Single-layer 1T‧-MoS2 under electron irradiation from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Pizzochero, Michele; Yazyev, Oleg V.

2018-04-01

Irradiation with high-energy particles has recently emerged as an effective tool for tailoring the properties of two-dimensional transition metal dichalcogenides. In order to carry out an atomically-precise manipulation of the lattice, a detailed understanding of the beam-induced events occurring at the atomic scale is necessary. Here, we investigate the response of 1T' -MoS2 to the electron irradiation by ab initio molecular dynamics means. Our simulations suggest that an electron beam with energy smaller than 75 keV does not result in any knock-on damage. The displacement threshold energies are different for the two nonequivalent sulfur atoms in 1T' -MoS2 and strongly depend on whether the top or bottom chalcogen layer is considered. As a result, a careful tuning of the beam energy can promote the formation of ordered defects in the sample. We further discuss the effect of the electron irradiation in the neighborhood of a defective site, the mobility of the sulfur vacancies created and their tendency to aggregate. Overall, our work provides useful guidelines for the imaging and the defect engineering of 1T' -MoS2 using electron microscopy.

Raman scattering tensors in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Tsuboi, Masamichi; Kumakura, Akiko; Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ushizawa, Koichi; Ueda, Toyotoshi

1997-03-01

Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.

Adsorption and dissociation of molecular hydrogen on orthorhombic β-Mo 2C and cubic δ-MoC (001) surfaces

DOE PAGES

Posada-Pérez, Sergio; Viñes, Francesc; Valero, Rosendo; ...

2016-10-03

Molybdenum carbides are increasingly used in heterogeneously catalyzed hydrogenation reactions, which imply the adsorption and dissociation of molecular hydrogen. In this paper, a systematic density functional theory based study, including or excluding dispersion terms, concerning the interaction and stability of H 2 with cubic δ-MoC(001) and orthorhombic β-Mo 2C(001) surfaces, is presented. In the latter case the two possible C or Mo terminations are considered. In addition, different situations for the H covered surfaces are examined. Computational results including dispersive forces predict an essentially spontaneous dissociation of H 2 on β-Mo 2C(001) independently of the surface termination, whereas on δ-MoC(001)more » molecular hydrogen dissociation implies a small but noticeable energy barrier. Furthermore, the ab initio thermodynamics formalism has been used to compare the stability of different H coverages. In conclusion, core level binding energies and vibrational frequencies are presented with the aim to assist the interpretation of yet unavailable data from X-ray photoelectron and infrared spectroscopies.« less

Equation of state of U2Mo up-to Mbar pressure range: Ab-initio study

NASA Astrophysics Data System (ADS)

Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.

2018-04-01

Experimentally, U2Mo is known to exist in tetragonal structure at ambient conditions. In contrast to experimental reports, the past theoretical studies carried out in this material do not find this phase to be stable structure at zero pressure. In order to examine this discrepancy between experiment and theory, we have performed ab-initio electronic band structure calculations on this material. In our theoretical study, we have attempted to search for lowest enthalpy structure at ambient as well at high pressure up to 200 GPa, employing evolutionary structure search algorithm in conjunction with ab-inito method. Our investigations suggest that a hexagonal structure with space group symmetry P6/mmm is the lowest enthalpy structure not only at ambient pressure but also up to pressure range of ˜200 GPa. To further, substantiate the results of these static lattice calculations the elastic and lattice dynamical stability has also been analysed. The theoretical isotherm derived from these calculations has been utilized to determine the Hugoniot of this material. Various physical properties such as zero pressure equilibrium volume, bulk modulus and its pressure derivative has also been derived from theoretical isotherm.

Electronic structure and transport properties of zigzag MoS2 nanoribbons

NASA Astrophysics Data System (ADS)

Sharma, Uma Shankar; Shah, Rashmi; Mishra, Pankaj Kumar

2018-05-01

In present study, electronic and transport properties of the 8zigzag MoS2 nanoribbons (8ZMoS2NRs) are investigated using ab-initio density functional theory [DFT]. The calculations were performed using nonequilibrium Green's function (NEGF) formalism based on DFT as implemented in the TranSiesta code. Results show that the defect can introduces few extra states into the energy gap, which lead nanoribbons to reveal a metallic characteristic. The voltage-current (VI) graph of 8ZMoS2NRs show a threshold current increases after introducing Mo defect in the devices. when introducing a Mo vacancy under low biases, the current will be suppressed—whereas under high biases, the current through the defected 8ZMoS2NRs will increases rapidly, due to the other channel being opened, that make possibility of 8ZMoS2NRs application in electronic devices such as voltage regulation.

A General Approach to Access Morphologies of Polyoxometalates in Solution by Using SAXS: An Ab Initio Modeling Protocol.

PubMed

Li, Mu; Wang, Weiyu; Yin, Panchao

2018-05-02

Herein, we reported a general protocol for an ab initio modeling approach to deduce structure information of polyoxometalates (POMs) in solutions from scattering data collected by the small-angle X-ray scattering (SAXS) technique. To validate the protocol, the morphologies of a serious of known POMs in either aqueous or organic solvents were analyzed. The obtained particle morphologies were compared and confirmed with previous reported crystal structures. To extend the feasibility of the protocol to an unknown system of aqueous solutions of Na 2 MoO 4 with the pH ranging from -1 to 8.35, the formation of {Mo 36 } clusters was probed, identified, and confirmed by SAXS. The approach was further optimized with a multi-processing capability to achieve fast analysis of experimental data, thereby, facilitating in situ studies of formations of POMs in solutions. The advantage of this approach is to generate intuitive 3D models of POMs in solutions without confining information such as symmetries and possible sizes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fermi arc electronic structure and Chern numbers in the type-II Weyl semimetal candidate Mo x W 1 - x Te 2

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

Belopolski, Ilya; Xu, Su-Yang; Ishida, Yukiaki

2016-08-15

It has recently been proposed that electronic band structures in crystals can give rise to a previously overlooked type of Weyl fermion, which violates Lorentz invariance and, consequently, is forbidden in particle physics. It was further predicted that Mo x W 1 - x Te 2 may realize such a type-II Weyl fermion. Here, we first show theoretically that it is crucial to access the band structure above the Fermi level ε F to show a Weyl semimetal in Mo x W 1 - x Te 2 . Then, we study Mo x W 1 - x Te 2 bymore » pump-probe ARPES and we directly access the band structure > 0.2 eV above ε F in experiment. By comparing our results with ab initio calculations, we conclude that we directly observe the surface state containing the topological Fermi arc. We propose that a future study of Mo x W 1 - x Te 2 by pump-probe ARPES may directly pinpoint the Fermi arc. Our work sets the stage for the experimental discovery of the first type-II Weyl semimetal in Mo x W 1 - x Te 2 .« less

Tuning the Electronic Properties, Effective Mass and Carrier Mobility of MoS2 Monolayer by Strain Engineering: First-Principle Calculations

NASA Astrophysics Data System (ADS)

Phuc, Huynh V.; Hieu, Nguyen N.; Hoi, Bui D.; Hieu, Nguyen V.; Thu, Tran V.; Hung, Nguyen M.; Ilyasov, Victor V.; Poklonski, Nikolai A.; Nguyen, Chuong V.

2018-01-01

In this paper, we studied the electronic properties, effective masses, and carrier mobility of monolayer MoS_2 using density functional theory calculations. The carrier mobility was considered by means of ab initio calculations using the Boltzmann transport equation coupled with deformation potential theory. The effects of mechanical biaxial strain on the electronic properties, effective mass, and carrier mobility of monolayer MoS_2 were also investigated. It is demonstrated that the electronic properties, such as band structure and density of state, of monolayer MoS_2 are very sensitive to biaxial strain, leading to a direct-indirect transition in semiconductor monolayer MoS_2. Moreover, we found that the carrier mobility and effective mass can be enhanced significantly by biaxial strain and by lowering temperature. The electron mobility increases over 12 times with a biaxial strain of 10%, while the carrier mobility gradually decreases with increasing temperature. These results are very useful for the future nanotechnology, and they make monolayer MoS_2 a promising candidate for application in nanoelectronic and optoelectronic devices.

Stacking stability of MoS2 bilayer: An ab initio study

NASA Astrophysics Data System (ADS)

Tao, Peng; Guo, Huai-Hong; Yang, Teng; Zhang, Zhi-Dong

2014-10-01

The study of the stacking stability of bilayer MoS2 is essential since a bilayer has exhibited advantages over single layer MoS2 in many aspects for nanoelectronic applications. We explored the relative stability, optimal sliding path between different stacking orders of bilayer MoS2, and (especially) the effect of inter-layer stress, by combining first-principles density functional total energy calculations and the climbing-image nudge-elastic-band (CI-NEB) method. Among five typical stacking orders, which can be categorized into two kinds (I: AA, AB and II: AA', AB', A'B), we found that stacking orders with Mo and S superposing from both layers, such as AA' and AB, is more stable than the others. With smaller computational efforts than potential energy profile searching, we can study the effect of inter-layer stress on the stacking stability. Under isobaric condition, the sliding barrier increases by a few eV/(ucGPa) from AA' to AB', compared to 0.1 eV/(ucGPa) from AB to [AB]. Moreover, we found that interlayer compressive stress can help enhance the transport properties of AA'. This study can help understand why inter-layer stress by dielectric gating materials can be an effective means to improving MoS2 on nanoelectronic applications.

Interfacial Coupling Effect on Electron Transport in MoS2/SrTiO3 Heterostructure: An Ab-initio Study.

PubMed

Bano, Amreen; Gaur, N K

2018-01-15

A variety of theoretical and experimental works have reported several potential applications of MoS 2 monolayer based heterostructures (HSs) such as light emitting diodes, photodetectors and field effect transistors etc. In the present work, we have theoretically performed as a model case study, MoS 2 monolayer deposited over insulating SrTiO 3 (001) to study the band alignment at TiO 2 termination. The interfacial characteristics are found to be highly dependent on the interface termination. With an insulating oxide material, a significant band gap (0.85eV) is found in MoS 2 /TiO 2 interface heterostructure (HS). A unique electronic band profile with an indirect band gap (0.67eV) is observed in MoS 2 monolayer when confined in a cubic environment of SrTiO 3 (STO). Adsorption analysis showed the chemisorption of MoS 2 on the surface of STO substrate with TiO 2 termination which is justified by the charge density calculations that shows the existence of covalent bonding at the interface. The fabrication of HS of such materials paves the path for developing the unprecedented 2D materials with exciting properties such as semiconducting devices, thermoelectric and optoelectronic applications.

Vibrational spectra (FT-IR, Raman and MI-IR) of α- and β-alanine

NASA Astrophysics Data System (ADS)

Rosado, Mário Túlio S.; Duarte, Maria Leonor R. S.; Fausto, Rui

1997-06-01

The vibrational spectra of α- and β-alaine molecules in both their zwitterionic and neutral forms are studied by FT-IR, Raman and MI-IR spectroscopy. Together with results from theoretical SCF-MO ab initio calculations, the spectroscopic data obtained under the various experimental conditions used in this study (crystalline phase; low temperature matrix isolated molecules) enable to undertake a detailed assignment of the vibrational spectra of the studied compounds.

Simulation of Phonon Spectra in Three-Component Two-Dimensional Crystals of Refractory-Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Alexeev, A. Yu.; Krivosheeva, A. V.; Shaposhnikov, V. L.; Borisenko, V. E.

2017-09-01

A model for ab initio calculation of the phonon properties of three-component solid solutions of refractory-metal dichalcogenides was developed based on the assumption that displacements of the same type of chalcogen atoms and decoupled displacements of the metal atoms were identical. The calculated phonon frequencies at the Γ-point for monomolecular layers of MoS2-xSex and MoS2-xTex agreed with existing experimental Raman spectra.

Comment on 'Parametrization of Stillinger-Weber potential based on a valence force field model: application to single-layer MoS2 and black phosphorus'.

PubMed

Midtvedt, Daniel; Croy, Alexander

2016-06-10

We compare the simplified valence-force model for single-layer black phosphorus with the original model and recent ab initio results. Using an analytic approach and numerical calculations we find that the simplified model yields Young's moduli that are smaller compared to the original model and are almost a factor of two smaller than ab initio results. Moreover, the Poisson ratios are an order of magnitude smaller than values found in the literature.

First-principles study of MoS2 and MoSe2 nanoclusters in the framework of evolutionary algorithm and density functional theory

NASA Astrophysics Data System (ADS)

Hashemi, Zohreh; Rafiezadeh, Shohreh; Hafizi, Roohollah; Hashemifar, S. Javad; Akbarzadeh, Hadi

2018-04-01

Evolutionary algorithm is combined with full-potential ab initio calculations to investigate conformational space of (MoS2)n and (MoSe2)n (n = 1-10) nanoclusters and to identify the lowest energy structural isomers of these systems. It is argued that within both BLYP and PBE functionals, these nanoclusters favor sandwiched planar configurations, similar to their ideal planar sheets. The second order difference in total energy (Δ2 E) of the lowest energy isomers is computed to estimate the abundance of the clusters at different sizes and to determine the magic sizes of (MoS2)n and (MoSe2)n nanoclusters. In order to investigate the electronic properties of nanoclusters, their energy gap is calculated by several methods, including hybrid functionals (B3LYP and PBE0), GW approach, and Δ scf method. At the end, the vibrational modes of the lowest lying isomers are calculated by using the force constants method and the IR active modes of the systems are identified. The vibrational spectra are used to calculate the Helmholtz free energy of the systems and then to investigate abundance of the nanoclusters at finite temperatures.

Phonon-coupled ultrafast interlayer charge oscillation at van der Waals heterostructure interfaces

NASA Astrophysics Data System (ADS)

Zheng, Qijing; Xie, Yu; Lan, Zhenggang; Prezhdo, Oleg V.; Saidi, Wissam A.; Zhao, Jin

2018-05-01

Van der Waals (vdW) heterostructures of transition-metal dichalcogenide (TMD) semiconductors are central not only for fundamental science, but also for electro- and optical-device technologies where the interfacial charge transfer is a key factor. Ultrafast interfacial charge dynamics has been intensively studied, however, the atomic scale insights into the effects of the electron-phonon (e-p) coupling are still lacking. In this paper, using time dependent ab initio nonadiabatic molecular dynamics, we study the ultrafast interfacial charge transfer dynamics of two different TMD heterostructures MoS2/WS2 and MoSe2/WSe2 , which have similar band structures but different phonon frequencies. We found that MoSe2/WSe2 has softer phonon modes compared to MoS2/WS2 , and thus phonon-coupled charge oscillation can be excited with sufficient phonon excitations at room temperature. In contrast, for MoS2/WS2 , phonon-coupled interlayer charge oscillations are not easily excitable. Our study provides an atomic level understanding on how the phonon excitation and e-p coupling affect the interlayer charge transfer dynamics, which is valuable for both the fundamental understanding of ultrafast dynamics at vdW hetero-interfaces and the design of novel quasi-two-dimensional devices for optoelectronic and photovoltaic applications.

Large theoretical thermoelectric power factor of suspended single-layer MoS{sub 2}

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

Babaei, Hasan, E-mail: babaei@illinois.edu, E-mail: babaei@auburn.edu; Mechanical Engineering Department, Auburn University, Auburn, Alabama 36849-5341; Khodadadi, J. M.

2014-11-10

We have calculated the semi-classical thermoelectric power factor of suspended single-layer (SL)- MoS{sub 2} utilizing electron relaxation times derived from ab initio calculations. Measurements of the thermoelectric power factor of SL-MoS{sub 2} on substrates reveal poor power factors. In contrast, we find the thermoelectric power factor of suspended SL-MoS{sub 2} to peak at ∼2.8 × 10{sup 4} μW/m K{sup 2} at 300 K, at an electron concentration of 10{sup 12} cm{sup −2}. This figure is higher than that in bulk Bi{sub 2}Te{sub 3}, for example. Given its relatively high thermal conductivity, suspended SL-MoS{sub 2} may hold promise for in-plane thin-film Peltiermore » coolers, provided reasonable mobilities can be realized.« less

Conformational distribution of baclofen analogues by 1H and 13C NMR analysis and ab initio HF MO STO-3G or STO-3G* calculations

NASA Astrophysics Data System (ADS)

Vaccher, Claude; Berthelot, Pascal; Debaert, Michel; Vermeersch, Gaston; Guyon, René; Pirard, Bernard; Vercauteren, Daniel P.; Dory, Magdalena; Evrard, Guy; Durant, François

1993-12-01

The conformations of 3-(substituted furan-2-yl) and 3-(substituted thien-2-yl)-γ-aminobutyric acid 1-9 in solution (D 2O) are estimated from high-resolution (300 MHz) 1H NMR coupling data. Conformations and populations of conformers are calculated by means of a modified Karplus-like relationship for the vicinal coupling constants. The results are compared with X-ray crystallographic investigations (torsion angles) and ab initio HF MO ST-3G or STO-3G* calculations. 1H NMR spectral analysis shows how 1-9 in solution retain the preferred g- conformation around the C3C4 bond, as found in the solid state, while a partial rotation is set up around the C2C3 bond: the conformations about C2C3 are all highly populated in solution. The 13C spin-lattice relaxation times are also discussed.

Thermal transport properties of bulk and monolayer MoS2: an ab-initio approach

NASA Astrophysics Data System (ADS)

Bano, Amreen; Khare, Preeti; Gaur, N. K.

2017-05-01

The transport properties of semiconductors are key to the performance of many solid-state devices (transistors, data storage, thermoelectric cooling and power generation devices, etc). In recent years simulation tools based on first-principles calculations have been greatly improved, being able to obtain the fundamental ground-state properties of materials accurately. The quasi harmonic thermal properties of bulk and monolayer of MoS2 has been computed with ab initio periodic simulations based of density functional theory (DFT). The temperature dependence of bulk modulus, specific heat, thermal expansion and gruneisen parameter have been calculated in our work within the temperature range of 0K to 900K with projected augmented wave (PAW) method using generalized gradient approximation (GGA). Our results show that the optimized lattice parameters are in good agreement with the earlier reported works and also for thermoelastic parameter, i.e. isothermal bulk modulus (B) at 0K indicates that monolayer MoS2 (48.5 GPa)is more compressible than the bulk structure (159.23 GPa). The thermal expansion of monolayer structure is slightly less than the bulk. Similarly, other parameters like heat capacity and gruneisen parameter shows different nature which is due to the confinement of 3 dimensional structure to 2 dimension (2D) for improving its transport characteristics.

A first-principles study on new high-pressure metastable polymorphs of MoO{sub 2}

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

Becker, Nils; Dronskowski, Richard; Jülich-Aachen Research Alliance

The pressure-dependence of the stabilities of several MoO{sub 2} phases has been investigated by density-functional theory (GGA/PBE/PAW). Out of a set of 15 MX{sub 2} structures, the [SnO{sub 2}(II)], [α-PbO{sub 2}], and a modified rutile structure type were identified as possible metastable MoO{sub 2} polymorphs based on the analysis of thermodynamic properties and dynamic stability. High-pressure calculations suggest an orthorhombic TiO{sub 2} structure, dubbed [ortho-TiO{sub 2}], as a high-pressure polymorph at around 25 GPa. Furthermore, we find that the previously reported rutile-type MoO{sub 2} may be understood as a modified rutile type similar to the [VO{sub 2}] structure. - Graphicalmore » abstract: First-principles electronic structure and thermochemical calculations reveal four structure candidates as possible metastable polymorphs of MoO{sub 2}. Most promising is a distorted rutile-type similar to the known [VO{sub 2}] structure. An orthorhombic polymorph is proposed as a high-pressure polymorph. Display Omitted - Highlights: • Three possible metastable structure candidates for MoO{sub 2}. • Undistorted rutile type is improbable, a new distorted rutile-type MoO{sub 2} was suggested. • Orthorhombic phase of MoO{sub 2} (ortho-TiO{sub 2} type) should form at 25 GPa. • ab initio thermochemical data provided for MoO{sub 2}.« less

Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

1981-09-01

Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

Systematic investigation of structural, electronic, optical and thermal properties of ternary MoAlB; an ab initio approach

NASA Astrophysics Data System (ADS)

Rajpoot, Priyanka; Rastogi, Anugya; Verma, U. P.

2018-02-01

Structural, electronic, optical and thermal properties of molybdenum aluminum boride (MoAlB) have been analyzed systematically using the full potential linearized augmented plane wave method based on density functional theory at ambient condition as well as high pressure and high temperature. Density of states and band structure calculation reflect the metallic character of MoAlB. In addition to this, the electron charge density calculation reveals the strong covalent bonding, in between ‘B’ atoms as well as ‘Mo’ and ‘B’ atoms. Optical parameters exhibit anisotropic nature and MoAlB become transparent in ultraviolet region for the radiation of energy above 25 eV. The thermal properties were investigated by using the quasi-harmonic Debye model at high temperature and high pressure.

Elastic and Photoelastic Properties of M(NO3)2, MO (M = Mg, Ca, Sr, Ba)

NASA Astrophysics Data System (ADS)

Zhuravlev, Yu. N.; Korabel'nikov, D. V.

2017-05-01

The paper deals with ab initio investigations of elastic and photoelastic properties of oxides and nitrates of alkaline-earth metals. In gradient approximation of the density functional theory (DFT), these properties are studied with the use of the linear combination of the atomic orbital technique. DFT calculations are done with the CRYSTAL 14 software package. The paper introduces the elastic and photoelastic constants, anisotropy parameters for single-crystalline phases and the elastic modules, hardness, Poisson ratio for polycrystalline phases. Such parameters as sonic speed, Debye temperature, thermal conductivity, and Gruneisen parameter are estimated herein. For the fist time, mechanical stability, anisotropy of elastic and photoelastic properties and their dependences are investigated ab initio in this paper. Experimental results on elastic and photoelastic properties of oxides and nitrates are in good agreement with theoretical calculations.

A MoO2 sheet as a promising electrode material: ultrafast Li-diffusion and astonishing Li-storage capacity

NASA Astrophysics Data System (ADS)

Zhou, Yungang; Geng, Cheng

2017-03-01

The potential of MoO2 crystal as an electrode material is reported, and nanostructural MoO2 systems, including nanoparticles, nanospheres, nanobelts and nanowires, were synthesized and proved to be advanced electrode materials. A two-dimensional (2D) geometric structure represents an extreme of surface-to-volume ratio, and thus is more suitable as an electrode material in general. Stimulated by the recent fabrication of 2D MoO2, we adopted an ab initio molecular dynamics simulation and density functional theory calculation to study the stability and electrochemical properties of a MoO2 sheet. Identified by a phonon dispersion curve and potential energy curve calculations, the MoO2 sheet proved to be dynamically and thermally stable. After lithiation, similar to most promising 2D structures, we found that a Li atom can strongly adsorb on a MoO2 sheet, and the lithiated MoO2 sheet presented excellent metallic properties. Note that, compared with most promising 2D structures, we unexpectedly revealed that the diffusion barrier of the Li atom on the MoO2 sheet was much lower and the storage capacity of the MoO2 sheet was much larger. The calculated energy barrier for the diffusion of Li on the MoO2 sheet was only 75 meV, and, due to multilayer adsorption, the theoretical capacity of the MoO2 sheet can reach up to 2513 mA h g-1. Benefiting from general properties, such as strong Li-binding and excellent conductivity, and unique phenomena, such as ultrafast diffusion capacity and astonishing storage capacity, we highlight a new promising electrode material for the Li-ion battery.

The capacity fading mechanism and improvement of cycling stability in MoS2-based anode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Shu, Haibo; Li, Feng; Hu, Chenli; Liang, Pei; Cao, Dan; Chen, Xiaoshuang

2016-01-01

Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance.Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance. Electronic supplementary information (ESI) available: Models and energetics of Li adsorption/intercalation onto MoS2 sheets, details of the phase diagram calculations, schematic illustration for the structural evolution of lithiated MoS2 nanosheets, AIMD trajectories for lithiated silicene/MoS2/silicene composites, and movies for recording the AIMD simulation results. See DOI: 10.1039/c5nr07909h

Spin Hall Effect and Weak Antilocalization in Graphene/Transition Metal Dichalcogenide Heterostructures.

PubMed

Garcia, Jose H; Cummings, Aron W; Roche, Stephan

2017-08-09

We report on a theoretical study of the spin Hall Effect (SHE) and weak antilocalization (WAL) in graphene/transition metal dichalcogenide (TMDC) heterostructures, computed through efficient real-space quantum transport methods, and using realistic tight-binding models parametrized from ab initio calculations. The graphene/WS 2 system is found to maximize spin proximity effects compared to graphene on MoS 2 , WSe 2 , or MoSe 2 with a crucial role played by disorder, given the disappearance of SHE signals in the presence of strong intervalley scattering. Notably, we found that stronger WAL effects are concomitant with weaker charge-to-spin conversion efficiency. For further experimental studies of graphene/TMDC heterostructures, our findings provide guidelines for reaching the upper limit of spin current formation and for fully harvesting the potential of two-dimensional materials for spintronic applications.

Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

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

None, None

2016-01-01

The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shellmore » reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).« less

Ab Initio High Pressure and Temperature Investigation on Cubic PbMoO3 Perovskite

NASA Astrophysics Data System (ADS)

Dar, Sajad Ahmad; Srivastava, Vipul; Sakalle, Umesh Kumar

2017-12-01

A combined high pressure and temperature investigation on recently reported cubic perovskite PbMoO3 have been performed within the most accurate density functional theory (DFT). The structure was found stable in cubic paramagnetic phase. The DFT calculated analytical and experimental lattice constant were found in good agreement. The analytical tolerance factor as well as the elastic properties further verifies the cubic stability for PbMoO3. The spin polarized electronic band structure and density of states presented metallic nature with symmetry in up and down states. The insignificant magnetic moment also confirms the paramagnetic nature for the compound. The high pressure elastic and mechanical study up to 35 GPa reveal the structural stability of the material in this pressure range. The compound was found to establish a ductile nature. The electrical conductivity obtained from the band structure results show a decreasing trend with increasing temperature. The temperature dependence of thermodynamic parameters such as specific heat ( C v), thermal expansion ( α) has also been evaluated.

Molecular Symmetry in Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Madhavan, P. V.; Written, J. L.

1987-05-01

A scheme is presented for the construction of the Fock matrix in LCAO-SCF calculations and for the transformation of basis integrals to LCAO-MO integrals that can utilize several symmetry unique lists of integrals corresponding to different symmetry groups. The algorithm is fully compatible with vector processing machines and is especially suited for parallel processing machines.

Effect of alloying on screw dislocation structure in Mo: atomistic modelling approach with ab-initio parametrization

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.

2005-03-01

The plastic deformation in bcc metals is realized by the motion of screw dislocations with a complex star-like non-planar core. In this case, the direct investigation of the solute effect by first principles electronic structure calculations is a challenging problem for which we follow a combined approach that includes atomistic dislocation modelling with ab-initio parametrization of interatomic interactions. The screw dislocation core structure in Mo alloys is described within the model of atomic row displacements along a dislocation line with the interatomic row potential estimated from total energy full-potential linear muffin-tin orbital (FLMTO) calculations with the generalized gradient approximation (GGA) for the exchange-correlation potential. We demonstrate (1) that the solute effect on the dislocation structure is different for ``hard'' and ``easy'' cores and (2) that the softener addition in a ``hard'' core gives rise to a structural transformation into a configuration with a lower energy through an intermediate state. The softener solute is shown to disturb locally the three-fold symmetry of the dislocation core and the dislocation structure tends to the split planar core.

High-pressure melting of molybdenum.

PubMed

Belonoshko, A B; Simak, S I; Kochetov, A E; Johansson, B; Burakovsky, L; Preston, D L

2004-05-14

The melting curve of the body-centered cubic (bcc) phase of Mo has been determined for a wide pressure range using both direct ab initio molecular dynamics simulations of melting as well as a phenomenological theory of melting. These two methods show very good agreement. The simulations are based on density functional theory within the generalized gradient approximation. Our calculated equation of state of bcc Mo is in excellent agreement with experimental data. However, our melting curve is substantially higher than the one determined in diamond anvil cell experiments up to a pressure of 100 GPa. An explanation is suggested for this discrepancy.

Conformational analysis of a trihydroxylated derivative of cinnamic acid—a combined Raman spectroscopy and Ab initio study

NASA Astrophysics Data System (ADS)

Fiuza, S. M.; Van Besien, E.; Milhazes, N.; Borges, F.; Marques, M. P. M.

2004-05-01

A conformational analysis of 3-(3,4,5-trihydroxyphenyl)-2-propenoic acid (3,4,5-trihydroxycinnamic acid, THPPE), a trihydroxylated cinnamic acid analogous to caffeic acid (a natural compound often present in diet), was carried out by Raman spectroscopy coupled to Ab initio MO calculations. Apart from the optimised geometrical parameters for the most stable conformers of this compound, and for one of its dimeric species, the corresponding harmonic vibrational frequencies, as well as potential-energy profiles for rotation around several bonds within the molecule, were obtained. Twenty one distinct conformers were found for THPPE, the lowest energy ones—THPPE 1 and THPPE 2—displaying a completely planar geometry. The conformational preferences of this system were thus found to be mainly ruled by the stabilising effect of π-electron delocalisation. At the light of these results, a complete assignment of the corresponding solid state Raman spectra was performed.

Fully ab initio calculation of the resonant one-phonon Raman intensity of graphene

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

We developed a fully ab initio, many-body perturbation theory approach for the calculation of resonant, one-phonon Raman spectra. Our general approach is applicable to any material and here we present its application to the case of graphene. Our diagrammatic, first-principles approach allows us to go beyond and improve on an earlier theoretical study by Basko, which relied on an analytical calculation in certain limits. We investigate the dependence of the G peak intensity on both the excitation energy and Fermi level. Furthermore, our method allows us to identify the relevant electronic quantum pathways and to demonstrate the importance of the contributions from non-resonant electronic transitions. We also applied our approach to the calculation of the resonant one-phonon Raman spectrum of MoS2, with our results being in good agreement with experimental data. SR acknowledges financial support from the National Research Fund (FNR) Luxembourg.

Quantum-chemical study of model chemisorption structures on copper-containing catalysts. Communicat ion 1. ab-initio calculations of CuCo and CuCo/sup +/

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

Kuzminskii, M.B.; Bagator'yants, A.A.; Kazanskii, V.B.

1986-08-01

The authors perform ab-initio calculations, by the SCF MO LCAO method, of the electronic and geometric structure of the systems CuCO /SUP n+/ (n=0, 1) and potential curves of CO, depending on the charge state of the copper, with variation of all geometric parameters. The calculations of open-shell electronic states were performed by the unrestricted SCF method in a minimal basis set (I, STO-3G for the C and O, and MINI-1' for the Cu) and in a valence two-exponential basis set (II, MIDI-1 for the C and O, and MIDI'2' for the Cu). The principal results from the calculation inmore » the more flexible basis II are presented and the agreement between the results obtained in the minimal basis I and these data is then analyzed qualitatively.« less

Berry curvature dipole in Weyl semimetal materials: An ab initio study

NASA Astrophysics Data System (ADS)

Zhang, Yang; Sun, Yan; Yan, Binghai

2018-01-01

Noncentrosymmetric metals are anticipated to exhibit a dc photocurrent in the nonlinear optical response caused by the Berry curvature dipole in momentum space. Weyl semimetals (WSMs) are expected to be excellent candidates for observing these nonlinear effects because they carry a large Berry curvature concentrated in small regions, i.e., near the Weyl points. We have implemented the semiclassical Berry curvature dipole formalism into an ab initio scheme and investigated the second-order nonlinear response for two representative groups of materials: the TaAs-family type-I WSMs and the MoTe2-family type-II WSMs. Both types of WSMs exhibited a Berry curvature dipole in which type-II Weyl points are usually superior to the type-I WSM because of the strong tilt. Corresponding nonlinear susceptibilities in several materials promise a nonlinear Hall effect in the dc field limit, which is within the experimentally detectable range.

Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital-configuration interaction based quantum master equation study

NASA Astrophysics Data System (ADS)

Kishi, Ryohei; Minami, Takuya; Fukui, Hitoshi; Takahashi, Hideaki; Nakano, Masayoshi

2008-06-01

The core molecule dependence of energy (exciton) migration in phenylacetylene nanostar dendrimers is investigated using the ab initio molecular orbital (MO)-configuration interaction based quantum master equation approach. We examine three kinds of core molecular species, i.e., benzene, anthracene, and pentacene, with different highest occupied MO-lowest unoccupied MO (HOMO-LUMO) gaps, which lead to different orbital interactions between the dendron parts and the core molecule. The nanostars bearing anthracene and pentacene cores are characterized by multistep exciton states with spatially well-segmented distributions: The exciton distributions of high-lying exciton states are spatially localized well in the periphery region, whereas those of low-lying exciton states are done in the core region. On the other hand, for the nanostar bearing benzene core, which also has multistep exciton states, the spatial exciton distributions of low-lying exciton states are delocalized over the dendron and the core regions. It is found that the former nanostars exhibit nearly complete exciton migration from the periphery to the core molecule in contrast to the latter one, in which significant exciton distribution remains in the dendron parts attached to the core after the exciton relaxation, although all these dendrimers exhibit fast exciton relaxation from the initially populated states. It is predicted from the analysis based on the MO correlation diagrams and the relative relaxation factor that the complete exciton migration to the core occurs not only when the HOMO-LUMO gap of the core molecule is nearly equal to that of the dendron parts attached to the core (anthracene case) but also when fairly smaller than that (pentacene case), whereas the complete migration is not achieved when the HOMO-LUMO gap of the core is larger than that of the dendron parts (benzene case). These results suggest that the fast and complete exciton migration of real dendrimers could be realized by adjusting the HOMO-LUMO gap of the core molecule to be smaller than that of dendron parts, although there exist more complicated relaxation processes as compared to simple dendritic aggregate models studied so far.

The formation of Colloidal 2D/3D MoS2 Nanostructures in Organic Liquid Environment

NASA Astrophysics Data System (ADS)

Durgun, Engin; Sen, H. Sener; Oztas, Tugba; Ortac, Bulend

2015-03-01

2D MoS2 nanosheets (2D MoS2 NS) and fullerene-like MoS2 nanostructures (3D MoS2 NS) with varying sizes are synthesized by nanosecond laser ablation of hexagonal crystalline 2H-MoS2 powder in methanol. Structural, chemical, and optical properties of MoS2 NS are characterized by optical microscopy, SEM, TEM, XRD, Raman and UV/VIS/NIR absorption spectroscopy techniques. Results of structural analysis show that the obtained MoS2 NS mainly present layered morphology from micron to nanometer surface area. Detailed analysis of the product also proves the existence of inorganic polyhedral fullerene-like 3D MoS2 NS generated by pulsed laser ablation in methanol. The possible factors which may lead to formation of both 2D and 3D MoS2 NS in methanol are examined by ab initio calculations and shown that it is correlated with vacancy formation. The hexagonal crystalline structure of MoS2 NS was determined by XRD analysis. The colloidal MoS2 NS solution presents broadband absorption edge tailoring from UV region to NIR region. Investigations of MoS2 NS show that the one step physical process of pulsed laser ablation-bulk MoS2 powder interaction in organic solution opens doors to the formation of ``two scales'' micron- and nanometer-sized layered and fullerene-like morphology MoS2 structures. This work was partially supported by TUBITAK under the Project No. 113T050 and Bilim Akademisi - The Science Academy, Turkey under the BAGEP program.

Plasmon modes of bilayer molybdenum disulfide: a density functional study

NASA Astrophysics Data System (ADS)

Torbatian, Z.; Asgari, R.

2017-11-01

We explore the collective electronic excitations of bilayer molybdenum disulfide (MoS2) using density functional theory together with random phase approximation. The many-body dielectric function and electron energy-loss spectra are calculated using an ab initio based model involving material-realistic physical properties. The electron energy-loss function of the bilayer MoS2 system is found to be sensitive to either electron or hole doping and this is due to the fact that the Kohn-Sham band dispersions are not symmetric for energies above and below the zero Fermi level. Three plasmon modes are predicted, a damped high-energy mode, one optical mode (in-phase mode) for which the plasmon dispersion exhibits \\sqrt q in the long wavelength limit originating from low-energy electron scattering and finally a highly damped acoustic mode (out-of-phase mode).

The role of electron-phonon interactions on the coherence lifetime of monolayer transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Stevens, C. E.; Dey, P.; Paul, J.; Wang, Z.; Zhang, H.; Romero, A. H.; Shan, J.; Hilton, D. J.; Karaiskaj, D.

2017-10-01

We investigate the excitonic dephasing of transition metal dichalcogenides, namely MoS2, MoSe2 and WSe2 atomic monolayer thick and bulk crystals, in order to understand the factors that determine the optical coherence in these materials. Coherent nonlinear optical spectroscopy, temperature dependent absorption combined with theoretical calculations of the phonon spectra, reveal the important role electron-phonon interactions plat in dephasing process. The temperature dependence of the electronic band gap and the excitonic linewidth combined with 'ab initio' calculations of the phonon energies and the phonon density of state reveal strong interaction with the E‧ and E″ phonon modes.

Graphene/MoS2 heterostructures as templates for growing two-dimensional metals: Predictions from ab initio calculations

NASA Astrophysics Data System (ADS)

Šljivančanin, Željko; Belić, Milivoj

2017-09-01

Preparation of single-atom-thick layers of ordinary metals has been a challenging task since their closely packed atoms lack layered structure with highly anisotropic bonding. Using computational modeling based on density functional theory we showed that graphene/MoS2 heterostructures can be used as suitable templates to grow stable two-dimensional (2D) clusters, as well as extended monoatomic layers of metals with nonlayered structure in the bulk. Considering gold and lithium as two metals with markedly different properties, we found that Li intercalants strengthen coupling between graphene (G) and MoS2, mainly due to electrostatic attraction of 2D materials with positively charged Li atoms. However, intercalation with large Au atoms gives rise to a significant increase in the distance between G and MoS2 and thus, weakens their interaction. In addition to strong preference for 2D growth, we demonstrated that Au intercalants weakly interact with both G and MoS2, and hence G /MoS2 vertical heterostructures could be a promising framework to prepare gold 2D structures with electronic properties closely resembling those of the hypothetical free-standing hexagonal gold monolayer.

Atomic and electronic properties of quasi-one-dimensional MOS2 nanowires

PubMed Central

Seivane, Lucas Fernandez; Barron, Hector; Botti, Silvana; Marques, Miguel Alexandre Lopes; Rubio, Ángel; López-Lozano, Xóchitl

2013-01-01

The structural, electronic and magnetic properties of quasi-one-dimensional MoS2 nanowires, passivated by extra sulfur, have been determined using ab initio density-functional theory. The nanostructures were simulated using several different models based on experimental electron microscopy images. It is found that independently of the geometrical details and the coverage of extra sulfur at the Mo-edge, quasi-one-dimensional metallic states are predominant in all the low-energy model structures despite their reduced dimensionality. These metallic states are localized mainly at the edges. However, the electronic and magnetic character of the NWs does not depend only on the S saturation but also on the symmetry configuration of the S edge atoms. Our results show that for the same S saturation the magnetization can be decreased by increasing the pairing of the S and Mo edge atoms. In spite of the observed pairing of S dimers at the Mo-edge, the nanowires do not experience a Peierls-like metal-insulator transition PMID:25429189

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

PubMed Central

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; Wang, Shibing; Lin, Yu; Zeng, Qiaoshi; Xu, Gang; Liu, Zhenxian; Solanki, G. K.; Patel, K. D.; Cui, Yi; Hwang, Harold Y.; Mao, Wendy L.

2015-01-01

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe2 up to ∼60 GPa using multiple experimental techniques and ab-initio calculations. MoSe2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSe2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides. PMID:26088416

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

DOE PAGES

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; ...

2015-06-19

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe 2 up to ~60 GPa using multiple experimental techniques and ab-initio calculations. MoSe 2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS 2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSemore » 2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides.« less

J1-J2 square lattice antiferromagnetism in the orbitally quenched insulator MoOPO4

NASA Astrophysics Data System (ADS)

Yang, L.; Jeong, M.; Babkevich, P.; Katukuri, V. M.; Náfrádi, B.; Shaik, N. E.; Magrez, A.; Berger, H.; Schefer, J.; Ressouche, E.; Kriener, M.; Živković, I.; Yazyev, O. V.; Forró, L.; Rønnow, H. M.

2017-07-01

We report magnetic and thermodynamic properties of a 4 d1 (Mo5 +) magnetic insulator MoOPO4 single crystal, which realizes a J1-J2 Heisenberg spin-1 /2 model on a stacked square lattice. The specific-heat measurements show a magnetic transition at 16 K which is also confirmed by magnetic susceptibility, ESR, and neutron diffraction measurements. Magnetic entropy deduced from the specific heat corresponds to a two-level degree of freedom per Mo5 + ion, and the effective moment from the susceptibility corresponds to the spin-only value. Using ab initio quantum chemistry calculations, we demonstrate that the Mo5 + ion hosts a purely spin-1 /2 magnetic moment, indicating negligible effects of spin-orbit interaction. The quenched orbital moments originate from the large displacement of Mo ions inside the MoO6 octahedra along the apical direction. The ground state is shown by neutron diffraction to support a collinear Néel-type magnetic order, and a spin-flop transition is observed around an applied magnetic field of 3.5 T. The magnetic phase diagram is reproduced by a mean-field calculation assuming a small easy-axis anisotropy in the exchange interactions. Our results suggest 4 d molybdates as an alternative playground to search for model quantum magnets.

Semiempirical models of shear modulus at shock temperatures and pressures

NASA Astrophysics Data System (ADS)

Elkin, Vaytcheslav; Mikhaylov, Vadim; Mikhaylova, Tatiana

2011-06-01

The work is devoted to a comparison of capabilities the Steinberg-Cochran-Guinan and Burakovsky-Preston models of shear modulus offer for the description of experimental and calculated (ab initio) data at temperatures and pressures representative of solid state behind the shock front. Also, the SCG model is modernized by changing from the (P,V) variables to the (V,T) ones and adding a free parameter. The resulted model is then referred to as the (V,T)-model. The three models are tested for 9 metals (Al, Be, Cu, K, Na, Mg, Mo, W, Ta) with using ab initio and experimental values of shear modulus in a wide range of pressures as well as longitudinal sound velocities behind the shock front.

Full hyperfine structure analysis of singly ionized molybdenum

NASA Astrophysics Data System (ADS)

Bouazza, Safa

2017-03-01

For a first time a parametric study of hyperfine structure of Mo II configuration levels is presented. The newly measured A and B hyperfine structure (hfs) constants values of Mo II 4d5, 4d45s and 4d35s2 configuration levels, for both 95 and 97 isotopes, using Fast-ion-beam laser-induced fluorescence spectroscopy [1] are gathered with other few data available in literature. A fitting procedure of an isolated set of these three lowest even-parity configuration levels has been performed by taking into account second-order of perturbation theory including the effects of closed shell-open shell excitations. Moreover the same study was done for Mo II odd-parity levels; for both parities two sets of fine structure parameters as well as the leading eigenvector percentages of levels and Landé-factor gJ, relevant for this paper are given. We present also predicted singlet, triplet and quintet positions of missing experimental levels up to 85000 cm-1. The single-electron hfs parameter values were extracted in their entirety for 97Mo II and for 95Mo II: for instance for 95Mo II, a4d 01 =-133.37 MHz and a5p 01 =-160.25 MHz for 4d45p; a4d 01 =-140.84 MHz, a5p 01 =-170.18 MHz and a5s 10 =-2898 MHz for 4d35s5p; a5s 10 =-2529 (2) MHz and a4d 01 =-135.17 (0.44) MHz for the 4d45s. These parameter values were analysed and compared with diverse ab-initio calculations. We closed this work with giving predicted values of magnetic dipole and electric quadrupole hfs constants of all known levels, whose splitting are not yet measured.

Temperature-dependent excitonic effects in the optical properties of single-layer MoS2

NASA Astrophysics Data System (ADS)

Molina-Sánchez, Alejandro; Palummo, Maurizia; Marini, Andrea; Wirtz, Ludger

2016-04-01

Temperature influences the performance of two-dimensional (2D) materials in optoelectronic devices. Indeed, the optical characterization of these materials is usually realized at room temperature. Nevertheless, most ab initio studies are still performed without including any temperature effect. As a consequence, important features are thus overlooked, such as the relative height of the excitonic peaks and their broadening, directly related to the temperature and to the nonradiative exciton relaxation time. We present ab initio calculations of the optical response of single-layer MoS2, a prototype 2D material, as a function of temperature using density functional theory and many-body perturbation theory. We compute the electron-phonon interaction using the full spinorial wave functions, i.e., fully taking into account the effects of spin-orbit interaction. We find that bound excitons (A and B peaks) and resonant excitons (C peak) exhibit different behavior with temperature, displaying different nonradiative linewidths. We conclude that the inhomogeneous broadening of the absorption spectra is mainly due to electron-phonon scattering mechanisms. Our calculations explain the shortcomings of previous (zero-temperature) theoretical spectra and match well with the experimental spectra acquired at room temperature. Moreover, we disentangle the contributions of acoustic and optical phonon modes to the quasiparticles and exciton linewidths. Our model also allows us to identify which phonon modes couple to each exciton state, which is useful for the interpretation of resonant Raman-scattering experiments.

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes.

PubMed

Fabbri, F; Rotunno, E; Cinquanta, E; Campi, D; Bonnini, E; Kaplan, D; Lazzarini, L; Bernasconi, M; Ferrari, C; Longo, M; Nicotra, G; Molle, A; Swaminathan, V; Salviati, G

2016-10-04

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS 2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS 2 indirect bandgap emission.

Excitonic structure of the optical conductivity in MoS2 monolayers

NASA Astrophysics Data System (ADS)

Ridolfi, Emilia; Lewenkopf, Caio H.; Pereira, Vitor M.

2018-05-01

We investigate the excitonic spectrum of MoS2 monolayers and calculate its optical absorption properties over a wide range of energies. Our approach takes into account the anomalous screening in two dimensions and the presence of a substrate, both cast by a suitable effective Keldysh potential. We solve the Bethe-Salpeter equation using as a basis a Slater-Koster tight-binding model parameterized to fit the ab initio MoS2 band structure calculations. The resulting optical conductivity is in good quantitative agreement with existing measurements up to ultraviolet energies. We establish that the electronic contributions to the C excitons arise not from states at the Γ point, but from a set of k points over extended portions of the Brillouin zone. Our results reinforce the advantages of approaches based on effective models to expeditiously explore the properties and tunability of excitons in TMD systems.

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes

PubMed Central

Fabbri, F.; Rotunno, E.; Cinquanta, E.; Campi, D.; Bonnini, E.; Kaplan, D.; Lazzarini, L.; Bernasconi, M.; Ferrari, C.; Longo, M.; Nicotra, G.; Molle, A.; Swaminathan, V.; Salviati, G.

