Au n +1 cluster or one Au atom capped on a Au n -1Rb cluster, and the turnover point from a two-dimensional to a three-dimensional structure occurs at n = 4. Moreover, the stability of the ground-state structures of these clusters has been examined via an analysis of the average atomic binding energies, fragmentation energies, and the second-order difference of energies as a function of cluster size. The results exhibit a pronounced even-odd alternation phenomenon. The same pronounced even-odd alternations are found for the HOMO-LUMO gap, VIPs, VEAs, and the chemical hardness. In addition, about one electron charge transfers from the Au n host to the Rb atom in each corresponding Au n Rb cluster.

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

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

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

A DFT study of the stability of SIAs and small SIA clusters in the vicinity of solute atoms in Fe

NASA Astrophysics Data System (ADS)

Becquart, C. S.; Ngayam Happy, R.; Olsson, P.; Domain, C.

2018-03-01

The energetics, defect volume and magnetic properties of single SIAs and small SIA clusters up to size 6 have been calculated by DFT for different configurations like the parallel 〈110〉 dumbbell, the non parallel 〈110〉 dumbbell and the C15 structure. The most stable configurations of each type have been further analyzed to determine the influence on their stability of various solute atoms (Ti, V, Cr, Mn, Co, Ni, Cu, Mo, W, Pd, Al, Si, P), relevant for steels used under irradiation. The results show that the presence of solute atoms does not change the relative stability order among SIA clusters. The small SIA clusters investigated can bind to both undersized and oversized solutes. Several descriptors have been considered to derive interesting trends from results. It appears that the local atomic volume available for the solute is the main physical quantity governing the binding energy evolution, whatever the solute type (undersized or oversized) and the cluster configuration (size and type).

Classification of ligand molecules in PDB with graph match-based structural superposition.

PubMed

Shionyu-Mitsuyama, Clara; Hijikata, Atsushi; Tsuji, Toshiyuki; Shirai, Tsuyoshi

2016-12-01

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.

Catalyst Architecture for Stable Single Atom Dispersion Enables Site-Specific Spectroscopic and Reactivity Measurements of CO Adsorbed to Pt Atoms, Oxidized Pt Clusters, and Metallic Pt Clusters on TiO2.

PubMed

DeRita, Leo; Dai, Sheng; Lopez-Zepeda, Kimberly; Pham, Nicholas; Graham, George W; Pan, Xiaoqing; Christopher, Phillip

2017-10-11

Oxide-supported precious metal nanoparticles are widely used industrial catalysts. Due to expense and rarity, developing synthetic protocols that reduce precious metal nanoparticle size and stabilize dispersed species is essential. Supported atomically dispersed, single precious metal atoms represent the most efficient metal utilization geometry, although debate regarding the catalytic activity of supported single precious atom species has arisen from difficulty in synthesizing homogeneous and stable single atom dispersions, and a lack of site-specific characterization approaches. We propose a catalyst architecture and characterization approach to overcome these limitations, by depositing ∼1 precious metal atom per support particle and characterizing structures by correlating scanning transmission electron microscopy imaging and CO probe molecule infrared spectroscopy. This is demonstrated for Pt supported on anatase TiO 2 . In these structures, isolated Pt atoms, Pt iso , remain stable through various conditions, and spectroscopic evidence suggests Pt iso species exist in homogeneous local environments. Comparing Pt iso to ∼1 nm preoxidized (Pt ox ) and prereduced (Pt metal ) Pt clusters on TiO 2 , we identify unique spectroscopic signatures of CO bound to each site and find CO adsorption energy is ordered: Pt iso ≪ Pt metal < Pt ox . Pt iso species exhibited a 2-fold greater turnover frequency for CO oxidation than 1 nm Pt metal clusters but share an identical reaction mechanism. We propose the active catalytic sites are cationic interfacial Pt atoms bonded to TiO 2 and that Pt iso exhibits optimal reactivity because every atom is exposed for catalysis and forms an interfacial site with TiO 2 . This approach should be generally useful for studying the behavior of supported precious metal atoms.

Titanium embedded cage structure formation in Al{sub n}Ti{sup +} clusters and their interaction with Ar

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

Torres, M. B., E-mail: begonia@ubu.es; Vega, A.; Balbás, L. C.

2014-05-07

Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al{sub n}Ti{sup +} [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > n{sub c} determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al{sub n}Ti{sup +}, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic propertiesmore » of singly titanium doped cationic clusters, Al{sub n}Ti{sup +} (n = 16–21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at n{sub c} = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (n{sub c} = 21) and their neutral counterparts (n{sub c} = 20). For the Al {sub n} Ti {sup +} · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al{sub n}Ti{sup +} clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For n{sub c} = 21, the smallest size of endohedral Ti doped cationic clusters, the Ar binding energy decreases drastically, whereas the Ar-cluster distance increases substantially, point to Ar physisorption, as assumed by the experimentalists. Calculated Ar adsorption energies agree well with available experimental binding energies.« less

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr5Ni3Si2 and V15Ni10Si that by twinning achieve 8-fold rotational point-group symmetry

PubMed Central

Pauling, Linus

1988-01-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 Å is assigned to rapidly solidified Cu5Ni3Si2 and V15Ni10Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45° twinning on the basal plane. PMID:16593915

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr(5)Ni(3)Si(2) and V(15)Ni(10)Si that by twinning achieve 8-fold rotational point-group symmetry.

PubMed

Pauling, L

1988-04-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 A is assigned to rapidly solidified Cu(5)Ni(3)Si(2) and V(15)Ni(10)Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45 degrees twinning on the basal plane.

Tuning the Photophysical Properties of Ru(II) Monometallic and Ru(II),Rh(III) Bimetallic Supramolecular Complexes by Selective Ligand Deuteration.

PubMed

Wagner, Alec T; Zhou, Rongwei; Quinn, Kevan S; White, Travis A; Wang, Jing; Brewer, Karen J

2015-07-02

A series of three new complexes of the design [(TL)2Ru(BL)](2+), two new complexes of the design [(TL)2Ru(BL)Ru(TL)2](4+), and three new complexes of the design [(TL)2Ru(BL)RhCl2(TL)](3+) (TL = bpy or d8-bpy; BL = dpp or d10-dpp; TL = terminal ligand; BL = bridging ligand; bpy = 2,2'-bipyridine; dpp = 2,3-bis(2-pyridyl)pyrazine) were synthesized and the (1)H NMR spectroscopy, electrochemistry, electronic absorbance spectroscopy, and photophysical properties studied. Incorporation of deuterated ligands into the molecular architecture simplifies the (1)H NMR spectra, allowing for complete (1)H assignment of [(d8-bpy)2Ru(dpp)](PF6)2 and partial assignment of [(bpy)2Ru(d10-dpp)](PF6)2. The electrochemistry for the deuterated and nondeuterated species showed nearly identical redox properties. Electronic absorption spectroscopy of the deuterated and nondeuterated complexes are superimposable with the lowest energy transition being Ru(dπ) → BL(π*) charge transfer in nature (BL = dpp or d10-dpp). Ligand deuteration impacts the excited-state properties with an observed increase in the quantum yield of emission (Φ(em)) and excited-state lifetime (τ) of the Ru(dπ) → d10-dpp(π*) triplet metal-to-ligand charge transfer ((3)MLCT) excited state when dpp is deuterated, and a decrease in the rate constant for nonradiative decay (knr). Choice of ligand deuteration between bpy and dpp strongly impacts the observed photophysical properties with BL = d10-dpp complexes showing an enhanced Φ(em) and τ, providing further support that the lowest electronic excited state populated via UV or visible excitation is the photoactive Ru(dπ) → dpp(π*) CT excited state. The Ru(II),Rh(III) complex incorporating the deuterated BL shows increased hydrogen production compared to the variants incorporating the protiated BL, while demonstrating identical dynamic quenching behaviors in the presence of sacrificial electron donor.

Cluster Beam Studies.

DTIC Science & Technology

1988-04-01

Continue on reverse if necessary and identify by block number) Cluster beams offer a means of depositing high-quality thin films at low...either directly inclustered vapors of nonvolatile materials or Indirectly by bombarding the film duringdeposition with clusters of inert gases. When a...electron volt energy per atom. The suprathermal energy of thej depositing atoms is thought to produce unique thin films (either in quality, or in the ability

Evaluating the component contribution to nonlinear optical performances using stable [Ni4O4] cuboidal clusters as models.

PubMed

Hao, Zhi-Min; Chao, Meng-Yao; Liu, Yan; Song, Ying-Lin; Yang, Jun-Yi; Ding, Lifeng; Zhang, Wen-Hua; Lang, Jian-Ping

2018-06-19

Five stable clusters sharing the cuboidal [Ni4O4] skeleton are subjected to third-order nonlinear optical (NLO) property measurements. Preliminary results suggest that the NLO property is largely defined by the cluster core skeleton and the directly coordinated atoms, with limited contribution from the heavy atoms peripherally attached to the aromatic ligands.

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

PubMed

Parnis, J Mark; Escobar-Cabrera, Eric; Thompson, Matthew G K; Jacula, J Paul; Lafleur, Rick D; Guevara-García, Alfredo; Martínez, Ana; Rayner, David M

2005-08-18

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Spectroscopic study on deuterated benzenes. III. Vibronic structure and dynamics in the S1 state

NASA Astrophysics Data System (ADS)

Kunishige, Sachi; Katori, Toshiharu; Kawabata, Megumi; Yamanaka, Takaya; Baba, Masaaki

2015-12-01

We observed the fluorescence excitation spectra and mass-selected resonance enhanced multiphoton ionization (REMPI) excitation spectra for the 6 01 , 6 01 10 1 , and 6 01 10 2 bands of the S1←S0 transition of jet-cooled deuterated benzene and assigned the vibronic bands of C6D6 and C6HD5. The 60 1 10 n (n = 0, 1, 2) and 00 0 transition energies were found to be dependent only on the number of D atoms (ND), which was reflected by the zero-point energy of each H/D isotopomer. In some isotopomers some bands, such as those of out-of-plane vibrations mixed with 611n, make the spectra complex. These included the 611021n level or combination bands with ν12 which are allowed because of reduced molecular symmetry. From the lifetime measurements of each vibronic band, some enhancement of the nonradiative intramolecular vibrational redistribution (IVR) process was observed. It was also found that the threshold excess energy of "channel three" was higher than the 6112 levels, which were similar for all the H/D isotopomers. We suggest that the channel three nonradiative process could be caused mainly by in-plane processes such as IVR and internal conversion at the high vibrational levels in the S1 state of benzene, although the out-of-plane vibrations might contribute to some degree.

Ion mobility studies of PdC{sub n}{sup +} clusters: Where are the fullerenes?

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

Shelimov, K.B.; Jarrold, M.F.

1995-12-14

Gas-phase ion mobility measurements have been used to study the structures and isomerization of PdC{sub n}{sup +} (n = 10-60) clusters. Non-fullerene isomers of PdC{sub n}{sup +} clusters are similar to those of C{sub n}{sup +} and MC{sub n}{sup +} (M = La and Nb) clusters, and include metal-containing mono- and bicyclic rings and graphite sheets. Neither endohedral nor nonendohedral PdC{sub n} {sup +} fullerene isomers are detected. When collisionally heated, PdC{sub n}{sup +} clusters efficiently convert into fullerenes, but the exothermicity of this process results in the loss of the Pd atom and the formation of a pure carbonmore » cluster cation. PdC{sub n}{sup +} bicyclic rings with an odd number of carbon atoms efficiently isomerize into monocyclic rings, while no evidence is found for this isomerization process for bicyclic rings with an even number of carbon atoms. 18 refs., 4 figs.« less

Analysis of Helium Segregation on Surfaces of Plasma-Exposed Tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Hu, Lin; Hammond, Karl; Wirth, Brian

2015-11-01

We report a systematic theoretical and atomic-scale computational study of implanted helium segregation on surfaces of tungsten, which is considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations, including molecular statics to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile helium clusters (of 1-7 He atoms) in the near-surface region are attracted to the surface due to an elastic interaction force. This thermodynamic driving force induces drift fluxes of these mobile clusters toward the surface, facilitating helium segregation. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, at rates much higher than in the bulk material. This cluster dynamics has significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

PubMed

Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

PubMed Central

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. PMID:26741367

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Characterization of Deuterated-xylene Scintillator as a Neutron Spectrometer

DOE PAGES

Di Fulvio, Angela; Becchetti, F. D.; Raymond, R. S.; ...

2016-11-16

We have experimentally characterized the neutron light output response functions of a deuterated-xylene scintillator for neutron energies lower than 10 MeV. We then used the response matrix to unfold the energy distribution of neutrons produced via several reactions, i.e. spontaneous fission, d(d,n)3He, 27Al(d,n)28Si, and 9Be(alpha,n)12C. Organic scintillators based on deuterated compounds show a fast response and good gamma-neutron discrimination capability, similar to proton-based scintillators. Deuterated scintillators can also effectively provide neutron spectra by unfolding measured data with the detector response matrix, without the need of time-of-flight. Deuteron recoils, produced by elastic collisions between deuterium and impinging neutrons, are preferentially forward-scattered.more » This non-isotropic reaction results in distinct peaks in the response functions to monoenergetic neutrons. In this work, we evaluated a custom-fabricated 7.62 cm x 7.62 cm deuterated-xylene (EJ301D) liquid scintillator. This liquid has a low volatility and higher flash point, compared to benzene-based deuterated detectors, e.g. EJ315 and NE230. We measured the EJ301D detector neutron response matrix (up to 6 MeV neutron energy) using an intense Cf252 source and the time-of-flight technique. The number of response functions obtained using our method is only limited by counting statistics and by the experimentally achievable energy resolution. Multi-channel unfolding was performed successfully for neutron spectra with different energy spectra.« less

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation

NASA Astrophysics Data System (ADS)

Zhou, Pan-Pan; Liu, Shubin; Ayers, Paul W.; Zhang, Rui-Qin

2017-10-01

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters' reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems.

A screened independent atom model for the description of ion collisions from atomic and molecular clusters

NASA Astrophysics Data System (ADS)

Lüdde, Hans Jürgen; Horbatsch, Marko; Kirchner, Tom

2018-05-01

We apply a recently introduced model for an independent-atom-like calculation of ion-impact electron transfer and ionization cross sections to proton collisions from water, neon, and carbon clusters. The model is based on a geometrical interpretation of the cluster cross section as an effective area composed of overlapping circular disks that are representative of the atomic contributions. The latter are calculated using a time-dependent density-functional-theory-based single-particle description with accurate exchange-only ground-state potentials. We find that the net capture and ionization cross sections in p-X n collisions are proportional to n α with 2/3 ≤ α ≤ 1. For capture from water clusters at 100 keV impact energy α is close to one, which is substantially different from the value α = 2/3 predicted by a previous theoretical work based on the simplest-level electron nuclear dynamics method. For ionization at 100 keV and for capture at lower energies we find smaller α values than for capture at 100 keV. This can be understood by considering the magnitude of the atomic cross sections and the resulting overlaps of the circular disks that make up the cluster cross section in our model. Results for neon and carbon clusters confirm these trends. Simple parametrizations are found which fit the cross sections remarkably well and suggest that they depend on the relevant bond lengths.

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.

Structures and stability of metal-doped Ge{sub n}M (n = 9, 10) clusters

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

Qin, Wei, E-mail: qinw@qdu.edu.cn; Xia, Lin-Hua; Zhao, Li-Zhen

The lowest-energy structures of neutral and cationic Ge{sub n}M (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge{sub 9} and Ge{sub 10} clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge{sub n} clusters. However, the neutral and cationic FeGe{sub 9,10},MnGe{sub 9,10} and Ge{sub 10}Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge{sub n} clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge{sub 9,10}Fe and Ge{sub 9}Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Thermodynamics of the clusterization process of cis isomers of unsaturated fatty acids at the air/water interface.

PubMed

Vysotsky, Yu B; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Aksenenko, E V; Miller, R

2009-04-02

In the framework of the semiempirical PM3 method, the thermodynamic parameters of cis isomers of unsaturated carboxylic acids at the air/water interface are studied. The model systems used are unsaturated cis fatty acid of the composition Delta = 12-15 and omega = 6-11, where Delta and omega refer to the number of carbon atoms between the functional group and double bond, and that between the double bond and methyl group, respectively. For dimers, trimers, and tetramers of the four acid series, the thermodynamic parameters of clusterization are calculated. It is shown that the position of the double bond does not significantly affect the values of thermodynamic parameters of formation and clusterization of carboxylic acids for equal chain lengths (n = Delta + omega). The calculated results show that for cis unsaturated fatty acid with odd Delta values the spontaneous clusterization threshold corresponds to n = 17-18 carbon atoms in the alkyl chain, while for monounsaturated acids with even Delta values this threshold corresponds to n = 18-19 carbon atoms in the alkyl chain. These differences in the clusterization threshold between the acids with even and odd Delta values are attributed to the formation of additional intermolecular hydrogen bonds between the ketonic oxygen atom of one monomer and the hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with odd Delta values or between the hydroxyl oxygen atom of one monomer and hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with even Delta values. The results obtained in the study agree satisfactorily with our experimental data for cis unsaturated nervonic (Delta15, omega9) and erucic acids (Delta13, omega9), and published data for some fatty acids, namely cis-16-heptadecenoic (Delta16, omega1), cis-9-hexadecenoic (Delta7, omega9), cis-11-eicosenoic (Delta11, omega9) and cis-9-octadecenoic acid (Delta9, omega9).

Symmetry analysis of the behavior of the family R6M23 compounds upon hydrogenation

NASA Astrophysics Data System (ADS)

Kuna, Agnieszka; Sikora, Wiesława

2011-06-01

Symmetry analysis was applied in this work to discuss the behavior of the family R6M23 compounds upon hydrogenation (deuteration), where different structural transformations and magnetic properties, depending on the type of R and M atoms and hydrogen (deuterium) concentrations, have been found. The crystallographic structure of these compounds is described by the Fm3m space group and contain 116 atoms per unit cell occupying the positions 24e(R), 4b, 24d, 32f1 and 32f2(M). Additionally in the elementary cell, there could be up to 100 atoms of hydrogen (or deuterium) occupying the interstitial positions 4a, 32f3, 96j1 and 96k1. The symmetry analysis in the frame of the theory of space groups and their representation gives the opportunity to find all possible transformations from high symmetry parent structure to the structures with symmetry belonging to one of its subgroups. For a given transformation it indicates possible displacements of atoms from initial positions in the parent structure, ordering of hydrogen over interstitial sites and also ordering of magnetic moments, described by the smallest possible number of free parameters. The analysis was carried out by means of the MODY computer program for vectors k = (0; 0; 0) and k = (0; 0; 1) describing the changes of translational symmetry and all positions occupied by the R, M and D atoms.

Molecular emulsions: from charge order to domain order.

PubMed

Perera, Aurélien

2017-10-25

Aqueous mixtures of small molecules, such as lower n-alkanols for example, are known to be micro-segregated, with domains in the nano-meter range. One consequence of this micro-segregation would be the existence of long range domain-domain oscillatory correlations in the various atom-atom pair correlation functions, and subsequent pre-peaks in the corresponding atom-atom structure factors, in the q-vector range corresponding to nano-sized domains. However, no such pre-peak have ever been observed in the large corpus of radiation scattering data published so far on aqueous mixtures of small n-alkanols. By using large scale simulations of aqueous-1propanol mixtures, it is shown herein that the origin for the absence of scattering pre-peak resides in the exact cancellation of the contributions of the various atom-atom correlation pre-peaks to the total scattered intensity. The mechanism for this cancellation is due to the differences in the long range oscillatory behaviour of the correlations (beyond 1 nm), which are exactly out-of-phase between same species and cross species. This is similar to the charge order observed in ionic melts, but differs from room temperature ionic liquids, where the segregation is between charged and neutral groups, instead of species segregation. The consequences of such cancellation in the experimental scattering data are examined, in relation to the possibility of detecting micro-segregation through such methods. In the particular case of aqueous-1propanol mixtures, it is shown the X-ray scattering leads an exact cancellation, while this cancellation in neutron scattering is seen to depend on the deuteration ratio between solvent and solute.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the 199Hg Atom

NASA Astrophysics Data System (ADS)

Sahoo, B. K.; Das, B. P.

2018-05-01

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P ,T -odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P ,T -odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to 199Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the ^{199}Hg Atom.

PubMed

Sahoo, B K; Das, B P

2018-05-18

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P,T-odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P,T-odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to ^{199}Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

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

Adams, W.H.; Adams, D.G.

Mice ingesting 30 to 50% D/sub 2/O (heavy water, deuterium oxide) developed a dose-dependent depression of formed peripheral blood elements in 4 to 9 days. The principal mechanism of anemia and thrombocytopenia is impaired hematopoiesis. Despite pancytopenia in the peripheral blood, bone marrow cellularity and morphology remained normal. Upon replacement of D/sub 2/O with tap water, platelet and neutrophil concentrations returned to normal within 48 to 72 hr. In contrast, blood lymphocyte concentrations remained low for several weeks. B-lymphocytes may be more affected by deuteration than other lymphocyte subsets. In vivo reticuloendothelial cell function, as assessed by /sup 51/Cr-labeled sheepmore » erythrocyte clearance, was unaffected by D/sub 2/O. Although a dose-dependent decrease in fluid intake occurred during deuteration, hematocytopenia was not a consequence of dehydration. In view of the known kinetics of D/sub 2/O in biological systems, the rapid response of myeloid elements to deuteration must be due primarily to the solvent (nonmetabolic) isotope effect. Prolonged deuteration has proven toxic when included in regimens for treatment of neoplasia, including leukemia, in animal models. The present study shows that modulation of hematopoiesis by D/sub 2/O is possible without invoking the toxicities associated with prolonged deuteration.« less

1997 Technical Digest Series. Volume 7: Applications of High Field and Short Wavelength Sources VII

DTIC Science & Technology

1997-03-01

clusters irradiated with ultrashort , high intensity laser pulses can exhibit "ionization ig- nition" which leads...8, 9]. 25-atom Ne clusters and 25-atom Ar clusters are modelled as irradiated by a 800 nm, 15 fs (fwhm) laser pulse with peak intensities ranging...Measurements of the spatial and spectral properties of ultrashort , intense laser pulses propagating in underdense plasmas demonstrate

Spectra of helium clusters with up to six atoms using soft-core potentials

NASA Astrophysics Data System (ADS)

Gattobigio, M.; Kievsky, A.; Viviani, M.

