Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry.

PubMed

Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

2017-02-01

Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C-C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

Mechanism of vibrational energy dissipation of free OH groups at the air-water interface.

PubMed

Hsieh, Cho-Shuen; Campen, R Kramer; Okuno, Masanari; Backus, Ellen H G; Nagata, Yuki; Bonn, Mischa

2013-11-19

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air-water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air-H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces.

Mechanism of vibrational energy dissipation of free OH groups at the air–water interface

PubMed Central

Hsieh, Cho-Shuen; Campen, R. Kramer; Okuno, Masanari; Backus, Ellen H. G.; Nagata, Yuki; Bonn, Mischa

2013-01-01

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air–water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air–H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces. PMID:24191016

Theoretical Studies on Structures and Relative Stability for Polynitrohexaazaadamantanes

NASA Astrophysics Data System (ADS)

Xu, Xiao-juan; Xiao, He-ming; Wang, Gui-xiang; Ju, Xue-hai

2006-10-01

The density function theory at the B3LYP/6-31G* level was employed to study the structures, including the total energies (EZPE), the geometries, the oxygen balances (OB100), the dipole moments, of polynitro-hexaazaadamantanes (PNHAAs) and the potential candidates of high energy density compounds (HEDCs). The structural parameters of PNHAAs, such as the the maximum N—NO2 bond length (LBmax), the least N—N Mulliken population (BN—N), the least negative charge on the nitro group (QNO2) and OB100, were studied to predict their relative stability or sensitivity (the easiness for initiating a detonation, high sensitivity means low stability). It was found that the same conclusion was drawn from the four parameters. With the number of nitro groups increasing, the stabilities of these compounds decrease. OB100 failed in identifying the isomers, but the EZPE energy and the dipole moment were considered to give more reliable results for the isomers.

Observation time scale, free-energy landscapes, and molecular symmetry

PubMed Central

Wales, David J.; Salamon, Peter

2014-01-01

When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely atomic clusters and alanine dipeptide, highlighting the connections to broken ergodicity, local equilibrium, and “feasible” symmetry operations of the molecular Hamiltonian. PMID:24374625

Quasiparticle semiconductor band structures including spin-orbit interactions.

PubMed

Malone, Brad D; Cohen, Marvin L

2013-03-13

We present first-principles calculations of the quasiparticle band structure of the group IV materials Si and Ge and the group III-V compound semiconductors AlP, AlAs, AlSb, InP, InAs, InSb, GaP, GaAs and GaSb. Calculations are performed using the plane wave pseudopotential method and the 'one-shot' GW method, i.e. G(0)W(0). Quasiparticle band structures, augmented with the effects of spin-orbit, are obtained via a Wannier interpolation of the obtained quasiparticle energies and calculated spin-orbit matrix. Our calculations explicitly treat the shallow semicore states of In and Ga, which are known to be important in the description of the electronic properties, as valence states in the quasiparticle calculation. Our calculated quasiparticle energies, combining both the ab initio evaluation of the electron self-energy and the vector part of the pseudopotential representing the spin-orbit effects, are in generally very good agreement with experimental values. These calculations illustrate the predictive power of the methodology as applied to group IV and III-V semiconductors.

Crown oxygen-doping graphene with embedded main-group metal atoms

NASA Astrophysics Data System (ADS)

Wu, Liyuan; Wang, Qian; Yang, Chuanghua; Quhe, Ruge; Guan, Pengfei; Lu, Pengfei

2018-02-01

Different main-group metal atoms embedded in crown oxygen-doping graphene (metal@OG) systems are studied by the density functional theory. The binding energies and electronic structures are calculated by using first-principles calculations. The binding energy of metal@OG system mainly depends on the electronegativity of the metal atom. The lower the value of the electronegativity, the larger the binding energy, indicating the more stable the system. The electronic structure of metal@OG arouses the emergence of bandgap and shift of Dirac point. It is shown that interaction between metal atom and crown oxygen-doping graphene leads to the graphene's stable n-doping, and the metal@OG systems are stable semiconducting materials, which can be used in technological applications.

Geometric and electronic structures of potassium-adsorbed rubrene complexes

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

Li, Tsung-Lung, E-mail: quantum@mail.ncyu.edu.tw; Lu, Wen-Cai, E-mail: wencailu@jlu.edu.cn; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130021

2015-06-28

The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules,more » the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced resemblance of the simulated to the experimental spectra. Fourth, the HOMO and LUMO are mainly the α and β components of the 2p orbitals of the backbone carbons, respectively.« less

Uncertainty relations, zero point energy and the linear canonical group

NASA Technical Reports Server (NTRS)

Sudarshan, E. C. G.

1993-01-01

The close relationship between the zero point energy, the uncertainty relations, coherent states, squeezed states, and correlated states for one mode is investigated. This group-theoretic perspective enables the parametrization and identification of their multimode generalization. In particular the generalized Schroedinger-Robertson uncertainty relations are analyzed. An elementary method of determining the canonical structure of the generalized correlated states is presented.

An experimental analysis of granivory in a desert ecosystem: Progress report

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

Brown, J.H.

1987-03-01

Controlled, replicated experiments are revealing the network of interactions that determine structure, dynamics, and energy transfer in a desert community that is functionally interconnected by the consumption of seeds (granivory). This community includes seed-eating rodents, ants, and birds, seed-producing annual and perennial plants, and other kinds of organisms that interact with these. The experiments entail removal of important species or functional groups of granivores or plants and supplementation of seed resources. The results demonstrate a large number of direct and indirect interactions that have important effects on the abundance of species and functional groups, the structure of the community, andmore » the dynamics of energy flow. The results suggest that networks of interaction are structured with sufficient overlap in resource requirements and interconnections through indirect pathways that community- and ecosystem-level processes, such as energy flow, are relatively insensitive to major perturbations in the abundance of particular species or functional groups. This preliminary finding has important implications for understanding the response of ecosystems to natural and human-caused perturbations, for the management of agricultural and other human-modified ecosystems, and for the design of perturbation-resistant networks for acquisition and distribution of human resources such energy and information. 44 refs.« less

Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy

NASA Astrophysics Data System (ADS)

Hay, Michael B.; Myneni, Satish C. B.

2007-07-01

Carboxyls play an important role in the chemistry of natural organic molecules (NOM) in the environment, and their behavior is dependent on local structural environment within the macromolecule. We studied the structural environments of carboxyl groups in dissolved NOM from the Pine Barrens (New Jersey, USA), and IHSS NOM isolates from soils and river waters using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. It is well established that the energies of the asymmetric stretching vibrations of the carboxylate anion (COO -) are sensitive to the structural environment of the carboxyl group. These energies were compiled from previous infrared studies on small organic acids for a wide variety of carboxyl structural environments and compared with the carboxyl spectral features of the NOM samples. We found that the asymmetric stretching peaks for all NOM samples occur within a narrow range centered at 1578 cm -1, suggesting that all NOM samples examined primarily contain very similar carboxyl structures, independent of sample source and isolation techniques employed. The small aliphatic acids containing hydroxyl (e.g., D-lactate, gluconate), ether/ester (methoxyacetate, acetoxyacetate), and carboxylate (malonate) substitutions on the α-carbon, and the aromatic acids salicylate ( ortho-OH) and furancarboxylate ( O-heterocycle), exhibit strong overlap with the NOM range, indicating that similar structures may be common in NOM. The width of the asymmetric peak suggests that the structural heterogeneity among the predominant carboxyl configurations in NOM is small. Changes in peak area with pH at energies distant from the peak at 1578 cm -1, however, may be indicative of a small fraction of other aromatic carboxyls and aliphatic structures lacking α-substitution. This information is important in understanding NOM-metal and mineral-surface complexation, and in building appropriate structural and mechanistic models of humic materials.

SASS: A symmetry adapted stochastic search algorithm exploiting site symmetry

NASA Astrophysics Data System (ADS)

Wheeler, Steven E.; Schleyer, Paul v. R.; Schaefer, Henry F.

2007-03-01

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.

Technology for aircraft energy efficiency

NASA Technical Reports Server (NTRS)

Klineberg, J. M.

1977-01-01

Six technology programs for reducing fuel use in U.S. commercial aviation are discussed. The six NASA programs are divided into three groups: Propulsion - engine component improvement, energy efficient engine, advanced turboprops; Aerodynamics - energy efficient transport, laminar flow control; and Structures - composite primary structures. Schedules, phases, and applications of these programs are considered, and it is suggested that program results will be applied to current transport derivatives in the early 1980s and to all-new aircraft of the late 1980s and early 1990s.

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

The Anh, Le, E-mail: letheanh@jaist.ac.jp; Lam, Pham Tien; Manoharan, Muruganathan

We present a first-principles study on the interstitial-mediated diffusion process of neutral phosphorus (P) atoms in a silicon crystal with the presence of mono-atomic hydrogen (H). By relaxing initial Si structures containing a P atom and an H atom, we derived four low-energy P-H-Si defect complexes whose formation energies are significantly lower than those of P-Si defect complexes. These four defect complexes are classified into two groups. In group A, an H atom is located near a Si atom, whereas in group B, an H atom is close to a P atom. We found that the H atom pairs withmore » P or Si atom and changes the nature bonding between P and Si atoms from out-of-phase conjugation to in-phase conjugation. This fact results in the lower formation energies compare to the cases without H atom. For the migration of defect complexes, we have found that P-H-Si defect complexes can migrate with low barrier energies if an H atom sticks to either P or Si atom. Group B complexes can migrate from one lattice site to another with an H atom staying close to a P atom. Group A complexes cannot migrate from one lattice site to another without a transfer of an H atom from one Si atom to another Si atom. A change in the structure of defect complexes between groups A and B during the migration results in a transfer of an H atom between P and Si atoms. The results for diffusion of group B complexes show that the presence of mono-atomic H significantly reduces the activation energy of P diffusion in a Si crystal, which is considered as a summation of formation energy and migration barrier energy, leading to the enhancement of diffusion of P atoms at low temperatures, which has been suggested by recent experimental studies.« less

Accurate calibration for the quantification of the Al content in AlGaN epitaxial layers by energy-dispersive X-ray spectroscopy in a Transmission Electron Microscope

NASA Astrophysics Data System (ADS)

Amari, H.; Lari, L.; Zhang, H. Y.; Geelhaar, L.; Chèze, C.; Kappers, M. J.; McAleese, C.; Humphreys, C. J.; Walther, T.

2011-11-01

Since the band structure of group III- nitrides presents a direct electronic transition with a band-gap energy covering the range from 3.4 eV for (GaN) to 6.2 eV (for AlN) at room temperature as well as a high thermal conductivity, aluminium gallium nitride (AlGaN) is a strong candidate for high-power and high-temperature electronic devices and short-wavelength (visible and ultraviolet) optoelectronic devices. We report here a study by energy-filtered transmission electron microscopy (EFTEM) and energy-dispersive X-ray spectroscopy (EDXS) of the micro structure and elemental distribution in different aluminium gallium nitride epitaxial layers grown by different research groups. A calibration procedure is out-lined that yields the Al content from EDXS to within ~1 at % precision.

Genetic algorithm prediction of two-dimensional group-IV dioxides for dielectrics

NASA Astrophysics Data System (ADS)

Singh, Arunima K.; Revard, Benjamin C.; Ramanathan, Rohit; Ashton, Michael; Tavazza, Francesca; Hennig, Richard G.

2017-04-01

Two-dimensional (2D) materials present a new class of materials whose structures and properties can differ from their bulk counterparts. We perform a genetic algorithm structure search using density-functional theory to identify low-energy structures of 2D group-IV dioxides A O2 (A =Si , Ge, Sn, Pb). We find that 2D SiO2 is most stable in the experimentally determined bi-tetrahedral structure, while 2D SnO2 and PbO2 are most stable in the 1 T structure. For 2D GeO2, the genetic algorithm finds a new low-energy 2D structure with monoclinic symmetry. Each system exhibits 2D structures with formation energies ranging from 26 to 151 meV/atom, below those of certain already synthesized 2D materials. The phonon spectra confirm their dynamic stability. Using the HSE06 hybrid functional, we determine that the 2D dioxides are insulators or semiconductors, with a direct band gap of 7.2 eV at Γ for 2D SiO2, and indirect band gaps of 4.8-2.7 eV for the other dioxides. To guide future applications of these 2D materials in nanoelectronic devices, we determine their band-edge alignment with graphene, phosphorene, and single-layer BN and MoS2. An assessment of the dielectric properties and electrochemical stability of the 2D group-IV dioxides shows that 2D GeO2 and SnO2 are particularly promising candidates for gate oxides and 2D SnO2 also as a protective layer in heterostructure nanoelectronic devices.

Structural, electronic and vibrational properties of LaF3 according to density functional theory and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Oreshonkov, A. S.; Roginskii, E. M.; Krylov, A. S.; Ershov, A. A.; Voronov, V. N.

2018-06-01

Crystal structure of LaF3 single crystal is refined in tysonite-type trigonal unit cell P c1 using density functional theory calculations and Raman spectroscopy. It is shown that trigonal structure with P c1 space group is more energy-efficient than hexagonal structure with space group P63 cm. Simulated Raman spectra obtained using LDA approximation is in much better agreement with experimental data than that obtained with PBE and PBEsol functionals of GGA. The calculated frequency value of silent mode B 2 in case of hexagonal structure P63 cm was found to be imaginary (unstable mode), thus the energy surface obtains negative curvature with respect to the corresponding normal coordinates of the mode which leads to instability of the hexagonal structure in harmonic approximation. The A 1g line at 214 cm‑1 in Raman spectra of LaF3 related to the translation of F2 ions along c axis can be connected with F2 ionic conductivity.

Complexes of carboxyl-containing polymer and monosubstituted bipyridinium salts

NASA Astrophysics Data System (ADS)

Merekalova, N. D.; Bondarenko, G. N.; Krylsky, D. W.; Zakirov, M. I.; Talroze, R. V.

2013-09-01

Semi-empirical PM3 method for the quantum calculations of molecular electronic structure based on NDDO integral approximation is used to investigate the complex formation of monosubstituted 4,4‧-bipyridinium salts BpyR (Hal) containing a halide anion interacting with the quaternary nitrogen atom and carboxylic group of the two-units construct. Significant effect of the BpyR (Hal) electronic structure is unveiled that contributes in two different structures of these salts, namely, partial charge transfer complex and ion pair structure, both having stable energy minima. We demonstrate that (i) the structure of the N-substituent modulates the energy and electronic characteristics of monosubstituted salts BpyR with chlorine and bromine anions and (ii) the coulomb interactions between quaternary N-atom, halogen anion, and the proton of carboxylic group stimulate the transformation of the charge transfer complex into the ion pair structure. Results of calculations are compared with the experimental FTIR spectra of blends of BpyR(Hal) with Eudragit copolymer.

Energy for Wild-Type Acetylcholine Receptor Channel Gating from Different Choline Derivatives

PubMed Central

Bruhova, Iva; Gregg, Timothy; Auerbach, Anthony

2013-01-01

Agonists, including the neurotransmitter acetylcholine (ACh), bind at two sites in the neuromuscular ACh receptor channel (AChR) to promote a reversible, global change in protein conformation that regulates the flow of ions across the muscle cell membrane. In the synaptic cleft, ACh is hydrolyzed to acetate and choline. Replacement of the transmitter’s ester acetyl group with a hydroxyl (ACh→choline) results in a +1.8 kcal/mol reduction in the energy for gating generated by each agonist molecule from a low- to high-affinity change of the transmitter binding site (ΔGB). To understand the distinct actions of structurally related agonist molecules, we measured ΔGB for 10 related choline derivatives. Replacing the hydroxyl group of choline with different substituents, such as hydrogen, chloride, methyl, or amine, increased the energy for gating (i.e., it made ΔGB more negative relative to choline). Extending the ethyl hydroxide tail of choline to propyl and butyl hydroxide also increased this energy. Our findings reveal the amount of energy that is available for the AChR conformational change provided by different, structurally related agonists. We speculate that a hydrogen bond between the choline hydroxyl and the backbone carbonyl of αW149 positions this agonist’s quaternary ammonium group so as to reduce the cation-π interaction between this moiety and the aromatic groups at the binding site. PMID:23442907

Ab initio electronic structure of the progestogen norethisterone and its 5 alpha-derivatives.

PubMed

Kubli-Garfias, Carlos; Vázquez, Ricardo; Cooney, Austin J; Larrea, Fernando

2002-11-01

The steroid 17 alpha-ethynyl-19-nor-4-androsten-17 beta-ol, 3-one (Norethisterone; NET) and its 5 alpha-dihydro (5 alpha-NET), 3 alpha- and 3 beta-tetrahydro derivatives (3 alpha,5 alpha- and 3 beta,5 alpha-NET), were comparatively studied by the ab initio quantum mechanics theory. Additionally, 5 alpha-androstan-3 beta,17 beta-diol (ADIOL) was also studied. The Hartree-Fock method and the 6-31G(*) basis set were used to obtain the lowest energy conformation, geometries, electronic structure and physicochemical properties of the steroids. The results showed bond distances and valence angles similar among all steroids, but some differences in dihedral angles in the A-B-ring system were observed. The electronic structure analysis showed that NET has both frontier orbitals that is, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) located at the C4-C5 pi-bond. In A-ring reduced derivatives, the HOMO was found at the 17 beta-OH and ethynyl groups. In the case of 5 alpha-NET, the LUMO was confined to the A-ring and its C3 carbonyl group while the two NET tetrahydro-reduced derivatives showed the LUMO at the 17 beta-OH and ethynyl groups. The energy changes of the rotational barrier of the 17 beta-OH group suggest that its movement is somewhat restricted by the 17 alpha-ethynyl group. Interestingly both groups at C17 form a single electrostatic potential with high electronic density. On the other side, the 19-nor condition increases the A-ring mobility. However, the 3 beta-OH group of 3 beta,5 alpha-NET may rotate without significant energy differences as compared to the same group in ADIOL. The electronic structure of NET and its A-ring reduced derivatives explains in some extent their interaction with androgen and progesterone receptors as well as their selectivity for the estrogen alpha-receptor.

Identification and properties of the non-cubic phases of Mg 2Pb

DOE PAGES

Li, Yuwei; Bian, Guang; Singh, David J.

2016-12-20

Mg 2Pb occurs in the cubic fluorite structure and is a semimetal with a band structure strongly affected by spin-orbit interaction on the Pb p states. Its properties are therefore of interest in the context of topological materials. In addition a different phase of Mg 2Pb was experimentally reported, but its crystal structure and properties remain unknown. Here we determine the structure of this phase using ab initio evolutionary methods and report its properties. The energy of one tetragonal phase, space group P4/ nmm, is 2 meV per atom higher than that of the ground state structure supporting the experimentalmore » observation. We find this tetragonal phase to be a compenstated anisotropic metal with strong spin orbit effects. As a result, many other metastable structures have also been identified, especially one orthorhombic structure, space group Pnma, of which energy is 17 meV per atom higher than that of ground state structure and which perhaps could be the phase that was reported based on similarity of lattice parameters.« less

Delayed neutron spectral data for Hansen-Roach energy group structure

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

Campbell, J.M.; Spriggs, G.D.

A detailed knowledge of delayed neutron spectra is important in reactor physics. It not only allows for an accurate estimate of the effective delayed neutron fraction {beta}{sub eff} but also is essential to calculating important reactor kinetic parameters, such as effective group abundances and the ratio of {beta}{sub eff} to the prompt neutron generation time. Numerous measurements of delayed neutron spectra for various delayed neutron precursors have been performed and reported in the literature. However, for application in reactor physics calculations, these spectra are usually lumped into one of the traditional six groups of delayed neutrons in accordance to theirmore » half-lives. Subsequently, these six-group spectra are binned into energy intervals corresponding to the energy intervals of a chosen nuclear cross-section set. In this work, the authors present a set of delayed neutron spectra that were formulated specifically to match Keepin`s six-group parameters and the 16-energy-group Hansen-Roach cross sections.« less

Physics and chemistry of MoS2 intercalation compounds

NASA Technical Reports Server (NTRS)

Woollam, J. A.; Somoano, R. B.

1977-01-01

An investigation is made of the physics and chemistry of MoS2 intercalation compounds. These compounds may be separated into two groups according to their stoichiometry, structure and superconducting properties. The first group consists of Na, Ca, and Sr intercalates, and the second group consists of K, Rb, and Cs intercalates. Particular attention is given to the structure of the electronic energy band and to the normal state and superconducting properties of these compounds.

STRUCTURAL DIVERSITY IN SOLID STATE CHEMISTRY:A Story of Squares and Triangles

NASA Astrophysics Data System (ADS)

Lee, Stephen

1996-10-01

A simple method for calculating the electronic energy of extended solids is discussed in this review. This method is based on the Huckel or tight-binding theory in which an explicit pairwise repulsion is added to the generally attractive forces of the partially filled valence electron bands. An expansion based on the power moments of the electronic density of states is discussed, and the structural energy difference theorem is reviewed. The repulsive energy is found to vary linearly with the second power moment of the electronic density of states. These results are then used to show why there is such a diversity of structure in the solid state. The elemental structures of the main group are rationalized by the above methods. It is the third and fourth power moments (which correspond in part to triangles and squares of bonded atoms) that account for much of the elemental structures of the main group elements of the periodic table. This serves as an introduction to further rationalizations of transition for noble metal alloy, binary and ternary telluride and selenide, and other intermetallic structures.Thus a cohesive picture of both covalent and metallic bonding is presented in this review, illustrating the importance of atomic orbitals and their overlap integrals.

Study of iridium silicide monolayers using density functional theory

NASA Astrophysics Data System (ADS)

Popis, Minh D.; Popis, Sylvester V.; Oncel, Nuri; Hoffmann, Mark R.; ćakır, Deniz

2018-02-01

In this study, we investigated physical and electronic properties of possible two-dimensional structures formed by Si (silicon) and Ir (iridium). To this end, different plausible structures were modeled by using density functional theory and the cohesive energies calculated for the geometry of optimized structures, with the lowest equilibrium lattice constants. Among several candidate structures, we identified three mechanically (via elastic constants and Young's modulus), dynamically (via phonon calculations), and thermodynamically stable iridium silicide monolayer structures. The lowest energy structure has a chemical formula of Ir2Si4 (called r-IrSi2), with a rectangular lattice (Pmmn space group). Its cohesive energy was calculated to be -0.248 eV (per IrSi2 unit) with respect to bulk Ir and bulk Si. The band structure indicates that the Ir2Si4 monolayer exhibits metallic properties. Other stable structures have hexagonal (P-3m1) and tetragonal (P4/nmm) cell structures with 0.12 and 0.20 eV/f.u. higher cohesive energies, respectively. Our calculations showed that Ir-Si monolayers are reactive. Although O2 molecules exothermically dissociate on the surface of the free-standing iridium silicide monolayers with large binding energies, H2O molecules bind to the monolayers with a rather weak interaction.

FAST TRACK COMMUNICATION: Preferential functionalization on zigzag graphene nanoribbons: first-principles calculations

NASA Astrophysics Data System (ADS)

Lee, Hoonkyung

2010-09-01

We investigate the functionalization of functional groups to graphene nanoribbons with zigzag and armchair edges using first-principles calculations. We find that the formation energy for the configuration of the functional groups functionalized to the zigzag edge is ~ 0.2 eV per functional group lower than that to the armchair edge. The formation energy difference arises from a structural deformation on the armchair edge by the functionalization whereas there is no structural deformation on the zigzag edge. Selective functionalization on the zigzag edge takes place at a condition of the temperature and the pressure of ~ 25 °C and 10 - 5 atm. Our findings show that selective functionalization can offer the opportunity for an approach to the separation of zigzag graphene nanoribbons with their solubility change.

Optical properties of boron-group (V) hexagonal nanowires: DFT investigation

NASA Astrophysics Data System (ADS)

Santhibhushan, B.; Soni, Mahesh; Srivastava, Anurag

2017-07-01

The paper presents structural, electronic and optical properties of boron-group V hexagonal nanowires (h-NW) within the framework of density functional theory. The h-NW of boron-group V compounds with an analogous diameter of 12 Å have been designed in (1 1 1) plane. Stability analysis performed through formation energies reveal that, the stability of these structures decreases with increasing atomic number of the group V element. The band nature predicts that these nanowires are good electrical conductors. Optical behaviour of the nanowires has been analysed through absorption coefficient, reflectivity, refractive index, optical conductivity and electron energy loss spectrum (EELS), that are computed from the frequency-dependent complex dielectric function. The analysis reveals high reactivity of BP and BAs h-NWs to the incident light especially in the IR and visible ranges, and the optical transparency of BN h-NW in the visible and UV ranges.

Electronic structure and optical properties of Eu(III) tris-β-diketonate adducts with 1,10-phenanthroline

NASA Astrophysics Data System (ADS)

Shurygin, A. V.; Korochentsev, V. V.; Cherednichenko, A. I.; Mirochnik, A. G.; Kalinovskaya, I. V.; Vovna, V. I.

2018-03-01

Adducts of tris-β-diketonates of the rare earth metal Eu(III) with 1,10-phenanthroline are studied by photoelectron spectroscopy and quantum chemistry methods. The electronic structure, peculiarities of the nature of chemical bonds, and the geometric structure of the adducts are determined. The interpretation of UV photoelectron spectra of vapors and X-ray photoelectron spectra of solid is carried out with the chosen technique. DFT/TDDFT methods make it possible to study the 1,10-phenanthroline molecule influence on the adduct electronic structure and to analyze the electronic effects of substitution of methyl groups by trifluoromethyl groups in the ligands. At transition from the tris-β-diketonate complexes to the adducts, it is observed an increase of the absorption region and a decrease in the energy gap that contributes to the efficiency growth in electronic excitation energy transfer in the ligand-metal. Moreover, phenanthroline displaces water groups, that are luminescence quenchers, from the first coordination sphere, closes coordination in the adduct, and blocks their further attachment. Both factors contribute to an increase in the luminescence intensity.

The impact of shock wave therapy at varied energy and dose levels on functional and structural changes in erectile tissue.

PubMed

Müller, Alexander; Akin-Olugbade, Yemi; Deveci, Serkan; Donohue, John F; Tal, Raanan; Kobylarz, Keith A; Palese, Michael; Mulhall, John P

2008-03-01

Only minimal literature exists on consequences of shock wave therapy (SWT) on erectile function in treatment of Peyronie's disease (PD). This study was undertaken to define SWT impact at varied energy/dose levels at different time points on functional and structural changes in erectile tissue. In 45 rats 2000 shock waves (sw) at 2 BAR were applied to the penis weekly sorted by one, two, and three sessions (high-dose/energy level, HD-1, HD-2, HD-3). Each group was followed for 1, 7, or 28 d before measuring intracavernosal pressure (ICP) and mean arterial pressure (MAP). Fifteen control animals (C1, C7, C28) underwent anesthesia alone. Another 15 animals were exposed to three SWT sessions applying 1000 sw at 1 BAR and analyzed identically (low-dose/energy level, LD-3-1, -7, -28). Terminal deoxynucleotidyl transferase biotin-dUTP nick-end labeling assay was used to define the apoptotic index (AI) and Masson's trichrome (MT) staining was prepared to evaluate smooth muscle-to-collagen ratios. ICP/MAP ratios for all C groups displayed a mean of 64%. All SWT groups demonstrated significantly reduced ICP/MAP ratios compared to their corresponding C groups (p<0.05). The LD-3 groups showed a trend toward improved ICP/MAP ratios. LD-3-28 demonstrated significant recovery compared to HD-3-28 (55+/-8% vs. 41+/-10%, p=0.004), but remained reduced compared to C28 (63+/-5%, p=0.03). No statistical differences were seen for MT staining in SWT groups compared to C (p>0.05). AIs for the LD-3 groups were significantly lower compared to the HD-3 groups (p<0.001), but all AIs were significantly increased compared to C groups (p<0.01). Overall, at both energy/dose levels, SWT resulted in a time- and treatment-dependent reduction of ICP/MAP ratios, which might be mediated partly through apoptosis and collagenization of corporal smooth muscle.

ISEE 3 observations of low-energy proton bidirectional events and their relation to isolated interplanetary magnetic structures

NASA Technical Reports Server (NTRS)

Marsden, R. G.; Sanderson, T. R.; Tranquille, C.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

The paper represents the results of a comprehensive survey of low-energy proton bidirectional anisotropies and associated transient magnetic structures as observed in the 35-1600 keV energy range on ISEE-3 during the last solar maximum. The majority of observed bidirectional flow (BDF) events (more than 70 percent) are associated with isolated magnetic structures which are postulated to be an interplanetary manifestation of coronal mass ejection (CME) events. The observed BDF events can be qualitatively grouped into five classes depending on the field signature of the related magnetic structure and the association (or lack of association) with an interplanetary shock. Concerning the topology of the CME-related magnetic structures, the observations are interpreted as being consistent with a detached bubble, comprising closed loops or tightly wound helices.

Production of Value-added Products by Lactic Acid Bacteria

USDA-ARS?s Scientific Manuscript database

Lactic acid bacteria (LAB) are a group of facultative anaerobic, catalase negative, nonmotile and nonsporeforming–Gram positive bacteria. Most LAB utilize high energy C sources including monomer sugars to produce energy to maintain cellular structure and function. This anaerobic fermentation proce...

Towards designing polymers for photovoltaic applications: A DFT and experimental study of polyazomethines with various chemical structures

NASA Astrophysics Data System (ADS)

Wojtkiewicz, Jacek; Iwan, Agnieszka; Pilch, Marek; Boharewicz, Bartosz; Wójcik, Kamil; Tazbir, Igor; Kaminska, Maria

2017-06-01

Theoretical studies of polyazomethines (PAZs) with various chemical structures designated for photovoltaic applications are presented. PAZ energy levels and optical properties were calculated within density-functional theory (DFT and TDDFT) framework for 28 oligomers (monomer, dimer and trimer) of PAZs. The correlations between chemical structure of PAZ and location of its highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels were examined. It turned out that the presence of triaminophenylene, dimethoxydiphenylene and fluorine group raises the orbital energies. As a consequence, it is a factor which improves the photovoltaic efficiency of solar cell built on the base of the corresponding PAZ and [6,6]-phenyl C61 butyric acid methyl ester (PCBM). On the contrary, quinone, 1,3,5-triazine and perfluorophenylene groups lower orbital energies and have negative influence on the photovoltaic efficiency. Moreover, calculations for methyl, ethyl and butyl analogs of P3HT as well as polythiophenes were performed and compared with the results obtained for PAZs. In addition experimental data are presented, which cover optical, electrochemical and electrical transport properties of the studied PAZs, allowing to determine HOMO and LUMO energies of the polymers and their conductivity. Finally, comparison between calculated and experimental results were made and discussed.

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

KASCADE-Grande measurements of energy spectra for elemental groups of cosmic rays

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Mayer, H. J.; Melissas, M.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2013-07-01

The KASCADE-Grande air shower experiment [1] consists of, among others, a large scintillator array for measurements of charged particles, N, and of an array of shielded scintillation counters used for muon counting, Nμ. KASCADE-Grande is optimized for cosmic ray measurements in the energy range 10 PeV to about 2000 PeV, where exploring the composition is of fundamental importance for understanding the transition from galactic to extragalactic origin of cosmic rays. Following earlier studies of the all-particle and the elemental spectra reconstructed in the knee energy range from KASCADE data [2], we have now extended these measurements to beyond 200 PeV. By analysing the two-dimensional shower size spectrum N vs. Nμ for nearly vertical events, we reconstruct the energy spectra of different mass groups by means of unfolding methods over an energy range where the detector is fully efficient. The procedure and its results, which are derived based on the hadronic interaction model QGSJET-II-02 and which yield a strong indication for a dominance of heavy mass groups in the covered energy range and for a knee-like structure in the iron spectrum at around 80 PeV, are presented. This confirms and further refines the results obtained by other analyses of KASCADE-Grande data, which already gave evidence for a knee-like structure in the heavy component of cosmic rays at about 80 PeV [3].

Medical Image Fusion Based on Feature Extraction and Sparse Representation

PubMed Central

Wei, Gao; Zongxi, Song

2017-01-01

As a novel multiscale geometric analysis tool, sparse representation has shown many advantages over the conventional image representation methods. However, the standard sparse representation does not take intrinsic structure and its time complexity into consideration. In this paper, a new fusion mechanism for multimodal medical images based on sparse representation and decision map is proposed to deal with these problems simultaneously. Three decision maps are designed including structure information map (SM) and energy information map (EM) as well as structure and energy map (SEM) to make the results reserve more energy and edge information. SM contains the local structure feature captured by the Laplacian of a Gaussian (LOG) and EM contains the energy and energy distribution feature detected by the mean square deviation. The decision map is added to the normal sparse representation based method to improve the speed of the algorithm. Proposed approach also improves the quality of the fused results by enhancing the contrast and reserving more structure and energy information from the source images. The experiment results of 36 groups of CT/MR, MR-T1/MR-T2, and CT/PET images demonstrate that the method based on SR and SEM outperforms five state-of-the-art methods. PMID:28321246

The Effects of Internal Rotation and 14N Quadrupole Coupling in N-Methyldiacetamide

NASA Astrophysics Data System (ADS)

Kannengießer, Raphaela; Eibl, Konrad; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

2015-06-01

Acetyl- and nitrogen containing substances play an important role in chemical, physical, and especially biological systems. This applies in particular for acetamides, which are structurally related to peptide bonds. In this work, N-methyldiacetamide, CH_3N(COCH_3)_2, was investigated by a combination of molecular beam Fourier transform microwave spectroscopy and quantum chemical calculations. In N-methyldiacetamide, at least three large amplitude motions are possible: (1) the internal rotation of the methyl group attached to the nitrogen atom and (2, 3) the internal rotations of both acetyl methyl groups. This leads to a rather complicated torsional fine structure of all rotational transitions with additional quadrupole hyperfine splittings caused by the 14N nucleus. Quantum chemical calculations were carried out at the MP2/6-311++G(d,p) level of theory to support the spectral assignment. Conformational analysis was performed by calculating a full potential energy surface depending on the orientation of the two acetyl groups. This yielded three stable conformers with a maximum energy difference of 35.2 kJ/mol. The spectrum of the lowest energy conformer was identified in the molecular beam. The quadrupole hyperfine structure as well as the internal rotation of two methyl groups could be assigned. For the N-methyl group and for one of the two acetyl methyl groups, barriers to internal rotation of 147 cm-1 and of 680 cm-1, respectively, were determined. The barrier of the last methyl group seems to be so high that no additional splittings could be resolved. Using the XIAM program, a global fit with a standard deviation on the order of our experimental accuracy could be achieved.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

The effects of explicit visual cues in reading biological diagrams

NASA Astrophysics Data System (ADS)

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

2017-03-01

Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and energy pyramid, were selected as the reading materials for the control group and reformatted in tree structure or with additional arrows as the diagrams for the treatment group. A quasi-experiment with an online reading test was conducted to examine the effect of the different image conditions on reading comprehension of the two groups. In total, 192 Taiwanese participants from year 7 were assigned randomly into either control group or treatment group according to the pre-test of relevant prior knowledge. The results indicated that not all explicit visual cues were significantly efficient. Only the explicit tree-structured diagrams cued significantly the key concepts of qualitative class-inclusion, parallel relations, and fish taxonomy. Meanwhile the effect of indexical arrows was not significant. The inconsistent effect of tree structure and arrows might be related to the extent of image reformation in which the tree-structured diagrams had undergone radical change of knowledge representation; meanwhile, the arrows had not changed the diagram structure of energy pyramid. The factor of prior knowledge was essential in considering the influence of image design as the effect of diagrams was very different for low and high prior knowledge students. Implications are drawn for the importance of visual design in textbooks.

Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; Fonda, Mark (Technical Monitor)

2001-01-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies were estimated for four types reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed that (1) when carbon-carbon bond cleavage involves two different types of functional groups, transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) the energy of carbon-carbon bond transformation is strongly dependent on the type of functional group that donates the shared electron-pair during cleavage, and the group that accepts the shared electron-pair during synthesis, and (3) the energetics of C-C bond transformation is determined primarily by the half-reaction energies of the couples: carbonyl/carboxylic acid, carboxylic acid/carbon dioxide, alcohol/carbonyl, and hydrocarbon/alcohol. The energy of hydrogen-transfer between carbon groups was found to depend on the functional group class of both the hydrogen-donor and hydrogen-acceptor. From these and other observations we concluded that the chemistry of the origin of metabolism (and to a lesser degree modem metabolism) is strongly constrained by the (1) limited disproportionation energy of organic substrates that can be dissipated in a few irreversible reactions, (2) the energy-dominance of few half-reaction couples in carbon-carbon bond transformation that establishes whether a chemical reaction is energetically irreversible, reversible or unfeasible, and (3) the dependence of the transformation-energy on the oxidation state of carbon groups (functional group type) which is contingent on prior reactions in the synthetic pathway.

Radical bonding: structure and stability of bis(phenalenyl) complexes of divalent metals from across the periodic table.

PubMed

Craciun, Smaranda; Donald, Kelling J

2009-07-06

We examine the bonding possibilities of the bis(phenalenyl) MP(2) sandwich complexes of the divalent metals M = Be, Mg, Ca, Sr, Ba, Zn, Cd, and Hg, at the B3LYP level of theory. The outcome is an extraordinarily diverse class of low symmetry bis(phenalenyl)metal complexes in which bonding preferences and binding enthalpies differ dramatically. The lowest energy group 2 metal MP(2) complexes include an intriguing eta(1),eta(3) BeP(2) structure, and bent eta(6),eta(6) systems for M = Ca, Sr, and Ba. The group 12 bis(phenalenyl) complexes are thermodynamically unstable eta(1),eta(1) slip-sandwich structures. To better understand changes in the structural preferences going from the (eta(6),eta(6)) group 2 to the (eta(1),eta(1)) group 12 complexes, we explored the bonding in the bis(phenalenyl) complexes of transition metals with stable +2 oxidations states between Ca and Zn in period 4. The computed binding enthalpies are large and negative for nearly all of the minimum energy bis(phenalenyl) complexes of the group 2 and the transition metals; they are tiny for MgP(2), and are quite positive for the group 12 systems. The structural preferences and stability of the complexes is a subtle negotiation of several influences: the (un)availability of (n - 1)d and np, orbitals for bonding, the cost of the rehybridization at carbon sites in the phenalenyl rings in preparation for bonding to the metals, and the (P---P) interaction between the phenalenyl radicals.

Rhythmic crowd bobbing on a grandstand simulator

NASA Astrophysics Data System (ADS)

Comer, A. J.; Blakeborough, A.; Williams, M. S.

2013-01-01

It is widely accepted that concerted human activity such as bouncing or bobbing can excite cantilever grandstands. Crowd coordination can be unwitting and may be exacerbated by structural motion caused by resonant structural response. This is an area of uncertainty in the design and analysis of modern grandstands. This paper presents experimental measurement and analysis of rhythmic crowd bobbing loads obtained from tests on a grandstand simulator with two distinct support conditions; (a) rigid, and; (b) flexible. It was found that significant structural vibration at the bobbing frequency did not increase the effective bobbing load. Structural motion at the bobbing frequency caused a reduction in the dynamic load factor (DLF) at the frequency of the second harmonic while those at the first and third harmonics were unaffected. Two plausible reasons for this are: (a) the bobbing group were unable to supply significant energy to the system at the frequency of the second harmonic; (b) the bobbing group altered their bobbing style to reduce the response of the grandstand simulator. It was deduced that the bobbing group did not absorb energy from the dynamic system. Furthermore, dynamic load factors for groups of test subjects bobbing on a rigid structure were typically greater than those of synthesised groups derived from individuals bobbing alone, possibly due to group effects such as audio and visual stimuli from neighbouring test subjects. Last, the vibration levels experienced by the test subjects appear to be below levels likely to cause discomfort. This is to be expected as the test subjects were themselves controlling the magnitude and duration of vibration for the bobbing tests considered.

Atomistic simulations of aromatic polyurea and polyamide for capacitive energy storage

NASA Astrophysics Data System (ADS)

Dong, Rui; Ranjan, V.; Buongiorno Nardelli, Marco; Bernholc, J.