2016-01-01

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS2 indirect bandgap emission. PMID:27698425

Oxygen Passivation Mediated Tunability of Trion and Excitons in MoS2

NASA Astrophysics Data System (ADS)

Gogoi, Pranjal Kumar; Hu, Zhenliang; Wang, Qixing; Carvalho, Alexandra; Schmidt, Daniel; Yin, Xinmao; Chang, Yung-Huang; Li, Lain-Jong; Sow, Chorng Haur; Neto, A. H. Castro; Breese, Mark B. H.; Rusydi, Andrivo; Wee, Andrew T. S.

2017-08-01

Using wide spectral range in situ spectroscopic ellipsometry with systematic ultrahigh vacuum annealing and in situ exposure to oxygen, we report the complex dielectric function of MoS2 isolating the environmental effects and revealing the crucial role of unpassivated and passivated sulphur vacancies. The spectral weights of the A (1.92 eV) and B (2.02 eV) exciton peaks in the dielectric function reduce significantly upon annealing, accompanied by spectral weight transfer in a broad energy range. Interestingly, the original spectral weights are recovered upon controlled oxygen exposure. This tunability of the excitonic effects is likely due to passivation and reemergence of the gap states in the band structure during oxygen adsorption and desorption, respectively, as indicated by ab initio density functional theory calculation results. This Letter unravels and emphasizes the important role of adsorbed oxygen in the optical spectra and many-body interactions of MoS2 .

Signature of type-II Weyl semimetal phase in MoTe2

NASA Astrophysics Data System (ADS)

Jiang, J.; Liu, Z. K.; Sun, Y.; Yang, H. F.; Rajamathi, C. R.; Qi, Y. P.; Yang, L. X.; Chen, C.; Peng, H.; Hwang, C.-C.; Sun, S. Z.; Mo, S.-K.; Vobornik, I.; Fujii, J.; Parkin, S. S. P.; Felser, C.; Yan, B. H.; Chen, Y. L.

2017-01-01

Topological Weyl semimetal (TWS), a new state of quantum matter, has sparked enormous research interest recently. Possessing unique Weyl fermions in the bulk and Fermi arcs on the surface, TWSs offer a rare platform for realizing many exotic physical phenomena. TWSs can be classified into type-I that respect Lorentz symmetry and type-II that do not. Here, we directly visualize the electronic structure of MoTe2, a recently proposed type-II TWS. Using angle-resolved photoemission spectroscopy (ARPES), we unravel the unique surface Fermi arcs, in good agreement with our ab initio calculations that have nontrivial topological nature. Our work not only leads to new understandings of the unusual properties discovered in this family of compounds, but also allows for the further exploration of exotic properties and practical applications of type-II TWSs, as well as the interplay between superconductivity (MoTe2 was discovered to be superconducting recently) and their topological order.

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes

NASA Astrophysics Data System (ADS)

Fabbri, F.; Rotunno, E.; Cinquanta, E.; Campi, D.; Bonnini, E.; Kaplan, D.; Lazzarini, L.; Bernasconi, M.; Ferrari, C.; Longo, M.; Nicotra, G.; Molle, A.; Swaminathan, V.; Salviati, G.

2016-10-01

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS2 indirect bandgap emission.

Interlayer excitons in MoSe2/WSe2 heterostructures from first principles

NASA Astrophysics Data System (ADS)

Gillen, Roland; Maultzsch, Janina

2018-04-01

Based on ab initio theoretical calculations of the optical spectra of vertical heterostructures of MoSe2 (or MoS2) and WSe2 sheets, we reveal two spin-orbit-split Rydberg series of excitonic states below the A excitons of MoSe2 and WSe2 with a significant binding energy on the order of 250 meV for the first excitons in the series. At the same time, we predict from accurate many-body G0W0 calculations that crystallographically aligned MoSe2/WSe2 heterostructures exhibit an indirect fundamental band gap. Due to the type-II nature of the MoSe2/WSe2 heterostructure, the indirect transition and the exciton Rydberg series corresponding to a direct transition exhibit a distinct interlayer nature with spatial charge separation of the coupled electrons and holes. Our calculations confirm the recent experimental observation of a doublet nature of the long-lived states in photoluminescence spectra of Mo X2/W Y2 heterostructures, and we attribute these two contributions to momentum-direct interlayer excitons at the K point of the hexagonal Brillouin zone and to momentum-indirect excitons at the indirect fundamental band gap. Our calculations further suggest a noticeable effect of stacking order on the electronic band gaps and on the peak energies of the interlayer excitons and their oscillation strengths.

Adsorption of small inorganic molecules on a defective MoS2 monolayer.

PubMed

González, César; Biel, Blanca; Dappe, Yannick J

2017-04-05

We present a theoretical study of molecular adsorption on defects on a MoS 2 monolayer. Based on Density Functional Theory, our calculations confirm that small inorganic molecules, such as CO 2 , CO, H 2 O, NO, NO 2 , H 2 and N 2 , remain bonded to the pristine monolayer through weak van der Waals interactions, suggesting that the molecules may easily diffuse over the clean monolayer. On the other hand, the introduction of defects can lead to three different situations, depending on the defect and the molecule considered: physisorption, chemical (strong) bonding to the metallic defects, namely the Mo substitutional atoms on the S vacancies, and dissociation, that can take place spontaneously at 0 K in some specific cases or by the effect of thermal agitation in molecules such as CO 2 or NO 2 on the S vacancy. Our energetic and electronic analyses provide an explanation to such bonding possibilities, showing that in the low interacting situations, the molecules tend to adopt a planar configuration parallel to the monolayer, while a molecular rotation is favored in order to facilitate the bond formation on the reactive sites. Finally, the ab initio based Scanning Tunneling Microscopy (STM) simulations show the fingerprint of each molecule adsorbed on the most reactive site. This work opens the way to the possibility of tuning the catalytic properties of MoS 2 by controlling the creation of specific defects in the MoS 2 monolayer.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Structural and thermodynamic study of dicesium molybdate Cs2Mo2O7: Implications for fast neutron reactors

NASA Astrophysics Data System (ADS)

Smith, A. L.; Kauric, G.; van Eijck, L.; Goubitz, K.; Wallez, G.; Griveau, J.-C.; Colineau, E.; Clavier, N.; Konings, R. J. M.

2017-09-01

The structure of α-Cs2Mo2O7 (monoclinic in space group P21 / c), which can form during irradiation in fast breeder reactors in the space between nuclear fuel and cladding, has been refined in this work at room temperature from neutron diffraction data. Furthermore, the compounds' thermal expansion and polymorphism have been investigated using high temperature X-ray diffraction combined with high temperature Raman spectroscopy. A phase transition has been observed at Ttr(α → β)=(621.9±0.8) K using Differential Scanning Calorimetry, and the structure of the β-Cs2Mo2O7 phase, orthorhombic in space group Pbcm, has been solved ab initio from the high temperature X-ray diffraction data. Furthermore, the low temperature heat capacity of α-Cs2Mo2O7 has been measured in the temperature range T=(1.9-313.2) K using a Quantum Design PPMS (Physical Property Measurement System) calorimeter. The heat capacity and entropy values at T=298.15 K have been derived as Cp,mo (Cs2Mo2O7 , cr , 298.15 K) = (211.9 ± 2.1) J K-1mol-1 and Smo (Cs2Mo2O7 , cr , 298.15 K) = (317.4 ± 4.3) J K-1mol-1 . When combined with the enthalpy of formation reported in the literature, these data yield standard entropy and Gibbs energy of formation as Δf Smo (Cs2Mo2O7 , cr , 298.15 K) = - (628.2 ± 4.4) J K-1mol-1 and Δf Gmo (Cs2Mo2O7 , cr , 298.15 K) = - (2115.1 ± 2.5) kJmol-1 . Finally, the cesium partial pressure expected in the gap between fuel and cladding following the disproportionation reaction 2Cs2MoO4=Cs2Mo2O7+2Cs(g)+ 1/2 O2(g) has been calculated from the newly determined thermodynamic functions.

Persistence of a surface state arc in the topologically trivial phase of MoTe2

NASA Astrophysics Data System (ADS)

Crepaldi, A.; Autès, G.; Sterzi, A.; Manzoni, G.; Zacchigna, M.; Cilento, F.; Vobornik, I.; Fujii, J.; Bugnon, Ph.; Magrez, A.; Berger, H.; Parmigiani, F.; Yazyev, O. V.; Grioni, M.

2017-01-01

The prediction of Weyl fermions in the low-temperature noncentrosymmetric 1 T' phase of MoTe2 still awaits clear experimental confirmation. Here, we report angle-resolved photoemission (ARPES) data and ab initio calculations that reveal a surface state arc dispersing between the valence and the conduction band, as expected for a Weyl semimetal. However, we find that the arc survives in the high-temperature centrosymmetric 1 T'' phase. Therefore, a surface Fermi arc is not an unambiguous fingerprint of a topologically nontrivial phase. We have also investigated the surface state spin texture of the 1 T' phase by spin-resolved ARPES, and identified additional topologically trivial spin-split states within the projected band gap at higher binding energies.

Interactions of foreign interstitial and substitutional atoms in bcc iron from ab initio calculations

NASA Astrophysics Data System (ADS)

You, Y.; Yan, M. F.

2013-05-01

C and N atoms are the most frequent foreign interstitial atoms (FIAs), and often incorporated into the surface layers of steels to enhance their properties by thermochemical treatments. Al, Si, Ti, V, Cr, Mn, Co, Ni, Cu, Nb and Mo are the most common alloying elements in steels, also can be called foreign substitutional atoms (FSAs). The FIA and FSA interactions play an important role in the diffusion of C and N atoms, and the microstructures and mechanical properties of surface modified layers. Ab initio calculations based on the density functional theory are carried out to investigate FIA interactions with FSA in ferromagnetic bcc iron. The FIA-FSA interactions are analyzed systematically from five aspects, including interaction energies, density of states (DOS), bond populations, electron density difference maps and local magnetic moments.

Hierarchical MoO3/SnS2 core-shell nanowires with enhanced electrochemical performance for lithium-ion batteries.

PubMed

Hu, Chenli; Shu, Haibo; Shen, Zihong; Zhao, Tianfeng; Liang, Pei; Chen, Xiaoshuang

2018-06-27

Two-dimensional (2D) tin disulfide (SnS2) is a promising anode material for lithium-ion batteries (LIBs) because of its high theoretical capacity. The main challenges associated with the SnS2 electrodes are the poor cycling stability and low rate capability due to structural degradation in the discharge/charge process. Here, a facile two-step synthesis method is developed to fabricate hierarchical MoO3/SnS2 core-shell nanowires, where ultrathin SnS2 nanosheets are vertically anchored on MoO3 nanobelts to induce a heterointerface. Benefiting from the unique structural and compositional characteristics, the hierarchical MoO3/SnS2 core-shell nanowires exhibit excellent electrochemical performance and deliver a high reversible capacity of 504 mA h g-1 after 100 stable cycles at a current density of 100 mA g-1, which is far superior to the MoO3 and SnS2 electrodes. An analysis of lithiation dynamics based on ab initio molecular dynamics simulations demonstrates that the formation of a hierarchical MoO3/SnS2 core-shell heterostructure can effectively suppress the rapid dissociation of shell-layer SnS2 nanosheets via the interfacial coupling effect and the central MoO3 backbone can trap and support the polysulfide in the discharge/charge process. The results are responsible for the high storage capacity and rate capability of MoO3/SnS2 electrode materials. This work provides a novel design strategy for constructing high-performance electrodes for LIBs.

Structural Evolution of Electrochemically Lithiated MoS2 Nanosheets and the Role of Carbon Additive in Li-Ion Batteries

PubMed Central

2016-01-01

Understanding the structure and phase changes associated with conversion-type materials is key to optimizing their electrochemical performance in Li-ion batteries. For example, molybdenum disulfide (MoS2) offers a capacity up to 3-fold higher (∼1 Ah/g) than the currently used graphite anodes, but they suffer from limited Coulombic efficiency and capacity fading. The lack of insights into the structural dynamics induced by electrochemical conversion of MoS2 still hampers its implementation in high energy-density batteries. Here, by combining ab initio density-functional theory (DFT) simulation with electrochemical analysis, we found new sulfur-enriched intermediates that progressively insulate MoS2 electrodes and cause instability from the first discharge cycle. Because of this, the choice of conductive additives is critical for the battery performance. We investigate the mechanistic role of carbon additive by comparing equal loading of standard Super P carbon powder and carbon nanotubes (CNTs). The latter offer a nearly 2-fold increase in capacity and a 45% reduction in resistance along with Coulombic efficiency of over 90%. These insights into the phase changes during MoS2 conversion reactions and stabilization methods provide new solutions for implementing cost-effective metal sulfide electrodes, including Li–S systems in high energy-density batteries. PMID:27818575

Signature of type-II Weyl semimetal phase in MoTe 2

DOE PAGES

Jiang, J.; Liu, Z. K.; Sun, Y.; ...

2017-01-13

Topological Weyl semimetal (TWS), a new state of quantum matter, has sparked enormous research interest recently. Possessing unique Weyl fermions in the bulk and Fermi arcs on the surface, TWSs offer a rare platform for realizing many exotic physical phenomena. TWSs can be classified into type-I that respect Lorentz symmetry and type-II that do not. Here, we directly visualize the electronic structure of MoTe 2, a recently proposed type-II TWS. Using angle-resolved photoemission spectroscopy (ARPES), we unravel the unique surface Fermi arcs, in good agreement with our ab initio calculations that have nontrivial topological nature. Our work not only leadsmore » to new understandings of the unusual properties discovered in this family of compounds, but also allows for the further exploration of exotic properties and practical applications of type-II TWSs, as well as the interplay between superconductivity (MoTe 2 was discovered to be superconducting recently) and their topological order.« less

Chloromethyl-oxirane and chloromethyl-thiirane in liquid phase: A joint experimental and quantum chemical study

NASA Astrophysics Data System (ADS)

Campetella, M.; Bencivenni, L.; Caminiti, R.; Zazza, C.; Di Trapani, S.; Martino, A.; Gontrani, L.

2016-07-01

The X-ray diffraction spectra of liquid chloromethyl-oxirane (ClMO) and chloromethyl-thiirane (ClMT) have been recorded for the first time. The interpretation of X-ray measurements was based on ab initio molecular dynamics simulations at finite temperature conditions. Both liquids show conformational equilibrium, which is discussed in terms of Gauche-2, Gauche-1 and Cis structures. The occurrence of the various forms estimated from X-ray and AIMD data has been compared with spectroscopy data from the literature, with the FTIR spectra of the liquids newly recorded in this work, and with theoretical in vacuo calculations.

Nanostructure of and structural defects in a Mo2BC hard coating investigated by transmission electron microscopy and atom probe tomography

NASA Astrophysics Data System (ADS)

Gleich, Stephan; Fager, Hanna; Bolvardi, Hamid; Achenbach, Jan-Ole; Soler, Rafael; Pradeep, Konda Gokuldoss; Schneider, Jochen M.; Dehm, Gerhard; Scheu, Christina

2017-08-01

In this work, the nanostructure of a Mo2BC hard coating was determined by several transmission electron microscopy methods and correlated with the mechanical properties. The coating was deposited on a Si (100) wafer by bipolar pulsed direct current magnetron sputtering from a Mo2BC compound target in Ar at a substrate temperature of 630 °C. Transmission electron microscopy investigations revealed structural features at various length scales: bundles (30 nm to networks of several micrometers) consisting of columnar grains (˜10 nm in diameter), grain boundary regions with a less ordered atomic arrangement, and defects including disordered clusters (˜1.5 nm in diameter) as well as stacking faults within the grains. The most prominent defect with a volume fraction of ˜0.5% is the disordered clusters, which were investigated in detail by electron energy loss spectroscopy and atom probe tomography. The results provide conclusive evidence that Ar is incorporated into the Mo2BC film as disordered Ar-rich Mo-B-C clusters of approximately 1.5 nm in diameter. Hardness values of 28 ± 1 GPa were obtained by nanoindentation tests. The Young's modulus of the Mo2BC coating exhibits a value of 462 ± 9 GPa, which is consistent with ab initio calculations for crystalline and defect free Mo2BC and measurements of combinatorically deposited Mo2BC thin films at a substrate temperature of 900 °C. We conclude that a reduction of the substrate temperature of 270 °C has no significant influence on hardness and Young's modulus of the Mo2BC hard coating, even if its nanostructure exhibits defects.

Anharmonic, dimensionality and size effects in phonon transport

NASA Astrophysics Data System (ADS)

Thomas, Iorwerth O.; Srivastava, G. P.

2017-12-01

We have developed and employed a numerically efficient semi- ab initio theory, based on density-functional and relaxation-time schemes, to examine anharmonic, dimensionality and size effects in phonon transport in three- and two-dimensional solids of different crystal symmetries. Our method uses third- and fourth-order terms in crystal Hamiltonian expressed in terms of a temperature-dependent Grüneisen’s constant. All input to numerical calculations are generated from phonon calculations based on the density-functional perturbation theory. It is found that four-phonon processes make important and measurable contribution to lattice thermal resistivity above the Debye temperature. From our numerical results for bulk Si, bulk Ge, bulk MoS2 and monolayer MoS2 we find that the sample length dependence of phonon conductivity is significantly stronger in low-dimensional solids.

Fast Mg2+ diffusion in Mo3(PO4)3O for Mg batteries.

PubMed

Rong, Ziqin; Xiao, Penghao; Liu, Miao; Huang, Wenxuan; Hannah, Daniel C; Scullin, William; Persson, Kristin A; Ceder, Gerbrand

2017-07-13

In this work, we identify a new potential Mg battery cathode structure Mo 3 (PO 4 ) 3 O, which is predicted to exhibit ultra-fast Mg 2+ diffusion and relatively high voltage based on first-principles density functional theory calculations. Nudged elastic band calculations reveal that the migration barrier of the percolation channel is only ∼80 meV, which is remarkably low, and comparable to the best Li-ion conductors. This low barrier is verified by ab initio molecular dynamics and kinetic Monte Carlo simulations. The voltage and specific energy are predicted to be ∼1.98 V and ∼173 W h kg -1 , respectively. If confirmed by experiments, this material would have the highest known Mg mobility among inorganic compounds.

Ab initio molecular orbital calculations on the associated complexes of lithium cyanide with ammonia

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

Mohandas, P.; Shivaglal, M.C.; Chandrasekhar, J.

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets are carried out on a series of complexes of NH{sub 3} with Li{sup +}, C{triple_bond}N{sup -}, LiCN, and its isomer LiNC. The BSSE-corrected interaction energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies are evaluated for 15 species. Complexes with trifurcated (C{sub 3v}) structures are calculated to be saddle points on the potential energy surfaces and have one imaginary frequency each. Calculated energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies of the various species considered are discussed in terms of the nature of associationmore » of LiCN with ammonia. The vibrational frequencies of the relevant complexed species are compared with the experimental frequencies reported earlier for solutions of lithium cyanide in liquid ammonia. 40 refs., 1 fig., 4 tabs.« less

Theoretical ultra-fast spectroscopy in transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Molina-Sanchez, Alejandro; Sangalli, Davide; Marini, Andrea; Wirtz, Ludger

Semiconducting 2D-materials like the transition metal dichalcogenides (TMDs) MoS2, MoSe2, WS2, WSe2 are promising alternatives to graphene for designing novel opto-electronic devices. The strong spin-orbit interaction along with the breaking of inversion symmetry in single-layer TMDs allow using the valley-index as a new quantum number. The practical use of valley physics depends on the lifetimes of valley-polarized excitons which are affected by scattering at phonons, impurities and by carrier-carrier interactions. The carrier dynamics can be monitored using ultra-fast spectroscopies such as pump-probe experiments. The carrier dynamics is simulated using non-equilibrium Green's function theory in an ab-initio framework. We include carrier relaxation through electron-phonon interaction. We obtain the transient absorption spectra of single-layer TMD and compare our simulations with recent pump-probe experiments

[Mo2(CN)11]:5- A detailed description of ligand-field spectra and magnetic properties by first-principles calculations.

PubMed

Hendrickx, Marc F A; Clima, S; Chibotaru, L F; Ceulemans, A

2005-10-06

An ab initio multiconfigurational approach has been used to calculate the ligand-field spectrum and magnetic properties of the title cyano-bridged dinuclear molybdenum complex. The rather large magnetic coupling parameter J for a single cyano bridge, as derived experimentally for this complex by susceptibility measurements, is confirmed to a high degree of accuracy by our CASPT2 calculations. Its electronic structure is rationalized in terms of spin-spin coupling between the two constituent hexacyano-monomolybdate complexes. An in-depth analysis on the basis of Anderson's kinetic exchange theory provides a qualitative picture of the calculated CASSCF antiferromagnetic ground-state eigenvector in the Mo dimer. Dynamic electron correlations as incorporated into our first-principles calculations by means of the CASPT2 method are essential to obtain quantitative agreement between theory and experiment.

Ab initio calculation of 1H, 17O, 27Al and 29Si NMR parameters, vibrational frequencies and bonding energetics in hydrous silica and Na-aluminosilicate glasses

NASA Astrophysics Data System (ADS)

Kubicki, J. D.; Sykes, D. G.

2004-10-01

Ab initio, molecular orbital (MO) calculations were performed on model systems of SiO 2, NaAlSi 3O 8 (albite), H 2O-SiO 2 and H 2O-NaAlSi 3O 8 glasses. Model nuclear magnetic resonance (NMR) isotropic chemical shifts (δ iso) for 1H, 17O, 27Al and 29Si are consistent with experimental data for the SiO 2, NaAlSi 3O 8, H 2O-SiO 2 systems where structural interpretations of the NMR peak assignments are accepted. For H 2O-NaSi 3AlO 8 glass, controversy has surrounded the interpretation of NMR and infrared (IR) spectra. Calculated δ iso1H, δ iso17O, δ iso27Al and δ iso29Si are consistent with the interpretation of Kohn et al. (1992) that Si-(OH)-Al linkages are responsible for the observed peaks in hydrous Na-aluminosilicate glasses. In addition, a theoretical vibrational frequency associated with the Kohn et al. (1992) model agrees well with the observed shoulder near 900 cm -1 in the IR and Raman spectra of hydrous albite glasses. MO calculations suggest that breaking this Si-(OH)-Al linkage requires ˜+56 to +82 kJ/mol which is comparable to the activation energies for viscous flow in hydrous aluminosilicate melts.

Ultrafast carrier thermalization and cooling dynamics in few-layer MoS2.

PubMed

Nie, Zhaogang; Long, Run; Sun, Linfeng; Huang, Chung-Che; Zhang, Jun; Xiong, Qihua; Hewak, Daniel W; Shen, Zexiang; Prezhdo, Oleg V; Loh, Zhi-Heng

2014-10-28

Femtosecond optical pump-probe spectroscopy with 10 fs visible pulses is employed to elucidate the ultrafast carrier dynamics of few-layer MoS2. A nonthermal carrier distribution is observed immediately following the photoexcitation of the A and B excitonic transitions by the ultrashort, broadband laser pulse. Carrier thermalization occurs within 20 fs and proceeds via both carrier-carrier and carrier-phonon scattering, as evidenced by the observed dependence of the thermalization time on the carrier density and the sample temperature. The n(-0.37 ± 0.03) scaling of the thermalization time with carrier density suggests that equilibration of the nonthermal carrier distribution occurs via non-Markovian quantum kinetics. Subsequent cooling of the hot Fermi-Dirac carrier distribution occurs on the ∼ 0.6 ps time scale via carrier-phonon scattering. Temperature- and fluence-dependence studies reveal the involvement of hot phonons in the carrier cooling process. Nonadiabatic ab initio molecular dynamics simulations, which predict carrier-carrier and carrier-phonon scattering time scales of 40 fs and 0.5 ps, respectively, lend support to the assignment of the observed carrier dynamics.

Vibrational and optical properties of MoS2: From monolayer to bulk

NASA Astrophysics Data System (ADS)

Molina-Sánchez, Alejandro; Hummer, Kerstin; Wirtz, Ludger

2015-12-01

Molybdenum disulfide, MoS2, has recently gained considerable attention as a layered material where neighboring layers are only weakly interacting and can easily slide against each other. Therefore, mechanical exfoliation allows the fabrication of single and multi-layers and opens the possibility to generate atomically thin crystals with outstanding properties. In contrast to graphene, it has an optical gap of ~1.9 eV. This makes it a prominent candidate for transistor and opto-electronic applications. Single-layer MoS2 exhibits remarkably different physical properties compared to bulk MoS2 due to the absence of interlayer hybridization. For instance, while the band gap of bulk and multi-layer MoS2 is indirect, it becomes direct with decreasing number of layers. In this review, we analyze from a theoretical point of view the electronic, optical, and vibrational properties of single-layer, few-layer and bulk MoS2. In particular, we focus on the effects of spin-orbit interaction, number of layers, and applied tensile strain on the vibrational and optical properties. We examine the results obtained by different methodologies, mainly ab initio approaches. We also discuss which approximations are suitable for MoS2 and layered materials. The effect of external strain on the band gap of single-layer MoS2 and the crossover from indirect to direct band gap is investigated. We analyze the excitonic effects on the absorption spectra. The main features, such as the double peak at the absorption threshold and the high-energy exciton are presented. Furthermore, we report on the the phonon dispersion relations of single-layer, few-layer and bulk MoS2. Based on the latter, we explain the behavior of the Raman-active A1g and E2g1 modes as a function of the number of layers. Finally, we compare theoretical and experimental results of Raman, photoluminescence, and optical-absorption spectroscopy.

Ab-initio study on the absorption spectrum of color change sapphire based on first-principles calculations with considering lattice relaxation-effect

NASA Astrophysics Data System (ADS)

Novita, Mega; Nagoshi, Hikari; Sudo, Akiho; Ogasawara, Kazuyoshi

2018-01-01

In this study, we performed an investigation on α-Al2O3: V3+ material, or the so-called color change sapphire, based on first-principles calculations without referring to any experimental parameter. The molecular orbital (MO) structure was estimated by the one-electron MO calculations using the discrete variational-Xα (DV-Xα) method. Next, the absorption spectra were estimated by the many-electron calculations using the discrete variational multi-electron (DVME) method. The effect of lattice relaxation on the crystal structures was estimated based on the first-principles band structure calculations. We performed geometry optimizations on the pure α-Al2O3 and with the impurity V3+ ion using Cambridge Serial Total Energy Package (CASTEP) code. The effect of energy corrections such as configuration dependence correction and correlation correction was also investigated in detail. The results revealed that the structural change on the α-Al2O3: V3+ resulted from the geometry optimization improved the calculated absorption spectra. By a combination of both the lattice relaxation-effect and the energy correction-effect improve the agreement to the experiment fact.

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

Jiang, J.; Liu, Z. K.; Sun, Y.

Topological Weyl semimetal (TWS), a new state of quantum matter, has sparked enormous research interest recently. Possessing unique Weyl fermions in the bulk and Fermi arcs on the surface, TWSs offer a rare platform for realizing many exotic physical phenomena. TWSs can be classified into type-I that respect Lorentz symmetry and type-II that do not. Here, we directly visualize the electronic structure of MoTe 2, a recently proposed type-II TWS. Using angle-resolved photoemission spectroscopy (ARPES), we unravel the unique surface Fermi arcs, in good agreement with our ab initio calculations that have nontrivial topological nature. Our work not only leadsmore » to new understandings of the unusual properties discovered in this family of compounds, but also allows for the further exploration of exotic properties and practical applications of type-II TWSs, as well as the interplay between superconductivity (MoTe 2 was discovered to be superconducting recently) and their topological order.« less

Signature of Type-II Weyl Semimetal Phase in MoTe2

NASA Astrophysics Data System (ADS)

Jiang, Juan; Liu, Zhongkai; Yang, Haifeng; Yang, Lexian; Chen, Cheng; Peng, Han; Hwang, Chan-Cuk; Mo, Sung-Kwan; Chen, Yulin; ShanghaiTech University Collaboration; Oxford University Collaboration; Lawrence Berkeley National Lab Collaboration; Pohang University of Science; Technology Collaboration

Topological Weyl semimetal (TWS) is a new state of quantum matter, which has sparked enormous research interest recently. Possessing unique Weyl fermions in the bulk and Fermi arcs on the surface, TWSs offer a rare platform for realizing many exotic physical phenomena. Here, by using angle-resolved photoemission spectroscopy, we directly visualize the electronic structure of MoTe2, a recently proposed type-II TWS, which do not respect Lorentz symmetry compared with type-I TWS. Furthermore, we unravel the unique surface Fermi arcs, in good agreement with our ab-initio calculations, which have non-trivial topological nature. Our work not only leads to new understandings of the unusual properties discovered in this family of compounds, but also allows for the further exploration of exotic properties and practical applications of type-II TWSs, as well as the interplay between superconductivity and their topological order.

Phosphorus vacancy cluster model for phosphorus diffusion gettering of metals in Si

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

Chen, Renyu; Trzynadlowski, Bart; Dunham, Scott T.

2014-02-07

In this work, we develop models for the gettering of metals in silicon by high phosphorus concentration. We first performed ab initio calculations to determine favorable configurations of complexes involving phosphorus and transition metals (Fe, Cu, Cr, Ni, Ti, Mo, and W). Our ab initio calculations found that the P{sub 4}V cluster, a vacancy surrounded by 4 nearest-neighbor phosphorus atoms, which is the most favorable inactive P species in heavily doped Si, strongly binds metals such as Cu, Cr, Ni, and Fe. Based on the calculated binding energies, we build continuum models to describe the P deactivation and Fe getteringmore » processes with model parameters calibrated against experimental data. In contrast to previous models assuming metal-P{sub 1}V or metal-P{sub 2}V as the gettered species, the binding of metals to P{sub 4}V satisfactorily explains the experimentally observed strong gettering behavior at high phosphorus concentrations.« less

Stacking-dependent interlayer coupling in trilayer MoS 2 with broken inversion symmetry

DOE PAGES

Yan, Jiaxu; Wang, Xingli; Tay, Beng Kang; ...

2015-11-13

The stacking configuration in few-layer two-dimensional (2D) materials results in different structural symmetries and layer-to-layer interactions, and hence it provides a very useful parameter for tuning their electronic properties. For example, ABA-stacking trilayer graphene remains semimetallic similar to that of monolayer, while ABC-stacking is predicted to be a tunable band gap semiconductor under an external electric field. Such stacking dependence resulting from many-body interactions has recently been the focus of intense research activities. Here we demonstrate that few-layer MoS 2 samples grown by chemical vapor deposition with different stacking configurations (AA, AB for bilayer; AAB, ABB, ABA, AAA for trilayer)more » exhibit distinct coupling phenomena in both photoluminescence and Raman spectra. By means of ultralow-frequency (ULF) Raman spectroscopy, we demonstrate that the evolution of interlayer interaction with various stacking configurations correlates strongly with layer-breathing mode (LBM) vibrations. Our ab initio calculations reveal that the layer-dependent properties arise from both the spin–orbit coupling (SOC) and interlayer coupling in different structural symmetries. Lastly, such detailed understanding provides useful guidance for future spintronics fabrication using various stacked few-layer MoS 2 blocks.« less

Stacking-dependent interlayer coupling in trilayer MoS 2 with broken inversion symmetry

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

Yan, Jiaxu; Wang, Xingli; Tay, Beng Kang

The stacking configuration in few-layer two-dimensional (2D) materials results in different structural symmetries and layer-to-layer interactions, and hence it provides a very useful parameter for tuning their electronic properties. For example, ABA-stacking trilayer graphene remains semimetallic similar to that of monolayer, while ABC-stacking is predicted to be a tunable band gap semiconductor under an external electric field. Such stacking dependence resulting from many-body interactions has recently been the focus of intense research activities. Here we demonstrate that few-layer MoS 2 samples grown by chemical vapor deposition with different stacking configurations (AA, AB for bilayer; AAB, ABB, ABA, AAA for trilayer)more » exhibit distinct coupling phenomena in both photoluminescence and Raman spectra. By means of ultralow-frequency (ULF) Raman spectroscopy, we demonstrate that the evolution of interlayer interaction with various stacking configurations correlates strongly with layer-breathing mode (LBM) vibrations. Our ab initio calculations reveal that the layer-dependent properties arise from both the spin–orbit coupling (SOC) and interlayer coupling in different structural symmetries. Lastly, such detailed understanding provides useful guidance for future spintronics fabrication using various stacked few-layer MoS 2 blocks.« less

Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

NASA Astrophysics Data System (ADS)

Huczyński, Adam; Janczak, Jan; Brzezinski, Bogumil

2012-12-01

A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic - monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8sbnd Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8sbnd Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.

Recent Progress in GW-based Methods for Excited-State Calculations of Reduced Dimensional Systems

NASA Astrophysics Data System (ADS)

da Jornada, Felipe H.

2015-03-01

Ab initio calculations of excited-state phenomena within the GW and GW-Bethe-Salpeter equation (GW-BSE) approaches allow one to accurately study the electronic and optical properties of various materials, including systems with reduced dimensionality. However, several challenges arise when dealing with complicated nanostructures where the electronic screening is strongly spatially and directionally dependent. In this talk, we discuss some recent developments to address these issues. First, we turn to the slow convergence of quasiparticle energies and exciton binding energies with respect to k-point sampling. This is very effectively dealt with using a new hybrid sampling scheme, which results in savings of several orders of magnitude in computation time. A new ab initio method is also developed to incorporate substrate screening into GW and GW-BSE calculations. These two methods have been applied to mono- and few-layer MoSe2, and yielded strong environmental dependent behaviors in good agreement with experiment. Other issues that arise in confined systems and materials with reduced dimensionality, such as the effect of the Tamm-Dancoff approximation to GW-BSE, and the calculation of non-radiative exciton lifetime, are also addressed. These developments have been efficiently implemented and successfully applied to real systems in an ab initio framework using the BerkeleyGW package. I would like to acknowledge collaborations with Diana Y. Qiu, Steven G. Louie, Meiyue Shao, Chao Yang, and the experimental groups of M. Crommie and F. Wang. This work was supported by Department of Energy under Contract No. DE-AC02-05CH11231 and by National Science Foundation under Grant No. DMR10-1006184.

Effect of protonation of the N-acetyl neuraminic acid residue of sialyl Lewis(X): a molecular orbital study with insights into its binding properties toward the carbohydrate recognition domain of E-selectin.

PubMed

Pichierri, Fabio; Matsuo, Yo

2002-08-01

Semiempirical molecular orbital (MO) calculations with an implicit treatment of the water environment were employed in order to assess whether the sialyl Lewis(X) (sLe(X)) tetrasaccharide binds to E-selectin in the anionic or neutral (i.e., protonated) state. The analysis of the frontier molecular orbitals, electrostatic potential surfaces, and conformational behavior of the sugar indicates that its neutral form possesses the necessary characteristics for binding. In particular, the LUMO level of the neutral sLe(X) molecule is localized both on the carboxylic group of the N-acetyl neuraminic acid (NeuNAc) residue and on the nearby glycosidic linkage. These two moieties interact with the Arg97 residue of E-selectin, as revealed by a recent crystal structure analysis of the E-selectin/sLe(X) complex. The energetics of this specific interaction was investigated with the aid of ab initio Hartree-Fock MO calculations, which resulted in a BSSE-corrected binding energy of 16.63 kcal/mol. Our observations could open up new perspectives in the design of sLe(X) mimics.

First- and second-order Raman scattering from MoTe2 single crystal

NASA Astrophysics Data System (ADS)

Caramazza, Simone; Collina, Arianna; Stellino, Elena; Ripanti, Francesca; Dore, Paolo; Postorino, Paolo

2018-02-01

We report on Raman experiments performed on a MoTe2 single crystal. The system belongs to the wide family of transition metal dichalcogenides which includes several of the most interesting two-dimensional materials for both basic and applied physics. Measurements were performed in the standard basal plane configuration, by placing the ab plane of the crystal perpendicular to the wave vector k i of the incident beam to explore the in-plane vibrational modes, and in the edge plane configuration with k i perpendicular to the crystal c axis, thus mainly exciting out-of-plane modes. For both configurations we performed a polarization-dependent study of the first-order Raman components and detailed computation of the corresponding selection rules. We were thus able to provide a complete assignment of the observed first-order Raman peaks, in agreement with previous literature results. A thorough analysis of the second-order Raman bands, as observed in both basal and edge plane configurations, provides new information and allows a precise assignment of these spectral structures. In particular, we have observed and assigned Raman active modes of the M point of the Brillouin zone previously predicted by ab initio calculations but never previously measured.

Adsorbate-induced shifts of electronic surface states: Cs on the (100) faces of tungsten, molybdenum, and tantalum

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

Soukiassian, P.; Riwan, R.; Lecante, J.

1985-04-15

The adsorption of cesium on the (100) faces of W, Mo, and Ta for coverages between 0 and 1 monolayer is studied by angle-resolved ultraviolet photoemission spectroscopy with use of synchro- tron radiation, by electron-energy-loss spectroscopy, and by low-energy electron diffraction. With increasing cesiation, the W(100) surface state at Gamma-bar located 0.3 eV below the Fermi level is shifted by up to 1.0 eV to larger binding energies while remaining sharp and intense. A similar behavior is observed on Ta(100), whereas on Mo(100) the shift of 0.9 eV of this surface state is accompanied by a pronounced attenuation of itsmore » intensity. These experimental shifts are shown to be in excellent agreement with all-electron local-density-functional results obtained with the full-potential linearized augmented-plane-wave method for Cs monolayers on the W(100) and Mo(100) surfaces. Based on these ab initio results, the electronic origin of the shifts is understood by the formation of strongly polarized covalent bonds between the d-like surface states and the Cs 6s--derived valence states. It is argued that even at high Cs coverages, the main electron-energy-loss peaks, which are observed between 1 and 2 eV, could be interpreted as Cs 6s..-->..6p--like interband transitions rather than as surface-plasmon peaks.« less

Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

PubMed

Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

2014-01-01

Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

Theoretical study of the potential energy surfaces and dynamics of CaNC/CaCN

NASA Astrophysics Data System (ADS)

Nanbu, Shinkoh; Minamino, Satoshi; Aoyagi, Mutsumi

1997-05-01

Potential energy surfaces for the ground and two low-lying electronically excited states of CaNC/CaCN, are calculated using the ab initio molecular orbital (MO) configuration interaction (CI) method. The absorption and emission spectra of the system are computed by performing time-dependent quantum dynamical calculations on these surfaces. The most stable geometries for the two lowest lying 12Σ+ and 12Π electronic states correspond to the calcium isocyanide (CaNC) structure. These two states are characterized by ionic bonding and the potential energy curves along the bending coordinate are relatively isotropic. The result of our wave packet dynamics shows that the characteristics of the experimental spectra observed by the laser-induced fluorescence spectroscopy can be explained by the Renner-Teller splitting.

Charge Redistribution in the β-NAPHTHOL-WATER Complex as Measured by High Resolution Stark Spectroscopy in the Gas Phase.

NASA Astrophysics Data System (ADS)

Fleisher, Adam J.; Pratt, David W.; Cembran, Alessandro; Gao, Jiali

2010-06-01

The extensively studied photoacid β-naphthol exhibits a large decrease in pKa upon irradiation with ultraviolet light, in the condensed phase. β-naphthol is almost 10 million times more acidic in the excited electronic state, compared to the ground state. Motivated by this fact, we report here the measurement of the electronic dipole moments of the β-naphthol-water complex in both electronic states, from which estimates of the charge transfer from solute to solvent in both states will be made. Comparisons to ab initio and density functional theory calculations will also be reported. N. Mataga and T. Kubota, Molecular Interactions and Electronic Spectra (Marcel Dekker, New York, 1970). Y. Mo, J. Gao, S.D. Peyerimhoff, J. Chem. Phys. 112, 5530 (2000).

Molecular Design of High Performance Molecular Devices Based on Direct Ab-initio Molecular Dynamics Method: Diffusion of Lithium Ion on Fluorinated Amorphous Carbon

NASA Astrophysics Data System (ADS)

Kawabata, Hiroshi; Iyama, Tetsuji; Tachikawa, Hiroto

2008-01-01

Hybrid density functional theory (DFT) calculations have been carried out for the lithium adsorbed on a fluorinated graphene surface (F-graphene, C96F24) to elucidate the effect of fluorination of amorphous carbon on the diffusion mechanism of lithium ion. Also, direct molecular orbital-molecular dynamics (MO-MD) calculation [H. Tachikawa and A. Shimizu: J. Phys. Chem. B 109 (2005) 13255] was applied to diffusion processes of the Li+ ion on F-graphene. The B3LYP/LANL2MB calculation showed that the Li+ ion is most stabilized around central position of F-graphene, and the energy was gradually instabilized for the edge region. The direct MO-MD calculations showed that the Li+ ion diffuses on the bulk surface region of F-graphite at 300 K. The nature of the interaction between Li+ and F-graphene was discussed on the basis of theoretical results.

Semiempirical models for description of shear modulus in wide ranges of temperatures and pressures of shock compression

NASA Astrophysics Data System (ADS)

El'Kin, V. M.; Mikhailov, V. N.; Mikhailova, T. Yu.

2011-12-01

In this paper, we discuss the potentials of the Steinberg-Cochran-Guinan (SCG) and Burakovsky-Preston (BP) models for the description of the shear-modulus behavior at temperatures and pressures that arise behind the shock-wave front. A modernized variant of the SCG model is suggested, which reduces to the introduction of a free parameter and the representation of the model in the volume-temperature coordinates (( V, T) model). A systematic comparison is performed of all three models of shear modulus with experimental data and data of ab initio calculations for metals such as Al, Be, Cu, K, Na, Mg, Mo, W, and Ta in a wide range of pressures. In addition, for Al, Cu, Mo, W, and Ta there is performed a comparison with the known temperature dependences of the shear modulus and with the results of measurements of the velocities of longitudinal sound behind the shock-wave front. It is shown that in the original form the SCG and BP models give overestimated values of the shear modulus as compared to the data of ab initio calculations and shock-wave experiments. The ( V, T) model, due to the use of a free parameter, makes it possible to optimally describe the totality of experimental and calculated data. The same result is achieved in the case of the BP model after a redefining of its initial parameters. The adequate description of the shear modulus in the range of high intermediate pressures characteristic of the solid-phase states behind the shock-wave front is accompanied in both cases by the violation of the correct asymptotic behavior of the shear modulus at ultrahigh compressions which is originally laid into the SCG and BP models.

Band nesting, massive Dirac fermions, and valley Landé and Zeeman effects in transition metal dichalcogenides: A tight-binding model

NASA Astrophysics Data System (ADS)

Bieniek, Maciej; Korkusiński, Marek; Szulakowska, Ludmiła; Potasz, Paweł; Ozfidan, Isil; Hawrylak, Paweł

2018-02-01

We present here the minimal tight-binding model for a single layer of transition metal dichalcogenides (TMDCs) MX 2(M , metal; X , chalcogen) which illuminates the physics and captures band nesting, massive Dirac fermions, and valley Landé and Zeeman magnetic field effects. TMDCs share the hexagonal lattice with graphene but their electronic bands require much more complex atomic orbitals. Using symmetry arguments, a minimal basis consisting of three metal d orbitals and three chalcogen dimer p orbitals is constructed. The tunneling matrix elements between nearest-neighbor metal and chalcogen orbitals are explicitly derived at K ,-K , and Γ points of the Brillouin zone. The nearest-neighbor tunneling matrix elements connect specific metal and sulfur orbitals yielding an effective 6 ×6 Hamiltonian giving correct composition of metal and chalcogen orbitals but not the direct gap at K points. The direct gap at K , correct masses, and conduction band minima at Q points responsible for band nesting are obtained by inclusion of next-neighbor Mo-Mo tunneling. The parameters of the next-nearest-neighbor model are successfully fitted to MX 2(M =Mo ; X =S ) density functional ab initio calculations of the highest valence and lowest conduction band dispersion along K -Γ line in the Brillouin zone. The effective two-band massive Dirac Hamiltonian for MoS2, Landé g factors, and valley Zeeman splitting are obtained.

The CH/π hydrogen bond: Implication in chemistry

NASA Astrophysics Data System (ADS)

Nishio, M.

2012-06-01

The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

Overcoming nanoscale friction barriers in transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Cammarata, Antonio; Polcar, Tomas

2017-08-01

We study the atomic contributions to the nanoscale friction in layered M X2 (M =Mo , W; X =S , Se, Te) transition metal dichalcogenides by combining ab initio techniques with group-theoretical analysis. Starting from stable atomic configurations, we propose a computational method, named normal-modes transition approximation (NMTA), to individuate possible sliding paths from only the analysis of the phonon modes of the stable geometry. The method provides a way to decompose the atomic displacements realizing the layer sliding in terms of phonon modes of the stable structure, so as to guide the selection and tuning of specific atomic motions promoting M X2 sheets gliding, and to adjust the corresponding energy barrier. The present results show that main contributions to the nanoscale friction are due to few low frequency phonon modes, corresponding to rigid shifts of M X2 layers. We also provide further evidences that a previously reported Ti-doped MoS2 phase is a promising candidate as new material with enhanced tribologic properties. The NMTA approach can be exploited to tune the energetic and the structural features of specific phonon modes, and, thanks to its general formulation, can also be applied to any solid state system, irrespective of the chemical composition and structural topology.

Twisted MoSe 2 bilayers with variable local stacking and interlayer coupling revealed by low-frequency Raman spectroscopy

DOE PAGES

Puretzky, Alexander A.; Liang, Liangbo; Li, Xufan; ...

2016-01-14

Unique twisted bilayers of MoSe 2 with multiple stacking orientations and interlayer couplings in the narrow range of twist angles, 60 ± 3°, are revealed by low-frequency Raman spectroscopy and theoretical analysis. The slight deviation from 60 allows the concomitant presence of patches featuring all three high-symmetry stacking configurations (2H or AA', AB', A'B) in one unique bilayer system. In this case, the periodic arrangement of the patches and their size strongly depend on the twist angle. Ab initio modeling predicts significant changes in frequencies and intensities of low-frequency modes versus stacking and twist angle. Experimentally, the variable stacking andmore » coupling across the interface is revealed by the appearance of two breathing modes corresponding to the mixture of the high-symmetry stacking configurations and unaligned regions of monolayers. Only one breathing mode is observed outside the narrow range of twist angles. This indicates a stacking transition to unaligned monolayers with mismatched atom registry without the in-plane restoring force required to generate a shear mode. As a result, the variable interlayer coupling and spacing in transition metal dichalcogenide bilayers revealed in this study may provide a new platform for optoelectronic applications of these materials.« less

Twisted MoSe 2 bilayers with variable local stacking and interlayer coupling revealed by low-frequency Raman spectroscopy

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

Puretzky, Alexander A.; Liang, Liangbo; Li, Xufan

Unique twisted bilayers of MoSe 2 with multiple stacking orientations and interlayer couplings in the narrow range of twist angles, 60 ± 3°, are revealed by low-frequency Raman spectroscopy and theoretical analysis. The slight deviation from 60 allows the concomitant presence of patches featuring all three high-symmetry stacking configurations (2H or AA', AB', A'B) in one unique bilayer system. In this case, the periodic arrangement of the patches and their size strongly depend on the twist angle. Ab initio modeling predicts significant changes in frequencies and intensities of low-frequency modes versus stacking and twist angle. Experimentally, the variable stacking andmore » coupling across the interface is revealed by the appearance of two breathing modes corresponding to the mixture of the high-symmetry stacking configurations and unaligned regions of monolayers. Only one breathing mode is observed outside the narrow range of twist angles. This indicates a stacking transition to unaligned monolayers with mismatched atom registry without the in-plane restoring force required to generate a shear mode. As a result, the variable interlayer coupling and spacing in transition metal dichalcogenide bilayers revealed in this study may provide a new platform for optoelectronic applications of these materials.« less

Ab Initio Study of the Electronic Structure, Elastic Properties, Magnetic Feature and Thermodynamic Properties of the Ba2NiMoO6 Material

NASA Astrophysics Data System (ADS)

Deluque Toro, C. E.; Mosquera Polo, A. S.; Gil Rebaza, A. V.; Landínez Téllez, D. A.; Roa-Rojas, J.