2011-11-01

In this paper, we investigate small clusters of helium atoms using the hyperspherical harmonic basis. We consider systems with A=2,3,4,5,6 atoms with an interparticle potential which does not present a strong repulsion at short distances. We use an attractive Gaussian potential that reproduces the values of the dimer binding energy, the atom-atom scattering length, and the effective range obtained with one of the widely used He-He interactions, the Aziz and Slaman potential, called LM2M2. In systems with more than two atoms, we consider a repulsive three-body force that, by construction, reproduces the trimer binding energy of the LM2M2 potential. With this model, consisting of the sum of a two- and three-body potential, we have calculated the spectrum of clusters formed by four, five, and six helium atoms. We have found that these systems present two bound states, one deep and one shallow, close to the threshold fixed by the energy of the (A-1)-atom system. Universal relations between the energies of the excited state of the A-atom system and the ground-state energy of the (A-1)-atom system are extracted, as well as the ratio between the ground state of the A-atom system and the ground-state energy of the trimer.

Perspective: Size selected clusters for catalysis and electrochemistry

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

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

DOE PAGES

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; ...

2018-03-15

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

NASA Astrophysics Data System (ADS)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; Vajda, Stefan

2018-03-01

Size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization, and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions, and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modeling based on density functional theory sampling of local minima and energy barriers or ab initio molecular dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Finally, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

Neutron inelastic scattering by amino acids

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

Thaper, C.L.; Sinha, S.K.; Dasannacharya, B.A.

Inelastic neutron scattering experiments on normal, N-deuterated glycine, normal and N-deuterated alanine, L-valine, L-tyrosine and, L-phenylalanine at 100 K, are reported. Coupling of the external modes to different hydrogens is discussed.

Effect of solute atom concentration on vacancy cluster formation in neutron-irradiated Ni alloys

NASA Astrophysics Data System (ADS)

Sato, Koichi; Itoh, Daiki; Yoshiie, Toshimasa; Xu, Qiu; Taniguchi, Akihiro; Toyama, Takeshi

2011-10-01

The dependence of microstructural evolution on solute atom concentration in Ni alloys was investigated by positron annihilation lifetime measurements. The positron annihilation lifetimes in pure Ni, Ni-0.05 at.%Si, Ni-0.05 at.%Sn, Ni-Cu, and Ni-Ge alloys were about 400 ps even at a low irradiation dose of 3 × 10 -4 dpa, indicating the presence of microvoids in these alloys. The size of vacancy clusters in Ni-Si and Ni-Sn alloys decreased with an increase in the solute atom concentration at irradiation doses less than 0.1 dpa; vacancy clusters started to grow at an irradiation dose of about 0.1 dpa. In Ni-2 at.%Si, irradiation-induced segregation was detected by positron annihilation coincidence Doppler broadening measurements. This segregation suppressed one-dimensional (1-D) motion of the interstitial clusters and promoted mutual annihilation of point defects. The frequency and mean free path of the 1-D motion depended on the solute atom concentration and the amount of segregation.

Molecular dynamics study of the melting of a supported 887-atom Pd decahedron.

PubMed

Schebarchov, D; Hendy, S C; Polak, W

2009-04-08

We employ classical molecular dynamics simulations to investigate the melting behaviour of a decahedral Pd(887) cluster on a single layer of graphite (graphene). The interaction between Pd atoms is modelled with an embedded-atom potential, while the adhesion of Pd atoms to the substrate is approximated with a Lennard-Jones potential. We find that the decahedral structure persists at temperatures close to the melting point, but that just below the melting transition, the cluster accommodates to the substrate by means of complete melting and then recrystallization into an fcc structure. These structural changes are in qualitative agreement with recently proposed models, and they verify the existence of an energy barrier preventing softly deposited clusters from 'wetting' the substrate at temperatures below the melting point.

Melting of isolated tin nanoparticles

PubMed

Bachels; Guntherodt; Schafer

2000-08-07

The melting of isolated neutral tin cluster distributions with mean sizes of about 500 atoms has been investigated in a molecular beam experiment by calorimetrically measuring the clusters' formation energies as a function of their internal temperature. For this purpose the possibility to adjust the temperature of the clusters' internal degrees of freedom by means of the temperature of the cluster source's nozzle was exploited. The melting point of the investigated tin clusters was found to be lowered by 125 K and the latent heat of fusion per atom is reduced by 35% compared to bulk tin. The melting behavior of the isolated tin clusters is discussed with respect to the occurrence of surface premelting.

Structural and magnetic evolution of bimetallic MnAu clusters driven by asymmetric atomic migration.

PubMed

Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

2014-03-12

The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L1(0) structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

Ultra-small rhenium clusters supported on graphene.

PubMed

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J; Mariscal, Marcelo M; Yacaman, Miguel José

2015-03-28

The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.

Ultra-small rhenium clusters supported on graphene

PubMed Central

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J.; Mariscal, Marcelo M.; Yacaman, Miguel José

2015-01-01

The adsorption of very small rhenium clusters (2 – 13 atoms) supported on graphene was studied with high annular dark field - scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones. PMID:25721176

Melting of Cu nanoclusters by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying

2003-04-01

We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to Tm, N= Tm,Bulk- αN-1/3, dropping from Tm,Bulk=1360 K to Tm,456=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

PubMed Central

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

Purification and characterization of two fully deuterated enzymes

NASA Technical Reports Server (NTRS)

Crespi, H. L.; Katz, J. J.; Parmerter, S.; Rokop, S.

1969-01-01

Comparative data reveal little difference between kinetic and thermal stabilities of pure preparations of two ordinary enzymes and their fully deuterated counterparts. The effects of temperature on the enzymes proved to be consistent with earlier results.

THE DISTRIBUTION OF DEUTERATED FORMALDEHYDE WITHIN ORION-KL

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

Favre, Cécile; Bergin, Edwin A.; Neill, Justin L.

2015-08-01

We report the first high angular resolution imaging (3.″4 × 3.″0) of deuterated formaldehyde (HDCO) toward Orion-KL, carried out with the Submillimeter Array. We find that the spatial distribution of the formaldehyde emission systematically differs from that of methanol: while methanol is found toward the inner part of the region, HDCO is found in colder gas that wraps around the methanol emission on four sides. The HDCO/H{sub 2}CO ratios are determined to be 0.003–0.009 within the region, up to an order of magnitude higher than the D/H measured for methanol. These findings strengthen the previously suggested hypothesis that there aremore » differences in the chemical pathways leading to HDCO (via deuterated gas-phase chemistry) and deuterated methanol (through conversion of formaldehyde into methanol on the surface of icy grain mantles)« less

Direct Detection of Hardly Detectable Hidden Chirality of Hydrocarbons and Deuterated Isotopomers by a Helical Polyacetylene through Chiral Amplification and Memory.

PubMed

Maeda, Katsuhiro; Hirose, Daisuke; Okoshi, Natsuki; Shimomura, Kouhei; Wada, Yuya; Ikai, Tomoyuki; Kanoh, Shigeyoshi; Yashima, Eiji

2018-03-07

We report the first direct chirality sensing of a series of chiral hydrocarbons and isotopically chiral compounds (deuterated isotopomers), which are almost impossible to detect by conventional optical spectroscopic methods, by a stereoregular polyacetylene bearing 2,2'-biphenol-derived pendants. The polyacetylene showed a circular dichroism due to a preferred-handed helix formation in response to the hardly detectable hidden chirality of saturated tertiary or chiroptical quaternary hydrocarbons, and deuterated isotopomers. In sharp contrast to the previously reported sensory systems, the chirality detection by the polyacetylene relies on an excess one-handed helix formation induced by the chiral hydrocarbons and deuterated isotopomers via significant amplification of the chirality followed by its static memory, through which chiral information on the minute and hidden chirality can be stored as an excess of a single-handed helix memory for a long time.

Structural, electronic and vibrational properties of GexCy (x+y=2-5) nanoclusters: A B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Goswami, Sohini; Saha, Sushmita; Yadav, R. K.

2015-11-01

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2-5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C-C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO-LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO-LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

Self-Learning Off-Lattice Kinetic Monte Carlo method as applied to growth on metal surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Kara, Abdelkader; Rahman, Talat

2007-03-01

We propose a new development in the Self-Learning Kinetic Monte Carlo (SLKMC) method with the goal of improving the accuracy with which atomic mechanisms controlling diffusive processes on metal surfaces may be identified. This is important for diffusion of small clusters (2 - 20 atoms) in which atoms may occupy Off-Lattice positions. Such a procedure is also necessary for consideration of heteroepitaxial growth. The new technique combines an earlier version of SLKMC [1] with the inclusion of off-lattice occupancy. This allows us to include arbitrary positions of adatoms in the modeling and makes the simulations more realistic and reliable. We have tested this new approach for the case of the diffusion of small 2D Cu clusters diffusion on Cu(111) and found good performance and satisfactory agreement with results obtained from previous version of SLKMC. The new method also helped reveal a novel atomic mechanism contributing to cluster migration. We have also applied this method to study the diffusion of Cu clusters on Ag(111), and find that Cu atoms generally prefer to occupy off-lattice sites. [1] O. Trushin, A. Kara, A. Karim, T.S. Rahman Phys. Rev B 2005

Atomically manufactured nickel-silicon quantum dots displaying robust resonant tunneling and negative differential resistance

NASA Astrophysics Data System (ADS)

Cheng, Jian-Yih; Fisher, Brandon L.; Guisinger, Nathan P.; Lilley, Carmen M.

2017-12-01

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni-Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni-Si clusters. The resonance energy is reproducible and the peak spacing of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I-V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. All of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

DOE PAGES

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.; ...

2017-05-22

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

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

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

Synthesis, Structure and Electrochemistry of Tetranuclear Oxygen-Centered Copper(II) Clusters with Acetylacetone and Benz-pyrazole Hydrolyzed Derivatives as Ligand.

PubMed

Vafazadeh, Rasoul; Willis, Anthony C

2016-01-01

Two copper(II) clusters Cu(4)OCl(6)(pyrazole)4, 1, and Cu(4)OBr(6)(Br-pyrazole)4, 2, have been synthesized by reacting acetylacetone and benzohydrazide (1:1 ratio) with CuX(2) (X = Cl for 1 and X= Br for 2) in methanol solutions. The structures of both clusters have been established by X-ray crystallography. The clusters contain four Cu, one O, six μ(2)-X atoms, and four pyrazole ligands. The pyrazoles was prepared in situ by the reaction of acetylacetone with benzohydrazide in methanol under reflux. In 2, the methine hydrogens of the pyrazole ligands have been replaced by bromine atoms. The four copper atoms encapsulate the central O atom in a tetrahedral arrangement. All copper atoms are five-coordinate and have similar coordination environments with slightly distorted trigonal bipyramidal geometry. The cyclic voltammogram of the clusters 1 and 2 show a one-electron quasi-reversible reduction wave in the region 0.485 to 0.731 V, and a one-electron quasi-reversible oxidation wave in the region 0.767 to 0.898 V. In 1, one irreversible oxidative response is observed on the positive of side of the voltammogram at 1.512 V and this can be assigned to Cu(II) to Cu(III) oxidation.

Factors driving stable growth of He clusters in W: first-principles study

NASA Astrophysics Data System (ADS)

Feng, Y. J.; Xin, T. Y.; Xu, Q.; Wang, Y. X.

2018-07-01

The evolution of helium (He) bubbles is responsible for the surface morphology variation and subsequent degradation of the properties of plasma-facing materials (PFMs) in nuclear fusion reactors. These severe problems unquestionably trace back to the behavior of He in PFMs, which is closely associated with the interaction between He and the matrix. In this paper, we decomposed the binding energy of the He cluster into three parts, those from W–W, W–He, and He–He interactions, using density functional theory. As a result, we clearly identified the main factors that determine a steplike decrease in the binding energy with increasing number of He atoms, which explains the process of self-trapping and athermal vacancy generation during He cluster growth in the PFM tungsten. The three interactions were found to synergetically shape the features of the steplike decrease in the binding energy. Fairly strong He–He repulsive forces at a short distance, which stem from antibonding states between He atoms, need to be released when additional He atoms are continuously bonded to the He cluster. This causes the steplike feature in the binding energy. The bonding states between W and He atoms in principle facilitate the decreasing trend of the binding energy. The decrease in binding energy with increasing number of He atoms implies that He clusters can grow stably.

Lithium-air batteries, method for making lithium-air batteries

DOEpatents

Vajda, Stefan; Curtiss, Larry A.; Lu, Jun; Amine, Khalil; Tyo, Eric C.

2016-11-15

The invention provides a method for generating Li.sub.2O.sub.2 or composites of it, the method uses mixing lithium ions with oxygen ions in the presence of a catalyst. The catalyst comprises a plurality of metal clusters, their alloys and mixtures, each cluster consisting of between 3 and 18 metal atoms. The invention also describes a lithium-air battery which uses a lithium metal anode, and a cathode opposing the anode. The cathode supports metal clusters, each cluster consisting of size selected clusters, taken from a range of between approximately 3 and approximately 18 metal atoms, and an electrolyte positioned between the anode and the cathode.

Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag24Au(SR)18](-) Nanocluster.

PubMed

Bootharaju, Megalamane S; Joshi, Chakra P; Parida, Manas R; Mohammed, Omar F; Bakr, Osman M

2016-01-18

Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18](-) cluster (SR: thiolate) using a pure [Ag25(SR)18](-) cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag(25-x)Au(x)(SR)18](-), x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18](-) reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced Electrochemistry of Individual Metal Clusters Electrodeposited Atom by Atom to Nanometer by Nanometer.

PubMed

Kim, Jiyeon; Dick, Jeffrey E; Bard, Allen J

2016-11-15

Metal clusters are very important as building blocks for nanoparticles (NPs) for electrocatalysis and electroanalysis in both fundamental and applied electrochemistry. Attention has been given to understanding of traditional nucleation and growth of metal clusters and to their catalytic activities for various electrochemical applications in energy harvesting as well as analytical sensing. Importantly, understanding the properties of these clusters, primarily the relationship between catalysis and morphology, is required to optimize catalytic function. This has been difficult due to the heterogeneities in the size, shape, and surface properties. Thus, methods that address these issues are necessary to begin understanding the reactivity of individual catalytic centers as opposed to ensemble measurements, where the effect of size and morphology on the catalysis is averaged out in the measurement. This Account introduces our advanced electrochemical approaches to focus on each isolated metal cluster, where we electrochemically fabricated clusters or NPs atom by atom to nanometer by nanometer and explored their electrochemistry for their kinetic and catalytic behavior. Such approaches expand the dimensions of analysis, to include the electrochemistry of (1) a discrete atomic cluster, (2) solely a single NP, or (3) individual NPs in the ensemble sample. Specifically, we studied the electrocatalysis of atomic metal clusters as a nascent electrocatalyst via direct electrodeposition on carbon ultramicroelectrode (C UME) in a femtomolar metal ion precursor. In addition, we developed tunneling ultramicroelectrodes (TUMEs) to study electron transfer (ET) kinetics of a redox probe at a single metal NP electrodeposited on this TUME. Owing to the small dimension of a NP as an active area of a TUME, extremely high mass transfer conditions yielded a remarkably high standard ET rate constant, k 0 , of 36 cm/s for outer-sphere ET reaction. Most recently, we advanced nanoscale scanning electrochemical microscopy (SECM) imaging to resolve the electrocatalytic activity of individual electrodeposited NPs within an ensemble sample yielding consistent high k 0 values of ≥2 cm/s for the hydrogen oxidation reaction (HOR) at different NPs. We envision that our advanced electrochemical approaches will enable us to systematically address structure effects on the catalytic activity, thus providing a quantitative guideline for electrocatalysts in energy-related applications.

Estimating carbon cluster binding energies from measured Cn distributions, n <= 10

NASA Astrophysics Data System (ADS)

Pargellis, A. N.

1990-08-01

Experimental data are presented for the cluster distribution of sputtered negative carbon clusters, C-n, with n≤10. Additionally, clusters have been observed with masses indicating they are CsC-2n, with n≤4. The C-n data are compared with the data obtained by other groups, for neutral and charged clusters, using a variety of sources such as evaporation, sputtering, and laser ablation. The data are used to estimate the cluster binding energies En, using the universal relation, En=(n-1)ΔHn+RTe [ln(Jn/J1)+0.5 ln(n)-α-(ΔSn-ΔS1)/R], derived from basic kinetic and thermodynamic relations. The estimated values agree astonishingly well with values from the literature, varying from published values by at most a few percent. In this equation, Jn is the observed current of n-atom clusters, ΔHn is the heat of vaporization, ΔH1=7.41 eV, and Te ≊0.25 eV (2900 K) is the effective source temperature. The relative change in cluster entropy during sublimation from the solid to vapor phase is approximated to first order by the relation (ΔSn-ΔS1)/R =3.1+0.9(n-2), and is fit to published data for n between 2 and 5 and temperatures between 2000 and 4000 K. The parameter α is empirical, obtained by fitting the data to known binding energies for Cn≤5 clusters. For evaporation sources, α must be zero, but α˜7 when sputtering with Cs+ ions, indicating the sputtered clusters appear to be in thermodynamic equilibrium, but not the atoms. Several possible mechanisms for the formation of clusters during sputtering are examined. One plausible mechanism is that atoms diffuse on the graphite surface to form clusters which are then desorbed by energetic, recoil atoms created in subsequent sputtering events.

Cluster generator

DOEpatents

Donchev, Todor I [Urbana, IL; Petrov, Ivan G [Champaign, IL

2011-05-31

Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

Planar CoB18- Cluster: a New Motif for - and Metallo-Borophenes

NASA Astrophysics Data System (ADS)

Chen, Teng-Teng; Jian, Tian; Lopez, Gary; Li, Wan-Lu; Chen, Xin; Li, Jun; Wang, Lai-Sheng

2016-06-01

Combined Photoelectron Spectroscopy (PES) and theoretical calculations have found that anion boron clusters (Bn-) are planar and quasi-planar up to B25-. Recent works show that anion pure boron clusters continued to be planar at B27-,B30-,B35- and B36-. B35- and B36- provide the first experimental evidence for the viability of the two-dimensional (2D) boron sheets (Borophene). The 2D to three-dimensional (3D) transitions are shown to happen at B40-,B39- and B28-, which possess cage-like structures. These fullerene-like boron cage clusters are named as Borospherene. Recently, borophenes or similar structures are claimed to be synthesized by several groups. Following an electronic design principle, a series of transition-metal-doped boron clusters (M©Bn-, n=8-10) are found to possess the monocyclic wheel structures. Meanwhile, CoB12- and RhB12- are revealed to adopt half-sandwich-type structures with the quasi-planar B12 moiety similar to the B12- cluster. Very lately, we show that the CoB16- cluster possesses a highly symmetric Cobalt-centered drum-like structure, with a new record of coordination number at 16. Here we report the CoB18- cluster to possess a unique planar structure, in which the Co atom is doped into the network of a planar boron cluster. PES reveals that the CoB18- cluster is a highly stable electronic system with the first adiabatic detachment energy (ADE) at 4.0 eV. Global minimum searches along with high-level quantum calculations show the global minimum for CoB18- is perfectly planar and closed shell (1A1) with C2v symmetry. The Co atom is bonded with 7 boron atoms in the closest coordination shell and the other 11 boron atoms in the outer coordination shell. The calculated vertical detachment energy (VDE) values match quite well with our experimental results. Chemical bonding analysis by the Adaptive Natural Density Partitioning (AdNDP) method shows the CoB18- cluster is π-aromatic with four 4-centered-2-electron (4c-2e) π bonds and one 19-centered-2-electron (19c-2e) π bond, 10 π electrons in total. This perfectly planar structure reveals the viability of creating a new class of hetero-borophenes and metallo-borophenes by doping metal atoms into the plane of monolayer boron atoms. This gives a new approach to design perspective hetero-borophenes and metallo-borophenes materials with tunable chemical, magnetic and optical properties.

Gas chromatographic--mass spectrometric quantitation of 16, 16-dimethyl-trans-delta 2-PGE1

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

Dimov, V.; Green, K.; Bygdeman, M.

1983-02-01

Di-deuterated and di-tritiated 16,16-dimethyl-trans-delta 2-PGE1 has been synthesized and used for development of a GC-MS method for quantitation of corresponding unlabelled drug in patient plasma. Although these carrier/internal standard molecules only contain 2 deuterium atoms the lower limit of detection at each injection is as low as about 40 pg. The maximum plasma levels of this drug following administration of vaginal suppositories used in clinical studies (1 mg 16,16-dimethyl-trans-delta 2-PGE1 methyl ester in 0.8 g Witepsol S-52) were 100-350 pg/ml i.e. in the same order of magnitude as earlier seen for 16,16-dimethyl-PGE2.

Electronic structures and thermochemical properties of the small silicon-doped boron clusters B(n)Si (n=1-7) and their anions.