2015-07-01

Materials for capacitive energy storage with high energy density and low loss are desired in many fields. We investigate several polymers with urea and amide functional groups using density functional theory and classical molecular dynamics simulations. For aromatic polyurea (APU) and para-aramid (PA), we find several nearly energetically degenerate ordered structures, while meta-aromatic polyurea (mAPU) tends to be rotationally disordered along the polymer chains. Simulated annealing of APU and PA structures results in the formation of hydrogen-bonded sheets, highlighting the importance of dipole-dipole interactions. In contrast, hydrogen bonding does not play a significant role in mAPU, hence the propensity to disorder. We find that the disordered structures with misaligned chains have significantly larger dielectric constants, due to significant increase in the free volume, which leads to easier reorientation of dipolar groups in the presence of an electric field. Large segment motion is still not allowed below the glass transition temperature, which explains the experimentally observed very low loss at high field and elevated temperature. However, the degree of disorder needs to be controlled, because highly entangled structures diminish the free dipoles and decrease permittivity. Among the considered materials, mAPU is the most promising dielectric for capacitive energy storage, but the concept of increasing permittivity while maintaining low loss through disorder-induced free volume increase is generally applicable and provides an alternative pathway for the design of high-performance dielectrics for capacitive energy storage.

Absolute surface energy calculations of Wurtzite (0001)/(000-1): a study of ZnO and GaN

NASA Astrophysics Data System (ADS)

Zhang, Jingzhao; Zhang, Yiou; Tse, Kinfai; Deng, Bei; Xu, Hu; Zhu, Junyi

The accurate absolute surface energies of (0001)/(000-1) surfaces of wurtzite structures are crucial in determining the thin film growth mode of important energy materials. However, the surface energies still remain to be solved due to the intrinsic difficulty of calculating dangling bond energy of asymmetrically bonded surface atoms. We used a pseudo-hydrogen passivation method to estimate the dangling bond energy and calculate the polar surfaces of ZnO and GaN. The calculations were based on the pseudo chemical potentials obtained from a set of tetrahedral clusters or simple pseudo-molecules, using density functional theory approaches, for both GGA and HSE. And the surface energies of (0001)/(000-1) surfaces of wurtzite ZnO and GaN we obtained showed relatively high self-consistencies. A wedge structure calculation with a new bottom surface passivation scheme of group I and group VII elements was also proposed and performed to show converged absolute surface energy of wurtzite ZnO polar surfaces. Part of the computing resources was provided by the High Performance Cluster Computing Centre, Hong Kong Baptist University. This work was supported by the start-up funding and direct Grant with the Project code of 4053134 at CUHK.

Linear solvation energy relationships: "rule of thumb" for estimation of variable values

USGS Publications Warehouse

Hickey, James P.; Passino-Reader, Dora R.

1991-01-01

For the linear solvation energy relationship (LSER), values are listed for each of the variables (Vi/100, π*, &betam, αm) for fundamental organic structures and functional groups. We give the guidelines to estimate LSER variable values quickly for a vast array of possible organic compounds such as those found in the environment. The difficulty in generating these variables has greatly discouraged the application of this quantitative structure-activity relationship (QSAR) method. This paper present the first compilation of molecular functional group values together with a utilitarian set of the LSER variable estimation rules. The availability of these variable values and rules should facilitate widespread application of LSER for hazard evaluation of environmental contaminants.

Solvation of Esters and Ketones in Supercritical CO2.

PubMed

Kajiya, Daisuke; Imanishi, Masayoshi; Saitow, Ken-ichi

2016-02-04

Vibrational Raman spectra for the C═O stretching modes of three esters with different functional groups (methyl, a single phenyl, and two phenyl groups) were measured in supercritical carbon dioxide (scCO2). The results were compared with Raman spectra for three ketones involving the same functional groups, measured at the same thermodynamic states in scCO2. The peak frequencies of the Raman spectra of these six solute molecules were analyzed by decomposition into the attractive and repulsive energy components, based on the perturbed hard-sphere theory. For all solute molecules, the attractive energy is greater than the repulsive energy. In particular, a significant difference in the attractive energies of the ester-CO2 and ketone-CO2 systems was observed when the methyl group is attached to the ester or ketone. This difference was significantly reduced in the solute systems with a single phenyl group and was completely absent in those with two phenyl groups. The optimized structures among the solutes and CO2 molecules based on quantum chemical calculations indicate that greater attractive energy is obtained for a system where the oxygen atom of the ester is solvated by CO2 molecules.

Mapping energy poverty in Huntington, West Virginia

NASA Astrophysics Data System (ADS)

Callicoat, Elizabeth Anne

Energy poverty is a growing phenomenon culminating from the combination of low to mid household income, deteriorating housing structures and rising household energy costs. Energy prices are increasing for all households, but the burden is proportionally larger for those with low to mid income. These groups must sacrifice to afford energy, and are often unable or do not have the autonomy to make structural improvements, especially if they rent their home. Data on residential dwellings from the Cabell County Tax Assessor's Office was used within a geographic information system to map where energy poverty likely exists within the city limits of Huntington, WV. It was found that one fifth of Huntington households are at a high risk of energy poverty, primarily located across the northern section of the city and in the center, surrounding Marshall University, Downtown and Cabell Huntington Hospital.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

Relaxed structure of typical nitro explosives in the excited state: Observation, implication and application

NASA Astrophysics Data System (ADS)

Chu, Genbai; Yang, Zuhua; Xi, Tao; Xin, Jianting; Zhao, Yongqiang; He, Weihua; Shui, Min; Gu, Yuqiu; Xiong, Ying; Xu, Tao

2018-04-01

Understanding the structural, geometrical, and chemical changes that occur after an electronic excitation is essential to elucidate the inherent mechanism of nitro explosives. Herein, relaxed structures of typical nitro explosives in the lowest singlet excited state are investigated using time-dependent density functional theory. During the excitation process, the nitro group is activated and relaxes via geometrical change. The five explosives RDX, HMX, CL-20, PETN, and LLM-105 exhibit similar relaxed structures, and the impact sensitivity is related to their excitation energy. High-sensitivity δ-HMX has a lower excitation energy for relaxed structure than β-HMX. This study offers novel insight into energetic materials.

Diverse roles of hydrogen in rhenium carbonyl chemistry: hydrides, dihydrogen complexes, and a formyl derivative.

PubMed

Li, Nan; Xie, Yaoming; King, R Bruce; Schaefer, Henry F

2010-11-04

Rhenium carbonyl hydride chemistry dates back to the 1959 synthesis of HRe(CO)₅ by Hieber and Braun. The binuclear H₂Re₂(CO)₈ was subsequently synthesized as a stable compound with a central Re₂(μ-H)₂ unit analogous to the B₂(μ-H)₂ unit in diborane. The complete series of HRe(CO)(n) (n = 5, 4, 3) and H₂Re₂(CO)(n) (n = 9, 8, 7, 6) derivatives have now been investigated by density functional theory. In contrast to the corresponding manganese derivatives, all of the triplet rhenium structures are found to lie at relatively high energies compared with the corresponding singlet structures consistent with the higher ligand field splitting of rhenium relative to manganese. The lowest energy HRe(CO)₅ structure is the expected octahedral structure. Low-energy structures for HRe(CO)(n) (n = 4, 3) are singlet structures derived from the octahedral HRe(CO)₅ structure by removal of one or two carbonyl groups. For H₂Re₂(CO)₉ a structure HRe₂(CO)₉(μ-H), with one terminal and one bridging hydrogen atom, lies within 3 kcal/mol of the structure Re₂(CO)₉(η²-H₂), similar to that of Re₂(CO)₁₀. For H₂Re₂(CO)(n) (n = 8, 7, 6) the only low-energy structures are doubly bridged singlet Re₂(μ-H)₂(CO)(n) structures. Higher energy dihydrogen complex structures are also found.

Hamiltonian approach to Ehrenfest expectation values and Gaussian quantum states

PubMed Central

Bonet-Luz, Esther

2016-01-01

The dynamics of quantum expectation values is considered in a geometric setting. First, expectation values of the canonical observables are shown to be equivariant momentum maps for the action of the Heisenberg group on quantum states. Then, the Hamiltonian structure of Ehrenfest’s theorem is shown to be Lie–Poisson for a semidirect-product Lie group, named the Ehrenfest group. The underlying Poisson structure produces classical and quantum mechanics as special limit cases. In addition, quantum dynamics is expressed in the frame of the expectation values, in which the latter undergo canonical Hamiltonian motion. In the case of Gaussian states, expectation values dynamics couples to second-order moments, which also enjoy a momentum map structure. Eventually, Gaussian states are shown to possess a Lie–Poisson structure associated with another semidirect-product group, which is called the Jacobi group. This structure produces the energy-conserving variant of a class of Gaussian moment models that have previously appeared in the chemical physics literature. PMID:27279764

A study of the effect of gamma and laser irradiation on the thermal, optical and structural properties of CR-39 nuclear track detector

NASA Astrophysics Data System (ADS)

Nouh, S. A.; Atta, M. R.; El-Melleegy, W. M.

2004-08-01

A comparative study of the effect of gamma and laser irradiation on the thermal, optical and structural properties of the CR-39 diglycol carbonate solid state nuclear track detector has been carried out. Samples from CR-39 polymer were classified into two main groups: the first group was irradiated by gamma rays with doses at levels between 20 and 300 kGy, whereas the second group was exposed to infrared laser radiation with energy fluences at levels between 0.71 and 8.53 J/cm(2). Non-isothermal studies were carried out using thermogravimetry, differential thermogravimetry and differential thermal analysis to obtain activation energy of decomposition and transition temperatures for the non-irradiated and all irradiated CR-39 samples. In addition, optical and structural property studies were performed on non-irradiated and irradiated CR-39 samples using refractive index and X-ray diffraction measurements. Variation in the onset temperature of decomposition T-o, activation energy of decomposition E-a, melting temperature T-m, refractive index n and the mass fraction of the amorphous phase after gamma and laser irradiation were studied. It was found that many changes in the thermal, optical and structural properties of the CR-39 polymer could be produced by gamma irradiation via degradation and cross-linking mechanisms. Also, the gamma dose has an advantage of increasing the correlation between thermal stability of the CR-39 polymer and bond formation created by the ionizing effect of gamma radiation. On the other hand, higher laser-energy fluences in the range 4.27-8.53 J/cm(2) decrease the melting temperature of the CR-39 polymer and this is most suitable for applications requiring molding of the polymer at lower temperatures.

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

2002-01-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations under Mild Aqueous Conditions

NASA Astrophysics Data System (ADS)

Weber, Arthur L.

2002-08-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (ΔG) were estimated for four types of reactions of biochemical importance - carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (ΔG < -3.5 kcal/mol), reversible (ΔG between +/-3.5 kcal/mol), or unfavorable (ΔG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

2017-01-01

The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

Nuclear spectroscopic studies. Progress report

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

Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.

1994-02-18

The Nuclear Physics group at UTK is involved in heavy-ion physics including both nuclear structure and reaction mechanisms. During the last year experimental work has been in 3 broad areas: structure of nuclei at high angular momentum, structure of nuclei far from stability, and ultra-relativistic heavy-ion physics. Results in these areas are described in this document under: properties of high-spin states, study of low-energy levels of nuclei far from stability, and high-energy heavy-ion physics (PHENIX, etc.). Another important component of the work is theoretical interpretation of experimental results (Joint Institute for Heavy Ion Research).

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

DOE PAGES

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles; ...

2017-06-20

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

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

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Towards designing polymers for photovoltaic applications: A DFT and experimental study of polyazomethines with various chemical structures.

PubMed

Wojtkiewicz, Jacek; Iwan, Agnieszka; Pilch, Marek; Boharewicz, Bartosz; Wójcik, Kamil; Tazbir, Igor; Kaminska, Maria

2017-06-15

Theoretical studies of polyazomethines (PAZs) with various chemical structures designated for photovoltaic applications are presented. PAZ energy levels and optical properties were calculated within density-functional theory (DFT and TDDFT) framework for 28 oligomers (monomer, dimer and trimer) of PAZs. The correlations between chemical structure of PAZ and location of its highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels were examined. It turned out that the presence of triaminophenylene, dimethoxydiphenylene and fluorine group raises the orbital energies. As a consequence, it is a factor which improves the photovoltaic efficiency of solar cell built on the base of the corresponding PAZ and [6,6]-phenyl C 61 butyric acid methyl ester (PCBM). On the contrary, quinone, 1,3,5-triazine and perfluorophenylene groups lower orbital energies and have negative influence on the photovoltaic efficiency. Moreover, calculations for methyl, ethyl and butyl analogs of P3HT as well as polythiophenes were performed and compared with the results obtained for PAZs. In addition experimental data are presented, which cover optical, electrochemical and electrical transport properties of the studied PAZs, allowing to determine HOMO and LUMO energies of the polymers and their conductivity. Finally, comparison between calculated and experimental results were made and discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantum Computational Calculations of the Ionization Energies of Acidic and Basic Amino Acids: Aspartate, Glutamate, Arginine, Lysine, and Histidine

NASA Astrophysics Data System (ADS)

de Guzman, C. P.; Andrianarijaona, M.; Lee, Y. S.; Andrianarijaona, V.

An extensive knowledge of the ionization energies of amino acids can provide vital information on protein sequencing, structure, and function. Acidic and basic amino acids are unique because they have three ionizable groups: the C-terminus, the N-terminus, and the side chain. The effects of multiple ionizable groups can be seen in how Aspartate's ionizable side chain heavily influences its preferred conformation (J Phys Chem A. 2011 April 7; 115(13): 2900-2912). Theoretical and experimental data on the ionization energies of many of these molecules is sparse. Considering each atom of the amino acid as a potential departing site for the electron gives insight on how the three ionizable groups affect the ionization process of the molecule and the dynamic coupling between the vibrational modes. In the following study, we optimized the structure of each acidic and basic amino acid then exported the three dimensional coordinates of the amino acids. We used ORCA to calculate single point energies for a region near the optimized coordinates and systematically went through the x, y, and z coordinates of each atom in the neutral and ionized forms of the amino acid. With the calculations, we were able to graph energy potential curves to better understand the quantum dynamic properties of the amino acids. The authors thank Pacific Union College Student Association for providing funds.

Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

PubMed

Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

2014-01-14

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.

High Energy Density Physics and Exotic Acceleration Schemes

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

Cowan, T.; /General Atomics, San Diego; Colby, E.

2005-09-27

The High Energy Density and Exotic Acceleration working group took as our goal to reach beyond the community of plasma accelerator research with its applications to high energy physics, to promote exchange with other disciplines which are challenged by related and demanding beam physics issues. The scope of the group was to cover particle acceleration and beam transport that, unlike other groups at AAC, are not mediated by plasmas or by electromagnetic structures. At this Workshop, we saw an impressive advancement from years past in the area of Vacuum Acceleration, for example with the LEAP experiment at Stanford. And wemore » saw an influx of exciting new beam physics topics involving particle propagation inside of solid-density plasmas or at extremely high charge density, particularly in the areas of laser acceleration of ions, and extreme beams for fusion energy research, including Heavy-ion Inertial Fusion beam physics. One example of the importance and extreme nature of beam physics in HED research is the requirement in the Fast Ignitor scheme of inertial fusion to heat a compressed DT fusion pellet to keV temperatures by injection of laser-driven electron or ion beams of giga-Amp current. Even in modest experiments presently being performed on the laser-acceleration of ions from solids, mega-amp currents of MeV electrons must be transported through solid foils, requiring almost complete return current neutralization, and giving rise to a wide variety of beam-plasma instabilities. As keynote talks our group promoted Ion Acceleration (plenary talk by A. MacKinnon), which historically has grown out of inertial fusion research, and HIF Accelerator Research (invited talk by A. Friedman), which will require impressive advancements in space-charge-limited ion beam physics and in understanding the generation and transport of neutralized ion beams. A unifying aspect of High Energy Density applications was the physics of particle beams inside of solids, which is proving to be a very important field for diverse applications such as muon cooling, fusion energy research, and ultra-bright particle and radiation generation with high intensity lasers. We had several talks on these and other subjects, and many joint sessions with the Computational group, the EM Structures group, and the Beam Generation group. We summarize our groups' work in the following categories: vacuum acceleration schemes; ion acceleration; particle transport in solids; and applications to high energy density phenomena.« less

Functional renormalization group approach to electronic structure calculations for systems without translational symmetry

NASA Astrophysics Data System (ADS)

Seiler, Christian; Evers, Ferdinand

2016-10-01

A formalism for electronic-structure calculations is presented that is based on the functional renormalization group (FRG). The traditional FRG has been formulated for systems that exhibit a translational symmetry with an associated Fermi surface, which can provide the organization principle for the renormalization group (RG) procedure. We here advance an alternative formulation, where the RG flow is organized in the energy-domain rather than in k space. This has the advantage that it can also be applied to inhomogeneous matter lacking a band structure, such as disordered metals or molecules. The energy-domain FRG (ɛ FRG) presented here accounts for Fermi-liquid corrections to quasiparticle energies and particle-hole excitations. It goes beyond the state of the art G W -BSE , because in ɛ FRG the Bethe-Salpeter equation (BSE) is solved in a self-consistent manner. An efficient implementation of the approach that has been tested against exact diagonalization calculations and calculations based on the density matrix renormalization group is presented. Similar to the conventional FRG, also the ɛ FRG is able to signalize the vicinity of an instability of the Fermi-liquid fixed point via runaway flow of the corresponding interaction vertex. Embarking upon this fact, in an application of ɛ FRG to the spinless disordered Hubbard model we calculate its phase boundary in the plane spanned by the interaction and disorder strength. Finally, an extension of the approach to finite temperatures and spin S =1 /2 is also given.

Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF

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

Breuer, Marian; Zarzycki, Piotr P.; Shi, Liang

2012-12-01

The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable force fieldmore » dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.« less

Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes.

PubMed

Liu, Kexi; Lei, Yinkai; Wang, Guofeng

2013-11-28

Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O2 adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N4 chelation, as well as the molecular and electronic structures for the O2 adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O2 on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d(z(2)), d(xy), d(xz), and d(yz)) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O2 adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

Dark energy domination in the Virgocentric flow

NASA Astrophysics Data System (ADS)

Chernin, A. D.; Karachentsev, I. D.; Nasonova, O. G.; Teerikorpi, P.; Valtonen, M. J.; Dolgachev, V. P.; Domozhilova, L. M.; Byrd, G. G.

2010-09-01

Context. The standard ΛCDM cosmological model implies that all celestial bodies are embedded in a perfectly uniform dark energy background, represented by Einstein's cosmological constant, and experience its repulsive antigravity action. Aims: Can dark energy have strong dynamical effects on small cosmic scales as well as globally? Continuing our efforts to clarify this question, we now focus on the Virgo Cluster and the flow of expansion around it. Methods: We interpret the Hubble diagram from a new database of velocities and distances of galaxies in the cluster and its environment, using a nonlinear analytical model, which incorporates the antigravity force in terms of Newtonian mechanics. The key parameter is the zero-gravity radius, the distance at which gravity and antigravity are in balance. Results: 1. The interplay between the gravity of the cluster and the antigravity of the dark energy background determines the kinematical structure of the system and controls its evolution. 2. The gravity dominates the quasi-stationary bound cluster, while the antigravity controls the Virgocentric flow, bringing order and regularity to the flow, which reaches linearity and the global Hubble rate at distances ⪆15 Mpc. 3. The cluster and the flow form a system similar to the Local Group and its outflow. In the velocity-distance diagram, the cluster-flow structure reproduces the group-flow structure with a scaling factor of about 10; the zero-gravity radius for the cluster system is also 10 times larger. Conclusions: The phase and dynamical similarity of the systems on the scales of 1-30 Mpc suggests that a two-component pattern may be universal for groups and clusters: a quasi-stationary bound central component and an expanding outflow around it, caused by the nonlinear gravity-antigravity interplay with the dark energy dominating in the flow component.

Distributions of methyl group rotational barriers in polycrystalline organic solids

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

Beckmann, Peter A., E-mail: pbeckman@brynmawr.edu, E-mail: wangxianlong@uestc.edu.cn; Conn, Kathleen G.; Division of Education and Human Services, Neumann University, One Neumann Drive, Aston, Pennsylvania 19014-1298

We bring together solid state {sup 1}H spin-lattice relaxation rate measurements, scanning electron microscopy, single crystal X-ray diffraction, and electronic structure calculations for two methyl substituted organic compounds to investigate methyl group (CH{sub 3}) rotational dynamics in the solid state. Methyl group rotational barrier heights are computed using electronic structure calculations, both in isolated molecules and in molecular clusters mimicking a perfect single crystal environment. The calculations are performed on suitable clusters built from the X-ray diffraction studies. These calculations allow for an estimate of the intramolecular and the intermolecular contributions to the barrier heights. The {sup 1}H relaxation measurements,more » on the other hand, are performed with polycrystalline samples which have been investigated with scanning electron microscopy. The {sup 1}H relaxation measurements are best fitted with a distribution of activation energies for methyl group rotation and we propose, based on the scanning electron microscopy images, that this distribution arises from molecules near crystallite surfaces or near other crystal imperfections (vacancies, dislocations, etc.). An activation energy characterizing this distribution is compared with a barrier height determined from the electronic structure calculations and a consistent model for methyl group rotation is developed. The compounds are 1,6-dimethylphenanthrene and 1,8-dimethylphenanthrene and the methyl group barriers being discussed and compared are in the 2–12 kJ mol{sup −1} range.« less

Conformational responses to changes in the state of ionization of titrable groups in proteins

NASA Astrophysics Data System (ADS)

Richman, Daniel Eric

Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H-bond) breaking on at least the mus timescale, and segmental unfolding were detected near titrating groups as pH decreased into the acidic range. The study identified local structural features and stabilities that modulate the magnitude of electrostatic effects. The data demonstrate that computational approaches to pK a calculations for surface groups must account for local fluctuations spanning a wide range of timescales. A comparative NMR spectroscopy study with the L25K and L125K variants of SNase, each with a Lys residue buried in the hydrophobic interior of the protein, determined locations, timescales, and amplitudes of backbone conformational reorganization coupled with ionization of the buried Lys residues. The L25K protein exhibited an ensemble of local fluctuations of the beta barrel in the hundreds of mus timescale and an ensemble of subglobally unfolded beta-barrel states in the hundreds of ms timescale with strong pH dependence. The L125K protein exhibited fluctuations of the helix around site 125 in the mus timescale, with negligible pH dependence. These data illustrate the diverse timescales and local structural properties of conformational reorganization coupled to ionization of buried groups, and the challenge to structure-based electrostatics calculations, which must capture these long-timescale processes.

Theory of Covalent Adsorbate Frontier Orbital Energies on Functionalized Light-Absorbing Semiconductor Surfaces.

PubMed

Yu, Min; Doak, Peter; Tamblyn, Isaac; Neaton, Jeffrey B

2013-05-16

Functional hybrid interfaces between organic molecules and semiconductors are central to many emerging information and solar energy conversion technologies. Here we demonstrate a general, empirical parameter-free approach for computing and understanding frontier orbital energies - or redox levels - of a broad class of covalently bonded organic-semiconductor surfaces. We develop this framework in the context of specific density functional theory (DFT) and many-body perturbation theory calculations, within the GW approximation, of an exemplar interface, thiophene-functionalized silicon (111). Through detailed calculations taking into account structural and binding energetics of mixed-monolayers consisting of both covalently attached thiophene and hydrogen, chlorine, methyl, and other passivating groups, we quantify the impact of coverage, nonlocal polarization, and interface dipole effects on the alignment of the thiophene frontier orbital energies with the silicon band edges. For thiophene adsorbate frontier orbital energies, we observe significant corrections to standard DFT (∼1 eV), including large nonlocal electrostatic polarization effects (∼1.6 eV). Importantly, both results can be rationalized from knowledge of the electronic structure of the isolated thiophene molecule and silicon substrate systems. Silicon band edge energies are predicted to vary by more than 2.5 eV, while molecular orbital energies stay similar, with the different functional groups studied, suggesting the prospect of tuning energy alignment over a wide range for photoelectrochemistry and other applications.

Exposure to digital marketing enhances young adults’ interest in energy drinks: An exploratory investigation

PubMed Central

Buchanan, Limin; Kelly, Bridget; Yeatman, Heather

2017-01-01

Young adults experience faster weight gain and consume more unhealthy food than any other age groups. The impact of online food marketing on “digital native” young adults is unclear. This study examined the effects of online marketing on young adults’ consumption behaviours, using energy drinks as a case example. The elaboration likelihood model of persuasion was used as the theoretical basis. A pre-test post-test experimental research design was adopted using mixed-methods. Participants (aged 18–24) were randomly assigned to control or experimental groups (N = 30 each). Experimental group participants’ attitudes towards and intended purchase and consumption of energy drinks were examined via surveys and semi-structured interviews after their exposure to two popular energy drink brands’ websites and social media sites (exposure time 8 minutes). Exposure to digital marketing contents of energy drinks improved the experimental group participants’ attitudes towards and purchase and consumption intention of energy drinks. This study indicates the influential power of unhealthy online marketing on cognitively mature young adults. This study draws public health attentions to young adults, who to date have been less of a focus of researchers but are influenced by online food advertising. PMID:28152016

Exposure to digital marketing enhances young adults' interest in energy drinks: An exploratory investigation.

PubMed

Buchanan, Limin; Kelly, Bridget; Yeatman, Heather

2017-01-01

Young adults experience faster weight gain and consume more unhealthy food than any other age groups. The impact of online food marketing on "digital native" young adults is unclear. This study examined the effects of online marketing on young adults' consumption behaviours, using energy drinks as a case example. The elaboration likelihood model of persuasion was used as the theoretical basis. A pre-test post-test experimental research design was adopted using mixed-methods. Participants (aged 18-24) were randomly assigned to control or experimental groups (N = 30 each). Experimental group participants' attitudes towards and intended purchase and consumption of energy drinks were examined via surveys and semi-structured interviews after their exposure to two popular energy drink brands' websites and social media sites (exposure time 8 minutes). Exposure to digital marketing contents of energy drinks improved the experimental group participants' attitudes towards and purchase and consumption intention of energy drinks. This study indicates the influential power of unhealthy online marketing on cognitively mature young adults. This study draws public health attentions to young adults, who to date have been less of a focus of researchers but are influenced by online food advertising.

The smallest quaternary ammonium salts with ether groups for high-performance electrochemical double layer capacitors† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02755a Click here for additional data file.

PubMed Central

Han, Taihee; Park, Min-Sik; Kim, Jeonghun; Kim, Jung Ho

2016-01-01

Electrochemical double layer capacitors (EDLCs) are energy storage devices that have been used for a wide range of electronic applications. In particular, the electrolyte is one of the important components, directly related to the capacitance and stability. Herein, we first report a series of the smallest quaternary ammonium salts (QASs), with ether groups on tails and tetrafluoroborate (BF4) as an anion, for use in EDLCs. To find the optimal structure, various QASs with different sized head groups and ether-containing tail groups were systematically compared. Comparing two nearly identical structures with and without ether groups, QASs with oxygen atoms showed improved capacitance, proving that ions with oxygen atoms move more easily than their counterparts at lower electric fields. Moreover, the ether containing QASs showed low activation energy values of conductivities, leading to smaller IR drops during the charge and discharge processes, resulting in an overall higher capacitance. PMID:28959391

First-principles prediction of low-energy structures for AlH3

NASA Astrophysics Data System (ADS)

Sun, Shoutian; Ke, Xuezhi; Chen, Changfeng; Tanaka, Isao

2009-01-01

We report density-functional calculations that predict ten different low-energy structures for aluminum hydride AlH3 with space groups Pnma , P6/mmm , I4/mcm , P4/mbm , P4/nmm , Pm3¯m , P21/m , P21/c , Pbcm , and P4/n . Phonon calculations within harmonic approximation reveal unstable modes in the P6/mmm , I4/mcm , P4/mbm , P4/nmm , Pm3¯m , P21/m , and P21/c structures, indicating that they are unstable at low temperatures. The calculations show that the thermodynamic stabilities for AlH3 with space groups Pnma , Pbcm , and P4/n are overall close to the existing α - and γ-AlH3 . From x-ray powder-diffraction patterns, the simulated main-peak positions for AlH3 (P4/n) are in good agreement with experimental δ-AlH3 . A full Rietveld analysis reveals that the fitting space groups R3¯c , Pbcm , and Pnma to the experimental x-ray powder-diffraction pattern of α-AlH3 gives almost the same satisfactory result.

Synthesis, structural and optical properties of (ALa)(FeMn)O6 (A = Ba and Sr) double perovskites

NASA Astrophysics Data System (ADS)

Kumar, Dinesh; Sudarshan, V.; Singh, Akhilesh Kumar

2018-05-01

Here, we report structural and optical properties of ALaFeMnO6 (A = Ba and Sr) double perovskite synthesized via auto-combustion followed by calcinations process. Rietveld refinement of structure using x-ray diffraction data reveals that BaLaFeMnO6 crystallizes into cubic crystal structure with space group Pm-3m while SrLaFeMnO6 crystallizes into rhombohedral crystal structure having space group R-3c. The absorption spectrum measurement using UV-Vis spectroscopy reveals that these samples are prefect insulator having energy band gap between conduction and valence band of the order of 6 eV.

Nitroxoline Molecule: Planar or Not? A Story of Battle between π-π Conjugation and Interatomic Repulsion.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Otlyotov, Arseniy A; Solyankin, Peter M; Rykov, Anatolii N; Shkurinov, Alexander P; Grikina, Olga E; Khaikin, Leonid S

2018-02-15

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO 2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO 2 group from the closest hydrogen, which overcomes the energy gain from the π-π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO 2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

NASICON-Structured Materials for Energy Storage.

PubMed

Jian, Zelang; Hu, Yong-Sheng; Ji, Xiulei; Chen, Wen

2017-05-01

The demand for electrical energy storage (EES) is ever increasing, which calls for better batteries. NASICON-structured materials represent a family of important electrodes due to its superior ionic conductivity and stable structures. A wide range of materials have been considered, where both vanadium-based and titanium-based materials are recommended as being of great interest. NASICON-structured materials are suitable for both the cathode and the anode, where the operation potential can be easily tuned by the choice of transition metal and/or polyanion group in the structure. NASICON-structured materials also represent a class of solid electrolytes, which are widely employed in all-solid-state ion batteries, all-solid-state air batteries, and hybrid batteries. NASICON-structured materials are reviewed with a focus on both electrode materials and solid-state electrolytes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic and magnetic properties of second main-group and second sub-group metals substitution for Al in delafossite CuAlO2

NASA Astrophysics Data System (ADS)

Liu, Qi-Jun; Liu, Fu-Sheng; Liu, Zheng-Tang

2015-07-01

A systematic theoretical investigation has been carried out for the structural, electronic and magnetic properties of second main-group and second sub-group metals substitution for Al in delafossite CuAlO2 in the framework of density functional theory. The structural parameters and formation energies were calculated and discussed. The appearance of enhanced p-type conductivity after doping has been analyzed. Moreover, it is shown that all dopants have relatively large magnetic moments, but their ferromagnetic states are unstable, showing that their potential application in dilute magnetic semiconductors is not applicable.

Nonlinear dissipative devices in structural vibration control: A review

NASA Astrophysics Data System (ADS)

Lu, Zheng; Wang, Zixin; Zhou, Ying; Lu, Xilin

2018-06-01

Structural vibration is a common phenomenon existing in various engineering fields such as machinery, aerospace, and civil engineering. It should be noted that the effective suppression of structural vibration is conducive to enhancing machine performance, prolonging the service life of devices, and promoting the safety and comfort of structures. Conventional linear energy dissipative devices (linear dampers) are largely restricted for wider application owing to their low performance under certain conditions, such as the detuning effect of tuned mass dampers subjected to nonstationary excitations and the excessively large forces generated in linear viscous dampers at high velocities. Recently, nonlinear energy dissipative devices (nonlinear dampers) with broadband response and high robustness are being increasingly used in practical engineering. At the present stage, nonlinear dampers can be classified into three groups, namely nonlinear stiffness dampers, nonlinear-stiffness nonlinear-damping dampers, and nonlinear damping dampers. Corresponding to each nonlinear group, three types of nonlinear dampers that are widely utilized in practical engineering are reviewed in this paper: the nonlinear energy sink (NES), particle impact damper (PID), and nonlinear viscous damper (NVD), respectively. The basic concepts, research status, engineering applications, and design approaches of these three types of nonlinear dampers are summarized. A comparison between their advantages and disadvantages in practical engineering applications is also conducted, to provide a reference source for practical applications and new research.

Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

Ab initio investigation of the first hydration shell of protonated glycine

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

Wei, Zhichao; Chen, Dong, E-mail: dongchen@henu.edu.cn, E-mail: boliu@henu.edu.cn; Zhao, Huiling

2014-02-28

The first hydration shell of the protonated glycine is built up using Monte Carlo multiple minimum conformational search analysis with the MMFFs force field. The potential energy surfaces of the protonated glycine and its hydration complexes with up to eight water molecules have been scanned and the energy-minimized structures are predicted using the ab initio calculations. First, three favorable structures of protonated glycine were determined, and the micro-hydration processes showed that water can significantly stabilize the unstable conformers, and then their first hydration shells were established. Finally, we found that seven water molecules are required to fully hydrate the firstmore » hydration shell for the most stable conformer of protonated glycine. In order to analyse the hydration process, the dominant hydration sites located around the ammonium and carboxyl groups are studied carefully and systemically. The results indicate that, water molecules hydrate the protonated glycine in an alternative dynamic hydration process which is driven by the competition between different hydration sites. The first three water molecules are strongly attached by the ammonium group, while only the fourth water molecule is attached by the carboxyl group in the ultimate first hydration shell of the protonated glycine. In addition, the first hydration shell model has predicted most identical structures and a reasonable accord in hydration energy and vibrational frequencies of the most stable conformer with the conductor-like polarizable continuum model.« less

Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Venkatesan, Perumal; Rajakannan, Venkatachalam; Venkataramanan, Natarajan S.; Ilangovan, Andivelu; Sundius, Tom; Thamotharan, Subbiah

2016-09-01

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular Nsbnd H⋯O and Osbnd H⋯O and intermolecular Nsbnd H⋯O and Csbnd H⋯O interactions along with carbonyl⋯carbonyl and Csbnd H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular Csbnd H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.

A comparison of community and trophic structure in five marine ecosystems based on energy budgets and system metrics

NASA Astrophysics Data System (ADS)

Gaichas, Sarah; Skaret, Georg; Falk-Petersen, Jannike; Link, Jason S.; Overholtz, William; Megrey, Bernard A.; Gjøsæter, Harald; Stockhausen, William T.; Dommasnes, Are; Friedland, Kevin D.; Aydin, Kerim

2009-04-01

Energy budget models for five marine ecosystems were compared to identify differences and similarities in trophic and community structure. We examined the Gulf of Maine and Georges Bank in the northwest Atlantic Ocean, the combined Norwegian/Barents Seas in the northeast Atlantic Ocean, and the eastern Bering Sea and the Gulf of Alaska in the northeast Pacific Ocean. Comparable energy budgets were constructed for each ecosystem by aggregating information for similar species groups into consistent functional groups. Several ecosystem indices (e.g., functional group production, consumption and biomass ratios, cumulative biomass, food web macrodescriptors, and network metrics) were compared for each ecosystem. The comparative approach clearly identified data gaps for each ecosystem, an important outcome of this work. Commonalities across the ecosystems included overall high primary production and energy flow at low trophic levels, high production and consumption by carnivorous zooplankton, and similar proportions of apex predator to lower trophic level biomass. Major differences included distinct biomass ratios of pelagic to demersal fish, ranging from highest in the combined Norwegian/Barents ecosystem to lowest in the Alaskan systems, and notable differences in primary production per unit area, highest in the Alaskan and Georges Bank/Gulf of Maine ecosystems, and lowest in the Norwegian ecosystems. While comparing a disparate group of organisms across a wide range of marine ecosystems is challenging, this work demonstrates that standardized metrics both elucidate properties common to marine ecosystems and identify key distinctions useful for fisheries management.

For or against structural realism? A verdict from high energy physics

NASA Astrophysics Data System (ADS)

Nounou, Antigone M.

2015-02-01

When it comes to supporting the main ontic structural realist thesis, that we are better off with a metaphysics purged of objects, its proponents have to meet several challenges, three of which are to ensure that objects can be recast in terms of structure alone at both the level of theory and the level of ontology, to justify on physical grounds that structure exists in the world in a way that affects the goings-on in it, and to show that the relation between objects and structure is non-reciprocal, so that structure is ontologically prior to objects but not the converse. Assuming-tacitly or explicitly-that the objects of physics can be thus recast using symmetry group structure, supporters of the thesis have, therefore, to meet the remaining challenges. The present paper discusses and contests two such attempts, which typify arguments in favor of ontic structural realism from high-energy physics.

Effect of cobalt doping on structural and optical properties of nanocrystalline La0.8Pb0.2CrO3 orthochromite

NASA Astrophysics Data System (ADS)

Zarrin, Naima; Shahidhusain

2018-04-01

We have synthesized nanocrystalline La0.8Pb0.2Cr1-xCoxO3 (0≤x≤0.3) through sol-gel process and studied their structural and optical properties. X-ray diffraction patterns reveal that the samples conform in the orthorhombic crystal symmetry with Pnma space group. Structural parameters are refined by Rietveld Refinement using Fullprof software. Lattice parameters and unit cell volume of doped samples are found to decrease with increase in Co doping. The optical energy band gapdecreases whereas Urbach energy increases with the increase in Co content.

Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

PubMed

Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

2015-01-01

A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

Chemical and quantum simulation of electron transfer through a polypeptide

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

Ungar, L.W.; Voth, G.A.; Newton, M.D.

1999-08-26

Quantum rate theory, molecular dynamics simulations, and semiempirical electronic structure calculations are used to fully investigate electron transfer mediated by a solvated polypeptide for the first time. Using a stationary-phase approximation, the nonadiabatic electron-transfer rate constant is calculated from the nuclear free energies and the electronic coupling between the initial and final states. The former are obtained from quantum path integral and classical molecular dynamics simulations; the latter are calculated using semiempirical electronic structure calculations and the generalized Mulliken-Hush method. Importantly, no parameters are fit to kinetic data. The simulated system consists of a solvated four-proline polypeptide with a tris(bipyridine)rutheniummore » donor group and an oxypentamminecobalt acceptor group. From the simulation data entropy and energy contributions to the free energies are distinguished. Quantum suppression of the barrier, including important solvent contributions, is demonstrated. Although free energy profiles along the reaction coordinate are nearly parabolic, pronounced departures from harmonic behavior are found for the separate energy and entropy functions. Harmonic models of the system are compared to simulation results in order to quantify anharmonic effects. Electronic structure calculations show that electronic coupling elements vary considerably with system conformation, even when the effective donor-acceptor separation remains roughly constant. The calculations indicate that electron transfer in a significant range of conformations linking the polypeptide to the acceptor may contribute to the overall rate constant. After correction for limitations of the solvent model, the simulations and calculations agree well with the experimental activation energy and Arrhenius prefactor.« less

Influence of functional groups on the C α-C β chain of L-phenylalanine and its derivatives

NASA Astrophysics Data System (ADS)

Ganesan, Aravindhan; Brunger, Michael; Wang, Feng

2010-07-01

L-phenylalanine ( L-phe) consists of three different functional groups, i.e., phenyl, carboxyl (-COOH) and amino (-NH 2), joining through the C α-C β bridge. Substitution of these groups produces 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA). Electronic structures of L-phe, PEA and PPA together with smaller "fragments" L-alanine and benzene were determined using density functional theory (DFT), from which core and valence shell ionization spectra were simulated. Comparison of the spectra reveals that core shell ionization energies clearly indicate that the carbon bridge is significantly affected by their functional group substitutions particularly at the C α site. In the valence space, quite unexpectedly, the frontier orbitals are concentrated on the benzene group although some energy splitting is observed. The orbitals which significantly affect the C α-C β carbon backbone are from the inner valence shell in the ionization energy region of 20-26 eV of the molecules.