2018-04-01

We report first-principles calculations of the elastic properties, electronic structure and magnetic behavior performed over the Ba2NiMoO6 double perovskite. Calculations are carried out through the full-potential linear augmented plane-wave method within the framework of the Density Functional Theory (DFT) with exchange and correlation effects in the Generalized Gradient and Local Density Approximations, including spin polarization. The elastic properties calculated are bulk modulus (B), the elastic constants (C 11, C 12 and C 44), the Zener anisotropy factor (A), the isotropic shear modulus (G), the Young modulus (Y) and the Poisson ratio (υ). Structural parameters, total energies and cohesive properties of the perovskite are studied by means of minimization of internal parameters with the Murnaghan equation, where the structural parameters are in good agreement with experimental data. Furthermore, we have explored different antiferromagnetic configurations in order to describe the magnetic ground state of this compound. The pressure and temperature dependence of specific heat, thermal expansion coefficient, Debye temperature and Grüneisen parameter were calculated by DFT from the state equation using the quasi-harmonic model of Debye. A specific heat behavior C V ≈ C P was found at temperatures below T = 400 K, with Dulong-Petit limit values, which is higher than those, reported for simple perovskites.

Metallic VS2 Monolayer Polytypes as Potential Sodium-Ion Battery Anode via ab Initio Random Structure Searching.

PubMed

Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai

2016-07-27

We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications.

Robust valley polarization of helium ion modified atomically thin MoS2

NASA Astrophysics Data System (ADS)

Klein, J.; Kuc, A.; Nolinder, A.; Altzschner, M.; Wierzbowski, J.; Sigger, F.; Kreupl, F.; Finley, J. J.; Wurstbauer, U.; Holleitner, A. W.; Kaniber, M.

2018-01-01

Atomically thin semiconductors have dimensions that are commensurate with critical feature sizes of future optoelectronic devices defined using electron/ion beam lithography. Robustness of their emergent optical and valleytronic properties is essential for typical exposure doses used during fabrication. Here, we explore how focused helium ion bombardement affects the intrinsic vibrational, luminescence and valleytronic properties of atomically thin MoS2 . By probing the disorder dependent vibrational response we deduce the interdefect distance by applying a phonon confinement model. We show that the increasing interdefect distance correlates with disorder-related luminscence arising 180 meV below the neutral exciton emission. We perform ab initio density functional theory of a variety of defect related morphologies, which yield first indications on the origin of the observed additional luminescence. Remarkably, no significant reduction of free exciton valley polarization is observed until the interdefect distance approaches a few nanometers, namely the size of the free exciton Bohr radius. Our findings pave the way for direct writing of sub-10 nm nanoscale valleytronic devices and circuits using focused helium ions.

Control of thermal conductivity with species mass in transition-metal dichalcogenides

NASA Astrophysics Data System (ADS)

Thomas, Iorwerth O.; Srivastava, G. P.

2018-04-01

In this paper, we examine how the behaviour of the thermal conductivity of bulk and monolayer transition-metal dichalcogenides XY2 in their 2-H form can be controlled with different choices of cation and anion masses. We employ a semi-ab-initio approach, which combines first-principles phonon eigensolutions, the elastic anharmonic Hamiltonian for phonon-phonon interactions, a quasi-harmonic scheme for the temperature-dependent Grüneisen's constant, and a relaxation-time solution of the Boltzmann transport equation. Our results confirm an earlier finding [Gu and Yang, Appl. Phys. Lett. 105, 131903 (2014)] that the thermal conductivity of 2-H MoS2 is lower than that of 2-H WS2 contrary to what would be expected from the relative masses of Mo and W and the relative stiffnesses of both compounds. In addition to confirming this anomaly as a result of the larger acoustic optical gap of WS2 relative to that of MoS2, it is found that where one constituent species is fixed, more profound changes on the thermal conductivity occur for different anion masses than for different cation masses. We explain how these behaviours arise from the dispersion relations of each compound and the anharmonic interactions of phonon modes, and its connection with the relative masses of the constituent species. This finding provides useful insight into which 2-H dichalcogenides might be suitable for which thermal applications.

Ab-initio quantum transport simulation of self-heating in single-layer 2-D materials

NASA Astrophysics Data System (ADS)

Stieger, Christian; Szabo, Aron; Bunjaku, Teutë; Luisier, Mathieu

2017-07-01

Through advanced quantum mechanical simulations combining electron transport and phonon transport from first-principles, self-heating effects are investigated in n-type transistors with single-layer MoS2, WS2, and black phosphorus as channel materials. The selected 2-D crystals all exhibit different phonon-limited mobility values, as well as electron and phonon properties, which have a direct influence on the increase in their lattice temperature and on the power dissipated inside their channel as a function of the applied gate voltage and electrical current magnitude. This computational study reveals (i) that self-heating plays a much more important role in 2-D materials than in Si nanowires, (ii) that it could severely limit the performance of 2-D devices at high current densities, and (iii) that black phosphorus appears less sensitive to this phenomenon than transition metal dichalcogenides.

Long-Chain Polysulfide Retention at the Cathode of Li–S Batteries

DOE PAGES

Kamphaus, Ethan P.; Balbuena, Perla B.

2016-02-10

Lithium–sulfur batteries present a complex interconnected chemistry where the three components—anode, electrolyte, and cathode—strongly interact with each other. One of the main issues associated with these interactions is the dissolution in the electrolyte solution of part of the sulfur reduction products (mainly long-chain polysulfides) during the discharge reactions at the cathode. These dissolved species can migrate and react at the anode surface producing undesired insulating films. A potential solution to mitigate this problem is to resort to additional materials which can act as anchors of the soluble species thus avoiding their migration. Density functional theory and ab initio molecular dynamicsmore » simulations are employed to investigate the ability of certain substrates to retain long-chain polysulfides (Li 2S 6 and Li 2S 8) at their surfaces in the presence of a pure solvent or a lithiated solution. Nanopores of graphene are first tested because the cathode is usually a mix of sulfur and carbon. Then, MoS 2 and Mo-doped graphene are evaluated because of the well-known Mo–S affinity. Finally, a material which has been reported successful in experimental studies, MnO 2, is analyzed and compared with another oxide surface, Fe 2O 3. Adsorption energies of the polysulfides to the surfaces and the detailed interactions of the Li ions and S atoms with the substrate are characterized via charge and geometric analyses. Both the Mo-containing materials and the oxides adsorb the polysulfides much more strongly than graphene nanopores do. However, some of these surfaces are found to be excessively reactive. Thus, a balance between affinity for S and moderate surface reactivity is found as a promising guideline for designing these materials.« less

Why Chemical Vapor Deposition Grown MoS2 Samples Outperform Physical Vapor Deposition Samples: Time-Domain ab Initio Analysis.

PubMed

Li, Linqiu; Long, Run; Prezhdo, Oleg V

2018-06-13

Two-dimensional transition metal dichalcogenides (TMDs) have drawn strong attention due to their unique properties and diverse applications. However, TMD performance depends strongly on material quality and defect morphology. Experiments show that samples grown by chemical vapor deposition (CVD) outperform those obtained by physical vapor deposition (PVD). Experiments also show that CVD samples exhibit vacancy defects, while antisite defects are frequently observed in PVD samples. Our time-domain ab initio study demonstrates that both antisites and vacancies accelerate trapping and nonradiative recombination of charge carriers, but antisites are much more detrimental than vacancies. Antisites create deep traps for both electrons and holes, reducing energy gaps for recombination, while vacancies trap primarily holes. Antisites also perturb band-edge states, creating significant overlap with the trap states. In comparison, vacancy defects overlap much less with the band-edge states. Finally, antisites can create pairs of electron and hole traps close to the Fermi energy, allowing trapping by thermal activation from the ground state and strongly contributing to charge scattering. As a result, antisites accelerate charge recombination by more than a factor of 8, while vacancies enhance the recombination by less than a factor of 2. Our simulations demonstrate a general principle that missing atoms are significantly more benign than misplaced atoms, such as antisites and adatoms. The study rationalizes the existing experimental data, provides theoretical insights into the diverse behavior of different classes of defects, and generates guidelines for defect engineering to achieve high-performance electronic, optoelectronic, and solar-cell devices.

Ideal strength of bcc molybdenum and niobium

NASA Astrophysics Data System (ADS)

Luo, Weidong; Roundy, D.; Cohen, Marvin L.; Morris, J. W.

2002-09-01

The behavior of bcc Mo and Nb under large strain was investigated using the ab initio pseudopotential density-functional method. We calculated the ideal shear strength for the {211}<111> and {011}<111> slip systems and the ideal tensile strength in the <100> direction, which are believed to provide the minimum shear and tensile strengths. As either material is sheared in either of the two systems, it evolves toward a stress-free tetragonal structure that defines a saddle point in the strain-energy surface. The inflection point on the path to this tetragonal ``saddle-point'' structure sets the ideal shear strength. When either material is strained in tension along <100>, it initially follows the tetragonal, ``Bain,'' path toward a stress-free fcc structure. However, before the strained crystal reaches fcc, its symmetry changes from tetragonal to orthorhombic; on continued strain it evolves toward the same tetragonal saddle point that is reached in shear. In Mo, the symmetry break occurs after the point of maximum tensile stress has been passed, so the ideal strength is associated with the fcc extremum as in W. However, a Nb crystal strained in <100> becomes orthorhombic at tensile stress below the ideal strength. The ideal tensile strength of Nb is associated with the tetragonal saddle point and is caused by failure in shear rather than tension. In dimensionless form, the ideal shear and tensile strengths of Mo (τ*=τm/G111=0.12, σ*=σm/E100=0.078) are essentially identical to those previously calculated for W. Nb is anomalous. Its dimensionless shear strength is unusually high, τ*=0.15, even though the saddle-point structure that causes it is similar to that in Mo and W, while its dimensionless tensile strength, σ*=0.079, is almost the same as that of Mo and W, even though the saddle-point structure is quite different.

Absence of quantum anomalous Hall state in 4 d transition-metal-doped B i2S e3 : An ab initio study

NASA Astrophysics Data System (ADS)

Deng, Bei; Liu, Feng; Zhu, Junyi

2017-11-01

The realization of insulating ferromagnetic states in topological insulator (TI) systems, with sufficiently high Curie temperatures (TC) and large magnetically induced gaps, has been the key bottleneck towards the realization of the quantum anomalous Hall effect (QAHE). Despite the limited reports on 3 d or 4 f transition-metal (TM)-doped B i2S e3 , there remains a lack of systematic studies on 4 d TMs, which may be potential candidates since the atomic sizes of 4 d TMs and that of Bi are similar. Here, we report a theoretical work that probes the magnetic behaviors of the 4 d TM-doped B i2S e3 system. We discovered that among the 4 d TMs, Nb and Mo can create magnetic moments of 1.76 and 2.96 μ B in B i2S e3 , respectively. While Mo yields a stable gapless antiferromagnetic ground state, Nb favors a strong ferromagnetic order, with the magnetic coupling strength (TC) ˜6 times of that induced by the traditional Cr impurity. Yet, we found that Nb is still unfavorable to support the QAH state in B i2S e3 because of the reduced correlation in the t2 g band that gives a gapless character. This rationale is not only successful in interpreting why Nb, the strongest candidate among 4 d TMs for achieving ferromagnetism in B i2S e3 , actually cannot lead to QAHE in the B i2S e3 system even with the assistance of codoping but also is particularly important to fully understand the mechanism of acquisition of insulating ferromagnetic states inside TI. On the other hand, we discovered that Mo-doped B i2S e3 favors strong antiferromagnetic states and may lead to superconducting states.

Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: experimental and theoretical investigations

NASA Astrophysics Data System (ADS)

Allaf, Abdul. W.; Kassem, M.; Alibrahim, M.; Boustani, Ihsan

1999-03-01

An attempt was made to observe the gas-phase infrared spectrum of Phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by an on-line process using phosphorus (III) oxychloride, OPCl as precursor passed over heated AgCN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands centered at 2165 and 1385 cm -1. These bands are assigned to, ν1 (CN stretch) and ν2 (OP stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Møller-Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN.

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Low-frequency Raman fingerprints of two-dimensional metal dichalcogenide layer stacking configurations

DOE PAGES

Puretzky, Alexander A.; Liang, Liangbo; Li, Xufan; ...

2015-05-12

In this study, stacked monolayers of two-dimensional (2D) materials present a new class of hybrid materials with tunable optoelectronic properties determined by their stacking orientation, order, and atomic registry. Atomic-resolution Z-contrast scanning transmission electron microscopy (AR-Z-STEM) and electron energy loss spectroscopy (EELS) can be used to determine the exact atomic registration between different layers, in few-layer 2D stacks, however fast optical characterization techniques are essential for rapid development of the field. Here, using two- and three-layer MoSe 2 and WSe 2 crystals synthesized by chemical vapor deposition we show that the generally unexplored low frequency (LF) Raman modes (< 50more » cm -1) that originate from interlayer vibrations can serve as fingerprints to characterize not only the number of layers, but also their stacking configurations. Ab initio calculations and group theory analysis corroborate the experimental assignments determined by AR-Z-STEM and show that the calculated LF mode fingerprints are related to the 2D crystal symmetries.« less

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

Puretzky, Alexander A.; Liang, Liangbo; Li, Xufan

In this study, stacked monolayers of two-dimensional (2D) materials present a new class of hybrid materials with tunable optoelectronic properties determined by their stacking orientation, order, and atomic registry. Atomic-resolution Z-contrast scanning transmission electron microscopy (AR-Z-STEM) and electron energy loss spectroscopy (EELS) can be used to determine the exact atomic registration between different layers, in few-layer 2D stacks, however fast optical characterization techniques are essential for rapid development of the field. Here, using two- and three-layer MoSe 2 and WSe 2 crystals synthesized by chemical vapor deposition we show that the generally unexplored low frequency (LF) Raman modes (< 50more » cm -1) that originate from interlayer vibrations can serve as fingerprints to characterize not only the number of layers, but also their stacking configurations. Ab initio calculations and group theory analysis corroborate the experimental assignments determined by AR-Z-STEM and show that the calculated LF mode fingerprints are related to the 2D crystal symmetries.« less

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

First-principles estimates of free energy barriers for Mg desolvation and intercalation at electrolyte/electrode interfaces

NASA Astrophysics Data System (ADS)

Wan, Liwen; Prendergast, David

2014-03-01

There is a growing interest in developing multivalent ion batteries that could, in principle, double or triple the energy density compared to the monovalent Li-ion batteries. However, the strong electrostatic interaction caused by the extra charge also makes it very challenging to find appropriate intercalation compounds that allow for relatively fast and reversible ion transport. An established working multivalent battery is comprised of Mg(AlCl2BuEt)2 salts in THF solution as the electrolyte, and Mg metal and Mo6S8 Chevrel phase as the anode and cathode, respectively. Currently, we lack a clear understanding of the mechanism for Mg desolvation and intercalation at the interface between the electrolyte and Chevrel phase surfaces, which is critical in designing new advanced battery systems with improved ion diffusion rate. Here, we present a theoretical investigation of the dynamics and kinetics of the Mg desolvation/intercalation process. The surface properties of Mo6S8 are studied for the first time using density functional theory (DFT) and its interaction with the electrolyte is simulated via an ab initio molecular dynamics (AIMD) approach. The free energy barrier for Mg diffusing through the interface is then calculated by performing a set of biased AIMD simulations. This work is supported as part of the Joint Center for Energy Storage Research (JCESR), an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

Selectivity in Ketenimine Cycloadditions. Photoelectron Hel Spectra of Ketenimines

NASA Astrophysics Data System (ADS)

Bernardi, Fernando; Bottoni, Andrea; Ballaglia, Arturo; Distefano, Giuseppe; Dondoni, Alessandro

1980-05-01

The first few bands in the photoelectron (Hel) spectra of ketenimines R1R2C-C=NR3(R1,R2=H, CH3, C5H6, CH2=CH; R3=alkyl or aryl group) are assigned to the corresponding molecular orbitals. The assignment is based on SCF-MO calculations made at three different levels (CNDO/2, ab-initio STO-3C and 4-31G) coupled with perturbational molecular orbital analyses. The π-orbitals of the unsaturated substituents are found to interact with one of the two perpendicular π-electron systems of the>C=C=N- residue, the critical factor being the position of attack of the substituent. The relevance of these results on the site selectivity observed in cycloaddition reactions of these species is discussed.

Theoretical and experimental studies on alpha/epsilon-hybrid peptides: design of a 14/12-helix from peptides with alternating (S)-C-linked carbo-epsilon-amino acid [(S)-epsilon-Caa((x))] and L-ala.

PubMed

Sharma, Gangavaram V M; Babu, Bommagani Shoban; Chatterjee, Deepak; Ramakrishna, Kallaganti V S; Kunwar, Ajit C; Schramm, Peter; Hofmann, Hans-Jörg

2009-09-04

An (S)-C-linked carbo-epsilon-amino acid [(S)-epsilon-Caa((x))] was prepared from the known (S)-delta-Caa. This monomer was utilized together with l-Ala to give novel alpha/epsilon-hybrid peptides in 1:1 alternation. Conformational analysis on penta- and hexapeptides by NMR (in CDCl(3)), CD, and MD studies led to the identification of robust 14/12-mixed helices. This is in agreement with the data from a theoretical conformational analysis on the basis of ab initio MO theory providing a complete overview on all formally possible hydrogen-bonded helix patterns of alpha/epsilon-hybrid peptides with 1:1 backbone alternation. The "new motif" of a mixed 14/12-helix was predicted as most stable in vacuum. Obviously, the formation of ordered secondary structures is also possible in peptide foldamers with amino acid constituents of considerable backbone lengths. Thus, alpha/epsilon-hybrid peptides expand the domain of foldamers and allow the introduction of desired functionalities via the alpha-amino acid constituents.

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

Interlayer Coupling and Gate-Tunable Excitons in Transition Metal Dichalcogenide Heterostructures

DOE PAGES

Gao, Shiyuan; Yang, Li; Spataru, Catalin Dan

2017-11-22

Bilayer van der Waals (vdW) heterostructures such as MoS 2/WS 2 and MoSe 2/WSe 2 have attracted much attention recently, particularly because of their type II band alignments and the formation of interlayer exciton as the lowest-energy excitonic state. In this work, we calculate the electronic and optical properties of such heterostructures with the first-principles GW+Bethe–Salpeter Equation (BSE) method and reveal the important role of interlayer coupling in deciding the excited-state properties, including the band alignment and excitonic properties. Our calculation shows that due to the interlayer coupling, the low energy excitons can be widely tuned by a vertical gatemore » field. In particular, the dipole oscillator strength and radiative lifetime of the lowest energy exciton in these bilayer heterostructures is varied by over an order of magnitude within a practical external gate field. We also build a simple model that captures the essential physics behind this tunability and allows the extension of the ab initio results to a large range of electric fields. In conclusion, our work clarifies the physical picture of interlayer excitons in bilayer vdW heterostructures and predicts a wide range of gate-tunable excited-state properties of 2D optoelectronic devices.« less

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

NASA Astrophysics Data System (ADS)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Electronic structure and magneto-optical Kerr effect spectra of ferromagnetic shape-memory Ni-Mn-Ga alloys: Experiment and density functional theory calculations

NASA Astrophysics Data System (ADS)

Uba, S.; Bonda, A.; Uba, L.; Bekenov, L. V.; Antonov, V. N.; Ernst, A.

2016-08-01

In this joint experimental and ab initio study, we focused on the influence of the chemical composition and martensite phase transition on the electronic, magnetic, optical, and magneto-optical properties of the ferromagnetic shape-memory Ni-Mn-Ga alloys. The polar magneto-optical Kerr effect (MOKE) spectra for the polycrystalline sample of the Ni-Mn-Ga alloy of Ni60Mn13Ga27 composition were measured by means of the polarization modulation method over the photon energy range 0.8 ≤h ν ≤5.8 eV in magnetic field up to 1.5 T. The optical properties (refractive index n and extinction coefficient k ) were measured directly by spectroscopic ellipsometry using the rotating analyzer method. To complement experiments, extensive first-principles calculations were made with two different first-principles approaches combining the advantages of a multiple scattering Green function method and a spin-polarized fully relativistic linear-muffin-tin-orbital method. The electronic, magnetic, and MO properties of Ni-Mn-Ga Heusler alloys were investigated for the cubic austenitic and modulated 7M-like incommensurate martensitic phases in the stoichiometric and off-stoichiometric compositions. The optical and MOKE properties of Ni-Mn-Ga systems are very sensitive to the deviation from the stoichiometry. It was shown that the ab initio calculations reproduce well experimental spectra and allow us to explain the microscopic origin of the Ni2MnGa optical and magneto-optical response in terms of interband transitions. The band-by-band decomposition of the Ni2MnGa MOKE spectra is presented and the interband transitions responsible for the prominent structures in the spectra are identified.

Environmentally sensitive theory of electronic and optical transitions in atomically thin semiconductors

NASA Astrophysics Data System (ADS)

Cho, Yeongsu; Berkelbach, Timothy C.

2018-01-01

We present an electrostatic theory of band-gap renormalization in atomically thin semiconductors that captures the strong sensitivity to the surrounding dielectric environment. In particular, our theory aims to correct known band gaps, such as that of the three-dimensional bulk crystal. Combining our quasiparticle band gaps with an effective-mass theory of excitons yields environmentally sensitive optical gaps as would be observed in absorption or photoluminescence. For an isolated monolayer of MoS2, the presented theory is in good agreement with ab initio results based on the G W approximation and the Bethe-Salpeter equation. We find that changes in the electronic band gap are almost exactly offset by changes in the exciton binding energy such that the energy of the first optical transition is nearly independent of the electrostatic environment, rationalizing experimental observations.

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

PubMed

Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

2014-07-03

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

Thakur, Anil; Sharma, Nalini; Chandel, Surjeet; Ahluwalia, P. K.

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Proximity enhanced quantum spin Hall state in graphene

DOE PAGES

Kou, Liangzhi; Hu, Feiming; Yan, Binghai; ...

2015-02-23

Graphene is the first model system of two-dimensional topological insulator (TI), also known as quantum spin Hall (QSH) insulator. The QSH effect in graphene, however, has eluded direct experimental detection because of its extremely small energy gap due to the weak spin–orbit coupling. Here we predict by ab initio calculations a giant (three orders of magnitude) proximity induced enhancement of the TI energy gap in the graphene layer that is sandwiched between thin slabs of Sb 2Te 3 (or MoTe 2). This gap (1.5 meV) is accessible by existing experimental techniques, and it can be further enhanced by tuning themore » interlayer distance via compression. We reveal by a tight-binding study that the QSH state in graphene is driven by the Kane–Mele interaction in competition with Kekulé deformation and symmetry breaking. As a result, the present work identifies a new family of graphene-based TIs with an observable and controllable bulk energy gap in the graphene layer, thus opening a new avenue for direct verification and exploration of the long-sought QSH effect in graphene.« less

Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method.

PubMed

Shrestha, Kushal; Jakubikova, Elena

2015-08-20

Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.

Interlayer excitons in a bulk van der Waals semiconductor.

PubMed

Arora, Ashish; Drüppel, Matthias; Schmidt, Robert; Deilmann, Thorsten; Schneider, Robert; Molas, Maciej R; Marauhn, Philipp; Michaelis de Vasconcellos, Steffen; Potemski, Marek; Rohlfing, Michael; Bratschitsch, Rudolf

2017-09-21

Bound electron-hole pairs called excitons govern the electronic and optical response of many organic and inorganic semiconductors. Excitons with spatially displaced wave functions of electrons and holes (interlayer excitons) are important for Bose-Einstein condensation, superfluidity, dissipationless current flow, and the light-induced exciton spin Hall effect. Here we report on the discovery of interlayer excitons in a bulk van der Waals semiconductor. They form due to strong localization and spin-valley coupling of charge carriers. By combining high-field magneto-reflectance experiments and ab initio calculations for 2H-MoTe 2 , we explain their salient features: the positive sign of the g-factor and the large diamagnetic shift. Our investigations solve the long-standing puzzle of positive g-factors in transition metal dichalcogenides, and pave the way for studying collective phenomena in these materials at elevated temperatures.Excitons, quasi-particles of bound electron-hole pairs, are at the core of the optoelectronic properties of layered transition metal dichalcogenides. Here, the authors unveil the presence of interlayer excitons in bulk van der Waals semiconductors, arising from strong localization and spin-valley coupling of charge carriers.

A theoretical study of the photoinduced desorption of I — from a CF3I dimer

NASA Astrophysics Data System (ADS)

Tossell, J. A.

1997-04-01

Ab initio SCF-MO calculations using effective core-potential basis sets are employed to evaluate ionization potentials and electron affinities for CF3I and the geometries and energies of the singlet and triplet states of the CF3I dimer. The calculated geometry of the single state of the dimer is in qualitative agreement with the experimental geometry for condensed phase CF3I. The calculated energy for vertical excitation from the singlet to the triplet state is 4.1 eV at the Hartree-Fock level and 4.5 eV after incorporation of correlation at the Moller-Plesset 2nd-order level, consistent with excitation by 193 nm (6.4 eV) light. The equilibrium geometry of the triplet consists essentially of a CF3I+, CF3I- ion pair, in which the Csbnd I bond distance in the anionic component has increased to 5.5Å, compared with 2.1Åin the neutral molecule. The calculated binding energy of the triplet ion pair is about 4 eV.

Ab initio theory of noble gas atoms in bcc transition metals.

PubMed

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; Gan, Jian

2018-06-18

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe). Our charge density analysis indicates that the strong polarization of nearest-neighbor metal atoms by noble gas interstitials is the electronic origin of their high formation energies. Such polarization becomes more significant with an increasing gas atom size and interstitial charge density in the host bcc metal, which explains the similar trend followed by the unrelaxed formation energies of noble gas interstitials. Upon allowing for local relaxation, nearby metal atoms move farther away from gas interstitials in order to decrease polarization, albeit at the expense of increasing the elastic strain energy. Such atomic relaxation is found to play an important role in governing both the energetics and site preference of noble gas atoms in bcc metals. Our most notable finding is that the fully relaxed formation energies of noble gas interstitials are strongly correlated with the elastic shear modulus of the bcc metal, and the physical origin of this unexpected correlation has been elucidated by our theoretical analysis based on the effective-medium theory. The kinetic behavior of noble gas atoms and their interaction with pre-existing vacancies in bcc transition metals have also been discussed in this work.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

An ab initio study on the four electronically lowest-lying states of CH 2 using the state-averaged complete active space second-order configuration interaction method

NASA Astrophysics Data System (ADS)

Yamaguchi, Yukio; Schaefer, Henry F., III

1997-12-01

Four electronically lowest-lying ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states of CH 2 have been investigated systematically using ab initio electronic structure theory. Complete active space (CAS) self-consistent-field (SCF) second-order configuration interaction (SOCI) and state-averaged (SA) CASSCF-SOCI levels of theory have been employed. The CASSCF reference wave function was constructed by minimizing the total energy of a specified state, while the SACASSCF reference wave function was obtained by minimizing the equally weighted total energy of the four ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states. The third excited state ( c˜ 1A 1 or 2 1A 1) is of particular theoretical interest because it is represented by the second root of CASSCF and SOCI Hamiltonian matrices. Theoretical treatments of states not the lowest of their symmetry require special attention due to their tendency of variational collapse to the lower-lying state(s). For these four lowest-lying states total energies and physical properties including dipole moments, harmonic vibrational frequencies, and associated infrared (IR) intensities were determined and compared with the results from the configuration interaction with single and double excitations (CISD) method and available experimental values. The CASSCF-SOCI method should provide the most reliable energetics and physical properties in the present study owing to its fully variational nature in the molecular orbital (MO) and CI spaces for a given state. It is demonstrated that the SACASSCF-SOCI wave functions produce results which are quite consistent with those from the CASSCF-SOCI method. Thus significantly increased application of the SACASSCF-SOCI method to the excited states of a wide variety of molecular systems is expected.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Geometric and electronic structures of silicon-sodium binary clusters. I. Ionization energy of SinNam

NASA Astrophysics Data System (ADS)

Kishi, Reiko; Iwata, Suehiro; Nakajima, Atsushi; Kaya, Koji

1997-08-01

Sodium doped silicon clusters (SinNam; 1⩽n⩽14, 1⩽m⩽5) produced by two types of laser vaporization were studied. The adsorption of Na atoms on the Sin clusters leads the substantial lowering of the ionization energy, Ei, of SinNam clusters. Their reactivity toward NO molecules was measured with a fast flow reactor, and the anticorrelation between the Eis and the reactivity was clearly observed; species having low Ei exhibit high reactivity and vice versa. Moreover, the clear parallelism between the Eis of SinNa and the EAs of Sin is found. This is consistent with the fact that the structure of SinNa clusters keeps the frame of the corresponding Sin cluster unchanged and that the electronic structure of SinNa is similar to that of the corresponding negative ion Sin-. In addition to the experimental studies, the geometries, adsorption energies, and vertical ionization energies of SinNa (n=1-7) were investigated with ab initio MO calculations including electron correlation; The Møller-Plesset perturbation theory was used and the configuration interaction (CI) calculation was carried out, particularly for a diatomic molecule, SiNa.

A HeI photoelectron spectrum of the [Al(CH 3) 3] 2 dimer

NASA Astrophysics Data System (ADS)

Wang, Dianxun; Qian, Ximei; Zheng, Shijun; Shi, Yizhong

1997-10-01

The HeI photoelectron spectrum (PES) of the [Al(CH 3) 3] 2 dimer is recorded for the first time. To assign the PES bands, an ab initio SCF MO calculation for the dimer has also been performed. The four splitting peaks of the first PE band are respectively designated to electron ionization of the four frontier 8b u, 13a g, 7b g, and 7b u orbitals of the dimer. They originate from the recombination of the two HOMO (5e') of the two monomers in the forming of the dimer. That is to say, during the formation of the dimer from the two monomers, the reduction of molecular symmetry (from the C 3h symmetry of the monomer to the C 2h symmetry of the dimer) leads to the undegeneration of the degenerate orbitals.

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

A theoretical and experimental study on the molecular and electronic structures of artemisinin and related drug molecules

NASA Astrophysics Data System (ADS)

Galasso, V.; Kovač, B.; Modelli, A.

2007-06-01

The equilibrium structures of artemisinin and a selection of its derivatives (potent antimalarial drugs) have been studied with the density functional theory ansatz B3LYP. Of the five rings of the artemisinin framework, it is only the pyranose ring B that exhibits a marked conformational flexibility, especially on addition of a pendant side chain at C-10. For the derivatives, the β isomer with the axial substituent group is found to be energetically more stable than the α isomer with the equatorial group. The assignment of the vibrational fundamentals has been supported by calculations on related model molecules and a normal coordinate analysis. This allows for a reliable characterization of the normal modes, mainly involving the peroxide linkage, in the claimed fingerprint region of 1,2,4-trioxanes. The electronic structures have also been studied by measuring and calculating significant features of the NMR, photoelectron and electron transmission spectra. In particular, a representative set of NMR chemical shifts and nuclear spin-spin coupling constants, obtained with DFT formalisms, compares favourably with experiment and fits expectation in terms of stereoelectronic effects of the vicinal oxygen lone pairs. Based on ab initio outer valence Green's function calculations, a consistent interpretation of the uppermost bands in the photoelectron spectra of artemisinin and derivatives has been advanced. The top ionization energies reflect a complex interaction of the various oxygen lone pair orbitals. Electron transmission spectroscopy is applied for the first time to compounds containing the peroxide bond and elucidates the empty level electronic structure of artemisinin and derivatives in the 0-6 eV energy range, with the support of MO calculations and comparison with the spectra of reference molecules. Electron attachment to the lowest-lying empty σ∗ MO, mainly localized on the O-O bridge, occurs at an energy (1.7 eV) exceptionally low for compounds not containing third-row or heavier elements.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

Structure and Bonding in Uranyl(VI) Peroxide and Crown Ether Complexes; Comparison of Quantum Chemical and Experimental Data.

PubMed

Vallet, Valérie; Grenthe, Ingmar

2017-12-18

The structure, chemical bonding, and thermodynamics of alkali ions in M[12-crown-4] + , M[15-crown-5] + , and M[18-crown-6] + , M[UO 2 (O 2 )(OH 2 ) 2 ] + 4,5 , and M[UO 2 (O 2 )(OH)(OH 2 )] n 1-n (n = 4, 5) complexes have been explored by using quantum chemical (QC) calculations at the ab initio level. The chemical bonding has been studied in the gas phase in order to eliminate solvent effects. QTAIM analysis demonstrates features that are very similar in all complexes and typical for electrostatic M-O bonds, but with the M-O bonds in the uranyl peroxide systems about 20 kJ mol -1 stronger than in the corresponding crown ether complexes. The regular decrease in bond strength with increasing M-O bond distance is consistent with predominantly electrostatic contributions. Energy decomposition of the reaction energies in the gas phase and solvent demonstrates that the predominant component of the total attractive (ΔE elec + ΔE orb ) energy contribution is the electrostatic component. There are no steric constraints for coordination of large cations to small rings, because the M + ions are located outside the ring plane, [O n ], formed by the oxygen donors in the ligands; coordination of ions smaller than the ligand cavity results in longer than normal M-O distances or in a change in the number of bonds, both resulting in weaker complexes. The Gibbs energies, enthalpies, and entropies of reaction calculated using the conductor-like screening model, COSMO, to account for solvent effects deviate significantly from experimental values in water, while those in acetonitrile are in much better agreement. Factors that might affect the selectivity are discussed, but our conclusion is that present QC methods are not accurate enough to describe the rather small differences in selectivity, which only amount to 5-10 kJ mol -1 . We can, however, conclude on the basis of QC and experimental data that M[crown ether] + complexes in the strongly coordinating water solvent are of outer-sphere type, [M(OH 2 ) n + ][crown ether], while those in weakly coordinating acetonitrile are of inner-sphere type, [M-crown ether] + . The observation that the M[UO 2 (O 2 )(OH)(OH 2 )] n 1-n complexes are more stable in solution than those of M[crown ether] + is an effect of the different charges of the rings.

An ab initio-based Er–He interatomic potential in hcp Er

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

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

An ab initio study of Cu-based delafossites as an alternative to nickel oxide in photocathodes: effects of Mg-doping and surface electronic features.

PubMed

Schiavo, Eduardo; Latouche, Camille; Barone, Vincenzo; Crescenzi, Orlando; Muñoz-García, Ana B; Pavone, Michele

2018-05-23

CuMO2 delafossites (M = Al, Ga, and Cr) are p-type semiconductor oxides that have been recently proposed as the electrode in p-type dye-sensitized solar cells (p-DSSC) which is an alternative to the standard, low-performing nickel oxide. To assess this potential application of delafossites, we report here a DFT-based investigation of the structural and electronic properties of CuAlO2, CuGaO2 and CuCrO2. In particular, we address the role of Mg doping to obtain the p-type semiconducting character: the substitution of an M3+ cation with Mg2+ is easier with Ga than with Al and Cr, and, in all cases, the hole introduced by Mg2+ leads to the formation of Cu2+ species. Moreover, we address surface electronic features in order to characterize the most exposed delafossite surface termination and, more importantly, to predict the valence band maximum energy value, which determines the p-DSSC open circuit potential. From analysis of all our results, CuGaO2 emerges as the most promising system that can boost the development of new photocathodes for p-DSSCs.

Band Gap Engineering of Titania Systems Purposed for Photocatalytic Activity

NASA Astrophysics Data System (ADS)

Thurston, Cameron

Ab initio computer aided design drastically increases candidate population for highly specified material discovery and selection. These simulations, carried out through a first-principles computational approach, accurately extrapolate material properties and behavior. Titanium Dioxide (TiO2 ) is one such material that stands to gain a great deal from the use of these simulations. In its anatase form, titania (TiO2 ) has been found to exhibit a band gap nearing 3.2 eV. If titania is to become a viable alternative to other contemporary photoactive materials exhibiting band gaps better suited for the solar spectrum, then the band gap must be subsequently reduced. To lower the energy needed for electronic excitation, both transition metals and non-metals have been extensively researched and are currently viable candidates for the continued reduction of titania's band gap. The introduction of multicomponent atomic doping introduces new energy bands which tend to both reduce the band gap and recombination loss. Ta-N, Nb-N, V-N, Cr-N, Mo-N, and W-N substitutions were studied in titania and subsequent energy and band gap calculations show a favorable band gap reduction in the case of passivated systems.

Strategic L2 Lexical Innovation: Case Study of a University-Level Ab Initio Learner of German.

ERIC Educational Resources Information Center

Ridley, Jennifer; Singleton, David

1995-01-01

This article presents a case study of one English-speaking ab initio learner of German. It found that in target language production tasks performed over a two-year period, the subject exhibited a particular tendency toward lexical innovation as a strategy to cope with the lack of target language lexical knowledge. (38 references) (MDM)

Behaviour of DFT-based approaches to the spin-orbit term of zero-field splitting tensors: a case study of metallocomplexes, MIII(acac)3 (M = V, Cr, Mn, Fe and Mo).

PubMed

Sugisaki, Kenji; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

2017-11-15

Spin-orbit contributions to the zero-field splitting (ZFS) tensor (D SO tensor) of M III (acac) 3 complexes (M = V, Cr, Mn, Fe and Mo; acac = acetylacetonate anion) are evaluated by means of ab initio (a hybrid CASSCF/MRMP2) and DFT (Pederson-Khanna (PK) and natural orbital-based Pederson-Khanna (NOB-PK)) methods, focusing on the behaviour of DFT-based approaches to the D SO tensors against the valence d-electron configurations of the transition metal ions in octahedral coordination. Both the DFT-based approaches reproduce trends in the D tensors. Significantly, the differences between the theoretical and experimental D (D = D ZZ - (D XX + D YY )/2) values are smaller in NOB-PK than in PK, emphasising the usefulness of the natural orbital-based approach to the D tensor calculations of transition metal ion complexes. In the case of d 2 and d 4 electronic configurations, the D SO (NOB-PK) values are considerably underestimated in the absolute magnitude, compared with the experimental ones. The D SO tensor analysis based on the orbital region partitioning technique (ORPT) revealed that the D SO contributions attributed to excitations from the singly occupied region (SOR) to the unoccupied region (UOR) are significantly underestimated in the DFT-based approaches to all the complexes under study. In the case of d 3 and d 5 configurations, the (SOR → UOR) excitations contribute in a nearly isotropic manner, which causes fortuitous error cancellations in the DFT-based D SO values. These results indicate that more efforts to develop DFT frameworks should be directed towards the reproduction of quantitative D SO tensors of transition metal complexes with various electronic configurations and local symmetries around metal ions.

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Resonant-Raman Intensities of N-layer Transition Metal Dichalcogenides from First Principles

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Froehlicher, Guillaume; Lorchat, Ettienne; Fernique, François; Molina-Sánchez, Alejandro; Berciaud, Stéphane; Wirtz, Ludger

Transition metal dichalcogenides (TMDs) have interesting optical and electronic properties that make them good candidates for nano-engineering applications. Raman spectroscopy provides information about the vibrational modes and optical spectrum at the same time: when the laser energy is close to an electronic transition, the intensity is increased due to resonance. We investigate these effects combining different ab initio methods: we obtain ground-state and vibrational properties from density functional theory and the optical absorption spectrum using GW corrections and the Bethe-Salpeter equation to account for the excitonic effects which are known to play an important role in TMDs. Using a quasi-static finite differences approach, we calculate the dielectric susceptibility for different light polarizations and different phonon modes in order to determine the Raman tensor of TMDs, in particular of multi-layer and bulk MoTe2. We explain recent experimental results for the splitting of high-frequency modes and deviations from the non-resonant Raman model. We also give a brief outlook on possible improvements of the methodology.

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

ERIC Educational Resources Information Center

Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

2016-01-01

The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

First-principles calculations of novel materials

NASA Astrophysics Data System (ADS)

Sun, Jifeng

Computational material simulation is becoming more and more important as a branch of material science. Depending on the scale of the systems, there are many simulation methods, i.e. first-principles calculation (or ab-initio), molecular dynamics, mesoscale methods and continuum methods. Among them, first-principles calculation, which involves density functional theory (DFT) and based on quantum mechanics, has become to be a reliable tool in condensed matter physics. DFT is a single-electron approximation in solving the many-body problems. Intrinsically speaking, both DFT and ab-initio belong to the first-principles calculation since the theoretical background of ab-initio is Hartree-Fock (HF) approximation and both are aimed at solving the Schrodinger equation of the many-body system using the self-consistent field (SCF) method and calculating the ground state properties. The difference is that DFT introduces parameters either from experiments or from other molecular dynamic (MD) calculations to approximate the expressions of the exchange-correlation terms. The exchange term is accurately calculated but the correlation term is neglected in HF. In this dissertation, DFT based first-principles calculations were performed for all the novel materials and interesting materials introduced. Specifically, the DFT theory together with the rationale behind related properties (e.g. electronic, optical, defect, thermoelectric, magnetic) are introduced in Chapter 2. Starting from Chapter 3 to Chapter 5, several representative materials were studied. In particular, a new semiconducting oxytelluride, Ba2TeO is studied in Chapter 3. Our calculations indicate a direct semiconducting character with a band gap value of 2.43 eV, which agrees well with the optical experiment (˜ 2.93 eV). Moreover, the optical and defects properties of Ba2TeO are also systematically investigated with a view to understanding its potential as an optoelectronic or transparent conducting material. We find relatively modest band masses for both electrons and holes suggesting applications. Optical properties show a infrared-red absorption when doped. This could potentially be useful for combining wavelength filtering and transparent conducting functions. Furthermore, our defect calculations show that Ba 2TeO is intrinsically p-type conducting under Ba-poor condition. However, the spontaneous formation of the donor defects may constrain the p-type transport properties and would need to be addressed to enable applications. Chapter 4 mainly devotes to the thermoelectric properties of the famous phase change material, Ge2Sb2Te5 (GST). GST has been used in data storage for more than a decade because of their fast phase switching between metastable crystalline (cubic) and amorphous phases. It also exhibits interesting thermoelectric properties, and we did a systematic study on the two crystalline phases (hexagonal and cubic) and the amorphous phase. We found a high Seebeck coefficient with a broad doping concentrations for both n-type and p-type, at and below room temperatures (300 K) for both the cubic and amorphous phases. This finding will be of crucial interests in further understand the thermoelectric properties experimentally and find device applications in the ultimate goal. Several magnetic materials that involve lanthanide elements are reported in Chapter 5. First of all, the electronic and magnetic properties of the BaLn2O4 (Ln = La-Lu, Y) family compound are studied. The series has been synthesized for the first time in single crystalline form, using a molten metal flux. They crystallize in the CaV 2O4 structure type with primitive orthorhombic symmetry (space group Pnma, #62). Our calculations show an insulating character with band gaps ranging from 3 eV to 4.5 eV for the three representative compounds, BaLa2O4, BaGd2O4 and BaLu 2O4. Moreover, the superexchange magnetism is also studied. Secondly, a strong correlated system with cerium is investigated. As expected, we find a value of 15 states eV-1 that stems from the Ce 4f orbitals at the Fermi energy which indicates intermetallic heavy fermion behavior. The Fermi surface calculation shows nesting feature which might be useful to further understand the antiferromagnetic magnetism. Thirdly, the DFT calculations of another lanthanide oxide involving transition element, LaMo16O44, are also presented. This material crystallizes with a complicated crystal structure consists of MoO6 magnetic clusters. The band structure calculations indicate a spin-polarized half metal feature that comes from different crystallographic sites of Mo since La occurs as trivalent with empty f shell thus no contribution to the magnetic moment. Last but not least, we studied the electronic properties of another newly found oxytellride that having lanthanide, Ba3Yb 2O5Te. We find a insulating behavior with a direct band-gap value of 1.9 eV using the DFT+U methodology.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

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

Roemelt, Michael, E-mail: michael.roemelt@theochem.rub.de

Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctionsmore » are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.« less

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2016-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2015-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

PubMed

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

Magneto-optical Kerr spectroscopy of noble metals

NASA Astrophysics Data System (ADS)

Uba, L.; Uba, S.; Antonov, V. N.

2017-12-01

Magneto-optical (MO) response of the noble metals Cu, Ag, and Au in the joint experimental and ab initio theoretical study is reported. The magneto-optical polar Kerr effect (MOKE) spectra of the noble-metal films were measured with the high sensitivity in the applied magnetic field of 1.5 T over the photon energy range 0.74-5.8 eV. Complete set of the optical conductivity tensor elements was determined precisely from the MOKE and the optical spectra measured at the same energy points. The importance of the off-diagonal intraband Drude-type transitions is demonstrated explicitly for each noble metal and found to be a substantial contribution to the observed spectra. It is shown that the first-principles calculations using the spin-polarized fully relativistic Dirac linear-muffin-tin-orbital method with the inclusion of correlation effects by GGA+U approach reproduce well the experimental spectra and allow to explain the microscopic origin of the noble metals' magneto-optical response in terms of interband transitions. Although the energy band structures of Cu, Ag, and Au are very similar, there are some distinctive differences in bandwidths and the energy positions of the bands (especially in X and L symmetry points), mainly due to different spin-orbit splitting and differences in the spatial extent of 3 d , 4 d , and 5 d valence wave functions of noble metals. It was found that the small differences in the band positions lead to significant differences in the MO properties of three noble metals. Although the spin-orbit interaction in Au is about six times larger than in Cu, and approximately two times larger than in Ag, the absolute value of Kerr rotation in Au is of the same magnitude as in Cu and one order of magnitude smaller as compared to Ag. The sharp Kerr effect spectral peak in Ag is not due to the electronic interband transitions, but rather to the plasma-edge splitting. The band-by-band decomposition of the Cu, Ag, and Au MO spectra is presented and the interband transitions responsible for the prominent structures in the spectra are identified. It has been found that main magneto-optical activity of noble metals in external magnetic field originates from interband transitions at well-defined small-volume regions of Brillouin zone located near the "neck" and "belly" of the Fermi surface.