PubMed

Tai, Truong Ba; Kadłubański, Paweł; Roszak, Szczepan; Majumdar, Devashis; Leszczynski, Jerzy; Nguyen, Minh Tho

2011-11-18

We perform a systematic investigation on small silicon-doped boron clusters B(n)Si (n=1-7) in both neutral and anionic states using density functional (DFT) and coupled-cluster (CCSD(T)) theories. The global minima of these B(n)Si(0/-) clusters are characterized together with their growth mechanisms. The planar structures are dominant for small B(n)Si clusters with n≤5. The B(6)Si molecule represents a geometrical transition with a quasi-planar geometry, and the first 3D global minimum is found for the B(7)Si cluster. The small neutral B(n)Si clusters can be formed by substituting the single boron atom of B(n+1) by silicon. The Si atom prefers the external position of the skeleton and tends to form bonds with its two neighboring B atoms. The larger B(7)Si cluster is constructed by doping Si-atoms on the symmetry axis of the B(n) host, which leads to the bonding of the silicon to the ring boron atoms through a number of hyper-coordination. Calculations of the thermochemical properties of B(n)Si(0/-) clusters, such as binding energies (BE), heats of formation at 0 K (ΔH(f)(0)) and 298 K (ΔH(f)([298])), adiabatic (ADE) and vertical (VDE) detachment energies, and dissociation energies (D(e)), are performed using the high accuracy G4 and complete basis-set extrapolation (CCSD(T)/CBS) approaches. The differences of heats of formation (at 0 K) between the G4 and CBS approaches for the B(n)Si clusters vary in the range of 0.0-4.6 kcal mol(-1). The largest difference between two approaches for ADE values is 0.15 eV. Our theoretical predictions also indicate that the species B(2)Si, B(4)Si, B(3)Si(-) and B(7)Si(-) are systems with enhanced stability, exhibiting each a double (σ and π) aromaticity. B(5)Si(-) and B(6)Si are doubly antiaromatic (σ and π) with lower stability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms.

PubMed

Albertí, Margarita; Huarte-Larrañaga, Fermín; Aguilar, Antonio; Lucas, José M; Pirani, Fernando

2011-05-14

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.

Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic Nim Cun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters.

PubMed

Singh, Raman K; Iwasa, Takeshi; Taketsugu, Tetsuya

2018-05-25

A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCu n -1 and Ni 2 Cu n -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cu n , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCu n -1 and Ni 2 Cu n -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters. The averaged binding energy, the fragmentation energies and the second-order energy differences signified that the Ni doped clusters can continue to gain an energy during the growth process. The electronic structures revealed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies of the LC-DFT are reliable and can be used to predict the vertical ionization potential and the vertical electron affinity of the systems. The reactivity descriptors such as the chemical potential, chemical hardness and electrophilic power, and the reactivity principle such as the minimum polarizability principle are operative for characterizing and rationalizing the electronic structures of these clusters. Moreover, doping of Ni atoms into the copper clusters carry most of the total spin magnetic moment. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

NASA Technical Reports Server (NTRS)

Walch, S.

1984-01-01

The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

Structure and properties of B20Si-/0/+ clusters

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Li, Yi De; Huang, Shou Guo

2018-06-01

A global search for the lowest energy structure of B20Si-, B20Si0 and B20Si+ clusters is conducted. Structural transitions at different charge states are observed. B20Si- is a 2D planar configuration with no polygonal holes, and Si atom occupies a peripheral position. B20Si+ adopts a 3D tubular shape, and each Si is bonded with four B atoms. But for B20Si0, competition among quasi-planar, tubular and cage like structures is found. These structures differ greatly from that of pure B21 - cluster. The structural transition may result from changes in the framework of bonding, sp 2 hybridization, and structural mechanics. Some of the clusters' properties including frontier molecular orbital, on-site charge on Si atom, electron density, and magnetism are also discussed.

Study of Pair and many-body interactions in rare-gas halide atom clusters using negative ion zero electron kinetic energy (ZEKE) and threshold photodetachment spectroscopy

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

Yourshaw, Ivan

1998-07-09

The diatomic halogen atom-rare gas diatomic complexes KrBr -, XeBr -, and KrCl - are studied in this work by zero electron kinetic energy (ZEKE) spectroscopy in order to characterize the weak intermolecular diatomic potentials of these species. Also, the ZEKE and threshold photodetachment spectra of the polyatomic clusters Ar nBr - (n = 2-9) and Ar nI - (n = 2-19) are studied to obtain information about the non-additive effects on the interactions among the atoms. This work is part of an ongoing effort to characterize the pair and many-body potentials of the complete series of rare gas halidemore » clusters. In these studies we obtain information about both the anionic and neutral clusters.« less

Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience

PubMed Central

Xavier, Paulrajpillai Lourdu; Chaudhari, Kamalesh; Baksi, Ananya; Pradeep, Thalappil

2012-01-01

Noble metal quantum clusters (NMQCs) are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature. PMID:22312454

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Formation of Core-Shell Ethane-Silver Clusters in He Droplets.

PubMed

Loginov, Evgeny; Gomez, Luis F; Sartakov, Boris G; Vilesov, Andrey F

2017-08-17

Ethane core-silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of ethane molecules followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of the C-H stretching vibrations of ethane. The spectra reveal a splitting of the vibrational bands, which is ascribed to interaction with Ag. A rigorous analysis of band intensities for a varying number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of a core of ethane that is covered by relatively small Ag clusters. This metastable structure is stabilized due to fast dissipation in superfluid helium droplets of the cohesion energy of the clusters.

Detonation of Meta-stable Clusters

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

Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.

2008-05-31

We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetahmore » code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.« less

Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

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

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

DOE PAGES

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; ...

2016-01-07

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

First principles study of vibrational dynamics of ceria-titania hybrid clusters

NASA Astrophysics Data System (ADS)

Majid, Abdul; Bibi, Maryam

2017-04-01

Density functional theory based calculations were performed to study vibrational properties of ceria, titania, and ceria-titania hybrid clusters. The findings revealed the dominance of vibrations related to oxygen when compared to those of metallic atoms in the clusters. In case of hybrid cluster, the softening of normal modes related to exterior oxygen atoms in ceria and softening/hardening of high/low frequency modes related to titania dimmers are observed. The results calculated for monomers conform to symmetry predictions according to which three IR and three Raman active modes were detected for TiO2, whereas two IR active and one Raman active modes were observed for CeO2. The comparative analysis indicates that the hybrid cluster CeTiO4 contains simultaneous vibrational fingerprints of the component dimmers. The symmetry, nature of vibrations, IR and Raman activity, intensities, and atomic involvement in different modes of the clusters are described in detail. The study points to engineering of CeTiO4 to tailor its properties for technological visible region applications in photocatalytic and electrochemical devices.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations.

PubMed

Yin, Shi; Bernstein, Elliot R

2016-10-21

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH) 1-3 - cluster anions are lower than those found for their respective FeS 1-3 - cluster anions. The experimental first VDEs for FeS 1-3 - clusters are observed to increase for the first two S atoms bound to Fe - ; however, due to the formation of an S-S bond for the FeS 3 - cluster, its first VDE is found to be ∼0.41 eV lower than the first VDE for the FeS 2 - cluster. The first VDEs of Fe(SH) 1-3 - cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS 1-3 - and Fe(SH) 1-3 - clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH) - is lower than that for FeS 2 - , but higher than that for Fe(SH) 2 - ; the first VDEs for FeS 2 (SH) - and FeS(SH) 2 - are close to that for FeS 3 - , but higher than that for Fe(SH) 3 - . The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Yin, Shi; Bernstein, Elliot R.

2016-10-01

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH)1-3- cluster anions are lower than those found for their respective FeS1-3- cluster anions. The experimental first VDEs for FeS1-3- clusters are observed to increase for the first two S atoms bound to Fe-; however, due to the formation of an S-S bond for the FeS3- cluster, its first VDE is found to be ˜0.41 eV lower than the first VDE for the FeS2- cluster. The first VDEs of Fe(SH)1-3- cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS1-3- and Fe(SH)1-3- clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH)- is lower than that for FeS2-, but higher than that for Fe(SH)2-; the first VDEs for FeS2(SH)- and FeS(SH)2- are close to that for FeS3-, but higher than that for Fe(SH)3-. The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

New Theoretical Developments in Exploring Electronically Excited States: Including Localized Configuration Interaction Singles and Application to Large Helium Clusters

NASA Astrophysics Data System (ADS)

Closser, Kristina Danielle

This thesis presents new developments in excited state electronic structure theory. Contrasted with the ground state, the electronically excited states of atoms and molecules often are unstable and have short lifetimes, exhibit a greater diversity of character and are generally less well understood. The very unusual excited states of helium clusters motivated much of this work. These clusters consist of large numbers of atoms (experimentally 103--109 atoms) and bands of nearly degenerate excited states. For an isolated atom the lowest energy excitation energies are from 1s → 2s and 1s → 2 p transitions, and in clusters describing the lowest energy band minimally requires four states per atom. In the ground state the clusters are weakly bound by van der Waals interactions, however in the excited state they can form well-defined covalent bonds. The computational cost of quantum chemical calculations rapidly becomes prohibitive as the size of the systems increase. Standard excited-state methods such as configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) can be used with ≈100 atoms, and are optimized to treat only a few states. Thus, one of our primary aims is to develop a method which can treat these large systems with large numbers of nearly degenerate excited states. Additionally, excited states are generally formed far from their equilibrium structures. Vertical excitations from the ground state induce dynamics in the excited states. Thus, another focus of this work is to explore the results of these forces and the fate of the excited states. Very little was known about helium cluster excited states when this work began, thus we first investigated the excitations in small helium clusters consisting of 7 or 25 atoms using CIS. The character of these excited states was determined using attachment/detachment density analysis and we found that in the n = 2 manifold the excitations could generally be interpreted as superpositions of atomic states with surface states appearing close to the atomic excitation energies and interior states being blue shifted by up to ≈2 eV. The dynamics resulting from excitation of He_7 were subsequently explored using ab initio molecular dynamics (AIMD). These simulations were performed with classical adiabatic dynamics coupled to a new state-following algorithm on CIS potential energy surfaces. Most clusters were found to completely dissociate and resulted in a single excited atomic state (90%), however, some trajectories formed bound, He*2 (3%), and a few yielded excited trimers (<0.5%). Comparisons were made with available experimental information on much larger clusters. Various applications of this state following algorithm are also presented. In addition to AIMD, these include excited-state geometry optimization and minimal energy path finding via the growing string method. When using state following we demonstrate that more physical results can be obtained with AIMD calculations. Also, the optimized geometries of three excited states of cytosine, two of which were not found without state following, and the minimal energy path between the lowest two singlet excited states of protonated formaldimine are offered as example applications. Finally, to address large clusters, a local variation of CIS was developed. This method exploits the properties of absolutely localized molecular orbitals (ALMOs) to limit the total number of excitations to scaling only linearly with cluster size, which results in formal scaling with the third power of the system size. The derivation of the equations and design of the algorithm are discussed in detail, and computational timings as well as a pilot application to the size dependence of the helium cluster spectrum are presented.

Observation of correlated electronic decay in expanding clusters triggered by near-infrared fields

PubMed Central

Schütte, B.; Arbeiter, M.; Fennel, T.; Jabbari, G.; Kuleff, A.I.; Vrakking, M.J.J.; Rouzée, A.

2015-01-01

When an excited atom is embedded into an environment, novel relaxation pathways can emerge that are absent for isolated atoms. A well-known example is interatomic Coulombic decay, where an excited atom relaxes by transferring its excess energy to another atom in the environment, leading to its ionization. Such processes have been observed in clusters ionized by extreme-ultraviolet and X-ray lasers. Here, we report on a correlated electronic decay process that occurs following nanoplasma formation and Rydberg atom generation in the ionization of clusters by intense, non-resonant infrared laser fields. Relaxation of the Rydberg states and transfer of the available electronic energy to adjacent electrons in Rydberg states or quasifree electrons in the expanding nanoplasma leaves a distinct signature in the electron kinetic energy spectrum. These so far unobserved electron-correlation-driven energy transfer processes may play a significant role in the response of any nano-scale system to intense laser light. PMID:26469997

Ab initio potential energy and dipole moment surfaces of the F(-)(H2O) complex.

PubMed

Kamarchik, Eugene; Toffoli, Daniele; Christiansen, Ove; Bowman, Joel M

2014-02-05

We present full-dimensional, ab initio potential energy and dipole moment surfaces for the F(-)(H2O) complex. The potential surface is a permutationally invariant fit to 16,114 coupled-cluster single double (triple)/aVTZ energies, while the dipole surface is a covariant fit to 11,395 CCSD(T)/aVTZ dipole moments. Vibrational self-consistent field/vibrational configuration interaction (VSCF/VCI) calculations of energies and the IR-spectrum are presented both for F(-)(H2O) and for the deuterated analog, F(-)(D2O). A one-dimensional calculation of the splitting of the ground state, due to equivalent double-well global minima, is also reported. Copyright © 2013 Elsevier B.V. All rights reserved.

Control of Wannier orbitals for generating tunable Ising interactions of ultracold atoms in an optical lattice

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

Inaba, Kensuke; Tamaki, Kiyoshi; Igeta, Kazuhiro

2014-12-04

In this study, we propose a method for generating cluster states of atoms in an optical lattice. By utilizing the quantum properties of Wannier orbitals, we create an tunable Ising interaction between atoms without inducing the spin-exchange interactions. We investigate the cause of errors that occur during entanglement generations, and then we propose an error-management scheme, which allows us to create high-fidelity cluster states in a short time.

A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24(-) cluster.

PubMed

Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Wang, Lai-Sheng; Boldyrev, Alexander I

2013-10-14

The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24(-) possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24(-) isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.

Preparation of a deuterated polymer: Simulating to produce a solid tritium radioactive source

NASA Astrophysics Data System (ADS)

Hu, Rui; Kan, Wentao; Xiong, Xiaoling; Wei, Hongyuan

2017-08-01

The preparation of a deuterated polymer was performed in order to simulate the production of the corresponding tritiated polymer as a solid tritium radioactive source. Substitution and addition reaction were used to introduce deuterium into the polymer. Proton nuclear magnetic resonance and FT-IR spectroscopy were used to investigate the extent and location of deuterium in the polymer, indicating an effectively deuterated polymer was produced. The thermal analysis showed that the final polymer product could tolerate the environmental temperature below 125 °C in its application. This research provides a prosperous method to prepare solid tritium radioactive source.

Evidence of quantum correlations in the H/D-transfer dynamics in the hydrogen bonds in partially deuterated benzoic acid crystals

NASA Astrophysics Data System (ADS)

Takeda, Sadamu; Tsuzumitani, Akihiko; Chatzidimitriou-Dreismann, C. A.

1992-10-01

A precise investigation of spin—lattice relaxation rates for protons and deuterons of partially deuterated benzoic acid crystals showed a remarkable quenching of the transfer rate of an HD pair in hydrogen-bonded dimeric units of carboxyl groups with increasing concentration of D in the surrounding hydrogen bonds. A similar effect was also observed for partially deuterated crystals of acetylenedicarboxylic acid. This finding supports recent theoretical predictions of thermally activated protonic quantum correlation in condensed matter and proposes a new mechanism for the proton transfer in hydrogen bonds in condensed matter.

Isotope Induced Proton Ordering in Partially Deuterated Aspirin

NASA Astrophysics Data System (ADS)

Schiebel, P.; Papoular, R. J.; Paulus, W.; Zimmermann, H.; Detken, A.; Haeberlen, U.; Prandl, W.

1999-08-01

We report the nuclear density distribution of partially deuterated aspirin, C8H5O4-CH2D, at 300 and 15 K, as determined by neutron diffraction coupled with maximum entropy method image reconstruction. While fully protonated and fully deuterated methyl groups in aspirin are delocalized at low temperatures due to quantum mechanical tunneling, we provide here direct evidence that in aspirin- CH2D at 15 K the methyl hydrogens are localized, while randomly distributed over three sites at 300 K. This is the first observation by diffraction methods of low-temperature isotopic ordering in condensed matter.

Deuterated methanol map towards L1544

NASA Astrophysics Data System (ADS)

Chacón-Tanarro, A.; Caselli, P.; Bizzocchi, L.; Pineda, J. E.; Spezzano, S.; Giuliano, B. M.; Lattanzi, V.; Punanova, A.

Pre-stellar cores are self-gravitating starless dense cores with clear signs of contraction and chemical evolution (Crapsi et al. 2005), considered to represent the initial conditions in the process of star formation (Caselli & Ceccarelli 2012). Theoretical studies predict that CO is one of the precursors of complex organic molecules (COMs) during this cold and dense phase (Tielens et al. 1982; Watanabe et al. 2002). Moreover, when CO starts to deplete onto dust grains (at densities of a few 104 cm-3), the formation of deuterated species is enhanced, as CO accelerates the destruction of important precursors of deuterated molecules (Dalgarno & Lepp 1984). Here, we present the CH_2DOH/CH_3OH column density map toward the pre-stellar core L1544 (Chacón-Tanarro et al., in prep.), taken with the IRAM 30 m antenna. The results are compared with the C17O (1-0) distribution across L1544. As methanol is formed on dust grains via hydrogenation of frozen-out CO, this work allows us to measure the deuteration on surfaces and compared it with gas phase deuteration, as well as CO freeze-out and dust properties. This is important to shed light on the basic chemical processes just before the formation of a stellar system.

Fast deuterium fractionation in magnetized and turbulent filaments

NASA Astrophysics Data System (ADS)

Körtgen, B.; Bovino, S.; Schleicher, D. R. G.; Stutz, A.; Banerjee, R.; Giannetti, A.; Leurini, S.

2018-04-01

Deuterium fractionation is considered as an important process to infer the chemical ages of prestellar cores in filaments. We present here the first magneto-hydrodynamical simulations including a chemical network to study deuterium fractionation in magnetized and turbulent filaments, with a line-mass of Mlin = 42 M⊙ pc-1 within a radius of R = 0.1 pc, and their substructures. The filaments typically show widespread deuterium fractionation with average values ≳ 0.01. For individual cores of similar age, we observe the deuteration fraction to increase with time, but also to be independent of their average properties such as density, virial or mass-to-magnetic flux ratio. We further find a correlation of the deuteration fraction with core mass, average H2 density and virial parameter only at late evolutionary stages of the filament and attribute this to the lifetime of the individual cores. Specifically, chemically old cores reveal higher deuteration fractions. Within the radial profiles of selected cores, we notice differences in the structure of the deuteration fraction or surface density, which we can attribute to their different turbulent properties. High deuteration fractions of the order 0.01 - 0.1 may be reached within approximately 200 kyrs, corresponding to two free-fall times, as defined for cylindrical systems, of the filaments.

Fast deuterium fractionation in magnetized and turbulent filaments

NASA Astrophysics Data System (ADS)

Körtgen, B.; Bovino, S.; Schleicher, D. R. G.; Stutz, A.; Banerjee, R.; Giannetti, A.; Leurini, S.

2018-07-01

Deuterium fractionation is considered as an important process to infer the chemical ages of prestellar cores in filaments. We present here the first magnetohydrodynamical simulations including a chemical network to study deuterium fractionation in magnetized and turbulent filaments, with a line-mass of Mlin = 42 M⊙ pc-1 within a radius of R= 0.1 pc, and their sub-structures. The filaments typically show widespread deuterium fractionation with average values ≳0.01. For individual cores of similar age, we observe the deuteration fraction to increase with time, but also to be independent of their average properties such as density, virial, or mass-to-magnetic flux ratio. We further find a correlation of the deuteration fraction with core mass, average H2 density, and virial parameter only at late evolutionary stages of the filament and attribute this to the lifetime of the individual cores. Specifically, chemically old cores reveal higher deuteration fractions. Within the radial profiles of selected cores, we notice differences in the structure of the deuteration fraction or surface density, which we can attribute to their different turbulent properties. High deuteration fractions of the order of 0.01-0.1 may be reached within approximately 200 kyr, corresponding to two free-fall times, as defined for cylindrical systems, of the filaments.

Detection and quantification of solute clusters in a nanostructured ferritic alloy

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

Miller, Michael K.; Larson, David J.; Reinhard, D. A.

2014-12-26

A series of simulated atom probe datasets were examined with a friends-of-friends method to establish the detection efficiency required to resolve solute clusters in the ferrite phase of a 14YWT nanostructured ferritic alloy. The size and number densities of solute clusters in the ferrite of the as-milled mechanically-alloyed condition and the stir zone of a friction stir weld were estimated with a prototype high-detection-efficiency (~80%) local electrode atom probe. High number densities, 1.8 × 10 24 m –3 and 1.2 × 10 24 m –3, respectively of solute clusters containing between 2 and 9 solute atoms of Ti, Y andmore » O and were detected for these two conditions. Furthermore, these results support first principle calculations that predicted that vacancies stabilize these Ti–Y–O– clusters, which retard diffusion and contribute to the excellent high temperature stability of the microstructure and radiation tolerance of nanostructured ferritic alloys.« less

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

DOE PAGES

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.; ...

2017-03-28

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

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

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Potential of transition metal atoms embedded in buckled monolayer g-C3N4 as single-atom catalysts.

PubMed

Li, Shu-Long; Yin, Hui; Kan, Xiang; Gan, Li-Yong; Schwingenschlögl, Udo; Zhao, Yong

2017-11-15

We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C 3 N 4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C 3 N 4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C 3 N 4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C 3 N 4 gives rise to promising single-atom catalysts at low temperature.

Penning ionization electron spectroscopy of CO 2 clusters in collision with metastable rare gas atoms

NASA Astrophysics Data System (ADS)

Maruyama, Ryo; Tanaka, Hideyasu; Yamakita, Yoshihiro; Misaizu, Fuminori; Ohno, Koichi

2000-09-01

Penning ionization electron spectra (PIES) of CO 2 clusters have been observed for the first time. An unusually fast electron band with excess kinetic energies of 1.4-2.9 eV with respect to the monomer band for the ionic X state was observed for CO 2 clusters in collision with He*(2 3S) atoms. While for PIES with Ne*(3 3P), no such unusual band was observed. The unusual band is ascribed to autoionization into stable structures of ionic clusters to which direct ionization processes are almost impossible due to very small Franck-Condon overlaps associated with a very large geometry difference between the ionic and neutral clusters.