A comparative theoretical study on the structural, electronic and nonlinear optical features of B12N12 and Al12N12 nanoclusters with the groups III, IV and V dopants

NASA Astrophysics Data System (ADS)

Shakerzadeh, Ehsan; Barazesh, Neda; Talebi, Sima Zargar

2014-12-01

The structural, electronic and nonlinear optical properties of the two important fullerene-like cages of B12N12 and Al12N12 nanostructures with the groups III, IV and V dopants are investigated through density functional theory (DFT) calculations. It has been found that doping process induces local deformation at bond lengths near the doping site. Natural bond orbital (NBO) analyses are also performed for scrutinizing the structural properties of the considered nanoclusters. The results indicate that the groups III, IV and V dopants remarkably narrow the energy gap of the B12N12 nanocluster. On the other hand, although the energy gap of Al12N12 nanocluster is insensitive to groups III and V dopants; the carbon, silicon and germanium dopants extremely reduce the energy gap of this cluster. It seems that the electronic character of the B12N12 and Al12N12 nanocluster is sensitive to the dopants and it could be adjusted by particular impurity. Moreover the considered dopants induce hyperpolarizability in both of the considered nanoclusters. Interestingly, the replacing aluminum atom by carbon one in Al12N12 nanocluster (CAl11N12) leads to an extremely large hyperpolarizability value of 4358.77 a.u., which is the largest one among the considered doped clusters. It shows that the doping process plays an important role in enhancing the first hyperpolarizability of the B12N12 and Al12N12 nanoclusters.

Report of Research at Technische Universitaet Darmstadt on Ultrahard Materials in the B-C-N-Si System

DTIC Science & Technology

2015-06-01

structure at the micro- and nanoscale. In other words, development of nanocomposites, multilayers, and superlattices via appropriate design and control of...C-B and C-N bonds as C-C and B-N bonds. Later, the same research group , based on first-principles total-energy, and dynamic phonon calculations...Vickers hardness values.7 Another research group employed an ab initio evolutionary algorithm42 to resolve the crystal structure of the observed

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

PubMed

Liu, Jie; Jiang, Xiangang; Cao, Yu; Zhang, Chen; Zhao, Guangyao; Zhao, Maoshuang; Feng, Li

2018-05-07

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Electronic structures and geometries of the XF{sub 3} (X = Cl, Br, I, At) fluorides

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

Sergentu, Dumitru-Claudiu; CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3; Amaouch, Mohamed

The potential energy surfaces of the group 17 XF{sub 3} (X = Cl, Br, I, At) fluorides have been investigated for the first time with multiconfigurational wave function theory approaches. In agreement with experiment, bent T-shaped C{sub 2v} structures are computed for ClF{sub 3}, BrF{sub 3}, and IF{sub 3}, while we predict that an average D{sub 3h} structure would be experimentally observed for AtF{sub 3}. Electron correlation and scalar relativistic effects strongly reduce the energy difference between the D{sub 3h} geometry and the C{sub 2v} one, along the XF{sub 3} series, and in the X = At case, spin-orbit couplingmore » also slightly reduces this energy difference. AtF{sub 3} is a borderline system where the D{sub 3h} structure becomes a minimum, i.e., the pseudo-Jahn-Teller effect is inhibited since electron correlation and scalar-relativistic effects create small energy barriers leading to the global C{sub 2v} minima, although both types of effects interfere.« less

Modulating the band structure and sub-bandgap absorption of Co-hyperdoped silicon by co-doping with shallow-level elements

NASA Astrophysics Data System (ADS)

Dong, Xiao; Fang, Xiuxiu; Wang, Yongyong; Song, Xiaohui; Lu, Zhansheng

2018-06-01

Hyperdoped group-III elements can lower the Fermi energy in the band structures of Co-hyperdoped silicon. When the Co-to-X (X = B, Al, Ga) ratio is 2:1, the intermediate band (IB) in the bandgap includes the Fermi energy and is partially filled by electrons, which is in accordance with the requirement of an IB material. The hyperdoped X atoms can cause the blueshift of the sub-bandgap absorption of the compound compared with the material with no shallow-level elements, which is due to the enlargement of the electronic excitation energy of the Co,X-co-doped silicon.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller than ˜ 10 H2O/SO 3-, which is consistent with experimental observations. The sulfonate groups are also found to have influence on the proton hopping directions. The temperature and water content effects on the PT pathways are also investigated. The morphological effects on proton solvation and transport in hydrated Nafion are investigated, by using the SCI-MS-EVB method. Two of the most significant morphological models of Nafion, the lamellar model and the cylinder model, are selected. The two models exhibit distinct PT patterns, which result in different proton diffusion rates. In both models, the interaction between protons and the sulfonate groups are proven to be the key to determining PT behavior. The proton solvation structure change as a function of the distance between protons and sulfonate groups has been analyzed. It is found that the increase of water cylinder radius or water layer height leads to the presence of more protons around the sulfonate groups. Furthermore, at a lower hydration level, the increased amount of protons around the sulfonate groups consists of more Zundel-like structures, which is influenced by the distinct morphological structures of Nafion.

Evaluation of multiple-scale 3D characterization for coal physical structure with DCM method and synchrotron X-ray CT.

PubMed

Wang, Haipeng; Yang, Yushuang; Yang, Jianli; Nie, Yihang; Jia, Jing; Wang, Yudan

2015-01-01

Multiscale nondestructive characterization of coal microscopic physical structure can provide important information for coal conversion and coal-bed methane extraction. In this study, the physical structure of a coal sample was investigated by synchrotron-based multiple-energy X-ray CT at three beam energies and two different spatial resolutions. A data-constrained modeling (DCM) approach was used to quantitatively characterize the multiscale compositional distributions at the two resolutions. The volume fractions of each voxel for four different composition groups were obtained at the two resolutions. Between the two resolutions, the difference for DCM computed volume fractions of coal matrix and pores is less than 0.3%, and the difference for mineral composition groups is less than 0.17%. This demonstrates that the DCM approach can account for compositions beyond the X-ray CT imaging resolution with adequate accuracy. By using DCM, it is possible to characterize a relatively large coal sample at a relatively low spatial resolution with minimal loss of the effect due to subpixel fine length scale structures.

Nanomechanical resonators based on group IV element monolayers

NASA Astrophysics Data System (ADS)

He, Ji-Dong; Sun, Jia-Sheng; Jiang, Jin-Wu

2018-04-01

We perform molecular dynamics simulations to investigate the energy dissipation of the resonant oscillation for the group IV monolayers of puckered configuration, in which the oscillation is driven with different actuation velocities. We find that, in the moderate actuation velocity regime, the nonlinear coupling between the resonant oscillation mode and other high-frequency modes will lead to the non-resonant motion of the system. For the larger actuation velocity, the effective strain generated during the resonant oscillating causes a structural transition from the puckered configuration into the planar configuration, which is a characteristic energy dissipation mechanism for the resonant oscillation of these group IV puckered monolayers. Our findings shed light on mechanical applications of the group IV monolayers in the nanomechanical resonator field.

Electron detachment of the hydrogen-bonded amino acid side-chain guanine complexes

NASA Astrophysics Data System (ADS)

Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

2007-07-01

The photoelectron spectra of the hydrogen-bonded amino acid side-chain-guanine complexes has been studied at the partial third order (P3) self-energy approximation of the electron propagator theory. The correlation between the vertical electron detachment energy and the charge distributions on the guanine moiety reveals that the vertical electron detachment energy (VDE) increases as the positive charge distribution on the guanine increases. The low VDE values determined for the negatively charged complexes of the guanine-side-chain-group of Asp/Glu suggest that the influence of the H-bonded anionic groups on the VDE of guanine could be more important than that of the anionic backbone structure. The even lower vertical electron detachment energy for guanine is thus can be expected in the H-bonded protein-DNA systems.

Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles.

PubMed

Panigrahi, Swati; Pal, Rahul; Bhattacharyya, Dhananjay

2011-12-01

Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H...O/N hydrogen bond mediated non-polar basepairs are also found to be significantly stable in terms of their interaction energy values. Few polar basepairs, having amino or carboxyl groups not hydrogen bonded to anything, such as G:G H:W C, show large flexibility. Most of the non-polar basepairs, except A:G s:s T and A:G w:s C, are found to be stable; indicating C-H...O/N interaction also plays a prominent role in stabilizing the basepairs. The sugar mediated basepairs show variability in their structures, due to the involvement of flexible ribose sugar. These presumably indicate that the most of the polar basepairs along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.

Towards solar energy storage in the photochromic dihydroazulene-vinylheptafulvene system.

PubMed

Cacciarini, Martina; Skov, Anders B; Jevric, Martyn; Hansen, Anne S; Elm, Jonas; Kjaergaard, Henrik G; Mikkelsen, Kurt V; Brøndsted Nielsen, Mogens

2015-05-11

One key challenge in the field of exploitation of solar energy is to store the energy and make it available on demand. One possibility is to use photochromic molecules that undergo light-induced isomerization to metastable isomers. Here we present efforts to develop solar thermal energy storage systems based on the dihydroazulene (DHA)/vinylheptafulvene (VHF) photo/thermoswitch. New DHA derivatives with one electron-withdrawing cyano group at position 1 and one or two phenyl substituents in the five-membered ring were prepared by using different synthetic routes. In particular, a diastereoselective reductive removal of one cyano group from DHAs incorporating two cyano groups at position 1 turned out to be most effective. Quantum chemical calculations reveal that the structural modifications provide two benefits relative to DHAs with two cyano groups at position 1: 1) The DHA-VHF energy difference is increased (i.e., higher energy capacity of metastable VHF isomer); 2) the Gibbs free energy of activation is increased for the energy-releasing VHF to DHA back-reaction. In fact, experimentally, these new derivatives were so reluctant to undergo the back-reaction at room temperature that they practically behaved as DHA to VHF one-way switches. Although lifetimes of years are at first attractive, which offers the ultimate control of energy release, for a real device it must of course be possible to trigger the back-reaction, which calls for further iterations in the future. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-activity correlations for organophosphorus ester anticholinesterases. Part 2: CNDO/2 calculations applied to ester hydrolysis rates

NASA Technical Reports Server (NTRS)

Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

1984-01-01

Quantitative structure-activity relationships are presented for the hydrolysis of organophosphorus esters, RR'P(O)X, where R and R' are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. CNDO/2 calculations provide values for molecular parameters that correlate with alkaline hydrolysis rates. For each subset of esters with the same leaving group, X, the CNDO-derived net atomic charge at the central phosphorus atom correlates well with the alkaline hydrolysis rate constants. For the whole set of esters with different leaving groups, equations are derived that relate charge, orbital energy and bond order to the hydrolysis rate constants.

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Renormalization group method based on the ionization energy theory

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

Arulsamy, Andrew Das, E-mail: sadwerdna@gmail.com; School of Physics, University of Sydney, Sydney, New South Wales 2006

2011-03-15

Proofs are developed to explicitly show that the ionization energy theory is a renormalized theory, which mathematically exactly satisfies the renormalization group formalisms developed by Gell-Mann-Low, Shankar and Zinn-Justin. However, the cutoff parameter for the ionization energy theory relies on the energy-level spacing, instead of lattice point spacing in k-space. Subsequently, we apply the earlier proofs to prove that the mathematical structure of the ionization-energy dressed electron-electron screened Coulomb potential is exactly the same as the ionization-energy dressed electron-phonon interaction potential. The latter proof is proven by means of the second-order time-independent perturbation theory with the heavier effective mass condition,more » as required by the electron-electron screened Coulomb potential. The outcome of this proof is that we can derive the heat capacity and the Debye frequency as a function of ionization energy, which can be applied in strongly correlated matter and nanostructures.« less

Scanning Electron Microscopy and Energy-Dispersive X-Ray Microanalysis of Set CEM Cement after Application of Different Bleaching Agents.

PubMed

Samiei, Mohammad; Janani, Maryam; Vahdati, Amin; Alemzadeh, Yalda; Bahari, Mahmoud

2017-01-01

The present study evaluated the element distribution in completely set calcium-enriched mixture (CEM) cement after application of 35% carbamide peroxide, 40% hydrogen peroxide and sodium perborate as commercial bleaching agents using an energy-dispersive x-ray microanalysis (EDX) system. The surface structure was also observed using the scanning electron microscope (SEM). Twenty completely set CEM cement samples, measuring 4×4 mm 2 , were prepared in the present in vitro study and randomly divided into 4 groups based on the preparation technique as follows: the control group; 35% carbamide peroxide group in contact for 30-60 min for 4 times; 40% hydrogen peroxide group with contact time of 15-20 min for 3 times; and sodium perborate group, where the powder and liquid were mixed and placed on CEM cement surface 4 times. Data were analyzed at a significance level of 0.05 through the one Way ANOVA and Tukey's post hoc tests. EDX showed similar element distribution of oxygen, sodium, calcium and carbon in CEM cement with the use of carbamide peroxide and hydroxide peroxide; however, the distribution of silicon was different ( P <0.05). In addition, these bleaching agents resulted in significantly higher levels of oxygen and carbon ( P <0.05) and a lower level of calcium ( P <0.05) compared to the control group. SEM of the control group showed plate-like and globular structure. Sodium perborate was similar to control group due to its weak oxidizing properties. Globular structures and numerous woodpecker holes were observed on the even surface on the carbamide peroxide group. The mean elemental distribution of completely set CEM cement was different when exposed to sodium perborate, carbamide peroxide and hydrogen peroxide.

Influence of hyperbaric oxygen on biomechanics and structural bone matrix in type 1 diabetes mellitus rats.

PubMed

Limirio, Pedro Henrique Justino Oliveira; da Rocha Junior, Huberth Alexandre; Morais, Richarlisson Borges de; Hiraki, Karen Renata Nakamura; Balbi, Ana Paula Coelho; Soares, Priscilla Barbosa Ferreira; Dechichi, Paula

2018-01-01

The aim of this study was to evaluate the biomechanics and structural bone matrix in diabetic rats subjected to hyperbaric oxygen therapy (HBO). Twenty-four male rats were divided into the following groups: Control; Control + HBO; Diabetic, and Diabetic + HBO. Diabetes was induced with streptozotocin (STZ) in the diabetic Groups. After 30 days, HBO was performed every 48h in HBO groups and all animals were euthanized 60 days after diabetic induction. The femur was submitted to a biomechanical (maximum strength, energy-to-failure and stiffness) and Attenuated Total Reflectance Fourier transform infrared (ATR-FTIR) analyses (crosslink ratio, crystallinity index, matrix-to-mineral ratio: Amide I + II/Hydroxyapatite (M:MI) and Amide III + Collagen/HA (M:MIII)). In biomechanical analysis, diabetic animals showed lower values of maximum strength, energy and stiffness than non-diabetic animals. However, structural strength and stiffness were increased in groups with HBO compared with non-HBO. ATR-FTIR analysis showed decreased collagen maturity in the ratio of crosslink peaks in diabetic compared with the other groups. The bone from the diabetic groups showed decreased crystallinity compared with non-diabetic groups. M:MI showed no statistical difference between groups. However, M:MIII showed an increased matrix mineral ratio in diabetic+HBO and control+HBO compared with control and diabetic groups. Correlations between mechanical and ATR-FTIR analyses showed significant positive correlation between collagen maturity and stiffness. Diabetes decreased collagen maturation and the mineral deposition process, thus reducing biomechanical properties. Moreover, the study showed that HBO improved crosslink maturation and increased maximum strength and stiffness in the femur of T1DM animals.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Nuclear structure and decay data evaluation in Europe

NASA Astrophysics Data System (ADS)

Negret, Alexandru; Balabanski, Dimiter; Dimitriou, Paraskevi; Elekes, Zoltan; Mertzimekis, Theo J.; Pascu, Sorin; Timar, Janos

2017-09-01

Nuclear Structure and Decay Data (NSDD) activities in Europe include mass-chain and individual nuclei evaluations as well as horizontal evaluations and compilations, data dissemination and educational activities. As such they are essential for a large range of applications from energy, environmental, and medical to basic research in nuclear structure and reactions, all of which are intensively pursued in Europe. Although the NSDD evaluation groups in Europe form part of the international network of NSDD evaluators, which is coordinated by the International Atomic Energy Agency, they are faced with some very distinct challenges. We shortly present the NSDD Data Centre at IFIN-HH, Bucharest and discuss possible actions to improve the situation for the entire European NSDD evaluation effort.

Boron difluoride dibenzoylmethane derivatives: Electronic structure and luminescence

NASA Astrophysics Data System (ADS)

Tikhonov, Sergey A.; Vovna, Vitaliy I.; Osmushko, Ivan S.; Fedorenko, Elena V.; Mirochnik, Anatoliy G.

2018-01-01

Electronic structure and optical properties of boron difluoride dibenzoylmethanate and four of its derivatives have been studied by X-ray photoelectron spectroscopy, absorption and luminescence spectroscopy and quantum chemistry (DFT, TDDFT). The relative quantum luminescence yields have been revealed to correlate with charge transfers of HOMO-LUMO transitions, energy barriers of aromatic substituents rotation and the lifetime of excited states in the investigated complexes. The bathochromic shift of intensive bands in the optical spectra has been observed to occur when the functional groups are introduced into p-positions of phenyl cycles due to destabilizing HOMO levels. Calculated energy intervals between electronic levels correlate well with XPS spectra structure of valence and core electrons.

Electronic properties and structural phase transition in A4 [M4O4] (A=Li, Na, K and Rb; M=Ag and Cu): A first principles study

NASA Astrophysics Data System (ADS)

Umamaheswari, R.; Yogeswari, M.; Kalpana, G.

2013-02-01

Self-consistent scalar relativistic band structure calculations for AMO (A=Li, Na, K and Rb; M=Ag and Cu) compounds have been performed using the tight-binding linear muffin-tin orbital (TB-LMTO) method within the local density approximation (LDA). At ambient conditions, these compounds are found to crystallize in tetragonal KAgO-type structure with two different space group I-4m2 and I4/mmm. Nowadays, hypothetical structures are being considered to look for new functional materials. AMO compounds have stoichiometry similar to eight-electron half-Heusler materials of type I-I-VI which crystallizes in cubic (C1b) MgAgAs-type structure with space group F-43m. For all these compounds, by interchanging the positions of atoms in the hypothetical cubic structure, three phases (α, β and γ) are formed. The energy-volume relation for these compounds in tetragonal KAgO-type structure and cubic α, β and γ phases of related structure have been obtained. Under ambient conditions these compounds are more stable in tetragonal KAgO-type (I4/mmm) structure. The total energies calculated within the atomic sphere approximation (ASA) were used to determine the ground state properties such as equilibrium lattice parameters, c/a ratio, bulk modulus, cohesive energy and are compared with the available experimental results. The results of the electronic band structure calculations at ambient condition show that LiCuO and NaMO are indirect band gap semiconductors whereas KMO and RbMO are direct band gap semiconductors. At high pressure the band gap decreases and the phenomenon of band overlap metallization occur. Also these compounds undergo structural phase transition from tetragonal I-4m2 phase to cubic α-phase and transition pressures were calculated.

Power, Profits, and Politics: Energy Security and Cooperation in Eurasia

NASA Astrophysics Data System (ADS)

Svyatets, Ekaterina

This study explores varying outcomes of energy cooperation, defined as diplomatic relations, bilateral trade, and investment in oil and natural gas. Tests of theories pertinent to energy security - broadly speaking, realism, liberalism, and domestic politics---reveal that they alone can offer only a narrow and one-sided explanation, not embracing the complexity of energy issues. Nevertheless, using them as a starting point, this study outlined a structured framework that incorporates three variables---economic potential, geopolitical rivalry, and domestic interest groups---that are applied to the cases of U.S.-Russia, U.S.-Azerbaijan, and Russia-Germany energy ties. This study concludes that if the economic potential (defined by geographic proximity and resource availability) is very high, such as in the case of Russia-Germany, states can overcome geopolitical rivalries and historical enmities in favor of energy cooperation. However, if the economic potential is relatively low (because of geographic obstacles or easily available alternative suppliers, as in the cases of U.S.-Russia and U.S.-Azerbaijan), then geopolitics prevails---for example, to bypass Russia or to limit American access to contracts in Russia when U.S.-Russian relations are strained. In all the cases explored here, domestic interest groups have mixed influence: if they are united along energy issues, they usually successfully achieve their energy policy goals, although the impact of these groups often becomes intertwined with state interests. In other situations, when powerful interest groups are divided or focused on non-energy-related issues (such as ethnic priorities), their influence over energy deals is much lower.

The value of a kurtosis metric in estimating the hazard to hearing of complex industrial noise exposures.

PubMed

Qiu, Wei; Hamernik, Roger P; Davis, Robert I

2013-05-01

A series of Gaussian and non-Gaussian equal energy noise exposures were designed with the objective of establishing the extent to which the kurtosis statistic could be used to grade the severity of noise trauma produced by the exposures. Here, 225 chinchillas distributed in 29 groups, with 6 to 8 animals per group, were exposed at 97 dB SPL. The equal energy exposures were presented either continuously for 5 d or on an interrupted schedule for 19 d. The non-Gaussian noises all differed in the level of the kurtosis statistic or in the temporal structure of the noise, where the latter was defined by different peak, interval, and duration histograms of the impact noise transients embedded in the noise signal. Noise-induced trauma was estimated from auditory evoked potential hearing thresholds and surface preparation histology that quantified sensory cell loss. Results indicated that the equal energy hypothesis is a valid unifying principle for estimating the consequences of an exposure if and only if the equivalent energy exposures had the same kurtosis. Furthermore, for the same level of kurtosis the detailed temporal structure of an exposure does not have a strong effect on trauma.

Structure of p-shell nuclei using three-nucleon interactions evolved with the similarity renormalization group

DOE PAGES

Jurgenson, E. D.; Maris, P.; Furnstahl, R. J.; ...

2013-05-13

The similarity renormalization group (SRG) is used to soften interactions for ab initio nuclear structure calculations by decoupling low- and high-energy Hamiltonian matrix elements. The substantial contribution of both initial and SRG-induced three-nucleon forces requires their consistent evolution in a three-particle basis space before applying them to larger nuclei. While, in principle, the evolved Hamiltonians are unitarily equivalent, in practice the need for basis truncation introduces deviations, which must be monitored. Here we present benchmark no-core full configuration calculations with SRG-evolved interactions in p-shell nuclei over a wide range of softening. As a result, these calculations are used to assessmore » convergence properties, extrapolation techniques, and the dependence of energies, including four-body contributions, on the SRG resolution scale.« less

Synthesis, structural and optical characterization of APbX{sub 3} (A=methylammonium, dimethylammonium, trimethylammonium; X=I, Br, Cl) hybrid organic-inorganic materials

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

Mancini, Alessandro; Quadrelli, Paolo; Amoroso, Giuseppe

2016-08-15

In this paper we report the synthesis, the crystal structure and the optical response of APbX{sub 3} (A=MA, DMA, and TMA; X=I, Br) hybrid organic-inorganic materials including some new phases. We observe that as the cation group increases in size, the optical absorption edge shifts to higher energies with energy steps which are systematic and independent on the anion. A linear correlation between the optical bad gap and the tolerance factor has been shown for the series of samples investigated. - Graphical abstract: The crystal structure and the optical response of the two series of hybrid organic-inorganic materials APbX{sub 3}more » (A=MA, DMA, and TMA; X=I, Br), which include some new phases, are reported. A dependence of crystal structure and band-gap with tolerance factor is shown. Display Omitted - Highlights: • DMAPbI{sub 3}, TMAPbI{sub 3} and TMAPbBr{sub 3} are reported as new hybrid organic-inorganic compounds. • Crystal structure and optical properties as a function of the number of methyl groups are provided. • Correlation between structure and optical properties are given as a function of tolerance factor.« less

Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding.

PubMed

Podjarny, A; Cachau, R E; Schneider, T; Van Zandt, M; Joachimiak, A

2004-04-01

The determination of several of aldose reductase-inhibitor complexes at subatomic resolution has revealed new structural details, including the specific interatomic contacts involved in inhibitor binding. In this article, we review the structures of the complexes of ALR2 with IDD 594 (resolution: 0.66 angstrom, IC50 (concentration of the inhibitor that produced half-maximal effect): 30 nM, space group: P2(1)), IDD 393 (resolution: 0.90 angstrom, IC50: 6 nM, space group: P1), fidarestat (resolution: 0.92 angstrom, IC50: 9 nM, space group: P2(1)) and minalrestat (resolution: 1.10 angstrom, IC50: 73 nM, space group: P1). The structures are compared and found to be highly reproductible within the same space group (root mean square (RMS) deviations: 0.15 approximately 0.3 angstrom). The mode of binding of the carboxylate inhibitors IDD 594 and IDD 393 is analysed. The binding of the carboxylate head can be accurately determined by the subatomic resolution structures, since both the protonation states and the positions of the atoms are very precisely known. The differences appear in the binding in the specificity pocket. The high-resolution structures explain the differences in IC50, which are confirmed both experimentally by mass spectrometry measures of VC50 and theoretically by free energy perturbation calculations. The binding of the cyclic imide inhibitors fidarestat and minalrestat is also described, focusing on the observation of a Cl(-) ion which binds simultaneously with fidarestat. The presence of this anion, binding also to the active site residue His110, leads to a mechanism in which the inhibitor can bind in a neutral state and then become charged inside the active site pocket. This mechanism can explain the excellent in vivo properties of cyclic imide inhibitors. In summary, the complete and detailed information supplied by the subatomic resolution structures can explain the differences in binding energy of the different inhibitors.

Structure/property relationships in polymer membranes for water purification and energy applications

NASA Astrophysics Data System (ADS)

Geise, Geoffrey

Providing sustainable supplies of purified water and energy is a critical global challenge for the future, and polymer membranes will play a key role in addressing these clear and pressing global needs for water and energy. Polymer membrane-based processes dominate the desalination market, and polymer membranes are crucial components in several rapidly developing power generation and storage applications that rely on membranes to control rates of water and/or ion transport. Much remains unknown about the influence of polymer structure on intrinsic water and ion transport properties, and these relationships must be developed to design next generation polymer membrane materials. For desalination applications, polymers with simultaneously high water permeability and low salt permeability are desirable in order to prepare selective membranes that can efficiently desalinate water, and a tradeoff relationship between water/salt selectivity and water permeability suggests that attempts to prepare such materials should rely on approaches that do more than simply vary polymer free volume. One strategy is to functionalize hydrocarbon polymers with fixed charge groups that can ionize upon exposure to water, and the presence of charged groups in the polymer influences transport properties. Additionally, in many emerging energy applications, charged polymers are exposed to ions that are very different from sodium and chloride. Specific ion effects have been observed in charged polymers, and these effects must be understood to prepare charged polymers that will enable emerging energy technologies. This presentation discusses research aimed at further understanding fundamental structure/property relationships that govern water and ion transport in charged polymer films considered for desalination and electric potential field-driven applications that can help address global needs for clean water and energy.

New crystal structures in hexagonal CuInS2 nanocrystals

NASA Astrophysics Data System (ADS)

Shen, Xiao; Hernández-Pagan, Emil A.; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo, Juan C.; MacDonald, Janet E.; Pennycook, Stephen J.; Pantelides, Sokrates T.

2013-03-01

CuInS2 is one of the best candidate materials for solar energy harvesting. Its nanocrystals with a hexagonal lattice structure that is different from the bulk chalcopyrite phase have been synthesized by many groups. The structure of these CuInS2 nanocrystals has been previously identified as the wurtzite structure in which the copper and indium atoms randomly occupy the cation sites. Using first-principles total energy and electronic structure calculations based on density functional theory, UV-vis absorption spectroscopy, X-ray diffraction, and atomic resolution Z-contrast images obtained in an aberration-corrected scanning transmission electron microscope, we show that CuInS2 nanocrystals do not form random wurtzite structure. Instead, the CuInS2 nanocrystals consist of several wurtzite- related crystal structures with ordered cation sublattices, some of which are reported for the first time here. This work is supported by the NSF TN-SCORE (JEM), by NSF (WZ), by ORNL's Shared Research Equipment User Program (JCI) sponsored by DOE BES, by DOE BES Materials Sciences and Engineering Division (SJP, STP), and used resources of the National Energy Research Scientific Computing Center, supported by the DOE Office of Science under Contract No. DE-AC02-05CH11231.

Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

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

Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed

2016-05-06

The molecular structure of fullerene (C{sub 60}) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electronmore » affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.« less

Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.

PubMed

Stafford, Amy J; Ensign, Daniel L; Webb, Lauren J

2010-11-25

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

NASA Astrophysics Data System (ADS)

Hey, John C.; Doyle, Emily J.; Chen, Yuting; Johnston, Roy L.

2018-03-01

We present putative global minima for the micro-hydrated sulfite SO32-(H2O)N and chlorate ClO32(H2O)N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems. This article is part of the theme issue `Modern theoretical chemistry'.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters.

PubMed

Hey, John C; Doyle, Emily J; Chen, Yuting; Johnston, Roy L

2018-03-13

We present putative global minima for the micro-hydrated sulfite SO 3 2- (H 2 O) N and chlorate ClO 3 - (H 2 O) N systems in the range 3≤ N ≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤ N ≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Authors.

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy

PubMed Central

Klatt, Judith M; Meyer, Steffi; Häusler, Stefan; Macalady, Jennifer L; de Beer, Dirk; Polerecky, Lubos

2016-01-01

We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (<5 μm). Aerobic chemolithotrophic activity of the SOB depended entirely on oxygen produced locally by cyanobacteria during high light conditions. In contrast, B/C mats formed at locations where oxygen in the water column was comparatively abundant (>45 μM) and continuously present. Here SOB were independent of the photosynthetic activity of cyanobacteria and outcompeted the cyanobacteria in the uppermost layer of the mat where energy sources for both functional groups were concentrated. Outcompetition of photosynthetic microbes in the presence of light was facilitated by the decoupling of aerobic chemolithotrophy and oxygenic phototrophy. Remarkably, the B/C mats conserved much less energy than the C/B mats, although similar amounts of light and chemical energy were available. Thus ecosystems do not necessarily develop towards optimal energy usage. Our data suggest that, when two independent sources of energy are available, the structure and activity of microbial communities is primarily determined by the continuous rather than the intermittent energy source, even if the time-integrated energy flux of the intermittent energy source is greater. PMID:26405833

Electron affinities and ionization energies of Cu and Ag delafossite compounds: A hybrid functional study

NASA Astrophysics Data System (ADS)

Miao, Mao-Sheng; Yarbro, Sam; Barton, Phillip T.; Seshadri, Ram

2014-01-01

Using density functional theory with a hybrid functional, we calculate the ionization energies and electron affinities of a series of delafossite compounds (AMO2: A =Cu, Ag; M =B, Al, Ga, In, Sc). The alignments of the valence band maximum and the conduction band minimum, which directly relate to the ionization energies and electron affinities, were obtained by calculations of supercell slab models constructed in a nonpolar orientation. Our calculations reveal that the ionization energy decreases with an increasing atomic number of group-III elements, and thus suggest an improved p-type doping propensity for heavier compounds. For keeping both a low ionization energy and a band gap of sufficient size, CuScO2 is superior to the Cu-based group-III delafossites. By analyzing the electronic structures, we demonstrate that the compositional trend of the ionization energies and electron affinities is the result of a combined effect of d-band broadening due to Cu(Ag)-Cu(Ag) coupling and a repositioning of the d-band center.

Stochastic annealing simulations of defect interactions among subcascades

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

Heinisch, H.L.; Singh, B.N.

1997-04-01

The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performedmore » on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.« less

Reduced graphene oxide as photocatalyst for CO2 reduction reaction(Conference Presentation)

NASA Astrophysics Data System (ADS)

Chang, Yu-Chung

2016-10-01

Photocatalytic conversion of carbon dioxide (CO2) to hydrocarbons such as methanol makes possible simultaneous solar energy harvesting and CO2 reduction. Our previous work is using graphene oxide (GO) as a promising photocatalyst for photocatalytic conversion of CO2 to methanol[1].When using graphene oxide as photocatalyst, the photocatalytic efficiency is 4-flod higher than TiO2 powder. GO has a lot of defects on the surface and those defects make sp2 carbon structure become sp3 carbon structure. The carbon structure change cause the GO has large energy gap about 2.7 eV to 3.2 eV. In order to remove the defect and reduce the energy gap of GO, Zhao et al. try to annealing GO powder in the nitrogen atmosphere at 900oC, the GO structure can be reduced to near graphene structure[2]. Zhu et al. do some low temperature annealing, it can control the structure and energy bandgap of GO by control annealing temperature. If the annealing temperature increase the bandgap of GO will be reduce[3]. So, we can using this annealing process to reduce the bandgap of the GO. In the varying temperature thermal reduction process, as the temperature increases from 130oC to 170oC, the functional groups of the graphene oxide will be reduced and band gap of graphene oxide will be narrowed at same time. The characteristic of thermal reduced graphene oxide were analyzed by SEM, XRD and Raman measurements. The band position was determined by UV/Vis. The reduction of functional groups correlates to red shift in light absorption and eventual quenching in the PL signal of RGOs. Combining hydrophobicity, light harvesting and PL quench, we get the highest yield of RGO150 (0.31 μmole g-1 -cat hr-1) is 1.7-fold higher than that of GO (0.18μmole g-1 -cat hr-1). This work investigates a modified method for using a thermal reduction process to reduce the energy gap of graphene oxide.

Diffraction studies of the high pressure phases of GaAs and GaP

NASA Technical Reports Server (NTRS)

Baublitz, M., Jr.; Ruoff, A. L.

1982-01-01

High pressure structural phase transitions of GaAs and GaP have been studied by energy dispersive X-ray diffraction with the radiation from the Cornell High Energy Synchrotron Source. GaAs began to transform at 172 + or - 7 kbar to an orthorhombic structure possibly belonging to space group Fmmm. GaP transformed to a tetragonal beta-Sn type phase at 215 + or - 8 kbar. Although pressure transmitting media were used to minimize shear stresses in the specimens, the high pressure diffraction results were interpreted as showing evidence for planar defects in the specimens.

Surface modification of EPDM rubber by plasma treatment.

PubMed

Grythe, Kai Frode; Hansen, Finn Knut

2006-07-04

The effect of argon, oxygen, and nitrogen plasma treatment of solvent cast EPDM rubber films has been investigated by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and surface energy measurements. Plasma treatment leads to changes in the surface energy from 25 to 70 mN/m. Treatment conditions influenced both the changes in surface energy and the stability, and it became more difficult to obtain good contact angle measurements after longer (> ca. 4 min) treatment times, probably because of an increasingly uneven surface structure. XPS analyses revealed that up to 20 at. % oxygen can be easily incorporated and that variations of approximately 5% can be controlled by the plasma conditions. Oxygen was mainly found in hydroxyl groups, but also as carbonyl and carboxyl. XPS analyses showed more stable surfaces than expected from contact angles, probably because XPS analysis is less surface sensitive than contact angle measurements. AFM measurements revealed different surface structures with the three gases. The surface roughness increased generally with treatment time, and dramatic changes could be observed at longer times. At short times, surface energy changes were much faster than the changes in surface structure, showing that plasma treatment conditions can be utilized to tailor both surface energies and surface structure of EPDM rubber.

The exponentiated Hencky energy: anisotropic extension and case studies

NASA Astrophysics Data System (ADS)

Schröder, Jörg; von Hoegen, Markus; Neff, Patrizio

2017-10-01

In this paper we propose an anisotropic extension of the isotropic exponentiated Hencky energy, based on logarithmic strain invariants. Unlike other elastic formulations, the isotropic exponentiated Hencky elastic energy has been derived solely on differential geometric grounds, involving the geodesic distance of the deformation gradient \\varvec{F} to the group of rotations. We formally extend this approach towards anisotropy by defining additional anisotropic logarithmic strain invariants with the help of suitable structural tensors and consider our findings for selected case studies.

Structural features, kinetics and SAR study of radical scavenging and antioxidant activities of phenolic and anilinic compounds

PubMed Central

2013-01-01

Background Phenolic compounds are widely distributed in plant kingdom and constitute one of the most important classes of natural and synthetic antioxidants. In the present study fifty one natural and synthetic structurally variant phenolic, enolic and anilinic compounds were examined as antioxidants and radical scavengers against DPPH, hydroxyl and peroxyl radicals. The structural diversity of the used phenolic compounds includes monophenols with substituents frequently present in natural phenols e.g. alkyl, alkoxy, ester and carboxyl groups, besides many other electron donating and withdrawing groups, in addition to polyphenols with 1–3 hydroxyl groups and aminophenols. Some common groups e.g. alkyl, carboxyl, amino and second OH groups were incorporated in ortho, meta and para positions. Results SAR study indicates that the most important structural feature of phenolic compounds required to possess good antiradical and antioxidant activities is the presence of a second hydroxyl or an amino group in o- or p-position because of their strong electron donating effect in these positions and the formation of a stable quinone-like products upon two hydrogen-atom transfer process; otherwise, the presence of a number of alkoxy (in o or p-position) and /or alkyl groups (in o, m or p-position) should be present to stabilize the resulted phenoxyl radical and reach good activity. Anilines showed also similar structural feature requirements as phenols to achieve good activities, except o-diamines which gave low activity because of the high energy of the resulted 1,2-dimine product upon the 2H-transfer process. Enols with ene-1,2-diol structure undergo the same process and give good activity. Good correlations were obtained between DPPH inhibition and inhibition of both OH and peroxyl radicals. In addition, good correlations were obtained between DPPH inhibition and antioxidant activities in sunflower oil and liver homogenate systems. Conclusions In conclusion, the structures of good anti radical and antioxidant phenols and anilines are defined. The obtained good correlations imply that measuring anti DPPH activity can be used as a simple predictive test for the anti hydroxyl and peroxyl radical, and antioxidant activities. Kinetic measurements showed that strong antioxidants with high activity have also high reaction rates indicating that factors stabilizing the phenoxyl radicals lower also the activation energy of the hydrogen transfer process. PMID:23497653

Spectroscopic Signatures and Structural Motifs of Dopamine: a Computational Study

NASA Astrophysics Data System (ADS)

Srivastava, Santosh Kumar; Singh, Vipin Bahadur

2016-06-01

Dopamine (DA) is an essential neurotransmitter in the central nervous system and it plays integral role in numerous brain functions including behaviour, cognition, emotion, working memory and associated learning. In the present work the conformational landscapes of neutral and protonated dopamine have been investigated in the gas phase and in aqueous solution by MP2 and DFT (M06-2X, ωB97X-D, B3LYP and B3LYP-D3) methods. Twenty lowest energy structures of neutral DA were subjected to geometry optimization and the gauche conformer, GIa, was found to be the lowest gas phase structure at the each level of theory in agreement with the experimental rotational spectroscopy. All folded gauche conformers (GI) where lone electron pair of the NH2 group is directed towards the π system of the aromatic ring ( 'non up' ) are found more stable in the gas phase. While in aqueous solution, all those gauche conformers (GII) where lone electron pair of the NH2 group is directed opposite from the π system of the aromatic ring ('up' structures) are stabilized significantly.Nine lowest energy structures, protonated at the amino group, are optimized at the same MP2/aug-cc-pVDZ level of theory. In the most stable gauche structures, g-1 and g+1, mainly electrostatic cation - π interaction is further stabilized by significant dispersion forces as predicted by the substantial differences between the DFT and dispersion corrected DFT-D3 calculations. In aqueous environment the intra-molecular cation- π distance in g-1 and g+1 isomers, slightly increases compared to the gas phase and the magnitude of the cation- π interaction is reduced relative to the gas phase, because solvation of the cation decreases its interaction energy with the π face of aromatic system. The IR intensity of the bound N-H+ stretching mode provides characteristic 'IR spectroscopic signatures' which can reflect the strength of cation- π interaction energy. The CC2 lowest lying S1 ( 1ππ* ) excited state of neutral dopamine is significantly red shifted upon protonation at amino site. E. Dragicevic, J. Schiemann and B. Liss, Neuroscience, 2015, 284, 798. Y. T. Chien et al. Science, 2010, 330, 1091. Cabezas etal., J. Phys. Chem. Lett. 2013, 4, 486.

Stability, Elastic Properties, and Deformation of LiBN2: A Potential High-Energy Material.