Comparitive study of fluorescence lifetime quenching of rhodamine 6G by MoS2 and Au-MoS2

NASA Astrophysics Data System (ADS)

Shakya, Jyoti; Kasana, Parath; Mohanty, T.

2018-04-01

Time resolved fluorescence study of Rhodamine 6G (R6G) in the presence of Molybdenum disulfide (MoS2) nanosheets and gold doped MoS2 (Au-MoS2) have been carried out and discussed. We have analyzed the fluorescence decay curves of R6G and it is observed that Au-MoS2 is a better fluorescence lifetime quencher as compare to MoS2 nanosheets. Also, the energy transfer efficiency and energy transfer rate from R6G to MoS2 and Au-MoS2 has been calculated and found higher for Au-MoS2.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

NASA Astrophysics Data System (ADS)

Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

2011-04-01

We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Effects of tungsten on uptake, transport and subcellular distribution of molybdenum in oilseed rape at two different molybdenum levels.

PubMed

Qin, Shiyu; Sun, Xuecheng; Hu, Chengxiao; Tan, Qiling; Zhao, Xiaohu; Xu, Shoujun

2017-03-01

Due to the similarities of molybdenum (Mo) with tungsten (W) in the physical structure and chemical properties, studies involving the two elements have mainly examined their competitive relationships. The objectives of this study were to assess the effects of equimolar W on Mo accumulation, transport and subcellular distribution in oilseed rape at two Mo levels with four treatments: Mo 1 (1μmol/L Mo, Low Mo), Mo 1 +W 1 (1μmol/L Mo+1μmol/LW, Low Mo with Low W), Mo 200 (200μmol/L Mo, High Mo) and Mo 200 +W 200 (200μmol/L Mo+200μmol/L Mo, High Mo with high W). The fresh weight and root growth were inhibited by equimolar W at both low and high Mo levels. The Mo concentration and accumulation in root was increased by equimolar W at the low Mo level, but that in the root and shoot was decreased at the high Mo level. Additionally, equimolar W increased the Mo concentrations of xylem and phloem sap at low Mo level, but decreased that of xylem and increased that of phloem sap at the high Mo level. Furthermore, equimolar W decreased the expression of BnMOT1 in roots and leaves at the low Mo level, and only decreased its expression in leaves at the high Mo level. The expression of BnMOT2 was also decreased in root for equimolar W compared with the low Mo level, but increased compared with high Mo level. Moreover, equimolar W increased the proportion of Mo in cell wall fraction in root and that of soluble fraction in leaves when compared with the low Mo level. The results suggest that cell wall and soluble fractions might be responsible for the adaptation of oilseed rape to W stress. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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.

An EXAFS study on the so-called {open_quotes}Co-Mo-S{close_quotes} phase in Co/C and CoMo/C, compared with a Moessbauer emission spectroscopy study

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

Craje, M.W.J.; Kraan, A.M. van der; Louwers, S.P.A.

1992-06-25

EXAFS was used in this paper to study 4 sulfided catalysts that have the same structure as their {sup 57}Co counterparts characterized by Mossbauer emission spectroscopy. The {open_quotes}Co-Mo-S{close_quotes} phase in Co/C is similar to CoMo/C due to a very highly dispersed Co species. Without Mo, the sulfidic Co results in a Co{sub 9}S{sub 8} phase during sulfidation at 673K, Mo prevents Co sintering in CoMo/C. 37 refs., 6 figs., 2 tabs.

Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.

PubMed

Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

2017-04-06

Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH 2 -phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules

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

Bruetzel, Linda K.; Fischer, Stefan; Salditt, Annalena

2016-02-15

We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 10{sup 6} photons/s at a beam size of 1.2 × 1.2 mm{sup 2} at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å{sup −1} down to 0.009 Å{sup −1} in SAXS configuration and of 0.26 Å{sup −1} up to 5.7 Å{sup −1} in wide-angle X-ray scattering (WAXS) mode. Tomore » determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5–24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å{sup −1} allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.« less

Symbolic programming language in molecular multicenter integral problem

NASA Astrophysics Data System (ADS)

Safouhi, Hassan; Bouferguene, Ahmed

It is well known that in any ab initio molecular orbital (MO) calculation, the major task involves the computation of molecular integrals, among which the computation of three-center nuclear attraction and Coulomb integrals is the most frequently encountered. As the molecular system becomes larger, computation of these integrals becomes one of the most laborious and time-consuming steps in molecular systems calculation. Improvement of the computational methods of molecular integrals would be indispensable to further development in computational studies of large molecular systems. To develop fast and accurate algorithms for the numerical evaluation of these integrals over B functions, we used nonlinear transformations for improving convergence of highly oscillatory integrals. These methods form the basis of new methods for solving various problems that were unsolvable otherwise and have many applications as well. To apply these nonlinear transformations, the integrands should satisfy linear differential equations with coefficients having asymptotic power series in the sense of Poincaré, which in their turn should satisfy some limit conditions. These differential equations are very difficult to obtain explicitly. In the case of molecular integrals, we used a symbolic programming language (MAPLE) to demonstrate that all the conditions required to apply these nonlinear transformation methods are satisfied. Differential equations are obtained explicitly, allowing us to demonstrate that the limit conditions are also satisfied.

Electronic structure and shearing in nanolaminated ternary carbides

NASA Astrophysics Data System (ADS)

Music, Denis; Sun, Zhimei; Voevodin, Andrey A.; Schneider, Jochen M.

2006-07-01

We have studied shearing in M 2AlC phases (M=Sc,Y,La,Ti,Zr,Hf,V,Nb,Ta,Cr,Mo,W) using ab initio calculations. We propose that these phases can be classified into two groups based on the valence electron concentration induced changes in C 44. One group comprises M=V B and VIB, where the C 44 values are approximately 170 GPa and independent of the corresponding MC. The other group includes M=IIIB and IVB, where the C 44 shows a linear dependency with the corresponding MC. This may be understood based on the electronic structure: shear resistant bands are filled in M 2AlC phases with M=V B and VIB, while they are not completely filled when M=IIIB and IVB. This notion is also consistent with our stress-strain analysis. These valence electron concentration induced changes in shear behaviour were compared to previously published valence electron concentration induced changes in compression behaviour [Z. Sun, D. Music, R. Ahuja, S. Li, J.M. Schneider, Phys. Rev. B 70 (2004) 092102]. These classification proposals exhibit identical critical valence electron concentration values for the group boundary. However, the physical mechanisms are not identical: the classification proposal for the bulk modulus is based on MC-A coupling, while shearing is based on MC-MC coupling.

Ab initio study of adsorption and diffusion of lithium on transition metal dichalcogenide monolayers

PubMed Central

Sun, Xiaoli

2017-01-01

Using first principles calculations, we studied the stability and electronic properties of transition metal dichalcogenide monolayers of the type MX2 (M = Ti, Zr, Hf, V, Nb, Ta, Mo, Cr, W; X= S, Se, Te). The adsorption and diffusion of lithium on the stable MX2 phase was also investigated for potential application as an anode for lithium ion batteries. Some of these compounds were found to be stable in the 2H phase and some are in the 1T or 1T' phase, but only a few of them were stable in both 2H/1T or 2H/1T' phases. The results show that lithium is energetically favourable for adsorption on MX2 monolayers, which can be semiconductors with a narrow bandgap and metallic materials. Lithium cannot be adsorbed onto 2H-WS2 and 2H-WSe2, which have large bandgaps of 1.66 and 1.96 eV, respectively. The diffusion energy barrier is in the range between 0.17 and 0.64 eV for lithium on MX2 monolayers, while for most of the materials it was found to be around 0.25 eV. Therefore, this work illustrated that most of the MX2 monolayers explored in this work can be used as promising anode materials for lithium ion batteries. PMID:29354342

Near-infrared luminescent cubic silicon carbide nanocrystals for in vivo biomarker applications: an ab initio Study

NASA Astrophysics Data System (ADS)

Gali, Adam; Zólyomi, Viktor; Somogyi, Bálint

2013-03-01

Small molecule-sized fluorescent emitters are needed as probes to image and track the locations of targeted nano-sized objects with minimal perturbation, and are much sought-after to probe biomolecules in living cells. For in vivo biological imaging, fluorescent biomarkers have to meet the following stringent requirements: (i) they should be non-toxic and bioinert, (ii) their hydrodynamical size should be sufficiently small for clearance, (iii) they should be photo-stable. Furthermore, it is highly desirable that (iv) they have intense, stable emission in the near-infrared range, and (v) they can be produced in relatively large amount for biological studies. Here we report time-density functional calculations on SiC-based QDs in the aspect of in vivo biological imaging applications. We find that Si-vacancy, divacancy, as well as single metal dopants such as Vanadium (V), Molybdenum (Mo) and Tungsten (W) in molecule-sized (1-2 nm) SiC QDs emit light efficiently in the near-infrared range. Furthermore, their emission wavelength varies on the size of host SiC QDs at less extent than that of pristine SiC QDs, thus sharper emission spectrum is expected even in a disperse size distribution of these QDs. These fluorescent SiC QDs are paramagnetic in the ground state. EU FP7 DIAMANT (Grant No. 270197)

Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

PubMed

Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

2015-04-21

Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Einstein coefficients and oscillator strengths for low lying state of CO molecules

NASA Astrophysics Data System (ADS)

Swer, S.; Syiemiong, A.; Ram, M.; Jha, A. K.; Saxena, A.

2018-04-01

Einstein Coefficients and Oscillator Strengths for different state of CO molecule have been calculated using LEROY'S LEVEL program and MOLCAS ab initio code. Using the wave function derived from Morse potential and transition dipole moment obtained from ab initio calculation, The potential energy functions were computed for these states using the spectroscopic constants. The Morse potential of these states and electronic transition dipole moment of the transition calculated in a recent ab initio study have been used in LEVEL program to produce transition dipole matrix element for a large number of bands. Einstein Coefficients have also been used to compute the radiative lifetimes of several vibrational levels and the calculated values are compared with other theoretical results and experimental values.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

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

Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

2015-05-15

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factormore » shows the presence of liquid state in the considered alloys.« less

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

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

Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K.; Thakur, Anil

2016-05-23

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70,.} Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30}, and Hg{sub 90}Pb{sub 10}) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the localmore » arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.« less

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

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40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

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40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

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40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

Outcomes of different bearings in total hip arthroplasty - implant survival, revision causes, and patient-reported outcome.

PubMed

Varnum, Claus

2017-03-01

Total hip arthroplasty (THA) is a common and successful treatment of patients suffering from severe osteoarthritis that significantly reduces pain and improves hip function and quality of life. Traditionally, the outcome of THA has been evaluated by orthopaedic surgeons and assessed in morbidity and mortality rates, and implant survival. As patients and surgeons may assess outcome after THA differently, patient-reported outcomes (PROMs) have gained much more interest and are today recognized as very important tools for evaluating the outcome and satisfaction after THA. One of the prognostic factors for the outcome of THA is the type of bearings. This PhD thesis focuses on the influence of different types of bearings on implant survival, revision causes, PROMs, and noises from THA. The aims of the thesis were: Study I: To examine the revision risk and to investigate the causes of revision of cementless ceramic-on-ceramic (CoC) THAs comparing them to those of "standard" metal-on-polyethylene (MoP) THAs. Study II: To compare the six-year revision risk for metal-on-metal (MoM) with that for MoP bearings in cementless stemmed THA, and further to study the revision risk for different designs of stemmed MoM THAs and the causes of revision. Study III: To examine the association between CoC, MoM, and MoP bearings and both generic and disease-specific PROMs, and furthermore to examine the incidence and types of noises from the three types of bearings and identify the effect of noises on PROM scores. In study I and III, we used data from the Danish Hip Arthroplasty Registry combined with data from the Civil Registration System and the Danish National Patient Registry. In study II, data from the Nordic Arthroplasty Register Association, containing data from hip arthroplasty registries in Denmark, Norway, Sweden, and Finland, was used. In study I, 11,096 patients operated from 2002 through 2009 with cementless THA were included. Of these, 16% had CoC THA and 84% had MoP THA. At 8.7-year follow-up, no difference in RR of revision for any cause was found for CoC compared to MoP THA. One cause of revision related only to CoC THA is ceramic fracture. Medical records were reviewed for patients who had revision surgery due to component failure, and six patients (0,34%) had been revised due to ceramic fracture. No other difference in prevalence of causes of revision was found when comparing CoC to MoP THA. Study II included 32,678 patients who were operated from 2002 through 2010 with cementless stemmed THA with either MoM bearings (11,567 patients, 35%) or MoP bearings (21,111 patients, 65%). At six-year follow-up, the RR of revision for any cause was significantly higher for MoM compared to MoP THA. When comparing different combinations of cup/stem with MoM to MoP bearings, there was an increased RR of revision for any cause for the ASR/Summit, ASR/Corail, and "other" combinations. There was a higher prevalence of revision due to aseptic loosening for MoM compared to MoP THA. In contrast, the prevalence of revision due to dislocation was lower for MoM THA. In study III, a set of questionnaires including HOOS, EQ-5D, UCLA activity score, and a questionnaire about noises from the THA was sendt to patients having THA with CoC, MoM, or MoP bearings. The response rate was 85% and among the 3,089 patients responding, 45% received CoC, 17% MoM, and 38% MoP THA. No differences in mean subscale scores were found for CoC and MoM compared to MoP THA, except for CoC THA that had a lower mean HOOS symptoms score than MoP THA. 27% of patients with CoC, 29% of patients with MoM, and 12% of patients with MoP bearings had experienced noises from the THA. For the three types of bearings, PROM scores from patients with noisy THA were significantly lower when compared to silent MoP THA, except for noisy CoC and MoM THA that had the same mean UCLA activity score as silent MoP THA.

Mechanism of corrosion of Ni base superalloys by molten Na2MoO4 at elevated temperatures

NASA Technical Reports Server (NTRS)

Misra, A. K.; Stearns, C. A.

1983-01-01

The corrosion of nickel base superalloy, U-700, by molten Na2MoO4 was studied in the temperature range of 750 deg to 950 deg C. After an induction period, the rate of corrosion is linear and catastrophic corrosion is observed. It is shown that the induction period is associated with the attainment of a minimum MoO3 activity in the melt, which corresponds to the equilibrium MoO3 activity for the reaction, 2MoO3(l) + Mo = 3MoO2(s). A mechanism is proposed to describe the catastrophic nature of corrosion, which involves transport of Ni++ through the melt resulting in formulation of NiO at the melt gas interface and basic fluxing of Cr2O3. The effect of the amount of Na2MoO4 on the corrosion kinetics was also studied. It is found that evaporation and the thermodynamic calculations for the Na2MoO4 - MoO3 system the activity of MoO3 is reduced considerably when dissolved in Na2MoO4, which causes a sharp decrease in the rate of evaporation of MoO3 from a Na2MoO4 - MoO3 melt.

Cracking in dissimilar laser welding of tantalum to molybdenum

NASA Astrophysics Data System (ADS)

Zhou, Xingwen; Huang, Yongde; Hao, Kun; Chen, Yuhua

2018-06-01

Dissimilar joining of tantalum (Ta) to molybdenum (Mo) is of great interest in high temperature structural component applications. However, few reports were found about joining of these two hard-to-weld metals. The objective of this experimental study was to assess the weldability of laser butt joining of 0.2 mm-thick Ta and Mo. In order to study cracking mechanism in Ta/Mo joint, similar Ta/Ta and Mo/Mo joints were compared under the same welding conditions. An optical microscope observation revealed presence of intergranular cracks in the Mo/Mo joint, while both transgranular and intergranular cracks were observed in Ta/Mo joint. The cracking mechanism of the Ta/Mo joint was investigated further by micro-hardness testing, micro X-ray diffraction and scanning electron microscopy. The results showed that solidification cracking tendency of Mo is a main reason for crack initiation in the Ta/Mo joint. Low ductility feature in fusion zone most certainly played a role in the transgranular propagation of cracking.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

PubMed

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

Fabrication of micro-cell UO2-Mo pellet with enhanced thermal conductivity

NASA Astrophysics Data System (ADS)

Kim, Dong-Joo; Rhee, Young Woo; Kim, Jong Hun; Kim, Keon Sik; Oh, Jang Soo; Yang, Jae Ho; Koo, Yang-Hyun; Song, Kun-Woo

2015-07-01

As one of accident tolerant fuel pellets which should have features of good thermal conductivity and high fission product retention, a micro-cell UO2-Mo pellet has been studied in the aspect of fabrication and thermal property. It was intended to develop the compatible process with conventional UO2 pellet fabrication process. The effects of processing parameters such as the size and density of UO2 granule and the size of Mo powder have been studied to produce sound and dense pellet with completely connected uniform Mo cell-walls. The micro-cell UO2-Mo pellet consists of many Mo micro-cells and UO2 in them. The thermal conductivity of the micro-cell UO2-Mo pellet was measured and compared to those of the UO2 pellet and the UO2-Mo pellet with dispersed form of Mo particles. The thermal conductivity of the micro-cell UO2-Mo pellet was much enhanced and was found to be influenced by the Mo volumetric fraction and pellet integrity. A continuous Mo micro-cell works as a heat conducting channel in the pellet, greatly enhancing the thermal conductivity of the micro cell UO2-Mo pellet.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

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40 CFR 86.007-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

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Ab initio quantum chemical calculations of the interaction between radioactive elements and imidazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Saravanan, A. V. Sai; Abishek, B.; Anantharaj, R.

2018-04-01

The fundamental natures of the molecular level interaction and charge transfer between specific radioactive elements and ionic liquids of 1-butyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide ([BMIM]+[NTf2]-), 1-Butyl-3-methylimidazolium ethylsulfate ([BMIM]+[ES]-) and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]+[BF4]-) were investigated utilising HF theory and B3LYP hybrid DFT. The ambiguity in reaction mechanism of the interacting species dictates to employ Effective Core Potential (ECP) basis sets such as UGBS, SDD, and SDDAll to account for the relativistic effects of deep core electrons in the system involving potential, heavy and hazardous radioactive elements present in nuclear waste. The SCF energy convergence of each system validates the characterisation of the molecular orbitals as a linear combination of atomic orbitals utilising fixed MO coefficients and the optimized geometry of each system is visualised based on which Mulliken partial charge analysis is carried out to account for the polarising behaviour of the radioactive element and charge transfer between the IL phase by comparison with the bare IL species.

Synthesis and Characterization of Molybdenum Doped ZnO Thin Films by SILAR Deposition Method

NASA Astrophysics Data System (ADS)

Radha, R.; Sakthivelu, A.; Pradhabhan, D.

2016-08-01

Molybdenum (Mo) doped zinc oxide (ZnO) thin films were deposited on the glass substrate by Successive Ionic Layer Adsorption and Reaction (SILAR) deposition method. The effect of Mo dopant concentration of 5, 6.6 and 10 mol% on the structural, morphological, optical and electrical properties of n-type Mo doped ZnO films was studied. The X-ray diffraction (XRD) results confirmed that the Mo doped ZnO thin films were polycrystalline with wurtzite structure. The field emission scanning electron microscopy (FESEM) studies shows that the surface morphology of the films changes with Mo doping. A blue shift of the optical band gap was observed in the optical studies. Effect of Mo dopant concentration on electrical conductivity was studied and it shows comparatively high electrical conductivity at 10 mol% of Mo doping concentration.

Molybdenum-carbon bond dissociation energies in Mo(CO) sub 6

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

Ganske, J.A.; Rosenfeld, R.N.

1990-05-17

The pressure dependence of the recombination rate constants for Mo(CO){sub n} (n = 3,4 and 5) with CO has been studied by time-resolved infrared laser absorption spectroscopy. These data, in conjunction with an RRKM model for unimolecular decay of the activated molecules (Mo(CO){sub 6})*, (Mo(CO){sub 5})*, and (Mo(CO){sub 4})*, have allowed the determination of the bond dissociation energies for several of the Mo-C bonds in Mo(CO){sub 6}. The first Mo-C bond dissociation energies for Mo(CO){sub 6}, Mo(CO){sub 5}, and Mo(CO){sub 4} are found to be DH{degree}((CO){sub 5}Mo{hor ellipsis}CO) = 35 {plus minus} 5 kcal/mol, DH{degree}((CO){sub 4}Mo{hor ellipsis}CO) = 27 {plusmore » minus} 5 kcal/mol, and DH{degree}((CO){sub 3}Mo{hor ellipsis}CO) = 31 {plus minus} 5 kcal/mol.« less

Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

NASA Astrophysics Data System (ADS)

Uhlíková, Tereza; Urban, Štěpán

2018-05-01

This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

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

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Rotational Spectroscopy of Two Tellurol Compounds : Ethyl and Vinyl-Tellurol

NASA Astrophysics Data System (ADS)

Motiyenko, R.; Margulès, L.; Goubet, M.; Møllendal, H.; Guillemin, J. C.

2009-06-01

Among the compounds containing a chalcogen, the tellurols (R-TeH) have been poorly investigated previously. Only H_2Te was studied in rotational spectroscopy. This fact can be explained by high toxicity and high chemical reactivity of these compounds. However quite recently, a new method allowing easily obtention of pure samples has been reported. Thanks to this approach, very high acidity of these tellurols in gas phase has been measured and photoelectron spectra have been recorded. It should be noted that, even if simple derivatives are known since a long time, no microwave spectrum of these compounds has been recorded previously. The determination of their rotational constants is however a determining step to have a quite complete knowledge of such systems and to be able to perform comparisons of their physicochemical properties with those of the corresponding thiols and selenols which have been more extensively studied. The rotational spectra of vinyl and ethyl-tellurol have been recorded in the frequency range up to 210 GHz. For both compounds gauche forms have been assigned due to rather distinguishable patterns of a-type transitions. The assignments were confirmed by comparison with the results of ab initio calculations. For ethyl-tellurol the rotational transitions were observed as doublets. The splittings are probably caused by tunneling effect between two equivalent configurations (gauche^+, gauche^-). The assignment and analysis of the rotational spectra of both molecules is in progress. The latest results will be reported. I. N. Kozin, P. Jensen, O. Polanz, S. Klee, L. Poteau, and J. Demaison, J. Mol. Spectrosc., 180 402-413 (1996) J. C. Guillemin, A. Bouayard, D. Vijaykumar, D. Chem. Commun., 1163-1164 (2000) J. C. Guillemin, El. H. Riague, J. F. Gal, P. C. Marris, O. Mo., M. Yanez, Chem. Eur. J. 11, 2145-2153 (2005) B. Khater, J. C. Guillemin, G. Bajor, T. Veszprémi, P. C. Marris, O. Mo., M. Yanez, Inorg. Chem. 112, 3053-3060 (2008) A. Baroni, Atti Accad. Naz. Lincei, Cl. Sci. Fis., Mat. Nat., Rend. 27, 238-242 (1938)

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

EPR/ENDOR and Theoretical Study of the Jahn-Teller-Active [HIPTN3N]MoVL Complexes (L = N-, NH).

PubMed

Sharma, Ajay; Roemelt, Michael; Reithofer, Michael; Schrock, Richard R; Hoffman, Brian M; Neese, Frank

2017-06-19

The molybdenum trisamidoamine (TAA) complex [Mo] {[3,5-(2,4,6-i-Pr 3 C 6 H 2 ) 2 C 6 H 3 NCH 2 CH 2 N]Mo} carries out catalytic reduction of N 2 to ammonia (NH 3 ) by protons and electrons at room temperature. A key intermediate in the proposed [Mo] nitrogen reduction cycle is nitridomolybdenum(VI), [Mo(VI)]N. The addition of [e - /H + ] to [Mo(VI)]N to generate [Mo(V)]NH might, in principle, follow one of three possible pathways: direct proton-coupled electron transfer; H + first and then e - ; e - and then H + . In this study, the paramagnetic Mo(V) intermediate {[Mo]N} - and the [Mo]NH transfer product were generated by irradiating the diamagnetic [Mo]N and {[Mo]NH} + Mo(VI) complexes, respectively, with γ-rays at 77 K, and their electronic and geometric structures were characterized by electron paramagnetic resonance and electron nuclear double resonance spectroscopies, combined with quantum-chemical computations. In combination with previous X-ray studies, this creates the rare situation in which each one of the four possible states of [e - /H + ] delivery has been characterized. Because of the degeneracy of the electronic ground states of both {[Mo(V)]N} - and [Mo(V)]NH, only multireference-based methods such as the complete active-space self-consistent field (CASSCF) and related methods provide a qualitatively correct description of the electronic ground state and vibronic coupling. The molecular g values of {[Mo]N} - and [Mo]NH exhibit large deviations from the free-electron value g e . Their actual values reflect the relative strengths of vibronic and spin-orbit coupling. In the course of the computational treatment, the utility and limitations of a formal two-state model that describes this competition between couplings are illustrated, and the implications of our results for the chemical reactivity of these states are discussed.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2001-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

First-Principles Study of Mo Segregation in MoNi(111): Effects of Chemisorbed Atomic Oxygen

PubMed Central

Yu, Yanlin; Xiao, Wei; Wang, Jianwei; Wang, Ligen

2015-01-01

Segregation at metal alloy surfaces is an important issue because many electrochemical and catalytic properties are directly correlated to the surface composition. We have performed density functional theory calculations for Mo segregation in MoNi(111) in the presence of chemisorbed atomic oxygen. In particular, the coverage dependence and possible adsorption-induced segregation phenomena are addressed by investigating segregation energies of the Mo atom in MoNi(111). The theoretical calculated results show that the Mo atom prefers to be embedded in the bulk for the clean MoNi(111), while it segregates to the top-most layer when the oxygen coverage is thicker than 1/9 monolayer (ML). Furthermore, we analyze the densities of states for the clean and oxygen-chemisorbed MoNi(111), and see a strong covalent bonding between Mo d-band states and O p-states. The present study provides valuable insight for exploring practical applications of Ni-based alloys as hydrogen evolution electrodes. PMID:28787811

Theoretical study on electronic properties of MoS{sub 2} antidot lattices

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

Shao, Li; Chen, Guangde; Ye, Honggang, E-mail: hgye@mail.xjtu.edu.cn

2014-09-21

Motivated by the state of the art method for etching hexagonal array holes in molybdenum disulfide (MoS{sub 2}), the electronic properties of MoS{sub 2} antidot lattices (MoS{sub 2}ALs) with zigzag edge were studied with first-principles calculations. Monolayer MoS{sub 2}ALs are semiconducting and the band gaps converge to constant values as the supercell area increases, which can be attributed to the edge effect. Multilayer MoS{sub 2}ALs and chemical adsorbed MoS{sub 2}ALs by F atoms show metallic behavior, while the structure adsorbed with H atoms remains to be semiconducting with a tiny bandgap. Our results show that forming periodically repeating structures inmore » MoS{sub 2} can develop a promising technique for engineering nano materials and offer new opportunities for designing MoS{sub 2}-based nanoscale electronic devices and chemical sensors.« less

Structural phase transition of BeTe: an ab initio molecular dynamics study.

PubMed

Alptekin, Sebahaddin

2017-08-11

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.

Ab-initio study of several static and dynamic properties of liquid palladium and platinum

NASA Astrophysics Data System (ADS)

González, L. E.; González, D. J.; Molla, Mohammad Riazuddin; Ahmed, A. Z. Ziauddin; Bhuiyan, G. M.

2017-08-01

We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.

Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

Two Rab5 Homologs Are Essential for the Development and Pathogenicity of the Rice Blast Fungus Magnaporthe oryzae

PubMed Central

Yang, Cheng D.; Dang, Xie; Zheng, Hua W.; Chen, Xiao F.; Lin, Xiao L.; Zhang, Dong M.; Abubakar, Yakubu S.; Chen, Xin; Lu, Guodong; Wang, Zonghua; Li, Guangpu; Zhou, Jie

2017-01-01

The rice blast fungus, Magnaporthe oryzae, infects many economically important cereal crops, particularly rice. It has emerged as an important model organism for studying the growth, development, and pathogenesis of filamentous fungi. RabGTPases are important molecular switches in regulation of intracellular membrane trafficking in all eukaryotes. MoRab5A and MoRab5B are Rab5 homologs in M. oryzae, but their functions in the fungal development and pathogenicity are unknown. In this study, we have employed a genetic approach and demonstrated that both MoRab5A and MoRab5B are crucial for vegetative growth and development, conidiogenesis, melanin synthesis, vacuole fusion, endocytosis, sexual reproduction, and plant pathogenesis in M. oryzae. Moreover, both MoRab5A and MoRab5B show similar localization in hyphae and conidia. To further investigate possible functional redundancy between MoRab5A and MoRab5B, we overexpressed MoRAB5A and MoRAB5B, respectively, in MoRab5B:RNAi and MoRab5A:RNAi strains, but neither could rescue each other’s defects caused by the RNAi. Taken together, we conclude that both MoRab5A and MoRab5B are necessary for the development and pathogenesis of the rice blast fungus, while they may function independently. PMID:28529514

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Magnetic and electronic properties of single-walled Mo2C nanotube: a first-principles study

NASA Astrophysics Data System (ADS)

Jalil, Abdul; Sun, Zhongti; Wang, Dayong; Wu, Xiaojun

2018-04-01

The structural, electronic, and magnetic properties of single-walled Mo2C nanotubes are investigated by using first-principles calculations. We establish that single-walled Mo2C nanotubes can be rolled up from a graphene-like Mo2C monolayer with H- or T-type phase, i.e. H-Mo2C and T-Mo2C nanotubes. The armchair-type T-Mo2C nanotubes are more energetically stable than H-Mo2C nanotubes with the same diameter, while zigzag-type H-Mo2C nanotubes are more energetically stable than T-Mo2C nanotubes. In particular, (8, 0) H-Mo2C nanotube are more stable than Mo2C monolayer due to structural deformation. All Mo2C nanotubes are magnetic metals, independent of their chirality, and the magnetic moments of Mo atoms in the outer layer are larger than the inner. The ionic and metallic bonds in Mo2C nanotubes and delocalized electrons around Mo atoms lead to the versatile electronic and magnetic properties in them, endowing them potential applications in catalysts and electronics.

Magnetic and electronic properties of single-walled Mo2C nanotube: a first-principles study.

PubMed

Jalil, Abdul; Sun, Zhongti; Wang, Dayong; Wu, Xiaojun

2018-04-18

The structural, electronic, and magnetic properties of single-walled Mo 2 C nanotubes are investigated by using first-principles calculations. We establish that single-walled Mo 2 C nanotubes can be rolled up from a graphene-like Mo 2 C monolayer with H- or T-type phase, i.e. H-Mo 2 C and T-Mo 2 C nanotubes. The armchair-type T-Mo 2 C nanotubes are more energetically stable than H-Mo 2 C nanotubes with the same diameter, while zigzag-type H-Mo 2 C nanotubes are more energetically stable than T-Mo 2 C nanotubes. In particular, (8, 0) H-Mo 2 C nanotube are more stable than Mo 2 C monolayer due to structural deformation. All Mo 2 C nanotubes are magnetic metals, independent of their chirality, and the magnetic moments of Mo atoms in the outer layer are larger than the inner. The ionic and metallic bonds in Mo 2 C nanotubes and delocalized electrons around Mo atoms lead to the versatile electronic and magnetic properties in them, endowing them potential applications in catalysts and electronics.

The modulation of Schottky barriers of metal-MoS2 contacts via BN-MoS2 heterostructures.

PubMed

Su, Jie; Feng, Liping; Zhang, Yan; Liu, Zhengtang

2016-06-22

Using first-principles calculations within density functional theory, we systematically studied the effect of BN-MoS2 heterostructure on the Schottky barriers of metal-MoS2 contacts. Two types of FETs are designed according to the area of the BN-MoS2 heterostructure. Results show that the vertical and lateral Schottky barriers in all the studied contacts, irrespective of the work function of the metal, are significantly reduced or even vanish when the BN-MoS2 heterostructure substitutes the monolayer MoS2. Only the n-type lateral Schottky barrier of Au/BN-MoS2 contact relates to the area of the BN-MoS2 heterostructure. Notably, the Pt-MoS2 contact with n-type character is transformed into a p-type contact upon substituting the monolayer MoS2 by a BN-MoS2 heterostructure. These changes of the contact natures are ascribed to the variation of Fermi level pinning, work function and charge distribution. Analysis demonstrates that the Fermi level pinning effects are significantly weakened for metal/BN-MoS2 contacts because no gap states dominated by MoS2 are formed, in contrast to those of metal-MoS2 contacts. Although additional BN layers reduce the interlayer interaction and the work function of the metal, the Schottky barriers of metal/BN-MoS2 contacts still do not obey the Schottky-Mott rule. Moreover, different from metal-MoS2 contacts, the charges transfer from electrodes to the monolayer MoS2, resulting in an increment of the work function of these metals in metal/BN-MoS2 contacts. These findings may prove to be instrumental in the future design of new MoS2-based FETs with ohmic contact or p-type character.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born-Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Infant growth and health outcomes associated with 3 compared with 6 mo of exclusive breastfeeding.

PubMed

Kramer, Michael S; Guo, Tong; Platt, Robert W; Sevkovskaya, Zinaida; Dzikovich, Irina; Collet, Jean-Paul; Shapiro, Stanley; Chalmers, Beverley; Hodnett, Ellen; Vanilovich, Irina; Mezen, Irina; Ducruet, Thierry; Shishko, George; Bogdanovich, Natalia

2003-08-01

Opinions and recommendations about the optimal duration of exclusive breastfeeding have been strongly divided, but few published studies have provided direct evidence on the relative risks and benefits of different breastfeeding durations in recipient infants. We examined the effects on infant growth and health of 3 compared with 6 mo of exclusive breastfeeding. We conducted an observational cohort study nested within a large randomized trial in Belarus by comparing 2862 infants exclusively breastfed for 3 mo (with continued mixed breastfeeding through >/= 6 mo) with 621 infants who were exclusively breastfed for >/= 6 mo. Regression to the mean, within-cluster correlation, and cluster- and individual-level confounding variables were accounted for by using multilevel regression analyses. From 3 to 6 mo, weight gain was slightly greater in the 3-mo group [difference: 29 g/mo (95% CI: 13, 45 g/mo)], as was length gain [difference: 1.1 mm (0.5, 1.6 mm)], but the 6-mo group had a faster length gain from 9 to 12 mo [difference: 0.9 mm/mo (0.3, 1.5 mm/mo)] and a larger head circumference at 12 mo [difference: 0.19 cm (0.07, 0.31 cm)]. A significant reduction in the incidence density of gastrointestinal infection was observed during the period from 3 to 6 mo in the 6-mo group [adjusted incidence density ratio: 0.35 (0.13, 0.96)], but no significant differences in risk of respiratory infectious outcomes or atopic eczema were apparent. Exclusive breastfeeding for 6 mo is associated with a lower risk of gastrointestinal infection and no demonstrable adverse health effects in the first year of life.

Acetylene and Ethylene Adsorption on a β-Mo 2C(100) Surface: A Periodic DFT Study on the Role of C- and Mo-Terminations for Bonding and Hydrogenation Reactions

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

Jimenez-Orozco, Carlos; Florez, Elizabeth; Moreno, Andres

Mo 2C catalysts are widely used in hydrogenation reactions; however, the role of the C and Mo terminations in these catalysts is not clear. Understanding the binding of adsorbates is key for explaining the activity of Mo 2C. The adsorption of acetylene and ethylene, probe molecules representing alkynes and olefins, respectively, was studied in this paper on a β-Mo 2C(100) surface with C and Mo terminations using calculations based on periodic density functional theory. Moreover, the role of the C/Mo molar ratio was investigated to compare the catalytic potential of cubic (δ-MoC) and orthorhombic (β-Mo 2C) surfaces. The geometry andmore » electronic properties of the clean δ-MoC(001) and β-Mo 2C(100) surfaces have a strong influence on the binding of unsaturated hydrocarbons. The adsorption of ethylene is weaker than that of acetylene on the surfaces of the cubic and orthorhombic systems; adsorption of the hydrocarbons was stronger on β-Mo 2C(100) than on δ-MoC(001). The C termination in β-Mo 2C(100) actively participates in both acetylene and ethylene adsorption and is not merely a spectator. Finally, the results of this work suggest that the β-Mo 2C(100)-C surface could be the one responsible for the catalytic activity during the hydrogenation of unsaturated C≡C and C=C bonds, while the Mo-terminated surface could be poisoned or transformed by the strong adsorption of C and CH x fragments.« less

Acetylene and Ethylene Adsorption on a β-Mo 2C(100) Surface: A Periodic DFT Study on the Role of C- and Mo-Terminations for Bonding and Hydrogenation Reactions

DOE PAGES

Jimenez-Orozco, Carlos; Florez, Elizabeth; Moreno, Andres; ...

2017-08-18

Mo 2C catalysts are widely used in hydrogenation reactions; however, the role of the C and Mo terminations in these catalysts is not clear. Understanding the binding of adsorbates is key for explaining the activity of Mo 2C. The adsorption of acetylene and ethylene, probe molecules representing alkynes and olefins, respectively, was studied in this paper on a β-Mo 2C(100) surface with C and Mo terminations using calculations based on periodic density functional theory. Moreover, the role of the C/Mo molar ratio was investigated to compare the catalytic potential of cubic (δ-MoC) and orthorhombic (β-Mo 2C) surfaces. The geometry andmore » electronic properties of the clean δ-MoC(001) and β-Mo 2C(100) surfaces have a strong influence on the binding of unsaturated hydrocarbons. The adsorption of ethylene is weaker than that of acetylene on the surfaces of the cubic and orthorhombic systems; adsorption of the hydrocarbons was stronger on β-Mo 2C(100) than on δ-MoC(001). The C termination in β-Mo 2C(100) actively participates in both acetylene and ethylene adsorption and is not merely a spectator. Finally, the results of this work suggest that the β-Mo 2C(100)-C surface could be the one responsible for the catalytic activity during the hydrogenation of unsaturated C≡C and C=C bonds, while the Mo-terminated surface could be poisoned or transformed by the strong adsorption of C and CH x fragments.« less

Eight RGS and RGS-like Proteins Orchestrate Growth, Differentiation, and Pathogenicity of Magnaporthe oryzae

PubMed Central

Zhang, Haifeng; Tang, Wei; Liu, Kaiyue; Huang, Qian; Zhang, Xin; Yan, Xia; Chen, Yue; Wang, Jiansheng; Qi, Zhongqiang; Wang, Zhengyi; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

2011-01-01

A previous study identified MoRgs1 as an RGS protein that negative regulates G-protein signaling to control developmental processes such as conidiation and appressorium formation in Magnaporthe oryzae. Here, we characterized additional seven RGS and RGS-like proteins (MoRgs2 through MoRgs8). We found that MoRgs1 and MoRgs4 positively regulate surface hydrophobicity, conidiation, and mating. Indifference to MoRgs1, MoRgs4 has a role in regulating laccase and peroxidase activities. MoRgs1, MoRgs2, MoRgs3, MoRgs4, MoRgs6, and MoRgs7 are important for germ tube growth and appressorium formation. Interestingly, MoRgs7 and MoRgs8 exhibit a unique domain structure in which the RGS domain is linked to a seven-transmembrane motif, a hallmark of G-protein coupled receptors (GPCRs). We have also shown that MoRgs1 regulates mating through negative regulation of Gα MoMagB and is involved in the maintenance of cell wall integrity. While all proteins appear to be involved in the control of intracellular cAMP levels, only MoRgs1, MoRgs3, MoRgs4, and MoRgs7 are required for full virulence. Taking together, in addition to MoRgs1 functions as a prominent RGS protein in M. oryzae, MoRgs4 and other RGS and RGS-like proteins are also involved in a complex process governing asexual/sexual development, appressorium formation, and pathogenicity. PMID:22241981

A theoretical study on reaction mechanisms and kinetics of thiophene hydrodesulfurization over MoS 2 catalysts

DOE PAGES

Jin, Qiu; Chen, Biaohua; Ren, Zhibo; ...

2018-02-10

In the present study, thiophene hydrodesulphurization (HDS) over the Mo-edge, the S-edge, and the Mo-S connection edge of MoS 2 catalyst with 50% sulfur coverage was studied using first-principles based microkinetic modeling. Two parallel HDS routes, i.e., direct desulfurization (DDS) and hydrogenation (HYD) were taken into account. It has been found that the major reaction route of thiophene HDS on the Mo- and the Mo-S edges is temperature dependent. In the low temperature range of 500–600 K, the HYD route is dominant, leading to the C 4H 8 formation. As the temperature increases, the DDS route becomes competitive with themore » HYD route. At the temperature above 650 K, the DDS route will be the dominant HDS reaction route on the Mo- and the Mo-S edges. The DDS route leading to the formation of C 4H 6 is the major thiophene HDS reaction route on the S-edge in the entire temperature range of 500–750 K. The microkinetic modeling results show the overall HDS activity on the S-edge is lower than it on the Mo- and the Mo-S edges. The Mo-S edge also provides a preferential reaction pathway, which facilitates 2-hydrothiophene migration from the Mo-edge to the S-edge, followed by remaining elementary steps with lower activation barriers in the DDS route.« less

A theoretical study on reaction mechanisms and kinetics of thiophene hydrodesulfurization over MoS 2 catalysts

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

Jin, Qiu; Chen, Biaohua; Ren, Zhibo

In the present study, thiophene hydrodesulphurization (HDS) over the Mo-edge, the S-edge, and the Mo-S connection edge of MoS 2 catalyst with 50% sulfur coverage was studied using first-principles based microkinetic modeling. Two parallel HDS routes, i.e., direct desulfurization (DDS) and hydrogenation (HYD) were taken into account. It has been found that the major reaction route of thiophene HDS on the Mo- and the Mo-S edges is temperature dependent. In the low temperature range of 500–600 K, the HYD route is dominant, leading to the C 4H 8 formation. As the temperature increases, the DDS route becomes competitive with themore » HYD route. At the temperature above 650 K, the DDS route will be the dominant HDS reaction route on the Mo- and the Mo-S edges. The DDS route leading to the formation of C 4H 6 is the major thiophene HDS reaction route on the S-edge in the entire temperature range of 500–750 K. The microkinetic modeling results show the overall HDS activity on the S-edge is lower than it on the Mo- and the Mo-S edges. The Mo-S edge also provides a preferential reaction pathway, which facilitates 2-hydrothiophene migration from the Mo-edge to the S-edge, followed by remaining elementary steps with lower activation barriers in the DDS route.« less

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kumar, Sanjay

2007-12-01

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

2017-04-01

From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

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

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

PubMed

Yang, Lina; Minnich, Austin J

2017-03-14

Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation

PubMed Central

Yang, Lina; Minnich, Austin J.

2017-01-01

Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 on Mg 2+ sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2014-04-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

Ni-Doping Effects on Oxygen Removal from an Orthorhombic Mo 2 C (001) Surface: A Density Functional Theory Study

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

Zhou, Mingxia; Cheng, Lei; Choi, Jae-Soon

Density functional theory (DFT) calculations were used to investigate the effect of Ni dopants on the removal of chemisorbed oxygen (O*) from the Mo-terminated (T-Mo) and C-terminated (Tc) Mo2C(001) surfaces. The removal of adsorbed oxygen from the catalytic site is essential to maintain the long-term activity and selectivity of the carbide catalysts in the deoxygenation process related to bio-oil stabilization and upgrading. In this contribution, the computed reaction energetics and reaction barriers of O* removal were compared among undoped and Ni-doped Mo2C(001) surfaces. The DFT calculations indicate that selected Ni-doped surfaces such as Ni adsorbed on T-Mo and Tc Mo2C(001)more » surfaces enable weaker binding of important reactive intermediates (O*, OH*) compared to the undoped counterparts, which is beneficial for the O* removal from the catalyst surface. This study thus confirms the promoting effect of the Ni dopant on O* removal reaction on the T-Mo Mo2C(001) and Tc Mo2C(001) surfaces. This computational prediction has been confirmed by the temperature-programmed reduction profiles of Mo2C and Ni-doped Mo2C catalysts, which had been passivated and stored in an oxygen environment.« less

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

Kumar, Prabhat, E-mail: prabhat89k@gmail.com; Singh, Megha; Sharma, Rabindar K.

In this report, the effect of plasma voltage on plasma assisted sulfurization (PAS) of vertically aligned molybdenum trioxide (α- MoO{sub 3}) nanoflakes (NFs) on glass substrates has been studied systematically. MoO{sub 3} NFs were deposited using plasma assisted sublimation process. These nanoflakes were subjected to H{sub 2}S/Ar plasma at two different plasma voltages 600 and 1000 volts; to study the effect of plasma ionization on degree of sulfurization of MoO{sub 3} into MoS{sub 2}. XRD and Raman analysis show that film sulfurized at 1000 volts have relatively higher degree of conversion into MoS{sub 2}, as more intense peaks of MoS{submore » 2} and MoO{sub 2} are obtained than that sulfurized at 600 volts. HRTEM of sulfurized film shows that outer surface of nanoflake has been converted into MoS{sub 2} (4-5 monolayers). Meanwhile, MoO{sub 3} was reduced into MoO{sub 2} as confirmed by XRD and Raman results. All the observed results are well in consonance with each other.« less

Solution-processed MoS(x) as an efficient anode buffer layer in organic solar cells.

PubMed

Li, Xiaodong; Zhang, Wenjun; Wu, Yulei; Min, Chao; Fang, Junfeng

2013-09-25

We reported a facile solution-processed method to fabricate a MoSx anode buffer layer through thermal decomposition of (NH4)2MoS4. Organic solar cells (OSCs) based on in situ growth MoSx as the anode buffer layer showed impressive improvements, and the power conversion efficiency was higher than that of conventional PEDOT:PSS-based device. The MoSx films obtained at different temperatures and the corresponding device performance were systematically studied. The results indicated that both MoS3 and MoS2 were beneficial to the device performance. MoS3 could result in higher Voc, while MoS2 could lead to higher Jsc. Our results proved that, apart from MoO3, molybdenum sulfides and Mo(4+) were also promising candidates for the anode buffer materials in OSCs.

Molybdenum L-Edge XAS Spectra of MoFe Nitrogenase

PubMed Central

Bjornsson, Ragnar; Delgado-Jaime, Mario U; Lima, Frederico A; Sippel, Daniel; Schlesier, Julia; Weyhermüller, Thomas; Einsle, Oliver; Neese, Frank; DeBeer, Serena

2015-01-01

A molybdenum L-edge X-ray absorption spectroscopy (XAS) study is presented for native and oxidized MoFe protein of nitrogenase as well as Mo-Fe model compounds. Recently collected data on MoFe protein (in oxidized and reduced forms) is compared to previously published Mo XAS data on the isolated FeMo cofactor in NMF solution and put in context of the recent Mo K-edge XAS study, which showed a MoIII assignment for the molybdenum atom in FeMoco. The L3-edge data are interpreted within a simple ligand-field model, from which a time-dependent density functional theory (TDDFT) approach is proposed as a way to provide further insights into the analysis of the molybdenum L3-edges. The calculated results reproduce well the relative spectral trends that are observed experimentally. Ultimately, these results give further support for the MoIII assignment in protein-bound FeMoco, as well as isolated FeMoco. PMID:26213424

Effect of molecular intercalation on the local structure of superconducting Nax(NH3)yMoSe2 system

NASA Astrophysics Data System (ADS)

Simonelli, L.; Paris, E.; Wakita, T.; Marini, C.; Terashima, K.; Miao, X.; Olszewski, W.; Ramanan, N.; Heinis, D.; Kubozono, Y.; Yokoya, T.; Saini, N. L.