Al6H18: A baby crystal of γ-AlH3

NASA Astrophysics Data System (ADS)

Kiran, B.; Kandalam, Anil K.; Xu, Jing; Ding, Y. H.; Sierka, M.; Bowen, K. H.; Schnöckel, H.

2012-10-01

Using global-minima search methods based on the density functional theory calculations of (AlH3)n (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring structures of AlH3 were predicted to be the preferred structures in which the Al atoms can have a maximum of five-fold coordination. Our calculations also reveal that the Al6H18 cluster, with its hexa-coordination of the Al atoms, resembles the unit-cell of γ-AlH3, thus Al6H18 is designated as the "baby crystal." The fragmentation energies of the (AlH3)n (n = 2-8) along with the dimerization energies for even n clusters indicate an enhanced stability of the Al6H18 cluster. Both covalent (hybridization) and ionic (charge) contribution to the bonding are the driving factors in stabilizing the isomers containing hexa-coordinated Al atoms.

Recent development in deciphering the structure of luminescent silver nanodots

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Yu, Junhua

2017-05-01

Matrix-stabilized silver clusters and stable luminescent few-atom silver clusters, referred to as silver nanodots, show notable difference in their photophysical properties. We present recent research on deciphering the nature of silver clusters and nanodots and understanding the factors that lead to variations in luminescent mechanisms. Due to their relatively simple structure, the matrix-stabilized clusters have been well studied. However, the single-stranded DNA (ssDNA)-stabilized silver nanodots that show the most diverse emission wavelengths and the best photophysical properties remain mysterious species. It is clear that their photophysical properties highly depend on their protection scaffolds. Analyses from combinations of high-performance liquid chromatography, inductively coupled plasma-atomic emission spectroscopy, electrophoresis, and mass spectrometry indicate that about 10 to 20 silver atoms form emissive complexes with ssDNA. However, it is possible that not all of the silver atoms in the complex form effective emission centers. Investigation of the nanodot structure will help us understand why luminescent silver nanodots are stable in aqueous solution and how to further improve their chemical and photophysical properties.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

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

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

Evolution of the properties of Al(n)N(n) clusters with size.

PubMed

Costales, Aurora; Blanco, M A; Francisco, E; Pandey, Ravindra; Martín Pendás, A

2005-12-29

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

Hydrides of Alkaline Earth–Tetrel (AeTt) Zintl Phases: Covalent Tt–H Bonds from Silicon to Tin

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

Auer, Henry; Guehne, Robin; Bertmer, Marko

Zintl phases form hydrides either by incorporating hydride anions (interstitial hydrides) or by covalent bonding of H to the polyanion (polyanionic hydrides), which yields a variety of different compositions and bonding situations. Hydrides (deuterides) of SrGe, BaSi, and BaSn were prepared by hydrogenation (deuteration) of the CrB-type Zintl phases AeTt and characterized by laboratory X-ray, synchrotron, and neutron diffraction, NMR spectroscopy, and quantum-chemical calculations. SrGeD4/3–x and BaSnD4/3–x show condensed boatlike six-membered rings of Tt atoms, formed by joining three of the zigzag chains contained in the Zintl phase. These new polyanionic motifs are terminated by covalently bound H atoms withmore » d(Ge–D) = 1.521(9) Å and d(Sn–D) = 1.858(8) Å. Additional hydride anions are located in Ae4 tetrahedra; thus, the features of both interstitial hydrides and polyanionic hydrides are represented. BaSiD2–x retains the zigzag Si chain as in the parent Zintl phase, but in the hydride (deuteride), it is terminated by H (D) atoms, thus forming a linear (SiD) chain with d(Si–D) = 1.641(5) Å.« less

Sixteenth International Conference on the physics of electronic and atomic collisions

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

Dalgarno, A.; Freund, R.S.; Lubell, M.S.

1989-01-01

This report contains abstracts of papers on the following topics: photons, electron-atom collisions; electron-molecule collisions; electron-ion collisions; collisions involving exotic species; ion- atom collisions, ion-molecule or atom-molecule collisions; atom-atom collisions; ion-ion collisions; collisions involving rydberg atoms; field assisted collisions; collisions involving clusters and collisions involving condensed matter.

Behaviors of transmutation elements Re and Os and their effects on energetics and clustering of vacancy and self-interstitial atoms in W

NASA Astrophysics Data System (ADS)

Li, Yu-Hao; Zhou, Hong-Bo; Jin, Shuo; Zhang, Ying; Deng, Huiqiu; Lu, Guang-Hong

2017-04-01

We investigate the behaviors of rhenium (Re) and osmium (Os) and their interactions with point defects in tungsten (W) using a first-principles method. We show that Re atoms are energetically favorable to disperse separately in bulk W due to the Re-Re repulsive interaction. Despite the attractive interaction between Os atoms, there is still a large activation energy barrier of 1.10 eV at the critical number of 10 for the formation of Os clusters in bulk W based on the results of the total nucleation free energy change. Interestingly, the presence of vacancy can significantly reduce the total nucleation free energy change of Re/Os clusters, suggesting that vacancy can facilitate the nucleation of Re/Os in W. Re/Os in turn has an effect on the stability of the vacancy clusters (V n ) in W, especially for small vacancy clusters. A single Re/Os atom can raise the total binding energies of V2 and V3 obviously, thus enhancing their formation. Further, we demonstrate that there is a strong attractive interaction between Re/Os and self-interstitial atoms (SIAs). Re/Os could increase the diffusion barrier of SIAs and decrease their rotation barrier, while the interstitial-mediated path may be the optimal diffusion path of Re/Os in W. Consequently, the synergistic effect between Re/Os and point defects plays a key role in Re/Os precipitation and the evolution of defects in irradiated W.

Synthesis of specifically deuterated S-benzylcysteines and of oxytocin and related diastereomers deuterated in the half-cystine positions

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

Upson, D.A.; Hruby, V.J.

1976-04-16

S-Benzylcysteine derivatives specifically deuterated at the ..cap alpha.. carbon only, the ..beta.. carbon only, and at both the ..cap alpha.. and ..beta.. carbons have been synthesized. These labeled compounds have been enzymatically resolved and the enantiomers and reacemates have been converted to the N-tert-butyloxycarbonyl derivatives. The deuterium labels were not exchanged under the conditions of the syntheses. Condensation of the sodium salt of diethyl ..cap alpha..-acetami-domalonate with benzyl chloromethyl sulfide followed by hydrolysis with DCl afforded S-benzyl-DL-(..cap alpha..-/sup 2/H/sub 1/) cysteine. Acetylation followed by treatment with hog renal acylase separated the stereoisomers. A Mannich reaction with (/sup 2/H/sub 2/) methylenemore » diacetate, diethyl ..cap alpha..-acetamido-..cap alpha..-dimethylamino(/sup 2/H/sub 2/)methylmalonate methiodide (15). Treatment of 15 with sodium benzylmercaptide gave diethyl ..cap alpha..-acetamido-..cap alpha..-benzylthio(/sup 2/H/sub 2/)methylmalonate, which was hydrolyzed with HCl to yield S-benzyl-DL-(..beta..,..beta..-/sup 2/H/sub 2/)cysteine or with DCl to afford S-benzyl-DL-(..cap alpha..,..beta..,..beta..,-/sup 2/H/sub 3/)cysteine. These compounds were resolved as before. The preparation of S-benzyl-DL-(..cap alpha..,..beta..,..beta..-/sup 2/H/sub 3/)cysteine required an efficient source of ethanol-d. This deuterated solvent was prepared in quantitative yield in 2 h from tetraethoxysilane, D/sub 2/O, and a catalytic amount of thionyl chloride. The protected deuterated amino acids were used in the preparation of several oxytocin analogues in which the specific deuteration appears in either the 1-hemicystine or the 6-hemicystine residues.« less

Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications.

PubMed

Hiruma-Shimizu, Kazumi; Shimizu, Hiroki; Thompson, Gary S; Kalverda, Arnout P; Patching, Simon G

2015-01-01

Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-β-D-glucoside (β-OG), n-dodecyl-β-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR.

Plasmon excitations in doped square-lattice atomic clusters

NASA Astrophysics Data System (ADS)

Wang, Yaxin; Yu, Ya-Bin

2017-12-01

Employing the tight-binding model, we theoretically study the properties of the plasmon excitations in doped square-lattice atomic clusters. The results show that the dopant atoms would blur the absorption spectra, and give rise to extra plasmon resonant peaks as reported in the literature; however, our calculated external-field induced oscillating charge density shows that no obvious evidences indicate the so-called local mode of plasmon appearing in two-dimensional-doped atomic clusters, but the dopants may change the symmetry of the charge distribution. Furthermore, we show that the disorder of the energy level due to dopant makes the absorption spectrum has a red- or blue-shift, which depends on the position of impurities; disorder of hopping due to dopant makes a blue- or red-shift, a larger (smaller) hopping gives a blue-shift (red-shift); and a larger (smaller) host-dopant and dopant-dopant intersite coulomb repulsion induces a blue-shift (red-shift).

Atomically precise organomimetic cluster nanomolecules assembled via perfluoroaryl-thiol SNAr chemistry

NASA Astrophysics Data System (ADS)

Qian, Elaine A.; Wixtrom, Alex I.; Axtell, Jonathan C.; Saebi, Azin; Jung, Dahee; Rehak, Pavel; Han, Yanxiao; Moully, Elamar Hakim; Mosallaei, Daniel; Chow, Sylvia; Messina, Marco S.; Wang, Jing Yang; Royappa, A. Timothy; Rheingold, Arnold L.; Maynard, Heather D.; Král, Petr; Spokoyny, Alexander M.

2017-04-01

The majority of biomolecules are intrinsically atomically precise, an important characteristic that enables rational engineering of their recognition and binding properties. However, imparting a similar precision to hybrid nanoparticles has been challenging because of the inherent limitations of existing chemical methods and building blocks. Here we report a new approach to form atomically precise and highly tunable hybrid nanomolecules with well-defined three-dimensionality. Perfunctionalization of atomically precise clusters with pentafluoroaryl-terminated linkers produces size-tunable rigid cluster nanomolecules. These species are amenable to facile modification with a variety of thiol-containing molecules and macromolecules. Assembly proceeds at room temperature within hours under mild conditions, and the resulting nanomolecules exhibit high stabilities because of their full covalency. We further demonstrate how these nanomolecules grafted with saccharides can exhibit dramatically improved binding affinity towards a protein. Ultimately, the developed strategy allows the rapid generation of precise molecular assemblies to investigate multivalent interactions.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Gold atoms and dimers on amorphous SiO(2): calculation of optical properties and cavity ringdown spectroscopy measurements.

PubMed

Del Vitto, Annalisa; Pacchioni, Gianfranco; Lim, Kok Hwa; Rösch, Notker; Antonietti, Jean-Marie; Michalski, Marcin; Heiz, Ulrich; Jones, Harold

2005-10-27

We report on the optical absorption spectra of gold atoms and dimers deposited on amorphous silica in size-selected fashion. Experimental spectra were obtained by cavity ringdown spectroscopy. Issues on soft-landing, fragmentation, and thermal diffusion are discussed on the basis of the experimental results. In parallel, cluster and periodic supercell density functional theory (DFT) calculations were performed to model atoms and dimers trapped on various defect sites of amorphous silica. Optically allowed electronic transitions were calculated, and comparisons with the experimental spectra show that silicon dangling bonds [[triple bond]Si(.-)], nonbridging oxygen [[triple bond]Si-O(.-)], and the silanolate group [[triple bond]Si-O(-)] act as trapping centers for the gold particles. The results are not only important for understanding the chemical bonding of atoms and clusters on oxide surfaces, but they will also be of fundamental interest for photochemical studies of size-selected clusters on surfaces.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Negative ion productions in high velocity collision between small carbon clusters and Helium atom target

NASA Astrophysics Data System (ADS)

M, Chabot; K, Béroff; T, Pino; G, Féraud; N, Dothi; Padellec A, Le; G, Martinet; S, Bouneau; Y, Carpentier

2012-11-01

We measured absolute double capture cross section of Cn+ ions (n=1,5) colliding, at 2.3 and 2.6 a.u velocities, with an Helium target atom and the branching ratios of fragmentation of the so formed electronically excited anions Cn-*. We also measured absolute cross section for the electronic attachment on neutral Cn clusters colliding at same velocities with He atom. This is to our knowledge the first measurement of neutral-neutral charge exchange in high velocity collision.

Tight-binding study of Si2Cn (n = 3 to 42) fullerene-like or nanodiamonds microclusters: are Si atoms isolated or adjacent?

NASA Astrophysics Data System (ADS)

Leleyter, M.; Olivi-Tran, N.

2008-12-01

We studied in tight-binding approximation involving spν hybridization (ν=2,3), some Si2Cn (n=3 to 42) microclusters. We then investigated, on one hand, fragments of fullerene-like structures (sp2), and on the other hand, nanodiamonds (sp3) of adamantane-type or a 44-atom nanodiamond (with 2 inner atoms which are assumed to play the role of bulk atoms). We compared the stabilities, i.e. the electronic energies of these clusters, according to the various positions of the 2 Si atoms. Results are very different in the two kinds of hybridization. Besides, they can be analysed according to two different points of view: either the clusters are considered as small particles with limited sizes, or they are assumed to be used as models in order to simulate the Si-atom behaviour in very larger systems. In sp2 hybridization (fullerene-like geometries), the most stable isomer is always encountered when the 2 Si atoms build a Si2 group, and this result holds for both viewpoints quoted above. Conversely, in sp3 hybridization (nanodiamonds), since Si atoms “prefer” sites having the minimum connectivity, they are never found in adjacent sites. We see that with a simple and fast computational method we can explain an experimental fact which is very interesting such as the relative position of two heteroatoms in the cluster. This enhances the generality and the fecondity in the tight binding approximation due essentially to the link between this model and the graph theory, link based on the topology of the clusters.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework

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

Kim, In Soo; Li, Zhanyong; Zheng, Jian

Installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 degrees C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and Xray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novelmore » catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support.« less

Atomic-scale structure and electronic properties of GaN/GaAs superlattices

NASA Astrophysics Data System (ADS)

Goldman, R. S.; Feenstra, R. M.; Briner, B. G.; O'Steen, M. L.; Hauenstein, R. J.

1996-12-01

We have investigated the atomic-scale structure and electronic properties of GaN/GaAs superlattices produced by nitridation of a molecular beam epitaxially grown GaAs surface. Using cross-sectional scanning tunneling microscopy (STM) and spectroscopy, we show that the nitrided layers are laterally inhomogeneous, consisting of groups of atomic-scale defects and larger clusters. Analysis of x-ray diffraction data in terms of fractional area of clusters (determined by STM), reveals a cluster lattice constant similar to bulk GaN. In addition, tunneling spectroscopy on the defects indicates a conduction band state associated with an acceptor level of NAs in GaAs. Therefore, we identify the clusters and defects as nearly pure GaN and NAs, respectively. Together, the results reveal phase segregation in these arsenide/nitride structures, in agreement with the large miscibility gap predicted for GaAsN.

Metallothionein-like multinuclear clusters of mercury(II) and sulfur in peat

USGS Publications Warehouse

Nagy, K.L.; Manceau, A.; Gasper, J.D.; Ryan, J.N.; Aiken, G.R.

2011-01-01

Strong mercury(II)-sulfur (Hg-SR) bonds in natural organic matter, which influence mercury bioavailability, are difficult to characterize. We report evidence for two new Hg-SR structures using X-ray absorption spectroscopy in peats from the Florida Everglades with added Hg. The first, observed at a mole ratio of organic reduced S to Hg (Sred/Hg) between 220 and 1140, is a Hg4Sx type of cluster with each Hg atom bonded to two S atoms at 2.34 ?? and one S at 2.53 ??, and all Hg atoms 4.12 ?? apart. This model structure matches those of metal-thiolate clusters in metallothioneins, but not those of HgS minerals. The second, with one S atom at 2.34 ?? and about six C atoms at 2.97 to 3.28 ??, occurred at S red/Hg between 0.80 and 4.3 and suggests Hg binding to a thiolated aromatic unit. The multinuclear Hg cluster indicates a strong binding environment to cysteinyl sulfur that might impede methylation. Along with a linear Hg(SR)2 unit with Hg - S bond lengths of 2.34 ?? at Sred/Hg of about 10 to 20, the new structures support a continuum in Hg-SR binding strength in natural organic matter. ?? 2011 American Chemical Society.

Interatomic scattering in energy dependent photoelectron spectra of Ar clusters

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

Patanen, M.; Benkoula, S.; Nicolas, C.

2015-09-28

Soft X-ray photoelectron spectra of Ar 2p levels of atomic argon and argon clusters are recorded over an extended range of photon energies. The Ar 2p intensity ratios between atomic argon and clusters’ surface and bulk components reveal oscillations similar to photoelectron extended X-ray absorption fine structure signal (PEXAFS). We demonstrate here that this technique allows us to analyze separately the PEXAFS signals from surface and bulk sites of free-standing, neutral clusters, revealing a bond contraction at the surface.

Comparative study of local atomic structures in Zr2CuxNi1-x (x = 0, 0.5, 1) metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2015-11-01

Extensive analysis has been performed to understand the key structural motifs accounting for the difference in glass forming ability in the Zr-Cu and Zr-Ni binary alloy systems. Here, the reliable atomic structure models of Zr2CuxNi1-x (x = 0, 0.5, 1) are constructed using the combination of X-ray diffraction experiments, ab initio molecular dynamics simulations and a constrained reverse Monte Carlo method. We observe a systematic variation of the interatomic distance of different atomic pairs with respect to the alloy composition. The ideal icosahedral content in all samples is limited, despite the high content of five-fold symmetry motifs. We also demonstrate that the population of Z-clusters in Zr2Cu glass is much higher than that in the Zr2Ni and Zr2Cu0.5Ni0.5 samples. And Z12 ⟨0, 0, 12, 0⟩ Voronoi polyhedra clusters prefer to form around Cu atoms, while Ni-centered clusters are more like Z11 ⟨0, 2, 8, 1⟩ clusters, which is less energetically stable compared to Z12 clusters. These two different structural properties may account for the higher glass forming ability of Zr2Cu alloy than that of Zr2Ni alloy.

NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

PubMed

Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

2014-10-01

Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

Super-reduced polyoxometalates: excellent molecular cluster battery components and semipermeable molecular capacitors.

PubMed

Nishimoto, Yoshio; Yokogawa, Daisuke; Yoshikawa, Hirofumi; Awaga, Kunio; Irle, Stephan

2014-06-25

Theoretical investigations are presented on the molecular and electronic structure changes that occur as α-Keggin-type polyoxometalate (POM(3-)) clusters [PM12O40](3-) (M = Mo, W) are converted toward their super-reduced POM(27-) state during the discharging process in lithium-based molecular cluster batteries. Density functional theory was employed in geometry optimization, and first-principles molecular dynamics simulations were used to explore local minima on the potential energy surface of neutral POM clusters adorned with randomly placed Li atoms as electron donors around the cluster surface. On the basis of structural, electron density, and molecular orbital studies, we present evidence that the super-reduction is accompanied by metal-metal bond formation, beginning from the 12th to 14th excess electron transferred to the cluster. Afterward, the number of metal-metal bonds increases nearly linearly with the number of additionally transferred excess electrons. In α-Keggin-type POMs, metal triangles are a prominently emerging structural feature. The origin of the metal triangle formation during super-reduction stems from the formation of characteristic three-center two-electron bonds in triangular metal atom sites, created under preservation of the POM skeleton via "squeezing out" of oxygen atoms bridging two metal atoms when the underlying metal atoms form covalent bonds. The driving force for this unusual geometrical and electronic structure change is a local Jahn-Teller distortion at individual transition-metal octahedral sites, where the triply degenerate t2 d orbitals become partially filled during reduction and gain energy by distortion of the octahedron in such a way that metal-metal bonds are formed. The bonding orbitals show strong contributions from mixing with metal-oxygen antibonding orbitals, thereby "shuffling away" excess electrons from the cluster center to the outside of the cage. The high density of negatively charged yet largely separated oxygen atoms on the surface of the super-reduced POM(27-) polyanion allows the huge Coulombic repulsion due to the presence of the excess electrons to be counterbalanced by the presence of Li countercations, which partially penetrate into the outer oxygen shell. This "semiporous molecular capacitor" structure is likely the reason for the effective electron uptake in POMs.

Dielectric properties of betaine phosphite and deuterated betaine phosphite films

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

Balashova, E. V., E-mail: balashova@mail.ioffe.ru; Krichevtsov, B. B.; Zaitseva, N. V.

2011-01-15

Polycrystalline films of betaine phosphite (BPI) and deuterated BPI have been grown by evaporation on LiNbO{sub 3}, {alpha}-SiO{sub 2}, {alpha}-Al{sub 2}O{sub 3}, and NdGaO{sub 3} substrates. These films consist of large single-crystal blocks in which the polar axis (b) lies in the substrate plane. The results of studying the dielectric properties of the films using interdigital electrodes, X-ray diffraction, and block images in a polarized-light microscope in reflection are reported. The film transition into the ferroelectric state at T = T{sub c} is accompanied by strong anomalies of the capacitance of the film/interdigital structure/substrate structure. The deuteration of BPI filmsmore » leads to an increase in their temperature T{sub c}: from T{sub c} = 200 K for BPI-based structures to T{sub c} = 280 K for structures with a high degree of deuteration (d {approx} 90%).« less

Boronization on NSTX using Deuterated Trimethylboron

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

W.R. Blanchard; R.C. Gernhardt; H.W. Kugel

2002-01-28

Boronization on the National Spherical Torus Experiment (NSTX) has proved to be quite beneficial with increases in confinement and density, and decreases in impurities observed in the plasma. The boron has been applied to the interior surfaces of NSTX, about every 2 to 3 weeks of plasma operation, by producing a glow discharge in the vacuum vessel using deuterated trimethylboron (TMB) in a 10% mixture with helium. Special NSTX requirements restricted the selection of the candidate boronization method to the use of deuterated boron compounds. Deuterated TMB met these requirements, but is a hazardous gas and special care in themore » execution of the boronization process is required. This paper describes the existing GDC, Gas Injection, and Torus Vacuum Pumping System hardware used for this process, the glow discharge process, and the automated control system that allows for remote operation to maximize both the safety and efficacy of applying the boron coating. The administrative requirements and the detailed procedure for the setup, operation and shutdown of the process are also described.« less

Special and general superatoms.