PubMed

Zhu, Chunye; Zhu, Wenjun; Yang, Yanqiang

2018-05-15

Searching for high-energy-density materials is of great interest in scientific research and for industrial applications. Using an unbiased structure prediction method and first-principles calculations, we investigated the phase stability of LiBN 2 from 0 to100 GPa. Two new structures with space groups P4̅2 1 m and Pnma were discovered. The theoretical calculations revealed that Pnma LiBN 2 is stable with respect to a mixture of 1 / 3 Li 3 N, BN, and 1 / 3 N 2 above 22 GPa. The electronic band structure revealed that Pnma LiBN 2 has an indirect band gap of 2.3 eV, which shows a nonmetallic feature. The Pnma phase has a high calculated bulk modulus and shear modulus, indicating its incompressible nature. The microscopic mechanism of the structural deformation was demonstrated by ideal tensile shear strength calculations. It is worth mentioning that Pnma LiBN 2 is dynamically stable under ambient conditions. The decomposition of this phase is exothermic, releasing an energy of approximately 1.23 kJ/g at the PBE level. The results provide new thoughts for designing and synthesizing novel high-energy compounds in ternary systems.

The structure of plant photosystem I super-complex at 2.8 Å resolution

PubMed Central

Mazor, Yuval; Borovikova, Anna; Nelson, Nathan

2015-01-01

Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment–pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines. DOI: http://dx.doi.org/10.7554/eLife.07433.001 PMID:26076232

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Electronic and thermal properties of germanene and stanene by first-principles calculations

NASA Astrophysics Data System (ADS)

Jomehpour Zaveh, S.; Roknabadi, M. R.; Morshedloo, T.; Modarresi, M.

2016-03-01

The electronic, vibrational and thermal properties of germanene and stanene have been investigated based on density functional theory (DFT) and density functional perturbation theory (DFPT). The electronic band structure, total and partial density of states and phonon dispersion spectrum and states are analyzed. The phonon spectrum is positive for all modes in the first Brillouin zone and there is a phonon energy band gap between acoustic and optical modes which is around 50 cm-1 for both structure. The constant-volume specific heats of two structures are calculated by using phonon spectrum and density of states. The spin-orbit coupling (SOC) opens a direct energy band gap at the Dirac point, softens phonon spectrum and decreases phonon group velocity of ZA mode.

Slow-light transmission with high group index and large normalized delay bandwidth product through successive defect rods on intrinsic photonic crystal waveguide

NASA Astrophysics Data System (ADS)

Elshahat, Sayed; Khan, Karim; Yadav, Ashish; Bibbò, Luigi; Ouyang, Zhengbiao

2018-07-01

We proposed a strategy with successive cavities as energy reservoirs of electromagnetic energy and light-speed reducers introduced in the first and second rows of rods on the walls of an intrinsic photonic crystal waveguide (PCW) for slow-light transmission in the PCW concerning applications for optical communication, optical computation and optical signal processing. Subsequently, plane-wave expansion method (PWE) is used for studying slow-light properties and finite-difference time-domain (FDTD) method to demonstrate the slow-light propagating property of our proposed structure. We obtained group index as exceedingly large as 6123 with normalized delay bandwidth product (NDBP) as high as 0.48. We designed a facile but more generalized structure that may provide a vital theoretical basis for further enhancing the storage capacity properties of slow light with wideband and high NDBP.

Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings

PubMed Central

Sun, Weichao; Ren, Haisheng; Tao, Ye; Xiao, Dong; Qin, Xin; Deng, Li; Shao, Mengyao; Gao, Jiali; Chen, Xiaohua

2015-01-01

The cooperative interactions among two aromatic rings with a S-containing group are described, which may participate in electron hole transport in proteins. Ab initio calculations reveal the possibility for the formations of the π∴S:π↔π:S∴π and π∴π:S↔π:π∴S five-electron bindings in the corresponding microsurrounding structures in proteins, both facilitating electron hole transport as efficient relay stations. The relay functionality of these two special structures comes from their low local ionization energies and proper binding energies, which varies with the different aromatic amino acids, S-containing residues, and the arrangements of the same aromatic rings according to the local microsurroundings in proteins. PMID:26120374

Molecular Eigensolution Symmetry Analysis and Fine Structure

PubMed Central

Harter, William G.; Mitchell, Justin C.

2013-01-01

Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

A hydro/organo/hybrid gelator: a peptide lipid with turning aspartame head groups.

PubMed

Mukai, Masaru; Minamikawa, Hiroyuki; Aoyagi, Masaru; Asakawa, Masumi; Shimizu, Toshimi; Kogiso, Masaki

2013-04-01

This work presents a novel bola-type peptide lipid which can gelate water, organic solvents, and water/organic-solvent mixtures. In its molecular structure, an amphiphilic dipeptide aspartame (L-α-aspartyl-L-phenylalanine methyl ester) is connected at both ends of an alkylene linker. The different morphologies in the hydrogel (helical nanotapes) and the organogel (tape-like nanostructures) were visualized by energy-filtering transmission electron microscopy (EF-TEM) and energy-filtering scanning electron microscopy (FE-SEM), and the molecular arrangement was examined using X-ray diffraction (XRD), infrared (IR) spectroscopy, and circular dichroism (CD) spectroscopy. Possessing a hydrophilic aspartic acid group and a (relatively) hydrophobic phenylalanine methyl ester group, the dipeptide head group can turn about in response to solvent polarity. As a consequence, the solvent condition changed the molecular packing of the gelator and affected the overall supramolecular structure of the gel. It is noted that the peptide lipid gelated mixed solvents of water and organic solvents such as dichloromethane, liquid-paraffin, olive-oil, silicone-oils, and so on. The present hybrid gel can simultaneously hold hydrophilic and hydrophobic functional materials. Copyright © 2013 Elsevier Inc. All rights reserved.

Inertial Frames Without the Relativity Principle: Breaking Lorentz Symmetry

NASA Astrophysics Data System (ADS)

Baccetti, Valentina; Tate, Kyle; Visser, Matt

2015-01-01

We investigate inertial frames in the absence of Lorentz invariance, reconsidering the usual group structure implied by the relativity principle. We abandon the relativity principle, discarding the group structure for the transformations between inertial frames, while requiring these transformations to be at least linear (to preserve homogeneity). In theories with a preferred frame (aether), the set of transformations between inertial frames forms a groupoid/pseudogroup instead of a group, a characteristic essential to evading the von Ignatowsky theorems. In order to understand the dynamics, we also demonstrate that the transformation rules for energy and momentum are in general affine. We finally focus on one specific and compelling model implementing a minimalist violation of Lorentz invariance.

Toward the identification of molecular cogs.

PubMed

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.

Structures including network and topology for identifying, locating and quantifying physical phenomena

DOEpatents

Richardson, John G.; Moore, Karen A.; Carrington, Robert A.

2006-04-25

A method and system for detecting, locating and quantifying a physical phenomena such as strain or a deformation in a structure. A plurality of laterally adjacent conductors may each include a plurality of segments. Each segment is constructed to exhibit a unit value representative of a defined energy transmission characteristic. A plurality of identity groups are defined with each identity group comprising a plurality of segments including at least one segment from each of the plurality of conductors. The segments contained within an identity group are configured and arranged such that each of their associated unit values may be represented by a concatenated digit string which is a unique number relative to the other identity groups. Additionally, the unit values of the segments within an identity group maintain unique ratios with respect to the other unit values in the identity group.

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Origin of polymorphism of the two-dimensional group-IV monochalcogenides

NASA Astrophysics Data System (ADS)

Wu, Minghui; Wei, Su-Huai; Huang, Li

2017-11-01

Unlike other two-dimensional (2D) isovalent materials, the 2D group IV monochalcogenides, M X (M =Si , Ge, Sn, and Pb; X =S , Se, and Te), are found to be either in a black phosphorene-derived distorted NaCl-type (d -NaCl) structure or a recently predicted P m a 2 structure. Both M and X atoms in the d -NaCl structure are threefold coordinated, whereas M and X in the P m a 2 structure are fourfold and twofold coordinated, respectively. Using first-principles total energy and electronic structure calculations and a global structural search technique, we systematically investigated the mechanism underlying the polymorphism of the 2D group-IV monochalcogenides. Our analysis show that the relative stability of the two distinct crystallographic phases depends on the strength of the M -M covalent bond and the electronegativity difference between the constituent elements M and X . For small cations, the covalency plays more important role, whereas for large cations the Coulomb interaction becomes more dominant. Therefore, the Si X and Ge X compounds assume the P m a 2 structure, whereas the M X compounds with heavy cation elements (M =Sn and Pb) tend to adopt the d -NaCl structure.

Low-energy spin dynamics of orthoferrites AFeO3 (A  =  Y, La, Bi)

NASA Astrophysics Data System (ADS)

Park, Kisoo; Sim, Hasung; Leiner, Jonathan C.; Yoshida, Yoshiyuki; Jeong, Jaehong; Yano, Shin-ichiro; Gardner, Jason; Bourges, Philippe; Klicpera, Milan; Sechovský, Vladimír; Boehm, Martin; Park, Je-Geun

2018-06-01

YFeO3 and LaFeO3 are members of the rare-earth orthoferrites family with Pbnm space group. Using inelastic neutron scattering, the low-energy spin excitations have been measured around the magnetic Brillouin zone center. Splitting of magnon branches and finite magnon gaps (∼2 meV) are observed for both compounds, where the Dzyaloshinsky–Moriya interactions account for most of this gap with some additional contribution from single-ion anisotropy. We also make comparisons with multiferroic BiFeO3 (R3c space group), in which similar behavior was observed. By taking into account all relevant local Dzyaloshinsky–Moriya interactions, our analysis allows for the precise determination of all experimentally observed parameters in the spin-Hamiltonian. We find that different properties of the Pbnm and R3c space group lead to the stabilization of a spin cycloid structure in the latter case but not in the former, which explains the difference in the levels of complexity of magnon band structures for the respective compounds.

Effects of the Hydroxyl Group on Phenyl Based Ligand/ERRγ Protein Binding

PubMed Central

2015-01-01

Bisphenol-A (4,4′-dihydroxy-2,2-diphenylpropane, BPA, or BPA-A) and its derivatives, when exposed to humans, may affect functions of multiple organs by specific binding to the human estrogen-related receptor γ (ERRγ). We carried out atomistic molecular dynamics (MD) simulations of three ligand compounds including BPA-A, 4-α-cumylphenol (BPA-C), and 2,2-diphenylpropane (BPA-D) binding to the ligand binding domain (LBD) of a human ERRγ to study the structures and energies associated with the binding. We used the implicit Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method to estimate the free energies of binding for the phenyl based compound/ERRγ systems. The addition of hydroxyl groups to the aromatic ring had only a minor effect on binding structures and a significant effect on ligand/protein binding energy in an aqueous solution. Free binding energies of BPA-D to the ERRγ were found to be considerably less than those of BPA-A and BPA-C to the ERRγ. These results are well correlated with those from experiments where no binding affinities were determined in the BPA-D/ERRγ complex. No conformational change was observed for the helix 12 (H-12) of ERRγ upon binding of these compounds preserving an active transcriptional conformation state. PMID:25098505

Proton transfer pathways, energy landscape, and kinetics in creatine-water systems.

PubMed

Ivchenko, Olga; Whittleston, Chris S; Carr, Joanne M; Imhof, Petra; Goerke, Steffen; Bachert, Peter; Wales, David J

2014-02-27

We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.

Multiloop functional renormalization group for general models

NASA Astrophysics Data System (ADS)

Kugler, Fabian B.; von Delft, Jan

2018-02-01

We present multiloop flow equations in the functional renormalization group (fRG) framework for the four-point vertex and self-energy, formulated for a general fermionic many-body problem. This generalizes the previously introduced vertex flow [F. B. Kugler and J. von Delft, Phys. Rev. Lett. 120, 057403 (2018), 10.1103/PhysRevLett.120.057403] and provides the necessary corrections to the self-energy flow in order to complete the derivative of all diagrams involved in the truncated fRG flow. Due to its iterative one-loop structure, the multiloop flow is well suited for numerical algorithms, enabling improvement of many fRG computations. We demonstrate its equivalence to a solution of the (first-order) parquet equations in conjunction with the Schwinger-Dyson equation for the self-energy.

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

Adsorption of amino acids by fullerenes and fullerene nanowhiskers

NASA Astrophysics Data System (ADS)

Hashizume, Hideo; Hirata, Chika; Fujii, Kazuko; Miyazawa, Kun'ichi

2015-12-01

We have investigated the adsorption of some amino acids and an oligopeptide by fullerene (C60) and fullerene nanowhiskers (FNWs). C60 and FNWs hardly adsorbed amino acids. Most of the amino acids used have a hydrophobic side chain. Ala and Val, with an alkyl chain, were not adsorbed by the C60 or FNWs. Trp, Phe and Pro, with a cyclic structure, were not adsorbed by them either. The aromatic group of C60 did not interact with the side chain. The carboxyl or amino group, with the frame structure of an amino acid, has a positive or negative charge in solution. It is likely that the C60 and FNWs would not prefer the charged carboxyl or amino group. Tri-Ala was adsorbed slightly by the C60 and FNWs. The carboxyl or amino group is not close to the center of the methyl group of Tri-Ala. One of the methyl groups in Tri-Ala would interact with the aromatic structure of the C60 and FNWs. We compared our results with the theoretical interaction of 20 bio-amino acids with C60. The theoretical simulations showed the bonding distance between C60 and an amino acid and the dissociation energy. The dissociation energy was shown to increase in the order, Val < Phe < Pro < Asp < Ala < Trp < Tyr < Arg < Leu. However, the simulation was not consistent with our experimental results. The adsorption of albumin (a protein) by C60 showed the effect on the side chains of Try and Trp. The structure of albumin was changed a little by C60. In our study Try and Tyr were hardly adsorbed by C60 and FNWs. These amino acids did not show a different adsorption behavior compared with other amino acids. The adsorptive behavior of mono-amino acids might be different from that of polypeptides.

Reexamine structures and relative stability of medium-sized silicon clusters: Low-lying endohedral fullerene-like clusters Si 30-Si 38

NASA Astrophysics Data System (ADS)

Yoo, Soohaeng; Shao, Nan; Zeng, X. C.

2009-10-01

We report improved results of lowest-lying silicon clusters Si 30-Si 38. A large population of low-energy clusters are collected from previous searches by several research groups and the binding energies of these clusters are computed using density-functional theory (DFT) methods. Best candidates (isomers with high binding energies) are identified from the screening calculations. Additional constrained search is then performed for the best candidates using the basin-hopping method combined with DFT geometry optimization. The obtained low-lying clusters are classified according to binding energies computed using either the Perdew-Burke-Ernzerhof (PBE) functional or the Becke exchange and Lee-Yang-Parr correlation (BLYP) functional. We propose to rank low-lying clusters according to the mean PBE/BLYP binding energies in view that the PBE functional tends to give greater binding energies for more compact clusters whereas the BLYP functional tends to give greater binding energies for less compact clusters or clusters composed of small-sized magic-number clusters. Except for Si 30, the new search confirms again that medium-size silicon clusters Si 31-Si 38 constructed with proper fullerene cage motifs are most promising to be the lowest-energy structures.

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.

PubMed

Lubin, Joseph H; Pacella, Michael S; Gray, Jeffrey J

2018-05-08

Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or complement to experimental structure determination is molecular simulation. Rosetta is one software suite that models protein-surface interactions, but Rosetta is normally benchmarked on soluble proteins. For surface interactions, the validity of the energy function is uncertain because it is a combination of independent parameters from energy functions developed separately for solution proteins and mineral surfaces. Here, we assess the performance of the RosettaSurface algorithm and test the accuracy of its energy function by modeling the adsorption of leucine/lysine (LK)-repeat peptides on methyl- and carboxy-terminated self-assembled monolayers (SAMs). We investigated how RosettaSurface predictions for this system compare with the experimental results, which showed that on both surfaces, LK-α peptides folded into helices and LK-β peptides held extended structures. Utilizing this model system, we performed a parametric analysis of Rosetta's Talaris energy function and determined that adjusting solvation parameters offered improved predictive accuracy. Simultaneously increasing lysine carbon hydrophilicity and the hydrophobicity of the surface methyl head groups yielded computational predictions most closely matching the experimental results. De novo models still should be interpreted skeptically unless bolstered in an integrative approach with experimental data.

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

NASA Astrophysics Data System (ADS)

Sherborne, Bradley; Shanmugasundaram, Veerabahu; Cheng, Alan C.; Christ, Clara D.; DesJarlais, Renee L.; Duca, Jose S.; Lewis, Richard A.; Loughney, Deborah A.; Manas, Eric S.; McGaughey, Georgia B.; Peishoff, Catherine E.; van Vlijmen, Herman

2016-12-01

In May and August, 2016, several pharmaceutical companies convened to discuss and compare experiences with Free Energy Perturbation (FEP). This unusual synchronization of interest was prompted by Schrödinger's FEP+ implementation and offered the opportunity to share fresh studies with FEP and enable broader discussions on the topic. This article summarizes key conclusions of the meetings, including a path forward of actions for this group to aid the accelerated evaluation, application and development of free energy and related quantitative, structure-based design methods.

Effects of a short-term whole body vibration intervention on bone mass and structure in elderly people.

PubMed

Gómez-Cabello, Alba; González-Agüero, Alejandro; Morales, Silvia; Ara, Ignacio; Casajús, José A; Vicente-Rodríguez, Germán

2014-03-01

We aimed to clarify whether a short-term whole body vibration training has a beneficial effect on bone mass and structure in elderly men and women. Randomised controlled trial. A total of 49 non-institutionalised elderly (20 men and 29 women) volunteered to participate in the study. Participants who met the inclusion criteria were randomly assigned to one of the study groups (whole body vibration or control). A total of 24 elderly trained squat positioned on a vibration platform 3 times per week for 11 weeks. Bone-related variables were assessed by dual-energy X-ray absorptiometry and peripheral quantitative computed tomography. Two-way repeated measures one-way analysis of variance (group by time) was used to determine the effects of the intervention on the bone-related variables and also to determinate the changes within group throughout the intervention period. Analysis of covariance was used to test the differences between groups for bone-related variables in pre- and post-training assessments and in the percentage of change between groups. All analysis were carried out including age, height, subtotal lean mass and daily calcium intake as covariates. 11 weeks of whole body vibration training led to no changes in none of the bone mineral content and bone mineral density parameters measured by dual-energy X-ray absorptiometry through the skeleton. At the tibia, total, trabecular and cortical volumetric bone mineral density decreased significantly in the whole body vibration group (all P<0.05). A short-term whole body vibration therapy is not enough to cause any changes on bone mineral content or bone mineral density and it only produces a slight variation on bone structure among elderly people. Copyright © 2013 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field.

PubMed

Kräutler, Vincent; Müller, Martin; Hünenberger, Philippe H

2007-10-15

The present article reports long timescale (200 ns) simulations of four beta-D-hexopyranoses (beta-D-glucose, beta-D-mannose, beta-D-galactose and beta-D-talose) using explicit-solvent (water) molecular dynamics and vacuum stochastic dynamics simulations together with the GROMOS 45A4 force field. Free-energy and solvation free-energy differences between the four compounds are also calculated using thermodynamic integration. Along with previous experimental findings, the present results suggest that the formation of intramolecular hydrogen-bonds in water is an 'opportunistic' consequence of the close proximity of hydrogen-bonding groups, rather than a major conformational driving force promoting this proximity. In particular, the conformational preferences of the hydroxymethyl group in aqueous environment appear to be dominated by 1,3-syn-diaxial repulsion, with gauche and solvation effects being secondary, and intramolecular hydrogen-bonding essentially negligible. The rotational dynamics of the exocyclic hydroxyl groups, which cannot be probed experimentally, is found to be rapid (10-100 ps timescale) and correlated (flip-flop hydrogen-bonds interconverting preferentially through an asynchronous disrotatory pathway). Structured solvent environments are observed between the ring and lactol oxygen atoms, as well as between the 4-OH and hydroxymethyl groups. The calculated stability differences between the four compounds are dominated by intramolecular effects, while the corresponding differences in solvation free energies are small. An inversion of the stereochemistry at either C(2) or C(4) from equatorial to axial is associated with a raise in free energy. Finally, the particularly low hydrophilicity of beta-D-talose appears to be caused by the formation of a high-occurrence hydrogen-bonded bridge between the 1,3-syn-diaxial 2-OH and 4-OH groups. Overall, good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds. However, this detailed comparison also reveals some discrepancies, suggesting the need (and providing a solid basis) for further refinement.

Quantum chemical calculations in the structural analysis of phloretin

NASA Astrophysics Data System (ADS)

Gómez-Zavaglia, Andrea

2009-07-01

In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance

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

Hou, Gao-Lei; Zhang, Jun; Valiev, Marat

2017-01-01

Pinonic acid, a C10-monocarboxylic acid with a hydrophilic –CO 2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene – an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of cis-pinonate anion (cPA–), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA– canmore » adopt two different structural configurations – open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The addition waters, which mainly interact with the negatively charged -CO 2– group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analysis suggests that the mono- and di- hydrates are likely to exist in humid atmospheric environment with high populations. The detailed molecular description of cPA– hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.« less

Comparative studies of structural, thermal, optical, and electrochemical properties of azines with different end groups with their azomethine analogues toward application in (opto)electronics.

PubMed

Sek, Danuta; Siwy, Mariola; Bijak, Katarzyna; Grucela-Zajac, Marzena; Malecki, Grzegorz; Smolarek, Karolina; Bujak, Lukasz; Mackowski, Sebastian; Schab-Balcerzak, Ewa

2013-10-10

Two series of azines and their azomethine analogues were prepared via condensation reaction of benzaldehyde, 2-hydroxybenzaldehyde, 4-pyridinecarboxaldehyde, 2-thiophenecarboxaldehyde, and 4-(diphenylamino)benzaldehyde with hydrazine monohydrate and 1,4-phenylenediamine, respectively. The structures of given compounds were characterized by FTIR, (1)H NMR, and (13)C NMR spectroscopy as well as elemental analysis. Optical, electrochemical, and thermal properties of all compounds were investigated by means of differential scanning calorimetry (DSC), UV-vis spectroscopy, stationary and time-resolved photoluminescence spectroscopy, and cycling voltammetry (CV). Additionally, the electronic properties, that is, orbital energies and resulting energy gap were calculated theoretically by density functional theory (DFT). Influence of chemical structure of the compounds on their properties was analyzed.

Effect of grain size on structural and dielectric properties of barium titanate piezoceramics synthesized by high energy ball milling

NASA Astrophysics Data System (ADS)

Verma, Narendra Kumar; Patel, Sandeep Kumar Singh; Kumar, Dinesh; Singh, Chandra Bhal; Singh, Akhilesh Kumar

2018-05-01

We have investigated the effect of sintering temperature on the densification behaviour, grain size, structural and dielectric properties of BaTiO3 ceramics, prepared by high energy ball milling method. The Powder x-ray diffraction reveals the tetragonal structure with space group P4mm for all the samples. The samples were sintered at four different temperatures, (T = 900°C, 1000°C, 1100°C, 1200°C and 1300°C). Density increased with increasing sintering temperature, reaching up to 97% at 1300°C. A grain growth was observed with increasing sintering temperature. Impedance analyses of the sintered samples at various temperatures were performed. Increase in dielectric constant and Curie temperature is observed with increasing sintering temperature.

Multiprobe characterization of plasma flows for space propulsion

NASA Astrophysics Data System (ADS)

Damba, Julius; Argente, P.; Maldonado, P. E.; Cervone, A.; Domenech-Garret, J. L.; Conde, L.

2018-02-01

Plasma engines for space propulsion generate plasma jets (also denominated plasma plumes) having supersonic ion groups with typical speeds in the order of tens of kilometers per second, which lies between electron and ion thermal speeds. Studies of the stationary plasma expansion process using a four-grid retarding field energy analyzer (RFEA), an emissive probe (EP) and a Langmuir probe (LP), all mounted on a three dimensionally (3D) displaced multiprobe structure are discussed. Specifically, the determination of plasma beam properties from the RFEA current-voltage (IV) characteristic curves is presented. The experimental results show the ion energy spectra to be essentially unchanged over 300 mm along the plasma-jet expansion axis of symmetry. The measured ion velocity distribution function (IVDF) results from the superposition of different ion groups and has two dominant populations: A low-energy group constituted of ions from the background plasma is produced by the interaction of the plasma jet with the walls of the vacuum chamber. The fast-ion population is composed of ions from the plasma beam moving at supersonic speeds with respect to the low-energy ions. The decreasing spatial profiles of the plasma-jet current density are compared with those of the low-energy ion group, which are not uniform along the axis of symmetry because of the small contributions from other ion populations with intermediate speeds.

A Sliding-Mode Triboelectric Nanogenerator with Chemical Group Grated Structure by Shadow Mask Reactive Ion Etching.

PubMed

Shang, Wanyu; Gu, Guang Qin; Yang, Feng; Zhao, Lei; Cheng, Gang; Du, Zu-Liang; Wang, Zhong Lin

2017-09-26

The sliding-mode triboelectric nanogenerator (S-TENG) with grated structure has important applications in energy harvest and active sensors; however its concavo-convex structure leads to large frictional resistance and abrasion. Here, we developed a S-TENG with a chemical group grated structure (S-TENG-CGG), in which the triboelectric layer's triboelectric potential has a positive-negative alternating charged structure. The triboelectric layer of the S-TENG-CGG was fabricated through a reactive ion etching process with a metal shadow mask with grated structure. In the etched region, the nylon film, originally positively charged as in friction with stainless steel, gained opposite triboelectric potential and became negatively charged because of the change of surface functional groups. The output signals of the S-TENG-CGG are alternating and the frequency is determined by both the segment numbers and the moving speed. The applications of the S-TENG-CGG in the charging capacitor and driving calculator are demonstrated. In the S-TENG-CGG, since there is no concavo-convex structure, the frictional resistance and abrasion are largely reduced, which enhances its performances in better stability and longer working time.

New group-V elemental bilayers: A tunable structure model with four-, six-, and eight-atom rings

NASA Astrophysics Data System (ADS)

Kong, Xiangru; Li, Linyang; Leenaerts, Ortwin; Liu, Xiong-Jun; Peeters, François M.

2017-07-01

Two-dimensional group-V elemental materials have attracted widespread attention due to their nonzero band gap while displaying high electron mobility. Using first-principles calculations, we propose a series of new elemental bilayers with group-V elements (Bi, Sb, As). Our study reveals the dynamical stability of four-, six-, and eight-atom ring structures, demonstrating their possible coexistence in such bilayer systems. The proposed structures for Sb and As are large-gap semiconductors that are potentially interesting for applications in future nanodevices. The Bi structures have nontrivial topological properties with a direct nontrivial band gap. The nontrivial gap is shown to arise from a band inversion at the Brillouin zone center due to the strong intrinsic spin-orbit coupling in Bi atoms. Moreover, we demonstrate the possibility of tuning the properties of these materials by enhancing the ratio of six-atom rings to four- and eight-atom rings, which results in wider nontrivial band gaps and lower formation energies.

Lorentz invariance with an invariant energy scale.

PubMed

Magueijo, João; Smolin, Lee

2002-05-13

We propose a modification of special relativity in which a physical energy, which may be the Planck energy, joins the speed of light as an invariant, in spite of a complete relativity of inertial frames and agreement with Einstein's theory at low energies. This is accomplished by a nonlinear modification of the action of the Lorentz group on momentum space, generated by adding a dilatation to each boost in such a way that the Planck energy remains invariant. The associated algebra has unmodified structure constants. We also discuss the resulting modifications of field theory and suggest a modification of the equivalence principle which determines how the new theory is embedded in general relativity.

Cost of Equity Estimation in Fuel and Energy Sector Companies Based on CAPM

NASA Astrophysics Data System (ADS)

Kozieł, Diana; Pawłowski, Stanisław; Kustra, Arkadiusz

2018-03-01

The article presents cost of equity estimation of capital groups from the fuel and energy sector, listed at the Warsaw Stock Exchange, based on the Capital Asset Pricing Model (CAPM). The objective of the article was to perform a valuation of equity with the application of CAPM, based on actual financial data and stock exchange data and to carry out a sensitivity analysis of such cost, depending on the financing structure of the entity. The objective of the article formulated in this manner has determined its' structure. It focuses on presentation of substantive analyses related to the core of equity and methods of estimating its' costs, with special attention given to the CAPM. In the practical section, estimation of cost was performed according to the CAPM methodology, based on the example of leading fuel and energy companies, such as Tauron GE and PGE. Simultaneously, sensitivity analysis of such cost was performed depending on the structure of financing the company's operation.

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole

NASA Astrophysics Data System (ADS)

Arjunan, V.; Raj, Arushma; Santhanam, R.; Marchewka, M. K.; Mohan, S.

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. 1H and 13C NMR chemical shifts and the electronic transitions of the molecule are also discussed.

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

PubMed Central

Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

2018-01-01

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance.

PubMed

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K-Y

2013-01-04

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH 2 ) 12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm 2 V -1 s -1 . It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm 2 V -1 s -1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed.

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance

PubMed Central

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K.-Y.

2013-01-01

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH2)12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm2 V−1 s−1. It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm2 V−1 s−1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed. PMID:24086795

Composition and structure of spontaneously adsorbed monolayers of n-perfluorocarboxylic acids on silver

NASA Astrophysics Data System (ADS)

Chau, Lai-Kwan; Porter, Marc D.

1990-03-01

Monolayer films of n-perfluorocarboxylic acids (CF 3(CF 2) nCOOH, where n = 0-2, 5-8) have been formed by spontaneous adsorption at silver. Infrared reflection spectroscopy, optical ellipsometry, and contact angle measurements indicate that these films exhibit low surface free energies, that the carboxylic acid group is symmetrically bound at the silver substrate as a carboxylate bridging ligand, and that the structure is composed of tilted (≈ 40° from the surface normal) perfluorocarbon chains and small structural defects.

Structure determination and characterization of two rare-earth molybdenum borate compounds: LnMoBO(6) (Ln = La, Ce).

PubMed

Zhao, Dan; Cheng, Wen-Dan; Zhang, Hao; Hang, Shu-Ping; Fang, Ming

2008-07-28

The structural, optical, and electronic properties of two rare-earth molybdenum borate compounds, LnMoBO(6) (Ln = La, Ce), have been investigated by means of single-crystal X-ray diffraction, elemental analyses, and spectral measurements, as well as calculations of energy band structures, density of states, and optical response functions by the density functional method. The title compounds, which crystallize in monoclinic space group P2(1)/c, possess a similar network of interconnected [Ce(2)(MoO(4))(2)](2+) chains and [BO(2)](-) wavy chains. Novel 1D molybdenum oxide chains are contained in their three-dimensional (3D) networks. The calculated results of crystal energy band structure by the density functional theory (DFT) method show that the solid-state compound LaMoBO(6) is a semiconductor with indirect band gaps.

Three-dimensional organic Dirac-line materials due to nonsymmorphic symmetry: A data mining approach

NASA Astrophysics Data System (ADS)

Geilhufe, R. Matthias; Bouhon, Adrien; Borysov, Stanislav S.; Balatsky, Alexander V.

2017-01-01

A data mining study of electronic Kohn-Sham band structures was performed to identify Dirac materials within the Organic Materials Database. Out of that, the three-dimensional organic crystal 5,6-bis(trifluoromethyl)-2-methoxy-1 H -1,3-diazepine was found to host different Dirac-line nodes within the band structure. From a group theoretical analysis, it is possible to distinguish between Dirac-line nodes occurring due to twofold degenerate energy levels protected by the monoclinic crystalline symmetry and twofold degenerate accidental crossings protected by the topology of the electronic band structure. The obtained results can be generalized to all materials having the space group P 21/c (No. 14, C2h 5) by introducing three distinct topological classes.

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

PubMed Central

Baskerville, Edward B.; Dobson, Andy P.; Bedford, Trevor; Allesina, Stefano; Anderson, T. Michael; Pascual, Mercedes

2011-01-01

Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts. PMID:22219719

Alternative expression of the Bloch wave group velocity in loss-less periodic media using the electromagnetic field energy

NASA Astrophysics Data System (ADS)

Deparis, Olivier; Lambin, Philippe

2018-01-01

In periodic optical media, the group velocity is defined as the gradient with respect to wave-vector of the corresponding Bloch mode frequency dispersion curve, forming the photonic band structure. Instead of deducing it from the numerically computed photonic crystal band structure, the group velocity can be calculated directly from the integral of the Poynting vector over the crystal unit cell, the physical meaning of which is immediately perceivable. The related formula, which can be regarded as the application of Hellmann-Feynman theorem to electromagnetism, has been reported previously though without proof. We provide hereafter a full derivation of that formula starting from Maxwell's equations and we discuss its usefulness in photonics.

Infrared multiple photon dissociation spectroscopy of group I and group II metal complexes with Boc-hydroxylamine.

PubMed

Dain, Ryan P; Gresham, Gary; Groenewold, Gary S; Steill, Jeffrey D; Oomens, Jos; Van Stipdonk, Michael J

2013-08-30

Hydroxamates are essential growth factors for some microbes, acting primarily as siderophores that solubilize iron for transport into a cell. Here we determined the intrinsic structure of 1:1 complexes between Boc-protected hydroxylamine and group I ([M(L)](+)) and group II ([M(L-H)](+)) cations, where M and L are the cation and ligand, respectively, which are convenient models for the functional unit of hydroxamate siderphores. The relevant complex ions were generated by electrospray ionization (ESI) and isolated and stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Infrared spectra of the isolated complexes were collected by monitoring (infrared) photodissociation yield as a function of photon energy. Experimental spectra were then compared to those predicted by density functional theory (DFT) calculations. The infrared multiple photon dissociation (IRMPD) spectra collected are in good agreement with those predicted to be lowest-energy by DFT. The spectra for the group I complexes contain six resolved absorptions that can be attributed to amide I and II type and hydroxylamine N-OH vibrations. Similar absorptions are observed for the group II cation complexes, with shifts of the amide I and amide II vibrations due to the change in structure with deprotonation of the hydroxylamine group. IRMPD spectroscopy unequivocally shows that the intrinsic binding mode for the group I cations involves the O atoms of the amide carbonyl and hydroxylamine groups of Boc-hydroxylamine. A similar binding mode is preferred for the group II cations, except that in this case the metal ion is coordinated by the O atom of the deprotonated hydroxylamine group. Copyright © 2013 John Wiley & Sons, Ltd.

Dietary boron does not affect tooth strength, micro-hardness, and density, but affects tooth mineral composition and alveolar bone mineral density in rabbits fed a high-energy diet.

PubMed

Hakki, Sema S; SiddikMalkoc; Dundar, Niyazi; Kayis, Seyit Ali; Hakki, Erdogan E; Hamurcu, Mehmet; Baspinar, Nuri; Basoglu, Abdullah; Nielsen, Forrest H; Götz, Werner

2015-01-01

The objective of this study was to determine whether dietary boron (B) affects the strength, density and mineral composition of teeth and mineral density of alveolar bone in rabbits with apparent obesity induced by a high-energy diet. Sixty female, 8-month-old, New Zealand rabbits were randomly assigned for 7 months into five groups as follows: (1) control 1, fed alfalfa hay only (5.91 MJ/kg and 57.5 mg B/kg); (2) control 2, high energy diet (11.76 MJ and 3.88 mg B/kg); (3) B10, high energy diet + 10 mg B gavage/kg body weight/96 h; (4) B30, high energy diet + 30 mg B gavage/kg body weight/96 h; (5) B50, high energy diet + 50 mg B gavage/kg body weight/96 h. Maxillary incisor teeth of the rabbits were evaluated for compression strength, mineral composition, and micro-hardness. Enamel, dentin, cementum and pulp tissue were examined histologically. Mineral densities of the incisor teeth and surrounding alveolar bone were determined by using micro-CT. When compared to controls, the different boron treatments did not significantly affect compression strength, and micro-hardness of the teeth, although the B content of teeth increased in a dose-dependent manner. Compared to control 1, B50 teeth had decreased phosphorus (P) concentrations. Histological examination revealed that teeth structure (shape and thickness of the enamel, dentin, cementum and pulp) was similar in the B-treated and control rabbits. Micro CT evaluation revealed greater alveolar bone mineral density in B10 and B30 groups than in controls. Alveolar bone density of the B50 group was not different than the controls. Although the B treatments did not affect teeth structure, strength, mineral density and micro-hardness, increasing B intake altered the mineral composition of teeth, and, in moderate amounts, had beneficial effects on surrounding alveolar bone.

Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain

NASA Astrophysics Data System (ADS)

Di Lella, Santiago; Petruk, Ariel A.; Armiño, Diego J. Alonso de; Álvarez, Rosa M. S.

2010-08-01

Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have revealed the existence of several water sites which were well correlated to both the bound water molecules observed in the crystal structure of the protein in the free state and to some of the hydroxyl groups of the carbohydrate ligand observed in the crystal structure of the complexed protein. In this work, we present a study using quantum mechanical methods (B3LYP/6-311++G(3df,3dp)//B3LYP/6-31+G(d)) to determine the energy involved in the binding of these water molecules to specific amino acids in the carbohydrate recognition domain of the protein. By modeling the hydroxyl groups of the carbohydrate by methanol, the energies associated to the local interactions between the ligand and the protein have been evaluated by replacing specific water molecules with methanol. The values of the binding energies have been compared to those previously obtained by the molecular dynamic method.

The influence of pre-existing basement structures on salt tectonics in the Upper Silurian Salina Group, Appalachian Basin, NE Pennsylvania: results from 3D seismic analysis and analogue modelling

NASA Astrophysics Data System (ADS)

Harding, M. R.; Rowan, C. J.

2013-12-01

The Upper Silurian Salina Group in Pennsylvania's Appalachian basin consists of several hundred feet of highly deformable and mobile salt that was a significant influence on the tectonic and structural development of the Appalachian Mountains during the late Paleozoic. Understanding how halokinesis and décollement thrusting of the Salina Group has contributed to the present-day structure of the Appalachian Basin is of intense current interest due to the energy resource potential of the overlying Marcellus Shale and underlying Utica Shale. Seismic data suggest that halokinesis of the Salina Group in the Appalachian Basin might be strongly influenced by the presence of preexisting faults in the underlying Neoproterozoic basement, which suggests that these structures may have interacted with the Salina Group or its interior during deformation. We examine these apparent interactions in more detail using high-resolution 3D seismic data from the Appalachian Basin of NE Pennsylvania to identify and characterize salt tectonic-related structures developed above and within the Salina Group during orogenesis, verify their geographic association with major basement faults, and document how reactivation of these preexisting faults might have influenced later deformation within and above the salt units. We also present the results of sandbox modelling of thin-skinned thrusting in a salt-analogue décollement. Multiple runs in the presence and absence of preexisting basement structures provide insight into how the modern structures observed in the seismic data initiated and evolved during progressively more intense orogenesis, and better constrain the physical processes that control the structural linkage through the Salina décollement.