2017-12-01

We have studied the local structure of layered Nax(NH3)yMoSe2 system by Mo K-edge extended X-ray absorption fine structure (EXAFS) measurements performed as a function of temperature. We find that molecular intercalation in MoSe2 largely affects the Mo-Se network while Mo-Mo seems to sustain small changes. The Einstein temperature (ΘE) of Mo-Mo distance hardly changes (∼264 K) indicating that bond strength of this distance remains unaffected by intercalation. On the other hand, Mo-Se distance suffers a softening, revealed by the decrease of ΘE from ∼364 K to ∼350 K. The results indicate that Na+ ion transported by NH3 molecules may enter between the two MoSe-layers resulting reduced Se-Se coupling. Therefore, increased hybridization between Se 4p and Mo 4d orbitals due to inter-layer disorder is the likely reason of metallicity in intercalated MoSe2 and superconductivity at low temperature.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

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

2011-01-01

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

On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

PubMed

Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R

2016-12-21

For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H d (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H d by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H d determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.

Compatibility studies on Mo-coating systems for nuclear fuel cladding applications

NASA Astrophysics Data System (ADS)

Koh, Huan Chin; Hosemann, Peter; Glaeser, Andreas M.; Cionea, Cristian

2017-12-01

To improve the safety factor of nuclear power plants in accident scenarios, molybdenum (Mo), with its high-temperature strength, is proposed as a potential fuel-cladding candidate. However, Mo undergoes rapid oxidation and sublimation at elevated temperatures in oxygen-rich environments. Thus, it is necessary to coat Mo with a protective layer. The diffusional interactions in two systems, namely, Zircaloy-2 (Zr2) on a Mo tube, and iron-chromium-aluminum (FeCrAl) on a Mo rod, were studied by aging coated Mo substrates in high vacuum at temperatures ranging from 650 °C to 1000° for 1000 h. The specimens were characterized using scanning electron microscopy (SEM), energy-dispersive spectrometry (EDS) and nanoindentation. In both systems, pores in the coating increased in size and number with increasing temperature over time, and cracks were also observed; intermetallic phases formed between the Mo and its coatings.

Spin-orbit coupled systems in the atomic limit: rhenates, osmates, iridates

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

Paramekanti, Arun; Singh, David J.; Yuan, Bo

Motivated by RIXS experiments on a wide range of complex heavy oxides, including rhenates, osmates, and iridates, we discuss the theory of RIXS for site-localized t 2g orbital systems with strong spin-orbit coupling. For such systems, we present exact diagonalization results for the spectrum at different electron fillings, showing that it accesses “single-particle” and “multiparticle” excitations. This leads to a simple picture for the energies and intensities of the RIXS spectra in Mott insulators such as double perovskites which feature highly localized electrons, and yields estimates of the spin-orbit coupling and Hund's coupling in correlated 5d oxides. We present newmore » higher resolution RIXS data at the Re L 3 edge in Ba 2YReO 6 which finds a previously unresolved peak splitting, providing further confirmation of our theoretical predictions. Using ab initio electronic structure calculations on Ba 2MReO 6 (with M=Re, Os, Ir) we show that while the atomic limit yields a reasonable effective Hamiltonian description of the experimental observations, effects such as t 2g–e g interactions and hybridization with oxygen are important. Our ab initio estimate for the strength of the intersite exchange coupling shows that, compared to the d 3 systems, the exchange is one or two orders of magnitude weaker in the d 2 and d 4 materials, which may partly explain the suppression of long-range magnetic order in the latter compounds. As a way to interpolate between the site-localized picture and our electronic structure band calculations, we discuss the spin-orbital levels of the MO 6 cluster. In conclusion, this suggests a possible role for intracluster excitons in Ba 2YIrO 6 which may lead to a weak breakdown of the atomic J eff = 0 picture and to small magnetic moments.« less

Spin-orbit coupled systems in the atomic limit: rhenates, osmates, iridates

DOE PAGES

Paramekanti, Arun; Singh, David J.; Yuan, Bo; ...

2018-06-11

Motivated by RIXS experiments on a wide range of complex heavy oxides, including rhenates, osmates, and iridates, we discuss the theory of RIXS for site-localized t 2g orbital systems with strong spin-orbit coupling. For such systems, we present exact diagonalization results for the spectrum at different electron fillings, showing that it accesses “single-particle” and “multiparticle” excitations. This leads to a simple picture for the energies and intensities of the RIXS spectra in Mott insulators such as double perovskites which feature highly localized electrons, and yields estimates of the spin-orbit coupling and Hund's coupling in correlated 5d oxides. We present newmore » higher resolution RIXS data at the Re L 3 edge in Ba 2YReO 6 which finds a previously unresolved peak splitting, providing further confirmation of our theoretical predictions. Using ab initio electronic structure calculations on Ba 2MReO 6 (with M=Re, Os, Ir) we show that while the atomic limit yields a reasonable effective Hamiltonian description of the experimental observations, effects such as t 2g–e g interactions and hybridization with oxygen are important. Our ab initio estimate for the strength of the intersite exchange coupling shows that, compared to the d 3 systems, the exchange is one or two orders of magnitude weaker in the d 2 and d 4 materials, which may partly explain the suppression of long-range magnetic order in the latter compounds. As a way to interpolate between the site-localized picture and our electronic structure band calculations, we discuss the spin-orbital levels of the MO 6 cluster. In conclusion, this suggests a possible role for intracluster excitons in Ba 2YIrO 6 which may lead to a weak breakdown of the atomic J eff = 0 picture and to small magnetic moments.« less

An experimental study of the behaviour of cerium/molybdenum ratios during subduction: Implications for tracing the slab component in the Lesser Antilles and Mariana Arc

NASA Astrophysics Data System (ADS)

Skora, Susanne; Freymuth, Heye; Blundy, Jon; Elliott, Tim; Guillong, Marcel

2017-09-01

Arc magmas are very distinct in their geochemical signatures, a consequence of trace element enriched components from the subducting slab that are incorporated into melts of the overlying mantle wedge. However, it is not always straightforward to distinguish such slab components from assimilation of crustal rocks during subsequent differentiation, given that both reservoirs can share similar geochemical characteristics. This has prompted the development of new tools, such as 98Mo/95Mo analyses used in combination with Ce/Mo measurements. The diverse range of δ98/95Mo in the surface environment gives rise to variable isotopic compositions of subducted Mo. Most diagnostic of these is the extremely isotopically heavy Mo in marine black shales, such as those drilled in the vicinity of the Lesser Antilles. However, subducting assemblages are invariably complex and differing melting behaviours and contrasting δ98/95Mo of various crustal components may counter-balance one another, requiring a more detailed investigation of the behaviour of Mo and Ce in the down-going slab. This study is dedicated to identifying possible hosts for Mo and Ce in sediments and basalt at sub-arc depths. New melting experiments were performed (3 GPa, 800-900 °C), using synthetic carbon-rich black shale and calcareous sediment compositions from the Lesser Antilles arc. In addition, new analyses of Mo concentrations and Ce/Mo data of previously published partial melting studies on altered oceanic crust and volcaniclastics (Mariana Arc) are presented. Our study suggests that sulfide and to a lesser extent rutile are the major hosts for Mo in eclogites, whereas the presence or absence of monazite (Ca-poor sediments), epidote (Ca-rich sediments) and carbonate (CaCO3-rich sediments) controls Ce concentrations in sediments. Redox conditions are found to be of great importance for the Ce/Mo ratios of slab components derived from these lithologies because of their influence on sulfide and epidote stability. It is further shown that rutile only hosts Mo at suitably reducing conditions, in concordance with previous studies. The combination of measured Ce/Mo with our experimental results thus places important constrains on phase petrology and redox conditions in the subducted slab.

Effects of heat treatment on U-Mo fuel foils with a zirconium diffusion barrier

NASA Astrophysics Data System (ADS)

Jue, Jan-Fong; Trowbridge, Tammy L.; Breckenridge, Cynthia R.; Moore, Glenn A.; Meyer, Mitchell K.; Keiser, Dennis D.

2015-05-01

A monolith fuel design based on U-Mo alloy has been selected as the fuel type for conversion of the United States' high performance research reactors (HPRRs) from highly enriched uranium (HEU) to low-enriched uranium (LEU). In this fuel design, a thin layer of zirconium is used to eliminate the direct interaction between the U-Mo fuel meat and the aluminum-alloy cladding during irradiation. The co-rolling process used to bond the Zr barrier layer to the U-Mo foil during fabrication alters the microstructure of both the U-10Mo fuel meat and the U-Mo/Zr interface. This work studied the effects of post-rolling annealing treatment on the microstructure of the co-rolled U-Mo fuel meat and the U-Mo/Zr interaction layer. Microscopic characterization shows that the grain size of U-Mo fuel meat increases with the annealing temperature, as expected. The grain sizes were ∼9, ∼13, and ∼20 μm for annealing temperature of 650, 750, and 850 °C, respectively. No abnormal grain growth was observed. The U-Mo/Zr interaction-layer thickness increased with the annealing temperature with an Arrhenius constant for growth of 184 kJ/mole, consistent with a previous diffusion-couple study. The interaction layer thickness was 3.2 ± 0.5 μm, 11.1 ± 2.1 μm, 27.1 ± 0.9 μm for annealing temperature of 650, 750, to 850 °C, respectively. The homogeneity of Mo improves with post rolling annealing temperature and with U-Mo coupon homogenization. The phases in the Zr/U-Mo interaction layer produced by co-rolling, however, differ from those reported in the previous diffusion couple studies.

Effects of heat treatment on U–Mo fuel foils with a zirconium diffusion barrier

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

Jue, Jan-Fong; Trowbridge, Tammy L.; Breckenridge, Cynthia R.

A monolith fuel design based on U–Mo alloy has been selected as the fuel type for conversion of the United States’ high performance research reactors (HPRRs) from highly enriched uranium (HEU) to low-enriched uranium (LEU). In this fuel design, a thin layer of zirconium is used to eliminate the direct interaction between the U–Mo fuel meat and the aluminum-alloy cladding during irradiation. The co-rolling process used to bond the Zr barrier layer to the U–Mo foil during fabrication alters the microstructure of both the U–10Mo fuel meat and the U–Mo/Zr interface. This work studied the effects of post-rolling annealing treatmentmore » on the microstructure of the co-rolled U–Mo fuel meat and the U–Mo/Zr interaction layer. Microscopic characterization shows that the grain size of U–Mo fuel meat increases with the annealing temperature, as expected. The grain sizes were ~9, ~13, and ~20 μm for annealing temperature of 650, 750, and 850 °C, respectively. No abnormal grain growth was observed. The U–Mo/Zr interaction-layer thickness increased with the annealing temperature with an Arrhenius constant for growth of 184 kJ/mole, consistent with a previous diffusion-couple study. The interaction layer thickness was 3.2 ± 0.5 μm, 11.1 ± 2.1 μm, 27.1 ± 0.9 μm for annealing temperature of 650, 750, to 850 °C, respectively. The homogeneity of Mo improves with post rolling annealing temperature and with U–Mo coupon homogenization. The phases in the Zr/U–Mo interaction layer produced by co-rolling, however, differ from those reported in the previous diffusion couple studies.« less

A mechanistic study on Decontamination of Methyl Orange Dyes from Aqueous Phase by Mesoporous Pulp Waste and Polyaniline

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

Li, Donglin; Yang, Yonggang; Li, Chaozheng

2017-04-15

The dispersion-corrected density functional theory (DFT-D3) is used to investigate the mechanism of mesoporous pulp waste (MPW) and polyaniline (PANI) adsorptive removal methyl orange (MO) dye from their aqueous solutions. The results are absolutely reliable because of the sufficiently accurate method although such big systems are studied. It is demonstrated that hydrogen bond and Van Der Waals interactions play a significant role in MO adsorption by MPW and PANI. For MO adsorption by MPW, hydrogen bond and Van Der Waals interactions are both weakened in S{sub 1} state. In contrast, hydrogen bond and Van Der Waals interactions between PANI andmore » MO are both enhanced in S{sub 1} state. The thermodynamic parameters such as enthalpy and free energy change reveal that the MO adsorption by MPW and PANI are spontaneous and exothermic. The adsorption of MO on MPW is less favorable in S{sub 1} state and the adsorption of MO on PANI is more favorable in S{sub 1} state. Therefore, the photoexcitation should be controlled during the MO adsorption by MPW and applied for MO adsorption by PANI. - Highlights: • The hydrogen bond and Van Der Waals interactions play a significant role in MO adsorption by MPW and PANI. • The influence of photoexcitation on adsorption has been studied firstly in our work. • The adsorption of MO on MPW is less favorable in S{sub 1} state and the adsorption of MO on PANI is more favorable in S{sub 1} state. • The MO adsorption by MPW and PANI are spontaneous and exothermic.« less

Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

2017-02-14

Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16 O 3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν 3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm -1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

Nonlinear effects in evolution - an ab initio study: A model in which the classical theory of evolution occurs as a special case.

PubMed

Clerc, Daryl G

2016-07-21

An ab initio approach was used to study the molecular-level interactions that connect gene-mutation to changes in an organism׳s phenotype. The study provides new insights into the evolutionary process and presents a simplification whereby changes in phenotypic properties may be studied in terms of the binding affinities of the chemical interactions affected by mutation, rather than by correlation to the genes. The study also reports the role that nonlinear effects play in the progression of organs, and how those effects relate to the classical theory of evolution. Results indicate that the classical theory of evolution occurs as a special case within the ab initio model - a case having two attributes. The first attribute: proteins and promoter regions are not shared among organs. The second attribute: continuous limiting behavior exists in the physical properties of organs as well as in the binding affinity of the associated chemical interactions, with respect to displacements in the chemical properties of proteins and promoter regions induced by mutation. Outside of the special case, second-order coupling contributions are significant and nonlinear effects play an important role, a result corroborated by analyses of published activity levels in binding and transactivation assays. Further, gradations in the state of perfection of an organ may be small or large depending on the type of mutation, and not necessarily closely-separated as maintained by the classical theory. Results also indicate that organs progress with varying degrees of interdependence, the likelihood of successful mutation decreases with increasing complexity of the affected chemical system, and differences between the ab initio model and the classical theory increase with increasing complexity of the organism. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

Maximum wind radius estimated by the 50 kt radius: improvement of storm surge forecasting over the western North Pacific

NASA Astrophysics Data System (ADS)

Takagi, Hiroshi; Wu, Wenjie

2016-03-01

Even though the maximum wind radius (Rmax) is an important parameter in determining the intensity and size of tropical cyclones, it has been overlooked in previous storm surge studies. This study reviews the existing estimation methods for Rmax based on central pressure or maximum wind speed. These over- or underestimate Rmax because of substantial variations in the data, although an average radius can be estimated with moderate accuracy. As an alternative, we propose an Rmax estimation method based on the radius of the 50 kt wind (R50). Data obtained by a meteorological station network in the Japanese archipelago during the passage of strong typhoons, together with the JMA typhoon best track data for 1990-2013, enabled us to derive the following simple equation, Rmax = 0.23 R50. Application to a recent strong typhoon, the 2015 Typhoon Goni, confirms that the equation provides a good estimation of Rmax, particularly when the central pressure became considerably low. Although this new method substantially improves the estimation of Rmax compared to the existing models, estimation errors are unavoidable because of fundamental uncertainties regarding the typhoon's structure or insufficient number of available typhoon data. In fact, a numerical simulation for the 2013 Typhoon Haiyan as well as 2015 Typhoon Goni demonstrates a substantial difference in the storm surge height for different Rmax. Therefore, the variability of Rmax should be taken into account in storm surge simulations (e.g., Rmax = 0.15 R50-0.35 R50), independently of the model used, to minimize the risk of over- or underestimating storm surges. The proposed method is expected to increase the predictability of major storm surges and to contribute to disaster risk management, particularly in the western North Pacific, including countries such as Japan, China, Taiwan, the Philippines, and Vietnam.

A Positive Move: 12th Annual College M&O Cost Study

ERIC Educational Resources Information Center

Agron, Joe

2006-01-01

Colleges placed more of an emphasis on maintenance and operations (M&O) this school year by increasing the amount spent on M&O as a percentage of total budget. According to "American School & University's" 12th annual College Maintenance and Operations Cost Study, spending on M&O as a percentage of total college budget increased to 11 percent from…

Elastic properties of fcc Fe-Mn-X (X = Cr, Co, Ni, Cu) alloys studied by the combinatorial thin film approach and ab initio calculations.

PubMed

Reeh, S; Kasprzak, M; Klusmann, C D; Stalf, F; Music, D; Ekholm, M; Abrikosov, I A; Schneider, J M

2013-06-19

The elastic properties of fcc Fe-Mn-X (X = Cr, Co, Ni, Cu) alloys with additions of up to 8 at.% X were studied by combinatorial thin film growth and characterization and by ab initio calculations using the disordered local moments (DLM) approach. The lattice parameter and Young's modulus values change only marginally with X. The calculations and experiments are in good agreement. We demonstrate that the elastic properties of transition metal alloyed Fe-Mn can be predicted by the DLM model.

Ab initio study of C + H3+ reactions

NASA Technical Reports Server (NTRS)

Talbi, D.; DeFrees, D. J.

1991-01-01

The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.

Transfer matrix approach to electron transport in monolayer MoS2/MoO x heterostructures

NASA Astrophysics Data System (ADS)

Li, Gen

2018-05-01

Oxygen plasma treatment can introduce oxidation into monolayer MoS2 to transfer MoS2 into MoO x , causing the formation of MoS2/MoO x heterostructures. We find the MoS2/MoO x heterostructures have the similar geometry compared with GaAs/Ga1‑x Al x As semiconductor superlattice. Thus, We employ the established transfer matrix method to analyse the electron transport in the MoS2/MoO x heterostructures with double-well and step-well geometries. We also considere the coupling between transverse and longitudinal kinetic energy because the electron effective mass changes spatially in the MoS2/MoO x heterostructures. We find the resonant peaks show red shift with the increasing of transverse momentum, which is similar to the previous work studying the transverse-momentum-dependent transmission in GaAs/Ga1‑x Al x As double-barrier structure. We find electric field can enhance the magnitude of peaks and intensify the coupling between longitudinal and transverse momentums. Moreover, higher bias is applied to optimize resonant tunnelling condition to show negative differential effect can be observed in the MoS2/MoO x system.

Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface.

PubMed

Cao, Jianwei; Zhang, Zhijun; Zhang, Chunfang; Bian, Wensheng; Guo, Yin

2011-01-14

Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

The study of molecular spectroscopy by ab initio methods

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1991-01-01

This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

Surface structure of bulk 2H-MoS2(0001) and exfoliated suspended monolayer MoS2: A selected area low energy electron diffraction study

NASA Astrophysics Data System (ADS)

Dai, Zhongwei; Jin, Wencan; Grady, Maxwell; Sadowski, Jerzy T.; Dadap, Jerry I.; Osgood, Richard M.; Pohl, Karsten

2017-06-01

We have used selected area low energy electron diffraction intensity-voltage (μLEED-IV) analysis to investigate the surface structure of crystalline 2H molybdenum disulfide (MoS2) and mechanically exfoliated and suspended monolayer MoS2. Our results show that the surface structure of bulk 2H-MoS2 is distinct from its bulk and that it has a slightly smaller surface relaxation at 320 K than previously reported at 95 K. We concluded that suspended monolayer MoS2 shows a large interlayer relaxation compared to the MoS2 sandwich layer terminating the bulk surface. The Debye temperature of MoS2 was concluded to be about 600 K, which agrees with a previous theoretical study. Our work has shown that the dynamical μLEED-IV analysis performed with a low energy electron microscope (LEEM) is a powerful technique for determination of the local atomic structures of currently extensively studied two-dimensional (2-D) materials.

Surface structure of bulk 2H-MoS 2 (0001) and exfoliated suspended monolayer MoS 2 : A selected area low energy electron diffraction study

DOE PAGES

Dai, Zhongwei; Jin, Wencan; Grady, Maxwell; ...

2017-02-10

Here, we used selected area low energy electron diffraction intensity-voltage (μLEED-IV) analysis to investigate the surface structure of crystalline 2H molybdenum disulfide (MoS 2) and mechanically exfoliated and suspended monolayer MoS 2. Our results show that the surface structure of bulk 2H-MoS 2 is distinct from its bulk and that it has a slightly smaller surface relaxation at 320 K than previously reported at 95 K. We concluded that suspended monolayer MoS 2 shows a large interlayer relaxation compared to the MoS 2 sandwich layer terminating the bulk surface. The Debye temperature of MoS 2 was concluded to be aboutmore » 600 K, which agrees with a previous theoretical study. Our work has shown that the dynamical μLEED-IV analysis performed with a low energy electron microscope (LEEM) is a powerful technique for determination of the local atomic structures of currently extensively studied two-dimensional (2-D) materials.« less

Charge disproportionation in tetragonal La2MoO5, a small band gap semiconductor influenced by direct Mo-Mo bonding.

PubMed

Colabello, Diane M; Camino, Fernando E; Huq, Ashfia; Hybertsen, Mark; Khalifah, Peter G

2015-01-28

The structure of the novel compound La2MoO5 has been solved from powder X-ray and neutron diffraction data and belongs to the tetragonal space group P4/m (no. 83) with a = 12.6847(3) Å and c = 6.0568(2) Å and with Z = 8. It consists of equal proportions of bioctahedral (Mo2O10) and square prismatic (Mo2O8) dimers, both of which contain direct Mo-Mo bonds and are arranged in 1D chains. The Mo-Mo bond length in the Mo2O10 dimers is 2.684(8) Å, while there are two types of Mo2O8 dimers with Mo-Mo bonds lengths of 2.22(2) and 2.28(2) Å. Although the average Mo oxidation state in La2MoO5 is 4+, the very different Mo-Mo distances reflect the fact that the Mo2O10 dimers contain only Mo(5+) (d(1)), while the prismatic Mo2O8 dimers only contain Mo(3+) (d(3)), a result directly confirmed by density function theory calculations. This is due to the complete disproportionation of Mo(4+), a phenomenon which has not previously been observed in solid-state compounds. La2MoO5 is diamagnetic, behavior which is not expected for a nonmetallic transition-metal oxide whose cation sites have an odd number of d-electrons. The resistivity displays the Arrhenius-type activated behavior expected for a semiconductor with a band gap of 0.5 eV, exhibiting an unusually small transport gap relative to other diamagnetic oxides. Diffuse reflectance studies indicate that La2MoO5 is a rare example of a stable oxide semiconductor with strong infrared absorbance. It is shown that the d-orbital splitting associated with the Mo2O8 and Mo2O10 dimeric units can be rationalized using simple molecular orbital bonding concepts.

Single crystal structure and SHG of defect pyrochlores CsB{sup V}MoO{sub 6} (B{sup V}=Nb,Ta)

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

Fukina, D.G., E-mail: dianafuk@yandex.ru; Suleimanov, E.V.; Yavetskiy, R.P.

2016-09-15

The crystal structure and non-linear optical properties of CsNbMoO{sub 6} and CsTaMoO{sub 6} defect pyrochlores have been studied. The single crystals of these compounds grown by the flux method possess an octahedral faceting and reach up to 50 µm in size. The crystal structures of CsB{sup V}MoO{sub 6} (B{sup V}=Nb, Ta) were investigated by X-ray diffraction method. Both compounds crystallize in the cubic symmetry with noncentrosymmetric space group F-43m. The second harmonic generation of CsNbMoO{sub 6} and CsTaMoO{sub 6}was found to be 1.6×10{sup −2} and 8.5×10{sup −4} of lithium niobate, correspondingly. It has been determined that distortions of [MO{sub 6}]more » polyhedra (M=Nb, Ta, Mo) as well as polarizability and covalency of Nb–O and Ta–O bonds have a great effect on the second harmonic generation. - Highlights: • CsNbMoO{sub 6} and CsTaMoO{sub 6} homogeneous single crystals have been grown. • The crystal structure of CsTaMoO{sub 6} has been studied. • Nonlinear optical properties of CsNbMoO{sub 6} and CsTaMoO{sub 6} have been found. • The microscopic origin of the second harmonic generation (SHG) response have been identified.« less

First-principles study of the surface properties of U-Mo system

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

Mei, Zhi-Gang; Liang, Linyun; Yacout, Abdellatif M.

U-Mo alloys are promising fuels for future high-performance research reactors with low enriched uranium. Surface properties, such as surface energy, are important inputs for mesoscale simulations (e.g., phase field method) of fission gas bubble behaviors in irradiated nuclear fuels. The lack of surface energies of U-Mo alloys prevents an accurate modeling of the morphology of gas bubbles and gas bubble-induced fuel swelling. To this end, we study the surface properties of U-Mo system, including bcc Mo, alpha-U, gamma-U, and gamma U-Mo alloys. All surfaces up to a maximum Miller index of three and two are calculated for cubic Mo andmore » gamma-U and non-cubic alpha-U, respectively. The equilibrium crystal shapes of bcc Mo, alpha-U and gamma-U are constructed using the calculated surface energies. The dominant surface orientations and the area fraction of each facet are determined from the constructed equilibrium crystal shape. The disordered gamma U-Mo alloys are simulated using the Special Quasirandom Structure method. The (1 1 0) and (1 0 0) surface energies of gamma U-7Mo and U-10Mo alloys are predicted to lie between those of gamma-U and bcc Mo, following a linear combination of the two constituents' surface energies. To better compare with future measurements of surface energies, the area fraction weighted surface energies of alpha-U, gamma-U and gamma U-7Mo and U-10Mo alloys are also predicted. (C) 2017 Published by Elsevier B.V.« less

Facile synthesis of high surface area molybdenum nitride and carbide

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

Roy, Aaron; Serov, Alexey; Artyushkova, Kateryna

2015-08-15

The synthesis of high surface area γ-Mo{sub 2}N and α-Mo{sub 2}C is reported (116 and 120 m{sup 2}/g) without the temperature programmed reduction of MoO{sub 3}. γ-Mo{sub 2}N was prepared in an NH{sub 3}-free synthesis using forming gas (7 at% H{sub 2}, N{sub 2}-balance) as the reactive atmosphere. Three precursors were studied ((NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}·4H{sub 2}O, (NH{sub 4}){sub 2} Mg(MoO{sub 4}){sub 2}, and MgMoO{sub 4}) along with the sacrificial support method (SSM) as a means of reducing the particle size of Mo{sub 2}N and Mo{sub 2}C. In situ X-ray diffraction (XRD) studies were carried out to identify reactionmore » intermediates, the temperature at which various intermediates form, and the average domain size of the Mo{sub 2}N products. Materials were synthesized in bulk and further characterized by XRD, HRTEM, XPS, and BET. - Highlights: • Facile synthesis of γ-Mo2N and α-Mo2C with surface area exceeding 100 m{sup 2}/g. • Sacrificial support method was used to achieve these high surface areas. • Materials can serve as catalysts or supports in (electro)chemical processes.« less

Ni-Doping Effects on Oxygen Removal from an Orthorhombic Mo 2C (001) Surface: A Density Functional Theory Study

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

Zhou, Mingxia; Cheng, Lei; Choi, Jae-Soon

Density functional theory (DFT) calculations were used in this paper to investigate the effect of Ni dopants on the removal of chemisorbed oxygen (O*) from the Mo-terminated (T Mo) and C-terminated (T C) Mo 2C(001) surfaces. The removal of adsorbed oxygen from the catalytic site is essential to maintain the long-term activity and selectivity of the carbide catalysts in the deoxygenation process related to bio-oil stabilization and upgrading. In this contribution, the computed reaction energetics and reaction barriers of O* removal were compared among undoped and Ni-doped Mo 2C(001) surfaces. The DFT calculations indicate that selected Ni-doped surfaces such asmore » Ni adsorbed on T Mo and T C Mo 2C(001) surfaces enable weaker binding of important reactive intermediates (O*, OH*) compared to the undoped counterparts, which is beneficial for the O* removal from the catalyst surface. This study thus confirms the promoting effect of the Ni dopant on O* removal reaction on the T Mo Mo 2C(001) and T C Mo 2C(001) surfaces. Finally, this computational prediction has been confirmed by the temperature-programmed reduction profiles of Mo 2C and Ni-doped Mo 2C catalysts, which had been passivated and stored in an oxygen environment.« less

Ni-Doping Effects on Oxygen Removal from an Orthorhombic Mo 2C (001) Surface: A Density Functional Theory Study

DOE PAGES

Zhou, Mingxia; Cheng, Lei; Choi, Jae-Soon; ...

2017-12-22

Density functional theory (DFT) calculations were used in this paper to investigate the effect of Ni dopants on the removal of chemisorbed oxygen (O*) from the Mo-terminated (T Mo) and C-terminated (T C) Mo 2C(001) surfaces. The removal of adsorbed oxygen from the catalytic site is essential to maintain the long-term activity and selectivity of the carbide catalysts in the deoxygenation process related to bio-oil stabilization and upgrading. In this contribution, the computed reaction energetics and reaction barriers of O* removal were compared among undoped and Ni-doped Mo 2C(001) surfaces. The DFT calculations indicate that selected Ni-doped surfaces such asmore » Ni adsorbed on T Mo and T C Mo 2C(001) surfaces enable weaker binding of important reactive intermediates (O*, OH*) compared to the undoped counterparts, which is beneficial for the O* removal from the catalyst surface. This study thus confirms the promoting effect of the Ni dopant on O* removal reaction on the T Mo Mo 2C(001) and T C Mo 2C(001) surfaces. Finally, this computational prediction has been confirmed by the temperature-programmed reduction profiles of Mo 2C and Ni-doped Mo 2C catalysts, which had been passivated and stored in an oxygen environment.« less

Fate and Transport of Molybdenum Disulfide Nanomaterials in Sand Columns

PubMed Central

Lanphere, Jacob D.; Luth, Corey J.; Guiney, Linda M.; Mansukhani, Nikhita D.; Hersam, Mark C.; Walker, Sharon L.

2015-01-01

Abstract Research and development of two-dimensional transition metal dichalcogenides (TMDC) (e.g., molybdenum disulfide [MoS2]) in electronic, optical, and catalytic applications has been growing rapidly. However, there is little known regarding the behavior of these particles once released into aquatic environments. Therefore, an in-depth study regarding the fate and transport of two popular types of MoS2 nanomaterials, lithiated (MoS2-Li) and Pluronic PF-87 dispersed (MoS2-PL), was conducted in saturated porous media (quartz sand) to identify which form would be least mobile in aquatic environments. The electrokinetic properties and hydrodynamic diameters of MoS2 as a function of ionic strength and pH were determined using a zeta potential analyzer and dynamic light scattering techniques. Results suggest that the stability is significantly decreased beginning at 10 and 31.6 mM KCl, for MoS2-PL and MoS2-Li, respectively. Transport study results from breakthrough curves, column dissections, and release experiments suggest that MoS2-PL exhibits a greater affinity to be irreversibly bound to quartz surfaces as compared with the MoS2-Li at a similar ionic strength. Derjaguin–Landau–Verwey–Overbeek theory was used to help explain the unique interactions between the MoS2-PL and MoS2-Li surfaces between particles and with the quartz collectors. Overall, the results suggest that the fate and transport of MoS2 is dependent on the type of MoS2 that enters the environment, where MoS2-PL will be least mobile and more likely be deposited in porous media from pluronic–quartz interactions, whereas MoS2-Li will travel greater distances and have a greater tendency to be remobilized in sand columns. PMID:25741176

Determination of band alignment at two-dimensional MoS2/Si van der Waals heterojunction

NASA Astrophysics Data System (ADS)

Goel, Neeraj; Kumar, Rahul; Mishra, Monu; Gupta, Govind; Kumar, Mahesh

2018-06-01

To understand the different mechanism occurring at the MoS2-silicon interface, we have fabricated a MoS2/Si heterojunction by exfoliating MoS2 on top of the silicon substrate. Raman spectroscopy and atomic force microscopy (AFM) measurement expose the signature of few-layers in the deposited MoS2 flake. Herein, the temperature dependence of the energy barrier and carrier density at the MoS2/Si heterojunction has been extensively investigated. Furthermore, to study band alignment at the MoS2/Si interface, we have calculated a valence band offset of 0.66 ± 0.17 eV and a conduction band offset of 0.42 ± 0.17 eV using X-ray and Ultraviolet photoelectron spectroscopy. We determined a type-II band alignment at the interface which is very conducive for the transport of photoexcited carriers. As a proof-of-concept application, we extend our analysis of the photovoltaic behavior of the MoS2/Si heterojunction. This work provides not only a comparative study between MoS2/p-Si and MoS2/n-Si heterojunctions but also paves the way to engineer the properties of the interface for the future integration of MoS2 with silicon.

Heat shock proteins MoSsb1, MoSsz1, and MoZuo1 attenuate MoMkk1-mediated CWI signaling and are important for growth and pathogenicity of Magnaporthe oryzae.

PubMed

Yang, Jie; Liu, Muxing; Liu, Xinyu; Yin, Ziyi; Sun, Yi; Zhang, Haifeng; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

2018-06-05

The mitogen-activated protein (MAP) kinase MoMkk1 governs the cell wall integrity (CWI) pathway in the rice blast fungus Magnaporthe oryzae. To understand the underlying mechanism, we have identified MoSsb1 as one of the MoMkk1-interacting proteins. MoSsb1 is a stress-seventy subfamily B (Ssb) protein homolog, sharing high amino acid sequence homology with the 70-kDa heat shock proteins (Hsp70s). Hsp70 proteins are a family of conserved and ubiquitously expressed chaperones that regulate protein biogenesis by promoting protein folding, preventing protein aggregation and controlling protein degradation. We found that MoSsb1 regulates the synthesis of nascent polypeptide chains and this regulation is achieved by being in complex with other members of heat shock proteins: Hsp70 MoSsz1 and 40-kDa heat shock protein (Hsp40) MoZuo1. MoSsb1 is important for the growth, conidiation and full virulence of the blast fungus and this role is also shared by MoSsz1 and MoZuo1. Importantly, MoSsb1, MoSsz1 and MoZuo1 are all involved in the regulation of the CWI MAP kinase pathway by modulating MoMkk1 biosynthesis. Our studies reveal novel insights into how MoSsb1, MoSsz1 and MoZuo1 affect CWI signaling that is involved in regulating growth, differentiation and virulence of M. oryzae and highlight the conserved functional mechanisms of Hsp proteins in pathogenic fungi.

Anti-site defected MoS2 sheet-based single electron transistor as a gas sensor

NASA Astrophysics Data System (ADS)

Sharma, Archana; Husain, Mushahid; Srivastava, Anurag; Khan, Mohd. Shahid

2018-05-01

To prevent harmful and poisonous CO gas molecules, catalysts are needed for converting them into benign substances. Density functional theory (DFT) calculations have been used to study the adsorption of CO and CO2 gas molecules on the surface of MoS2 monolayer with Mo atom embedded at S-vacancy site (MoS). The strong interaction between Mo metal with pristine MoS2 sheet suggests its strong binding nature. Doping Mo into MoS2 sheet enhances CO and CO2 adsorption strength. The sensing response of MoS-doped MoS2 system to CO and CO2 gas molecules is obtained in the single electron transistor (SET) environment by varying bias voltage. Doping reduces charging energy of the device which results in fast switching of the device from OFF to ON state.

Molybdenum Cycling in Upwelling Sediments: An Example from Namibian Margin Sediments

NASA Astrophysics Data System (ADS)

Arnold, G. L.; Goldhammer, T.; Formolo, M.; Brunner, B.; Ferdelman, T.

2008-12-01

The paleo-redox application of molybdenum (Mo) isotopes is strongly tied to our knowledge of the modern marine Mo cycle. Elemental mass balance indicates that ~47% of the Mo supplied to the oceans is removed to deep sea sediments, leaving the remaining Mo to "near-shore" reducing sediments (1). The Black Sea is likely the best studied reducing environment with regards to Mo isotopes, yet accounts for only a small fraction of the Mo mass balance. The accumulation of Mo in continental margin sediments has been recently re-assessed and may account for a larger fraction of the marine Mo reservoir than previously thought (2). In the presence of sulfide, the molybdate anion is transformed, by the replacement of oxygen with sulfur, to particle reactive oxy-thiomolybdates (3). This is often cited as the mechanism by which Mo removal proceeds in the Black Sea where sulfide concentrations in the water are high. In contrast, in continental margin settings, the removal mechanism is poorly understood, and the extent to which sulfur cycling plays a role remains un-quantified. To better understand removal/cycling processes in a continental margin setting, where sulfide may only be present in the pore waters and not in the water column, Mo was studied in an array of marine settings off the Namibian coast. Surface sediments were collected across a transect from near-shore/high productivity to deep water/low productivity sediments. These sediments were incubated in bag experiments to study the relationship between sulfur and Mo cycling. Molybdenum concentrations in the Namibian sediments range from detrital values at the lowest productivity site to 25 ppm in surface sediments with high productivity. Preliminary results allude to a correlation between sulfate reduction rates and Mo accumulation in these sediments. Detailed studies of Mo, Mo isotopes, other trace metals, and sulfur investigations from both sediment cores and bag experiments will be presented. (1)Bertine and Turekian (1973), Geochim. Cosmochim. Acta 87, 1415. (2)McManus et al. (2006), Geochim. Cosmochim. Acta 70, 4643. (3)Erickson and Helz (2000) Geochim. Cosmochim. Acta 64, 1149.

Enhancement of photodetection characteristics of MoS2 field effect transistors using surface treatment with copper phthalocyanine.

PubMed

Pak, Jinsu; Jang, Jingon; Cho, Kyungjune; Kim, Tae-Young; Kim, Jae-Keun; Song, Younggul; Hong, Woong-Ki; Min, Misook; Lee, Hyoyoung; Lee, Takhee

2015-11-28

Recently, two-dimensional materials such as molybdenum disulfide (MoS2) have been extensively studied as channel materials for field effect transistors (FETs) because MoS2 has outstanding electrical properties such as a low subthreshold swing value, a high on/off ratio, and good carrier mobility. In this study, we characterized the electrical and photo-responsive properties of MoS2 FET when stacking a p-type organic copper phthalocyanine (CuPc) layer on the MoS2 surface. We observed that the threshold voltage of MoS2 FET could be controlled by stacking the CuPc layers due to a charge transfer phenomenon at the interface. Particularly, we demonstrated that CuPc/MoS2 hybrid devices exhibited high performance as a photodetector compared with the pristine MoS2 FETs, caused by more electron-hole pairs separation at the p-n interface. Furthermore, we found the optimized CuPc thickness (∼2 nm) on the MoS2 surface for the best performance as a photodetector with a photoresponsivity of ∼1.98 A W(-1), a detectivity of ∼6.11 × 10(10) Jones, and an external quantum efficiency of ∼12.57%. Our study suggests that the MoS2 vertical hybrid structure with organic material can be promising as efficient photodetecting devices and optoelectronic circuits.

Optical and structural properties of Mo-doped NiTiO3 materials synthesized via modified Pechini methods

NASA Astrophysics Data System (ADS)

Pham, Thanh-Truc; Kang, Sung Gu; Shin, Eun Woo

2017-07-01

In this study, molybdenum (Mo)-doped nickel titanate (NiTiO3) materials were successfully synthesized as a function of Mo content through a modified Pechini method followed by a solvothermal treatment process. Various characterization methods were employed to investigate the optical and structural properties of the materials. XRD patterns clearly showed that the NiTiO3 structure maintained a single phase with no observed crystalline structure transformations, even after the addition of 10 wt.% Mo. In the Raman spectra and XRD patterns, peak positions shifted with a change in Mo content, confirming that the NiTiO3 lattice was doped with Mo. On the other hand, Mo doping of NiTiO3 materials changed their optical properties. DRS-UV demonstrated that the addition of Mo increased photon absorption within the UV region. Relaxation processes were inhibited by Mo doping, which was evident in the PL spectra. Structural properties of the prepared materials were studied via FE-SEM and HR-TEM. The measured surface area increased proportionally with Mo content due to a reduction in grain size of the materials.

Functional thiols as repair and doping agents of defective MoS2 monolayers

NASA Astrophysics Data System (ADS)

Förster, Anja; Gemming, Sibylle; Seifert, Gotthard

2018-06-01

Recent experimental and theoretical studies indicate that thiols (R-SH) can be used to repair sulfur vacancy defects in MoS2 monolayers (MLs). This density functional theory study investigates how the thiol repair mechanism process can be used to dope MoS2 MLs. Fluorinated thiols as well as amine-containing ones are used to p- and n-dope the MoS2 ML, respectively. It is shown that functional groups are only physisorbed on the repaired MoS2 surface. This explains the reversible doping with fluorinated thiols.

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Kubo–Greenwood approach to conductivity in dense plasmas with average atom models

DOE PAGES

Starrett, C. E.

2016-04-13

In this study, a new formulation of the Kubo–Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman–Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman–Evans formula. Again, results based on this expression are in good agreement withmore » ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.« less

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

NASA Astrophysics Data System (ADS)

Autrey, Daniel; Choo, Jaebum; Laane, Jaan

2000-10-01

The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Nuclear shielding constants by density functional theory with gauge including atomic orbitals

NASA Astrophysics Data System (ADS)

Helgaker, Trygve; Wilson, Philip J.; Amos, Roger D.; Handy, Nicholas C.

2000-08-01

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems.

Ab-initio calculations on melting of thorium

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

Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

2016-05-23

Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a{sub 0}){sup 3} and (1.02a{sub 0}){sup 3} and (1.04a{sub 0}){sup 3} increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a{sub 0} = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures asmore » melting point. The melting point of 2100 K is close to the experimental value of 2023 K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.« less

Ab initio study of Pd carbonyls and CO/Pd(110)

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

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

Molecular adsorption properties of CO and H2O on Au-, Cu-, and AuxCuy-doped MoS2 monolayer

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Gökoğlu, Gökhan; Üzengi Aktürk, Olcay

2017-12-01

In this study, we investigate the adsorption properties of Au, Cu, and AuxCuy nanoclusters on MoS2 sheet and the interactions of the adsorbed systems with CO and H2O molecules by using first principles calculations. Results indicate that Au, Cu, or AuxCuy strongly binds to MoS2 monolayer resulting in enhanced chemical activity and sensitivity toward CO and H2O molecules compared to bare MoS2 monolayer. Although both CO and H2O molecules bind weakly to pristine MoS2 monolayer, CO strongly binds to MoS2 sheet in the presence of Au, Cu atoms or AuxCuy clusters. Semiconductor MoS2 monolayer turns into metal upon Au or Cu adsorption. AuxCuy nanocluster adsorption decreases the band gap of MoS2 monolayer acting as a n-type dopant. AuxCuy-doped MoS2 systems have improved adsorption properties for CO and H2O molecules, so the conclusions provided in this study can be useful as a guide for next generation device modeling.

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Cohort profile: the Motorik-Modul Longitudinal Study: physical fitness and physical activity as determinants of health development in German children and adolescents.

PubMed

Wagner, Matthias O; Bös, Klaus; Jekauc, Darko; Karger, Claudia; Mewes, Nadine; Oberger, Jennifer; Reimers, Anne K; Schlenker, Lars; Worth, Annette; Woll, Alexander

2014-10-01

The Motorik-Modul (MoMo) Longitudinal Study aims to contribute to long-term improvement in the health of German children and adolescents by focusing on: (i) the development of physical fitness and physical activity (including period effects); (ii) the individual and physical/social environmental determinants of the development of physical fitness and physical activity; and (iii) the impact of physical fitness and physical activity on the development of physical and mental health. The MoMo Longitudinal Study began with a nationwide representative sample of 4529 children and adolescents who ranged in age from 4-17 years at the study baseline (2003-2006). The first survey wave of the MoMo Longitudinal Study was conducted between 2009 and 2012, with two subsequent survey waves to be conducted between 2014 and 2016 and 2018 and 2020, respectively. The MoMo Longitudinal Study includes a physical fitness test profile, a physical activity questionnaire, and subjective and objective measures of health from the German Health Interview and Examination Survey (KiGGS). Data access is provided on request (alexander.woll@kit.edu). For further information, including a complete list of publications please visit www.motorik-modul.de. Published by Oxford University Press on behalf of the International Epidemiological Association © The Author 2013; all rights reserved.

XAS Study at Mo and Co K-Edges of the Sulfidation of a CoMo / Al2O3 Hydrotreating Catalyst

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

Pichon, C.; Gandubert, A. D.; Legens, C.

2007-02-02

Because of its impact on environment, the removal of sulfur is an indispensable step, called hydrotreatment, in the refining of petroleum. One of the most commonly used hydrotreating catalysts is CoMo-type catalyst which is composed of molybdenum disulfide slabs promoted by cobalt atoms (CoMoS phase) and well dispersed on a high specific area alumina. As far as the highest sulfur content allowed in gasoline and diesel is continually decreasing, more and more efficient and active hydrotreating catalysts are required. In order to optimize the reactivity of the CoMo-type catalyst in hydrotreatment, a better understanding of the processes used to producemore » the active phase (CoMoS slabs) of the catalyst is necessary. The study reported here deals with the sulfiding mechanism of the slabs and the influence of temperature on the phenomenon. Ex situ X-ray absorption spectroscopy (XANES and EXAFS) was used to study the evolution of the structure of CoMo-type catalyst sulfided at various temperatures (from 293 to 873 K). XAS analysis was performed at both molybdenum and cobalt K-edges to obtain a cross-characterization of the sulfidation of the slabs. It evidenced the formation of various compounds, including two molybdenum oxides, MoS3 (or MoS3-like compound) and Co9S8, at specific steps of the sulfiding process. It showed the role of intermediate played by MoS3 (or MoS3-like compound) during the formation of the slabs and the competition between the appearance of promoted slabs (CoMoS phase) and Co9S8. At last, it leaded to the proposal of a mechanism for the sulfidation of the catalyst.« less

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

OPAL: prediction of MoRF regions in intrinsically disordered protein sequences.