PubMed

Luo, Zhixun; Castleman, A Welford

2014-10-21

Bridging the gap between atoms and macroscopic matter, clusters continue to be a subject of increasing research interest. Among the realm of cluster investigations, an exciting development is the realization that chosen stable clusters can mimic the chemical behavior of an atom or a group of the periodic table of elements. This major finding known as a superatom concept was originated experimentally from the study of aluminum cluster reactivity conducted in 1989 by noting a dramatic size dependence of the reactivity where cluster anions containing a certain number of Al atoms were unreactive toward oxygen while the other species were etched away. This observation was well interpreted by shell closings on the basis of the jellium model, and the related concept (originally termed "unified atom") spawned a wide range of pioneering studies in the 1990s pertaining to the understanding of factors governing the properties of clusters. Under the inspiration of a superatom concept, advances in cluster science in finding stable species not only shed light on magic clusters (i.e., superatomic noble gas) but also enlightened the exploration of stable clusters to mimic the chemical behavior of atoms leading to the discovery of superhalogens, alkaline-earth metals, superalkalis, etc. Among them, certain clusters could enable isovalent isomorphism of precious metals, indicating application potential for inexpensive superatoms for industrial catalysis, while a few superalkalis were found to validate the interesting "harpoon mechanism" involved in the superatomic cluster reactivity; recently also found were the magnetic superatoms of which the cluster-assembled materials could be used in spin electronics. Up to now, extensive studies in cluster science have allowed the stability of superatomic clusters to be understood within a few models, including the jellium model, also aromaticity and Wade-Mingos rules depending on the geometry and metallicity of the cluster. However, the scope of application of the jellium model and modification of the theory to account for nonspherical symmetry and nonmetal-doped metal clusters are still illusive to be further developed. It is still worth mentioning that a superatom concept has also been introduced in ligand-stabilized metal clusters which could also follow the major shell-closing electron count for a spherical, square-well potential. By proposing a new concept named as special and general superatoms, herein we try to summarize all these investigations in series, expecting to provide an overview of this field with a primary focus on the joint undertakings which have given rise to the superatom concept. To be specific, for special superatoms, we limit to clusters under a strict jellium model and simply classify them into groups based on their valence electron counts. While for general superatoms we emphasize on nonmetal-doped metal clusters and ligand-stabilized metal clusters, as well as a few isovalent cluster systems. Hopefully this summary of special and general superatoms benefits the further development of cluster-related theory, and lights up the prospect of using them as building blocks of new materials with tailored properties, such as inexpensive isovalent systems for industrial catalysis, semiconductive superatoms for transistors, and magnetic superatoms for spin electronics.

Diffusion Monte Carlo studies of MB-pol (H2O)2-6 and (D2O)2-6 clusters: Structures and binding energies

NASA Astrophysics Data System (ADS)

Mallory, Joel D.; Mandelshtam, Vladimir A.

2016-08-01

We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

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

Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong

2015-07-29

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. Themore » higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.« less

Probing the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters by density functional calculations

NASA Astrophysics Data System (ADS)

Lu, Sheng-Jie

2018-05-01

We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

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.

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales.

PubMed

Huang, Shiping

2017-11-13

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

NASA Astrophysics Data System (ADS)

Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

2016-05-01

Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales

NASA Astrophysics Data System (ADS)

Huang, Shiping

2017-11-01

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

H2 Ortho-to-para Conversion on Grains: A Route to Fast Deuterium Fractionation in Dense Cloud Cores?

NASA Astrophysics Data System (ADS)

Bovino, S.; Grassi, T.; Schleicher, D. R. G.; Caselli, P.

2017-11-01

Deuterium fractionation, I.e., the enhancement of deuterated species with respect to non-deuterated ones, is considered to be a reliable chemical clock of star-forming regions. This process is strongly affected by the ortho-to-para H2 ratio. In this Letter we explore the effect of the ortho-para (o-p) H2 conversion on grains on the deuteration timescale in fully-depleted dense cores, including the most relevant uncertainties that affect this complex process. We show that (I) the o-p H2 conversion on grains is not strongly influenced by the uncertainties on the conversion time and the sticking coefficient, and (II) that the process is controlled by the temperature and the residence time of ortho-H2 on the surface, I.e., by the binding energy. We find that for binding energies between 330 and 550 K, depending on the temperature, the o-p H2 conversion on grains can shorten the deuterium fractionation timescale by orders of magnitude, opening a new route for explaining the large observed deuteration fraction D frac in dense molecular cloud cores. Our results suggest that the star formation timescale, when estimated through the timescale to reach the observed deuteration fractions, might be shorter than previously proposed. However, more accurate measurements of the binding energy are needed in order to better assess the overall role of this process.

Role of radial nonuniformities in the interaction of an intense laser with atomic clusters

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

Holkundkar, Amol R.; Gupta, N. K.

A model for the interaction of an intense laser with atomic clusters is presented. The model takes into account the spatial nonuniformities of the cluster as it evolves in time. The cluster is treated as a stratified sphere having an arbitrary number of layers. Electric and magnetic fields are obtained by solving the vector Helmholtz equation coupled with one-dimensional Lagrangian hydrodynamics. Results are compared with the uniform density nanoplasma model. Enhancement in the amount of energy absorbed is seen over the uniform density model. In some cases the absorbed energy increases by as much as a factor of 40.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

A model for sputtering from solid surfaces bombarded by energetic clusters

NASA Astrophysics Data System (ADS)

Benguerba, Messaoud

2018-04-01

A model is developed to explain and predict the sputtering from solid surfaces bombarded by energetic clusters, on the basis of shock wave generated at the impact of cluster. Under the shock compression the temperature increases causing the vaporization of material that requires an internal energy behind the shock, at least, of about twice the cohesive energy of target. The sputtering is treated as a gas of vaporized particles from a hemispherical volume behind the shock front. The sputter yield per cluster atoms is given as a universal function depending on the ratio of target to cluster atomic density and the ratio of cluster velocity to the velocity calculated on the basis of an internal energy equals about twice cohesive energy. The predictions of the model for self sputter yield of copper, gold, tungsten and of silver bombarded by C60 clusters agree well, with the corresponding data simulated by molecular dynamics.

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

Alexandrova, Anastassia N.; Nayhouse, Michael J.; Huynh, Mioy T.

CAl₄²-/- (D₄h, ¹A₁g) is is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al₄, facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl₄²-/- (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, evenmore » though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al₄. From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn₄²-/-.« less

Structural, electronic and magnetic properties of Ti n Mo ( n = 1 - 7) clusters

NASA Astrophysics Data System (ADS)

Zhang, Ge; Zhai, Zhongyuan; Sheng, Yong

2017-04-01

The ground state structures of TinMo and Tin+1 (n = 1 - 7) clusters and their structural, electronic and magnetic properties are investigated with the density functional method at B3LYP/LanL2DZ level. One Mo atom substituted Tin+1 structure is the dominant growth pattern, and the TinMo clusters exhibit enhanced structural stabilities according to the averaged binding energies. The electronic properties are also discussed by investigating chemical hardness and HOMO-LUMO energy gap. The results reveal that Ti3Mo and Ti5Mo keep higher chemical stabilities when compared with the other clusters. For all the studied clusters, the Mo atoms always get electrons from Ti atoms and present negative charges. Moreover, the doping of Mo in the bare titanium clusters can alter the magnetic moments of them. Ti3Mo and Ti5Mo show relatively large total magnetic moments, which may be related to the presence of exchange splitting behavior in their densities of states. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-70589-8

Re-solution of xenon clusters in plutonium dioxide under the collision cascade impact: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Seitov, D. D.; Nekrasov, K. A.; Kupryazhkin, A. Ya.; Gupta, S. K.; Akilbekov, A. T.

2017-09-01

The interaction of xenon clusters with the collision cascades in the PuO2 crystals is investigated using the molecular dynamics simulation and the approximation of the pair interaction potentials. The potentials of interaction of Xe atoms with the surrounding particles in the crystal lattice are suggested, that are valid in the range of high collision energies. The cascades created by the recoil 235U ions formed as the plutonium α-decay product are considered, and the influence of such cascades on the structure of the xenon clusters is analyzed. It is shown, that the cascade-cluster interaction leads to release of the xenon atoms from the clusters and their subsequent re-solution in the crystal bulk.

Understanding the Cu-Zn brass alloys using a short-range-order cluster model: significance of specific compositions of industrial alloys

PubMed Central

Hong, H. L.; Wang, Q.; Dong, C.; Liaw, Peter K.

2014-01-01

Metallic alloys show complex chemistries that are not yet understood so far. It has been widely accepted that behind the composition selection lies a short-range-order mechanism for solid solutions. The present paper addresses this fundamental question by examining the face-centered-cubic Cu-Zn α-brasses. A new structural approach, the cluster-plus-glue-atom model, is introduced, which suits specifically for the description of short-range-order structures in disordered systems. Two types of formulas are pointed out, [Zn-Cu12]Zn1~6 and [Zn-Cu12](Zn,Cu)6, which explain the α-brasses listed in the American Society for Testing and Materials (ASTM) specifications. In these formulas, the bracketed parts represent the 1st-neighbor cluster, and each cluster is matched with one to six 2nd-neighbor Zn atoms or with six mixed (Zn,Cu) atoms. Such a cluster-based formulism describes the 1st- and 2nd-neighbor local atomic units where the solute and solvent interactions are ideally satisfied. The Cu-Ni industrial alloys are also explained, thus proving the universality of the cluster-formula approach in understanding the alloy selections. The revelation of the composition formulas for the Cu-(Zn,Ni) industrial alloys points to the common existence of simple composition rules behind seemingly complex chemistries of industrial alloys, thus offering a fundamental and practical method towards composition interpretations of all kinds of alloys. PMID:25399835

Understanding the Cu-Zn brass alloys using a short-range-order cluster model: Significance of specific compositions of industrial alloys

DOE PAGES

Hong, H. L.; Wang, Q.; Dong, C.; ...

2014-11-17

Metallic alloys show complex chemistries that are not yet understood so far. It has been widely accepted that behind the composition selection lies a short-range-order mechanism for solid solutions. The present paper addresses this fundamental question by examining the face-centered-cubic Cu-Zn α-brasses. A new structural approach, the cluster-plus-glue-atom model, is introduced, which suits specifically for the description of short-range-order structures in disordered systems. Two types of formulas are pointed out, [Zn-Cu 12]Zn 1~6 and [Zn-Cu 12](Zn,Cu) 6, which explain the α-brasses listed in the American Society for Testing and Materials (ASTM) specifications. In these formulas, the bracketed parts represent themore » 1 st-neighbor cluster, and each cluster is matched with one to six 2 nd-neighbor Zn atoms or with six mixed (Zn,Cu) atoms. Such a cluster-based formulism describes the 1 st- and 2 nd-neighbor local atomic units where the solute and solvent interactions are ideally satisfied. The Cu-Ni industrial alloys are also explained, thus proving the universality of the cluster-formula approach in understanding the alloy selections. As a result, the revelation of the composition formulas for the Cu-(Zn,Ni) industrial alloys points to the common existence of simple composition rules behind seemingly complex chemistries of industrial alloys, thus offering a fundamental and practical method towards composition interpretations of all kinds of alloys.« less

Cluster-impact fusion, or beam-contaminant fusion? (abstract)a),b)

NASA Astrophysics Data System (ADS)

Lo, Daniel H.; Petrasso, Richard D.; Wenzel, Kevin W.

1992-10-01

Beuhler, Friedlander, and Friedman (BFF) reported anomalously huge D-D fusion rates while bombarding deuterated targets with (D2O)N+ clusters (N˜25-1000) accelerated to ≊325 keV [R. J. Beuhler et al., Phys. Rev. Lett. 63, 1292 (1989); R. J. Beuhler et al., J. Phys. Chem. 94, 7665 (1990)] [i.e., ≊0.3 keV lab energy for D in (D2O)100+]. However, from our analysis of BFF's fusion product spectra, we conclude that their D lab energy was ˜50 keV. Therefore, no gross anomalies exist. Also, from our analysis of the BFF beam-ranging experiments through 500 μg/cm2 of Au, we conclude that light-ion-beam contaminants (e.g., D+ of order 100 keV) have not been ruled out, and are the probable cause of their fusion reactions. This work was supported by LLNL Subcontract B116798, Department of Energy (DOE) Grant No. DE-FG02-91ER54109, DOE Magnetic Fusion Energy Technology Fellowship Program (D. H. Lo), and DOE Fusion Energy Postdoctoral Research Program (Kevin W. Wenzel).

Structural, electronic, vibrational and optical properties of Bin clusters

NASA Astrophysics Data System (ADS)

Liang, Dan; Shen, Wanting; Zhang, Chunfang; Lu, Pengfei; Wang, Shumin

2017-10-01

The neutral, anionic and cationic bismuth clusters with the size n up to 14 are investigated by using B3LYP functional within the regime of density functional theory and the LAN2DZ basis set. By analysis of the geometries of the Bin (n = 2-14) clusters, where cationic and anionic bismuth clusters are largely similar to those of neutral ones, a periodic effect by adding units with one to four atoms into smaller cluster to form larger cluster is drawn for the stable structures of bismuth clusters. An even-odd alteration is shown for the properties of the clusters, such as the calculated binding energies and dissociation energies, as well as frontier orbital energies, electron affinities, ionization energies. All the properties indicate that the Bi4 cluster is the most possible existence in bismuth-containing materials, which supports the most recent experiment. The orbital compositions, infrared and Raman activities and the ultraviolet absorption of the most possible tetramer bismuth cluster are given in detail to reveal the periodic tendency of adding bismuth atoms and the stability of tetramer bismuth cluster.

Transfer-free synthesis of graphene-like atomically thin carbon films on SiC by ion beam mixing technique

NASA Astrophysics Data System (ADS)

Zhang, Rui; Chen, Fenghua; Wang, Jinbin; Fu, Dejun

2018-03-01

Here we demonstrate the synthesis of graphene directly on SiC substrates at 900 °C using ion beam mixing technique with energetic carbon cluster ions on Ni/SiC structures. The thickness of 7-8 nm Ni films was evaporated on the SiC substrates, followed by C cluster ion bombarding. Carbon cluster ions C4 were bombarded at 16 keV with the dosage of 4 × 1016 atoms/cm2. After thermal annealing process Ni silicides were formed, whereas C atoms either from the decomposition of the SiC substrates or the implanted contributes to the graphene synthesis by segregating and precipitating process. The limited solubility of carbon atoms in silicides, involving SiC, Ni2Si, Ni5Si2, Ni3Si, resulted in diffusion and precipitation of carbon atoms to form graphene on top of Ni and the interface of Ni/SiC. The ion beam mixing technique provides an attractive production method of a transfer-free graphene growth on SiC and be compatible with current device fabrication.

Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

NASA Astrophysics Data System (ADS)

Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

2016-08-01

Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size.

Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

PubMed Central

Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

2016-01-01

Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size. PMID:27476577

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

Ding, Jun; Ma, Evan; Asta, Mark

Using molecular dynamics simulations, we have studied the atomic correlations characterizing the second peak in the radial distribution function (RDF) of metallic glasses and liquids. The analysis was conducted from the perspective of different connection schemes of atomic packing motifs, based on the number of shared atoms between two linked coordination polyhedra. The results demonstrate that the cluster connections by face-sharing, specifically with three common atoms, are most favored when transitioning from the liquid to glassy state, and exhibit the stiffest elastic response during shear deformation. These properties of the connections and the resultant atomic correlations are generally the samemore » for different types of packing motifs in different alloys. Splitting of the second RDF peak was observed for the inherent structure of the equilibrium liquid, originating solely from cluster connections; this trait can then be inherited in the metallic glass formed via subsequent quenching of the parent liquid through the glass transition, in the absence of any additional type of local structural order. In conclusion, increasing ordering and cluster connection during cooling, however, may tune the position and intensity of the split peaks.« less

Ideal gas thermodynamic properties for the phenyl, phenoxy, and o-biphenyl radicals

NASA Technical Reports Server (NTRS)

Burcat, A.; Zeleznik, F. J.; Mcbride, B. J.

1985-01-01

Ideal gas thermodynamic properties of the phenyl and o-biphenyl radicals, their deuterated analogs and the phenoxy radical were calculated to 5000 K using estimated vibrational frequencies and structures. The ideal gas thermodynamic properties of benzene, biphenyl, their deuterated analogs and phenyl were also calculated.

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Predicting stability limits for pure and doped dicationic noble gas clusters undergoing coulomb explosion: A parallel tempering based study.

PubMed

Ghorai, Sankar; Chaudhury, Pinaki

2018-05-30

We have used a replica exchange Monte-Carlo procedure, popularly known as Parallel Tempering, to study the problem of Coulomb explosion in homogeneous Ar and Xe dicationic clusters as well as mixed Ar-Xe dicationic clusters of varying sizes with different degrees of relative composition. All the clusters studied have two units of positive charges. The simulations reveal that in all the cases there is a cutoff size below which the clusters fragment. It is seen that for the case of pure Ar, the value is around 95 while that for Xe it is 55. For the mixed clusters with increasing Xe content, the cutoff limit for suppression of Coulomb explosion gradually decreases from 95 for a pure Ar to 55 for a pure Xe cluster. The hallmark of this study is this smooth progression. All the clusters are simulated using the reliable potential energy surface developed by Gay and Berne (Gay and Berne, Phys. Rev. Lett. 1982, 49, 194). For the hetero clusters, we have also discussed two different ways of charge distribution, that is one in which both positive charges are on two Xe atoms and the other where the two charges are at a Xe atom and at an Ar atom. The fragmentation patterns observed by us are such that single ionic ejections are the favored dissociating pattern. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Nature's polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo-O clusters.

PubMed

Kowalewski, Björn; Poppe, Juliane; Demmer, Ulrike; Warkentin, Eberhard; Dierks, Thomas; Ermler, Ulrich; Schneider, Klaus

2012-06-13

Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo(8), three Mo(5-7), and one Mo(3) clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)(3) protein complex. The structurally identical Mo(8) clusters (three layers of two, four, and two MoO(n) octahedra) are distinguishable from the [Mo(8)O(26)](4-) cluster formed in acidic solutions by two displaced MoO(n) octahedra implicating three kinetically labile terminal ligands. Stabilization in the covalent Mo(8) cluster is achieved by Mo bonding to Hisα156-N(ε2) and Gluα129-O(ε1). The absence of covalent protein interactions in the noncovalent Mo(8) cluster is compensated by a more extended hydrogen-bond network involving three pronounced histidines. One displaced MoO(n) octahedron might serve as nucleation site for an inhomogeneous Mo(5-7) cluster largely surrounded by bulk solvent. In the Mo(3) cluster located on the 3-fold axis, the three accurately positioned His140-N(ε2) atoms of the α subunits coordinate to the Mo atoms. The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host-guest system. Template, nucleation/protection, and catalyst functions of the polypeptide as well as perspectives for designing new clusters are discussed.

Temperature-Dependent Evolution of the Oxidation States of Cobalt and Platinum in Co 1–xPt x Clusters under H 2 and CO + H 2 Atmospheres

DOE PAGES

Yang, Bing; Khadra, Ghassan; Tuaillon-Combes, Juliette; ...

2016-08-25

In this study, Co 1–xPt x clusters of 2.9-nm size with a range of atomically precise Pt/Co atomic ratios (x = 0, 0.25, 0.5, 0.75, 1) were synthesized using the mass-selected low-energy cluster beam deposition (LECBD) technique and soft-landed onto an amorphous alumina thin film prepared by atomic layer deposition (ALD). Utilizing ex situ X-ray photoemission spectroscopy (XPS), the oxidation state of the as-made clusters supported on Al 2O 3 was determined after both a 1-h-long exposure to air and aging for several weeks while exposed to air. Next, the aged cluster samples were characterized by grazing-incidence X-ray absorption spectroscopymore » (GIXAS) and then pretreated with diluted hydrogen and further exposed to the mixture of diluted CO and H 2 up to 225°C at atmospheric pressure, and the temperature-dependent evolutions of the particle size/shape and the oxidation states of the individual metal components within the clusters were monitored using in situ grazing-incidence small-angle X-ray scattering and X-ray absorption spectroscopy (GISAXS/GIXAS). The changes in the oxidation states of Co and Pt exhibited a nonlinear dependence on the Pt/Co atomic ratio of the clusters. For example, a low Pt/Co ratio (x ≤ 0.5) facilitates the formation of Co(OH) 2, whereas a high Pt/Co ratio (x = 0.75) stabilizes the Co 3O 4 composition instead through the formation of a Co–Pt core–shell structure where the platinum shell inhibits the reduction of cobalt in the core of the Co 1–xPt x alloy clusters. Finally, the obtained results indicate methods for optimizing the composition and structure of binary alloy clusters for catalysis.« less

Redistribution of carbonyl stretch mode energy in isolated and solvated N-methylacetamide: kinetic energy spectral density analyses.