Experimental investigation of change of energy of infragavity waves in dependence on spectral characteristics of an irregular wind waves in coastal zone

NASA Astrophysics Data System (ADS)

Saprykina, Yana; Divinskii, Boris

2013-04-01

An infragravity waves are long waves with periods of 20 - 300 s. Most essential influence of infragarvity waves on dynamic processes is in a coastal zone, where its energy can exceed the energy of wind waves. From practical point of view, the infragravity waves are important, firstly, due to their influence on sand transport processes in a coastal zone. For example, interacting with group structure of wind waves the infragravity waves can define position of underwater bars on sandy coast. Secondly, they are responsible on formation of long waves in harbors. Main source of infragravity waves is wave group structure defined by sub-nonlinear interactions of wind waves (Longuet-Higgins, Stewart, 1962). These infragravity waves are bound with groups of wind waves and propagate with wave group velocity. Another type of infragravity waves are formed in a surf zone as a result of migration a wave breaking point (Symonds, et al., 1982). What from described above mechanisms of formation of infragravity waves prevails, till now it is unknown. It is also unknown how energy of infragravity waves depends on energy of input wind waves and how it changes during nonlinear wave transformation in coastal zone. In our work on the basis of the analysis of data of field experiment and numerical simulation a contribution of infragravity waves in total wave energy in depending on integral characteristics of an irregular wave field in the conditions of a real bathymetry was investigated. For analysis the data of field experiment "Shkorpilovtsy-2007" (Black sea) and data of numerical modeling of Boussinesq type equation with extended dispersion characteristics (Madsen et al., 1997) were used. It was revealed that infragravity waves in a coastal zone are defined mainly by local group structure of waves, which permanently changes due to nonlinearity, shoaling and breaking processes. Free infragravity waves appearing after wave breaking exist together with bound infragravity waves. There are no clear total dependences of energy of infrragravity waves from energy of wind waves and mean period of infragravity waves from mean period of wind waves. But significant wave height of infragravity waves depends on relative water depth (wave height of wind waves divided on water depth). There are different types of this dependence for breaking and non-breaking waves. The influence of peak period, significant wave height and directional spreading of initial wave spectrum on these dependences are discussed. The peculiarities of spectra of infragravity waves for non-breaking, breaking and multibreaking wind waves are shown. This work is supported by the RFBR, project 12-05-00965. References: Longuet-Higgins, M. S., R. W. Stewart, 1962. Radiation stress and mass transport in gravity waves, with an application to surf beats. J. Fluid Mech., 13, pp. 481-504. Symonds G., D.A. Huntley, A.J. Bowen, 1982. Two dimensional surf beat: long wave generation by a time-varying breakpoint. J. of Geoph. Res., 87(C), pp.492-498. Madsen P.A., Sorensen O.R., Shaffer H.A. 1997. Surf zone dynamics simulated by a Boussinesq type model. Coastal Engineering, 32, p. 255-287.

Single or functionalized fullerenes interacting with heme group

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

Costa, Wallison Chaves; Diniz, Eduardo Moraes, E-mail: eduardo.diniz@ufma.br

The heme group is responsible for iron transportation through the bloodstream, where iron participates in redox reactions, electron transfer, gases detection etc. The efficiency of such processes can be reduced if the whole heme molecule or even the iron is somehow altered from its original oxidation state, which can be caused by interactions with nanoparticles as fullerenes. To verify how such particles alter the geometry and electronic structure of heme molecule, here we report first principles calculations based on density functional theory of heme group interacting with single C{sub 60} fullerene or with C{sub 60} functionalized with small functional groupsmore » (−CH{sub 3}, −COOH, −NH{sub 2}, −OH). The calculations shown that the system heme + nanoparticle has a different spin state in comparison with heme group if the fullerene is functionalized. Also a functional group can provide a stronger binding between nanoparticle and heme molecule or inhibit the chemical bonding in comparison with single fullerene results. In addition heme molecule loses electrons to the nanoparticles and some systems exhibited a geometry distortion in heme group, depending on the binding energy. Furthermore, one find that such nanoparticles induce a formation of spin up states in heme group. Moreover, there exist modifications in density of states near the Fermi energy. Although of such changes in heme electronic structure and geometry, the iron atom remains in the heme group with the same oxidation state, so that processes that involve the iron might not be affected, only those that depend on the whole heme molecule.« less

Dependence of the third-order coefficients in Landau free energies for bcc --> fcc structural transition on hydrogen concentration in zirconium hydrides

NASA Astrophysics Data System (ADS)

Ashida, Yuh; Yamamoto, Masahiro; Naito, Shizuo; Mabuchi, Mahito; Hashino, Tomoyasu

1997-08-01

Young's modulus E and the modulus of rigidity G of zirconium hydrides ZrHx(0.9⩽x⩽1.65) at 941 and 1001 K have been obtained as a function of hydrogen concentration c by measuring resonance frequencies for bending and torsion vibrations of a polycrystalline wire. As c increases, observed E and G increase in the bcc β phase, slightly increase linearly in the β+δ phase, and then decrease in the fcc δ phase. On the basis of a phenomenological free energy in terms of strain components taking account of space group symmetry, two types of Landau expansion of the free energies for the β phase in terms of the strain components which play an important role in the structural phase transition between the β and the δ phases are examined. The observed E and G are assumed to be the same as the second-order coefficients of the free energy for the Bain distortions, which occur at the structural phase transition. The dependence of the third-order coefficients on c permits the expanded free energies to describe the fact that the β phase is more stable than the δ phase at low c.

Initial mechanisms for the dissociation of carbon from electronically-excited nitrotoluene molecules

NASA Astrophysics Data System (ADS)

Yuan, Bing; Eilers, Hergen

2017-12-01

We calculated the photoinduced decomposition of various nitrotoluene molecules, resulting in the formation of atomic carbon, at the B3LYP/6-311++G(d,p) level of theory using Gaussian 09. In addition, we used TD-DFT (B3LYP/6-311++G(d,p)) to calculate the excitation energies. The results confirm our previously reported experimental results. Specifically, we show that the absorption of 226 nm (5.49 eV) light can lead to the decomposition of nitrotoluene molecules and the formation of atomic carbon. One 226 nm photon is sufficient for the dissociation of carbon from 2-NT and 4-NT molecules. During the dissociation process, the CH3 group provides the dissociated carbon atom and the NO2 group accepts the H atoms from either the CH3 group or the benzene ring before carbon exits the molecular system. For the second and third carbon dissociation of 2-NT, the energy barriers are 6.70 eV and 7.43 eV, respectively, and two 226 nm photons would need to be absorbed by the molecule. If extra NO is present during the first carbon dissociation of 2-NT, it gets involved in the last two decomposition steps and forms a C=NH-N=O structure which stabilizes the decomposition products and lowers the energy barrier from 5.22 eV to 4.70 eV. However, for the second and third carbon dissociation of 2-NT, the NO molecules have no apparent effect. For nitrotoluene molecules with two or three NO2 groups (i.e., 2,4-DNT, 2,6-DNT, 3,4-DNT, and 2,4,6-TNT), the first carbon dissociation energies are between 5.26 eV and 5.57 eV. The carbon dissociation pathways for these molecules are similar to those of 2-NT. In 2,4-DNT, the lowest energy barriers for the second and third carbon dissociation are 6.54 eV and 6.60 eV, respectively, which are about 1 eV higher than the energy barrier for the first carbon dissociation. In case of 2,4-DNT/NO and 2,4,6-TNT/NO, NO acts as a catalyst in the first carbon dissociation processes and forms a C=NH-N=O structure which lowers the energy barriers by 0.48 eV and 0.89 eV, respectively.

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems.

PubMed

Freed, Karl F

2009-02-14

A new extension of the lattice cluster theory is developed to describe the influence of monomer structure and local correlations on the free energy of strongly interacting and self-assembling polymer systems. This extension combines a systematic high dimension (1/d) and high temperature expansion (that is appropriate for weakly interacting systems) with a direct treatment of strong interactions. The general theory is illustrated for a binary polymer blend whose two components contain "sticky" donor and acceptor groups, respectively. The free energy is determined as an explicit function of the donor-acceptor contact probabilities that depend, in turn, on the local structure and both the strong and weak interactions.

First principles study of electronic and structural properties of single walled zigzag boron nitride nanotubes doped with the elements of group IV

NASA Astrophysics Data System (ADS)

Bahari, Ali; jalalinejad, Amir; Bagheri, Mosahhar; Amiri, Masoud

2017-11-01

In this paper, structural and electronic properties and stability of (10, 0) born nitride nanotube (BNNT) are considered within density functional theory by doping group IV elements of the periodic table. The HOMO-LUMO gap has been strongly modified and treated a dual manner by choosing B or N sites for dopant atoms. Formation energy calculation shows that B site doping is more stable than N site doping. Results also show that all dopants turn the pristine BNNT into a p-type semiconductor except for carbon-doped BNNT at B site.

Sphalerons in composite and nonstandard Higgs models

NASA Astrophysics Data System (ADS)

Spannowsky, Michael; Tamarit, Carlos

2017-01-01

After the discovery of the Higgs boson and the rather precise measurement of all electroweak boson's masses the local structure of the electroweak symmetry breaking potential is already quite well established. However, despite being a key ingredient to a fundamental understanding of the underlying mechanism of electroweak symmetry breaking, the global structure of the electroweak potential remains entirely unknown. The existence of sphalerons, unstable solutions of the classical action of motion that are interpolating between topologically distinct vacua, is a direct consequence of the Standard Model's SU (2 )L gauge group. Nevertheless, the sphaleron energy depends on the shape of the Higgs potential away from the minimum and can therefore be a litmus test for its global structure. Focusing on two scenarios, the minimal composite Higgs model SO (5 )/SO (4 ) or an elementary Higgs with a deformed electroweak potential, we calculate the change of the sphaleron energy compared to the Standard Model prediction. We find that the sphaleron energy would have to be measured to O (10 )% accuracy to exclude sizeable global deviations from the Standard Model Higgs potential. We further find that because of the periodicity of the scalar potential in composite Higgs models a second sphaleron branch with larger energy arises.

Cohesive energy and structural parameters of binary oxides of groups IIA and IIIB from diffusion quantum Monte Carlo

DOE PAGES

Santana, Juan A.; Krogel, Jaron T.; Kent, Paul R. C.; ...

2016-05-03

We have applied the diffusion quantum Monte Carlo (DMC) method to calculate the cohesive energy and the structural parameters of the binary oxides CaO, SrO, BaO, Sc 2O 3, Y 2O 3 and La 2O 3. The aim of our calculations is to systematically quantify the accuracy of the DMC method to study this type of metal oxides. The DMC results were compared with local and semi-local Density Functional Theory (DFT) approximations as well as with experimental measurements. The DMC method yields cohesive energies for these oxides with a mean absolute deviation from experimental measurements of 0.18(2) eV, while withmore » local and semi-local DFT approximations the deviation is 3.06 and 0.94 eV, respectively. For lattice constants, the mean absolute deviation in DMC, local and semi-local DFT approximations, are 0.017(1), 0.07 and 0.05 , respectively. In conclusion, DMC is highly accurate method, outperforming the local and semi-local DFT approximations in describing the cohesive energies and structural parameters of these binary oxides.« less

Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown.

PubMed

Gresh, Nohad; Perahia, David; de Courcy, Benoit; Foret, Johanna; Roux, Céline; El-Khoury, Lea; Piquemal, Jean-Philip; Salmon, Laurent

2016-12-15

Zn-metalloproteins are a major class of targets for drug design. They constitute a demanding testing ground for polarizable molecular mechanics/dynamics aimed at extending the realm of quantum chemistry (QC) to very long-duration molecular dynamics (MD). The reliability of such procedures needs to be demonstrated upon comparing the relative stabilities of competing candidate complexes of inhibitors with the recognition site stabilized in the course of MD. This could be necessary when no information is available regarding the experimental structure of the inhibitor-protein complex. Thus, this study bears on the phosphomannose isomerase (PMI) enzyme, considered as a potential therapeutic target for the treatment of several bacterial and parasitic diseases. We consider its complexes with 5-phospho-d-arabinonohydroxamate and three analog ligands differing by the number and location of their hydroxyl groups. We evaluate the energy accuracy expectable from a polarizable molecular mechanics procedure, SIBFA. This is done by comparisons with ab initio quantum-chemistry (QC) calculations in the following cases: (a) the complexes of the four ligands in three distinct structures extracted from the entire PMI-ligand energy-minimized structures, and totaling up to 264 atoms; (b) the solvation energies of several energy-minimized complexes of each ligand with a shell of 64 water molecules; (c) the conformational energy differences of each ligand in different conformations characterized in the course of energy-minimizations; and (d) the continuum solvation energies of the ligands in different conformations. The agreements with the QC results appear convincing. On these bases, we discuss the prospects of applying the procedure to ligand-macromolecule recognition problems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

East Europe Report, Economic and Industrial Affairs, No. 2435

DTIC Science & Technology

1983-08-12

was as shown in Table 4. Age Structure of Energy Boilers in 1978, in Percent Table 4 Category under 20 yrs. .20- 40 yrs. 40 or more Total 79.3...converted energy into electricity. In this group, over 50 percent of the boilers have been operated for 20 years or more, and 24.3 percent for more than 40 ...Lodz 38. Bydgoszcz Refrigeration Equipment Factory in Bydgoszcz 39. Scientific-Production Center for Semiconductors (all production units) 40

Neutron scattering study of yttrium iron garnet

NASA Astrophysics Data System (ADS)

Shamoto, Shin-ichi; Ito, Takashi U.; Onishi, Hiroaki; Yamauchi, Hiroki; Inamura, Yasuhiro; Matsuura, Masato; Akatsu, Mitsuhiro; Kodama, Katsuaki; Nakao, Akiko; Moyoshi, Taketo; Munakata, Koji; Ohhara, Takashi; Nakamura, Mitsutaka; Ohira-Kawamura, Seiko; Nemoto, Yuichi; Shibata, Kaoru

2018-02-01

The nuclear and magnetic structure and full magnon dispersions of yttrium iron garnet Y3Fe5O12 have been studied using neutron scattering. The refined nuclear structure is distorted to a trigonal space group of R 3 ¯ . The highest-energy dispersion extends up to 86 meV. The observed dispersions are reproduced by a simple model with three nearest-neighbor-exchange integrals between 16 a (octahedral) and 24 d (tetrahedral) sites, Ja a, Ja d, and Jd d, which are estimated to be 0.00 ±0.05 , -2.90 ±0.07 , and -0.35 ±0.08 meV, respectively. The lowest-energy dispersion below 14 meV exhibits a quadratic dispersion as expected from ferromagnetic magnons. The imaginary part of q -integrated dynamical spin susceptibility χ″(E ) exhibits a square-root energy dependence at low energies. The magnon density of state is estimated from χ″(E ) obtained on an absolute scale. The value is consistent with the single chirality mode for the magnon branch expected theoretically.

Caloric Restriction in Older Adults-Differential Effects of Weight Loss and Reduced Weight on Brain Structure and Function.

PubMed

Prehn, Kristin; Jumpertz von Schwartzenberg, Reiner; Mai, Knut; Zeitz, Ulrike; Witte, A Veronica; Hampel, Dierk; Szela, Anna-Maria; Fabian, Sonja; Grittner, Ulrike; Spranger, Joachim; Flöel, Agnes

2017-03-01

Dietary modifications such as caloric restriction (CR) have been suggested as a means to improve memory and prevent age-related decline. However, it is unclear whether those effects remain stable over time or are related specifically to negative energy balance during the weight loss phase of CR. Using a randomized interventional design, we investigated changes in recognition memory and neural correlates in postmenopausal obese women (n = 19): 1) after intense weight loss in the course of a 12-week low-caloric diet (reduced body weight and negative energy balance) and 2) after having sustained the reduced weight over 4 more weeks (reduced body weight, but energy balance equilibrium). Participants were contrasted to a control group (n = 18) instructed not to change dietary habits. In the CR group, we found improved recognition memory, paralleled by increased gray matter volume in inferior frontal gyrus and hippocampus, and augmented hippocampal resting-state functional connectivity to parietal areas. Moreover, effects were specific for transient negative energy balance and could not be detected after subsequent weight maintenance. Our data demonstrate for the first time in humans that beneficial effects of CR on brain structure and function are due to weight loss rather than an overall reduced weight. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Real-space finite-difference approach for multi-body systems: path-integral renormalization group method and direct energy minimization method.

PubMed

Sasaki, Akira; Kojo, Masashi; Hirose, Kikuji; Goto, Hidekazu

2011-11-02

The path-integral renormalization group and direct energy minimization method of practical first-principles electronic structure calculations for multi-body systems within the framework of the real-space finite-difference scheme are introduced. These two methods can handle higher dimensional systems with consideration of the correlation effect. Furthermore, they can be easily extended to the multicomponent quantum systems which contain more than two kinds of quantum particles. The key to the present methods is employing linear combinations of nonorthogonal Slater determinants (SDs) as multi-body wavefunctions. As one of the noticeable results, the same accuracy as the variational Monte Carlo method is achieved with a few SDs. This enables us to study the entire ground state consisting of electrons and nuclei without the need to use the Born-Oppenheimer approximation. Recent activities on methodological developments aiming towards practical calculations such as the implementation of auxiliary field for Coulombic interaction, the treatment of the kinetic operator in imaginary-time evolutions, the time-saving double-grid technique for bare-Coulomb atomic potentials and the optimization scheme for minimizing the total-energy functional are also introduced. As test examples, the total energy of the hydrogen molecule, the atomic configuration of the methylene and the electronic structures of two-dimensional quantum dots are calculated, and the accuracy, availability and possibility of the present methods are demonstrated.

Insights into the use of polyethylene oxide in energy storage/conversion devices: a critical review

NASA Astrophysics Data System (ADS)

Arya, Anil; Sharma, A. L.

2017-11-01

In this review, the latest updates in poly (ethylene oxide) based electrolytes are summarized. The ultimate goal of researchers globally is towards the development of free-standing solid polymeric separators for energy storage devices. This single free-standing solid polymeric separator may replace the liquid and separator (organic/inorganic) used in existing efficient/smart energy technology. As an example, polyethylene oxide (PEO) consists of an electron donor-rich group which provides coordinating sites to the cation for migration. Owing to this exclusive structure, PEO exhibits some remarkable properties, such as a low glass transition temperature, excellent flexibility, and the ability to make complexation with various metal salts which are unattainable by another polymer host. Hence, the PEO is an emerging candidate that has been most examined or is currently under consideration for application in energy storage devices. This review article first provides a detailed study of the PEO properties, characteristics of the constituents of the polymer electrolyte, and suitable approaches for the modification of polymer electrolytes. Then, the synthesization and characterizations techniques are outlined. The structures, characteristics, and performance during charge-discharge of four types of electrolyte/separators (liquid, plasticized, and dispersed and intercalated electrolyte) are highlighted. The suitable ion transport mechanism proposed by researchers in different renowned groups have been discussed for the better understanding of the ion dynamics in such systems.

Studies of QCD structure in high-energy collisions

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

Nadolsky, Pavel M.

2016-06-26

”Studies of QCD structure in high-energy collisions” is a research project in theoretical particle physics at Southern Methodist University funded by US DOE Award DE-SC0013681. The award furnished bridge funding for one year (2015/04/15-2016/03/31) between the periods funded by Nadolsky’s DOE Early Career Research Award DE-SC0003870 (in 2010-2015) and a DOE grant DE-SC0010129 for SMU Department of Physics (starting in April 2016). The primary objective of the research is to provide theoretical predictions for Run-2 of the CERN Large Hadron Collider (LHC). The LHC physics program relies on state-of-the-art predictions in the field of quantum chromodynamics. The main effort ofmore » our group went into the global analysis of parton distribution functions (PDFs) employed by the bulk of LHC computations. Parton distributions describe internal structure of protons during ultrarelivistic collisions. A new generation of CTEQ parton distribution functions (PDFs), CT14, was released in summer 2015 and quickly adopted by the HEP community. The new CT14 parametrizations of PDFs were obtained using benchmarked NNLO calculations and latest data from LHC and Tevatron experiments. The group developed advanced methods for the PDF analysis and estimation of uncertainties in LHC predictions associated with the PDFs. We invented and refined a new ’meta-parametrization’ technique that streamlines usage of PDFs in Higgs boson production and other numerous LHC processes, by combining PDFs from various groups using multivariate stochastic sampling. In 2015, the PDF4LHC working group recommended to LHC experimental collaborations to use ’meta-parametrizations’ as a standard technique for computing PDF uncertainties. Finally, to include new QCD processes into the global fits, our group worked on several (N)NNLO calculations.« less

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

NASA Astrophysics Data System (ADS)

Henke, Paul S.; Mak, Chi H.

2014-08-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

PubMed

Henke, Paul S; Mak, Chi H

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Neutron spectra measurement and calculations using data libraries CIELO, JEFF-3.2 and ENDF/B-VII.1 in iron benchmark assemblies

NASA Astrophysics Data System (ADS)

Jansky, Bohumil; Rejchrt, Jiri; Novak, Evzen; Losa, Evzen; Blokhin, Anatoly I.; Mitenkova, Elena

2017-09-01

The leakage neutron spectra measurements have been done on benchmark spherical assemblies - iron spheres with diameter of 20, 30, 50 and 100 cm. The Cf-252 neutron source was placed into the centre of iron sphere. The proton recoil method was used for neutron spectra measurement using spherical hydrogen proportional counters with diameter of 4 cm and with pressure of 400 and 1000 kPa. The neutron energy range of spectrometer is from 0.1 to 1.3 MeV. This energy interval represents about 85 % of all leakage neutrons from Fe sphere of diameter 50 cm and about of 74% for Fe sphere of diameter 100 cm. The adequate MCNP neutron spectra calculations based on data libraries CIELO, JEFF-3.2 and ENDF/B-VII.1 were done. Two calculations were done with CIELO library. The first one used data for all Fe-isotopes from CIELO and the second one (CIELO-56) used only Fe-56 data from CIELO and data for other Fe isotopes were from ENDF/B-VII.1. The energy structure used for calculations and measurements was 40 gpd (groups per decade) and 200 gpd. Structure 200 gpd represents lethargy step about of 1%. This relatively fine energy structure enables to analyze the Fe resonance neutron energy structure. The evaluated cross section data of Fe were validated on comparisons between the calculated and experimental spectra.

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

Gifford, Jason S.; Grace, Robert C.; Rickerson, Wilson H.

This report serves as a resource for policymakers who wish to learn more about levelized cost of energy (LCOE) calculations, including cost-based incentives. The report identifies key renewable energy cost modeling options, highlights the policy implications of choosing one approach over the other, and presents recommendations on the optimal characteristics of a model to calculate rates for cost-based incentives, FITs, or similar policies. These recommendations shaped the design of NREL's Cost of Renewable Energy Spreadsheet Tool (CREST), which is used by state policymakers, regulators, utilities, developers, and other stakeholders to assist with analyses of policy and renewable energy incentive paymentmore » structures. Authored by Jason S. Gifford and Robert C. Grace of Sustainable Energy Advantage LLC and Wilson H. Rickerson of Meister Consultants Group, Inc.« less

A Computational Study of Structure and Reactivity of N-Substitued-4-Piperidones Curcumin Analogues and Their Radical Anions.

PubMed

Martínez-Cifuentes, Maximiliano; Weiss-López, Boris; Araya-Maturana, Ramiro

2016-12-02

In this work, a computational study of a series of N -substitued-4-piperidones curcumin analogues is presented. The molecular structure of the neutral molecules and their radical anions, as well as their reactivity, are investigated. N -substituents include methyl and benzyl groups, while substituents on the aromatic rings cover electron-donor and electron-acceptor groups. Substitutions at the nitrogen atom do not significantly affect the geometry and frontier molecular orbitals (FMO) energies of these molecules. On the other hand, substituents on the aromatic rings modify the distribution of FMO. In addition, they influence the capability of these molecules to attach an additional electron, which was studied through adiabatic (AEA) and vertical electron affinities (VEA), as well as vertical detachment energy (VDE). To study electrophilic properties of these structures, local reactivity indices, such as Fukui ( f ⁺) and Parr ( P ⁺) functions, were calculated, and show the influence of the aromatic rings substituents on the reactivity of α,β-unsaturated ketones towards nucleophilic attack. This study has potential implications for the design of curcumin analogues based on a 4-piperidone core with desired reactivity.

Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

PubMed

Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

2016-05-05

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

The Nature of the Interactions in Triethanolammonium-Based Ionic Liquids. A Quantum Chemical Study.

PubMed

Fedorova, Irina V; Safonova, Lyubov P

2018-05-10

Structural features and interionic interactions play a crucial role in determining the overall stability of ionic liquids and their physicochemical properties. Therefore, we performed high-level quantum-chemical study of different cation-anion pairs representing the building units of protic ionic liquids based on triethanolammonium cation and anions of sulfuric, nitric, phosphoric, and phosphorus acids to provide essential insight into these phenomena at the molecular level. It was shown that every structure is stabilized through multiple H bonds between the protons in the N-H and O-H groups of the cation and different oxygen atoms of the anion acid. Using atoms in molecules topological parameters and natural bond orbital analysis, we determined the nature and strength of these interactions. Our calculations suggest that the N-H group of the cation has more proton donor-like character than the O-H group that makes the N-H···O hydrogen bonds stronger. A close relation between the binding energies of these ion pairs and experimental melting points was established: the smaller the absolute value of the binding energy between ions, the lower is the melting point.

Theoretical studies of the transition state structures and free energy barriers for base-catalyzed hydrolysis of amides

PubMed Central

Xiong, Ying; Zhan, Chang-Guo

2010-01-01

The transition state structures and free energy barriers for the rate-determining step (i.e. the formation of a tetrahedral intermediate) of base-catalyzed hydrolysis of a series of amides in aqueous solution have been studied by performing first-principle electronic structure calculations using a hybrid supermolecule-polarizable continuum approach. The calculated results and a revisit of recently reported experimental proton inventory data reveal that the favorable transition state structure optimized for the tetrahedral intermediate formation of hydroxide ion-catalyzed hydrolysis of formamide may have three solvating water molecules remaining on the attacking hydroxide oxygen and two additional water molecules attached to the carbonyl oxygen of formamide. The calculated results have also demonstrated interesting substituent effects on the optimized transition state geometries, on the transition-state stabilization, and on the calculated free energy barriers for the base-catalyzed hydrolysis of amides. When some or all of the hydrogen atoms of formamide are replaced by methyl groups, the total number of water molecules hydrogen-bonding with the attacking hydroxide in the transition state decreases from three for formamide to two for N-methylacetamide, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). The larger substituents of the amide hinder the solvent water molecules approaching the attacking hydroxide oxygen in the transition state and, therefore, destabilize the transition state structure and increase the free energy barrier. By using the optimized most favorable transition state structures, the calculated free energy barriers, i.e. 21.6 (or 21.7), 22.7, 23.1, and 26.0 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively, are in good agreement with the available experimental free energy barriers, i.e. 21.2, 21.5, 22.6, and 24.1 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively. PMID:17107116

Effects of mid-foot contact area ratio on lower body kinetics/kinematics in sagittal plane during stair descent in women.

PubMed

Lee, Jinkyu; Hong, Yoon No Gregory; Shin, Choongsoo S

2016-07-01

The mid-foot contact area relative to the total foot contact area can facilitate foot arch structure evaluation. A stair descent motion consistently provides initial fore-foot contact and utilizes the foot arch more actively for energy absorption. The purpose of this study was to compare ankle and knee joint angle, moment, and work in sagittal plane during stair descending between low and high Mid-Foot-Contact-Area (MFCA) ratio group. The twenty-two female subjects were tested and classified into two groups (high MFCA and low MFCA) using their static MFCA ratios. The ground reaction force (GRF) and kinematics of ankle and knee joints were measured while stair descending. During the period between initial contact and the first peak in vertical GRF (early absorption phase), ankle negative work for the low MFCA ratio group was 33% higher than that for the high MFCA ratio group (p<0.05). However, ankle negative work was not significantly different between the two groups during the period between initial contact and peak dorsiflexion angle (early absorption phase+late absorption phase). The peak ankle dorsiflexion angle was smaller in the low MFCA ratio group (p<0.05). Our results suggest that strategy of energy absorption at the ankle and foot differs depending upon foot arch types classified by MFCA. The low MFCA ratio group seemed to absorb more impact energy using strain in the planar fascia during early absorption phase, whereas the high MFCA ratio group absorbed more impact energy using increased dorsiflexion during late absorption phase. Copyright © 2016 Elsevier B.V. All rights reserved.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials.

PubMed

Qi, Xuejun; Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite's chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials

PubMed Central

Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite’s chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface. PMID:28301544

Microscopic structure and properties changes of cassava stillage residue pretreated by mechanical activation.

PubMed

Liao, Zhengda; Huang, Zuqiang; Hu, Huayu; Zhang, Yanjuan; Tan, Yunfang

2011-09-01

This study has focused on the pretreatment of cassava stillage residue (CSR) by mechanical activation (MA) using a self-designed stirring ball mill. The changes in surface morphology, functional groups and crystalline structure of pretreated CSR were examined by using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) under reasonable conditions. The results showed that MA could significantly damage the crystal structure of CSR, resulting in the variation of surface morphology, the increase of amorphous region ratio and hydrogen bond energy, and the decrease in crystallinity and crystalline size. But no new functional groups generated during milling, and the crystal type of cellulose in CSR still belonged to cellulose I after MA. Copyright © 2011 Elsevier Ltd. All rights reserved.

DFT study of the effect of substitution on the molecular structure of copper phthalocyanine

NASA Astrophysics Data System (ADS)

Kaur, Prabhjot; Sachdeva, Ritika; Singh, Sukhwinder; Saini, G. S. S.

2016-05-01

To study the effect of sulfonic acid group as substituent on the molecular structure of an organic compound copper Phthalocyanine, the optimized geometry, mulliken charges, energies and dipole momemts of copper phthalocyanine and copper phthalocyaninetetrasulfonic acid tetra sodium salt have been investigated using density functional theory. Also to predict the change in reactive sites after substitution, molecular electrostatic potential maps for both the molecules have been calculated.

Photon energy lifter.

PubMed

Gaburro, Zeno; Ghulinyan, Mher; Riboli, Francesco; Pavesi, Lorenzo; Recati, Alessio; Carusotto, Iacopo

2006-08-07

We propose a time-dependent, spatially periodic photonic structure which is able to shift the carrier frequency of an optical pulse which propagates through it. Taking advantage of the slow group velocity of light in periodic photonic structures, the wavelength conversion process can be performed with an efficiency close to 1 and without affecting the shape and the coherence of the pulse. Quantitative Finite Difference Time Domain simulations are performed for realistic systems with optical parameters of conventional silicon technology.

Enhanced fluorescence from CdSe/ZnS quantum dot nanophosphors embedded in a one-dimensional photonic crystal backbone structure.

PubMed

Min, Kyungtaek; Choi, Serok; Choi, Yunkyoung; Jeon, Heonsu

2014-11-06

A nano-engineered phosphor structure that produces enhanced fluorescence is reported. Two kinds of polymer materials with different refractive indices are spin-coated alternately to realize a one-dimensional (1D) photonic crystal (PC) phosphor platform, in which CdSe/ZnS core-shell quantum dots (QDs) were embedded as a fluorescence agent. The 1D PC phosphor structure is designed to match the pump photon energy with one of the photonic band-edges (PBEs), where the photon group velocity becomes zero, and thus the interaction between pump photons and fluorescent centres strengthened. A reference phosphor structure is also designed and fabricated; however, it has no PBE and exhibited bulk-like photonic properties. The fluorescence intensity from the 1D PC phosphors is examined during the pump photon energy scanning across the PBE. It is found that fluorescence from the 1D PC phosphor reaches its maximum when the pump photon energy coincides with the PBE, which is consistent with the theoretical prediction. In comparison with the reference phosphor, the fluorescence from the 1D PC phosphor is measured to be enhanced by a factor of 1.36.

Magnetic field adjustment structure and method for a tapered wiggler

DOEpatents

Halbach, Klaus

1988-03-01

An improved method and structure is disclosed for adjusting the magnetic field generated by a group of electromagnet poles spaced along the path of a charged particle beam to compensate for energy losses in the charged particles which comprises providing more than one winding on at least some of the electromagnet poles; connecting one respective winding on each of several consecutive adjacent electromagnet poles to a first power supply, and the other respective winding on the electromagnet pole to a different power supply in staggered order; and independently adjusting one power supply to independently vary the current in one winding on each electromagnet pole in a group whereby the magnetic field strength of each of a group of electromagnet poles may be changed in smaller increments.

Magnetic field adjustment structure and method for a tapered wiggler

DOEpatents

Halbach, Klaus

1988-01-01

An improved method and structure is disclosed for adjusting the magnetic field generated by a group of electromagnet poles spaced along the path of a charged particle beam to compensate for energy losses in the charged particles which comprises providing more than one winding on at least some of the electromagnet poles; connecting one respective winding on each of several consecutive adjacent electromagnet poles to a first power supply, and the other respective winding on the electromagnet pole to a different power supply in staggered order; and independently adjusting one power supply to independently vary the current in one winding on each electromagnet pole in a group whereby the magnetic field strength of each of a group of electromagnet poles may be changed in smaller increments.

Citizen's actions

NASA Technical Reports Server (NTRS)

1975-01-01

The role played by individual citizens as consumers of energy was examined, with emphasis on studying ways in which their action could result in energy conservation. It was shown that there are ways that energy can be conserved in this way, with citizens acting either individually or in groups. The potential savings are significant, but the actual savings may be quite small. The citizens need to be motivated to save and to believe in a conservation ethic; developing such an ethic is difficult, and perhaps not responsive to the shotgun approach now being attempted. The true course of action may be to synthesize new societal structures that provide the maximum evolution of culture within the limitation of scarce energy resources.

UNIDENTIFIED INFRARED EMISSION BANDS: PAHs or MAONs?

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

Sun Kwok; Yong Zhang, E-mail: sunkwok@hku.hk

2013-07-01

We suggest that the carrier of the unidentified infrared emission (UIE) bands is an amorphous carbonaceous solid with mixed aromatic/aliphatic structures, rather than free-flying polycyclic aromatic hydrocarbon molecules. Through spectral fittings of the astronomical spectra of the UIE bands, we show that a significant amount of the energy is emitted by the aliphatic component, implying that aliphatic groups are an essential part of the chemical structure. Arguments in favor of an amorphous, solid-state structure rather than a gas-phase molecule as a carrier of the UIE are also presented.

The origin of luminescence from di[4-(4-diphenylaminophenyl)phenyl]sulfone (DAPSF), a blue light emitter: an X-ray excited optical luminescence (XEOL) and X-ray absorption near edge structure (XANES) study.

PubMed

Zhang, Duo; Zhang, Hui; Zhang, Xiaohong; Sham, Tsun-Kong; Hu, Yongfeng; Sun, Xuhui

2016-03-07

The electronic structure and optical properties of di[4-(4-diphenylaminophenyl)phenyl]sulfone (denoted as DAPSF), a highly efficient fluorophor, have been investigated using X-ray excited optical luminescence (XEOL) and X-ray absorption near edge structure (XANES) spectroscopy at excitation energies across the C, N, O K-edges and the sulfur K-edge. The results indicate that the blue luminescence is mainly related to the sulfur functional group.

The anti-obesity effect of starch in a whole grain-like structural form.

PubMed

Luo, Kaiyun; Wang, Xufeng; Zhang, Genyi

2018-06-13

Obesity is a risk factor for many chronic diseases, and the anti-obesity effect of starch in a whole grain-like structural form (WGLSF) prepared through co-gelation with oat β-glucan and alginate was studied using high-fat (HF) induced obese male C57BL/6J mice. In vitro human fecal fermentation of WGLSF-starch showed a slower rate of fermentation and a higher production of butyric acid (132.0 μmol per 50 mg sample) when compared to the physical mixture counterpart of starch, β-glucan, and alginate (PM) (110.5 μmol per 50 mg) or β-glucan itself (96.2 μmol per 50 mg). The body weight gain of obese mice fed with a HF-WGLSF diet was significantly reduced (42.0% lower than the HF group, 30.2% lower than the physical mixture) with decreased cell size in white adipose tissue and similar levels of serum lipid profiles to the control of the low-fat (LF) group. Western blotting experiments showed the down-regulated lipogenic transcription factor of SREBP-1c and fatty acid synthase (FAS), but the lipid-oxidation related transcription factors of peroxisome proliferator-activated receptor-α (PPAR-α) and phosphorylated AMP-activated protein kinase (p-AMPK) were up-regulated. Energy metabolism analysis revealed increased lipid-sourced energy expenditure with higher heat production and respiratory exchange ratios. Consistently, the expression of hypothalamic pro-opiomelanocortin (POMC), favoring energy expenditure, was increased significantly while the neuropeptide Y (NPY) was reduced. Thus, the increased energy expenditure stimulated by starch in a whole-grain-like structural form is responsible for the reduced body weight gain of obese mice fed with a high fat-based diet.

Characterization of Ultrasound Energy Diffusion Due to Small-Size Damage on an Aluminum Plate Using Piezoceramic Transducers

PubMed Central

Lu, Guangtao; Feng, Qian; Li, Yourong; Wang, Hao; Song, Gangbing

2017-01-01

During the propagation of ultrasonic waves in structures, there is usually energy loss due to ultrasound energy diffusion and dissipation. The aim of this research is to characterize the ultrasound energy diffusion that occurs due to small-size damage on an aluminum plate using piezoceramic transducers, for the future purpose of developing a damage detection algorithm. The ultrasonic energy diffusion coefficient is related to the damage distributed in the medium. Meanwhile, the ultrasonic energy dissipation coefficient is related to the inhomogeneity of the medium. Both are usually employed to describe the characteristics of ultrasound energy diffusion. The existence of multimodes of Lamb waves in metallic plate structures results in the asynchronous energy transport of different modes. The mode of Lamb waves has a great influence on ultrasound energy diffusion as a result, and thus has to be chosen appropriately. In order to study the characteristics of ultrasound energy diffusion in metallic plate structures, an experimental setup of an aluminum plate with a through-hole, whose diameter varies from 0.6 mm to 1.2 mm, is used as the test specimen with the help of piezoceramic transducers. The experimental results of two categories of damages at different locations reveal that the existence of damage changes the energy transport between the actuator and the sensor. Also, when there is only one dominate mode of Lamb wave excited in the structure, the ultrasound energy diffusion coefficient decreases approximately linearly with the diameter of the simulated damage. Meanwhile, the ultrasonic energy dissipation coefficient increases approximately linearly with the diameter of the simulated damage. However, when two or more modes of Lamb waves are excited, due to the existence of different group velocities between the different modes, the energy transport of the different modes is asynchronous, and the ultrasonic energy diffusion is not strictly linear with the size of the damage. Therefore, it is recommended that only one dominant mode of Lamb wave should be excited during the characterization process, in order to ensure that the linear relationship between the damage size and the characteristic parameters is maintained. In addition, the findings from this paper demonstrate the potential of developing future damage detection algorithms using the linear relationships between damage size and the ultrasound energy diffusion coefficient or ultrasonic energy dissipation coefficient when a single dominant mode is excited. PMID:29207530

Two-photon or higher-order absorbing optical materials and methods of use

NASA Technical Reports Server (NTRS)

Marder, Seth (Inventor); Perry, Joseph (Inventor)

2012-01-01

Compositions capable of simultaneous two-photon absorption and higher order absorptivities are provided. Compounds having a donor-pi-donor or acceptor-pi-acceptor structure are of particular interest, where the donor is an electron donating group, acceptor is an electron accepting group, and pi is a pi bridge linking the donor and/or acceptor groups. The pi bridge may additionally be substituted with electron donating or withdrawing groups to alter the absorptive wavelength of the structure. Also disclosed are methods of generating an excited state of such compounds through optical stimulation with light using simultaneous absorption of photons of energies individually insufficient to achieve an excited state of the compound, but capable of doing so upon simultaneous absorption of two or more such photons. Applications employing such methods are also provided, including controlled polymerization achieved through focusing of the light source(s) used.

Effect of auxiliary group for p-type organic dyes in NiO-based dye-sensitized solar cells: The first principal study

NASA Astrophysics Data System (ADS)

Li, Juan; Zhang, Shijie; Shao, Di; Yang, Zhenqing; Zhang, Wansong

2018-03-01

Auxiliary acceptor groups play a crucial role in D-A-π-A structured organic dyes. In this paper, we designed three D-A-π-A structured organic molecules based on the prototype dye QT-1, named ME18-ME20, and further investigated their electronic and optical properties with density functional theory (DFT) and time-dependent DFT (TDDFT). The calculated results indicate that the scope and intensity of dyes' absorption spectra have some outstanding changes by inserting auxiliary groups. ME20 has not only 152 nm redshifts to long wave orientation, but also 78% increased oscillator strength compared to QT-1, and its absorption spectrum broadens region even up to 1400 nm. Then, we studied the reason that the effect of the introduced different auxiliary acceptor groups in these dyes through their ground states geometries and energy levels, electron transfer and recombination rate.