PubMed

Sharma, Ronesh; Raicar, Gaurav; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

2018-06-01

Intrinsically disordered proteins lack stable 3-dimensional structure and play a crucial role in performing various biological functions. Key to their biological function are the molecular recognition features (MoRFs) located within long disordered regions. Computationally identifying these MoRFs from disordered protein sequences is a challenging task. In this study, we present a new MoRF predictor, OPAL, to identify MoRFs in disordered protein sequences. OPAL utilizes two independent sources of information computed using different component predictors. The scores are processed and combined using common averaging method. The first score is computed using a component MoRF predictor which utilizes composition and sequence similarity of MoRF and non-MoRF regions to detect MoRFs. The second score is calculated using half-sphere exposure (HSE), solvent accessible surface area (ASA) and backbone angle information of the disordered protein sequence, using information from the amino acid properties of flanks surrounding the MoRFs to distinguish MoRF and non-MoRF residues. OPAL is evaluated using test sets that were previously used to evaluate MoRF predictors, MoRFpred, MoRFchibi and MoRFchibi-web. The results demonstrate that OPAL outperforms all the available MoRF predictors and is the most accurate predictor available for MoRF prediction. It is available at http://www.alok-ai-lab.com/tools/opal/. ashwini@hgc.jp or alok.sharma@griffith.edu.au. Supplementary data are available at Bioinformatics online.

VTVH-MCD study of the Delta nifB Delta nifZ MoFe protein from Azotobacter vinelandii.

PubMed

Cotton, Marcia S; Rupnik, Kresimir; Broach, Robyn B; Hu, Yilin; Fay, Aaron W; Ribbe, Markus W; Hales, Brian J

2009-04-08

NifZ is a member of a series of proteins associated with the maturation of the nitrogenase MoFe protein. An MCD spectroscopic study was undertaken on the Delta nifB Delta nifZ MoFe protein generated in the absence of both NifZ and NifB (deletion of NifB generates an apo-MoFe protein lacking the FeMo cofactor). Results presented here show that, in the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, representing a P-cluster precursor that is electronically identical to the analogous clusters observed in the Delta nifH MoFe protein. These results suggest that the MoFe protein is synthesized in a stepwise fashion where NifZ is specifically required for the formation of the second P-cluster.

Doping effect on monolayer MoS2 for visible light dye degradation - A DFT study

NASA Astrophysics Data System (ADS)

Cheriyan, Silpa; Balamurgan, D.; Sriram, S.

2018-04-01

The electronic and optical properties of, Nitrogen (N), Cobalt (Co), and Co-N co-doped monolayers of MoS2 has been studied by using density functional theory (DFT) for visible light photocatalytic activity. From the calculations, it has been observed that the band gap of monolayer MoS2 has been reduced while doping. However, the band gaps of pristine and N doped MoS2 monolayers only falls in the visible region while for Co and Co-N co-doped systems, the band gap shifted to IR region. The optical calculation also confirms the results. The formation energy values of the doped system reaveal that MoS2 monolayer drops its stability while doping. To evaluate the photocatalytic response, band edge potentials of pristine and N-MoS2 are calculated, and the observed results show that compared to N-doped MoS2 monolayer, pure MoS2 is highly suitable for visible light photocatalytic dye degradation.

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

PubMed

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

A review on ab initio studies of static, transport, and optical properties of polystyrene under extreme conditions for inertial confinement fusion applications

NASA Astrophysics Data System (ADS)

Hu, S. X.; Collins, L. A.; Boehly, T. R.; Ding, Y. H.; Radha, P. B.; Goncharov, V. N.; Karasiev, V. V.; Collins, G. W.; Regan, S. P.; Campbell, E. M.

2018-05-01

Polystyrene (CH), commonly known as "plastic," has been one of the widely used ablator materials for capsule designs in inertial confinement fusion (ICF). Knowing its precise properties under high-energy-density conditions is crucial to understanding and designing ICF implosions through radiation-hydrodynamic simulations. For this purpose, systematic ab initio studies on the static, transport, and optical properties of CH, in a wide range of density and temperature conditions (ρ = 0.1 to 100 g/cm3 and T = 103 to 4 × 106 K), have been conducted using quantum molecular dynamics (QMD) simulations based on the density functional theory. We have built several wide-ranging, self-consistent material-properties tables for CH, such as the first-principles equation of state, the QMD-based thermal conductivity (κQMD) and ionization, and the first-principles opacity table. This paper is devoted to providing a review on (1) what results were obtained from these systematic ab initio studies; (2) how these self-consistent results were compared with both traditional plasma-physics models and available experiments; and (3) how these first-principles-based properties of polystyrene affect the predictions of ICF target performance, through both 1-D and 2-D radiation-hydrodynamic simulations. In the warm dense regime, our ab initio results, which can significantly differ from predictions of traditional plasma-physics models, compared favorably with experiments. When incorporated into hydrocodes for ICF simulations, these first-principles material properties of CH have produced significant differences over traditional models in predicting 1-D/2-D target performance of ICF implosions on OMEGA and direct-drive-ignition designs for the National Ignition Facility. Finally, we will discuss the implications of these studies on the current small-margin ICF target designs using a CH ablator.

Spin-orbit coupled potential energy surfaces and properties using effective relativistic coupling by asymptotic representation.

PubMed

Ndome, Hameth; Eisfeld, Wolfgang

2012-08-14

A new method has been reported recently [H. Ndome, R. Welsch, and W. Eisfeld, J. Chem. Phys. 136, 034103 (2012)] that allows the efficient generation of fully coupled potential energy surfaces (PESs) including derivative and spin-orbit (SO) coupling. The method is based on the diabatic asymptotic representation of the molecular fine structure states and an effective relativistic coupling operator and therefore is called effective relativistic coupling by asymptotic representation (ERCAR). The resulting diabatic spin-orbit coupling matrix is constant and the geometry dependence of the coupling between the eigenstates is accounted for by the diabatization. This approach allows to generate an analytical model for the fully coupled PESs without performing any ab initio SO calculations (except perhaps for the atoms) and thus is very efficient. In the present work, we study the performance of this new method for the example of hydrogen iodide as a well-established test case. Details of the diabatization and the accuracy of the results are investigated in comparison to reference ab initio calculations. The energies of the adiabatic fine structure states are reproduced in excellent agreement with reference ab initio data. It is shown that the accuracy of the ERCAR approach mainly depends on the quality of the underlying ab initio data. This is also the case for dissociation and vibrational level energies, which are influenced by the SO coupling. A method is presented how one-electron operators and the corresponding properties can be evaluated in the framework of the ERCAR approach. This allows the computation of dipole and transition moments of the fine structure states in good agreement with ab initio data. The new method is shown to be very promising for the construction of fully coupled PESs for more complex polyatomic systems to be used in quantum dynamics studies.

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE PAGES

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

2016-05-10

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

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

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Summary of Research/Publications

NASA Technical Reports Server (NTRS)

1997-01-01

Summary of research/publications include:(1) Comment on broadening of water microwave lines by collisions with helium atoms; (2) Calculations of ion-molecule deuterium fractionation reactions involving HD; (3) Ab initio predictions on the rotational spectra of carbon-chain carbene molecules; (4) Theoretical IR spectra of ionized naphthalene; (5) Improved collisional excitation rates for interstellar water; (6) Calculations on the competition between association and reaction for C3H+ + H2; (7) Theoretical infrared spectra of some model polycyclic aromatic hydrocarbons: effect of ionization; (8) Calculations concerning interstellar isomeric abundance ratios for C3H and C3H2; (9) New calculations on the ion-molecule processes C2H2+ + H2 C2H3+ + H and C2H2+ + H2 C2H4+; (10) Anisotropic rigid rotor potential energy function for H2O-H2; (11) A correlated ab initio study of linear carbon-chain radicals CnH (n=2-7); (12) Ab initio characterization of MgCCH, MgCCH+, and MgC2 and pathways to their formation in the interstellar medium; (13) Why HOC+ is detectable in interstellar clouds: The rate of the reaction between HOC+ and H2; (14) A correlated ab initio study of the X 2A 1 and A 2E states of MgCH3; (15) On the stability of interstellar carbon clusters: The rate of the reaction between C3 and O; and (16) The rate of the reaction between CN and C2H2 at interstellar temperatures.

Effects of hydrogen on the structural and optical properties of MoSe2 grown by hot filament chemical vapor deposition

NASA Astrophysics Data System (ADS)

Wang, B. B.; Zhu, M. K.; Levchenko, I.; Zheng, K.; Gao, B.; Xu, S.; Ostrikov, K.

2017-10-01

The role of reactive environment and hydrogen specifically in growth and structure of molybdenum selenide (MoSe2) nanomaterials is presently debated, and it is not clear whether hydrogen can promote the growth of MoSe2 sheets and alter their electronic properties. To find efficient, convenient methods for controlling the nucleation, growth and resultant properties of MoSe2 nanomaterials, MoSe2 nanoflakes were synthesized on silicon substrates by hot filament chemical vapor deposition using molybdenum trioxide and selenium powders in pure hydrogen, nitrogen gases and hydrogen-nitrogen mixtures. The structures and composition of synthesized MoSe2 nanoflakes were studied using the advanced characterization instruments including field emission scanning electron microscopy, micro-Raman spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy and energy dispersive X-ray spectrometry. The analysis of the growth process indicates that hydrogen can improve the formation of MoSe2 nanoflakes and significantly alter their properties due to the high reduction capacity of hydrogen and the creation of more nucleation centers of MoSe2 nanoflakes on the silicon surface. The study of photoluminescent (PL) properties reveals that the MoSe2 nanoflakes can generate a strong PL band at about 631 nm, differently from the plain MoSe2 nanoflakes. The major difference in the PL properties may be related to the edges of MoSe2 nanoflakes. These results can be used to control the growth and structure of MoSe2-based nanomaterials and contribute to the development of advanced MoSe2-based optoelectronic devices.

Molybdenum Isotopic Composition of the Archean Mantle As Inferred from Studies of Komatiites

NASA Astrophysics Data System (ADS)

Greber, N. D.; Puchtel, I. S.; Nagler, T. F.; Mezger, K.

2014-12-01

Molybdenum isotopic composition has been shown to be a powerful tool in studies of planetary processes, e.g. estimating core formation temperatures [1,2]. However, Mo isotope compositions of terrestrial reservoirs are not well constrained. In order to better constrain the Mo isotopic composition of the early Earth's mantle, komatiites from four locations were analyzed for their Mo concentrations and isotopic compositions. Komatiites are particularly appropriate for this type of study because they formed by high degrees of partial melting of the mantle leading to a complete base metal sulfide removal from the residual mantle and the production of sulfur-undersaturated melts and thus a quantitative removal of Mo from the source into the melt. All samples, except for two strongly altered specimens specifically chosen to study the effects of secondary alteration, are very fresh having preserved most of their primary mineralogy. The Mo concentrations in komatiites range from 10 to 120 ng/g. Fresh komatiites have lighter δ98Mo (NIST SRM 3134 = 0.25‰, [3]) than altered samples. The estimated primary Mo isotope compositions of the studied komatiite melts range from 0.02 ± 0.16‰ to 0.19 ± 0.14‰ and are therefore indistinguishable within analytical uncertainty (2SD) from published values for chondritic meteorites (0.09 ± 0.04 ‰; 2SD; [2]) and lighter than the proposed average for Earth's continental crust (0.3 to 0.4‰ [4]). All data combined, although overlapping in errors, show a consistent trend of lighter δ98Mo and lower Mo concentrations in more melt-depleted mantle sources, indicating incompatible behaviour of Mo and preferential mobilization of heavy Mo isotopes during mantle melting. [1] Hin et al. (2013) EPSL, 379 [2] Burkhardt et al. (2014) EPSL, 391 [3] Nägler, et al. (2014) GGR, 38. [4] Voegelin et al. (2014) Lithos, 190-191.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc) 2 ] - (Pc=phthalocyanine) and Dy 4 K 2 ([Dy 4 K 2 O(OtBu) 12 ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H 3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

Investigation on nonlinear optical properties of MoS2 nanoflake, grown on silicon and quartz substrates

NASA Astrophysics Data System (ADS)

Bayesteh, S.; Mortazavi, S. Z.; Reyhani, A.

2018-03-01

In this study, MoS2 was directly synthesized by one-step thermal chemical vapour deposition (TCVD), on different substrates including Si/SiO2 and quartz, using MoO3 and sulfide powders as precursor. The XRD patterns demonstrate the high crystallinity of MoS2 on Si/SiO2 and quartz substrates. SEM confirmed the formation of MoS2 grown on both substrates. According to line width and frequency difference between the E1 2g and A1g in Raman spectroscopy, it is inferred that the MoS2 grown on Si/SiO2 substrate is monolayer and the MoS2 grown on quartz substrate is multilayer. Moreover, by assessment of MoS2 nanoflake band gap via UV-visible analysis, it verified the formation of few layer structures. In addition, the open-aperture and close-aperture Z-scan techniques were employed to study the nonlinear optical properties including nonlinear absorption and nonlinear refraction of the synthesized MoS2. All experiments were performed using a diode laser with a wavelength of 532 nm as light source. The monolayer MoS2 synthesized on Si/SiO2, display considerable two-photon absorption. However, the multilayer MoS2 synthesized on quartz displayed saturable absorption (SA). It is noticeable that both samples demonstrate obvious self-defocusing behaviour.

Study on Tribological Properties of CoCrMo Alloys against Metals and Ceramics as Bearing Materials for Artificial Cervical Disc

NASA Astrophysics Data System (ADS)

Xiang, Dingding; Song, Jian; Wang, Song; Liao, Zhenhua; Liu, Yuhong; Tyagi, Rajnesh; Liu, Weiqiang

2018-02-01

CoCrMo alloys are believed to be a kind of potential material for artificial cervical disc. However, the tribological properties of CoCrMo alloys against different metals and ceramics are not systematically studied. In this study, the tribological behaviors of CoCrMo alloys against metals (316L, Ti6Al4V) and ceramics (Si3N4, ZrO2) were focused under dry friction and 25 wt.% newborn calf serum (NCS)-lubricated conditions using a ball-on-disc apparatus under reciprocating motion. The microstructure, composition and hardness of CoCrMo alloys were characterized using x-ray diffraction, scanning electron microscopy (SEM) and hardness testers, respectively. The contact angles of the CoCrMo alloys with deionized water and 25 wt.% NCS were measured by the OCA contact angle measuring instrument. The maximum wear width, wear depth and wear volume were measured by three-dimensional white light interference. The morphology and the EDX analysis of the wear marks on CoCrMo alloys were examined by SEM to determine the basic mechanism of friction and wear. The dominant wear mechanism in dry friction for CoCrMo alloys against all pairings was severe abrasive wear, accompanied with a lot of material transfer. Under 25 wt.% NCS-lubricated condition, the wear mechanism for CoCrMo alloys against ceramics (Si3N4, ZrO2) was also mainly severe abrasive wear. However, severe abrasive wear and electrochemical corrosion occurred for the CoCrMo-316L pairing under lubrication. Severe abrasive wear, adhesive wear and electrochemical corrosion occurred for the CoCrMo-Ti6Al4V pairing under lubrication. According to the results, the tribological properties of CoCrMo alloys against ceramics were better than those against metals. The CoCrMo-ZrO2 pairing displayed the best tribological behaviors and could be taken as a potential candidate bearing material for artificial cervical disc.

Creep Rupture Analysis and Life Estimation of 1.25Cr-0.5Mo, 2.25Cr-1Mo and Modified 9Cr-1Mo Steel: A Comparative Study

NASA Astrophysics Data System (ADS)

Roy, Prabir Kumar

2018-04-01

This paper highlights a comparative assessment of creep life of 1.25Cr-0.5Mo, 2.25Cr-1Mo and modified 9Cr-1Mo steels based on accelerated creep rupture tests. Creep rupture test data have been analysed and creep life of the above mentioned materials have been assessed using Larson Miller parameter at the stress levels of 60 and 42 MPa for different temperatures. Limiting steam temperatures for minimum design life of 105 h at 42 and 60 MPa for the above mentioned steels have also been calculated. Microstructural studies for the three above mentioned steels are also done.

Gate Tunable Transport in Graphene/MoS₂/(Cr/Au) Vertical Field-Effect Transistors.

PubMed

Nazir, Ghazanfar; Khan, Muhammad Farooq; Aftab, Sikandar; Afzal, Amir Muhammad; Dastgeer, Ghulam; Rehman, Malik Abdul; Seo, Yongho; Eom, Jonghwa

2017-12-28

Two-dimensional materials based vertical field-effect transistors have been widely studied due to their useful applications in industry. In the present study, we fabricate graphene/MoS₂/(Cr/Au) vertical transistor based on the mechanical exfoliation and dry transfer method. Since the bottom electrode was made of monolayer graphene (Gr), the electrical transport in our Gr/MoS₂/(Cr/Au) vertical transistors can be significantly modified by using back-gate voltage. Schottky barrier height at the interface between Gr and MoS₂ can be modified by back-gate voltage and the current bias. Vertical resistance (R vert ) of a Gr/MoS₂/(Cr/Au) transistor is compared with planar resistance (R planar ) of a conventional lateral MoS₂ field-effect transistor. We have also studied electrical properties for various thicknesses of MoS₂ channels in both vertical and lateral transistors. As the thickness of MoS₂ increases, R vert increases, but R planar decreases. The increase of R vert in the thicker MoS₂ film is attributed to the interlayer resistance in the vertical direction. However, R planar shows a lower value for a thicker MoS₂ film because of an excess of charge carriers available in upper layers connected directly to source/drain contacts that limits the conduction through layers closed to source/drain electrodes. Hence, interlayer resistance associated with these layers contributes to planer resistance in contrast to vertical devices in which all layers contribute interlayer resistance.

Role of graphene inter layer on the formation of the MoS2-CZTS interface during growth

NASA Astrophysics Data System (ADS)

Vishwakarma, Manoj; Thota, Narayana; Karakulina, Olesia; Hadermann, Joke; Mehta, B. R.

2018-05-01

The growth of MoS2 layer near the Mo/CZTS interface during sulphurization process can have an impact on back contact cell parameters (series resistance and fill factor) depending upon the thickness or quality of MoS2. This study reports the dependence of the thickness of interfacial MoS2 layer on the growth of graphene at the interface between molybdenum back contact and deposited CZTS layer. The graphene layer reduces the accumulation of Zn/ZnS, Sn/SnO2 and formation of pores near the MoS2-CZTS interface. The use of graphene as interface layer can be potentially useful for improving the quality of Mo/MoS2/CZTS interface.

Elevated Temperature Tensile Tests on DU–10Mo Rolled Foils

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

Schulthess, Jason

2014-09-01

Tensile mechanical properties for uranium-10 wt.% molybdenum (U–10Mo) foils are required to support modeling and qualification of new monolithic fuel plate designs. It is expected that depleted uranium-10 wt% Mo (DU–10Mo) mechanical behavior is representative of the low enriched U–10Mo to be used in the actual fuel plates, therefore DU-10Mo was studied to simplify material processing, handling, and testing requirements. In this report, tensile testing of DU-10Mo fuel foils prepared using four different thermomechanical processing treatments were conducted to assess the impact of foil fabrication history on resultant tensile properties.

Phase relations in the system CuMoS

USGS Publications Warehouse

Dawei, H.; Chang, L.L.Y.; Knowles, C.R.

1990-01-01

Phase relations in the system CuMoS were studied in the temperature range 500-1000 ??C by using the conventional sealed, evacuated glass capsule technique. Reflected-light microscopy, X-ray powder diffraction and electron microprobe analysis were used for phase characterization. The chevrel-type phase, CuxMo3S4, is stable above 600??C, and forms equilibrium assemblages with the cubic Cu2S solid solution, copper, molybdenum, Mo2S3 and MoS2. Its solid solution ranges from Cu1.50-2.00Mo3S4 at 700??C to Cu1.22-2.00Mo3S4 at 1000 ??C. ?? 1990.

Impact of reduced graphene oxide on MoS{sub 2} grown by sulfurization of sputtered MoO{sub 3} and Mo precursor films

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

Pacley, Shanee, E-mail: shanee.pacley@us.af.mil; Brausch, Jacob; Beck-Millerton, Emory

2016-07-15

Monolayer molybdenum disulfide (MoS{sub 2}), a two dimensional semiconducting dichalcogenide material with a bandgap of 1.8–1.9 eV, has demonstrated promise for future use in field effect transistors and optoelectronics. Various approaches have been used for MoS{sub 2} processing, the most common being chemical vapor deposition. During chemical vapor deposition, precursors such as Mo, MoO{sub 3}, and MoCl{sub 5} have been used to form a vapor reaction with sulfur, resulting in thin films of MoS{sub 2}. Currently, MoO{sub 3} ribbons and powder, and MoCl{sub 5} powder have been used. However, the use of ribbons and powder makes it difficult to growmore » large area-continuous films. Sputtering of Mo is an approach that has demonstrated continuous MoS{sub 2} film growth. In this paper, the authors compare the structural properties of MoS{sub 2} grown by sulfurization of pulse vapor deposited MoO{sub 3} and Mo precursor films. In addition, they have studied the effects that reduced graphene oxide (rGO) has on MoS{sub 2} structure. Reports show that rGO increases MoS{sub 2} grain growth during powder vaporization. Herein, the authors report a grain size increase for MoS{sub 2} when rGO was used during sulfurization of both sputtered Mo and MoO{sub 3} precursors. In addition, our transmission electron microscopy results show a more uniform and continuous film growth for the MoS{sub 2} films produced from Mo when compared to the films produced from MoO{sub 3}. Atomic force microscopy images further confirm this uniform and continuous film growth when Mo precursor was used. Finally, x-ray photoelectron spectroscopy results show that the MoS{sub 2} films produced using both precursors were stoichiometric and had about 7–8 layers in thickness, and that there was a slight improvement in stoichiometry when rGO was used.« less

Charge Disproportionation in Tetragonal La 2MoO 5 , a Small Band Gap Semiconductor Influenced by Direct Mo–Mo Bonding

DOE PAGES

Colabello, Diane M.; Camino, Fernando E.; Huq, Ashfia; ...

2014-12-31

The structure of the novel compound La 2MoO 5 has been solved from powder X-ray and neutron diffraction data and belongs to the tetragonal space group P4/m (no. 83) with a = 12.6847(3) Å and c = 6.0568(2) Å and with Z = 8. It consists of equal proportions of bioctahedral (Mo 2O 10) and square prismatic (Mo 2O 8) dimers, both of which contain direct Mo-Mo bonds and are arranged in 1D chains. The Mo-Mo bond length in the Mo 2O 10dimers is 2.684(8) Å, while there are two types of Mo 2O 8 dimers with Mo-Mo bonds lengthsmore » of 2.22(2) and 2.28(2) Å. Although the average Mo oxidation state in La 2MoO 5 is 4+, the very different Mo-Mo distances reflect the fact that the Mo 2O 10 dimers contain only Mo5+ (d(1)), while the prismatic Mo2O8 dimers only contain Mo 3+ (d 3), a result directly confirmed by density function theory calculations. This is due to the complete disproportionation of Mo 4+, a phenomenon which has not previously been observed in solid-state compounds. La 2MoO 5 is diamagnetic, behavior which is not expected for a nonmetallic transition-metal oxide whose cation sites have an odd number of d-electrons. The resistivity displays the Arrhenius-type activated behavior expected for a semiconductor with a band gap of 0.5 eV, exhibiting an unusually small transport gap relative to other diamagnetic oxides. Diffuse reflectance studies indicate that La 2MoO 5 is a rare example of a stable oxide semiconductor with strong infrared absorbance. Lastly, we show that the d-orbital splitting associated with the Mo 2O 8 and Mo 2O 10 dimeric units can be rationalized using simple molecular orbital bonding concepts.« less

Conformational properties and electronic structure of tetrahydrotetrazines studied by photoelectron spectroscopy and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Muchall, Heidi M.; Rademacher, Paul

1997-11-01

The photoelectron (PE) spectra of tetrahydro-1,2,3,4-tetrazines 1 and 2 and tetrahydro-1,2,4,5-tetrazines 3-5 have been recorded and their conformations have been investigated by ab initio SCF calculations. While v-tetrazine 2 is planar, tetrazines 1 and 3-5 each possess two low-energy conformations, according to ab initio HF and Becke3LYP methods. Attempts to assign ionization potentials to molecular orbitals obtained by semiempirical PM3 calculations indicate that this method is not suited for the compounds studied. Best results were obtained when the ab initio hybrid method Becke3LYP of the density functional theory was employed. Two conformers of 1 and 3-5 are present in the gas phase and their PE spectra are superimposed one upon the other. For v-tetrazine 1, ionizations arising from half-chair and unsymmetrical boat conformers have similar energies and cannot be separated in the PE spectrum. For s-tetrazine 3, on the other hand, the spectrum clearly shows different ionizations of both half-chairs, 3ee and 3ae.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

NASA Astrophysics Data System (ADS)

Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.

PubMed

Wang, Linjun; Long, Run; Prezhdo, Oleg V

2015-04-01

Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.

The C4H radical and the diffuse interstellar bands. An ab initio study

NASA Technical Reports Server (NTRS)

Kolbuszewski, Marcin

1994-01-01

An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

Optimization of the dissolution of molybdenum disks. FY-16 results

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

Tkac, Peter; Rotsch, David A.; Chemerisov, Sergey D.

2016-09-01

Argonne National Laboratory is providing technical development assistance to NorthStar Medical Technologies LLC in its pursuit of two pathways for production of molybdenum-99: the 98Mo(n,γ) 99Mo reaction and the photonuclear reaction, 100Mo(γ,n) 99Mo. Processing of irradiated targets, from either production mode, requires dissolution of the target material in H 2O 2 followed by a concentration step, addition of ferric ion to precipitate impurities, and conversion of the final solution to 5M potassium hydroxide solution of potassium molybdate. Currently, NorthStar is using pressed and sintered Mo disks as targets. Several options are being considered for the design of Mo targets formore » the production of 99Mo using the (γ,n) reaction. In the current design, the target holder contains a series of sintered Mo disks lined up perpendicular to two incident electron beams, one entering from each side of the target stack. In this configuration, the front-most disks absorb most of the heat from the electron beam and need to be thinner to allow for better cooling, while the middle of the target can be thicker. Distribution of the total mass of Mo allows for larger masses of Mo material and thus larger production batches of 99Mo. A limitation of the sintering approach is the production of very thin disks. Recent advances in 3D printing allow for much thinner target components can be achieved than when the traditional press-and-sinter approach is used. We have demonstrated that several factors can play important roles in dissolution behavior: particle size of Mo metal used for production of targets, sintering conditions, degree of open porosity, and thickness of the sintered Mo targets. Here we report experimental results from studies of small-scale dissolution of sintered Mo disks fabricated from various recycled and commercial Mo materials, and dissolution of 3D-printed Mo disks that were fabricated by Oak Ridge National Laboratory (ORNL). We also report on large-scale dissolution studies with 600 g batches of sintered Mo disks.« less

Ab initio study on electronically excited states of lithium isocyanide, LiNC

NASA Astrophysics Data System (ADS)

Yasumatsu, Hisato; Jeung, Gwang-Hi

2014-01-01

The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.

FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes.

PubMed

Melikova, S M; Rutkowski, K S; Rospenk, M

2017-09-05

The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T~118-158K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane. Copyright © 2017 Elsevier B.V. All rights reserved.

An Ab Initio Study of Alkali-C60 Complexes

NASA Astrophysics Data System (ADS)

Frick, Nathan; Hira, A. S.; Ray, A. K.

2003-03-01

We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).

X-ray absorption and Raman spectroscopy studies of molybdenum environments in borosilicate waste glasses

NASA Astrophysics Data System (ADS)

McKeown, David A.; Gan, Hao; Pegg, Ian L.

2017-05-01

Mo-containing high-level nuclear waste borosilicate glasses were investigated as part of an effort to improve Mo loading while avoiding yellow phase crystallization. Previous work showed that additions of vanadium decrease yellow phase formation and increases Mo solubility. X-ray absorption spectroscopy (XAS) and Raman spectroscopy were used to characterize Mo environments in HLW borosilicate glasses and to investigate possible structural relationships between Mo and V. Mo XAS spectra for the glasses indicate isolated tetrahedral Mo6+O4 with Mo-O distances near 1.75 Å. V XANES indicate tetrahedral V5+O4 as the dominant species. Raman spectra show composition dependent trends, where Mo-O symmetrical stretch mode frequencies (ν1) are sensitive to the mix of alkali and alkaline earth cations, decreasing by up to 10 cm-1 for glasses that change from Li+ to Na+ as the dominant network-modifying species. This indicates that MoO4 tetrahedra are isolated from the borosilicate network and are surrounded, at least partly, by Na+ and Li+. Secondary ν1 frequency effects, with changes up to 7 cm-1, were also observed with increasing V2O5 and MoO3 content. These secondary trends may indicate MoO4-MoO4 and MoO4-VO4 clustering, suggesting that V additions may stabilize Mo in the matrix with respect to yellow phase formation.

4-d magnetism: Electronic structure and magnetism of some Mo-based alloys

NASA Astrophysics Data System (ADS)

Liu, Yong; Bose, S. K.; Kudrnovský, J.

2017-02-01

We report results of a first-principles density-functional study of alloys of the 4 d -element Mo with group IV elements Si, Ge and Sn in zinc blende (ZB) and rock salt (RS) structures. The study was motivated by a similar study of ours based on the 4 d -element Tc, which showed the presence of half-metallic states with integer magnetic moment (1μB) per formula unit in TcX (X=C, Si, Ge) alloys. The calculated Curie temperatures for the ferromagnetic (FM) phases were low, around or less than 300 K. Searching for the possibility of 4 d -based alloys with higher Curie temperatures we have carried out the study involving the elements Mo, Ru and Rh. Among these the most promising case appears to be that involving the element Mo. Among the MoX (X=Si, Ge, Sn) alloys in ZB and RS structures, both MoGe and MoSn in ZB structures are found to possess an integer magnetic moment of 2μB per formula unit. ZB MoSn can be classified as a marginal/weak half-metal or a spin gapless semiconductor, while ZB MoGe would be best described as a gapless magnetic semiconductor. The calculated Curie temperatures are in the range 300-700 K. Considering the theoretical uncertainty in the band gaps due not only to the treatment of exchange and correlation effects, but density functional theory itself, these classifications may change somewhat, but both merit investigation from the viewpoint of potential spintronic application. Based on their higher Curie temperatures, Mo-based alloys would serve such purpose better than the previously reported Tc-based ones.

Differentiation and activation of equine monocyte-derived dendritic cells are not correlated with CD206 or CD83 expression

PubMed Central

Moyo, Nathifa A; Marchi, Emanuele; Steinbach, Falko

2013-01-01

Dendritic cells (DC) are the main immune mediators inducing primary immune responses. DC generated from monocytes (MoDC) are a model system to study the biology of DC in vitro, as they represent inflammatory DC in vivo. Previous studies on the generation of MoDC in horses indicated that there was no distinct difference between immature and mature DC and that the expression profile was distinctly different from humans, where CD206 is expressed on immature MoDC whereas CD83 is expressed on mature MoDC. Here we describe the kinetics of equine MoDC differentiation and activation, analysing both phenotypic and functional characteristics. Blood monocytes were first differentiated with equine granulocyte–macrophage colony-stimulating factor and interleukin-4 generating immature DC (iMoDC). These cells were further activated with a cocktail of cytokines including interferon-γ) but not CD40 ligand to obtain mature DC (mMoDC). To determine the expression of a broad range of markers for which no monoclonal antibodies were available to analyse the protein expression, microarray and quantitative PCR analysis were performed to carry out gene expression analysis. This study demonstrates that equine iMoDC and mMoDC can be distinguished both phenotypically and functionally but the expression pattern of some markers including CD206 and CD83 is dissimilar to the human system. PMID:23461413

Mechanistic studies on the reactions of PhS(-) or [MoS(4)](2)(-) with [M(4)(SPh)(10)](2)(-) (M = Fe or Co).

PubMed

Cui, Zhen; Henderson, Richard A

2002-08-12

Kinetic studies, using stopped-flow spectrophotometry, on the reactions of [M(4)(SPh)(10)](2)(-) (M = Fe or Co) with PhS(-) to form [M(SPh)(4)](2)(-) are described, as are the reactions between [M(4)(SPh)(10)](2)(-) and [MoS(4)](2)(-) to form [S(2)MoS(2)Fe(SPh)(2)](2)(-) or [S(2)MoS(2)CoS(2)MoS(2)](2)(-). The kinetics of the reactions with PhS(-) are consistent with an initial associative substitution mechanism involving attack of PhS(-) at one of the tetrahedral M sites of [M(4)(SPh)(10)](2)(-) to form [M(4)(SPh)(11)](3)(-). Subsequent or concomitant cleavage of a micro-SPh ligand, at the same M, initiates a cascade of rapid reactions which result ultimately in the complete rupture of the cluster and formation of [M(SPh)(4)](2)(-). The kinetics of the reaction between [M(4)(SPh)(10)](2)(-) and [MoS(4)](2)(-) indicate an initial dissociative substitution mechanism at low concentrations of [MoS(4)](2)(-), in which rate-limiting dissociation of a terminal thiolate from [M(4)(SPh)(10)](2)(-) produces [M(4)(SPh)(9)](-) and the coordinatively unsaturated M site is rapidly attacked by a sulfido group of [MoS(4)](2)(-). It is proposed that subsequent chelation of the MoS(4) ligand results in cleavage of an M-micro-SPh bond, initiating a cascade of reactions which lead to the ultimate break-up of the cluster and formation of the products, [S(2)MoS(2)Fe(SPh)(2)](2)(-) or [S(2)MoS(2)CoS(2)MoS(2)](2)(-). With [Co(4)(SPh)(10)](2)(-), at higher concentrations of [MoS(4)](2)(-), a further substitution pathway is evident which exhibits a second order dependence on the concentration of [MoS(4)](2)(-). The mechanistic picture of cluster disruption which emerges from these studies rationalizes the "all or nothing" reactivity of [M(4)(SPh)(10)](2)(-).

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

NASA Astrophysics Data System (ADS)

Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.

2017-08-01

The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

NASA Astrophysics Data System (ADS)

Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

2005-02-01

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

Decohesion models informed by first-principles calculations: The ab initio tensile test

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-10-01

Extreme deformation and homogeneous fracture can be readily studied via ab initio methods by subjecting crystals to numerical "tensile tests", where the energy of locally stable crystal configurations corresponding to elongated and fractured states are evaluated by means of density functional method calculations. The information obtained can then be used to construct traction curves of cohesive zone models in order to address fracture at the macroscopic scale. In this work, we perform an in depth analysis of traction curves and how ab initio calculations must be interpreted to rigorously parameterize an atomic scale cohesive zone model, using crystalline Ag as an example. Our analysis of traction curves reveal the existence of two qualitatively distinct decohesion criteria: (i) an energy criterion whereby the released elastic energy equals the energy cost of creating two new surfaces and (ii) an instability criterion that occurs at a higher and size independent stress than that of the energy criterion. We find that increasing the size of the simulation cell renders parts of the traction curve inaccessible to ab initio calculations involving the uniform decohesion of the crystal. We also find that the separation distance below which a crack heals is not a material parameter as has been proposed in the past. Finally, we show that a large energy barrier separates the uniformly stressed crystal from the decohered crystal, resolving a paradox predicted by a scaling law based on the energy criterion that implies that large crystals will decohere under vanishingly small stresses. This work clarifies confusion in the literature as to how a cohesive zone model is to be parameterized with ab initio "tensile tests" in the presence of internal relaxations.

Coming Up Short: 35th Annual M&O Cost Study

ERIC Educational Resources Information Center

Agron, Joe

2006-01-01

As the nation's school buildings age and deteriorate, spending on maintenance and operations (M&O) remains paltry, especially when compared with historical figures. This article presents the findings of "American School & University's" 35th annual Maintenance and Operations Cost Study. According to the M&O Cost Study, the median school district…

Heart failure after conventional metal-on-metal hip replacements

PubMed Central

Gillam, Marianne H; Pratt, Nicole L; Inacio, Maria C S; Roughead, Elizabeth E; Shakib, Sepehr; Nicholls, Stephen J; Graves, Stephen E

2017-01-01

Background and purpose — It is unclear whether metal particles and ions produced by mechanical wear and corrosion of hip prostheses with metal-on-metal (MoM) bearings have systemic adverse effects on health. We compared the risk of heart failure in patients with conventional MoM total hip arthroplasty (THA) and in those with metal-on-polyethylene (MoP) THA. Patients and methods — We conducted a retrospective cohort study using data from the Australian Government Department of Veterans’ Affairs health claims database on patients who received conventional THA for osteoarthritis between 2004 and 2012. The MoM THAs were classified into groups: Articular Surface Replacement (ASR) XL Acetabular System, other large-head (LH) (> 32 mm) MoM, and small-head (SH) (≤ 32 mm) MoM. The primary outcome was hospitalization for heart failure after THA. Results — 4,019 patients with no history of heart failure were included (56% women). Men with an ASR XL THA had a higher rate of hospitalization for heart failure than men with MoP THA (hazard ratio (HR) = 3.2, 95% CI: 1.6–6.5). No statistically significant difference in the rate of heart failure was found with the other LH MoM or SH MoM compared to MoP in men. There was no statistically significant difference in heart failure rate between exposure groups in women. Interpretation — An association between ASR XL and hospitalization for heart failure was found in men. While causality between ASR XL and heart failure could not be established in this study, it highlights an urgent need for further studies to investigate the possibility of systemic effects associated with MoM THA. PMID:27759468

Human monocyte-derived dendritic cells exposed to microorganisms involved in hypersensitivity pneumonitis induce a Th1-polarized immune response.

PubMed

Bellanger, Anne-Pauline; Pallandre, Jean-René; Borg, Christophe; Loeffert, Sophie; Gbaguidi-Haore, Houssein; Millon, Laurence

2013-08-01

Hypersensitivity pneumonitis (HP) is an immunoallergic disease characterized by a prominent interstitial infiltrate composed predominantly of lymphocytes secreting inflammatory cytokines. Dendritic cells (DCs) are known to play a pivotal role in the lymphocytic response. However, their cross talk with microorganisms that cause HP has yet to be elucidated. This study aimed to investigate the initial interactions between human monocyte-derived DCs (MoDCs) and four microorganisms that are different in nature (Saccharopolyspora rectivirgula [actinomycetes], Mycobacterium immunogenum [mycobacteria], and Wallemia sebi and Eurotium amstelodami [filamentous fungi]) and are involved in HP. Our objectives were to determine the cross talk between MoDCs and HP-causative agents and to determine whether the resulting immune response varied according to the microbial extract tested. The phenotypic activation of MoDCs was measured by the increased expression of costimulatory molecules and levels of cytokines in supernatants. The functional activation of MoDCs was measured by the ability of MoDCs to induce lymphocytic proliferation and differentiation in a mixed lymphocytic reaction (MLR). E. amstelodami-exposed (EA) MoDCs expressed higher percentages of costimulatory molecules than did W. sebi-exposed (WS), S. rectivirgula-exposed (SR), or M. immunogenum-exposed (MI) MoDCs (P < 0.05, Wilcoxon signed-rank test). EA-MoDCs, WS-MoDCs, SR-MoDCs, and MI-MoDCs induced CD4(+) T cell proliferation and a Th1-polarized immune response. The present study provides evidence that, although differences were initially observed between MoDCs exposed to filamentous fungi and MoDCs exposed to bacteria, a Th1 response was ultimately promoted by DCs regardless of the microbial extract tested.

First-principles study on the electronic structure and elastic properties of Mo2NiB2 doped with V

NASA Astrophysics Data System (ADS)

Li, Jinming; Li, Xiaobo; Gao, Haiyun; Peng, Dian

2018-04-01

The content of this study is to analyze the electronic structure and elastic properties that the different structures of Mo2NiB2 and doping with V of the tetragonal M3B2 (Mo2Ni1‑xVxB2 and Mo2‑yNi1‑yV2yB2) (x = 0.25, 0.5, 0.75 and y = 0.125, 0.25, 0.375) by first-principles calculations based on density functional theory (DFT) combined with the projection-plus-wave method. But the calculated formation energy shows that V atoms prefer to substitute the Mo and Ni atoms of the tetragonal Mo2NiB2. Moreover, with the increase of V content, the formation enthalpy of tetragonal Mo2NiB2 is reduced, and the formation enthalpy of Mo1.625Ni0.625V0.75B2 is the least as ‑53.23 kJ/mol. The calculated elastic constant suffices the condition of mechanical stability, indicate that they are stable. The calculated elastic modulus illustrates that Mo2NiB2 having better mechanical properties when V elements are at Mo and Ni sites instead of Ni sites. The calculated and analyzed density of states of Mo1.625Ni0.625V0.75B2 has the smallest the density of states at the Fermi level indicating that it has the more stable structure. For the theoretical analysis of the first-principles calculations, the addition of 15 atom% of the V and V doping modes of Mo and Ni are preferentially replaced by V atoms of Mo2NiB2 ternary boride has the best performance.

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

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

Holst, Bastian; French, Martin; Redmer, Ronald

2011-06-15

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

Ab initio R-matrix calculations of e+-molecule scattering

NASA Technical Reports Server (NTRS)

Danby, Grahame; Tennyson, Jonathan

1990-01-01

The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.

Ab initio molecular dynamics simulations of the initial stages of solid-electrolyte interphase formation on lithium ion battery graphitic anodes.

PubMed

Leung, Kevin; Budzien, Joanne L

2010-07-07

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

In silico simulations of tunneling barrier measurements for molecular orbital-mediated junctions: A molecular orbital theory approach to scanning tunneling microscopy

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

Terryn, Raymond J.; Sriraman, Krishnan; Olson, Joel A., E-mail: jolson@fit.edu

A new simulator for scanning tunneling microscopy (STM) is presented based on the linear combination of atomic orbitals molecular orbital (LCAO-MO) approximation for the effective tunneling Hamiltonian, which leads to the convolution integral when applied to the tip interaction with the sample. This approach intrinsically includes the structure of the STM tip. Through this mechanical emulation and the tip-inclusive convolution model, dI/dz images for molecular orbitals (which are closely associated with apparent barrier height, ϕ{sub ap}) are reported for the first time. For molecular adsorbates whose experimental topographic images correspond well to isolated-molecule quantum chemistry calculations, the simulator makes accuratemore » predictions, as illustrated by various cases. Distortions in these images due to the tip are shown to be in accord with those observed experimentally and predicted by other ab initio considerations of tip structure. Simulations of the tunneling current dI/dz images are in strong agreement with experiment. The theoretical framework provides a solid foundation which may be applied to LCAO cluster models of adsorbate–substrate systems, and is extendable to emulate several aspects of functional STM operation.« less

Applications of molybdenum-95 NMR spectroscopy. 7. Studies of metal-metal bonded systems including aqueous molybdenum(IV) and molybdenum(V). Crystal and molecular structure of Na/sub 2/(Mo/sub 3/O/sub 4/((O/sub 2/CCH/sub 2/)/sub 2/NCH/sub 3/)/sub 3/). 7H/sub 2/O

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

Ghellar, S.F.; Hambley, T.W.; Brownlee, R.T.

1983-03-23

Solution /sup 95/Mo NMR studies are reported on spin-coupled polynuclear systems of Mo(V), Mo(IV), and Mo(II). Resonances occur at low fields compared to mononuclear species. The chemical shifts of the Mo(IV)-aquo ion in 4 M p-toluenesulfonic and methanesulfonic acid media and those of the Mo(IV) complexes containing oxalate, EDTA, and methyliminodiacetate ligands (whose solid-state structures are based on the (Mo/sub 3/O/sub 4/)/sup 4 +/ cluster) fall in the narrow range of 172 ppm spanning 990-1162 ppm. As the known chemical shift scale for the /sup 95/Mo nucleus covers 7000 ppm, this observation indicates that the /sup 95/Mo nucleus is inmore » a similar chemical environment in each of the species examined and, taken with published evidence, confirms formulation of the Mo(IV)-aquo ion as (Mo/sub 3/O/sub 4/(H/sub 2/O)/sub 9/)/sup 4 +/. Two resonances are detected in the above range for Mo(IV)/sub aq/ in 4 M hydrochloric acid and for ((Mo/sub 3/O/sub 4/)/sub 2/(PDTA)/sub 3/)/sup 4 -/. Additional resonances appear at 539-608 ppm in the methanesulfonic acid, hydrochloric acid, and EDTA systems when stored in air. These are assigned to (Mo/sup v//sub 2/O/sub 4/)/sup 2 +/-based species by comparison with the observed resonances of the Mo(V)-aquo ion, (Mo/sup v//sub 2/O/sub 4/(H/sub 2/O)/sub 6/)/sup 2 +/, in the relevant acid media and with (Mo/sup v//sub 2/O/sub 4/(EDTA))/sup 2 -/ in H/sub 2/O. The (Mo/sup v//sub 2/O/sub 4/(PDTA))/sup 2 -/ anion exhibits two resonances associated with inequivalent molybdenum sites. Resonances for (Mo/sup II//sub 2/(O/sub 2/CR)/sub 4/) (R = CF/sub 3/, n-Pr), which contain formal quadruple bonds, have been observed for the first time and are the most deshielded /sup 95/Mo NMR signals detected to date. The methyliminodiacetate complex, Na/sub 2/(Mo/sub 3/O/sub 4/((O/sub 2/CCH/sub 2/)/sub 2/NCH/sub 3/)/sub 3/).7H/sub 2/O, was isolated. Its crystal structure contains a discrete trinuclear (Mo/sup IV//sub 3/O/sub 4/((O/sub 2/CCH/sub 2/)/sub 2/NCH/sub 3/)/sub 3/)/sup 2 -/ anion whose symmetry approaches C/sub 3v/.« less

The variation of molybdenum isotopes within the weathering system of the black shales

NASA Astrophysics Data System (ADS)

Jianming, Z.

2016-12-01

Jian-Ming Zhu 1,2, De-Can Tan 2, Liang Liang 2, Wang Jing21 State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences, Beijing, 100083, China 2 State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China Molybdenum (Mo) stable isotopes have been developed as a tracer to indicate the evolution of the atmospheric and oceanic oxygenation related with continent weathering, and to reveal the extent of ancient oceanic euxinia. Molybdenum isotopic variation within the weathering system of basalts has been studied, and was presented the whole trend with heavier isotopes preferentially removed during weathering processes. However, there are few researches to study the variation of Mo isotopes during black shale weathering, especiall on the behavoir of Mo isotopes within the perfect shales' profiles. Here, the weathering profiles of Mo and selenium(Se)-rich carbonaceous rocks in Enshi southwest Hubei Province were selected. The Mo isotopes was measured on Nu Plasma II's MC-ICP-MS using 97Mo-100Mo double spike, and δ98/95Mo was reported relative to NIST 3134. A comprehensive set of Mo isotopic composition and concentration data from the unweathered, weakly and intensely weathered rocks were collected. The δ98/95Mo in fresh shales (220±248 mg/kg Mo, 1SD, n=41) from Shadi and Yutangba drill cores varies from 0.41‰ to 0.99‰ with an average of 0.67±0.16‰, while the strongly weathered shales (19.9±5.8 mg/kg Mo, 1SD, n=5) from Shadi profiles are isotopically heavier with average δ98/95Mo values of 1.03±0.10‰ (1SD, n=5). The Locally altered shales exposed in a quarry at Yutangba are highly enriched in Mo, varing from 31 to 2377 mg/kg with an average of 428 ±605mg/kg (1SD, n=24), approximately 2 times greater than that in fresh shales samples. These rocks are presented a significant variation in δ98/95Mo values varing from -0.24 ‰ to -3.99 ‰ with average -1.67±1.57‰, showing the extremely negative δ98/95Mo values existed in natural samples. This suggested that Mo isotopes can be fractionated during shales weathering processes, with lighter isotopes preferentially removed. This finding is in contrast to the previous knowledge from basalt weathering, and requires further study.