PubMed

Jeon, Jonggu; Cho, Minhaeng

2011-12-07

The vibrational energy transfer from the excited carbonyl stretch mode in N-deuterated N-methylacetamide (NMA-d), both in isolation and in a heavy water cluster, is studied with nonequilibrium molecular dynamics (NEMD) simulations, employing a quantum mechanical/molecular mechanical (QM∕MM) force field at the semiempirical PM3 level. The nonequilibrium ensemble of vibrationally excited NMA-d is prepared by perturbing the positions and velocities of the carbonyl C and O atoms and its NEMD trajectories are obtained with a leap-frog algorithm properly modified for the initial perturbation. In addition to the time-domain analysis of the kinetic and potential energies, a novel method for the spectral analysis of the atomic kinetic energies is developed, in terms of the spectral density of kinetic energy, which provides the time-dependent changes of the frequency-resolved kinetic energies without the complications of normal mode analysis at every MD time step. Due to the QM description of the solute electronic structure, the couplings among the normal modes are captured more realistically than with classical force fields. The energy transfer in the isolated NMA-d is found to proceed first from the carbonyl bond to other modes with time scales of 3 ps or less, and then among the other modes over 3-21 ps. In the solvated NMA-d, most of the excess energy is first transferred to other intramolecular modes within 5 ps, which is subsequently dissipated to solvent with 7-19 ps time scales. The contribution of the direct energy transfer from the carbonyl bond to solvent was only 5% with ~7 ps time scale. Solvent reorganization that leads to destabilization of the electrostatic interactions is found to be crucial in the long time relaxation of the excess energy, while the water intramolecular modes do not contribute significantly. Detailed mode-specific energy transfer pathways are deduced for the isolated and solvated NMA-d and they show that the energy transfer in NMA-d is a highly cooperative process among the intramolecular modes and there is no single dominant pathway with more than 30% of transient contribution. © 2011 American Institute of Physics

Atomic and electronic structure of the silicon and silicon-metal Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, KSi{sub 20} nanoparticles

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

Borshch, N. A., E-mail: ssd18@phys.vsu.ru; Pereslavtseva, N. S.; Kurganskii, S. I.

The results of atomic-structure optimization and calculation of the electronic structure of the Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, and KSi{sub 20} clusters are reported. The PM3 and AM1 semiempirical methods were used in the calculations. It is shown that the Na and K atoms stabilize the fullerene-like silicon structure. The effect of configuration of the clusters on their electronic structure is analyzed.

Anomalous small-angle scattering as a way to solve the Babinet principle problem

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

Boiko, M. E., E-mail: m.e.boiko@mail.ioffe.ru; Sharkov, M. D.; Boiko, A. M.

2013-12-15

X-ray absorption spectra (XAS) have been used to determine the absorption edges of atoms present in a sample under study. A series of small-angle X-ray scattering (SAXS) measurements using different monochromatic X-ray beams at different wavelengths near the absorption edges is performed to solve the Babinet principle problem. The sizes of clusters containing atoms determined by the method of XAS were defined in SAXS experiments. In contrast to differential X-ray porosimetry, anomalous SAXS makes it possible to determine sizes of clusters of different atomic compositions.

Anomalous small-angle scattering as a way to solve the Babinet principle problem

NASA Astrophysics Data System (ADS)

Boiko, M. E.; Sharkov, M. D.; Boiko, A. M.; Bobyl, A. V.

2013-12-01

X-ray absorption spectra (XAS) have been used to determine the absorption edges of atoms present in a sample under study. A series of small-angle X-ray scattering (SAXS) measurements using different monochromatic X-ray beams at different wavelengths near the absorption edges is performed to solve the Babinet principle problem. The sizes of clusters containing atoms determined by the method of XAS were defined in SAXS experiments. In contrast to differential X-ray porosimetry, anomalous SAXS makes it possible to determine sizes of clusters of different atomic compositions.

A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

ERIC Educational Resources Information Center

Glendening, Eric D.; Halpern, Arthur M.

2012-01-01

An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

Experimental methods of molecular matter-wave optics.

PubMed

Juffmann, Thomas; Ulbricht, Hendrik; Arndt, Markus

2013-08-01

We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.

Systematization of actinides using cluster analysis

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

Kopyrin, A.A.; Terent`eva, T.N.; Khramov, N.N.

1994-11-01

A representation of the actinides in multidimensional property space is proposed for systematization of these elements using cluster analysis. Literature data for their atomic properties are used. Owing to the wide variation of published ionization potentials, medians are used to estimate them. Vertical dendograms are used for classification on the basis of distances between the actinides in atomic-property space. The properties of actinium and lawrencium are furthest removed from the main group. Thorium and mendelevium exhibit individualized properties. A cluster based on the einsteinium-fermium pair is joined by californium.

Anharmonic frequencies of CX2Y2 (X, Y = O, N, F, H, D) isomers and related systems obtained from vibrational multiconfiguration self-consistent field theory.

PubMed

Pfeiffer, Florian; Rauhut, Guntram

2011-10-13

Accurate anharmonic frequencies are provided for molecules of current research, i.e., diazirines, diazomethane, the corresponding fluorinated and deuterated compounds, their dioxygen analogs, and others. Vibrational-state energies were obtained from state-specific vibrational multiconfiguration self-consistent field theory (VMCSCF) based on multilevel potential energy surfaces (PES) generated from explicitly correlated coupled cluster, CCSD(T)-F12a, and double-hybrid density functional calculations, B2PLYP. To accelerate the vibrational structure calculations, a configuration selection scheme as well as a polynomial representation of the PES have been exploited. Because experimental data are scarce for these systems, many calculated frequencies of this study are predictions and may guide experiments to come.

Photoelectron spectroscopy and density functional theory study of TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3) clusters.

PubMed

Zhang, Zeng-Guang; Xu, Hong-Guang; Zhao, Yuchao; Zheng, Weijun

2010-10-21

Small titanium-aluminum oxide clusters, TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3), were studied by using anion photoelectron spectroscopy. The adiabatic detachment energies of TiAlO(y) (-) (y=1-3) were estimated to be 1.11±0.05, 1.70±0.08, and 2.47±0.08eV based on their photoelectron spectra; those of TiAl(2)O(2) (-) and TiAl(2)O(3) (-) were estimated to be 1.17±0.08 and 2.2±0.1eV, respectively. The structures of these clusters were determined by comparison of density functional calculations with the experimental results. The structure of TiAlO(-) is nearly linear with the O atom in the middle. That of TiAlO(2) (-) is a kite-shaped structure. TiAlO(3) (-) has a kite-shaped TiAlO(2) unit with the third O atom attaching to the Ti atom. TiAl(2)O(2) (-) has two nearly degenerate Al-O-Ti-O-Al chain structures that can be considered as cis and trans forms. TiAl(2)O(3) (-) has two low-lying isomers, kite structure and book structure. The structures of these clusters indicate that the Ti atom tends to bind to more O atoms.

Experimental and theoretical study on Raman spectra of magnesium fluoride clusters and solids.

PubMed

Neelamraju, S; Bach, A; Schön, J C; Fischer, D; Jansen, M

2012-11-21

In this study, the Raman and IR spectra of a large number of isomers of MgF(2) clusters and of possible bulk polymorphs of MgF(2) are calculated and compared with experimental data observed using a low-temperature atom beam deposition. The bulk polymorphs were taken from earlier work, while the cluster modifications for the neutral (MgF(2))(n) (n = 1-10) clusters and charged clusters (up to the trimer anion and cation, (Mg(3)F(7))(-) and (Mg(3)F(5))(+), respectively) are determined in the present work by global energy landscape explorations using simulated annealing. These theoretical calculations are complemented by an experimental study on both the vapor phase and the deposited films of MgF(2), which are generated in a low-temperature atom beam deposition setup for the synthesis of MgF(2) bulk phases. The MgF(2) vapor and film are characterized via Raman spectroscopy of the MgF(2) gas phase species embedded in an Ar-matrix and of the MgF(2)-films deposited onto a cooled substrate, respectively. We find that, in the vapor phase, there are monomers and dimers and charged species to be present in our experimental setup. Furthermore, the results suggest that in the amorphous bulk MgF(2), rutile-like domains are present and MgF(2) clusters similar to those in the matrix. Finally, peaks at about 800 cm(-1), which are in the same range as the A(g) modes of clusters with dangling fluorine atoms connected to three-coordinated Mg atoms, indicate that such dangling bonds are also present in amorphous MgF(2).

Nanopores creation in boron and nitrogen doped polycrystalline graphene: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Izadifar, Mohammadreza; Abadi, Rouzbeh; Nezhad Shirazi, Ali Hossein; Alajlan, Naif; Rabczuk, Timon

2018-05-01

In the present paper, molecular dynamic simulations have been conducted to investigate the nanopores creation on 10% of boron and nitrogen doped polycrystalline graphene by silicon and diamond nanoclusters. Two types of nanoclusters based on silicon and diamond are used to investigate their effect for the fabrication of nanopores. Therefore, three different diameter sizes of the clusters with five kinetic energies of 10, 50, 100, 300 and 500 eV/atom at four different locations in boron or nitrogen doped polycrystalline graphene nanosheets have been perused. We also study the effect of 3% and 6% of boron doped polycrystalline graphene with the best outcome from 10% of doping. Our results reveal that the diamond cluster with diameter of 2 and 2.5 nm fabricates the largest nanopore areas on boron and nitrogen doped polycrystalline graphene, respectively. Furthermore, the kinetic energies of 10 and 50 eV/atom can not fabricate nanopores in some cases for silicon and diamond clusters on boron doped polycrystalline graphene nanosheets. On the other hand, silicon and diamond clusters fabricate nanopores for all locations and all tested energies on nitrogen doped polycrystalline graphene. The area sizes of nanopores fabricated by silicon and diamond clusters with diameter of 2 and 2.5 nm are close to the actual area size of the related clusters for the kinetic energy of 300 eV/atom in all locations on boron doped polycrystalline graphene. The maximum area and the average maximum area of nanopores are fabricated by the kinetic energy of 500 eV/atom inside the grain boundary at the center of the nanosheet and in the corner of nanosheet with diameters of 2 and 3 nm for silicon and diamond clusters on boron and nitrogen doped polycrystalline graphene.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Water Oxidation Catalysis via Size-Selected Iridium Clusters

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

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

Electronic structure and properties of magnetic defects in Co(1+x)Al(1-x) and Fe(1+x)Al(1-x) alloys. Ph.D. Thesis - Paris Univ.

NASA Technical Reports Server (NTRS)

Abbe, D.

1984-01-01

CoAl and FeAl compounds are developed along two directions. Magnetic susceptibility and specific heat at low temperature on (NiCo)Al and (CoFe)Al ternary alloys are in good agreement with band calculations. Results on magnetization and specific heat under field at low temperature on nonstoichiometric compounds show clearly the importance of the nearest neighbor effects. In the case of CoAl, the isolated cobalt atoms substituting aluminum are characterized by a Kondo behavior, and, for FeAl, the isolated extra iron atoms are magnetic and polarize the matrix. Moreover, for the two compounds, clusters of higher order play a considerable part in the magnetic properties for CoAl, these clusters also seem to be characterized by a Kondo behavior, for FeAl, these clusters whose moment is higher than in the case of isolated atoms, could be constituted of excess parts of iron atoms.

Composition-dependent metallic glass alloys correlate atomic mobility with collective glass surface dynamics.

PubMed

Nguyen, Duc; Zhu, Zhi-Guang; Pringle, Brian; Lyding, Joseph; Wang, Wei-Hua; Gruebele, Martin

2016-06-22

Glassy metallic alloys are richly tunable model systems for surface glassy dynamics. Here we study the correlation between atomic mobility, and the hopping rate of surface regions (clusters) that rearrange collectively on a minute to hour time scale. Increasing the proportion of low-mobility copper atoms in La-Ni-Al-Cu alloys reduces the cluster hopping rate, thus establishing a microscopic connection between atomic mobility and dynamics of collective rearrangements at a glass surface made from freshly exposed bulk glass. One composition, La60Ni15Al15Cu10, has a surface resistant to re-crystallization after three heating cycles. When thermally cycled, surface clusters grow in size from about 5 glass-forming units to about 8 glass-forming units, evidence of surface aging without crystal formation, although its bulk clearly forms larger crystalline domains. Such kinetically stable glass surfaces may be of use in applications where glassy coatings stable against heating are needed.

Nonempirical calculations of the structure and stability of ALi/sub 2k/ lithium clusters of group-two elements

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

Klimenko, N.M.; Musaev, D.G.; Gorbik, A.A.

Nonempirical Hartree-Fock calculations of the geometric and relative energetic characteristics of linear ALi/sub 2/ molecules and square ALi/sub 4/ molecules, where A = Be, Mg, Ca, and Zn, have been performed. The results for BeLi/sup +/, BeLi/sup 2/, BeLi/sub 4/, and MgLi/sub 2/ have been refined with consideration of the electron correlation in the framework of the theory of self-consistent electron pairs (SCEP). It has been shown that the stability of ALi/sub 2k/ increases with increasing size of the cluster and that the energy of the singlet-triplet transitions does not exceed 0.5-1.5 eV in all cases. The interactions between themore » atoms in the clusters have a cooperative character: the overlapping Q(Li-Li) between the Li atoms is no less significant than the overlapping Q(A-Li) between the Li atoms and the central atom A.« less

Properties of Vacancy Complexes with Hydrogen and Helium Atoms in Tungsten from First Principles

DOE PAGES

Samolyuk, German D.; Osetsky, Yury N.; Stoller, Roger E.

2016-12-03

Tungsten and its alloys are the primary candidate materials for plasma-facing components in fusion reactors. The material is exposed to high-energy neutrons and the high flux of helium and hydrogen atoms. In this paper, we have studied the properties of vacancy clusters and their interaction with H and He in W using density functional theory. Convergence of calculations with respect to modeling cell size was investigated. It is demonstrated that vacancy cluster formation energy converges with small cells with a size of 6 × 6 × 6 (432 lattice sites) enough to consider a microvoid of up to six vacanciesmore » with high accuracy. Most of the vacancy clusters containing fewer than six vacancies are unstable. Introducing He or H atoms increases their binding energy potentially making gas-filled bubbles stable. Finally, according to the results of the calculations, the H 2 molecule is unstable in clusters containing six or fewer vacancies.« less

The adsorption of helium atoms on small cationic gold clusters.

PubMed

Goulart, Marcelo; Gatchell, Michael; Kranabetter, Lorenz; Kuhn, Martin; Martini, Paul; Gitzl, Norbert; Rainer, Manuel; Postler, Johannes; Scheier, Paul; Ellis, Andrew M

2018-04-04

Adducts formed between small gold cluster cations and helium atoms are reported for the first time. These binary ions, Aun+Hem, were produced by electron ionization of helium nanodroplets doped with neutral gold clusters and were detected using mass spectrometry. For a given value of n, the distribution of ions as a function of the number of added helium atoms, m, has been recorded. Peaks with anomalously high intensities, corresponding to so-called magic number ions, are identified and interpreted in terms of the geometric structures of the underlying Aun+ ions. These features can be accounted for by planar structures for Aun+ ions with n ≤ 7, with the addition of helium having no significant effect on the structures of the underlying gold cluster ions. According to ion mobility studies and some theoretical predictions, a 3-D structure is expected for Au8+. However, the findings for Au8+ in this work are more consistent with a planar structure.

Ultracold few fermionic atoms in needle-shaped double wells: spin chains and resonating spin clusters from microscopic Hamiltonians emulated via antiferromagnetic Heisenberg and t-J models

NASA Astrophysics Data System (ADS)

Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi

2016-07-01

Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.

Ferroelectric films of deuterated glycine phosphite: Structure and dielectric properties

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Svinarev, F. B.; Lemanov, V. V.

2013-05-01

Polycrystalline textured films of deuterated glycine phosphite consisting of single-crystal blocks with lateral dimensions ˜(50-100) μm and a thickness d ˜ (1-5) μm have been grown by evaporation on NdGaO3(100) and α-Al2O3 substrates with preliminarily deposited interdigitated electrodes, as well as on Al substrates. The c* ( Z) crystallographic axis in the blocks is normal to the film plane, and the a ( X) axis and the polar axis b ( Y) are oriented in the film plane. The temperature dependences of the capacitance of the structures measured with the interdigitated electrode system reveal a strong dielectric anomaly at the film transition to the ferroelectric state. The phase transition temperature T c depends on the degree of deuteration D of the glycine phosphite. The maximum value T c = 275 K obtained in the structures studied corresponds to a degree of deuteration of the glycine phosphite D ˜ 50%. The frequency behavior of the dielectric hysteresis loops in glycine phosphite films differs radically from that of the previously studied films of deuterated betaine phosphite, which evidences that polarization switching in these structures proceeds by different mechanisms. It has been that application of a dc bias to the electrodes changes the shape of the dielectric hysteresis loops and shifts them along the electric field axis. The shift of the loops depends on the sign, magnitude, and time of application of the bias. Possible mechanisms underlying the induced unipolarity are discussed.

Experimental Observations of Nuclear Activity in Deuterated Materials Subjected to a Low-Energy Photon Beam

NASA Technical Reports Server (NTRS)

Steinetz, Bruce M.; Benyo, Theresa L.; Pines, Vladimir; Pines, Marianna; Forsley, Lawrence P.; Westmeyer, Paul A.; Chait, Arnon; Becks, Michael D.; Martin, Richard E.; Hendricks, Robert C.;

H{sub 2} Ortho-to-para Conversion on Grains: A Route to Fast Deuterium Fractionation in Dense Cloud Cores?

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

Bovino, S.; Grassi, T.; Schleicher, D. R. G.

Deuterium fractionation, i.e., the enhancement of deuterated species with respect to non-deuterated ones, is considered to be a reliable chemical clock of star-forming regions. This process is strongly affected by the ortho-to-para H{sub 2} ratio. In this Letter we explore the effect of the ortho–para (o–p) H{sub 2} conversion on grains on the deuteration timescale in fully-depleted dense cores, including the most relevant uncertainties that affect this complex process. We show that (i) the o–p H{sub 2} conversion on grains is not strongly influenced by the uncertainties on the conversion time and the sticking coefficient, and (ii) that the processmore » is controlled by the temperature and the residence time of ortho-H{sub 2} on the surface, i.e., by the binding energy. We find that for binding energies between 330 and 550 K, depending on the temperature, the o–p H{sub 2} conversion on grains can shorten the deuterium fractionation timescale by orders of magnitude, opening a new route for explaining the large observed deuteration fraction D {sub frac} in dense molecular cloud cores. Our results suggest that the star formation timescale, when estimated through the timescale to reach the observed deuteration fractions, might be shorter than previously proposed. However, more accurate measurements of the binding energy are needed in order to better assess the overall role of this process.« less

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

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Magnetic behavior of Si-Ge bond in SixGe4-x nano-clusters

NASA Astrophysics Data System (ADS)

Nahali, Masoud; Mehri, Ali

2018-06-01

The structure of SixGe4-x nano-clusters were optimized by MPW1B95 level of theory using MG3S and SDB-aug-cc-PVTZ basis set. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. Since the Si-Si bond is stronger than Si-Ge and Ge-Ge bonds, the Si-Si, Si-Ge, and Ge-Ge diagonal bonds determine the precedence of the stability in these nano-clusters. The hybrid meta density functional calculations were carried out to investigate the adsorption of CO on all possible SixGe4-x nano-clusters. It was found that the silicon atom generally makes a stronger bond with CO than germanium and thereby preferentially affects the shape of structures having higher multiplicity. In Si-Ge structures with higher spin more than 95% of spins accumulate on positions with less bonds to other atoms of the cluster. Through CO adsorption on these clusters bridge structures are made that behave as spin bridge which conduct the spin from the nano-cluster surface to the adsorbate atoms. A better understanding of bridged structures was achieved upon introducing the 'spin bridge' concept. Based on exhaustive spin density analysis, it was found that the reason for the extra negative charge on oxygen in the bridged structures is the relocation of spin from the surface through the bridge.

Mechanistic Details and Reactivity Descriptors in Oxidation and Acid Catalysis of Methanol

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

Deshlahra, Prashant; Carr, Robert T.; Chai, Song-Hai

2015-02-06

Acid and redox reaction rates of CH₃OH-O₂ mixtures on polyoxometalate (POM) clusters, together with isotopic, spectroscopic, and theoretical assessments of catalyst properties and reaction pathways, were used to define rigorous descriptors of reactivity and to probe the compositional effects for oxidative dehydrogenation (ODH) and dehydration reactions. ³¹P-MAS NMR, transmission electron microscopy and titrations of protons with di-tert-butylpyridine during catalysis showed that POM clusters retained their Keggin structure upon dispersion on SiO₂ and after use in CH₃OH reactions. The effects of CH₃OH and O₂ pressures and of D-substitution on ODH rates show that C-H activation in molecularly adsorbed CH₃OH is themore » sole kinetically relevant step and leads to reduced centers as intermediates present at low coverages; their concentrations, measured from UV-vis spectra obtained during catalysis, are consistent with the effects of CH₃OH/O₂ ratios predicted from the elementary steps proposed. First-order ODH rate constants depend strongly on the addenda atoms (Mo vs W) but weakly on the central atom (P vs Si) in POM clusters, because C-H activation steps inject electrons into the lowest unoccupied molecular orbitals (LUMO) of the clusters, which are the d-orbitals at Mo⁶⁺ and W⁶⁺ centers. H-atom addition energies (HAE) at O-atoms in POM clusters represent the relevant theoretical probe of the LUMO energies and of ODH reactivity. The calculated energies of ODH transition states at each O-atom depend linearly on their HAE values with slopes near unity, as predicted for late transition states in which electron transfer and C-H cleavage are essentially complete. HAE values averaged over all accessible O-atoms in POM clusters provide the appropriate reactivity descriptor for oxides whose known structures allow accurate HAE calculations. CH₃OH dehydration proceeds via parallel pathways mediated by late carbenium-ion transition states; effects of composition on dehydration reactivity reflect changes in charge reorganizations and electrostatic forces that stabilize protons at Brønsted acid sites.« less

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

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

Mao, Jianjun; Li, Shasha; Chu, Xingli

2015-11-14

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

High-accuracy calculations of the rotation-vibration spectrum of {{\\rm{H}}}_{3}^{+}

NASA Astrophysics Data System (ADS)

Tennyson, Jonathan; Polyansky, Oleg L.; Zobov, Nikolai F.; Alijah, Alexander; Császár, Attila G.