QSAR for cholinesterase inhibition by organophosphorus esters and CNDO/2 calculations for organophosphorus ester hydrolysis. [quantitative structure-activity relationship, complete neglect of differential overlap

NASA Technical Reports Server (NTRS)

Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

1985-01-01

Quantitative structure-activity relationships were derived for acetyl- and butyrylcholinesterase inhibition by various organophosphorus esters. Bimolecular inhibition rate constants correlate well with hydrophobic substituent constants, and with the presence or absence of cationic groups on the inhibitor, but not with steric substituent constants. CNDO/2 calculations were performed on a separate set of organophosphorus esters, RR-primeP(O)X, where R and R-prime are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. For each subset with the same X, the CNDO-derived net atomic charge at the central phosphorus atom in the ester correlates well with the alkaline hydrolysis rate constant. For the whole set of esters with different X, two equations were derived that relate either charge and leaving group steric bulk, or orbital energy and bond order to the hydrolysis rate constant.

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters

PubMed Central

Saier, Milton H.

2000-01-01

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects. PMID:10839820

Identification of new 2,5-diketopiperazine derivatives as simultaneous effective inhibitors of αβ-tubulin and BCRP proteins: Molecular docking, Structure-Activity Relationships and virtual consensus docking studies

NASA Astrophysics Data System (ADS)

Fani, Najmeh; Sattarinezhad, Elham; Bordbar, Abdol-Khalegh

2017-06-01

In the first part of this paper, docking method was employed in order to study the binding mechanism of breast cancer resistance protein (BCRP) with a group of previously synthesized TPS-A derivatives which known as potent inhibitors of this protein to get insight into drug binding site of BCRP and to explore structure-activity relationship of these compounds. Molecular docking results showed that most of these compounds bind in the binding site of BCRP at the interface between the membrane and outer environment. In the second part, a group of designed TPS-A derivatives which showed good binding energies in the binding site of αβ-tubulin in the previous study were chosen to study their binding energies in the binding site of BCRP to investigate their simultaneous inhibitory effect on both αβ-tubulin and BCRP. The results showed that all of these compounds bind to the binding site of BCRP with relatively suitable binding energies and therefore could be potential inhibitors of both αβ-tubulin and BCRP proteins. Finally, virtual consensus docking method was utilized with the aim of design of new 2,5-diketopiperazine derivatives with significant inhibitory effect on both αβ-tubulin and BCRP proteins. For this purpose binding energies of a library of 2,5-diketopiperazine derivatives in the binding sites of αβ-tubulin and BCRP was investigated by using AutoDock and AutoDock vina tools. Molecular docking results revealed that a group of 36 compounds among them exhibit strong anti-tubulin and anti-BCRP activity.

Correlating molecular spectroscopy and molecular chemometrics to explore carbohydrate functional groups and utilization of coproducts from biofuel and biobrewing processing.

PubMed

Chen, Limei; Zhang, Xuewei; Yu, Peiqiang

2014-06-04

Dried distillers grains with solubles (DDGS) was coproducts from bioethanol and biobrewing industry. It was an excellent resource of protein and energy feedstuff in China. Conventional studies often focus on traditional nutritional profiles. To data, there is little research on molecular structure-nutrition interaction of carbohydrate in coproducts. In this study, five kinds of corn-grain based DDGS and two kinds of barley-grain based DDGS were collected from different manufactures in the north of China. They were coded as "1, 2, 3, 4, 5, 6, and 7", respectively. The primary purposes of this project were to investigate the molecular structure-nutrition interaction of carbohydrate in coproducts, in terms of (1) carbohydrate-related chemical composition and nutrient profiles, (2) predicted values for energy in coproducts for animal, and (3) in situ digestion of dry matter. The result showed that acid detergent fiber content in corn DDGS and barley DDGS had negative correlation with structural carbohydrate peak area, cellulose compounds, and carbohydrate component peaks (first, second, and total peak area), which were measured with molecular spectroscopy. The correlation between carbohydrate peak area (second and total) and digestible fiber (tdNDF) were negative. There were no correlation between carbohydrate spectral intensities and energy values, carbohydrate subfractions partitioned by CNCPS system, and in situ rumen degradation. The results indicate that carbohydrate spectral profiles (functional groups) are associated with the carbohydrate nutritive values in coproducts from biofuel and biobrewing processing.

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

PubMed Central

Koorehdavoudi, Hana; Bogdan, Paul

2016-01-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity. PMID:27297496

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

NASA Astrophysics Data System (ADS)

Koorehdavoudi, Hana; Bogdan, Paul

2016-06-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.

Crystal Structures, Surface Stability, and Water Adsorption Energies of La-Bastnäsite via Density Functional Theory and Experimental Studies

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

Srinivasan, Sriram Goverapet; Shivaramaiah, Radha; Kent, Paul R. C.

2016-07-11

Bastnasite is a fluoro-carbonate mineral that is the largest source of rare earth elements such as Y, La and Ce. With increasing demand for REE in many emerging technologies, there is an urgent need for improving the efficiency of ore beneficiation by froth flotation. In order to design improved flotation agents that can selectively bind to the mineral surface, a fundamental understanding of the bulk and surface properties of bastnasite is essential. Density functional theory calculations using the PBEsol exchange correlation functional and the DFT-D3 dispersion correction reveal that the most stable form of La bastnsite is isomorphic to themore » structure of Ce bastnasite belonging to the P2c space group, while the Inorganic Crystal Structure Database structure in the P2m space group is ca. 11.3 kJ/mol higher in energy per LaFCO 3 formula unit. We report powder X-ray diffraction measurements on synthetic of La bastnasite to support these theoretical findings. Six different surfaces are studied by DFT, namely [100], [0001], [101], [102], [104] and [112]. Among these, the [100] surface is the most stable with a surface energy of 0.73 J/m 2 in vacuum and 0.45 J/m 2 in aqueous solution. We predicted the shape of a La bastnasite nanoparticle via thermodynamic Wulff construction to be a hexagonal prism with [100] and [0001] facets, chiseled at its ends by the [101] and [102] facets. The average surface energy of the nanoparticle in the gas phase is estimated to be 0.86 J/m 2, in good agreement with a value of 1.11 J/m 2 measured by calorimetry. The calculated adsorption energy of a water molecule varies widely with the surface plane and specific adsorption sites on a given surface. Moreover, the first layer of water molecules is predicted to adsorb strongly on the La-bastnasite surface, in agreement with water adsorption calorimetry experiments. Our work provides an important step towards a detailed atomistic understanding of the bastnasite water interface and designing collector molecules that can bind specifically to bastnasite.« less

Test particle simulation study of whistler wave packets observed near Comet Giacobini-Zinner

NASA Astrophysics Data System (ADS)

Kaya, N.; Matsumoto, H.; Tsurutani, B. T.

1989-01-01

Nonlinear interactions of water group ions with large-amplitude whistler wave packets detected at the leading edge of steepened magnetosonic waves observed near Comet Giacobini-Zinner (GZ) are studied using test particle simulations of water-ion interactions with a model wave based on GZ data. Some of the water ions are found to be decelerated in the steepened portion of the magnetosonic wave to the resonance velocity with the whistler wave packets. Through resonance and related nonlinear interaction with the large-amplitude whistler waves, the water ions become trapped by the packet. An energy balance calculation demonstrates that the trapped ions lose their kinetic energy during the trapped motion in the packet. Thus, the nonlinear trapping motion in the wave structure leads to effective energy transfer from the water group ions to the whistler wave packets in the leading edge of the steepened MHD waves.

Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phase

NASA Astrophysics Data System (ADS)

Holmes, Tiffani M.; Doskocz, Jacek; Wright, Terrance; Hill, Glake A.

The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the bond OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine.

The effect of different π-bridge configuration on bi-anchored triphenylamine and phenyl modified triphenylamine based dyes for dye sensitized solar cell (DSSC) application: A theoretical approach.

PubMed

Pounraj, P; Mohankumar, V; Pandian, M Senthil; Ramasamy, P

2018-01-01

Twenty eight bi-anchored triphenylamine (TH-1 to TH-14) and phenyl modified triphenylamine (PH-TH-1 to PH-TH-14) based metal free organic dyes are designed for DSSC application. The electronic effect of different π-bridge configurations in donor-π-bridge-acceptor (D-π-A) 2 structure was theoretically simulated and verified using density functional theory (DFT) and time dependent density functional theory (TD-DFT). The triphenylamine and phenyl modified triphenylamine groups are used as donor and cyanoacrylic acid group is used as acceptor. Thiophene and cyanovinyl groups are used as π-bridge. The ground state molecular structure was optimized by density functional theory and the electronic absorption spectra were calculated by time dependent density functional theory. The light harvesting efficiency (LHE), dye regeneration energy (ΔG reg ) and electron injection energy (ΔG inject ) are determined by computational examination. It is observed that, when the number of π-bridge increases, the band gap of the dye decreases. Also the absorption maximum and molar extinction coefficient of the dyes are increased. Theoretical result shows that the thiophene-cyanovinyl and thiophene-thiophene-cyanovinyl-cyanovinyl configurations give broader and red shifted absorption spectrum compared to other configurations. Also the results of phenyl modified triphenylamine (PH-TH) dyes clearly show better absorption and dye regeneration energy compared to TH dyes. Copyright © 2017 Elsevier Inc. All rights reserved.

'Part of the solution': Developing sustainable energy through co-operatives and learning

NASA Astrophysics Data System (ADS)

Duguid, Fiona C. B.

After five years of development, WindShare Co-operative in Toronto, Ontario became the first urban wind turbine in North America and the first co-operatively owned and operated wind turbine in Canada. The development of WindShare Co-operative has spurred the growth of a green energy co-operative sector in Ontario. This study, which included 27 interviews and a focus group with members of WindShare Co-operative, focuses on the roles of community-based green energy co-operatives in advancing sustainable energy development and energy literacy. Sustainable energy development is firmly rooted in the triple bottom line of environmental, social and economic success, and green energy co-operatives can be a way to help achieve those successes. Green energy co-operatives are structures for providing renewable energy generation or energy conservation practices, both of which have important environmental impacts regarding climate change and pollution levels. Co-operative structures are supported by processes that include local ownership, democracy, participation, community organizing, learning and social change. These processes have a significant social impact by creating a venue for people to be directly involved in the energy industry, by involving learning through participation in a community-based organization, and by advancing energy literacy within the membership and the general public. In regards to the economic impacts, green energy co-operatives foster a local economy and local investment opportunities, which have repercussions regarding building expertise within Ontario's green energy and co-operative development future, and more generally, captures members' interest because they have a direct stake in the co-operative. This thesis shows that green energy co-operatives, like WindShare, play an important role in advancing sustainable energy development, energy literacy and the triple bottom line. Members of WindShare expressed resounding feelings of pride, efficacy and understanding of WindShare's role in sustainable energy. WindShare Co-operative provided the structure whereby members felt a part of the solution in terms of sustainable energy development. Policies and practices at all levels of government should encourage the advancement of green energy co-operatives to support Canada's efforts at public involvement in combating climate change and pollution.

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole.

PubMed

Arjunan, V; Raj, Arushma; Santhanam, R; Marchewka, M K; Mohan, S

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. (1)H and (13)C NMR chemical shifts and the electronic transitions of the molecule are also discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Effects of dietary fibre on subjective appetite, energy intake and body weight: a systematic review of randomized controlled trials.

PubMed

Wanders, A J; van den Borne, J J G C; de Graaf, C; Hulshof, T; Jonathan, M C; Kristensen, M; Mars, M; Schols, H A; Feskens, E J M

2011-09-01

Dietary fibres are believed to reduce subjective appetite, energy intake and body weight. However, different types of dietary fibre may affect these outcomes differently. The aim of this review was to systematically investigate the available literature on the relationship between dietary fibre types, appetite, acute and long-term energy intake, and body weight. Fibres were grouped according to chemical structure and physicochemical properties (viscosity, solubility and fermentability). Effect rates were calculated as the proportion of all fibre-control comparisons that reduced appetite (n = 58 comparisons), acute energy intake (n = 26), long-term energy intake (n = 38) or body weight (n = 66). For appetite, acute energy intake, long-term energy intake and body weight, there were clear differences in effect rates depending on chemical structure. Interestingly, fibres characterized as being more viscous (e.g. pectins, β-glucans and guar gum) reduced appetite more often than those less viscous fibres (59% vs. 14%), which also applied to acute energy intake (69% vs. 30%). Overall, effects on energy intake and body weight were relatively small, and distinct dose-response relationships were not observed. Short- and long-term effects of dietary fibres appear to differ and multiple mechanisms relating to their different physicochemical properties seem to interplay. This warrants further exploration. © 2011 The Authors. obesity reviews © 2011 International Association for the Study of Obesity.

QM/MM MD and free energy simulations of G9α-like protein (GLP) and its mutants: Understanding the factors that determine the product specificity

DOE PAGES

Chu, Yuzhuo; Yao, Jianzhuang; Guo, Hong

2012-05-18

Certain lysine residues on histone tails could be methylated by protein lysine methyltransferases (PKMTs) using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Since the methylation states of the target lysines play a fundamental role in the regulation of chromatin structure and gene expression, it is important to study the property of PKMTs that allows a specific number of methyl groups (one, two or three) to be added (termed as product specificity). It has been shown that the product specificity of PKMTs may be controlled in part by the existence of specific residues at the active site. One of the best examplesmore » is a Phe/Tyr switch found in many PKMTs. Here quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed on wild type G9a-like protein (GLP) and its F1209Y and Y1124F mutants for understanding the energetic origin of the product specificity and the reasons for the change of product specificity as a result of single-residue mutations at the Phe/Tyr switch as well as other positions. The free energy barriers of the methyl transfer processes calculated from our simulations are consistent with experimental data, supporting the suggestion that the relative free energy barriers may determine, at least in part, the product specificity of PKMTs. The changes of the free energy barriers as a result of the mutations are also discussed based on the structural information obtained from the simulations. Furthermore, the results suggest that the space and active-site interactions around the -amino group of the target lysine available for methyl addition appear to among the key structural factors in controlling the product specificity and activity of PKMTs.« less

Spin-dependent delay time in ferromagnet/insulator/ferromagnet heterostructures

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

Xie, ZhengWei; Zheng Shi, De; Lv, HouXiang

2014-07-07

We study theoretically spin-dependent group delay and dwell time in ferromagnet/insulator/ferromagnet (FM/I/FM) heterostructure. The results indicate that, when the electrons with different spin orientations tunnel through the FM/I/FM junction, the spin-up process and the spin-down process are separated on the time scales. As the self-interference delay has the spin-dependent features, the variations of spin-dependent dwell-time and spin-dependent group-delay time with the structure parameters appear different features, especially, in low incident energy range. These different features show up as that the group delay times for the spin-up electrons are always longer than those for spin-down electrons when the barrier height ormore » incident energy increase. In contrast, the dwell times for the spin-up electrons are longer (shorter) than those for spin-down electrons when the barrier heights (the incident energy) are under a certain value. When the barrier heights (the incident energy) exceed a certain value, the dwell times for the spin-up electrons turn out to be shorter (longer) than those for spin-down electrons. In addition, the group delay time and the dwell time for spin-up and down electrons also relies on the comparative direction of magnetization in two FM layers and tends to saturation with the thickness of the barrier.« less

Density functional theory study of adsorption geometries and electronic structures of azo-dye-based molecules on anatase TiO2 surface for dye-sensitized solar cell applications.

PubMed

Prajongtat, Pongthep; Suramitr, Songwut; Nokbin, Somkiat; Nakajima, Koichi; Mitsuke, Koichiro; Hannongbua, Supa

2017-09-01

Structural and electronic properties of eight isolated azo dyes (ArNNAr', where Ar and Ar' denote the aryl groups containing benzene and naphthalene skeletons, respectively) were investigated by density functional theory (DFT) based on the B3LYP/6-31G(d,p) and TD-B3LYP/6-311G(d,p) methods The effect of methanol solvent on the structural and electronic properties of the azo dyes was elucidated by employing a polarizable continuum model (PCM). Then, the azo dyes adsorbed onto the anatase TiO 2 (101) slab surface through a carboxyl group. The geometries and electronic structures of the adsorption complexes were determined using periodic DFT based on the PWC/DNP method. The calculated adsorption energies indicate that the adsorbed dyes preferentially take configuration of the bidentate bridging rather than chelating or monodentate ester-type geometries. Furthermore, the azo compounds having two carboxyl groups are coordinated to the TiO 2 surface more preferentially through the carboxyl group connecting to the benzene skeleton than through that connecting to the naphthalene skeleton. The dihedral angles (Φ B-N ) between the benzene- and naphthalene-skeleton moieties are smaller than 10° for the adsorbed azo compounds containing one carboxyl group. In contrast, Φ B-N > 30° are obtained for the adsorbed azo compounds containing two carboxyl groups. The almost planar conformations of the former appear to strengthen both π-electrons conjugation and electronic coupling between low-lying unoccupied molecular orbitals of the azo dyes and the conduction band of TiO 2 . On the other hand, such coupling is very weak for the latter, leading to a shift of the Fermi level of TiO 2 in the lower-energy direction. The obtained results are useful to the design and synthesize novel azo-dye-based molecules that give rise to higher photovoltaic performances of the dye-sensitized solar cells. Copyright © 2017 Elsevier Inc. All rights reserved.

The role of energetic ions from plasma in the creation of nanostructured materials and stable polymer surface treatments

NASA Astrophysics Data System (ADS)

Bilek, M. M. M.; Newton-McGee, K.; McKenzie, D. R.; McCulloch, D. G.

2006-01-01

Plasma processes for the synthesis of new materials as thin films have enabled the production of a wide variety of new materials. These include meta-stable phases, which are not readily found in nature, and more recently, materials with structure on the nanoscale. Study of plasma synthesis processes at the fundamental level has revealed that ion energy, depositing flux and growth surface temperature are the critical parameters affecting the microstructure and the properties of the thin film materials formed. In this paper, we focus on the role of ion flux and impact energy in the creation of thin films with nanoscale structure in the form of multilayers. We describe three synthesis strategies, based on the extraction of ions from plasma sources and involving modulation of ion flux and ion energy. The microstructure, intrinsic stress and physical properties of the multilayered samples synthesized are studied and related back to the conditions at the growth surface during deposition. When energetic ions of a non-condensing species are used, it is possible to place active groups on the surfaces of materials such as polymers. These active groups can then be used as bonding sites in subsequent chemical attachment of proteins or other macromolecules. If the energy of the non-condensing ions is increased to a few keV then modified layers buried under the surface can be produced. Here we describe a method by which the aging effect, which is often observed in plasma surface modifications on polymers, can be reduced and even eliminated using high energy ion bombardment.

Wind/seismic comparisons for upgrading existing structures

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

Giller, R.A.

1989-10-01

This paper depicts the analysis procedures and methods used to evaluate three existing building structures for extreme wind loads. The three structures involved in this evaluation are located at the US Department of Energy's Hanford Site near Richland, Washington. This site is characterized by open flat grassland with few surrounding obstructions and has extreme winds in lieu of tornados as a design basis accident condition. This group of buildings represents a variety of construction types, including a concrete stack, a concrete load-bearing wall structure, and a rigid steel-frame building. The three structures included in this group have recently been evaluatedmore » for response to the design basis earthquake that included non-linear time history effects. The resulting loads and stresses from the wind analyses were compared to the loads and stresses resulting from seismic analyses. This approach eliminated the need to prepare additional capacity calculations that were already contained in the seismic evaluations. 4 refs., 5 figs., 5 tabs.« less

The spectroscopic impact of interactions with the four Gouterman orbitals from peripheral decoration of porphyrins with simple electron withdrawing and donating groups.

PubMed

Zhang, Angel; Kwan, Lydia; Stillman, Martin J

2017-11-07

Tetrapyrroles are of great interest for solar cell and photodynamic therapy applications due to their structural analogy with chlorophyll, a natural photosensitizer. Unsubstituted symmetric porphyrins exhibit weak absorption in the red region which makes them unsuitable for these applications. The push-pull peripheral decoration modifies the energies of the frontier molecular orbitals, which in turn influences the tetrapyrrole's spectroscopic properties. The absorption, magnetic circular dichroism, and emission spectra were measured for four zinc tetratolylporphyrin compounds substituted peripherally with a fused dimethoxybenzo group as an electron withdrawing group (EWG) on one pyrrole and on the opposite pyrrole, a single acetamido (1), a nitro (2), a proton (3), or a benzoylamino (4) substituent. Unusually, the magnetic circular dichroism spectrum of 2 exhibited a negative A term for the lowest energy absorption band (the Q band) and its emission spectrum was also unlike those of 1, 3, and 4. A complete computational analysis was carried out to obtain the energies and electron distribution, shown by electron density surfaces, of the four Gouterman MOs. TD-DFT calculations showed that for 2, ΔLUMO was greater than ΔHOMO, which accounted for the observed negative A term. The trend in the estimated MCD A term magnitudes, normalized to the absorbance as [A/(dipole strength) BM], provides experimental confirmation of the computationally determined ratio of ΔLUMO/ΔHOMO data. The value of ΔHOMO was confirmed by the trend in oscillator strengths. A series of fictive porphyrins (F1-F5) incorporating simple push-pull substituents were designed and their electronic structures were investigated using TD-DFT calculations. The substituents in the five fictive molecules illustrate the differential effect of the donor and acceptor groups in the β-position of the pyrroles on the relative stabilities of the four Gouterman orbitals. NO 2 groups result in the greatest splitting of the LUMO pair. We show that on using strong EWGs, opposite electron donating groups result in a ΔLUMO > 0, which red-shifts the Q band and introduces a strong dipole. With the nitro and formyl EWGs, ΔLUMO becomes greater than ΔHOMO, resulting in a complex electronic structure of the Q band, recognizable by a negative A term suggesting a design objective for future photosensitizers.

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

Report of the Office of Science and Technology Policy Working Group on Basic Research in the Department of Energy

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

Not Available

1978-06-01

The OSTP Working Group was commissioned to advise on the scope and quality of basic research conducted by and on behalf of DOE. The Group formed Subgroups in these areas: large-scale solar, fossil, fusion, small technology, and geothermal, environment and life sciences, social sciences, transportation, and fission. Work of the Subgroups forms the basis of much of this report, which has five sections. Following the introduction, preface, and executive summary (Section II), there is discussion of broad problem areas as they pertain to research (Section III). Section IV consists of general recommendations regarding policies for, as well as management andmore » scope of, research within the DOE: this section has four parts: Part A pertains to research in programmatic areas under the aegis of the Assistant Secretaries; Part B deals with the role and structure of the Office of Energy Research; Part C is concerned with broad research issues; and Part D addresses DOE Laboratories and Energy Research Centers. In Section V, research needs and opportunities for selected programs are discussed.« less

Highly resistive C-doped hydride vapor phase epitaxy-GaN grown on ammonothermally crystallized GaN seeds

NASA Astrophysics Data System (ADS)

Iwinska, Malgorzata; Piotrzkowski, Ryszard; Litwin-Staszewska, Elzbieta; Sochacki, Tomasz; Amilusik, Mikolaj; Fijalkowski, Michal; Lucznik, Boleslaw; Bockowski, Michal

2017-01-01

GaN crystals were grown by hydride vapor phase epitaxy (HVPE) and doped with C. The seeds were high-structural-quality ammonothermally crystallized GaN. The grown crystals were highly resistive at 296 K and of high structural quality. High-temperature Hall effect measurements revealed p-type conductivity and a deep acceptor level in the material with an activation energy of 1 eV. This is in good agreement with density functional theory calculations based on hybrid functionals as presented by the Van de Walle group. They obtained an ionization energy of 0.9 eV when C was substituted for N in GaN and acted as a deep acceptor.

Structural and spectroscopic study of the europium complex with N-(diphenylphosphoryl)pyrazine-2-carboxamide

NASA Astrophysics Data System (ADS)

Pham, Y. H.; Trush, V. A.; Amirkhanov, V. M.; Gawryszewska, P.

2017-12-01

This work presents a study of the Eu3+ complex with N-(diphenylphosphoryl)pyrazine-2-carboxamide (HL) and diphenylphosphinate ions (Ph2POO-) as co-ligands with the aim of probing the specific energetic and structural characteristics that influence the ligand-to-metal energy transfer and luminescence efficiency. The compound [Eu2(L)2(μ-Ph2POO)2(κ-OP(O)Ph2)2(CH3OH)2] crystallizes as a dimer with the space group P 1 bar . Absorption and emission (295, 77 K) spectra as well as luminescence decay times were used to characterize the photophysical properties of the complex in the solid state. Very effective energy transfer from ligands to Eu3+ ion was demonstrated.

Correlations between Energy and Displacement Demands for Performance-Based Seismic Engineering

NASA Astrophysics Data System (ADS)

Mollaioli, Fabrizio; Bruno, Silvia; Decanini, Luis; Saragoni, Rodolfo

2011-01-01

The development of a scientific framework for performance-based seismic engineering requires, among other steps, the evaluation of ground motion intensity measures at a site and the characterization of their relationship with suitable engineering demand parameters (EDPs) which describe the performance of a structure. In order to be able to predict the damage resulting from earthquake ground motions in a structural system, it is first necessary to properly identify ground motion parameters that are well correlated with structural response and, in turn, with damage. Since structural damage during an earthquake ground motion may be due to excessive deformation or to cumulative cyclic damage, reliable methods for estimating displacement demands on structures are needed. Even though the seismic performance is directly related to the global and local deformations of the structure, energy-based methodologies appear more helpful in concept, as they permit a rational assessment of the energy absorption and dissipation mechanisms that can be effectively accomplished to balance the energy imparted to the structure. Moreover, energy-based parameters are directly related to cycles of response of the structure and, therefore, they can implicitly capture the effect of ground motion duration, which is ignored by conventional spectral parameters. Therefore, the identification of reliable relationships between energy and displacement demands represents a fundamental issue in both the development of more reliable seismic code provisions and the evaluation of seismic vulnerability aimed at the upgrading of existing hazardous facilities. As these two aspects could become consistently integrated within a performance-based seismic design methodology, understanding how input and dissipated energy are correlated with displacement demands emerges as a decisive prerequisite. The aim of the present study is the establishment of functional relationships between input and dissipated energy (that can be considered as parameters representative of the amplitude, frequency content and duration of earthquake ground motions) and displacement-based response measures that are well correlated to structural and non-structural damage. For the purpose of quantifying the EDPs to be related to the energy measures, for comprehensive range of ground motion and structural characteristics, both simplified and more accurate numerical models will be used in this study for the estimation of local and global displacement and energy demands. Parametric linear and nonlinear time-history analyses will be performed on elastic and inelastic SDOF and MDOF systems, in order to assume information on the seismic response of a wide range of current structures. Hysteretic models typical of frame force/displacement behavior will be assumed for the local inelastic cyclic response of the systems. A wide range of vibration periods will be taken into account so as to define displacement, interstory drift and energy spectra for MDOF systems. Various scalar measures related to the deformation demand will be used in this research. These include the spectral displacements, the peak roof drift ratio, and the peak interstory drift ratio. A total of about 900 recorded ground motions covering a broad variety of condition in terms of frequency content, duration and amplitude will be used as input in the dynamic analyses. The records are obtained from 40 earthquakes and grouped as a function of magnitude of the event, source-to-site condition and site soil condition. In addition, in the data-set of records a considerable number of near-fault signals is included, in recognition of the particular significance of pulse-like time histories in causing large seismic demands to the structures.

Optimization of selected molecular orbitals in group basis sets.

PubMed

Ferenczy, György G; Adams, William H

2009-04-07

We derive a local basis equation which may be used to determine the orbitals of a group of electrons in a system when the orbitals of that group are represented by a group basis set, i.e., not the basis set one would normally use but a subset suited to a specific electronic group. The group orbitals determined by the local basis equation minimize the energy of a system when a group basis set is used and the orbitals of other groups are frozen. In contrast, under the constraint of a group basis set, the group orbitals satisfying the Huzinaga equation do not minimize the energy. In a test of the local basis equation on HCl, the group basis set included only 12 of the 21 functions in a basis set one might ordinarily use, but the calculated active orbital energies were within 0.001 hartree of the values obtained by solving the Hartree-Fock-Roothaan (HFR) equation using all 21 basis functions. The total energy found was just 0.003 hartree higher than the HFR value. The errors with the group basis set approximation to the Huzinaga equation were larger by over two orders of magnitude. Similar results were obtained for PCl(3) with the group basis approximation. Retaining more basis functions allows an even higher accuracy as shown by the perfect reproduction of the HFR energy of HCl with 16 out of 21 basis functions in the valence basis set. When the core basis set was also truncated then no additional error was introduced in the calculations performed for HCl with various basis sets. The same calculations with fixed core orbitals taken from isolated heavy atoms added a small error of about 10(-4) hartree. This offers a practical way to calculate wave functions with predetermined fixed core and reduced base valence orbitals at reduced computational costs. The local basis equation can also be used to combine the above approximations with the assignment of local basis sets to groups of localized valence molecular orbitals and to derive a priori localized orbitals. An appropriately chosen localization and basis set assignment allowed a reproduction of the energy of n-hexane with an error of 10(-5) hartree, while the energy difference between its two conformers was reproduced with a similar accuracy for several combinations of localizations and basis set assignments. These calculations include localized orbitals extending to 4-5 heavy atoms and thus they require to solve reduced dimension secular equations. The dimensions are not expected to increase with increasing system size and thus the local basis equation may find use in linear scaling electronic structure calculations.

Phase structure of NJL model with weak renormalization group

NASA Astrophysics Data System (ADS)

Aoki, Ken-Ichi; Kumamoto, Shin-Ichiro; Yamada, Masatoshi

2018-06-01

We analyze the chiral phase structure of the Nambu-Jona-Lasinio model at finite temperature and density by using the functional renormalization group (FRG). The renormalization group (RG) equation for the fermionic effective potential V (σ ; t) is given as a partial differential equation, where σ : = ψ bar ψ and t is a dimensionless RG scale. When the dynamical chiral symmetry breaking (DχSB) occurs at a certain scale tc, V (σ ; t) has singularities originated from the phase transitions, and then one cannot follow RG flows after tc. In this study, we introduce the weak solution method to the RG equation in order to follow the RG flows after the DχSB and to evaluate the dynamical mass and the chiral condensate in low energy scales. It is shown that the weak solution of the RG equation correctly captures vacuum structures and critical phenomena within the pure fermionic system. We show the chiral phase diagram on temperature, chemical potential and the four-Fermi coupling constant.

Annealing induced atomic rearrangements on (Ga,In) (N,As) probed by hard X-ray photoelectron spectroscopy and X-ray absorption fine structure.

PubMed

Ishikawa, Fumitaro; Higashi, Kotaro; Fuyuno, Satoshi; Morifuji, Masato; Kondow, Masahiko; Trampert, Achim

2018-04-13

We study the effects of annealing on (Ga 0.64 ,In 0.36 ) (N 0.045 ,As 0.955 ) using hard X-ray photoelectron spectroscopy and X-ray absorption fine structure measurements. We observed surface oxidation and termination of the N-As bond defects caused by the annealing process. Specifically, we observed a characteristic chemical shift towards lower binding energies in the photoelectron spectra related to In. This phenomenon appears to be caused by the atomic arrangement, which produces increased In-N bond configurations within the matrix, as indicated by the X-ray absorption fine structure measurements. The reduction in the binding energies of group-III In, which occurs concomitantly with the atomic rearrangements of the matrix, causes the differences in the electronic properties of the system before and after annealing.

SFG and AFM Studies of Polymer Surface Monolayers

NASA Astrophysics Data System (ADS)

Somorjai, Gabor A.

2003-03-01

Sum frequency generation vibrational spectroscopy and atomic force microscopy techniques were utilized to study the structure and composition of polymer surfaces ranging from polyethylene and polypropylene to copolymers of polyurethane and polystyrene. The surface methyl groups aligned perpendicular to the surface above the glass transition temperature of polypropylene. Large side groups such as the phenyl group on polystyrene is also near the surface normal at the polymer-air interface. At the air interface hydrophobic groups are dominant on the polymer surface while at solid-water interface hydrophilic groups segregate to the surface. Minimizing surface energy is the cause of readjusting the surface composition at polymer-water interfaces as compared to polymer-air interfaces. Upon stretching the soft component of two-component polymer systems segregates to the surface and both the surface structure and the surface composition undergo reversible or irreversible changes depending on the magnitude of the stretch. Since the heart beat forces bio-polymers to stretch over 40 million times a year the molecular behavior due to stretching has important physiological consequences.

A theory of self-organized zonal flow with fine radial structure in tokamak

NASA Astrophysics Data System (ADS)

Zhang, Y. Z.; Liu, Z. Y.; Xie, T.; Mahajan, S. M.; Liu, J.

2017-12-01

The (low frequency) zonal flow-ion temperature gradient (ITG) wave system, constructed on Braginskii's fluid model in tokamak, is shown to be a reaction-diffusion-advection system; it is derived by making use of a multiple spatiotemporal scale technique and two-dimensional (2D) ballooning theory. For real regular group velocities of ITG waves, two distinct temporal processes, sharing a very similar meso-scale radial structure, are identified in the nonlinear self-organized stage. The stationary and quasi-stationary structures reflect a particular feature of the poloidal group velocity. The equation set posed to be an initial value problem is numerically solved for JET low mode parameters; the results are presented in several figures and two movies that show the spatiotemporal evolutions as well as the spectrum analysis—frequency-wave number spectrum, auto power spectrum, and Lissajous diagram. This approach reveals that the zonal flow in tokamak is a local traveling wave. For the quasi-stationary process, the cycle of ITG wave energy is composed of two consecutive phases in distinct spatiotemporal structures: a pair of Cavitons growing and breathing slowly without long range propagation, followed by a sudden decay into many Instantons that carry negative wave energy rapidly into infinity. A spotlight onto the motion of Instantons for a given radial position reproduces a Blob-Hole temporal structure; the occurrence as well as the rapid decay of Caviton into Instantons is triggered by zero-crossing of radial group velocity. A sample of the radial profile of zonal flow contributed from 31 nonlinearly coupled rational surfaces near plasma edge is found to be very similar to that observed in the JET Ohmic phase [J. C. Hillesheim et al., Phys. Rev. Lett. 116, 165002 (2016)]. The theory predicts an interior asymmetric dipole structure associated with the zonal flow that is driven by the gradients of ITG turbulence intensity.

Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

PubMed

Rancova, Olga; Sulskus, Juozas; Abramavicius, Darius

2012-07-12

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

Crystal structure of methylprednisolone acetate form II, C 24H 32O 6

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

Wheatley, Austin M.; Kaduk, James A.; Gindhart, Amy M.

The crystal structure of methylprednisolone acetate form II, C 24H 32O 6, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Methylprednisolone acetate crystallizes in space groupP2 12 12 1(#19) witha= 8.17608(2),b= 9.67944(3),c= 26.35176(6) Å,V= 2085.474(6) Å 3, andZ= 4. Both hydroxyl groups act as hydrogen bond donors, resulting in a two-dimensional hydrogen bond network in theabplane. C–H…O hydrogen bonds also contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1412.

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

PubMed

Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

2015-07-30

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Raman scattering-based multiconformational analysis for probing the structural differences between acetylcholine and acetylthiocholine.

PubMed

Hernández, Belén; Houzé, Pascal; Pflüger, Fernando; Kruglik, Sergei G; Ghomi, Mahmoud

2017-05-10

Acetylcholine is the first discovered neurotransmitter that has received a great attention regarding its capability of binding to several cellular targets. The chemical composition of acetylcholine, including a positively charged trimethylammonium and a carbonyl group, as well as its conformational flexibility was pointed out as the key factors in the stabilization of its interactions. Here, the possibilities offered by a Raman scattering-based multiconformatioal analysis to access the most stable conformers of acetylcholine, is discussed. To control the validity of this protocol, acetylcholine and one of its closely structured analogues, acetylthiocholine, were simultaneously analyzed. Solution Raman spectra revealed distinct and well resolved strong markers for each molecule. Density functional theory calculations were consistent with the fact that the energy order of the low energy conformers is considerably affected by the acyloxy oxygen→sulfur atom substitution. Raman spectra were calculated on the basis of the thermal average of the spectra arising from the low energy conformers. It has been evidenced that the carbonyl and trimethylammonium groups are the most favorable hydration sites in aqueous environment. Taking into account the large gap between the carbonyl bond-stretch and aliphatic bending bands, Raman spectra also allowed separation of the HOH bending vibrations arising from the bound and bulk water molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

Reaction mechanisms at 4H-SiC/SiO2 interface during wet SiC oxidation

NASA Astrophysics Data System (ADS)

Akiyama, Toru; Hori, Shinsuke; Nakamura, Kohji; Ito, Tomonori; Kageshima, Hiroyuki; Uematsu, Masashi; Shiraishi, Kenji

2018-04-01

The reaction processes at the interface between SiC with 4H structure (4H-SiC) and SiO2 during wet oxidation are investigated by electronic structure calculations within the density functional theory. Our calculations for 4H-SiC/SiO2 interfaces with various orientations demonstrate characteristic features of the reaction depending on the crystal orientation of SiC: On the Si-face, the H2O molecule is stable in SiO2 and hardly reacts with the SiC substrate, while the O atom of H2O can form Si-O bonds at the C-face interface. Two OH groups are found to be at least necessary for forming new Si-O bonds at the Si-face interface, indicating that the oxidation rate on the Si-face is very low compared with that on the C-face. On the other hand, both the H2O molecule and the OH group are incorporated into the C-face interface, and the energy barrier for OH is similar to that for H2O. By comparing the calculated energy barriers for these reactants with the activation energies of oxide growth rate, we suggest the orientation-dependent rate-limiting processes during wet SiC oxidation.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

PubMed

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

2D lateral heterostructures of group-III monochalcogenide: Potential photovoltaic applications

NASA Astrophysics Data System (ADS)

Cheng, Kai; Guo, Yu; Han, Nannan; Jiang, Xue; Zhang, Junfeng; Ahuja, Rajeev; Su, Yan; Zhao, Jijun

2018-04-01

Solar photovoltaics provides a practical and sustainable solution to the increasing global energy demand. Using first-principles calculations, we investigate the energetics and electronic properties of two-dimensional lateral heterostructures by group-III monochalcogenides and explore their potential applications in photovoltaics. The band structures and formation energies from supercell calculations demonstrate that these heterostructures retain semiconducting behavior and might be synthesized in laboratory using the chemical vapor deposition technique. According to the computed band offsets, most of the heterojunctions belong to type II band alignment, which can prevent the recombination of electron-hole pairs. Besides, the electronic properties of these lateral heterostructures can be effectively tailored by the number of layers, leading to a high theoretical power conversion efficiency over 20%.

Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations

NASA Astrophysics Data System (ADS)

Hao, Ge-Fei; Tan, Ying; Yu, Ning-Xi; Yang, Guang-Fu

2011-03-01

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4), which has been identified as a significant target for a great family of herbicides with diverse chemical structures, is the last common enzyme responsible for the seventh step in the biosynthetic pathway to heme and chlorophyll. Among the existing PPO inhibitors, diphenyl-ether is the first commercial family of PPO inhibitors and used as agriculture herbicides for decades. Most importantly, diphenyl-ether inhibitors have been found recently to possess the potential in Photodynamic therapy (PDT) to treat cancer. Herein, molecular dynamics simulations, approximate free energy calculations and hydrogen bond energy calculations were integrated together to uncover the structure-activity relationships of this type of PPO inhibitors. The calculated binding free energies are correlated very well with the values derived from the experimental k i data. According to the established computational models and the results of approximate free energy calculation, the substitution effects at different position were rationalized from the view of binding free energy. Some outlier ( e.g. LS) in traditional QSAR study can also be explained reasonably. In addition, the hydrogen bond energy calculation and interaction analysis results indicated that the carbonyl oxygen on position-9 and the NO2 group at position-8 are both vital for the electrostatic interaction with Arg98, which made a great contribution to the binding free energy. These insights from computational simulations are not only helpful for understanding the molecular mechanism of PPO-inhibitor interactions, but also beneficial to the future rational design of novel promising PPO inhibitors.

New applications of renormalization group methods in nuclear physics.