Coupled Mo-U abundances and isotopes in a small marine euxinic basin: Constraints on processes in euxinic basins

NASA Astrophysics Data System (ADS)

Bura-Nakić, Elvira; Andersen, Morten B.; Archer, Corey; de Souza, Gregory F.; Marguš, Marija; Vance, Derek

2018-02-01

Sedimentary molybdenum (Mo) and uranium (U) abundances, as well as their isotope systematics, are used to reconstruct the evolution of the oxygenation state of the surface Earth from the geological record. Their utility in this endeavour must be underpinned by a thorough understanding of their behaviour in modern settings. In this study, Mo-U concentrations and their isotope compositions were measured in the water column, sinking particles, sediments and pore waters of the marine euxinic Lake Rogoznica (Adriatic Sea, Croatia) over a two year period, with the aim of shedding light on the specific processes that control Mo-U accumulation and isotope fractionations in anoxic sediment. Lake Rogoznica is a 15 m deep stratified sea-lake that is anoxic and euxinic at depth. The deep euxinic part of the lake generally shows Mo depletions consistent with near-quantitative Mo removal and uptake into sediments, with Mo isotope compositions close to the oceanic composition. The data also, however, show evidence for periodic additions of isotopically light Mo to the lake waters, possibly released from authigenic precipitates formed in the upper oxic layer and subsequently processed through the euxinic layer. The data also show evidence for a small isotopic offset (∼0.3‰ on 98Mo/95Mo) between particulate and dissolved Mo, even at highest sulfide concentrations, suggesting minor Mo isotope fractionation during uptake into euxinic sediments. Uranium concentrations decrease towards the bottom of the lake, where it also becomes isotopically lighter. The U systematics in the lake show clear evidence for a dominant U removal mechanism via diffusion into, and precipitation in, euxinic sediments, though the diffusion profile is mixed away under conditions of increased density stratification between an upper oxic and lower anoxic layer. The U diffusion-driven precipitation is best described with an effective 238U/235U fractionation of +0.6‰, in line with other studied euxinic basins. Combining the Mo and U systematics in Lake Rogoznica and other euxinic basins, it is apparent that the two different uptake mechanisms of U and Mo can lead to spatially and temporally variable Mo/U and Mo-U isotope systematics that depend on the rate of water renewal versus removal to sediment, the sulfide concentration, and the geometry of the basin. This study further emphasises the potential of combining multiple observations, from Mo-U enrichment and isotope systematics, for disentangling the various processes via which redox conditions control the chemistry of modern and ancient sediments.

Adsorption of DNA/RNA nucleobases onto single-layer MoS2 and Li-Doped MoS2: A dispersion-corrected DFT study

NASA Astrophysics Data System (ADS)

Sadeghi, Meisam; Jahanshahi, Mohsen; Ghorbanzadeh, Morteza; Najafpour, Ghasem

2018-03-01

The kind of sensing platform in nano biosensor plays an important role in nucleic acid sequence detection. It has been demonstrated that graphene does not have an intrinsic band gap; therefore, transition metal dichalcogenides (TMDs) are desirable materials for electronic base detection. In the present work, a comparative study of the adsorption of the DNA/RNA nucleobases [Adenine (A), Cytosine (C) Guanine (G), Thymine (T) and Uracil (U)] onto the single-layer molybdenum disulfide (MoS2) and Li-doped MoS2 (Li-MoS2) as a sensing surfaces was investigated by using Dispersion-corrected Density Functional Theory (D-DFT) calculations and different measure of equilibrium distances, charge transfers and binding energies for the various nucleobases were calculated. The results revealed that the interactions between the nucleobases and the MoS2 can be strongly enhanced by introducing metal atom, due to significant charge transfer from the Li atom to the MoS2 when Lithium is placed on top of the MoS2. Furthermore, the binding energies of the five nucleobases were in the range of -0.734 to -0.816 eV for MoS2 and -1.47 to -1.80 eV for the Li-MoS2. Also, nucleobases were adsorbed onto MoS2 sheets via the van der Waals (vdW) force. This high affinity and the renewable properties of the biosensing platform demonstrated that Li-MoS2 nanosheet is biocompatible and suitable for nucleic acid analysis.

Influence of defects and doping on phonon transport properties of monolayer MoSe2

NASA Astrophysics Data System (ADS)

Yan, Zhequan; Yoon, Mina; Kumar, Satish

2018-07-01

The doping of monolayer MoSe2 by tungsten (W) can suppress the Se vacancy concentration, but how doping and resulting change in defect concentration can tune its thermal properties is not understood yet. We use first-principles density functional theory (DFT) along with the phonon Boltzmann transport equation (BTE) to study the phonon transport properties of pristine MoSe2 and W doped MoSe2 with and without the presence of Se vacancies. We found that for samples without Se vacancy, the W doping could enhance the thermal transport of monolayer MoSe2 due to reduced three-phonon scattering phase space. For example, we observed that the 16.7% W doping increases the thermal conductivity of the monolayer MoSe2 with 2% Se vacancy by 80% if all vacancies can be suppressed by W-doping. However, the W doping in the defective MoSe2 amplifies the influence of the phonon scattering caused by the Se vacancies, which results in a further decrease in thermal conductivity of monolayer MoSe2 with defects. This is found to be related with higher phonon density of states of Mo0.83W0.17Se2 and larger mass difference between W and Se atoms compared to Mo and Se atoms. This study deciphers the effect of defects and doping on the thermal conductivity of monolayer MoSe2, which helps us understand the mechanism of defect-induced phonon transport, and provides insights into enhancing the heat dissipation in MoSe2-based electronic devices.

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures.

PubMed

Glass, Jennifer B; Axler, Richard P; Chandra, Sudeep; Goldman, Charles R

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2-4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state.

Intrauterine growth restriction programs an accelerated age-related increase in cardiovascular risk in male offspring

PubMed Central

Dasinger, John Henry; Intapad, Suttira; Backstrom, Miles A.; Carter, Anthony J.

2016-01-01

Placental insufficiency programs an increase in blood pressure associated with a twofold increase in serum testosterone in male growth-restricted offspring at 4 mo of age. Population studies indicate that the inverse relationship between birth weight and blood pressure is amplified with age. Thus, we tested the hypothesis that intrauterine growth restriction programs an age-related increase in blood pressure in male offspring. Growth-restricted offspring retained a significantly higher blood pressure at 12 but not at 18 mo of age compared with age-matched controls. Blood pressure was significantly increased in control offspring at 18 mo of age relative to control counterparts at 12 mo; however, blood pressure was not increased in growth-restricted at 18 mo relative to growth-restricted counterparts at 12 mo. Serum testosterone levels were not elevated in growth-restricted offspring relative to control at 12 mo of age. Thus, male growth-restricted offspring no longer exhibited a positive association between blood pressure and testosterone at 12 mo of age. Unlike hypertension in male growth-restricted offspring at 4 mo of age, inhibition of the renin-angiotensin system with enalapril (250 mg/l for 2 wk) did not abolish the difference in blood pressure in growth-restricted offspring relative to control counterparts at 12 mo of age. Therefore, these data suggest that intrauterine growth restriction programs an accelerated age-related increase in blood pressure in growth-restricted offspring. Furthermore, this study suggests that the etiology of increased blood pressure in male growth-restricted offspring at 12 mo of age differs from that at 4 mo of age. PMID:27147668

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures

PubMed Central

Glass, Jennifer B.; Axler, Richard P.; Chandra, Sudeep; Goldman, Charles R.

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state. PMID:22993512

Capabilities of CdTe-Based Detectors With {mathrm {MoO}}_{x} Contacts for Detection of X- and gamma -Radiation

NASA Astrophysics Data System (ADS)

Maslyanchuk, O. L.; Solovan, M. M.; Brus, V. V.; Kulchynsky, V. V.; Maryanchuk, P. D.; Fodchuk, I. M.; Gnatyuk, V. A.; Aoki, T.; Potiriadis, C.; Kaissas, Y.

2017-05-01

The charge transport mechanism and spectrometric properties of the X-ray and γ-ray detectors, fabricated by the deposition of molybdenum oxide thin films onto semi-insulating p-CdTe crystals were studied. The current transport processes in the Mo-MoOx/p-CdTe/MoOx-Mo structure are well described in the scope of the carrier's generation in the space-charge region and the space-charge-limited current models. The lifetime of charge carriers, the energy of hole traps, and the density of discrete trapping centers were determined from the comparison of the experimental data and calculations. Spectrometric properties of Mo-MoOx/p-CdTe/MoOx-Mo structures were also investigated. It is shown that the investigated heterojunctions have demonstrated promising characteristics for practical application in X-ray and γ-ray detector fabrication.

Controlled growth of MoS2 nanopetals on the silicon nanowire array using the chemical vapor deposition method

NASA Astrophysics Data System (ADS)

Chen, Shang-Min; Lin, Yow-Jon

2018-01-01

In order to get a physical/chemical insight into the formation of nanoscale semiconductor heterojunctions, MoS2 flakes are deposited on the silicon nanowire (SiNW) array by chemical vapor deposition (CVD). In this study, H2O2 treatment provides a favorable place where the formation of Sisbnd O bonds on the SiNW surfaces that play important roles (i.e., the nucleation centers, catalyst control centers or ;seeds;) can dominate the growth of MoS2 on the SiNWs. Using this configuration, the effect of a change in the S/MoO3 mass ratio (MS/MMoO3) on the surface morphology of MoS2 is studied. It is shown that an increase in the value of MS/MMoO3 leads to the increased nucleation rate, increasing the size of MoS2 nanopetals. This study provides valuable scientific information for directly CVD-grown edge-oriented MoS2/SiNWs heterojunctions for various nanoscale applications, including hydrogen evolution reaction and electronic and optoelectronic devices.

Theoretical study on the top- and enclosed-contacted single-layer MoS{sub 2} piezotronic transistors

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

Liu, Wei, E-mail: wliu@binn.cas.cn, E-mail: zlwang@gatech.edu; Zhou, Yongli; Zhang, Aihua

Recently, the piezotronic effect has been observed in two-dimensional single-layer MoS{sub 2} materials, which have potential applications in force and pressure triggered or controlled electronic devices, sensors, and human-machine interfaces. However, classical theory faces the difficulty in explaining the mechanism of the piezotronic effect for the top- and enclosed-contacted MoS{sub 2} transistors, since the piezoelectric charges are assumed to exist only at the edge of the MoS{sub 2} flake that is far from the electronic transport pathway. In the present study, we identify the piezoelectric charges at the MoS{sub 2}/metal-MoS{sub 2} interface by employing both the density functional theory andmore » finite element method simulations. This interface is on the transport pathway of both top- and enclosed-contacted MoS{sub 2} transistors, thus it is capable of controlling their transport properties. This study deepens the understanding of piezotronic effect and provides guidance for the design of two-dimensional piezotronic devices.« less

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Combined photothermal and photodynamic therapy delivered by PEGylated MoS2 nanosheets

NASA Astrophysics Data System (ADS)

Liu, Teng; Wang, Chao; Cui, Wei; Gong, Hua; Liang, Chao; Shi, Xiaoze; Li, Zhiwei; Sun, Baoquan; Liu, Zhuang

2014-09-01

Single- or few-layered transitional metal dichalcogenides, as a new genus of two-dimensional nanomaterials, have attracted tremendous attention in recent years, owing to their various intriguing properties. In this study, chemically exfoliated MoS2 nanosheets are modified with lipoic acid-terminated polyethylene glycol (LA-PEG), obtaining PEGylated MoS2 (MoS2-PEG) with high stability in physiological solutions and no obvious toxicity. Taking advantage of its ultra-high surface area, the obtained MoS2-PEG is able to load a photodynamic agent, chlorin e6 (Ce6), by physical adsorption. In vitro experiments reveal that Ce6 after being loaded on MoS2-PEG shows remarkably increased cellular uptake and thus significantly enhanced photodynamic therapeutic efficiency. Utilizing the strong, near-infrared (NIR) absorbance of the MoS2 nanosheets, we further demonstrate photothermally enhanced photodynamic therapy using Ce6-loaded MoS2-PEG for synergistic cancer killing, in both in vitro cellular and in vivo animal experiments. Our study presents a new type of multifunctional nanocarrier for the delivery of photodynamic therapy, which, if combined with photothermal therapy, appears to be an effective therapeutic approach for cancer treatment.Single- or few-layered transitional metal dichalcogenides, as a new genus of two-dimensional nanomaterials, have attracted tremendous attention in recent years, owing to their various intriguing properties. In this study, chemically exfoliated MoS2 nanosheets are modified with lipoic acid-terminated polyethylene glycol (LA-PEG), obtaining PEGylated MoS2 (MoS2-PEG) with high stability in physiological solutions and no obvious toxicity. Taking advantage of its ultra-high surface area, the obtained MoS2-PEG is able to load a photodynamic agent, chlorin e6 (Ce6), by physical adsorption. In vitro experiments reveal that Ce6 after being loaded on MoS2-PEG shows remarkably increased cellular uptake and thus significantly enhanced photodynamic therapeutic efficiency. Utilizing the strong, near-infrared (NIR) absorbance of the MoS2 nanosheets, we further demonstrate photothermally enhanced photodynamic therapy using Ce6-loaded MoS2-PEG for synergistic cancer killing, in both in vitro cellular and in vivo animal experiments. Our study presents a new type of multifunctional nanocarrier for the delivery of photodynamic therapy, which, if combined with photothermal therapy, appears to be an effective therapeutic approach for cancer treatment. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03753g

MoMip11, a MoRgs7-interacting protein, functions as a scaffolding protein to regulate cAMP signaling and pathogenicity in the rice blast fungus Magnaporthe oryzae.

PubMed

Yin, Ziyi; Zhang, Xiaofang; Wang, Jingzhen; Yang, Lina; Feng, Wanzhen; Chen, Chen; Gao, Chuyun; Zhang, Haifeng; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

2018-05-04

The rice blast fungus Magnaporthe oryzae has eight regulators of G-protein signaling (RGS) and RGS-like proteins (MoRgs1 to MoRgs8) that exhibit both distinct and shared regulatory functions in the growth, differentiation and pathogenicity of the fungus. We found MoRgs7 with a unique RGS-seven transmembrane (7-TM) domain motif is localized to the highly dynamic tubule-vesicular compartments during early appressorium differentiation followed by gradually degradation. To explore whether this involves an active signal perception of MoRgs7, we identified a Gbeta-like/RACK1 protein homolog in M. oryzae MoMip11 that interacts with MoRgs7. Interestingly, MoMip11 selectively interacted with several components of the cAMP regulatory pathway, including Gα MoMagA and the high-affinity phosphodiesterase MoPdeH. We further showed that MoMip11 promotes MoMagA activation and suppresses MoPdeH activity thereby upregulating intracellular cAMP levels. Moreover, MoMip11 is required for the response to multiple stresses, a role also shared by Gbeta-like/RACK1 adaptor proteins. In summary, we revealed a unique mechanism by which MoMip11 links MoRgs7 and G-proteins to reugulate cAMP signaling, stress responses and pathogenicity of M. oryzae. Our studies revealed the multitude of regulatory networks that govern growth, development and pathogenicity in this important causal agent of rice blast. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Structure and electronic properties of Cu nanoclusters supported on Mo 2C(001) and MoC(001) surfaces

DOE PAGES

Posada-Pérez, Sergio; Viñes, Francesc; Rodríguez, José A.; ...

2015-09-15

In this study, the atomic structure and electronic properties of Cu n nanoclusters (n = 4, 6, 7, and 10) supported on cubic nonpolar δ-MoC(001) and orthorhombic C- or Mo-terminated polar β-Mo 2C(001) surfaces have been investigated by means of periodic density functional theory based calculations. The electronic properties have been analyzed by means of the density of states, Bader charges, and electron localization function plots. The Cu nanoparticles supported on β-Mo 2C(001), either Mo- or C-terminated, tend to present a two-dimensional structure whereas a three-dimensional geometry is preferred when supported on δ-MoC(001), indicating that the Mo:C ratio and themore » surface polarity play a key role determining the structure of supported clusters. Nevertheless, calculations also reveal important differences between the C- and Mo-terminated β-Mo 2C(001) supports to the point that supported Cu particles exhibit different charge states, which opens a way to control the reactivity of these potential catalysts.« less

Network structure of Mo-oxide glasses

NASA Astrophysics Data System (ADS)

Fabian, M.; Svab, E.; Milanova, M.; Krezhov, K.

2017-01-01

The structure of molybdate glasses have been investigated by neutron and high-energy X-ray diffraction coupled with Reverse Monte Carlo (RMC) simulation technique. From the modelling the partial atomic correlation functions g ij(r), the coordination number distributions CN ij and bond angle distributions have been revealed. For binary 90MoO3-10Nd2O3 glass composition the fraction of MoO4/MoO6 was 0.55/0.25. Three type of ternary system have been studied, where the most important structural units was authenticated. For MoO3-Nd2O3-B2O3 sample mixed MoO4-BO4 and MoO4-BO3 linkages form pronounced intermediate-range order. In case of MoO3-ZnO-B2O3 series the BO3 and BO4 units are linked to MoO4 and/or ZnO4, forming mixed MoO4-BO4(BO3), MoO4-ZnO4 and ZnO4-BO4(BO3) bond-linkages.

Large-area snow-like MoSe2 monolayers: synthesis, growth mechanism, and efficient electrocatalyst application.

PubMed

Huang, Jingwen; Liu, Huiqiang; Jin, Bo; Liu, Min; Zhang, Qingchun; Luo, Liqiong; Chu, Shijin; Chu, Sheng; Peng, Rufang

2017-07-07

This study explores the large-area synthesis of controllable morphology, uniform, and high-quality monolayer. MoSe 2 is essential for its potential application in optoelectronics, photocatalysis, and renewable energy sources. In this study, we successfully synthesized snow-like MoSe 2 monolayers using a simple chemical vapor deposition method. Results reveal that snow-like MoSe 2 is a single crystal with a hexagonal structure, a thickness of ∼0.9 nm, and a lateral dimension of up to 20 μm. The peak position of the photoluminescence spectra is ∼1.52 eV corresponding to MoSe 2 monolayer. The growth mechanism of the snow-like MoSe 2 monolayer was investigated and comprised a four-step process during growth. Finally, we demonstrate that the snow-like MoSe 2 monolayers are ideal electrocatalysts for hydrogen evolution reactions (HERs), reflected by a low Tafel slope of ∼68 mV/decade. Compared with the triangular-shaped MoSe 2 monolayer, the hexangular snow-like shape with plentiful edges is superior for perfect electrocatalysts for HERs or transmission devices of optoelectronic signals.

Comparison of metal ion concentrations and implant survival after total hip arthroplasty with metal-on-metal versus metal-on-polyethylene articulations

PubMed Central

Dahlstrand, Henrik; Stark, André; Wick, Marius C; Anissian, Lucas; Hailer, Nils P; Weiss, Rüdiger J

2017-01-01

Background and purpose Large metal-on-metal (MoM) articulations are associated with metal wear and corrosion, leading to increased metal ion concentrations and unacceptable revision rates. There are few comparative studies of 28-mm MoM articulations with conventional metal-on-polyethylene (MoP) couplings. We present a long-term follow-up of a randomized controlled trial comparing MoM versus MoP 28-mm articulations, focused on metal ions and implant survival. Patients and methods 85 patients with a mean age of 65 years at surgery were randomized to a MoM (Metasul) or a MoP (Protasul) bearing. After 16 years, 38 patients had died and 4 had undergone revision surgery. 13 patients were unavailable for clinical follow-up, leaving 30 patients (n = 14 MoM and n = 16 MoP) for analysis of metal ion concentrations and clinical outcome. Results 15-year implant survival was similar in both groups (MoM 96% [95% CI 88–100] versus MoP 97% [95% CI 91–100]). The mean serum cobalt concentration was 4-fold higher in the MoM (1.5 μg/L) compared with the MoP cohort (0.4 μg/L, p < 0.001) and the mean chromium concentration was double in the MoM (2.2 μg/L) compared with the MoP cohort (1.0 μg/L, p = 0.05). Mean creatinine levels were similar in both groups (MoM 93 μmol/L versus MoP 92 μmol/L). Harris hip scores differed only marginally between the MoM and MoP cohorts. Interpretation This is the longest follow-up of a randomized trial on 28-mm MoM articulations, and although implant survival in the 2 groups was similar, metal ion concentrations remained elevated in the MoM cohort even in the long term. PMID:28699417

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

NASA Astrophysics Data System (ADS)

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

2016-07-01

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

2016-07-07

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Photoemission and Auger-electron spectroscopic study of the Chevrel-phase compound FexMo6S8

NASA Astrophysics Data System (ADS)

Fujimori, A.; Sekita, M.; Wada, H.

1986-05-01

The electronic structure of the Chevrel-phase compound FexMo6S8 has been studied by photoemission and Auger-electron spectroscopy. Core-level shifts suggest a large charge transfer from the Fe atoms to the Mo6S8 clusters and a small Mo-to-S charge transfer within the cluster. Line-shape asymmetry in the core levels indicates that the density of states (DOS) at the Fermi level has a finite S 3p component as well as the dominant Mo 3d character. Satellite structure and exchange splitting in the Fe core levels point to weak Fe 3d-S 3p hybridization in spite of the short Fe-S distances comparable to that in FeS. The x-ray and ultraviolet valence-band photoemission spectra and the Mo 4d partial DOS obtained by deconvoluting the Mo M4,5VV Auger spectrum are compared with existing band-structure calculations, and the Mo 4d-S 3p bonding character, the structure of the Mo 4d-derived conduction band etc., are discussed. In particular, it is shown that the conduction-band structure is sensitive to the noncubic distortion of the crystal through changes in the intercluster Mo 4d-S 3p hybridization. A pronounced final-state effect is found in the Mo M4,5N2,3V Auger spectrum and is attributed to strong 4p-4d intershell coupling.

CO2-assisted fabrication of novel heterostructures of h-MoO3/1T-MoS2 for enhanced photoelectrocatalytic performance

NASA Astrophysics Data System (ADS)

Zhu, Chuanhui; Xu, Qun; Liu, Wei; Ren, Yumei

2017-12-01

Combining the peculiar properties of different ingredients in one ultimate material is an efficient route to achieve the desired functional materials. Compared to 2H-MoS2, 1T-MoS2 nanosheets display the perfect performance of hydrogen evolution reaction (HER) because of the excellent electronic conductivity. However, how to further realize HER in the visual and near-infrared (NIR) region is a great challenge. Herein, we develop an efficient method to locally pattern h-MoO3 on the ultrathin metallic 1T-MoS2 nanosheets and obtain the novel heterostructures of h-MoO3/1T-MoS2. The enhanced photoelectrochemical performance of the as-prepared heterostructures has been demonstrated. Our study indicates it is originated from the synergistic effect between h-MoO3 and 1T-MoS2, i.e., the strong optical absorption of h-MoO3 in the visible and NIR region, the excellent electronic conductivity of 1T-MoS2 and as well as the efficient separation of the photo-induced carriers from the heterostructures.

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Yoder, Bruce L; Maze, Joshua T; Raghavachari, Krishnan; Jarrold, Caroline Chick

2005-03-01

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.

Excitatory and inhibitory innervation of the mouse orofacial motor nuclei: A stereological study.

PubMed

Faunes, Macarena; Oñate-Ponce, Alejandro; Fernández-Collemann, Sara; Henny, Pablo

2016-03-01

Neurons in the trigeminal (Mo5), facial (Mo7), ambiguus (Amb), and hypoglossal (Mo12) motor nuclei innervate jaw, facial, pharynx/larynx/esophagus, and tongue muscles, respectively. They are essential for movements subserving feeding, exploration of the environment, and social communication. These neurons are largely controlled by sensory afferents and premotor neurons of the reticular formation, where central pattern generator circuits controlling orofacial movements are located. To provide a description of the orofacial nuclei of the adult mouse and to ascertain the influence of excitatory and inhibitory afferents upon them, we used stereology to estimate the number of motoneurons as well as of varicosities immunopositive for glutamate (VGluT1+, VGluT2+) and GABA/glycine (known as VIAAT+ or VGAT+) vesicular transporters in the Mo5, Mo7, Amb, and Mo12. Mo5, Mo7, Amb, and Mo12 contain ∼1,000, ∼3,000, ∼600, and ∼1,700 cells, respectively. VGluT1+, VGluT2+, and VIAAT+ varicosities respectively represent: 28%, 41%, and 31% in Mo5; 2%, 49%, and 49% in Mo7; 12%, 42%, and 46% in Amb; and 4%, 54%, and 42% in Mo12. The Mo5 jaw-closing subdivision shows the highest VGluT1+ innervation. Noticeably, the VGluT2+ and VIAAT+ varicosity density in Mo7 is 5-fold higher than in Mo5 and 10-fold higher than in Amb and Mo12. The high density of terminals in Mo7 likely reflects the convergence and integration of numerous inputs to motoneurons subserving the wide range of complex behaviors to which this nucleus contributes. Also, somatic versus neuropil location of varicosities suggests that most of these afferents are integrated in the dendritic trees of Mo7 neurons. © 2015 Wiley Periodicals, Inc.

Investigation on nonlinear optical properties of MoS2 nanoflakes grown on silicon and quartz substrates

NASA Astrophysics Data System (ADS)

Bayesteh, Samaneh; Zahra Mortazavi, Seyedeh; Reyhani, Ali

2018-05-01

In this study, MoS2 nanoflakes were directly grown on different substrates—Si/SiO2 and quartz—by one-step thermal chemical vapor deposition using MoO3 and sulfide powders as precursors. Scanning electron microscopy and x-ray diffraction patterns demonstrated the formation of MoS2 structures on both substrates. Moreover, UV-visible and photoluminescence analysis confirmed the formation of MoS2 few-layer structures. According to Raman spectroscopy, by assessment of the line width and frequency shift differences between the and A 1g, it was inferred that the MoS2 grown on the silicon substrate was monolayer and that grown on the quartz substrate was multilayer. In addition, open-aperture and close-aperture Z-scan techniques were employed to study the nonlinear optical properties including nonlinear absorption and nonlinear refraction of the grown MoS2. All experiments were performed using a diode laser with a wavelength of 532 nm as the light source. It is noticeable that both samples demonstrate obvious self-defocusing behavior. The monolayer MoS2 grown on the silicon substrate displayed considerable two-photon absorption while, the multilayer MoS2 synthesized on the quartz exhibited saturable absorption. In general, few-layered MoS2 would be useful for the development of nanophotonic devices like optical limiters, optical switchers, etc.

Influence of inserted Mo layer on the thermal stability of perpendicularly magnetized Ta/Mo/Co{sub 20}Fe{sub 60}B{sub 20}/MgO/Ta films

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

Li, Minghua, E-mail: mhli@ustb.edu.cn; Department of Electrical Engineering, University of California, Los Angeles, California 90095; Lu, Jinhui

2016-04-15

We studied the thermal stability of perpendicular magnetic anisotropy (PMA) in Ta/Mo/CoFeB/MgO/Ta films with and without inserted Mo layers. In the absence of a Mo layer, the films show PMA at annealing temperatures below 300 °C. On the other hand, the insertion of a Mo layer preserves PMA at annealing temperatures of up to 500 °C; however, a higher annealing temperature leads to the collapse of PMA. X-ray photoelectron spectroscopy (XPS) and high-resolution transmission electron microscopy (HRTEM) were used to study the microstructure of the films to understand the deterioration of PMA. The XPS results show that the segregation ofmore » Ta is partly suppressed by inserting a Mo layer. Once inserted, Mo does not remain at the interface of Ta and CoFeB but migrates to the surface of the films. The HRTEM results show that the crystallization of the MgO (001) texture is improved owing to the higher annealing temperature of the Mo inserted sample. A smooth and clear CoFeB/MgO interface is evident. The inserted Mo layer not only helps to obtain sharper and smoother interfaces but also contributes to the crystallization after the higher annealing temperature of films.« less

High pressure stability of lithium metatitanate and metazirconate: Insight from experiments & ab-initio calculations

NASA Astrophysics Data System (ADS)

Chitnis, Abhishek; Chakraborty, B.; Tripathi, B. M.; Tyagi, A. K.; Garg, Nandini

2018-02-01

Lithium metatitanate (LTO) and lithium metazirconate (LZO) are lithium rich ceramics which can be used as tritium breeder materials for thermonuclear reactors. In-situ x-ray diffraction and ab-initio studies at high pressure show that LTO has a higher bulk modulus than that of LZO. In fact these studies indicate that they are the least compressible of the known lithium rich ceramics like Li2O or Li4SiO4, which are potential candidates for blanket materials. These studies show that the TiO6 octahedra are responsible for the higher bulk modulus of LTO when compared to that of LZO. It has also been shown that the compressibility and distortion of the softer LiO6 octahedra can be controlled by altering the stacking sequence of the more rigid covalently bonded octahedra. This knowledge can be used by chemists to design new lithium based ceramics with higher bulk modulus. It was observed that LTO was stable upto 34 GPa. Ab initio DFT calculations helped to understand the anisotropy in compressibility of both LZO and LTO. This study also shows, that even though the empirical potentials developed by Vijaykumar et al. successfully determine the ambient pressure structure of lithium metatitanate, they cannot be used at non ambient conditions like high pressure [1].

X-ray absorption and Raman spectroscopy studies of molybdenum environments in borosilicate waste glasses

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

McKeown, David A.; Gan, Hao; Pegg, Ian L.

2017-05-01

Mo-containing high-level nuclear waste borosilicate glasses were investigated as part of an effort to improve Mo loading while avoiding yellow phase crystallization. Previous work showed that additions of vanadium decrease yellow phase formation and increases Mo solubility. X-ray absorption spectroscopy (XAS) and Raman spectroscopy were used to characterize Mo environments in HLW borosilicate glasses and to investigate possible structural relationships between Mo and V. Mo XAS spectra for the glasses indicate isolated tetrahedral Mo6+O4 with Mo-O distances near 1.75 Å. V XANES indicate tetrahedral V5+O4 as the dominant species. Raman spectra show composition dependent trends, where Mo-O symmetrical stretch modemore » frequencies (ν1) are sensitive to the mix of alkali and alkaline earth cations, decreasing by up to 10 cm-1 for glasses that change from Li+ to Na+ as the dominant network-modifying species. This indicates that MoO4 tetrahedra are isolated from the borosilicate network and are surrounded, at least partly, by Na+ and Li+. Secondary ν1 frequency effects, with changes up to 7 cm-1, were also observed with increasing V2O5 and MoO3 content. These secondary trends may indicate MoO4-MoO4 and MoO4-VO4 clustering, suggesting that V additions may stabilize Mo in the matrix with respect to yellow phase formation.« less

Probing microstructure and phase evolution of α-MoO 3 nanobelts for sodium-ion batteries by in situ transmission electron microscopy

DOE PAGES

Xia, Weiwei; Xu, Feng; Zhu, Chongyang; ...

2016-07-15

The fundamental electrochemical reaction mechanisms and the phase transformation pathways of layer-structured α-MoO 3 nanobelt during the sodiation/desodiation process to date remain largely unknown. In this study, to observe the real-time sodiation/desodiaton behaviors of α-MoO 3 during electrochemical cycling, we construct a MoO 3 anode sodium-ion battery inside a transmission electron microscope (TEM). Utilizing in situ TEM and electron diffraction pattern (EDP) observation, α-MoO 3 nanobelts are found to undergo a unique multi-step phase transformation. Upon the first sodiation, α-MoO 3 nanobelts initially form amorphous Na xMoO3 phase and are subsequently sodiated into intermediate phase of crystalline NaMoO 2, finallymore » resulting in the crystallized Mo nanograins embedded within the Na 2O matrix. During the first desodiation process, Mo nanograins are firstly re-oxidized into intermediate phase NaMoO 2 that is further transformed into amorphous Na 2MoO 3, resulting in an irreversible phase transformation. Upon subsequent sodiation/desodiation cycles, however, a stable and reversible phase transformation between crystalline Mo and amorphous Na2MoO 3 phases has been revealed. In conclusion, our work provides an in-deepth understanding of the phase transformation pathways of α-MoO 3 nanobelts upon electrochemical sodiation/desodiation processes, with the hope of assistance in designing sodium-ion batteries with enhanced performance.« less

MoCAP proteins regulated by MoArk1-mediated phosphorylation coordinate endocytosis and actin dynamics to govern development and virulence of Magnaporthe oryzae

PubMed Central

Yang, Jun; Chen, Deng; Liu, Muxing; Zhang, Haifeng; Zheng, Xiaobo; Wang, Ping; Peng, Youliang; Zhang, Zhengguang

2017-01-01

Actin organization is a conserved cellular process that regulates the growth and development of eukaryotic cells. It also governs the virulence process of pathogenic fungi, such as the rice blast fungus Magnaporthe oryzae, with mechanisms not yet fully understood. In a previous study, we found that actin-regulating kinase MoArk1 displays conserved functions important in endocytosis and actin organization, and MoArk1 is required for maintaining the growth and full virulence of M. oryzae. To understand how MoArk1 might function, we identified capping protein homologs from M. oryzae (MoCAP) that interact with MoArk1 in vivo. MoCAP is heterodimer consisting of α and β subunits MoCapA and MoCapB. Single and double deletions of MoCAP subunits resulted in abnormal mycelial growth and conidia formation. The ΔMocap mutants also exhibited reduced appressorium penetration and invasive hyphal growth within host cells. Furthermore, the ΔMocap mutants exhibited delayed endocytosis and abnormal cytoskeleton assembly. Consistent with above findings, MoCAP proteins interacted with MoAct1, co-localized with actin during mycelial development, and participated in appressorial actin ring formation. Further analysis revealed that the S85 residue of MoCapA and the S285 residue of MoCapB were subject to phosphorylation by MoArk1 that negatively regulates MoCAP functions. Finally, the addition of exogenous phosphatidylinositol 4,5-bisphosphate (PIP2) failed to modulate actin ring formation in ΔMocap mutants, in contrast to the wild-type strain, suggesting that MoCAP may also mediate phospholipid signaling in the regulation of the actin organization. These results together demonstrate that MoCAP proteins whose functions are regulated by MoArk1 and PIP2 are important for endocytosis and actin dynamics that are directly linked to growth, conidiation and pathogenicity of M. oryzae. PMID:28542408

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

2011-01-28

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

Dietary menhaden oil contributes to hepatic lipidosis in laying hens.

PubMed

Van Elswyk, M E; Hargis, B M; Williams, J D; Hargis, P S

1994-05-01

Clinical and epidemiological investigations have indicated that there may be substantial human cardiovascular benefits associated with increased consumption of n-3 fatty acids commonly found in fish oils. Recent studies have indicated that egg yolk n-3 fatty acid content is significantly increased when hens are fed diets enriched with selected fish oils such as menhaden oil (MO). In the present study, reproductively active females but not males exhibited increased hepatic lipidosis following 6 mo of feeding 3% MO. Hens fed 3% animal-vegetable oil (AV) did not exhibit hepatic lipid accumulation. Serum triglyceride and cholesterol concentrations were reduced (P < or = .05) in hens fed MO. Subsequently, yolk and total egg weights of hens fed MO were decreased as compared with those of hens fed AV. A significant interaction of dietary MO and exogenous 17 beta-estradiol was noted among chick liver and gallbladder weights. These data suggest that dietary MO and estradiol may interact in a manner that enhances the lipogenic activity of the liver, thereby inducing hepatic lipidosis in laying hens.

SPE-LEEM Studies on the Surface and Electronic Structure of 2-D Transition Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Yeh, Po-Chun; Jin, Wencan; Zaki, Nader; Zhang, Datong; Sadowski, Jerzy; Al-Mahboob, Abdullah; van de Zande, Arend; Chenet, Daniel; Dadap, Jerry; Herman, Irving; Sutter, Petter; Hone, James; Osgood, Richard

2014-03-01

In this work, we studied the surface and electronic structure of monolayer and few-layer exfoliated MoS2 and WSe2, as well as chemical-vapor-deposition (CVD) grown MoS2, using Spectroscopic Photoemission and Low Energy Electron Microscope (SPE-LEEM). LEEM measurements reveal that, unlike exfoliated MoS2, CVD-grown MoS2 exhibits grain-boundary alterations due to surface strain. However, LEEM and micro-probe low energy electron diffraction show that the quality of CVD-grown MoS2 is comparable to that of exfoliated MoS2. Micrometer-scale angle-resolved photoemission spectroscopy (ARPES) measurement on exfoliated MoS2 and WSe2 single-crystals provides direct evidence for the shifting of the valence band maximum from Γ to K, when the layer number is thinned down to one, as predicted by density functional theory. Our measurements of the k-space resolved electronic structure allow for further comparison with other theoretical predictions and with transport measurements. Session I and II

Catalytic Oxidation by Transition Metal Ions in Zeolites.

DTIC Science & Technology

1984-09-28

exotic schemes were developed. It was previously demonstrated that MoCI5 may be reacted with a HYu (here Yu denotes a steam-stabilized or...34ultrastable" zeolite) to form a MoYu zeolite and HC1 which is removed from the system.1 In this study, MoYu zeolites have been prepared by reacting HYu with Mo

Mo(CO)/sub 6/-promoted reductive cleavage of the carbon-sulfur bond

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

Luh, T.Y.; Wong, C.S.

1985-12-13

In order to study the reductive cleavage of carbon-sulfur bonds by Mo(CO/sub 6/, various organosulfur compounds are reacted with Mo(CO)/sub 6/ in THF. Results of these experiments demonstrate that benzylic-, aryl-, or ..cap alpha..-acyl-activated carbon-sulfur bonds are reduced by treatment with Mo(CO)/sub 6/. 1 table.

Free energy of formation of Mo2C and the thermodynamic properties of carbon in solid molybdenum

NASA Technical Reports Server (NTRS)

Seigle, L. L.; Chang, C. L.; Sharma, T. P.

1979-01-01

As part of a study of the thermodynamical properties of interstitial elements in refractory metals, the free energy of formation of Mo2C is determined, and the thermodynamical properties of C in solution in solid Mo evaluated. The activity of C in the two-phase region Mo + Mo2C is obtained from the C content of iron rods equilibrated with metal + carbide powder mixtures. The free energy of formation of alpha-Mo2C is determined from the activity data. The thermodynamic properties of C in the terminal solid solution are calculated from available data on the solid solubility of C in Mo. Lattice distortion due to misfit of the C atoms in the interstitial sites appears to play a significant role in determining the thermodynamic properties of C in solid Mo.

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

2013-02-28

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

Mo-CBP3, an Antifungal Chitin-Binding Protein from Moringa oleifera Seeds, Is a Member of the 2S Albumin Family

PubMed Central

Freire, José E. C.; Vasconcelos, Ilka M.; Moreno, Frederico B. M. B.; Batista, Adelina B.; Lobo, Marina D. P.; Pereira, Mirella L.; Lima, João P. M. S.; Almeida, Ricardo V. M.; Sousa, Antônio J. S.; Monteiro-Moreira, Ana C. O.; Oliveira, José T. A.; Grangeiro, Thalles B.

2015-01-01

Mo-CBP3 is a chitin-binding protein from M. oleifera seeds that inhibits the germination and mycelial growth of phytopathogenic fungi. This protein is highly thermostable and resistant to pH changes, and therefore may be useful in the development of new antifungal drugs. However, the relationship of MoCBP3 with the known families of carbohydrate-binding domains has not been established. In the present study, full-length cDNAs encoding 4 isoforms of Mo-CBP3 (Mo-CBP3-1, Mo-CBP3-2, Mo-CBP3-3 and Mo-CBP3-4) were cloned from developing seeds. The polypeptides encoded by the Mo-CBP3 cDNAs were predicted to contain 160 (Mo-CBP3-3) and 163 amino acid residues (Mo-CBP3-1, Mo-CBP3-2 and Mo-CBP3-4) with a signal peptide of 20-residues at the N-terminal region. A comparative analysis of the deduced amino acid sequences revealed that Mo-CBP3 is a typical member of the 2S albumin family, as shown by the presence of an eight-cysteine motif, which is a characteristic feature of the prolamin superfamily. Furthermore, mass spectrometry analysis demonstrated that Mo-CBP3 is a mixture of isoforms that correspond to different mRNA products. The identification of Mo-CBP3 as a genuine member of the 2S albumin family reinforces the hypothesis that these seed storage proteins are involved in plant defense. Moreover, the chitin-binding ability of Mo-CBP3 reveals a novel functionality for a typical 2S albumin. PMID:25789746

MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

PubMed

Sharma, Ronesh; Bayarjargal, Maitsetseg; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

2018-01-21

Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences. Two separate independent propensity scores are computed via incorporating physicochemical properties and HMM profiles, these scores are combined to predict final MoRF propensity score for a given residue. The first score reflects the characteristics of a query residue to be part of MoRF region based on the composition and similarity of assumed MoRF and flank regions. The second score reflects the characteristics of a query residue to be part of MoRF region based on the properties of flanks associated around the given residue in the query protein sequence. The propensity scores are processed and common averaging is applied to generate the final prediction score of MoRFpred-plus. Performance of the proposed predictor is compared with available MoRF predictors, MoRFchibi, MoRFpred, and ANCHOR. Using previously collected training and test sets used to evaluate the mentioned predictors, the proposed predictor outperforms these predictors and generates lower false positive rate. In addition, MoRFpred-plus is a downloadable predictor, which makes it useful as it can be used as input to other computational tools. https://github.com/roneshsharma/MoRFpred-plus/wiki/MoRFpred-plus:-Download. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ultrafast charge transfer between MoTe2 and MoS2 monolayers

NASA Astrophysics Data System (ADS)

Pan, Shudi; Ceballos, Frank; Bellus, Matthew Z.; Zereshki, Peymon; Zhao, Hui

2017-03-01

High quality and stable electrical contact between metal and two-dimensional materials, such as transition metal dichalcogenides, is a necessary requirement that has yet to be achieved in order to successfully exploit the advantages that these materials offer to electronics and optoelectronics. MoTe2, owing to its phase changing property, can potentially offer a solution. A recent study demonstrated that metallic phase of MoTe2 connects its semiconducting phase with very low resistance. To utilize this property to connect other two-dimensional materials, it is important to achieve efficient charge transfer between MoTe2 and other semiconducting materials. Using MoS2 as an example, we report ultrafast and efficient charge transfer between MoTe2 and MoS2 monolayers. In the transient absorption measurements, an ultrashort pump pulse is used to selectively excite electrons in MoTe2. The appearance of the excited electrons in the conduction band of MoS2 is monitored by using a probe pulse that is tuned to the resonance of MoS2. We found that electrons transfer to MoS2 on a time scale of at most 0.3 ps. The transferred electrons give rise to a large transient absorption signal at both A-exciton and B-exciton resonances due to the screening effect. We also observed ultrafast transfer of holes from MoS2 to MoTe2. Our results suggest the feasibility of using MoTe2 as a bridge material to connect MoS2 and other transition metal dichalcogenides, and demonstrate a new transition metal dichalcogenide heterostructure involving MoTe2, which extends the spectral range of such structures to infrared.

Bio-dissolution of Ni, V and Mo from spent petroleum catalyst using iron oxidizing bacteria.

PubMed

Pradhan, Debabrata; Kim, Dong J; Roychaudhury, Gautam; Lee, Seoung W

2010-01-01

Bioleaching studies of spent petroleum catalyst containing Ni, V and Mo were carried out using iron oxidizing bacteria. Various leaching parameters such as Fe(II) concentration, pulp density, pH, temperature and particle size were studied to evaluate their effects on the leaching efficiency as well as the kinetics of dissolution. The percentage of leaching of Ni and V were higher than Mo. The leaching process followed a diffusion controlled model and the product layer was observed to be impervious due to formation of ammonium jarosite (NH(4))Fe(3)(SO(4))(2)(OH)(6). Apart from this, the lower leaching efficiency of Mo was due to a hydrophobic coating of elemental sulfur over Mo matrix in the spent catalyst. The diffusivities of the attacking species for Ni, V and Mo were also calculated.

Predictors of adolescent compliance with oral hygiene instructions during two-arch multibracket fixed orthodontic treatment.

PubMed

Al-Jewair, Thikriat S; Suri, Sunjay; Tompson, Bryan D

2011-05-01

To determine compliance with oral hygiene instructions (OHI) of adolescents receiving two-arch multibracket fixed appliances and identify its predictive factors. Forty-one patients in a longitudinal study were provided standardized OHI and assessed at baseline: before bonding (T0mo), approximately 30 days after bonding (T1mo), and approximately 150 days (T5mo) after bonding straight-wire appliances simultaneously in the maxillary and mandibular arches. Oral hygiene (OH) performance was measured using plaque and gingival indices. Compliance predictors were identified from questionnaires administered to patients and their parents and from patients' charts. OH performance worsened from T0mo to T1mo but then improved from T1mo to T5mo. At T5mo, 73% of the sample had good OH. Univariate analyses found perceived severity of malocclusion, school performance, and parental marital status to be significant predictors of good OH performance at T5mo. Multiple logistic regressions identified having married parents and good academic performance in school as significant predictors. In the sample studied, after initially worsening, compliance with OHI improved at 5 months after bonding. Adolescents with married parents and those reporting good academic performance in school were found more likely to have complied with OHI provided at baseline and to perform better OH.

A novel SWCNT-polyoxometalate nanohybrid material as an electrode for electrochemical supercapacitors

NASA Astrophysics Data System (ADS)

Chen, Han-Yi; Al-Oweini, Rami; Friedl, Jochen; Lee, Ching Yi; Li, Linlin; Kortz, Ulrich; Stimming, Ulrich; Srinivasan, Madhavi

2015-04-01

A novel nanohybrid material that combines single-walled carbon nanotubes (SWCNTs) with a polyoxometalate (TBA)5[PVV2MoVI10O40] (TBA-PV2Mo10, TBA: [(CH3(CH2)3)4N]+, tetra-n-butyl ammonium) is investigated for the first time as an electrode material for supercapacitors (SCs) in this study. The SWCNT-TBA-PV2Mo10 material has been prepared by a simple solution method which electrostatically attaches anionic [PV2Mo10O40]5- anions with organic TBA cations on the SWCNTs. The electrochemical performance of SWCNT-TBA-PV2Mo10 electrodes is studied in an acidic aqueous electrolyte (1 M H2SO4) by galvanostatic charge/discharge and cyclic voltammetry. In this SWCNT-TBA-PV2Mo10 nanohybrid material, TBA-PV2Mo10 provides redox activity while benefiting from the high electrical conductivity and high double-layer capacitance of the SWCNTs that improve both energy and power density. An assembled SWCNT-TBA-PV2Mo10 symmetric SC exhibits a 39% higher specific capacitance as compared to a symmetric SC employing only SWCNTs as electrode materials. Furthermore, the SWCNT-TBA-PV2Mo10 SC exhibits excellent cycling stability, retaining 95% of its specific capacitance after 6500 cycles.