2017-12-01

Calculation of the rotation-vibration spectrum of {{{H}}}3+, as well as of its deuterated isotopologues, with near-spectroscopic accuracy requires the development of sophisticated theoretical models, methods, and codes. The present paper reviews the state-of-the-art in these fields. Computation of rovibrational states on a given potential energy surface (PES) has now become standard for triatomic molecules, at least up to intermediate energies, due to developments achieved by the present authors and others. However, highly accurate Born-Oppenheimer energies leading to highly accurate PESs are not accessible even for this two-electron system using conventional electronic structure procedures (e.g. configuration-interaction or coupled-cluster techniques with extrapolation to the complete (atom-centered Gaussian) basis set limit). For this purpose, highly specialized techniques must be used, e.g. those employing explicitly correlated Gaussians and nonlinear parameter optimizations. It has also become evident that a very dense grid of ab initio points is required to obtain reliable representations of the computed points extending from the minimum to the asymptotic limits. Furthermore, adiabatic, relativistic, and quantum electrodynamic correction terms need to be considered to achieve near-spectroscopic accuracy during calculation of the rotation-vibration spectrum of {{{H}}}3+. The remaining and most intractable problem is then the treatment of the effects of non-adiabatic coupling on the rovibrational energies, which, in the worst cases, may lead to corrections on the order of several cm-1. A promising way of handling this difficulty is the further development of effective, motion- or even coordinate-dependent, masses and mass surfaces. Finally, the unresolved challenge of how to describe and elucidate the experimental pre-dissociation spectra of {{{H}}}3+ and its isotopologues is discussed.

Theory of Positron Annihilation in Helium-Filled Bubbles in Plutonium

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

Sterne, P A; Pask, J E

2003-02-13

Positron annihilation lifetime spectroscopy is a sensitive probe of vacancies and voids in materials. This non-destructive measurement technique can identify the presence of specific defects in materials at the part-per-million level. Recent experiments by Asoka-Kumar et al. have identified two lifetime components in aged plutonium samples--a dominant lifetime component of around 182 ps and a longer lifetime component of around 350-400ps. This second component appears to increase with the age of the sample, and accounts for only about 5 percent of the total intensity in 35 year-old plutonium samples. First-principles calculations of positron lifetimes are now used extensively to guidemore » the interpretation of positron lifetime data. At Livermore, we have developed a first-principles finite-element-based method for calculating positron lifetimes for defects in metals. This method is capable of treating system cell sizes of several thousand atoms, allowing us to model defects in plutonium ranging in size from a mono-vacancy to helium-filled bubbles of over 1 nm in diameter. In order to identify the defects that account for the observed lifetime values, we have performed positron lifetime calculations for a set of vacancies, vacancy clusters, and helium-filled vacancy clusters in delta-plutonium. The calculations produced values of 143ps for defect-free delta-Pu and 255ps for a mono-vacancy in Pu, both of which are inconsistent with the dominant experimental lifetime component of 182ps. Larger vacancy clusters have even longer lifetimes. The observed positron lifetime is significantly shorter than the calculated lifetimes for mono-vacancies and larger vacancy clusters, indicating that open vacancy clusters are not the dominant defect in the aged plutonium samples. When helium atoms are introduced into the vacancy cluster, the positron lifetime is reduced due to the increased density of electrons available for annihilation. For a mono-vacancy in Pu containing one helium atom, the calculated lifetime is 190 ps, while a di-vacancy containing two helium atoms has a positron lifetime of 205 ps. In general, increasing the helium density in a vacancy cluster or He-filled bubble reduces the positron lifetime, so that the same lifetime value can arise fi-om a range of vacancy cluster sizes with different helium densities. In order to understand the variation of positron lifetime with vacancy cluster size and helium density in the defect, we have performed over 60 positron lifetime calculations with vacancy cluster sizes ranging from 1 to 55 vacancies and helium densities ranging fi-om zero to five helium atoms per vacancy. The results indicate that the experimental lifetime of 182 ps is consistent with the theoretical value of 190 ps for a mono-vacancy with a single helium atom, but that slightly better agreement is obtained for larger clusters of 6 or more vacancies containing 2-3 helium atoms per vacancy. For larger vacancy clusters with diameters of about 3-5 nm or more, the annihilation with helium electrons dominates the positron annihilation rate; the observed lifetime of 180ps is then consistent with a helium concentration in the range of 3 to 3.5 Hehacancy, setting an upper bound on the helium concentration in the vacancy clusters. In practice, the single lifetime component is most probably associated with a family of helium-filled bubbles rather than with a specific unique defect size. The longer 350-400ps lifetime component is consistent with a relatively narrow range of defect sizes and He concentration. At zero He concentration, the lifetime values are matched by small vacancy clusters containing 6-12 vacancies. With increasing vacancy cluster size, a small amount of He is required to keep the lifetime in the 350-400 ps range, until the value saturates for larger helium bubbles of more than 50 vacancies (bubble diameter > 1.3 nm) at a helium concentration close to 1 He/vacancy. These results, taken together with the experimental data, indicate that the features observed in TEM data by Schwartz et al are not voids, but are in fact helium-filled bubbles with a helium pressure of around 2-3 helium atoms per vacancy, depending on the bubble size. This is consistent with the conclusions of recently developed models of He-bubble growth in aged plutonium.« less

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-11-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance.

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

PubMed Central

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-01-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance. PMID:27901129

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

Improvements in Ionized Cluster-Beam Deposition

NASA Technical Reports Server (NTRS)

Fitzgerald, D. J.; Compton, L. E.; Pawlik, E. V.

1986-01-01

Lower temperatures result in higher purity and fewer equipment problems. In cluster-beam deposition, clusters of atoms formed by adiabatic expansion nozzle and with proper nozzle design, expanding vapor cools sufficiently to become supersaturated and form clusters of material deposited. Clusters are ionized and accelerated in electric field and then impacted on substrate where films form. Improved cluster-beam technique useful for deposition of refractory metals.

Evidence for a Catalytically and Kinetically Competent Enzyme–Substrate Cross-Linked Intermediate in Catalysis by Lipoyl Synthase

PubMed Central

2015-01-01

Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N6-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe–4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5′-deoxyadenosyl 5′-radical (5′-dA•). In the LS reaction, two equivalents of 5′-dA• are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe–4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N6-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe–4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe–4S]0 clusters. PMID:24901788

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

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

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Carbon atom and cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, E.; Doerner, R. P.; Shimada, M.; Tynan, G. R.

2008-08-01

Exit-angle resolved carbon atom and cluster (C2 and C3) sputtering yields are measured during different noble gas (Xe, Kr, Ar, Ne, and He) ion bombardments from a plasma, for low incident energies (75-225 eV). A quadrupole mass spectrometer (QMS) is used to detect the fraction of sputtered neutrals that is ionized in the plasma and to obtain the angular distribution by changing the angle between the target normal and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles in the region between the sample and the QMS. The effective elastic scattering cross sections of C, C2, and C3 with the different bombarding gas neutrals are obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. The total sputtering yield (C+C2+C3) for each bombarding gas is obtained from weight-loss measurements and the sputtering yield for C, C2, and C3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. We observe undercosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases and a clear decrease of the atom to cluster (C2 and C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne, and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

Antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.

1988-06-28

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

NASA Astrophysics Data System (ADS)

Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

2018-06-01

Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.

Understanding the detection of carbon in austenitic high-Mn steel using atom probe tomography.

PubMed

Marceau, R K W; Choi, P; Raabe, D

2013-09-01

A high-Mn TWIP steel having composition Fe-22Mn-0.6C (wt%) is considered in this study, where the need for accurate and quantitative analysis of clustering and short-range ordering by atom probe analysis requires a better understanding of the detection of carbon in this system. Experimental measurements reveal that a high percentage of carbon atoms are detected as molecular ion species and on multiple hit events, which is discussed with respect to issues such as optimal experimental parameters, correlated field evaporation and directional walk/migration of carbon atoms at the surface of the specimen tip during analysis. These phenomena impact the compositional and spatial accuracy of the atom probe measurement and thus require careful consideration for further cluster-finding analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

The First Non-Dispersive High-Resolution Spectroscopy of an X-ray-bright Galaxy Cluster

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroya; Hitomi Collaboration

2018-06-01

The Hitomi X-ray Observatory was equipped with the Soft X-ray Spectrometer (SXS), an X-ray microcalorimeter that achieved an energy resolution of 5 eV (@0.5-10 keV) for extended objects. This offered an unprecedented benchmark of atomic modeling and database for hot collisional plasmas, revealing both successes and challenges in the current atomic codes that are widely used by the X-ray astronomy community. I will review the Hitomi observations of the brightest part of the Perseus Cluster, whose X-ray spectrum is dominated by thermal emission from the intra-cluster medium (ICM). The SXS successfully measured the turbulent velocities and metal abundances of the ICM, which radically altered our understanding of the dynamics and chemical enrichment in this object. At the same time, the high-resolution X-ray data led to significant improvement in the atomic models, such as AtomDB and SPEX -- I will briefly overview how this improvement was made. Nevertheless, there are still significant discrepancies among the public atomic models, causing systematic uncertainties in measurements of the temperature, abundance, and degree of the resonance scattering. Requirements for future improvements will be summarized in this context.

Effect of local structures on crystallization in deeply undercooled metallic glass-forming liquids

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

Jiang, S. Q.; Li, M. Z., E-mail: maozhili@ruc.edu.cn; Wu, Z. W.

2016-04-21

The crystallization mechanism in deeply undercooled ZrCu metallic glass-forming liquids was investigated via molecular dynamics simulations. It was found that the crystallization process is mainly controlled by the growth of crystal nuclei formed by the BCC-like atomic clusters, consistent with experimental speculations. The crystallization rate is found to relate to the number of growing crystal nuclei in the crystallization process. The crystallization rate in systems with more crystal nuclei is significantly hindered by the larger surface fractions of crystal nuclei and their different crystalline orientations. It is further revealed that in the crystallization in deeply undercooled regions, the BCC-like crystalmore » nuclei are formed from the inside of the precursors formed by the FCC-like atomic clusters, and growing at the expense of the precursors. Meanwhile, the precursors are expanding at the expense of the outside atomic clusters. This process is consistent with the so-called Ostwald step rule. The atomic structures of metallic glasses are found to have significant impact on the subsequent crystallization process. In the Zr{sub 85}Cu{sub 15} system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.« less

Molecular differences between deuterated and protonated polystyrenes using reversed-phase high-performance liquid chromatography.

PubMed

Kayillo, Sindy; Gray, Michael J; Shalliker, R Andrew; Dennis, Gary R

2005-05-06

Isotopic substitution is a technique used to highlight particular bonds within a molecule for kinetic, spectroscopic and structure analysis. It is presumed that although some properties such as stretching frequencies will not be the same for substituted analogues, the chemical interactions will not vary appreciably as a function of labelling. Reversed-phase liquid chromatography has been used to demonstrate that there are significant differences between the chromatographic behaviour of a sequence of deuterated and protonated oligomeric polystyrenes. Two-dimensional reversed-phase liquid chromatography was used to show that even the diasteromers of the oligomers (n = 5) have retention mechanisms that are dependent on the subtle changes to the molecular conformation and electronic structure, which are a consequence of deuteration.

Release of deuterated (E)-2-nonenal during beer aging from labeled precursors synthesized before boiling.

PubMed

Liégeois, Catherine; Meurens, Nicolas; Badot, Camille; Collin, Sonia

2002-12-18

Although lipid autoxidation in the boiling kettle is a key determinant of the cardboard flavor of aged beers, recent results show that mashing is another significant source of wort nonenal potential, the well-known indicator of how a beer will release (E)-2-nonenal during storage. Although unstable, deuterated (E)-2-nonenal nitrogen adducts created during mashing can in some cases partially persist in the pitching wort, to release deuterated (E)-2-nonenal during beer aging. In the experiment described here, the relative contributions of mashing and boiling were estimated at 30 and 70%, respectively. The presence of oxygen during mashing and, to a lesser extent, high lipoxygenase activity can intensify the stale cardboard flavor.

The electrooxidation mechanism of formic acid on platinum and on lead ad-atoms modified platinum studied with the kinetic isotope effect

NASA Astrophysics Data System (ADS)

Bełtowska-Brzezinska, M.; Łuczak, T.; Stelmach, J.; Holze, R.

2014-04-01

Kinetics and mechanism of formic acid (FA) oxidation on platinum and upd-lead ad-atoms modified platinum electrodes have been studied using unlabelled and deuterated compounds. Poisoning of the electrode surface by CO-like species was prevented by suppression of dissociative chemisorption of FA due to a fast competitive underpotential deposition of lead ad-atoms on the Pt surface from an acidic solution containing Pb2+ cations. Modification of the Pt electrode with upd lead induced a catalytic effect in the direct electrooxidation of physisorbed FA to CO2. With increasing degree of H/D substitution, the rate of this reaction decreased in the order: HCOOH > DCOOH ≥ HCOOD > DCOOD. HCOOH was oxidized 8.5-times faster on a Pt/Pb electrode than DCOOD. This primary kinetic isotope effect proves that the C-H- and O-H-bonds are simultaneously cleaved in the rate determining step. A secondary kinetic isotope effect was found in the dissociative chemisorption of FA in the hydrogen adsorption-desorption range on a bare Pt electrode after H/D exchange in the C-H bond, wherein the influence of deuterium substitution in the O-H group was negligibly small. Thus the C-H bond cleavage is accompanied by the C-OH and not the O-H bond split in the FA decomposition, producing CO-like species on the Pt surface sites.

DFT STUDY OF CO AND NO ADSORPTION ON BORON NITRIDE (BN)n = 3 - 5 NANOCLUSTERS

NASA Astrophysics Data System (ADS)

Zahedi, Ehsan; Pangh, Abdolhakim; Ghorbanpour, Hamed

2015-11-01

Interaction of CO and NO molecules by different orientations on (BN)n=3-5 clusters have been studied at the B3LYP/6-311+G* level of theory. Total electronic energies have been corrected for geometrical counterpoise (gCP) and dispersion (D3) energies at the B3LYP/6-31G* level. Formation of a new sigma bond between the gas and (BN)3 cluster, atom in molecules (AIM) results, density of states spectrums (DOS), molecular electrostatic potential (MEP) surfaces, and visualization of wave function of molecular orbitals in the nearest bonding regions to the Fermi level have confirmed that adsorption of CO by carbon end atom, and NO by nitrogen end atom is covalent in nature, so that the charge transfer is occurred from gas molecule to the cluster.

Study on the structural transition of CoNi nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xia, J. H.; Gao, Xue-Mei

2018-04-01

In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co147Ni414 cluster becomes a core-shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co147Ni414 crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.

Electronic and molecular structure of carbon grains

NASA Technical Reports Server (NTRS)

Almloef, Jan; Luethi, Hans-Peter

1990-01-01

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

First principles calculations for interaction of tyrosine with (ZnO)3 cluster

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-04-01

First Principles Calculations have been performed to study interactions of Phenol ring of Tyrosine (C6H5OH) with (ZnO)3 atomic cluster. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/C6H5OH have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations. The compatibility of the results with previous studies has been presented here.

Synthesis of Two-Electron Bimetallic Cu-Ag and Cu-Au Clusters by using [Cu13 (S2 CNn Bu2 )6 (C≡CPh)4 ]+ as a Template.

PubMed

Silalahi, Rhone P Brocha; Chakrahari, Kiran Kumarvarma; Liao, Jian-Hong; Kahlal, Samia; Liu, Yu-Chiao; Chiang, Ming-Hsi; Saillard, Jean-Yves; Liu, C W

2018-03-02

Atomically precise Cu-rich bimetallic superatom clusters have been synthesized by adopting a galvanic exchange strategy. [Cu@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ] (1) was used as a template to generate compositionally uniform clusters [M@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ], where M=Ag (2), Au (3). Structures of 1, 2 and 3 were determined by single crystal X-ray diffraction and the results were supported by ESI-MS. The anatomies of clusters 1-3 are very similar, with a centred cuboctahedral cationic core that is surrounded by six di-butyldithiocarbamate (dtc) and four phenylacetylide ligands. The doped Ag and Au atoms were found to preferentially occupy the centre of the 13-atom cuboctahedral core. Experimental and theoretical analyses of the synthesized clusters revealed that both Ag and Au doping result in significant changes in cluster stability, optical characteristics and enhancement in luminescence properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photofragment slice imaging studies of pyrrole and the Xe{center_dot}{center_dot}{center_dot}pyrrole cluster

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

Rubio-Lago, L.; Zaouris, D.; Sakellariou, Y.

The photolysis of pyrrole has been studied in a molecular beam at wavelengths of 250, 240, and 193.3 nm, using two different carrier gases, He and Xe. A broad bimodal distribution of H-atom fragment velocities has been observed at all wavelengths. Near threshold at both 240 and 250 nm, sharp features have been observed in the fast part of the H-atom distribution. Under appropriate molecular beam conditions, the entire H-atom loss signal from the photolysis of pyrrole at both 240 and 250 nm (including the sharp features) disappear when using Xe as opposed to He as the carrier gas. Wemore » attribute this phenomenon to cluster formation between Xe and pyrrole, and this assumption is supported by the observation of resonance enhanced multiphoton ionization spectra for the (Xe{center_dot}{center_dot}{center_dot}pyrrole) cluster followed by photofragmentation of the nascent cation cluster. Ab initio calculations are presented for the ground states of the neutral and cationic (Xe{center_dot}{center_dot}{center_dot}pyrrole) clusters as a means of understanding their structural and energetic properties.« less

Study of clusters using negative ion photodetachment spectroscopy

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

Zhao, Yuexing

1995-12-01

The weak van der Waals interaction between an open-shell halogen atom and a closed-shell atom or molecule has been investigated using zero electron kinetic energy (ZEKE) spectroscopy. This technique is also applied to study the low-lying electronic states in GaAs and GaAs -. In addition, the spectroscopy and electron detachment dynamics of several small carbon cluster anions are studied using resonant multiphoton detachment spectroscopy.

Infrared Multiple Photon Dissociation Spectroscopy Of Metal Cluster-Adducts

NASA Astrophysics Data System (ADS)

Cox, D. M.; Kaldor, A.; Zakin, M. R.

1987-01-01

Recent development of the laser vaporization technique combined with mass-selective detection has made possible new studies of the fundamental chemical and physical properties of unsupported transition metal clusters as a function of the number of constituent atoms. A variety of experimental techniques have been developed in our laboratory to measure ionization threshold energies, magnetic moments, and gas phase reactivity of clusters. However, studies have so far been unable to determine the cluster structure or the chemical state of chemisorbed species on gas phase clusters. The application of infrared multiple photon dissociation IRMPD to obtain the IR absorption properties of metal cluster-adsorbate species in a molecular beam is described here. Specifically using a high power, pulsed CO2 laser as the infrared source, the IRMPD spectrum for methanol chemisorbed on small iron clusters is measured as a function of the number of both iron atoms and methanols in the complex for different methanol isotopes. Both the feasibility and potential utility of IRMPD for characterizing metal cluster-adsorbate interactions are demonstrated. The method is generally applicable to any cluster or cluster-adsorbate system dependent only upon the availability of appropriate high power infrared sources.

Application of a parallel genetic algorithm to the global optimization of medium-sized Au-Pd sub-nanometre clusters

NASA Astrophysics Data System (ADS)

Hussein, Heider A.; Demiroglu, Ilker; Johnston, Roy L.

2018-02-01

To contribute to the discussion of the high activity and reactivity of Au-Pd system, we have adopted the BPGA-DFT approach to study the structural and energetic properties of medium-sized Au-Pd sub-nanometre clusters with 11-18 atoms. We have examined the structural behaviour and stability as a function of cluster size and composition. The study suggests 2D-3D crossover points for pure Au clusters at 14 and 16 atoms, whereas pure Pd clusters are all found to be 3D. For Au-Pd nanoalloys, the role of cluster size and the influence of doping were found to be extensive and non-monotonic in altering cluster structures. Various stability criteria (e.g. binding energies, second differences in energy, and mixing energies) are used to evaluate the energetics, structures, and tendency of segregation in sub-nanometre Au-Pd clusters. HOMO-LUMO gaps were calculated to give additional information on cluster stability and a systematic homotop search was used to evaluate the energies of the generated global minima of mono-substituted clusters and the preferred doping sites, as well as confirming the validity of the BPGA-DFT approach.

Ejection of Coulomb Crystals from a Linear Paul Ion Trap for Ion-Molecule Reaction Studies.

PubMed

Meyer, K A E; Pollum, L L; Petralia, L S; Tauschinsky, A; Rennick, C J; Softley, T P; Heazlewood, B R

2015-12-17

Coulomb crystals are being increasingly employed as a highly localized source of cold ions for the study of ion-molecule chemical reactions. To extend the scope of reactions that can be studied in Coulomb crystals-from simple reactions involving laser-cooled atomic ions, to more complex systems where molecular reactants give rise to multiple product channels-sensitive product detection methodologies are required. The use of a digital ion trap (DIT) and a new damped cosine trap (DCT) are described, which facilitate the ejection of Coulomb-crystallized ions onto an external detector for the recording of time-of-flight (TOF) mass spectra. This enables the examination of reaction dynamics and kinetics between Coulomb-crystallized ions and neutral molecules: ionic products are typically cotrapped, thus ejecting the crystal onto an external detector reveals the masses, identities, and quantities of all ionic species at a selected point in the reaction. Two reaction systems are examined: the reaction of Ca(+) with deuterated isotopologues of water, and the charge exchange between cotrapped Xe(+) with deuterated isotopologues of ammonia. These reactions are examples of two distinct types of experiment, the first involving direct reaction of the laser-cooled ions, and the second involving reaction of sympathetically-cooled heavy ions to form a mixture of light product ions. Extensive simulations are conducted to interpret experimental results and calculate optimal operating parameters, facilitating a comparison between the DIT and DCT approaches. The simulations also demonstrate a correlation between crystal shape and image shape on the detector, suggesting a possible means for determining crystal geometry for nonfluorescing ions.