PubMed

Furnstahl, R J; Hebeler, K

2013-12-01

We review recent developments in the use of renormalization group (RG) methods in low-energy nuclear physics. These advances include enhanced RG technology, particularly for three-nucleon forces, which greatly extends the reach and accuracy of microscopic calculations. We discuss new results for the nucleonic equation of state with applications to astrophysical systems such as neutron stars, new calculations of the structure and reactions of finite nuclei, and new explorations of correlations in nuclear systems.

Mitochondrial energy metabolism dysfunction involved in reproductive toxicity of mice caused by endosulfan and protective effects of vitamin E.

PubMed

Wang, Na; Qian, Hong-Yan; Zhou, Xian-Qing; Li, Yan-Bo; Sun, Zhi-Wei

2012-08-01

The experiment was designed to study the mechanism of reproductive toxicity caused by endosulfan in mice and protective effects of vitamin E. The experiment was composed of three groups: the control group did not receive any endosulfan and vitamin E; the endosulfan exposed group received 0.8 mg/kg/d endosulfan and 0mg/kg/d vitamin E; and the endosulfan+vitamin E group received 0.8 mg/kg/d endosulfan and 100mg/kg/d vitamin E. The results showed that vitamin E significantly reversed the decline of the concentration and motility rate of sperm, and inhibited the increase of sperm abnormality rate caused by endosulfan. The activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), and lactate dehydrogenase-C4 (LDH-C4) and the level of adenosine triphosphate (ATP) in the endosulfan+vitamin E group were higher while the malondialdehyde (MDA) content was significantly lower than those of the endosulfan exposed group. The results from pathology and electron microscope observed showed vitamin E decreased the cavities formation by desquamating of spermatogenic cells, stopped the ruptures and disappearances of mitochondrial cristaes in spermatogenic cells, and prevented the breakages and partial dissolvings of sperm tails induced by endosulfan. It is likely that endosulfan could directly damage sperm structures by oxidative stress, leading to a decrease in sperm quantity and quality. It also could indirectly cause a decline in reproductive function by damaging the structure of mitochondria, resulting in energy metabolism dysfunction, which could be one of the mechanisms behind the reproductive toxicity induced by endosulfan. It was inferred that vitamin E helps maintain the structural integrities of sperm architecture and prevent mitochondrial dysfunction through inhibiting oxidative stress, and thereby prevent the reproductive dysfunctions caused by endosulfan. Copyright © 2012 Elsevier Inc. All rights reserved.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

NASA Astrophysics Data System (ADS)

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-01

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Integrated Multi-Color Light Emitting Device Made with Hybrid Crystal Structure

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang Hyouk (Inventor)

2017-01-01

An integrated hybrid crystal Light Emitting Diode ("LED") display device that may emit red, green, and blue colors on a single wafer. The various embodiments may provide double-sided hetero crystal growth with hexagonal wurtzite III-Nitride compound semiconductor on one side of (0001) c-plane sapphire media and cubic zinc-blended III-V or II-VI compound semiconductor on the opposite side of c-plane sapphire media. The c-plane sapphire media may be a bulk single crystalline c-plane sapphire wafer, a thin free standing c-plane sapphire layer, or crack-and-bonded c-plane sapphire layer on any substrate. The bandgap energies and lattice constants of the compound semiconductor alloys may be changed by mixing different amounts of ingredients of the same group into the compound semiconductor. The bandgap energy and lattice constant may be engineered by changing the alloy composition within the cubic group IV, group III-V, and group II-VI semiconductors and within the hexagonal III-Nitrides.

Integrated Multi-Color Light Emitting Device Made with Hybrid Crystal Structure

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang Hyouk (Inventor)

2016-01-01

An integrated hybrid crystal Light Emitting Diode ("LED") display device that may emit red, green, and blue colors on a single wafer. The various embodiments may provide double-sided hetero crystal growth with hexagonal wurtzite III-Nitride compound semiconductor on one side of (0001) c-plane sapphire media and cubic zinc-blended III-V or II-VI compound semiconductor on the opposite side of c-plane sapphire media. The c-plane sapphire media may be a bulk single crystalline c-plane sapphire wafer, a thin free standing c-plane sapphire layer, or crack-and-bonded c-plane sapphire layer on any substrate. The bandgap energies and lattice constants of the compound semiconductor alloys may be changed by mixing different amounts of ingredients of the same group into the compound semiconductor. The bandgap energy and lattice constant may be engineered by changing the alloy composition within the cubic group IV, group III-V, and group II-VI semiconductors and within the hexagonal III-Nitrides.

Local expansion flows of galaxies: quantifying acceleration effect of dark energy

NASA Astrophysics Data System (ADS)

Chernin, A. D.; Teerikorpi, P.

2013-08-01

The nearest expansion flow of galaxies observed around the Local group is studied as an archetypical example of the newly discovered local expansion flows around groups and clusters of galaxies in the nearby Universe. The flow is accelerating due to the antigravity produced by the universal dark energy background. We introduce a new acceleration measure of the flow which is the dimensionless ``acceleration parameter" Q (x) = x - x-2 depending on the normalized distance x only. The parameter is zero at the zero-gravity distance x = 1, and Q(x) ∝ x, when x ≫ 1. At the distance x = 3, the parameter Q = 2.9. Since the expansion flows have a self-similar structure in normalized variables, we expect that the result is valid as well for all the other expansion flows around groups and clusters of galaxies on the spatial scales from ˜ 1 to ˜ 10 Mpc everywhere in the Universe.

A computational analysis of the binding model of MDM2 with inhibitors

NASA Astrophysics Data System (ADS)

Hu, Guodong; Wang, Dunyou; Liu, Xinguo; Zhang, Qinggang

2010-08-01

It is a new and promising strategy for anticancer drug design to block the MDM2-p53 interaction using a non-peptide small-molecule inhibitor. We carry out molecular dynamics simulations to study the binding of a set of six non-peptide small-molecule inhibitors with the MDM2. The relative binding free energies calculated using molecular mechanics Poisson-Boltzmann surface area method produce a good correlation with experimentally determined results. The study shows that the van der Waals energies are the largest component of the binding free energy for each complex, which indicates that the affinities of these inhibitors for MDM2 are dominated by shape complementarity. The A-ligands and the B-ligands are the same except for the conformation of 2,2-dimethylbutane group. The quantum mechanics and the binding free energies calculation also show the B-ligands are the more possible conformation of ligands. Detailed binding free energies between inhibitors and individual protein residues are calculated to provide insights into the inhibitor-protein binding model through interpretation of the structural and energetic results from the simulations. The study shows that G1, G2 and G3 group mimic the Phe19, Trp23 and Leu26 residues in p53 and their interactions with MDM2, but the binding model of G4 group differs from the original design strategy to mimic Leu22 residue in p53.

Atomization methods for forming magnet powders

DOEpatents

Sellers, Charles H.; Branagan, Daniel J.; Hyde, Timothy A.

2000-01-01

The invention encompasses methods of utilizing atomization, methods for forming magnet powders, methods for forming magnets, and methods for forming bonded magnets. The invention further encompasses methods for simulating atomization conditions. In one aspect, the invention includes an atomization method for forming a magnet powder comprising: a) forming a melt comprising R.sub.2.1 Q.sub.13.9 B.sub.1, Z and X, wherein R is a rare earth element; X is an element selected from the group consisting of carbon, nitrogen, oxygen and mixtures thereof; Q is an element selected from the group consisting of Fe, Co and mixtures thereof; and Z is an element selected from the group consisting of Ti, Zr, Hf and mixtures thereof; b) atomizing the melt to form generally spherical alloy powder granules having an internal structure comprising at least one of a substantially amorphous phase or a substantially nanocrystalline phase; and c) heat treating the alloy powder to increase an energy product of the alloy powder; after the heat treatment, the alloy powder comprising an energy product of at least 10 MGOe. In another aspect, the invention includes a magnet comprising R, Q, B, Z and X, wherein R is a rare earth element; X is an element selected from the group consisting of carbon, nitrogen, oxygen and mixtures thereof; Q is an element selected from the group consisting of Fe, Co and mixtures thereof; and Z is an element selected from the group consisting of Ti, Zr, Hf and mixtures thereof; the magnet comprising an internal structure comprising R.sub.2.1 Q.sub.13.9 B.sub.1.

Assessment of Ca and P content variation in enamel during an eight-week bleaching protocol using energy dispersive X-ray fluorescence

NASA Astrophysics Data System (ADS)

Sorozini, M.; Dos Santos, R. S.; Silva, E. M.; Dos Anjos, M. J.; Perez, C. R.

2017-05-01

Tooth bleaching is a simple technique performed with gels based on hydrogen peroxide molecules responsible for removing the tooth structure's pigmentation. The effects of the overuse of these agents on the tooth structure are not well established. Energy dispersive X-ray fluorescence (EDXRF) can be employed to analyze objects of biological origin as bone and tooth. It is very suitable analytical technique to detect demineralization processes in these tissues. The objective of this study was to use x-ray fluorescence to evaluate the effects on mineral content of enamel submitted to eight-week protocols of home bleaching gels (10% carbamide peroxide and 9.5% hydrogen peroxide), as well as bleaching strips. Four enamel fragments obtained from five teeth were subjected to bleaching for 8 weeks: Group 1- artificial saliva; Group 2-10% carbamide peroxide gel, 6 h daily; Group 3-9.5% hydrogen peroxide gel, two 30-minute applications; and Group 4-bleaching strips, twice daily for 30 min. The change in mineral content was assessed weekly using X-ray fluorescence (Artax 200). Differences were basically found in Group 4 for the concentrations of Ca and P after treatment with bleaching strips containing 10% hydrogen peroxide. For the Ca/P ratio, the differences were found in Group 2-15% carbamide peroxide (p < 0.05). X-ray fluorescence proved to be a suitable method for the evaluation of the mineral content, presenting the advantage of being able to evaluate the same area at different stages of the methodology.

Predicted electric-field-induced hexatic structure in an ionomer membrane

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.

2009-08-01

Coarse-grained molecular-dynamics simulations were used to study the morphological changes induced in a Nafion®-like ionomer by the imposition of a strong electric field. We observe the formation of structures aligned along the direction of the applied field. The polar head groups of the ionomer sidechains aggregate into clusters, which then form rodlike formations which assemble into a hexatic array aligned with the direction of the field. Occasionally these lines of sulfonates and protons form a helical structure. Upon removal of the electric field, the hexatic array of rodlike structures persists and has a lower calculated free energy than the original isotropic morphology.

Development of the relaxation-assisted 2DIR method for accessing structures of molecules and its application for studying the energy transport on a molecular level

NASA Astrophysics Data System (ADS)

Kasyanenko, Valeriy Mitrofanovich

Measuring the three-dimensional structure of molecules, dynamics of structural changes, and energy transport on a molecular scale is important for many areas of natural science. Supplementing the widely used methods of x-ray diffraction, NMR, and optical spectroscopies, a two-dimensional infrared spectroscopy (2DIR) method was introduced about a decade ago. The 2DIR method measures pair-wise interactions between vibrational modes in molecules, thus acquiring molecular structural constraints such as distances between vibrating groups and the angles between their transition dipoles. The 2DIR method has been applied to a variety of molecular systems but in studying larger molecules such as proteins and peptides the method is facing challenges associated with the congestion of their vibrational spectra and delocalized character of their vibrational modes. To help extract structural information from such spectra and make efficient use of vibrational modes separated by large distances, a novel relaxation-assisted 2DIR method (RA 2DIR) has recently been proposed, which exploits the transport of excess vibrational energy from the initially excited mode. With the goal of further development of RA 2DIR, we applied it to a variety of molecular systems, including model compounds, transition-metal complexes, and isomers. The experiments revealed several novel effects which both enhance the power of RA 2DIR and bring a deeper understanding to the fundamental process of energy transport on a molecular level. We demonstrated that RA 2DIR can enhance greatly (27-fold) the cross-peak amplitude among spatially remote modes, which leads to an increase of the range of distances accessible for structural measurements by several fold. We demonstrated that the energy transport time correlates with the intermode distance. This correlation offers a new way for identifying connectivity patterns in molecules. We developed two models of energy transport in molecules. In one, a spatial overlap of vibrational modes determines the rate of energy transfer. Another model uses generalizations of Marcus theory of electron transfer applied to anharmonic vibrational transitions. These theoretical models reproduce well the main features of RA 2DIR measurements in a set of isomers where the energy transport is found to be affected by the three-dimensional structure as well as in transition-metal complexes, where the energy transport has to go through relatively weak coordination bonds and can be different from that occurring via covalent bonds.

Economic impact of nutritional grouping in dairy herds.

PubMed

Kalantari, A S; Armentano, L E; Shaver, R D; Cabrera, V E

2016-02-01

This article evaluates the estimated economic impact of nutritional grouping in commercial dairy herds using a stochastic Monte Carlo simulation model. The model was initialized by separate data sets obtained from 5 commercial dairy herds. These herds were selected to explore the effect of herd size, structure, and characteristics on the economics and efficiency of nutrient usage according to nutritional grouping strategies. Simulated status of each cow was updated daily together with the nutrient requirements of net energy for lactation (NEL) and metabolizable protein (MP). The amount of energy consumed directly affected body weight (BW) and body condition score (BCS) changes. Moreover, to control the range of observed BCS in the model, constraints on lower (2.0) and upper (4.5) bounds of BCS were set. Each month, the clustering method was used to homogeneously regroup the cows according to their nutrient concentration requirements. The average NEL concentration of the group and a level of MP (average MP, average MP+0.5SD, or average MP+1SD) were considered to formulate the group diet. The calculated income over feed costs gain (IOFC, $/cow per yr) of having >1 nutritional group among the herds ranged from $33 to $58, with an average of $39 for 2 groups and $46 for 3 groups, when group was fed at average NEL concentration and average MP+1SD concentration. The improved IOFC was explained by increased milk sales and lower feed costs. Higher milk sales were a result of fewer cows having a milk loss associated with low BCS in multi-group scenarios. Lower feed costs in multi-group scenarios were mainly due to less rumen-undegradable protein consumption. The percentage of total NEL consumed captured in milk for >1 nutritional group was slightly lower than that for 1 nutritional group due to better distribution of energy throughout the lactation and higher energy retained in body tissue, which resulted in better herd BCS distribution. The percentage of fed N captured in milk increased with >1 group and was the most important factor for improved economic efficiency of grouping strategies. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Octahedral tilt transitions in the relaxor ferroelectric Na{sub 1/2}Bi{sub 1/2}TiO{sub 3}

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

Meyer, Kai-Christian, E-mail: meyer@mm.tu-darmstadt.de; Gröting, Melanie; Albe, Karsten

2015-07-15

The kinetics of octahedral tilt transitions in the lead-free relaxor material sodium bismuth titanate Na{sub 1/2}Bi{sub 1/2}TiO{sub 3} (NBT) is investigated by electronic structure calculations within density functional theory. Energy barriers for transitions between tetragonal, rhombohedral and orthorhombic tilts in cation configurations with [001]- and [111]-order on the A-sites are determined by nudged elastic band calculations. By tilting entire layers of octahedra simultaneously we find that the activation energy is lower for structures with 001-order compared to such with 111-order. The energetic coupling between differently tilted layers is, however, negligibly small. By introducing a single octahedral defect we create localmore » tilt disorder and find that the deformation energy of the neighboring octahedra is less in a rhombohedral than in a tetragonal structure. By successively increasing the size of clusters of orthorhombic defects in a rhombohedral matrix with 001-order, we determine a critical cluster size of about 40 Å . Thus groups of about ten octahedra can be considered as nuclei for polar nanoregions, which are the cause of the experimentally observed relaxor behavior of NBT. - Graphical abstract: Nine orthorhombic oxygen octahedral tilt defects in a rhombohedral tilt configuration. - Highlights: • Chemical order influences energy barriers of octahedral tilt transitions. • The octahedral deformation energy is lower in rhombohedral phases. • Tilt defect clusters are more likely in rhombohedral structures. • Tilt defect clusters can act as nuclei for polar nanoregions.« less

Investigation of low-loss spectra and near-edge fine structure of polymers by PEELS

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

Heckmann, W.

Transmission electron microscopy has changed from a purely imaging method to an analytical method. This has been facilitated particularly by equipping electron microscopes with energy filters and with parallel electron energy loss spectrometers (PEELS). Because of their relatively high energy resolution (1 to 2 eV) they provide information not only on the elements present but also on the type of bonds between the molecular groups. Polymers are radiation sensitive and the molecular bonds change as the spectrum is being recorded. This can be observed with PEEL spectrometers that are able to record spectra with high sensitivity and in rapid succession.

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

NASA Astrophysics Data System (ADS)

Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

2017-04-01

We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms . Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

Energy structure of MHD flow coupling with outer resistance circuit

NASA Astrophysics Data System (ADS)

Huang, Z. Y.; Liu, Y. J.; Chen, Y. Q.; Peng, Z. L.

2015-08-01

Energy structure of MHD flow coupling with outer resistance circuit is studied to illuminate qualitatively and quantitatively the energy relation of this basic MHD flow system with energy input and output. Energy structure are analytically derived based on the Navier-Stocks equations for two-dimensional fully-developed flow and generalized Ohm's Law. The influences of applied magnetic field, Hall parameter and conductivity on energy structure are discussed based on the analytical results. Associated energies in MHD flow are deduced and validated by energy conservation. These results reveal that energy structure consists of two sub structures: electrical energy structure and internal energy structure. Energy structure and its sub structures provide an integrated theoretical energy path of the MHD system. Applied magnetic field and conductivity decrease the input energy, dissipation by fluid viscosity and internal energy but increase the ratio of electrical energy to input energy, while Hall parameter has the opposite effects. These are caused by their different effects on Bulk velocity, velocity profiles, voltage and current in outer circuit. Understanding energy structure helps MHD application designers to actively adjust the allocation of different parts of energy so that it is more reasonable and desirable.

Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations

NASA Astrophysics Data System (ADS)

McCarrick, Margaret A.; Kollman, Peter A.

1999-03-01

The relative binding free energies in HIV protease of haloperidol thioketal (THK) and three of its derivatives were examined with free energy calculations. THK is a weak inhibitor (IC50 = 15 μM) for which two cocrystal structures with HIV type 1 proteases have been solved [Rutenber, E. et al., J. Biol. Chem., 268 (1993) 15343]. A THK derivative with a phenyl group on C2 of the piperidine ring was expected to be a poor inhibitor based on experiments with haloperidol ketal and its 2- phenyl derivative (Caldera, P., personal communication). Our calculations predict that a 5-phenyl THK derivative, suggested based on examination of the crystal structure, will bind significantly better than THK. Although there are large error bars as estimated from hysteresis, the calculations predict that the 5-phenyl substituent is clearly favored over the 2-phenyl derivative as well as the parent compound. The unfavorable free energies of solvation of both phenyl THK derivatives relative to the parent compound contributed to their predicted binding free energies. In a third simulation, the change in binding free energy for 5-benzyl THK relative to THK was calculated. Although this derivative has a lower free energy in the protein, its decreased free energy of solvation increases the predicted ΔΔG(bind) to the same range as that of the 2-phenyl derivative.

Low-energy and very-low energy total cross sections for electron collisions with N2

NASA Astrophysics Data System (ADS)

Kitajima, Masashi; Kishino, Takaya; Okumura, Takuma; Kobayashi, Naomasa; Sayama, Atsushi; Mori, Yuma; Hosaka, Kouichi; Odagiri, Takeshi; Hoshino, Masamitsu; Tanaka, Hiroshi

2017-06-01

Absolute grand total cross sections for electron scattering from N2 are obtained in the energy range from 20 eV down to 5 meV with very narrow electron energy width of 9 meV using the threshold-photoelectron source. Total cross sections obtained in the present study are compared with the previous experimentally obtained results. At the very-low energy region below 50 meV, the present total cross sections are somewhat smaller than those reported by the Aarhus group [S.V. Hoffmann et al., Rev. Sci. Instrum. 73, 4157 (2002)], which has been the only experimental work that provided the total cross sections in the very-low energy region. The energy positions of the peaks in the total cross sections due to the 2Πg shape resonance are obtained with higher accuracy, due to the improved uncertainty of the energy position in the present measurement compared to the previous works. The resonance structure in the total cross sections due to the Feshbach resonances of N2 at around 11.5 eV are also observed. Analysis of the resonant structure was carried out in order to determine the values of resonance width of Feshbach resonances of N2. Contribution to the Topical Issue: "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

Molecular simulation of dispersion and mechanical stability of organically modified layered silicates in polymer matrices

NASA Astrophysics Data System (ADS)

Fu, Yao-Tsung

The experimental analysis of nanometer-scale separation processes and mechanical properties at buried interfaces in nanocomposites has remained difficult. We have employed molecular dynamics simulation in relation to available experimental data to alleviate such limitations and gain insight into the dispersion and mechanical stability of organically modified layered silicates in hydrophobic polymer matrices. We analyzed cleavage energies of various organically modified silicates as a function of the cation exchange capacity, surfactant head group chemistry, and chain length using MD simulations with the PCFF-PHYLLOSILICATE force field. The range of the cleavage energy is between 25 and 210 mJ/m2 upon the molecular structures and packing of surfactants. As a function of chain length, the cleavage energy indicates local minima for interlayer structures comprised of loosely packed layers of alkyl chains and local maxima for interlayer structures comprised of densely packed layers of alkyl chains between the layers. In addition, the distribution of cationic head groups between the layers in the equilibrium state determines whether large increases in cleavage energy due to Coulomb attraction. We have also examined mechanical bending and failure mechanisms of layered silicates on the nanometer scale using molecular dynamics simulation in comparison to a library of TEM data of polymer nanocomposites. We investigated the energy of single clay lamellae as a function of bending radius and different cation density. The layer energy increases particularly for bending radii below 20 nm and is largely independent of cation exchange capacity. The analysis of TEM images of agglomerated and exfoliated aluminosilicates of different CEC in polymer matrices at small volume fractions showed bending radii in excess of 100 nm due to free volumes in the polymer matrix. At a volume fraction >5%, however, bent clay layers were found with bending radii <20 nm and kinks as a failure mechanism in good agreement with simulation results. We have examined thermal conductivity of organically modified layered silicates using molecular dynamics simulation in comparison to experimental results by laser measurement. The thermal conductivity slightly increased from 0.08 to 0.14 Wm-1K-1 with increasing chain length, related to the gallery spacing and interlayer density of the organic material.

Contribution of energy values to the analysis of global searching molecular dynamics simulations of transmembrane helical bundles.

PubMed Central

Torres, Jaume; Briggs, John A G; Arkin, Isaiah T

2002-01-01

Molecular interactions between transmembrane alpha-helices can be explored using global searching molecular dynamics simulations (GSMDS), a method that produces a group of probable low energy structures. We have shown previously that the correct model in various homooligomers is always located at the bottom of one of various possible energy basins. Unfortunately, the correct model is not necessarily the one with the lowest energy according to the computational protocol, which has resulted in overlooking of this parameter in favor of experimental data. In an attempt to use energetic considerations in the aforementioned analysis, we used global searching molecular dynamics simulations on three homooligomers of different sizes, the structures of which are known. As expected, our results show that even when the conformational space searched includes the correct structure, taking together simulations using both left and right handedness, the correct model does not necessarily have the lowest energy. However, for the models derived from the simulation that uses the correct handedness, the lowest energy model is always at, or very close to, the correct orientation. We hypothesize that this should also be true when simulations are performed using homologous sequences, and consequently lowest energy models with the right handedness should produce a cluster around a certain orientation. In contrast, using the wrong handedness the lowest energy structures for each sequence should appear at many different orientations. The rationale behind this is that, although more than one energy basin may exist, basins that do not contain the correct model will shift or disappear because they will be destabilized by at least one conservative (i.e. silent) mutation, whereas the basin containing the correct model will remain. This not only allows one to point to the possible handedness of the bundle, but can be used to overcome ambiguities arising from the use of homologous sequences in the analysis of global searching molecular dynamics simulations. In addition, because clustering of lowest energy models arising from homologous sequences only happens when the estimation of the helix tilt is correct, it may provide a validation for the helix tilt estimate. PMID:12023229

Structural Dynamics in Metal Tris-hydroxyquinolines: Interconversion of Meridianal and Facial Alq3 Isomers

NASA Astrophysics Data System (ADS)

Ferris, Kim; Sapochak, Linda; Burrows, Paul; Rodovsky, Deanna; Marmolejo, Theresa

2004-03-01

While previous work investigating the charge transport properties of Alq3 has indicated that the meridianal (mer) conformation of Alq3 is predominant species, recent work suggesting identification of a facial (fac) form raises again the question of heterogeneity. Electronic structure computations from our group have noted that the energy difference(in parenthesis) between the mer and fac conformations is highly sensitive to basis set description (8.6 kcal/mol//3-21g*/SCF; 6.9 kcal/mol//6-31g*/SCF), electron correlation (6.0 kcal/mol//3-21g*/MP2; 4.7 kcal/mol//6-31g*/MP2), and solvent effects (4.4 kcal/mol/3-21g*/SCF/DMSO). Given these small energy differences, we have conducted a series of Hartree-Fock and first principles electronic structure computations on the interconversion of these structural forms, and will report on the structural and energetic aspects of the transformation. The likely reaction path involves lengthening of the Al-N bond to the point where a pentacoordinate intermediate or transition state would be formed, followed by flipping of the ligand through rotation around the Al-O bond. Following Schmidbauer's earlier work, we note that transformation involving only one ligand will actually lead to a facial isomer. Preliminary characterization of this transition state suggests that the activation energy is approximately 20-25 kcal/mol above the mer conformation. The authors gratefully acknowledge financial support from PNNL Laboratory Directed Research and Development Project and the U.S. Department of Energy, Office of Science, Materials Sciences Division.

Impact of an Energy Drink on the Structure of Stomach and Pancreas of Albino Rat: Can Omega-3 Provide a Protection?

PubMed

Ayuob, Nasra; ElBeshbeishy, Rana

2016-01-01

A controversy developed between the benefits of energy drinks (EDs) versus the possible health threats since its revolution. Lack of information was a call to assess the effect of chronic consumption of Power Horse (PH) as one of the EDs, on the structure of pancreas and fundic mucosa of stomach in rats, and possible protective role of Omega-3. Thirty two adult male albino rats were divided equally into 4 groups; control received group which only received a standard diet, Omega-3 group, PH group which given PH and PH plus Omega-3 group received both PH plus Omega-3 for 4 weeks. Biochemical assessment of blood glucose, serum insulin, gastrin, tumor necrosis factor alpha (TNF-α) and inducible nitric oxide synthetase (iNOS) was performed. The antioxidant activity and histopathological examination of both pancreatic tissue and fundic mucosa of stomach were assessed. Administration of PH significantly increased serum insulin and glucose levels while it significantly reduced serum gastrin level compared to control. PH also caused oxidants/antioxidants imbalance in both pancreas and fundic mucosa. The latter revealed degenerative changes and increased apoptosis which was evident by increased caspase-3 immunoexpression. Pancreas exhibited signs of β-cells overstimulation. Fundic mucosa showed reduced number of parietal cells, gastrin hormone expression compared to control group. Omega-3 administration could alleviate, to some extent, these changes. It significantly decreased TNF-α, iNOS and reduced glutathione (GSH) as well as significantly increasing superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities compared to the group which received PH alone. Power Horse intake significantly injures islet cells, pancreatic acini as well as the glandular cells of the fundic mucosa. Omega-3 decreases these detrimental effects mostly through its antioxidant and anti-inflammatory action.

Lead optimization mapper: automating free energy calculations for lead optimization.

PubMed

Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P; Summa, Christopher M; Jaber, Vivian R; Lim, Nathan M; Mobley, David L

2013-09-01

Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license.

Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters

PubMed Central

Zhang, Minhua; Bao, Zhihao; Zhao, Qin; Guo, Hui; Xu, Ke; Wang, Chengcheng

2014-01-01

Energy-coupling factor (ECF) transporters are a unique group of ATP-binding cassette (ABC) transporters responsible for micronutrient uptake from the environment. Each ECF transporter is composed of an S component (or EcfS protein) and T/A/A′ components (or EcfT/A/A′ proteins; ECF module). Among the group II ECF transporters, several EcfS proteins share one ECF module; however, the underlying mechanism remains unknown. Here we report the structure of a group II ECF transporter–pantothenate transporter from Lactobacillus brevis (LbECF-PanT), which shares the ECF module with the folate and hydroxymethylpyrimidine transporters (LbECF-FolT and LbECF-HmpT). Structural and mutational analyses revealed the residues constituting the pantothenate-binding pocket. We found that although the three EcfS proteins PanT, FolT, and HmpT are dissimilar in sequence, they share a common surface area composed of the transmembrane helices 1/2/6 (SM1/2/6) to interact with the coupling helices 2/3 (CH2/3) of the same EcfT. CH2 interacts mainly with SM1 via hydrophobic interactions, which may modulate the sliding movement of EcfS. CH3 binds to a hydrophobic surface groove formed by SM1, SM2, and SM6, which may transmit the conformational changes from EcfA/A′ to EcfS. We also found that the residues at the intermolecular surfaces in LbECF-PanT are essential for transporter activity, and that these residues may mediate intermolecular conformational transmission and/or affect transporter complex stability. In addition, we found that the structure of EcfT is conformationally dynamic, which supports its function as a scaffold to mediate the interaction of the ECF module with various EcfS proteins to form different transporter complexes. PMID:25512487

Small Water Cluster Cations

NASA Astrophysics Data System (ADS)

Novakovskaya, Yu. V.; Stepanov, N. F.

Structures of water cluster cations (H_{2}O)^{+}_{n} with n ≤ 5 are optimized at the unrestricted Hartree-Fock level with the 4 - 31 + +G** basis set. Energetic characteristics of the cations are then estimated taking into account the second order perturbation corrections (MP2). After the electron detachment from a neutral cluster, the structure of the latter substantially changes, so that OH and H3O+ fragments can be distinguished in it. In some cations H3O+ is so strongly bonded to water molecules that it is reasonable to speak of the [H2n-1On-1]+ fragments. According to the position of OH, the structures form two groups. In one group, OH acts exclusively as the proton acceptor in H-bonds with water molecules, thus being terminal in the chain-like structures; in the other group it is directly bonded to H3O and, as a proton donor, forms an H-bond with water molecule. Cluster cations do not tend to dissociate into the fragments. However, an external influence of ≤ 0.4 eV is sufficient for the cations of the first group to dissociate into a free OH radical and a protonated cluster H+(H2O)n-1. Extrapolation of the calculated adiabatic ionization potentials of the water clusters to n → ∞ provides a value of 8.6 eV, which can be considered as an estimation of the electron work function of water. This value is close to the experimental photoelectric thresholds of amorphous ice (8.7 ± 0.1 eV) and water (9.39 ± 0.3 eV). Solvation of the electron lowers the value, and an energy of 7 eV can be sufficient for initiating conductivity. This prediction is in accord with the experiment: irradiating ice with ultraviolet light of the photon energy 6.5-6.8 eV initiates photoconductivity, and hydrogen peroxide and H3O+ ions are observed.

Excitonic states and defect physics of two-dimensional group-IV monochalcogenides.

NASA Astrophysics Data System (ADS)

Gomes, Lidia; Carvalho, Alexandra; Trevisanutto, Paolo; Rodin, Aleksandr; Neto, Antonio

Layered group-IV monochalcogenides have become an important group of materials within the ever-growing family of two-dimensional crystals. Among the binary IV-VI compounds, SnS, SnSe, GeS, and GeSe form a subgroup with orthorhombic structure which has shown exciting particularities and has been considered of high potential for numerous application. We give a brief overview of some important properties of the 2D form of this group and focus on recent results addressing the excitonic properties and the impact of the introduction of point defects on their structures. Vacancies and oxygen defects are modeled using first principles calculations. Energetic and structural analysis of five different models for chemisorbed oxygen atoms, reveals a better resistance of these materials to oxidation if compared to their isostructural partner, phosphorene. We also discuss a parallel work where quasi-particle band structure and excitonic properties of GeS and GeSe monolayers are investigated through ab initio GW and Bethe-Salpeter equation calculations. Within the main results, we show that the optical spectra of both materials are dominated by excitonic effects, however, GeS presents a remarkably larger binding energy of 1 eV. NRF-CRP award Novel 2D materials with tailored properties: beyond graphene (R-144-000-295-281) 1.

Thermal, structural, functional, optical and magnetic studies of pure and Ba doped CdO nanoparticles.

PubMed

Sivakumar, S; Venkatesan, A; Soundhirarajan, P; Khatiwada, Chandra Prasad

2015-12-05

In this research, a chemical precipitation method was used to synthesize undoped and doped cadmium oxide nanoparticles and studied by TG-DTA, XRD, FT-IR, SEM, with EDX and antibacterial activities, respectively. The melting points, thermal stability and the kinetic parameters like entropy (ΔS), enthalpy (ΔH), Gibb's energy (ΔG), activation energy (E), frequency factor (A) were evaluated from TG-DTA measurements. X-ray diffraction analysis (XRD) brought out the information about the synthesized products exist in spherical in shape with cubic structure. The functional groups and band area of the samples were established by Fourier transform infrared (FT-IR) spectroscopy. The direct and indirect band gap energy of pure and doped samples were determined by UV-Vis-DRS. The surface morphological, elemental compositions and particles sizes were evaluated by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Finally, antibacterial activities indicated the Gram-positive and Gram-negative bacteria are more active in transporter, dehydrogenize and periplasmic enzymatic activities of pure and doped samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Discrete kinetic models from funneled energy landscape simulations.

PubMed

Schafer, Nicholas P; Hoffman, Ryan M B; Burger, Anat; Craig, Patricio O; Komives, Elizabeth A; Wolynes, Peter G

2012-01-01

A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

Molecular design of novel fullerene-based acceptors for enhancing the open circuit voltage in polymer solar cells

NASA Astrophysics Data System (ADS)

Tajbakhsh, Mahmood; Kariminasab, Mohaddeseh; Ganji, Masoud Darvish; Alinezhad, Heshmatollah

2017-12-01

Organic solar cells, especially bulk hetero-junction polymer solar cells (PSCs), are the most successful structures for applications in renewable energy. The dramatic improvement in the performance of PSCs has increased demand for new conjugated polymer donors and fullerene derivative acceptors. In the present study, quantum chemical calculations were performed for several representative fullerene derivatives in order to determine their frontier orbital energy levels and electronic structures, thereby helping to enhance their performance in PSC devices. We found correlations between the theoretical lowest unoccupied molecular orbital levels and electrophilicity index of various fullerenes with the experimental open circuit voltage of photovoltaic devices according to the poly(3-hexylthiophene) (P3HT):fullerene blend. The correlations between the structure and descriptors may facilitate screening of the best fullerene acceptor for the P3HT donor. Thus, we considered fullerenes with new functional groups and we predicted the output factors for the corresponding P3HT:fullerene blend devices. The results showed that fullerene derivatives based on thieno-o-quinodimethane-C60 with a methoxy group will have enhanced photovoltaic properties. Our results may facilitate the design of new fullerenes and the development of favorable acceptors for use in photovoltaic applications.

Valence-Band Electronic Structures of High-Pressure-Phase PdF2-type Platinum-Group Metal Dioxides MO2 (M = Ru, Rh, Ir, and Pt)

NASA Astrophysics Data System (ADS)

Soda, Kazuo; Kobayashi, Daichi; Mizui, Tatsuya; Kato, Masahiko; Shirako, Yuichi; Niwa, Ken; Hasegawa, Masashi; Akaogi, Masaki; Kojitani, Hiroshi; Ikenaga, Eiji; Muro, Takayuki

2018-04-01

The valence-band electronic structures of high-pressure-phase PdF2-type (HP-PdF2-type) platinum-group metal dioxides MO2 (M = Ru, Rh, Ir, and Pt) were studied by synchrotron radiation photoelectron spectroscopy and first-principles calculations. The obtained photoelectron spectra for HP-PdF2-type RuO2, RhO2, and IrO2 agree well with the calculated valence-band densities of states (DOSs) for these compounds, indicating their metallic properties, whereas the DOS of HP-PdF2-type PtO2 (calculated in the presence and absence of spin-orbit interactions) predicts that this material may be metallic or semimetallic, which is inconsistent with the electric conductivity reported to date and the charging effect observed in current photoelectron measurements. Compared with the calculated results, the valence-band spectrum of PtO2 appears to have shifted toward the high-binding-energy side and reveals a gradual intensity decrease toward the Fermi energy EF, implying a semiconductor-like electronic structure. Spin-dependent calculations predict a ferromagnetic ground state with a magnetization of 0.475 μB per formula unit for HP-PdF2-type RhO2.

A "Career" Work Ethic versus Just a Job

ERIC Educational Resources Information Center

Porter, Gayle

2005-01-01

Purpose: To provide current information on managers' expectations of their employees, toward structuring future research on amount of time and energy devoted to work. Design/methodology/approach: Qualitative data, acquired through focus groups and interviews, provide a sample of the perceptions of 57 managers in the mid-Atlantic region of the USA…

Syntheses, structural characterization, and DPPH radical scavenging activity of cocrystals of caffeine with 1- and 2-naphthoxyacetic acids

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Seethalakshmi, P. G.; Sumathi, D.; Bhuvanesh, N.; Kumaresan, S.

2013-03-01

Caffeine:1-naphthoxyacetic acid [(caf)(1-naa)] and caffeine:2-naphthoxyacetic acid [(caf)(2-naa)] cocrystals have been synthesized and single crystals were grown by slow evaporation technique. The structures of the grown crystals were elucidated using single crystal X-ray diffraction analysis. Both the cocrystals belong to the monoclinic crystallographic system with space group P21/c, Z = 4, and α = γ = 90°, whereas β = 111.4244(18)° for [(caf)(1-naa)] and β = 109.281(6)° for [(caf)(2-naa)]. The crystal packing is predominantly stabilized by hydrogen bonding and π-π stacking interactions. The presence of unionized -COOH functional group in both the cocrystals was identified by FTIR spectral analysis. Thermal behavior and stability of both the cocrystals were studied by TGA/DTA analyses. Solvent-free formation of these cocrystals was confirmed by powder X-ray diffraction analyses. The theoretical energy of cocrystals showed that the formers have higher energy than cocrystals 1 and 2. DPPH radical scavenging activity of cocrystals 1 and 2 is slightly greater than the formers.

Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

PubMed

Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

2013-05-01

Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantum-chemical, NMR and X-ray diffraction studies on (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane.

PubMed

Zapata-Torres, Gerald; Cassels, Bruce K; Parra-Mouchet, Julia; Mascarenhas, Yvonne P; Ellena, Javier; De Araujo, A S

2008-06-01

Time-averaged conformations of (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane hydrochloride (MDMA, "ecstasy") in D(2)O, and of its free base and trifluoroacetate in CDCl(3), were deduced from their (1)H NMR spectra and used to calculate their conformer distribution. Their rotational potential energy surface (PES) was calculated at the RHF/6-31G(d,p), B3LYP/6-31G(d,p), B3LYP/cc-pVDZ and AM1 levels. Solvent effects were evaluated using the polarizable continuum model. The NMR and theoretical studies showed that, in the free base, the N-methyl group and the ring are preferentially trans. This preference is stronger in the salts and corresponds to the X-ray structure of the hydrochloride. However, the energy barriers separating these forms are very low. The X-ray diffraction crystal structures of the anhydrous salt and its monohydrate differed mainly in the trans or cis relationship of the N-methyl group to the alpha-methyl, although these two forms interconvert freely in solution.

Structural phase transitions in GaAs to 108 GPa

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

Weir, S.T.; Vohra, Y.K.; Vanderborgh, C.A.