Molybdenum Hydride and Dihydride Complexes Bearing Diphosphine Ligands with a Pendant Amine: Formation of Complexes With Bound Amines

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

Zhang, Shaoguang; Bullock, R. Morris

2015-07-06

CpMo(CO)(PNP)H complexes (PNP = (R2PCH2)2NMe, R = Et or Ph) were synthesized by displacement of two CO ligands of CpMo(CO)3H by the PNP ligand; these complexes were characterized by IR and variable temperature 1H and 31P NMR spectroscopy. CpMo(CO)(PNP)H complexes are formed as mixture of cis and trans-isomers. Both cis-CpMo(CO)(PEtNMePEt)H and trans-CpMo(CO)(PPhNMePPh)H were analyzed by single crystal X-ray diffraction. Electrochemical oxidation of CpMo(CO)(PEtNMePEt)H and CpMo(CO)(PPhNMePPh)H in CH3CN are both irreversible at slow scan rates and quasi-reversible at higher scan rates, with E1/2 = -0.36 V (vs. Cp2Fe+/0) for CpMo(CO)(PEtNMePEt)H and E1/2 = -0.18 V for CpMo(CO)(PPhNMePPh)H. Hydride abstraction from CpMo(CO)(PNP)Hmore » with [Ph3C]+[A]- (A = B(C6F5)4 or BArF4; [ArF = 3,5-bis(trifluoromethyl)phenyl]) afforded “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes that feature the amine bound to the metal. Displacement of the κ3 Mo-N bond by CD3CN gives [CpMo(CO)(PNP)(CD3CN)]+. The kinetics of this reaction were studied by NMR spectroscopy, providing the activation parameters ΔH‡ = 22.1 kcal/mol, ΔS‡ = 1.89 cal/(mol·K), Ea = 22.7 kcal/mol. Protonation of CpMo(CO)(PEtNMePEt)H affords [CpMo(CO)(κ2-PEtNMePEt)(H)2]+ as a Mo dihydride complex, which loses H2 to generate [CpMo(CO)(κ3-PEtNMePEt)]+ at room temperature. CpMo(CO)(dppp)H (dppp = 1,2-bis(diphenylphosphino)propane) was studied as a Mo diphosphine analogue without a pendant amine, and the product of protonation of this complex gives [CpMo(CO)(dppp)(H)2]+. Our results show that the pendant amine has a strong driving force to form stable “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes, and also promotes hydrogen elimination from [CpMo(CO)(PNP)(H)2]+ complexes by formation of Mo-N dative bond. We thank the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy. We thank Monte Helm, Elliott Hulley and Deanna Miller for help on the crystallography, and Ming Fang for assistance on the electrochemical experiments.« less

Molybdenum disulfide and water interaction parameters

NASA Astrophysics Data System (ADS)

Heiranian, Mohammad; Wu, Yanbin; Aluru, Narayana R.

2017-09-01

Understanding the interaction between water and molybdenum disulfide (MoS2) is of crucial importance to investigate the physics of various applications involving MoS2 and water interfaces. An accurate force field is required to describe water and MoS2 interactions. In this work, water-MoS2 force field parameters are derived using the high-accuracy random phase approximation (RPA) method and validated by comparing to experiments. The parameters obtained from the RPA method result in water-MoS2 interface properties (solid-liquid work of adhesion) in good comparison to the experimental measurements. An accurate description of MoS2-water interaction will facilitate the study of MoS2 in applications such as DNA sequencing, sea water desalination, and power generation.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Operator evolution for ab initio electric dipole transitions of 4He

DOE PAGES

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

2015-07-24

A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

Three-cluster dynamics within an ab initio framework

DOE PAGES

Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

2013-09-26

In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core ( 4He) polarization effects.« less

Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models

NASA Technical Reports Server (NTRS)

Rammacher, W.; Cuntz, M.

1991-01-01

Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

PubMed

Aalbergsjø, Siv G; Pauwels, Ewald; Van Yperen-De Deyne, Andy; Van Speybroeck, Veronique; Sagstuen, Einar

2014-08-28

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments.

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 86.094-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the Administrator may deem such certificate void ab initio. (4) In any case in which certification of... fraud or other misconduct as makes the certification invalid ab initio. (6) The manufacturer may request...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

Molybdenum Cycling During Crust Formation and Destruction

NASA Astrophysics Data System (ADS)

Greaney, A. T.; Rudnick, R. L.

2016-12-01

Molybdenum geochemistry has become an important tool for tracking the redox state of the early atmosphere and oceans as well as the emergence and sustainability of Mo-cofactored enzymes. However, in order for Mo to be enriched in the oceans, it must first be weathered out of the crust. Sulfides that weather in the presence of atmospheric O2have historically been deemed the predominant crustal source of Mo. Here, we test this assumption by determining the mineralogical hosts of Mo in Archean, Proterozoic, and Phanerozoic upper crustal rocks, using LA-ICP-MS. We also investigate Mo behavior during igneous differentiation and continental crust formation. We find that molybdenite, MoS2, is a weatherable sulfide source of Mo, but common igneous sulfides are not because their Mo concentrations are too low. However, molybdenite is uncommon in the upper continental crust. By contrast, volcanic glass is much more abundant and is a significant weatherable source of Mo that readily breaks down to release oxidized, soluble Mo whether or not atmospheric O2is present. Other common crustal mineral hosts of Mo are Ti-bearing phases like titanite, ilmenite, magnetite, and rutile that are resistant to weathering. Significant Mo depletion (relative to Ce and Pr) is observed in nearly every granitic rock analyzed in our study, but is not observed in OIB or MORB (Jenner and O'Neill, 2012). There are two possible reasons for this: 1) Mo is removed from cooling plutons during fluid expulsion, or 2) Mo is fractionated during igneous differentiation. The first scenario is a likely explanation given the solubility of oxidized Mo. However, correlations between Mo/Ce and Nb/La in several plutonic suites suggest a fractionating phase like rutile may sequester Mo in the lower crust. Additionally, a correlation between Mo/Ce and inferred tectonic setting (enrichments observed in rift-related plutons) suggest an overall tectonic influence on the availability of Mo in the upper crust.

Fe (hydro) oxide controls Mo isotope fractionation during the weathering of granite

NASA Astrophysics Data System (ADS)

Wang, Zhibing; Ma, Jinlong; Li, Jie; Wei, Gangjian; Zeng, Ti; Li, Lei; Zhang, Le; Deng, Wenfeng; Xie, Luhua; Liu, Zhifeng

2018-04-01

Understanding the fractionation mechanisms of Mo isotopes and seeking the main hosts of light δ98/95Mo during chemical weathering of continental rocks is a prerequisite for constraining heavy δ98/95Mo input into rivers. This study investigates the Mo concentrations and δ98/95Mo values of bulk samples, chemical extractions, and clay fractions of weathering products in a granite weathering profile in Guangdong province, South China, as well as in surrounding stream water. Results from bulk samples show that the τ MoTiO2 values systematically decrease from 59.1% to -77.0%, and δ98/95Mo values systematically increase from -1.46‰ to -0.17‰, upwards in the profile (from 30 to 0 m depth). Atmospheric input has a limited effect on δ98/95Mo variations in the weathering profile. Adsorption and desorption processes of Fe (hydro) oxide are the dominant factors controlling the variations in δ98/95Mo, with light Mo isotopes preferentially adsorbed by Fe (hydro) oxide, and released during desorption process, whereas the incongruent dissolution of primary minerals has little effect. Organic materials and the clay fraction are not the main hosts of light δ98/95Mo, as indicated by the results of chemical extractions, which show that a large proportion (41.5-86.2%) of total Mo with light δ98/95Mo (-1.57‰ to -0.59‰) is associated with Fe (hydro) oxide. Moreover, a significant positive correlation exists between Mo concentrations and δ98/95Mo in the Fe (hydro) oxide extractions from bulk samples. Finally, δ98/95Mo in stream water indicates the release of heavier δ98/95Mo into river water during the chemical weathering of granite rock. The results advance our understanding the mechanisms of Mo isotope fractionation during chemical weathering and its isotopic mass balance in Earth's surface system.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

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

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen

2015-02-09

In this study, the response of titanate pyrochlores (A 2Ti 2O 7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O 2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization inmore » titanate pyrochlores under laser, electron and ion irradiations.« less

Magnetic and Electronic Properties of h-BN Nanosheets with Nonmetal Atoms Adsorbed: an Ab Initio Study

NASA Astrophysics Data System (ADS)

Luo, M.; Yin, H. H.; Chu, J. H.

2018-04-01

The magnetic properties of the h-BN monolayer with nonmetal atoms are studied by ab initio methods. Different dopants (C, Cl, F, and O) and doping sites are considered. Magnetic behavior is observed in the two-dimensional (2D) BN system with C, Cl, and O atoms. On the other hand, the O adsorbed system shows a more stable formed structure among above three magnetic materials, we study the ferromagnetic (FM) interaction in 2D-BN system with two O adatoms. Interestingly, as the O-O distance increases, the interaction between two O adatoms prefers to a long-range FM coupling. This phenomenon could be well described by a simple Heisenberg model.

Ab-initio adsorption study of chitosan on functionalized graphene: critical role of van der Waals interactions.

PubMed

Rahman, R; Mazumdar, D

2012-03-01

We investigate the adsorption process of an organic biomolecule (chitosan) on epoxy-functionalized graphene using ab-initio density functional methods incorporating van-der-waals (vdW) interactions. The role of London dispersion force on the cohesive energy and conformal preference of the molecule is quantitatively elucidated. Functionalizing graphene with epoxy leads to weak hydrogen-bond interactions with chitosan. Binding energy values increase by over an order of magnitude after including vdW corrections, implying that dispersive interactions dominate the physisorption process. Conformal study show binding upto 30 kcal/mol when the molecule is oriented with the hydroxyl group approaching the functionalized graphene. Our study advances the promise of functionalized graphene for a variety of applications.

Combined experimental and ab initio study of the electronic structure of narrow-diameter single-wall carbon nanotubes with predominant (6,4),(6,5) chirality

NASA Astrophysics Data System (ADS)

de Blauwe, K.; Mowbray, D. J.; Miyata, Y.; Ayala, P.; Shiozawa, H.; Rubio, A.; Hoffmann, P.; Kataura, H.; Pichler, T.

2010-09-01

Narrow diameter tubes and especially (6,5) tubes with a diameter of 0.75 nm are currently one of the most studied carbon nanotubes because their unique optical and especially luminescence response makes them exceptionally suited for biomedical applications. Here we report on a detailed analysis of the electronic structure of nanotubes with (6,5) and (6,4) chiralities using a combined experimental and theoretical approach. From high-energy spectroscopy involving x-ray absorption and photoemission spectroscopy the detailed valence- and conduction-band response of these narrow diameter tubes is studied. The observed electronic structure is in sound agreement with state of the art ab initio calculations using density-functional theory.

Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

NASA Technical Reports Server (NTRS)

Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

2000-01-01

The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

Investigating the Geochemical Model for Molybdenum Mineralization in the JEB Tailings Management Facility at McClean Lake, Saskatchewan: An X-ray Absorption Spectroscopy Study.

PubMed

Blanchard, Peter E R; Hayes, John R; Grosvenor, Andrew P; Rowson, John; Hughes, Kebbi; Brown, Caitlin

2015-06-02

The geochemical model for Mo mineralization in the JEB Tailings Management Facility (JEB TMF), operated by AREVA Resources Canada at McClean Lake, Saskatchewan, was investigated using X-ray Absorption Near-Edge Spectroscopy (XANES), an elemental-specific technique that is sensitive to low elemental concentrations. Twenty five samples collected during the 2013 sampling campaign from various locations and depths in the TMF were analyzed by XANES. Mo K-edge XANES analysis indicated that the tailings consisted primarily of Mo(6+) species: powellite (CaMoO4), ferrimolybdite (Fe2(MoO4)3·8H2O), and molybdate adsorbed on ferrihydrite (Fe(OH)3 - MoO4). A minor concentration of a Mo(4+) species in the form of molybdenite (MoS2) was also present. Changes in the Mo mineralization over time were inferred by comparing the relative amounts of the Mo species in the tailings to the independently measured aqueous Mo pore water concentration. It was found that ferrimolybdite and molybdate adsorbed on ferrihydrite initially dissolves in the TMF and precipitates as powellite.

Lattice structures and electronic properties of MO/MoSe2 interface from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhang, Yu; Tang, Fu-Ling; Xue, Hong-Tao; Lu, Wen-Jiang; Liu, Jiang-Fei; Huang, Min

2015-02-01

Using first-principles plane-wave calculations within density functional theory, we theoretically studied the atomic structure, bonding energy and electronic properties of the perfect Mo (110)/MoSe2 (100) interface with a lattice mismatch less than 4.2%. Compared with the perfect structure, the interface is somewhat relaxed, and its atomic positions and bond lengths change slightly. The calculated interface bonding energy is about -1.2 J/m2, indicating that this interface is very stable. The MoSe2 layer on the interface has some interface states near the Fermi level, the interface states are mainly caused by Mo 4d orbitals, while the Se atom almost have no contribution. On the interface, Mo-5s and Se-4p orbitals hybridize at about -6.5 to -5.0 eV, and Mo-4d and Se-4p orbitals hybridize at about -5.0 to -1.0 eV. These hybridizations greatly improve the bonding ability of Mo and Se atom in the interface. By Bader charge analysis, we find electron redistribution near the interface which promotes the bonding of the Mo and MoSe2 layer.

Design of a Fission 99 Mo Recovery Process and Implications toward Mo Adsorption Mechanism on Titania and Alumina Sorbents

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

Stepinski, Dominique C.; Youker, Amanda J.; Krahn, Elizabeth O.

2017-03-01

Molybdenum-99 is a parent of the most widely used medical isotope technetium-99m. Proliferation concerns have prompted development of alternative Mo production methods utilizing low enriched uranium. Alumina and titania sorbents were evaluated for separation of Mo from concentrated uranyl nitrate solutions. System, mass transfer, and isotherm parameters were determined to enable design of Mo separation processes under a wide range of conditions. A model-based approach was utilized to design representative commercial-scale column processes. The designs and parameters were verified with bench-scale experiments. The results are essential for design of Mo separation processes from irradiated uranium solutions, selection of support materialmore » and process optimization. Mo uptake studies show that adsorption decreases with increasing concentration of uranyl nitrate; howeveL, examination of Mo adsorption as a function of nitrate ion concentration shows no dependency, indicating that uranium competes with Mo for adsorption sites. These results are consistent with reports indicating that Mo forms inner-sphere complexes with titania and alumina surface groups.« less

Effect of Mo on Microstructures and Wear Properties of In Situ Synthesized Ti(C,N)/Ni-Based Composite Coatings by Laser Cladding.

PubMed

Wu, Fan; Chen, Tao; Wang, Haojun; Liu, Defu

2017-09-06

Using Ni60 alloy, C, TiN and Mo mixed powders as the precursor materials, in situ synthesized Ti(C,N) particles reinforcing Ni-based composite coatings are produced on Ti6Al4V alloys by laser cladding. Phase constituents, microstructures and wear properties of the composite coatings with 0 wt % Mo, 4 wt % Mo and 8 wt % Mo additions are studied comparatively. Results indicate that Ti(C,N) is formed by the in situ metallurgical reaction, the (Ti,Mo)(C,N) rim phase surrounding the Ti(C,N) ceramic particle is synthesized with the addition of Mo, and the increase of Mo content is beneficial to improve the wear properties of the cladding coatings. Because of the effect of Mo, the grains are remarkably refined and a unique core-rim structure that is uniformly dispersed in the matrix appears; meanwhile, the composite coatings with Mo addition exhibit high hardness and excellent wear resistance due to the comprehensive action of dispersion strengthening, fine grain strengthening and solid solution strengthening.

Effect of Mo on Microstructures and Wear Properties of In Situ Synthesized Ti(C,N)/Ni-Based Composite Coatings by Laser Cladding

PubMed Central

Chen, Tao; Wang, Haojun

2017-01-01

Using Ni60 alloy, C, TiN and Mo mixed powders as the precursor materials, in situ synthesized Ti(C,N) particles reinforcing Ni-based composite coatings are produced on Ti6Al4V alloys by laser cladding. Phase constituents, microstructures and wear properties of the composite coatings with 0 wt % Mo, 4 wt % Mo and 8 wt % Mo additions are studied comparatively. Results indicate that Ti(C,N) is formed by the in situ metallurgical reaction, the (Ti,Mo)(C,N) rim phase surrounding the Ti(C,N) ceramic particle is synthesized with the addition of Mo, and the increase of Mo content is beneficial to improve the wear properties of the cladding coatings. Because of the effect of Mo, the grains are remarkably refined and a unique core-rim structure that is uniformly dispersed in the matrix appears; meanwhile, the composite coatings with Mo addition exhibit high hardness and excellent wear resistance due to the comprehensive action of dispersion strengthening, fine grain strengthening and solid solution strengthening. PMID:28878190

Quality of Life After Open Radical Prostatectomy Compared with Robot-assisted Radical Prostatectomy.

PubMed

Wallerstedt, Anna; Nyberg, Tommy; Carlsson, Stefan; Thorsteinsdottir, Thordis; Stranne, Johan; Tyritzis, Stavros I; Stinesen Kollberg, Karin; Hugosson, Jonas; Bjartell, Anders; Wilderäng, Ulrica; Wiklund, Peter; Steineck, Gunnar; Haglind, Eva

2018-01-20

Surgery for prostate cancer has a large impact on quality of life (QoL). To evaluate predictors for the level of self-assessed QoL at 3 mo, 12 mo, and 24 mo after robot-assisted laparoscopic (RALP) and open radical prostatectomy (ORP). The LAParoscopic Prostatectomy Robot Open study, a prospective, controlled, nonrandomised trial of more than 4000 men who underwent radical prostatectomy at 14 centres. Here we report on QoL issues after RALP and ORP. The primary outcome was self-assessed QoL preoperatively and at 3 mo, 12 mo, and 24 mo postoperatively. A direct validated question of self-assessed QoL on a seven-digit visual scale was used. Differences in QoL were analysed using logistic regression, with adjustment for confounders. QoL did not differ between RALP and ORP postoperatively. Men undergoing ORP had a preoperatively significantly lower level of self-assessed QoL in a multivariable analysis compared with men undergoing RALP (odds ratio: 1.21, 95% confidence interval: 1.02-1.43), that disappeared when adjusted for preoperative preparedness for incontinence, erectile dysfunction, and certainty of being cured (odds ratio: 1.18, 95% confidence interval: 0.99-1.40). Incontinence and erectile dysfunction increased the risk for poor QoL at 3 mo, 12 mo, and 24 mo postoperatively. Biochemical recurrence did not affect QoL. A limitation of the study is the nonrandomised design. QoL at 3 mo, 12 mo, and 24 mo after RALP or ORP did not differ significantly between the two techniques. Poor QoL was associated with postoperative incontinence and erectile dysfunction but not with early cancer relapse, which was related to thoughts of death and waking up at night with worry. We did not find any difference in quality of life at 3 mo, 12 mo, and 24 mo when open and robot-assisted surgery for prostate cancer were compared. Postoperative incontinence and erectile dysfunction were associated with poor quality of life. Copyright © 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Contributions of phase, sulfur vacancies, and edges to the hydrogen evolution reaction catalytic activity of porous molybdenum disulfide nanosheets

DOE PAGES

Yin, Ying; Han, Jiecai; Zhang, Yumin; ...

2016-06-07

Molybdenum disulfide (MoS 2) is a promising nonprecious catalyst for the hydrogen evolution reaction (HER) that has been extensively studied due to its excellent performance, but the lack of understanding of the factors that impact its catalytic activity hinders further design and enhancement of MoS 2-based electrocatalysts. Here, by using novel porous (holey) metallic 1T phase MoS 2 nanosheets synthesized by a liquid-ammonia-assisted lithiation route, we systematically investigated the contributions of crystal structure (phase), edges, and sulfur vacancies (S-vacancies) to the catalytic activity toward HER from five representative MoS 2 nanosheet samples, including 2H and 1T phase, porous 2H andmore » 1T phase, and sulfur-compensated porous 2H phase. Superior HER catalytic activity was achieved in the porous 1T phase MoS 2 nanosheets that have even more edges and S-vacancies than conventional 1T phase MoS 2. A comparative study revealed that the phase serves as the key role in determining the HER performance, as 1T phase MoS 2 always outperforms the corresponding 2H phase MoS 2 samples, and that both edges and S-vacancies also contribute significantly to the catalytic activity in porous MoS 2 samples. Then, using combined defect characterization techniques of electron spin resonance spectroscopy and positron annihilation lifetime spectroscopy to quantify the S-vacancies, the contributions of each factor were individually elucidated. Furthermore, this study presents new insights and opens up new avenues for designing electrocatalysts based on MoS 2 or other layered materials with enhanced HER performance.« less

Contributions of phase, sulfur vacancies, and edges to the hydrogen evolution reaction catalytic activity of porous molybdenum disulfide nanosheets

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

Yin, Ying; Han, Jiecai; Zhang, Yumin

Molybdenum disulfide (MoS 2) is a promising nonprecious catalyst for the hydrogen evolution reaction (HER) that has been extensively studied due to its excellent performance, but the lack of understanding of the factors that impact its catalytic activity hinders further design and enhancement of MoS 2-based electrocatalysts. Here, by using novel porous (holey) metallic 1T phase MoS 2 nanosheets synthesized by a liquid-ammonia-assisted lithiation route, we systematically investigated the contributions of crystal structure (phase), edges, and sulfur vacancies (S-vacancies) to the catalytic activity toward HER from five representative MoS 2 nanosheet samples, including 2H and 1T phase, porous 2H andmore » 1T phase, and sulfur-compensated porous 2H phase. Superior HER catalytic activity was achieved in the porous 1T phase MoS 2 nanosheets that have even more edges and S-vacancies than conventional 1T phase MoS 2. A comparative study revealed that the phase serves as the key role in determining the HER performance, as 1T phase MoS 2 always outperforms the corresponding 2H phase MoS 2 samples, and that both edges and S-vacancies also contribute significantly to the catalytic activity in porous MoS 2 samples. Then, using combined defect characterization techniques of electron spin resonance spectroscopy and positron annihilation lifetime spectroscopy to quantify the S-vacancies, the contributions of each factor were individually elucidated. Furthermore, this study presents new insights and opens up new avenues for designing electrocatalysts based on MoS 2 or other layered materials with enhanced HER performance.« less

Molybdenum speciation and burial pathway in weakly sulfidic environments: Insights from XAFS

NASA Astrophysics Data System (ADS)

Wagner, Meghan; Chappaz, Anthony; Lyons, Timothy W.

2017-06-01

Sedimentary molybdenum (Mo) accumulation is a robust proxy for sulfidic conditions in both modern and ancient aquatic systems and has been used to infer changing marine redox chemistry throughout Earth's history. Accurate interpretation of any proxy requires a comprehensive understanding of its biogeochemical cycling, but knowledge gaps remain concerning the geochemical mechanism(s) leading to Mo burial in anoxic sediments. Better characterization of Mo speciation should provide mechanistic insight into sedimentary Mo accumulation, and therefore in this study we investigate Mo speciation from both modern (Castle Lake, USA) and ancient (Doushantuo Formation, China) environments using X-ray Absorption Near Edge Structure (XANES) spectroscopy. By utilizing a series of laboratory-synthesized oxythiomolybdate complexes-many containing organic ligands-we expand the number of available standards to encompass a greater range of known Mo chemistry and test the linkage between Mo and total organic carbon (TOC). In weakly euxinic systems ([H2S(aq)] < 11 μM), or where sulfide is restricted to pore waters, natural samples are best represented by a linear combination of MoO3, MoOxS4-x2- (intermediate thiomolybdates), and [MoOx(cat)4-x]2- (cat = catechol, x = 2 or 3). These results suggest a revised model for how Mo accumulates in weakly sulfidic sediments, including a previously unrecognized role for organic matter in early sequestration of Mo and a de-emphasized importance for MoS42- (tetrathiomolybdate).

Hydrothermal synthesis of flower-like MoS2 nanospheres for electrochemical supercapacitors.

PubMed

Zhou, Xiaoping; Xu, Bin; Lin, Zhengfeng; Shu, Dong; Ma, Lin

2014-09-01

Flower-like MoS2 nanospheres were synthesized by a hydrothermal route. The structure and surface morphology of the as-prepared MoS2 was characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The supercapacitive behavior of MoS2 in 1 M KCl electrolyte was studied by means of cyclic voltammetry (CV), constant current charge-discharge cycling (CD) and electrochemical impedance spectroscopy (EIS). The XRD results indicate that the as-prepared MoS2 has good crystallinity. SEM images show that the MoS2 nanospheres have uniform sizes with mean diameter about 300 nm. Many nanosheets growing on the surface make the MoS2 nanospheres to be a flower-like structure. The specific capacitance of MoS2 is 122 F x g(-1) at 1 A x g(-1) or 114 F x g(-1) at 2 mv s(-1). All the experimental results indicate that MoS2 is a promising electrode material for electrochemical supercapacitors.

Electrochemical preparation of carbon films with a Mo2C interlayer in LiCl-NaCl-Na2CO3 melts

NASA Astrophysics Data System (ADS)

Ge, Jianbang; Wang, Shuai; Zhang, Feng; Zhang, Long; Jiao, Handong; Zhu, Hongmin; Jiao, Shuqiang

2015-08-01

The electrodeposition of carbon films with a Mo2C interlayer was investigated in LiCl-NaCl-Na2CO3 melts at 900 °C. Cyclic voltammetry was applied to study the electrochemical reaction mechanism on Mo and Pt electrodes, indicating that, two reduction reactions including carbon deposition and carbon monoxide evolution, may take place on the two electrodes simultaneously during the cathodic sweep. Carbon films with a continuous Mo2C interlayer were prepared by constant voltage electrolysis, showing a good adhesion between Mo substrate and carbon films. The carbon films with a Mo2C interlayer were characterized using X-ray diffraction measurement, Raman spectroscopy, scanning electron microscopy and transmission electron microscopy. The results reveal that carbon materials deposited on the electrodes are mainly composed of graphite and carbon diffusion in Mo (or Mo2C) leads to the formation and growth of Mo2C interlayer.

Development and characterization of (Ti, Mo)C carbides reinforced Fe-based surface composite coating produced by laser cladding

NASA Astrophysics Data System (ADS)

Wang, Xinhong; Zhang, Min; Qu, Shiyao

2010-09-01

In this study, in situ multiple carbides reinforced Fe-based surface composite coatings were fabricated successfully by laser cladding a precursor mixture of graphite, ferrotitanium (Fe-Ti) and ferromolybdenum (Fe-Mo) powders. The results showed that (Ti, Mo)C particles with flower-like and cuboidal shapes were in situ formed during the solidification and most shapes of (Ti, Mo)C particles were diversiform according to different contents of Fe-Mo powder in the Fe-Ti-Mo-C system. The growth morphology of the reinforcing (Ti, Mo)C carbide has typically faceted features, indicating that the lateral growth mechanism is still predominant growth mode under rapid solidification conditions. Increasing the amount of Fe-Mo in the reactants led to a decrease of carbide size and an increase of volume fraction of carbides. The coatings had good cracking resistance when the amounts of Fe-Mo were controlled within a range of 15 wt%.

Molybdenum modified phosphate glasses studied by 31P MAS NMR and Raman spectroscopy.

PubMed

Szumera, Magdalena

2015-02-25

Glasses have been synthesized in the system P2O5-SiO2-K2O-MgO-CaO modified by addition of MoO3. Glasses were prepared by conventional fusion method from 40 g batches. The influence of Mo-cations on the analysed glass structure was investigated by means of Raman and (31)P MAS-NMR techniques. It has been found that molybdate units can form Mo[MoO4/MoO6]-O-P and/or Mo[MoO4/MoO6]-O-Si bonds with non-bridging oxygens atoms of Q2 methaphosphate units, resulting in the transformation of chain methaphosphate structure into pyrophosphate and finally into orthophosphate structure. It has been also found that increasing amount of MoO3 in the structure of investigated glasses causes their gradual depolymerization and molybdenum ions in the analysed glass matrix act as modifying cations. Copyright © 2014 Elsevier B.V. All rights reserved.

The nonconservative property of dissolved molybdenum in the western Taiwan Strait: Relevance of submarine groundwater discharges and biological utilization

NASA Astrophysics Data System (ADS)

Wang, Deli; Xia, Weiwei; Lu, Shuimiao; Wang, Guizhi; Liu, Qian; Moore, Willard S.; Arthur Chen, Chen-Tung

2016-01-01

This study examined dissolved Mo and sedimentary Mo along with hydrochemical parameters in the western Taiwan Strait (WTS) in May and August 2012. The results demonstrate that dissolved Mo could be depleted of as high as 10-20 nM during our May sampling period when the nutrient-enriched Min-Zhe coastal current ceased and spring blooms developed. The negative correlation between Chl-a and dissolved Mo suggests the possible involvement of high algal productivity in removing dissolved Mo out of the water column. Specific oceanographic settings (little currents) permitted a high sedimentary enrichment of Mo (>6 µg/g Mo) within the highly productive waters outside the Jiulong River mouth. Possibly, the high algal productivities and consequent organic matter sinks provide a pathway of Mo burial from water columns into sediments. Dissolved Mo was relatively high in groundwater samples, but we observed that submarine groundwater discharges (SGDs) only contributed to a relatively small percentage of the total dissolved Mo pool in WTS. It is probably attributable to the immediate removal of SGD-released Mo ions via adsorption onto newly formed Mn oxides once exposed to oxygenated seawater, followed by an elevated sedimentary Mo accumulation near the SGDs (˜5 µg/g). In addition to metal oxide particle scavenging and sulfide precipitation, we estimated that biological uptake along with Mo adsorption onto organic matter carriers could finally provide more than 10% of the annual sedimentary Mo accumulation in WTS.

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

Dietary toxicity of soluble and insoluble molybdenum to northern bobwhite quail (Colinus virginianus).

PubMed

Stafford, Jennifer M; Lambert, Charles E; Zyskowski, Justin A; Engfehr, Cheryl L; Fletcher, Oscar J; Clark, Shanna L; Tiwary, Asheesh; Gulde, Cynthia M; Sample, Bradley E

2016-03-01

Limited data are available on the effects of molybdenum (Mo) on avian wildlife, which impairs evaluation of ecological exposure and risk. While Mo is an essential trace nutrient in birds, little is known of its toxicity to birds exposed to molybdenum disulfide (MoS2), the predominant form found in molybdenite ore. The chemical form and bioavailability of Mo is important in determining its toxicity. Avian toxicity tests typically involve a soluble form of Mo, such as sodium molybdate dihydrate (SMD, Na2MoO4·2H2O); however MoS2 is generally insoluble, with low bioaccessibility under most environmental conditions. The current study monitored survival and general health (body weight and food consumption) of 9-day old northern bobwhite exposed to soluble Mo (SMD) and ore-related Mo (MoS2) in their diet for 30 days. Toxicity and bioavailability (e.g. tissue distribution) of the two Mo forms were compared. Histopathology evaluations and serum, kidney, liver, and bone tissue sample analyses were conducted. Copper, a nutrient integrally associated with Mo toxicity, was also measured in the diet and tissue. No treatment-related mortality occurred and no treatment-related lesions were recorded for either Mo form. Tissue analyses detected increased Mo concentrations in serum, kidney, liver, and bone tissues following exposure to SMD, with decreasing concentrations following a post-exposure period. For the soluble form, a No-Observed-Adverse-Effect Concentration (NOAEC) of 1200 mg Mo as SMD/kg feed (134 mg SMD/kg body weight/day) was identified based on body weight and food consumption. No adverse effects were observed in birds exposed to MoS2 at the maximum dose of 5000 mg MoS2/kg feed (545 mg MoS2/kg body weight/day). These results show that effects associated with MoS2, the more environmentally prevalent and less bioavailable Mo form, are much less than those observed for SMD. These data should support more realistic representations of exposure and risks to avian receptors from environmental Mo.

An ab initio study of ion induced charge transfer dynamics in collision of carbon ions with thymine.

PubMed

Bacchus-Montabonel, Marie-Christine; Tergiman, Yvette Suzanne

2011-05-28

Charge transfer in collisions of carbon ions on a thymine target has been studied theoretically in a wide collision range by means of ab initio quantum chemistry molecular methods. The process appears markedly anisotropic in the whole energy domain, significantly favoured in the perpendicular orientation. A specific decrease of the charge transfer cross sections at low collision energies may be pointed out and could induce an enhancement of the complementary fragmentation processes for collision energies down to about 10 eV, as observed for the low-electron fragmentation process. Such feature may be of important interest in ion-induced biomolecular radiation damage. This journal is © the Owner Societies 2011

Ab Initio Density Functional Calculations and Infra-Red Study of CO Interaction with Pd Atoms on θ-Al2O3 (010) Surface.

PubMed

Narula, Chaitanya K; Allard, Lawrence F; Wu, Zili

2017-07-24

The ab initio density functional theoretical studies show that energetics favor CO oxidation on single Pd atoms supported on θ-alumina. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show that carbonates are formed as intermediates when single supported Pd atoms are exposed to a gaseous mixture of CO + O 2 . The rapid agglomeration of Pd atoms under CO oxidation conditions even at 6 °C leads to the presence of Pd particles along with single atoms during CO oxidation experiments. Thus, the observed CO oxidation has contributions from both single Pd atoms and Pd particles.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

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

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

PubMed Central

Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.

2015-01-01

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219

Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride

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

Koskelo, J., E-mail: jaakko.koskelo@helsinki.fi; Juurinen, I.; Ruotsalainen, K. O.

2014-12-28

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting futuremore » experiments.« less

Ab initio calculation of the G peak intensity of graphene: Laser-energy and Fermi-energy dependence and importance of quantum interference effects

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

2017-05-01

We present the results of a diagrammatic, fully ab initio calculation of the G peak intensity of graphene. The flexibility and generality of our approach enables us to go beyond the previous analytical calculations in the low-energy regime. We study the laser and Fermi energy dependence of the G peak intensity and analyze the contributions from resonant and nonresonant electronic transitions. In particular, we explicitly demonstrate the importance of quantum interference and nonresonant states for the G peak process. Our method of analysis and computational concept is completely general and can easily be applied to study other materials as well.

Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

PubMed

Koukounas, Constantine; Mavridis, Aristides

2008-11-06

The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

PubMed

Xiao, H Y; Weber, W J; Zhang, Y; Zu, X T; Li, S

2015-02-09

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

Ab Initio Study of Interfacial Structure Transformation of Amorphous Carbon Catalyzed by Ti, Cr, and W Transition Layers.

PubMed

Li, Xiaowei; Li, Lei; Zhang, Dong; Wang, Aiying

2017-11-29

Amorphous carbon (a-C) films composited with transition layers exhibit the desirable improvement of adhesion strength between films and substrate, but the further understanding on the interfacial structure transformation of a-C structure induced by transition layers is still lacked. In this paper, using ab initio calculations, we comparatively studied the interfacial structure between Ti, Cr, or W transition layers and a-C film from the atomic scale, and demonstrated that the addition of Ti, Cr, or W catalyzed the graphitic transformation of a-C structure at different levels, which provided the theoretical guidance for designing a multilayer nanocomposite film for renewed application.

Synthesis of α-MoO3 nano-flakes by dry oxidation of RF sputtered Mo thin films and their application in gas sensing

NASA Astrophysics Data System (ADS)

Dwivedi, Priyanka; Dhanekar, Saakshi; Das, Samaresh

2016-11-01

Synthesis of orthorhombic (α) MoO3 nano-flakes by dry oxidation of RF sputtered Mo thin film is presented. The influence of Mo thickness variation, oxidation temperature and time on the crystallographic structure, surface morphology and roughness of MoO3 thin films was studied using SEM, AFM, XRD and Raman spectroscopy. A structural study shows that MoO3 is polycrystalline in nature with an α phase. It was noticed that oxidation temperature plays an important role in the formation of nano-flakes. The synthesis technique proposed is simple and suitable for large scale productions. The synthesis parameters were optimized for the fabrication of sensors. Chrome gold-based IDE (interdigitated electrodes) structures were patterned for the electrical detection of organic vapors. Sensors were exposed to wide range 5-100 ppm of organic vapors like ethanol, acetone, IPA (isopropanol alcohol) and water vapors. α-MoO3 nano-flakes have demonstrated selective sensing to acetone in the range of 10-100 ppm at 150 °C. The morphology of such nanostructures has potential in applications such as sensor devices due to their high surface area and thermal stability.

Orbital Dimer Model for the Spin-Glass State in Y 2 Mo 2 O 7

DOE PAGES

Thygesen, Peter M. M.; Paddison, Joseph A. M.; Zhang, Ronghuan; ...

2017-02-08

The formation of a spin glass generally requires that magnetic exchange interactions are both frustrated and disordered. Consequently, the origin of spin-glass behavior in Y 2Mo 2O 7-in which magnetic Mo 4+ ions occupy a frustrated pyrochlore lattice with minimal compositional disorder-has been a longstanding question. Here, we use neutron and x-ray pair-distribution function (PDF) analysis to develop a disorder model that resolves apparent incompatibilities between previously reported PDF, extended x-rayabsorption fine structure spectroscopy, and NMR studies, and provides a new and physical explanation of the exchange disorder responsible for spin-glass formation. We show that Mo 4+ ions displace accordingmore » to a local "two-in-two-out" rule on each Mo 4 tetrahedron, driven by orbital dimerization of Jahn-Teller active Mo 4+ ions. Long-range orbital order is prevented by the macroscopic degeneracy of dimer coverings permitted by the pyrochlore lattice. Cooperative O 2- displacements yield a distribution of Mo-O-Mo angles, which in turn introduces disorder into magnetic interactions. In conclusion, our study demonstrates experimentally how frustration of atomic displacements can assume the role of compositional disorder in driving a spin-glass transition.« less

Orbital Dimer Model for the Spin-Glass State in Y_{2}Mo_{2}O_{7}.

PubMed

Thygesen, Peter M M; Paddison, Joseph A M; Zhang, Ronghuan; Beyer, Kevin A; Chapman, Karena W; Playford, Helen Y; Tucker, Matthew G; Keen, David A; Hayward, Michael A; Goodwin, Andrew L

2017-02-10

The formation of a spin glass generally requires that magnetic exchange interactions are both frustrated and disordered. Consequently, the origin of spin-glass behavior in Y_{2}Mo_{2}O_{7}-in which magnetic Mo^{4+} ions occupy a frustrated pyrochlore lattice with minimal compositional disorder-has been a longstanding question. Here, we use neutron and x-ray pair-distribution function (PDF) analysis to develop a disorder model that resolves apparent incompatibilities between previously reported PDF, extended x-ray-absorption fine structure spectroscopy, and NMR studies, and provides a new and physical explanation of the exchange disorder responsible for spin-glass formation. We show that Mo^{4+} ions displace according to a local "two-in-two-out" rule on each Mo_{4} tetrahedron, driven by orbital dimerization of Jahn-Teller active Mo^{4+} ions. Long-range orbital order is prevented by the macroscopic degeneracy of dimer coverings permitted by the pyrochlore lattice. Cooperative O^{2-} displacements yield a distribution of Mo-O-Mo angles, which in turn introduces disorder into magnetic interactions. Our study demonstrates experimentally how frustration of atomic displacements can assume the role of compositional disorder in driving a spin-glass transition.

Montreal Cognitive Assessment (MoCA): validation study for frontotemporal dementia.

PubMed

Freitas, Sandra; Simões, Mário R; Alves, Lara; Duro, Diana; Santana, Isabel

2012-09-01

The Montreal Cognitive Assessment (MoCA) is a brief instrument developed for the screening of milder forms of cognitive impairment, having surpassed the well-known limitations of the Mini-Mental State Examination (MMSE). The aim of the present study was to validate the MoCA as a cognitive screening test for behavioral-variant frontotemporal dementia (bv-FTD) by examining its psychometric properties and diagnostic accuracy. Three matched subgroups of participants were considered: bv-FTD (n = 50), Alzheimer disease (n = 50), and a control group of healthy adults (n = 50). Compared with the MMSE, the MoCA demonstrated consistently superior psychometric properties and discriminant capacity, providing comprehensive information about the patients' cognitive profiles. The diagnostic accuracy of MoCA for bv-FTD was extremely high (area under the curve AUC [MoCA] = 0.934, 95% confidence interval [CI] = 0.866-.974; AUC [MMSE] = 0.772, 95% CI = 0.677-0.850). With a cutoff below 17 points, the MoCA results for sensitivity, specificity, positive predictive value, negative predictive value, and classification accuracy were significantly superior to those of the MMSE. The MoCA is a sensitive and accurate instrument for screening the patients with bv-FTD and represents a better option than the MMSE.

Micro-structural study and Rietveld analysis of fast reactor fuels: U-Mo fuels

NASA Astrophysics Data System (ADS)

Chakraborty, S.; Choudhuri, G.; Banerjee, J.; Agarwal, Renu; Khan, K. B.; Kumar, Arun

2015-12-01

U-Mo alloys are the candidate fuels for both research reactors and fast breeder reactors. In-reactor performance of the fuel depends on the microstructural stability and thermal properties of the fuel. To improve the fuel performance, alloying elements viz. Zr, Mo, Nb, Ti and fissium are added in the fuel. The first reactor fuels are normally prepared by injection casting. The objective of this work is to compare microstructure, phase-fields and hardness of as-cast four different U-Mo alloy (2, 5, 10 and 33 at.% Mo) fuels with the equilibrium microstructure of the alloys. Scanning electron microscope with energy dispersive spectrometer and optical microscope have been used to characterize the morphology of the as-cast and annealed alloys. The monoclinic α'' phase in as-cast U-10 at.% Mo alloy has been characterized through Rietveld analysis. A comparison of metallographic and Rietveld analysis of as-cast (dendritic microstructure) and annealed U-33 at.% Mo alloy, corresponding to intermetallic compound, has been reported here for the first time. This study will provide in depth understanding of microstructural and phase evolution of U-Mo alloys as fast reactor fuel.

Is There a Cardiotoxicity Associated With Metallic Head Hip Prostheses? A Cohort Study in the French National Health Insurance Databases.

PubMed

Lassalle, Marion; Colas, Sandrine; Rudnichi, Annie; Zureik, Mahmoud; Dray-Spira, Rosemary

2018-07-01

There are four distinguishable types of THA devices in wide use, as defined by the femoral and acetabular bearing surfaces: metal-on-polyethylene (MoP), ceramic-on-polyethylene (CoP), metal-on-metal (MoM), and ceramic-on-ceramic (CoC). Metallic head THAs (MoP and MoM) can potentially induce cardiac toxicity because cobalt species, generated at the head-neck trunnion, and in the case of MoM devices, at the articular surface as well, can be absorbed systemically. However, studies have provided inconsistent results. The purpose of this study was to assess the risk of dilated cardiomyopathy (DCM) or heart failure (HF) associated with metallic head THAs using data from the French national health insurance databases. Between 2008 and 2011 in France, 399,968 patients ≥ 55 years had a first THA. A total of 127,481 were excluded after we applied the exclusion criteria regarding arthroplasty and 17,137 as a result of a history of DCM/HF, recorded in the French national health insurance reimbursement databases, between January 1, 2006, and the date of inclusion. The final cohort included 255,350 individuals (43% men; mean age 72 ± 9 years). Of them, 93,581 (37%) had been implanted with MoP, 58,095 (23%) with CoP, 11,298 (4%) with MoM, and 92,376 (36%) with CoC THAs. Patients were followed until December 2015. Patients with incident DCM/HF were identified by a new entitlement to the long-term disease scheme or a first hospitalization with a diagnosis of DCM or HF. MoP and CoP THAs are generally implanted in old patients, whereas MoM and CoC are mostly indicated in young, active male patients. Thus, to consider the specific indications of the bearing couples, analyses were separately performed in two distinct subcohorts, one comprising patients with MoP or CoP and one comprising patients with MoM or CoC THA. In each subcohort, the DCM/HF risk was compared between patients with metallic head versus nonmetallic head THAs (MoP versus CoP, MoM versus CoC). Hazard ratios (adjusted HRs) of incident DCM/HF were estimated using Cox models adjusted for baseline sex, age, THA characteristics (fixation technique with cement, use of a modular femoral neck), and comorbidities at baseline. Cox models were stratified by sex and age. The crude incidence of DCM/HF per 100 person-years was 2.4 in patients with MoP, 1.8 with CoP, 1.2 with MoM, and 1.1 with CoC THAs. Overall, metallic head THAs were associated with a slight increase in DCM/HF risk (MoP versus CoP: adjusted HR, 1.08; 95% confidence interval [CI], 1.05-1.12; p < 0.001; MoM versus CoC: adjusted HR, 1.11; 95% CI, 1.03-1.19; p = 0.007). In the MoM-CoC subcohort, the risk tended to be more pronounced with MoM versus CoC THAs in women (MoM versus CoC: adjusted HR, 1.20; 95% CI, 1.07-1.35; p = 0.002) and patients aged ≥ 75 years (MoM versus CoC: adjusted HR, 1.16; 95% CI, 1.04-1.29; p = 0.009). Metallic head THAs were associated with a slightly increased DCM/HF risk, especially with MoM in women and older patients. Some caveats should be mentioned: severity of DCM or HF was not available and residual confounding cannot be ruled out despite considering many covariates. Our findings suggest that cardiac function should be regularly monitored in patients with metallic head THAs. Further investigations should be planned on large international cohorts. Level III, therapeutic study.

Hydrogen attack in Cr-Mo steels. [3Cr-1. 5Mo and 2. 25Cr-1Mo steels

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

Ruoff, S.; Stone, D.; Wanagel, J.

Experiments conducted upon 3Cr-1.5Mo steel at elevated temperatures (600 C), and high pressure hydrogen (2000 psi), have shown a greater resistence to hydrogen attack compared with similar studies of 2.25Cr-lMo steels. Hydrogen exposure tests with and without an applied stress have been performed on both types of steels. Results of similar conditions show clear evidence of hydrogen attack in 2.25Cr-lMo steel, however, for the 3Cr-1.5Mo steel with exposure time up to 80 days without an applied stress no evidence of hydrogen attack is observed. For stress-rupture tests using stresses of 14 and 16 ksi, the 3Cr-1.5Mo steel showed no effectsmore » of hydrogen attack, and no damage was observed using a SEM.« less