Rotational Spectrum, Conformational Composition, Intramolecular Hydrogen Bonding, and Quantum Chemical Calculations of Mercaptoacetonitrile (HSCH2C≡N), a Compound of Potential Astrochemical Interest.

PubMed

Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

2016-03-31

The microwave spectra of mercaptoacetonitrile (HSCH2C≡N) and one deuterated species (DSCH2C≡N) were investigated in the 7.5-124 GHz spectral interval. The spectra of two conformers denoted SC and AP were assigned. The H-S-C-C chain of atoms is synclinal in SC and anti-periplanar in AP. The ground state of SC is split into two substates separated by a comparatively small energy difference resulting in closely spaced transitions with equal intensities. Several transitions of the parent species of SC deviate from Watson's Hamiltonian. Only slight improvements were obtained using a Hamiltonian that takes coupling between the two substates into account. Deviations from Watson's Hamiltonian were also observed for the parent species of AP. However, the spectrum of the deuterated species, which was investigated only for the SC conformer, fits satisfactorily to Watson's Hamiltonian. Relative intensity measurements found SC to be lower in energy than AP by 3.8(3) kJ/mol. The strength of the intramolecular hydrogen bond between the thiol and cyano groups was estimated to be ∼2.1 kJ/mol. The microwave work was augmented by quantum chemical calculations at CCSD and MP2 levels using basis sets of minimum triple-ζ quality. Mercaptoacetonitrile has astrochemical interest, and the spectra presented herein should be useful for a potential identification of this compound in the interstellar medium. Three different ways of generating mercaptoacetonitrile from compounds already found in the interstellar medium were explored by quantum chemical calculations.

A cluster expansion model for predicting activation barrier of atomic processes

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

Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in

2013-06-15

We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEBmore » results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.« less

Molybdenum and carbon atom and carbon cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, Eider

Exit-angle resolved Mo atom sputtering yield under Xe ion bombardment and carbon atom and cluster (C2 and C3) sputtering yields under Xe, Kr, Ar, Ne and He ion bombardment from a plasma are measured for low incident energies (75--225 eV). An energy-resolved quadrupole mass spectrometer (QMS) is used to detect the fraction of un-scattered sputtered neutrals that become ionized in the plasma; the angular distribution is obtained by changing the angle between the target and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles between the sample and the QMS. The elastic scattering cross-sections of C, C2 and C3 with the different bombarding gas neutrals is obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. Because the results obtained with the QMS are relative, the Mo atom sputtering results are normalized to the existing data in the literature and the total sputtering yield for carbon (C+C 2+C3) for each bombarding gas is obtained from weight loss measurements. The absolute sputtering yield for C, C2 and C 3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. The angular sputtering distribution for Mo has a maximum at theta=60°, and this maximum becomes less pronounced as the incident ion energy increases. The results of the Monte Carlo TRIDYN code simulation for the angular distribution of Mo atoms sputtered by Xe bombardment are in agreement with the experiments. For carbon sputtering under-cosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases are also observed. The C, C2 and C3 sputtering yield data shows a clear decrease of the atom to cluster (C/C2 and C/C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

Gas chromatography-mass spectrometric studies of O-alkyl O-2-(N,N-dialkylamino) ethyl alkylphosphonites(phosphonates) for chemical weapons convention verification.

PubMed

Saeidian, Hamid; Babri, Mehran; Ramezani, Atefeh; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-01-01

The electron ionization (EI) mass spectra of a series of O-alkyl O-2-(N,N-dialkylaminolethyl alkylphosphonites(phosphonates), which are precursors of nerve agents, were studied for Chemical Weapons Convention (CWC) verification. General El fragmentation pathways were constructed and discussed. Proposed fragment structures were confirmed through analyzing fragment ions of deuterated analogs and density functional theory (DFT) calculations. The observed fragment ions are due to different fragmentation pathways such as hydrogen and McLafferty+1 rearrangements, alkene, amine and alkoxy elimination by alpha- or beta-cleavage process. Fragment ions distinctly allow unequivocal identification of the interested compounds including those of isomeric compounds. The presence and abundance of fragment ions were found to depend on the size and structure of the alkyl group attached to nitrogen, phosphorus and oxygen atoms.

Photoredox-catalyzed deuteration and tritiation of pharmaceutical compounds

PubMed Central

Loh, Yong Yao; Nagao, Kazunori; Hoover, Andrew J.; Hesk, David; Rivera, Nelo R.; Colletti, Steven L.; Davies, Ian W.; MacMillan, David W. C.

2018-01-01

Deuterium- and tritium-labeled pharmaceutical compounds are pivotal diagnostic tools in drug discovery research, providing vital information about the biological fate of drugs and drug metabolites. Herein we demonstrate that a photoredox-mediated hydrogen atom transfer protocol can efficiently and selectively install deuterium (D) and tritium (T) at α-amino sp3 carbon-hydrogen bonds in a single step, using isotopically labeled water (D2O or T2O) as the source of hydrogen isotope. In this context, we also report a convenient synthesis of T2O from T2, providing access to high-specific-activity T2O. This protocol has been successfully applied to the high incorporation of deuterium and tritium in 18 drug molecules, which meet the requirements for use in ligand-binding assays and absorption, distribution, metabolism, and excretion studies. PMID:29123019

Vibrational Mode-Specific Reaction of Methane on a Nickel Surface

NASA Astrophysics Data System (ADS)

Beck, Rainer D.; Maroni, Plinio; Papageorgopoulos, Dimitrios C.; Dang, Tung T.; Schmid, Mathieu P.; Rizzo, Thomas R.

2003-10-01

The dissociation of methane on a nickel catalyst is a key step in steam reforming of natural gas for hydrogen production. Despite substantial effort in both experiment and theory, there is still no atomic-scale description of this important gas-surface reaction. We report quantum state-resolved studies, using pulsed laser and molecular beam techniques, of vibrationally excited methane reacting on the nickel (100) surface. For doubly deuterated methane (CD2H2), we observed that the reaction probability with two quanta of excitation in one C-H bond was greater (by as much as a factor of 5) than with one quantum in each of two C-H bonds. These results clearly exclude the possibility of statistical models correctly describing the mechanism of this process and attest to the importance of full-dimensional calculations of the reaction dynamics.

Vibrational mode-specific reaction of methane on a nickel surface.

PubMed

Beck, Rainer D; Maroni, Plinio; Papageorgopoulos, Dimitrios C; Dang, Tung T; Schmid, Mathieu P; Rizzo, Thomas R

2003-10-03

The dissociation of methane on a nickel catalyst is a key step in steam reforming of natural gas for hydrogen production. Despite substantial effort in both experiment and theory, there is still no atomic-scale description of this important gas-surface reaction. We report quantum state-resolved studies, using pulsed laser and molecular beam techniques, of vibrationally excited methane reacting on the nickel (100) surface. For doubly deuterated methane (CD2H2), we observed that the reaction probability with two quanta of excitation in one C-H bond was greater (by as much as a factor of 5) than with one quantum in each of two C-H bonds. These results clearly exclude the possibility of statistical models correctly describing the mechanism of this process and attest to the importance of full-dimensional calculations of the reaction dynamics.

Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

NASA Technical Reports Server (NTRS)

Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

1994-01-01

We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

Solid polystyrene and deuterated polystyrene light output response to fast neutrons

NASA Astrophysics Data System (ADS)

Simpson, R.; Danly, C.; Glebov, V. Yu.; Hurlbut, C.; Merrill, F. E.; Volegov, P. L.; Wilde, C.

2016-04-01

The Neutron Imaging System has proven to be an important diagnostic in studying DT implosion characteristics at the National Ignition Facility. The current system depends on a polystyrene scintillating fiber array, which detects fusion neutrons born in the DT hotspot as well as neutrons that have scattered to lower energies in the surrounding cold fuel. Increasing neutron yields at NIF, as well as a desire to resolve three-dimensional information about the fuel assembly, have provided the impetus to build and install two additional next-generation neutron imaging systems. We are currently investigating a novel neutron imaging system that will utilize a deuterated polystyrene (CD) fiber array instead of standard hydrogen-based polystyrene (CH). Studies of deuterated xylene or deuterated benzene liquid scintillator show an improvement in imaging resolution by a factor of two [L. Disdier et al., Rev. Sci. Instrum. 75, 2134 (2004)], but also a reduction in light output [V. Bildstein et al., Nucl. Instrum. Methods Phys. Res., Sect. A 729, 188 (2013); M. I. Ojaruega, Ph.D. thesis, University of Michigan, 2009; M. T. Febbraro, Ph.D. thesis, University of Michigan, 2014] as compared to standard plastic. Tests of the relative light output of deuterated polystyrene and standard polystyrene were completed using 14 MeV fusion neutrons generated through implosions of deuterium-tritium filled capsules at the OMEGA laser facility. In addition, we collected data of the relative response of these two scintillators to a wide energy range of neutrons (1-800 MeV) at the Weapons Neutrons Research Facility. Results of these measurements are presented.

Solid polystyrene and deuterated polystyrene light output response to fast neutrons.

PubMed

Simpson, R; Danly, C; Glebov, V Yu; Hurlbut, C; Merrill, F E; Volegov, P L; Wilde, C

2016-04-01

The Neutron Imaging System has proven to be an important diagnostic in studying DT implosion characteristics at the National Ignition Facility. The current system depends on a polystyrene scintillating fiber array, which detects fusion neutrons born in the DT hotspot as well as neutrons that have scattered to lower energies in the surrounding cold fuel. Increasing neutron yields at NIF, as well as a desire to resolve three-dimensional information about the fuel assembly, have provided the impetus to build and install two additional next-generation neutron imaging systems. We are currently investigating a novel neutron imaging system that will utilize a deuterated polystyrene (CD) fiber array instead of standard hydrogen-based polystyrene (CH). Studies of deuterated xylene or deuterated benzene liquid scintillator show an improvement in imaging resolution by a factor of two [L. Disdier et al., Rev. Sci. Instrum. 75, 2134 (2004)], but also a reduction in light output [V. Bildstein et al., Nucl. Instrum. Methods Phys. Res., Sect. A 729, 188 (2013); M. I. Ojaruega, Ph.D. thesis, University of Michigan, 2009; M. T. Febbraro, Ph.D. thesis, University of Michigan, 2014] as compared to standard plastic. Tests of the relative light output of deuterated polystyrene and standard polystyrene were completed using 14 MeV fusion neutrons generated through implosions of deuterium-tritium filled capsules at the OMEGA laser facility. In addition, we collected data of the relative response of these two scintillators to a wide energy range of neutrons (1-800 MeV) at the Weapons Neutrons Research Facility. Results of these measurements are presented.

The Chemistry of Multiply Deuterated Molecules in Protoplanetary Disks: I. The Outer Disk

NASA Technical Reports Server (NTRS)

Willacy, K.

2007-01-01

We present new models of the deuterium chemistry in protoplanetary disks, including, for the first time, multiply deuterated species. We use these models to explore whether observations in combination with models can give us clues as to which desorption processes occur in disks.We find, in common with other authors, that photodesorption can allow strongly bound molecules such as HDO to exist in the gas phase in a layer above the midplane. Models including this process give the best agreement with the observations. In the midplane, cosmic-ray heating can desorb weakly bound molecules such as CO and N2. We find the observations suggest that N2 is gaseous in this region, but that CO must be retained on the grains to account for the observed DCO+/HCO+. This could be achieved by CO having a higher binding energy than N2 (as may be the case when these molecules are accreted onto water ice) or by a smaller cosmic-ray desorption rate for CO than assumed here, as suggested by recent theoretical work. For gaseous molecules the calculated deuteration can be greatly changed by chemical processing in the disk from the input molecular cloud values. On the grains singly deuterated species tend to retain the D/H ratio set in the molecular cloud, whereas multiply deuterated species are more affected by the disk chemistry. Consequently, the D/H ratios observed in comets may be partly set in the parent cloud and partly in the disk, depending on the molecule.

Solid polystyrene and deuterated polystyrene light output response to fast neutrons

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

Simpson, R., E-mail: raspberry@lanl.gov; Danly, C.; Merrill, F. E.

The Neutron Imaging System has proven to be an important diagnostic in studying DT implosion characteristics at the National Ignition Facility. The current system depends on a polystyrene scintillating fiber array, which detects fusion neutrons born in the DT hotspot as well as neutrons that have scattered to lower energies in the surrounding cold fuel. Increasing neutron yields at NIF, as well as a desire to resolve three-dimensional information about the fuel assembly, have provided the impetus to build and install two additional next-generation neutron imaging systems. We are currently investigating a novel neutron imaging system that will utilize amore » deuterated polystyrene (CD) fiber array instead of standard hydrogen-based polystyrene (CH). Studies of deuterated xylene or deuterated benzene liquid scintillator show an improvement in imaging resolution by a factor of two [L. Disdier et al., Rev. Sci. Instrum. 75, 2134 (2004)], but also a reduction in light output [V. Bildstein et al., Nucl. Instrum. Methods Phys. Res., Sect. A 729, 188 (2013); M. I. Ojaruega, Ph.D. thesis, University of Michigan, 2009; M. T. Febbraro, Ph.D. thesis, University of Michigan, 2014] as compared to standard plastic. Tests of the relative light output of deuterated polystyrene and standard polystyrene were completed using 14 MeV fusion neutrons generated through implosions of deuterium-tritium filled capsules at the OMEGA laser facility. In addition, we collected data of the relative response of these two scintillators to a wide energy range of neutrons (1-800 MeV) at the Weapons Neutrons Research Facility. Results of these measurements are presented.« less

In Situ Scanning Tunneling Microscopy Topography Changes of Gold (111) in Aqueous Sulfuric Acid Produced by Electrochemical Surface Oxidation and Reduction and Relaxation Phenomena

NASA Astrophysics Data System (ADS)

Pasquale, M. A.; Nieto, F. J. Rodríguez; Arvia, A. J.

The electrochemical formation and reduction of O-layers on gold (111) films in 1 m sulfuric acid under different potentiodynamic routines are investigated utilizing in situ scanning tunneling microscopy. The surface dynamics is interpreted considering the anodic and cathodic reaction pathways recently proposed complemented with concurrent relaxation phenomena occurring after gold (111) lattice mild disruption (one gold atom deep) and moderate disruption (several atoms deep). The dynamics of both oxidized and reduced gold topographies depends on the potentiodynamic routine utilized to form OH/O surface species. The topography resulting from a mild oxidative disruption is dominated by quasi-2D holes and hillocks of the order of 5 nm, involving about 500-600 gold atoms each, and their coalescence. A cooperative turnover process at the O-layer, in which the anion ad-layer and interfacial water play a key role, determines the oxidized surface topography. The reduction of these O-layers results in gold clusters, their features depending on the applied potential routine. A moderate oxidative disruption produces a surface topography of hillocks and holes several gold atoms high and deep, respectively. The subsequent reduction leads to a spinodal gold pattern. Concurrent coalescence appears to be the result of an Ostwald ripening that involves the surface diffusion of both gold atoms and clusters. These processes produce an increase in surface roughness and an incipient gold faceting. The dynamics of different topographies can be qualitatively explained employing the arguments from colloidal science theory. For 1.1 V ≤ E ≅ Epzc weak electrostatic repulsions favor gold atom/cluster coalescence, whereas for E < Epzc the attenuated electrostatic repulsions among gold surfaces stabilize small clusters over the substrate producing string-like patterns.

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

Chezhina, N.V., E-mail: chezhina@nc2490.spb.edu; Korolev, D.A.; Zhuk, N.A.

On the basis of the results of magnetic susceptibility and ESR studies of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions iron atoms in the solid solutions of cubic modification of bismuth niobate were found to exist as Fe(III) monomers and exchange bound Fe(III)-O-Fe(III) dimers with antiferro- and ferromagnetic type of superexchange. The exchange parameters and the distribution of monomers and dimers in the solid solutions were calculated as a function of paramagnetic atom content. - Graphical abstract: The study of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions showed that the introduction of iron atoms into the structure ofmore » Bi{sub 3}NbO{sub 7} stabilizes the cubic structure of bismuth niobate making the phase transition tetragonal ↔ cubic structure irreversible. In the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions we observe the formation of dimers with antiferro- and ferromagnetic exchange. Such clusters are partially retained even at the infinite dilution of the solid solution, which testifies for their rigidity. A sufficiently high parameter of ferromagnetic exchange in a dimer (+53 cm{sup −1}) seems to result from iron atoms being located in the vicinity of oxygen vacancy. - Highlights: • The reversible transition cubic – tetragonal modifications in Bi{sub 3}NbO{sub 7} becomes irreversible. • Only cubic modification of Bi{sub 3}Nb{sub 1-x}Fe{sub x}O{sub 7-δ} is stable due to clusters of Fe atoms. • These clusters are sufficiently strong and retained even at the infinite dilution. • The calculations of magnetic susceptibility give the distribution of the clusters and single atoms.« less

Investigation on structure, electronic and magnetic properties of Cr doped (ZnO)12 clusters: First-principles calculations

NASA Astrophysics Data System (ADS)

Liu, Huan; Zhang, Jian-Min

2018-05-01

The structural, electronic, and magnetic properties of (ZnO)12 clusters doped with Cr atoms have been investigated by using spin-polarized first-principles calculations. The exohedral a3 isomer is favorable than endohedral a2 isomer. The isomer a1 and a5 respectively have the narrowest and biggest gap between highest unoccupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) of 0.473 and 1.291 eV among these five monodoped isomers. The magnetic moment may be related to the local environment around the Cr atom that the a2 isomer whose total magnetic moment is 6 μB while the other monodoped isomers which all isomers have nearly total magnetic moments 4 μB . For Cr-doped (ZnO)12 on a1 or a3 isomer, the DOS of spin-up channel cross the Fermi level EF showing a finite magnitude near the Fermi level which might be useful for half metallic character. For the bidoped cases, the exohedral isomers are found to be most favorable. Including all bipoed isomers of substitutional, exohedral and endohedral bidoped clusters, the total magnetic moment of the ferromagnetic (antiferromagnetic) state is 8 (0) μB and the HOMO-LUMO gap of antiferromagnetic state is slightly larger than that of ferromagnetic state. The magnetic coupling between the Cr atoms in bidoped configurations is mainly governed by the competition between direct Cr and Cr atoms antiferromagnetic interaction and the ferromagnetic interaction between two Cr atoms via O atom due to strong p-d hybridization. Most importantly, we show that the exohedral bidoped (ZnO)12 clusters favor the ferromagnetic state, which may have the future applications in spin-dependent magneto-optical and magneto-electrical devices.

Diffusion Monte Carlo studies of MB-pol (H{sub 2}O){sub 2−6} and (D{sub 2}O){sub 2−6} clusters: Structures and binding energies

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

Mallory, Joel D.; Mandelshtam, Vladimir A.

2016-08-14

We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H{sub 2}O){sub 2−6} clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitivemore » to the isotope substitution. Most remarkably, the ground state of the (H{sub 2}O){sub 6} hexamer is represented by four distinct cage structures, while that of (D{sub 2}O){sub 6} is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H{sub 2}O){sub 6} and (D{sub 2}O){sub 6}, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

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

Oka, Yurie, E-mail: ok-yu@fuji.waseda.jp; Yanao, Tomohiro, E-mail: yanao@waseda.jp; Koon, Wang Sang, E-mail: koon@cds.caltech.edu

2015-04-07

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internalmore » centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Oka, Yurie; Yanao, Tomohiro; Koon, Wang Sang

2015-04-01

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.

Synthesis of stereospecifically deuterated desoxypodophyllotoxins and 1H-nmr assignment of desoxypodophyllotoxin

NASA Technical Reports Server (NTRS)

Pullockaran, A. J.; Kingston, D. G.; Lewis, N. G.

1989-01-01

[4 beta- 2H1]Desoxypodophyllotoxin [3], [4 alpha- 2H1]desoxypodophyllotoxin [4], and [4, 4- 2 H2]desoxypodophyllotoxin [9] were prepared from podophyllotoxin [1] via its chloride [5]. A complete assignment of the 1H-nmr spectrum of desoxypodophyllotoxin [2] was made on the basis of the spectra of the deuterated compounds [3] and [4].

Hydrogen/deuterium exchange studies of native rabbit MM-CK dynamics.

PubMed

Mazon, Hortense; Marcillat, Olivier; Forest, Eric; Vial, Christian

2004-02-01

Creatine kinase (CK) isoenzymes catalyse the reversible transfer of a phosphoryl group from ATP onto creatine. This reaction plays a very important role in the regulation of intracellular ATP concentrations in excitable tissues. CK isoenzymes are highly resistant to proteases in native conditions. To appreciate localized backbone dynamics, kinetics of amide hydrogen exchange with deuterium was measured by pulse-labeling the dimeric cytosolic muscle CK isoenzyme. Upon exchange, the protein was digested with pepsin, and the deuterium content of the resulting peptides was determined by liquid chromatography coupled to mass spectrometry (MS). The deuteration kinetics of 47 peptides identified by MS/MS and covering 96% of the CK backbone were analyzed. Four deuteration patterns have been recognized: The less deuterated peptides are located in the saddle-shaped core of CK, whereas most of the highly deuterated peptides are close to the surface and located around the entrance to the active site. Their exchange kinetics are discussed by comparison with the known secondary and tertiary structures of CK with the goal to reveal the conformational dynamics of the protein. Some of the observed dynamic motions may be linked to the conformational changes associated with substrate binding and catalytic mechanism.

X-ray structure determination and deuteration of nattokinase.

PubMed

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-11-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.