1989-01-15

The III-V compound GaAs was studied using energy-dispersive x-ray diffraction with a synchro- tron source up to a pressure of 108 GPa. When the pressure was increased to 16.6 GPa, the GaAs sample transformed from the zinc-blende structure to an orthorhombic structure (GaAs(II)), space group Pmm2, consisting of a primitive orthorhombic lattice with a basis of (0,0,0) and (0,(1/2,..cap alpha..), where ..cap alpha.. = 0.35. Upon a further increase of pressure to 24 +- 1 GPa, GaAs(II) transformed to another orthorhombic structure (GaAs(III)), space group Imm2, consisting of a body-centered orthorhombic lattice with a basis of (0,0,0) and (0, (1/2,..delta..),more » where ..delta.. is 0.425 at 28.1 GPa. With increasing pressure, ..delta.. approached (1/2 and the GaAs(III) structure gradually assumed the symmetry of the simple hexagonal structure. The transition to the simple hexagonal structure (GaAs(IV)) was completed in the vicinity of 60--80 GPa. The structure remains simple hexagonal up to at least 108 GPa, the highest pressure reached in this study.« less

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus

DOE PAGES

Laino, Aldana; Lopez-Zavala, Alonso A.; Garcia-Orozco, Karina D.; ...

2017-09-11

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus ( PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, andmore » it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant ( K m) was 1.7 mM with a k cat of 75 s –1. Two crystal structures are presented, the apo PvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.« less

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus

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

Laino, Aldana; Lopez-Zavala, Alonso A.; Garcia-Orozco, Karina D.

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus ( PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, andmore » it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant ( K m) was 1.7 mM with a k cat of 75 s –1. Two crystal structures are presented, the apo PvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.« less

The stability of DOTA-chelated radiopharmaceuticals within 225Ac decay pathway studied with density functional theory.

NASA Astrophysics Data System (ADS)

Karolak, Aleksandra; Khabibullin, Artem; Budzevich, Mikalai; Martinez, M.; Doliganski, Michael; McLaughlin, Mark; Woods, Lilia; Morse, David

Ligand structures encapsulating metal ions play a central role as contrast agents in Magnetic Resonance Imaging (MRI) or as agents delivering toxic cargo directly to tumor cells in targeted cancer therapy. The structural stability and interaction with solutions of such complexes are the key elements in understanding the foundation of delivery process. We present a comparative study for the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to radioactive isotopes of 225Ac, 221Fr, 217At, 213Bi and a control 68Gd. Using density functional theory methods we investigate the structural stability of complexes for cancer therapy including binding energies, charge transfer, electron densities. The van der Waals interactions are included in the simulations to take into account weak dispersion forces present in such structures. Our results reveal that Ac-DOTA, Bi-DOTA and Gd-DOTA are the most stable complexes in the group. We also show that the water environment is a key ingredient for the structural coordination of the DOTA structures. Support from the US Department of Energy under Grant No. DE-FG02-06ER46297 is acknowledged.

Structure family and polymorphous phase transition in the compounds with soft sublattice: Cu{sub 2}Se as an example

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

Qiu, Wujie; State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050; Lu, Ping

Quite a few interesting but controversial phenomena, such as simple chemical composition but complex structures, well-defined high-temperature cubic structure but intriguing phase transition, coexist in Cu{sub 2}Se, originating from the relatively rigid Se framework and “soft” Cu sublattice. However, the electrical transport properties are almost uninfluenced by such complex substructures, which make Cu{sub 2}Se a promising high-performance thermoelectric compound with extremely low thermal conductivity and good power factor. Our work reveals that the crystal structure of Cu{sub 2}Se at the temperature below the phase-transition point (∼400 K) should have a group of candidate structures that all contain a Se-dominated face-centered-cubic-likemore » layered framework but nearly random site occupancy of atoms from the “soft” Cu sublattice. The energy differences among those structures are very low, implying the coexistence of various structures and thus an intrinsic structure complexity with a Se-based framework. Detailed analyses indicate that observed structures should be a random stacking of those representative structure units. The transition energy barriers between each two of those structures are estimated to be zero, leading to a polymorphous phase transition of Cu{sub 2}Se at increasing temperature. Those are all consistent with experimental observations.« less

Using experimental studies and theoretical calculations to analyze the molecular mechanism of coumarin, p-hydroxybenzoic acid, and cinnamic acid

NASA Astrophysics Data System (ADS)

Hsieh, Tiane-Jye; Su, Chia-Ching; Chen, Chung-Yi; Liou, Chyong-Huey; Lu, Li-Hwa

2005-05-01

Three natural products, Coumarin ( 1), p-hydroxybenzoic acid ( 2), trans-cinnamic acid ( 3) were isolated from the natural plant of indigenous cinnamon and the structures including relative stereochemistry were elucidated on the basis of spectroscopic data and theoretical calculations. Their sterochemical structures were determined by NMR spectroscopy, mass spectroscopy, and X-ray crystallography. The p-hydroxybenzoic acid complex with water is reported to show the existence of two hydrogen bonds. The two hydrogen bonds are formed in the water molecule of two hydrogen-accepting oxygen of carbonyl group of the p-hydroxybenzoic acid. The intermolecular interaction two hydrogen bond of the model system of the water- p-hydroxybenzoic acid was investigated. An experimental study and a theoretical analysis using the B3LYP/6-31G* method in the GAUSSIAN-03 package program were conducted on the three natural products. The theoretical results are supplemented by experimental data. Optimal geometric structures of three compounds were also determined. The calculated molecular mechanics compared quite well with those obtained from the experimental data. The ionization potentials, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, energy gaps, heat of formation, atomization energies, and vibration frequencies of the compounds were also calculated. The results of the calculations show that three natural products are stable molecules with high reactive and various other physical properties. The study also provided an explicit understanding of the sterochemical structure and thermodynamic properties of the three natural products.

The Energy Industry Profile of ISO/DIS 19115-1: Facilitating Discovery and Evaluation of, and Access to Distributed Information Resources

NASA Astrophysics Data System (ADS)

Hills, S. J.; Richard, S. M.; Doniger, A.; Danko, D. M.; Derenthal, L.; Energistics Metadata Work Group

2011-12-01

A diverse group of organizations representative of the international community involved in disciplines relevant to the upstream petroleum industry, - energy companies, - suppliers and publishers of information to the energy industry, - vendors of software applications used by the industry, - partner government and academic organizations, has engaged in the Energy Industry Metadata Standards Initiative. This Initiative envisions the use of standard metadata within the community to enable significant improvements in the efficiency with which users discover, evaluate, and access distributed information resources. The metadata standard needed to realize this vision is the initiative's primary deliverable. In addition to developing the metadata standard, the initiative is promoting its adoption to accelerate realization of the vision, and publishing metadata exemplars conformant with the standard. Implementation of the standard by community members, in the form of published metadata which document the information resources each organization manages, will allow use of tools requiring consistent metadata for efficient discovery and evaluation of, and access to, information resources. While metadata are expected to be widely accessible, access to associated information resources may be more constrained. The initiative is being conducting by Energistics' Metadata Work Group, in collaboration with the USGIN Project. Energistics is a global standards group in the oil and natural gas industry. The Work Group determined early in the initiative, based on input solicited from 40+ organizations and on an assessment of existing metadata standards, to develop the target metadata standard as a profile of a revised version of ISO 19115, formally the "Energy Industry Profile of ISO/DIS 19115-1 v1.0" (EIP). The Work Group is participating on the ISO/TC 211 project team responsible for the revision of ISO 19115, now ready for "Draft International Standard" (DIS) status. With ISO 19115 an established, capability-rich, open standard for geographic metadata, EIP v1 is expected to be widely acceptable within the community and readily sustainable over the long-term. The EIP design, also per community requirements, will enable discovery, evaluation, and access to types of information resources considered important to the community, including structured and unstructured digital resources, and physical assets such as hardcopy documents and material samples. This presentation will briefly review the development of this initiative as well as the current and planned Work Group activities. More time will be spent providing an overview of the EIP v1, including the requirements it prescribes, design efforts made to enable automated metadata capture and processing, and the structure and content of its documentation, which was written to minimize ambiguity and facilitate implementation. The Work Group considers EIP v1 a solid initial design for interoperable metadata, and first step toward the vision of the Initiative.

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

PubMed Central

Soares, C M; Martel, P J; Mendes, J; Carrondo, M A

1998-01-01

The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity. PMID:9545034

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside Sn2 Reactions: a Reaction Force and Atomic Contribution Analysis.

PubMed

Pedraza-González, Laura Milena; Galindo, Johan Fabian; Gonzalez, Ronald; Reyes, Andrés

2016-10-09

The solvent effect on the nucleophile and leaving group atoms of the prototypical F - + CH 3 Cl → CH 3 F + Cl - backside bimolecular nucleophilic substitution reaction (S N 2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE 0 and ΔE ↕ of Y - + CH 3 X → YCH 3 + X - (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Inter-subunit electrostatic interactions in ferritin molecule: comparison with inter-molecular interactions in crystals

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Hogyoku, Michiru; Nagayama, Kuniaki

1996-10-01

We evaluated the contribution of electrostatic interactions to the stability of macromolecular assembly in a horse L ferritin molecule composed of 24 subunits and the three-dimensional crystal of the ferritin molecules with numerical calculation of Poisson-Boltzmann equation based on dielectric model. The calculation showed that the electrostatic energy both favors the assembly of the 24 subunits and the crystalline assembly of the ferritin molecules (i.e., 24-mers). Short-range interactions less than 5 Å such as salt bridges and hydrogen bonds were important for both the subunit assembly and the crystalline assembly. To elucidate the strong stabilization by electrostatic interactions in both the ferritin 24-mer and its crystal, we analyzed the contribution of individual atoms. It revealed that the stabilization was arising from buried salt bridges or hydrogen bonds, which yielded more than 5 kcal/mol in some interactions. These large electrostatic stabilization and also the unexpected small ionic strength dependence was different from those of bovine pancreatic trypsin inhibitor (BPTI) orthorhombic and pig-insulin cubic crystals previously calculated. We also evaluated changes of the accessible surface area (ASA) and hydration free energy in accordance with the process of the subunit assembly. The change of hydration free energy, which was very large (i.e. ˜ + 100 kcal/mol/subunit) and unfavorable for the assembly, was proportional to the electrostatic hydration energy (i.e. Born energy change in hydration process). Hydrophobic groups were likely to appear more frequently than hydrophilic groups at the subunit interfaces. These results suggest that the molecular structure of the ferritin 24-mer and the crystal structure of the 24-mers were both stabilized by local electrostatic interactions, in particular. We view protein crystals as an extension of the protein oligomer to an infinite number of subunits association.

Ammonia IRMS-TPD measurements and DFT calculation on acidic hydroxyl groups in CHA-type zeolites.

PubMed

Suzuki, Katsuki; Sastre, German; Katada, Naonobu; Niwa, Miki

2007-12-07

Brønsted acidity of H-chabazite (CHA) zeolites (Si : Al(2) = 4.2) was investigated by means of ammonia infrared-mass spectrometry/temperature-programmed desorption (IRMS-TPD) methods and density functional calculations. Four IR bands were observed at 3644, 3616, 3575 and 3538 cm(-1), and they were ascribable to the acidic OH groups on four nonequivalent oxygen sites in the CHA structure. The absorption band at 3538 cm(-1) was attributed to the O(4)H in the 6-membered ring (MR), and ammonia adsorption energy (DeltaU) of this OH group was the lowest among the 4 kinds of OH groups. The other 3 bands were assigned to the acidic OH groups in 8MR. It was observed that the DeltaU in 8 and 6MR were 131 (+/-3) and 101 kJ mol(-1), respectively. On the other hand, the density functional theory (DFT) calculations within periodic boundary conditions yielded the adsorption energies on these OH groups in 8 and 6MR to be ca. 130 and 110 kJ mol(-1), respectively, in good agreement with the experimentally-observed values.

First principles calculations of interactions of ZrCl4 precursors with the bare and hydroxylated ZrO2 surfaces

NASA Astrophysics Data System (ADS)

Iskandarova, I. M.; Knizhnik, A. A.; Bagatur'yants, A. A.; Potapkin, B. V.; Korkin, A. A.

2004-05-01

First-principles calculations have been performed to determine the structures and relative energies of different zirconium chloride groups chemisorbed on the tetragonal ZrO2(001) surface and to study the effects of the surface coverage with metal chloride groups and the degree of hydroxylation on the adsorption energies of metal precursors. It is shown that the molecular and dissociative adsorption energies of the ZrCl4 precursor on the bare t-ZrO2(001) surface are too small to hold ZrCl4 molecules on the surface during an atomic layer deposition (ALD) cycle at temperatures higher than 300°C. On the contrary, it has been found that molecular adsorption on the fully hydroxylated zirconia surface leads to the formation of a stable adsorbed complex. This strong adsorption of ZrCl4 molecules can lead to a decrease in the film growth rate of the ALD process at lower temperatures (<200°C). The energies of interaction between adsorbed ZrCl4 groups at a 50% surface coverage has been found to be relatively small, which explains the maximum film growth rate observed in the ZrCl4:H2O ALD process. Moreover, we found that the adsorbed ZrCl4 precursors after hydrolysis give rise to very stable hydroxyl groups, which can be responsible for film growth at high temperatures (up to 900°C).

Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations.

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

Valiev, Marat; Yang, Jie; Adams, Joseph

2007-11-29

Protein kinases catalyze the transfer of the γ-phosphoryl group from ATP, a key regulatory process governing signalling pathways in eukaryotic cells. The structure of the active site in these enzymes is highly conserved implying common catalytic mechanism. In this work we investigate the reaction process in cAPK protein kinase (PKA) using a combined quantum mechanics and molecular mechanics approach. The novel computational features of our work include reaction pathway determination with nudged elastic band methodology and calculation of free energy profiles of the reaction process taking into account finite temperature fluctuations of the protein environment. We find that the transfermore » of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.« less

Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation

NASA Astrophysics Data System (ADS)

Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.

2016-07-01

Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

Ab initio study of the structural phase transitions of the double perovskites Sr2MWO6 (M=Zn, Ca, Mg)

NASA Astrophysics Data System (ADS)

Petralanda, U.; Etxebarria, I.

2014-02-01

We study the interplay of structural distortions in double perovskites Sr2MWO6 (M = Zn, Ca, Mg) by means of first-principles calculations and group theoretical analysis. Structure relaxations of the cubic, tetragonal, and monoclinic phases show that the ground states of the three compounds are monoclinic, although the energy difference between the monoclinic and tetragonal structures is very small in the case of Sr2MgWO6. The symmetry analysis of the distortions involved in the experimental and calculated low-temperature structures shows that the amplitude of two primary distortions associated to rigid rotations of the MX6 and WO6 octahedra are dominant, although the amplitude of a third mode related to deformations of the MX6 groups can not be neglected. The energy maps of the space spanned by the three relevant modes are calculated, and the couplings among the modes are evaluated, showing that the role of a hard secondary mode (in the Landau sense) coupled trilinearly to the two primary instabilities is crucial to stabilize the monoclinic ground state. Results suggest that the key role of the trilinear coupling among three modes could be rather common. A phenomenological theory including the effects of the chemical pressure is also developed. We find that the evolution of the stiffness constants in terms of the atomic substitution follows an accurate linear dependence and that the influence of quantum saturation of the order parameters could stabilize the tetragonal phase of Sr2MgWO6.

Crystallographic controls on the frictional behavior of dry and water-saturated sheet structure minerals

USGS Publications Warehouse

Moore, Diane E.; Lockner, D.A.

2004-01-01

We compare the frictional strengths of 17 sheet structure mineral powders, measured under dry and water-saturated conditions, to identify the factors that cause many of them to be relatively weak. The dry coefficient of friction ?? ranges upward from 0.2 for graphite, leveling off at 0.8 for margarite, clintonite, gibbsite, kaolinite, and lizardite. The values of ?? (dry) correlate directly with calculated (001) interlayer bond strengths of the minerals. This correlation occurs because shear becomes localized along boundary and Riedel shears and the platy minerals in them rotate into alignment with the shear planes. For those gouges with ?? (dry) < 0.8, shear occurs by breaking the interlayer bonds to form new cleavage surfaces. Where ?? (dry) = 0.8, consistent with Byerlee's law, the interlayer bonds are sufficiently strong that other frictional processes dominate. The transition in dry friction mechanisms corresponds to calculated surface energies of 2-3 J/m2. Adding water causes ?? to decrease for every mineral tested except graphite. If the minerals are separated into groups with similar crystal structures, ?? (wet) increases with increasing interlayer bond strength within each group. This relationship also holds for the swelling clay montmorillonite, whose water-saturated strength is consistent with the strengths of nonswelling clays of similar crystal structure. Water in the saturated gouges forms thin, structured films between the plate surfaces. The polar water molecules are bonded to the plate surfaces in proportion to the mineral's surface energy, and ?? (wet) reflects the stresses required to shear through the water films. Copyright 2004 by the American Geophysical Union.

Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

PubMed

Gu, Quanli; Knee, J L

2012-09-14

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

Effects of pulsed electromagnetic field (PEMF) on the tensile biomechanical properties of diabetic wounds at different phases of healing

PubMed Central

Cheing, Alex K. K.; Ng, Gabriel Y. F.; Cheing, Gladys L. Y.

2018-01-01

The present study investigated the effects of pulsed electromagnetic field (PEMF) on the tensile biomechanical properties of diabetic wounds at different phases of healing. Two intensities of PEMF were adopted for comparison. We randomly assigned 111 10-week-old male streptozotocin-induced diabetic Sprague-Dawley rats to two PEMF groups and a sham control group. Six-millimetre biopsy punched full thickness wounds were made on the lateral side of their hindlimbs. The PEMF groups received active PEMF delivered at 25 Hz with intensity of either 2 mT or 10 mT daily, while the sham group was handled in a similar way except they were not exposed to PEMF. Wound tissues were harvested for tensile testing on post-wounding days 3, 5, 7, 10, 14 and 21. Maximum load, maximum stress, energy absorption capacity, Young’s modulus and thickness of wound tissue were measured. On post-wounding day 5, the PEMF group that received 10-mT intensity had significantly increased energy absorption capacity and showed an apparent increase in the maximum load. However, the 10-mT PEMF group demonstrated a decrease in Young’s modulus on day 14. The 10-mT PEMF groups showed a significant increase in the overall thickness of wound tissue whereas the 2-mT group showed a significant decrease in the overall maximum stress of the wounds tissue. The present findings demonstrated that the PEMF delivered at 10 mT can improve energy absorption capacity of diabetic wounds in the early healing phase. However, PEMF (both 2-mT and 10-mT) seemed to impair the material properties (maximum stress and Young’s modulus) in the remodelling phase. PEMF may be a useful treatment for promoting the recovery of structural properties (maximum load and energy absorption capacity), but it might not be applied at the remodelling phase to avoid impairing the recovery of material properties. PMID:29324868

Experimental and theoretical IR and Raman spectra of picolinic, nicotinic and isonicotinic acids

NASA Astrophysics Data System (ADS)

Koczoń, P.; Dobrowolski, J. Cz.; Lewandowski, W.; Mazurek, A. P.

2003-07-01

The experimental and theoretical (B3PW91/6-311++G**) vibrational (IR and Raman) spectra of picolinic, nicotinic and isonicotinic acids (pyridine-2-, -3-, and -4-carboxylic acid, respectively) were studied. Three stable calculated structures were found for picolinic acid: the structure with intramolecular hydrogen COOH⋯N bond, and the two without hydrogen bond. For the nicotinic acid two stable theoretical structures differ in orientation of the COOH group with respect to the nitrogen atom, whereas for the isonicotinic acid only one form was stable. The theoretical vibrational spectra of the three acids were interpreted by means of potential energy distributions (PEDs) using VEDA 3 program. Next, selected experimental bands were assigned based on the scaled theoretical wavenumbers. Finally, the wavenumbers and intensities for the three isomeric acids were compared and discussed in terms of location of the carboxylic group.

Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations1[W

PubMed Central

Green, Abigail R.; Lewis, Kevin M.; Barr, John T.; Jones, Jeffrey P.; Lu, Fachuang; Ralph, John; Vermerris, Wilfred; Sattler, Scott E.; Kang, ChulHee

2014-01-01

Using S-adenosyl-methionine as the methyl donor, caffeic acid O-methyltransferase from sorghum (Sorghum bicolor; SbCOMT) methylates the 5-hydroxyl group of its preferred substrate, 5-hydroxyconiferaldehyde. In order to determine the mechanism of SbCOMT and understand the observed reduction in the lignin syringyl-to-guaiacyl ratio of three brown midrib12 mutants that carry COMT gene missense mutations, we determined the apo-form and S-adenosyl-methionine binary complex SbCOMT crystal structures and established the ternary complex structure with 5-hydroxyconiferaldehyde by molecular modeling. These structures revealed many features shared with monocot ryegrass (Lolium perenne) and dicot alfalfa (Medicago sativa) COMTs. SbCOMT steady-state kinetic and calorimetric data suggest a random bi-bi mechanism. Based on our structural, kinetic, and thermodynamic results, we propose that the observed reactivity hierarchy among 4,5-dihydroxy-3-methoxycinnamyl (and 3,4-dihydroxycinnamyl) aldehyde, alcohol, and acid substrates arises from the ability of the aldehyde to stabilize the anionic intermediate that results from deprotonation of the 5-hydroxyl group by histidine-267. Additionally, despite the presence of other phenylpropanoid substrates in vivo, sinapaldehyde is the preferential product, as demonstrated by its low Km for 5-hydroxyconiferaldehyde. Unlike its acid and alcohol substrates, the aldehydes exhibit product inhibition, and we propose that this is due to nonproductive binding of the S-cis-form of the aldehydes inhibiting productive binding of the S-trans-form. The S-cis-aldehydes most likely act only as inhibitors, because the high rotational energy barrier around the 2-propenyl bond prevents S-trans-conversion, unlike alcohol substrates, whose low 2-propenyl bond rotational energy barrier enables rapid S-cis/S-trans-interconversion. PMID:24948836

Overview of crew member energy expenditure during Shuttle Flight 61-8 EASE/ACCESS task performance

NASA Technical Reports Server (NTRS)

Horrigan, D. J.; Waligora, J. W.; Stanford, J.; Edwards, B. F.

1987-01-01

The energy expenditure of the Shuttle Flight 61-B crewmembers during the extravehicular performance of Experimental Assembly of Structures in EVA (EASE) and Assembly Concept of Construction of Space Structures (ACCESS) construction system tasks are reported. These data consist of metabolic rate time profiles correlated with specific EASE and ACCESS tasks and crew comments. Average extravehicular activity metabolic rates are computed and compared with those reported from previous Apollo, Shylab, and Shuttle flights. These data reflect total energy expenditure and not that of individual muscle groups such as hand and forearm. When correlated with specific EVA tasks and subtasks, the metabolic profile data is expected to be useful in planning future EVA protocols. For example, after experiencing high work rates and apparent overheating during some Gemini EVAs, it was found useful to carefully monitor work rates in subsequent flights to assess the adequacy of cooling garments and as an aid to preplanning EVA procedures. This presentation is represented by graphs and charts.

Polymer solar cells with enhanced open-circuit voltage and efficiency

NASA Astrophysics Data System (ADS)

Chen, Hsiang-Yu; Hou, Jianhui; Zhang, Shaoqing; Liang, Yongye; Yang, Guanwen; Yang, Yang; Yu, Luping; Wu, Yue; Li, Gang

2009-11-01

Following the development of the bulk heterojunction structure, recent years have seen a dramatic improvement in the efficiency of polymer solar cells. Maximizing the open-circuit voltage in a low-bandgap polymer is one of the critical factors towards enabling high-efficiency solar cells. Study of the relation between open-circuit voltage and the energy levels of the donor/acceptor in bulk heterojunction polymer solar cells has stimulated interest in modifying the open-circuit voltage by tuning the energy levels of polymers. Here, we show that the open-circuit voltage of polymer solar cells constructed based on the structure of a low-bandgap polymer, PBDTTT, can be tuned, step by step, using different functional groups, to achieve values as high as 0.76 V. This increased open-circuit voltage combined with a high short-circuit current density results in a polymer solar cell with a power conversion efficiency as high as 6.77%, as certified by the National Renewable Energy Laboratory.

Developing hybrid approaches to predict pKa values of ionizable groups

PubMed Central

Witham, Shawn; Talley, Kemper; Wang, Lin; Zhang, Zhe; Sarkar, Subhra; Gao, Daquan; Yang, Wei

2011-01-01

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups, which ionization is expected to cause conformational changes, termed “problematic” residues, then applies a special protocol on them, while the rest of the pKa’s are predicted with rigid backbone approach as implemented in multi-conformation continuum electrostatics (MCCE) method. The backbone representative conformations for “problematic” groups are generated with either molecular dynamics simulations with charged and uncharged amino acid or with ab-initio local segment modeling. The corresponding ensembles are then used to calculate the pKa of the “problematic” residues and then the results are averaged. PMID:21744395

Giant piezoelectricity of monolayer group IV monochalcogenides

NASA Astrophysics Data System (ADS)

Fei, Ruixiang; Li, Wenbin; Li, Ju; Yang, Li

We predict enormous, anisotropic piezoelectric effects in intrinsic monolayer group IV monochalcogenides (MX, M =Sn or Ge, X =Se or S), including SnSe, SnS, GeSe, and GeS. Using first-principle simulations based on the modern theory of polarization, we find that their piezoelectric coefficients are about one to two orders of magnitude larger than those of other 2D materials, such as MoS2 and GaSe, and bulk quartz and AlN which are widely used in industry. This enhancement is a result of the unique ``puckered'' C2v symmetry and electronic structure of monolayer group IV monochalcogenides. Given the achieved experimental advances in the fabrication of monolayers, their flexible character, and ability to withstand enormous strain, these 2D structures with giant piezoelectric effects may be promising for a broad range of applications such as nano-sized sensors, piezotronics, and energy harvesting in portable electronic devices.

Anomalous group velocity at the high energy range of real 3D photonic nanostructures

NASA Astrophysics Data System (ADS)

Botey, Muriel; Martorell, Jordi; Lozano, Gabriel; Míguez, Hernán; Dorado, Luis A.; Depine, Ricardo A.

2010-05-01

We perform a theoretical study on the group velocity for finite thin artificial opal slabs made of a reduced number of layers in the spectral range where the light wavelength is on the order of the lattice parameter. The vector KKR method including extinction allows us to evaluate the finite-size effects on light propagation in the ΓL and ΓX directions of fcc close-packed opal films made of dielectric spheres. The group is index determined from the phase delay introduced by the structure to the forwardly transmitted electric field. We show that for certain frequencies, light propagation can either be superluminal -positive or negative- or approach zero depending on the crystal size and absorption. Such anomalous behavior can be attributed to the finite character of the structure and provides confirmation of recently emerged experimental results.

Mixed-Timescale Per-Group Hybrid Precoding for Multiuser Massive MIMO Systems

NASA Astrophysics Data System (ADS)

Teng, Yinglei; Wei, Min; Liu, An; Lau, Vincent; Zhang, Yong

2018-05-01

Considering the expensive radio frequency (RF) chain, huge training overhead and feedback burden issues in massive MIMO, in this letter, we propose a mixed-timescale per-group hybrid precoding (MPHP) scheme under an adaptive partially-connected RF precoding structure (PRPS), where the RF precoder is implemented using an adaptive connection network (ACN) and M analog phase shifters (APSs), where M is the number of antennas at the base station (BS). Exploiting the mixed-time stage channel state information (CSI) structure, the joint-design of ACN and APSs is formulated as a statistical signal-to-leakage-and-noise ratio (SSLNR) maximization problem, and a heuristic group RF precoding (GRFP) algorithm is proposed to provide a near-optimal solution. Simulation results show that the proposed design advances at better energy efficiency (EE) and lower hardware cost, CSI signaling overhead and computational complexity than the conventional hybrid precoding (HP) schemes.

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

Comparative DFT study of structure, reactivity and IR spectra of phosphorus-containing dendrons with Pdbnd Nsbnd Pdbnd S linkages, vinyl and azide functional groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Gottis, S.; Laurent, R.; Kovalenko, V. I.

2015-07-01

Fourier transform IR spectra of the first generation dendrons built from thiophosphoryl core with terminal Psbnd Cl groups, vinyl (G1) and azide (G2) functional group at the level of the core have been recorded. The optimized geometries of low energy isomers of G1 and G2 have been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. DFT is used for analyzing the properties of each structural part (core, branches, surface). It was found that the repeated branching units of G1 and G2 contain planar sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd Prbond2 fragments. DFT results for the structure of G1 and G2 are in good agreement with X-ray diffraction measurements. A complete vibrational assignment is proposed for different parts of G1 and G2. The global and local reactivity descriptors have been used to characterize the reactivity pattern of the core functional and terminal groups. Natural bond orbital (NBO) analysis has been applied to comparative study of charge delocalization. Our study reveals why azide group linked to phosphorus has a different reactivity when compared to organic azides.

Electron transport through rectifying self-assembled monolayer diodes on silicon: Fermi-level pinning at the molecule-metal interface.

PubMed

Lenfant, S; Guerin, D; Tran Van, F; Chevrot, C; Palacin, S; Bourgoin, J P; Bouloussa, O; Rondelez, F; Vuillaume, D

2006-07-20

We report the synthesis and characterization of molecular rectifying diodes on silicon using sequential grafting of self-assembled monolayers of alkyl chains bearing a pi group at their outer end (Si/sigma-pi/metal junctions). We investigate the structure-performance relationships of these molecular devices, and we examine the extent to which the nature of the pi end group (change in the energy position of their molecular orbitals) drives the properties of these molecular diodes. Self-assembled monolayers of alkyl chains (different chain lengths from 6 to 15 methylene groups) functionalized by phenyl, anthracene, pyrene, ethylene dioxythiophene, ethylene dioxyphenyl, thiophene, terthiophene, and quaterthiophene were synthesized and characterized by contact angle measurements, ellipsometry, Fourier transform infrared spectroscopy, and atomic force microscopy. We demonstrate that reasonably well-packed monolayers are obtained in all cases. Their electrical properties were assessed by dc current-voltage characteristics and high-frequency (1-MHz) capacitance measurements. For all of the pi groups investigated here, we observed rectification behavior. These results extend our preliminary work using phenyl and thiophene groups (Lenfant et al., Nano Lett. 2003, 3, 741). The experimental current-voltage curves were analyzed with a simple analytical model, from which we extracted the energy position of the molecular orbital of the pi group in resonance with the Fermi energy of the electrodes. We report experimental studies of the band lineup in these silicon/alkyl pi-conjugated molecule/metal junctions. We conclude that Fermi-level pinning at the pi group/metal interface is mainly responsible for the observed absence of a dependence of the rectification effect on the nature of the pi groups, even though the groups examined were selected to have significant variations in their electronic molecular orbitals.

High-energy Collision-induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

PubMed Central

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

2014-01-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote-fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers. PMID:24781458

High-energy collision-induced dissociation by MALDI TOF/TOF causes charge-remote fragmentation of steroid sulfates.

PubMed

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B; Holy, Timothy E; Gross, Michael L

2014-08-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

PubMed

Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

2017-04-18

The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

Some metal oxides and their applications for creation of Microsystems (MEMS) and Energy Harvesting Devices (EHD)

NASA Astrophysics Data System (ADS)

Denishev, K.

2016-10-01

This is a review of a part of the work of the Technological Design Group at Technical University of Sofia, Faculty of Electronic Engineering and Technologies, Department of Microelectronics. It is dealing with piezoelectric polymer materials and their application in different microsystems (MEMS) and Energy Harvesting Devices (EHD), some organic materials and their applications in organic (OLED) displays, some transparent conductive materials etc. The metal oxides Lead Zirconium Titanate (PZT) and Zinc Oxide (ZnO) are used as piezoelectric layers - driving part of different sensors, actuators and EHD. These materials are studied in term of their performance in dependence on the deposition conditions and parameters. They were deposited as thin films by using RF Sputtering System. As technological substrates, glass plates and Polyethylenetherephtalate (PET) foils were used. For characterization of the materials, a test structure, based on Surface Acoustic Waves (SAW), was designed and prepared. The layers were characterized by Fourier Transform Infrared spectroscopy (FTIR). The piezoelectric response was tested at variety of mechanical loads (tensile strain, stress) in static and dynamic (multiple bending) mode. The single-layered and double-layered structures were prepared for piezoelectric efficiency increase. A structure of piezoelectric energy transformer is proposed and investigated.

Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

PubMed Central

Xia, Fei; Dou, Yong; Zhou, Xingming; Yang, Xuejun; Xu, Jiaqing; Zhang, Yang

2009-01-01

Background In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design. Results RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%. Conclusion To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (ViennaPackage – 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU. PMID:19208138

Formation of Triboelectric Series via Atomic-Level Surface Functionalization for Triboelectric Energy Harvesting.

PubMed

Shin, Sung-Ho; Bae, Young Eun; Moon, Hyun Kyung; Kim, Jungkil; Choi, Suk-Ho; Kim, Yongho; Yoon, Hyo Jae; Lee, Min Hyung; Nah, Junghyo

2017-06-27

Triboelectric charging involves frictional contact of two different materials, and their contact electrification usually relies on polarity difference in the triboelectric series. This limits the choices of materials for triboelectric contact pairs, hindering research and development of energy harvest devices utilizing triboelectric effect. A progressive approach to resolve this issue involves modification of chemical structures of materials for effectively engineering their triboelectric properties. Here, we describe a facile method to change triboelectric property of a polymeric surface via atomic-level chemical functionalizations using a series of halogens and amines, which allows a wide spectrum of triboelectric series over single material. Using this method, tunable triboelectric output power density is demonstrated in triboelectric generators. Furthermore, molecular-scale calculation using density functional theory unveils that electrons transferred through electrification are occupying the PET group rather than the surface functional group. The work introduced here would open the ability to tune triboelectric property of materials by chemical modification of surface and facilitate the development of energy harvesting devices and sensors exploiting triboelectric effect.

First-principles simulations of transition metal ions in silicon as potential quantum bits

NASA Astrophysics Data System (ADS)

Ma, He; Seo, Hosung; Galli, Giulia

Optically active spin defects in semiconductors have gained increasing attention in recent years for use as potential solid-state quantum bits (or qubits). Examples include the nitrogen-vacancy center in diamond, transition metal impurities, and rare earth ions. In this talk, we present first-principles theoretical results on group 6 transition metal ion (Chromium, Molybdenum and Tungsten) impurities in silicon, and we investigate their potential use as qubits. We used density functional theory (DFT) to calculate defect formation energies and we found that transition metal ions have lower formation energies at interstitial than substitutional sites. We also computed the electronic structure of the defects with particular attention to the position of the defect energy levels with respect to the silicon band edges. Based on our results, we will discuss the possibility of implementing qubits in silicon using group 6 transition metal ions. This work is supported by the National Science Foundation (NSF) through the University of Chicago MRSEC under Award Number DMR-1420709.

Effects of substituents in silyl groups on the absorption, fluorescence and structural properties of 1,3,6,8-tetrasilylpyrenes.

PubMed

Maeda, Hajime; Suzuki, Tsubasa; Segi, Masahito

2018-05-09

1,3,6,8-Tetrasilylpyrenes and related germyl and stannyl derivatives were synthesized, and their absorption and fluorescence spectroscopic and structural properties were elucidated. The results show that the UV-vis absorption maxima of these substances in CH2Cl2 solutions shift to longer wavelengths as the size of the alkyl groups and numbers of phenyl groups on silicon increase. Fluorescence quantum yields of tetrasilylpyrenes in cyclohexane are larger than that of pyrene, and a pentamethyldisilyl derivative has an emission efficiency of 0.79. Except in the case of the SiMe2H derivative, excimer emission was not observed in concentrated solutions of these substances. The SiMe2H and SiMe3 derivatives were shown to form CT complexes with tetracyanoethylene in CH2Cl2 solutions. The calculated energy barriers for rotation of the silyl groups about the Si-C bond increase as the steric bulk of the silyl group increases. 29Si NMR chemical shifts were found to depend on the sizes of the alkyl groups and numbers of phenyl groups. Data arising from theoretical calculations suggest that the silyl groups act as electron-donating groups, and the donating ability of the groups decreases in the order SiR3 > GeR3 > SnR3.

Combined MCD/DFT/TDDFT Study of the Electronic Structure of Axially Pyridine Coordinated Metallocorroles.

PubMed

Rhoda, Hannah M; Crandall, Laura A; Geier, G Richard; Ziegler, Christopher J; Nemykin, Victor N

2015-05-18

A series of metallocorroles were investigated by UV-vis and magnetic circular dichroism spectroscopies. The diamagnetic distorted square-pyramidal main-group corrole Ga(tpfc)py (2), the diamagnetic distorted octahedral transition-metal adduct Co(tpfc)(py)2 (3), and paramagnetic distorted octahedral transition-metal complex Fe(tpfc)(py)2 (4) [H3tpfc = tris(perfluorophenyl)corrole] were studied to investigate similarities and differences in the electronic structure and spectroscopy of the closed- and open-shell metallocorroles. Similar to the free-base H3tpfc (1), inspection of the MCD Faraday B-terms for all of the macrocycles presented in this report revealed that a ΔHOMO < ΔLUMO [ΔHOMO is the energy difference between two highest energy corrole-centered π-orbitals and ΔLUMO is the energy difference between two lowest energy corrole-centered π*-orbitals originating from ML ± 4 and ML ± 5 pairs of perimeter] condition is present for each complex, which results in an unusual sign-reversed sequence for π-π* transitions in their MCD spectra. In addition, the MCD spectra of the cobalt and the iron complexes were also complicated by a number of charge-transfer states in the visible region. Iron complex 4 also exhibits a low-energy absorption in the NIR region (1023 nm). DFT and TDDFT calculations were used to elaborate the electronic structures and provide band assignments in UV-vis and MCD spectra of the metallocorroles. DFT and TDDFT calculations predict that the orientation of the axial pyridine ligand(s) has a very minor influence on the calculated electronic structures and absorption spectra in the target systems.

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

Thayer, K.J.

The past year has seen several of the Physics Division`s new research projects reach major milestones with first successful experiments and results: the atomic physics station in the Basic Energy Sciences Research Center at the Argonne Advanced Photon Source was used in first high-energy, high-brilliance x-ray studies in atomic and molecular physics; the Short Orbit Spectrometer in Hall C at the Thomas Jefferson National Accelerator (TJNAF) Facility that the Argonne medium energy nuclear physics group was responsible for, was used extensively in the first round of experiments at TJNAF; at ATLAS, several new beams of radioactive isotopes were developed andmore » used in studies of nuclear physics and nuclear astrophysics; the new ECR ion source at ATLAS was completed and first commissioning tests indicate excellent performance characteristics; Quantum Monte Carlo calculations of mass-8 nuclei were performed for the first time with realistic nucleon-nucleon interactions using state-of-the-art computers, including Argonne`s massively parallel IBM SP. At the same time other future projects are well under way: preparations for the move of Gammasphere to ATLAS in September 1997 have progressed as planned. These new efforts are imbedded in, or flowing from, the vibrant ongoing research program described in some detail in this report: nuclear structure and reactions with heavy ions; measurements of reactions of astrophysical interest; studies of nucleon and sub-nucleon structures using leptonic probes at intermediate and high energies; atomic and molecular structure with high-energy x-rays. The experimental efforts are being complemented with efforts in theory, from QCD to nucleon-meson systems to structure and reactions of nuclei. Finally, the operation of ATLAS as a national users facility has achieved a new milestone, with 5,800 hours beam on target for experiments during the past fiscal year.« less

Instability of the layered orthorhombic post-perovskite phase of SrTiO3 and other candidate orthorhombic phases under pressure

NASA Astrophysics Data System (ADS)

Bhandari, Churna; Lambrecht, Walter R. L.

2018-06-01

While the tetragonal antiferro-electrically distorted (AFD) phase with space group I 4 / mcm is well known for SrTiO3 to occur below 105 K, there are also some hints in the literature of an orthorhombic phase, either at the lower temperature or at high pressure. A previously proposed orthorhombic layered structure of SrTiO3, known as the post-perovskite or CaIrO3 structure with space group Cmcm is shown to have significantly higher energy than the cubic or tetragonal phase and to have its minimum volume at larger volume than cubic perovskite. The Cmcm structure is thus ruled out. We also study an alternative Pnma phase obtained by two octahedral rotations about different axes. This phase is found to have slightly lower energy than the I 4 / mcm phase in spite of the fact that its parent, in-phase tilted P 4 / mbm phase is not found to occur. Our calculated enthalpies of formation show that the I 4 / mcm phase occurs at slightly higher volume than the cubic phase and has a negative transition pressure relative to the cubic phase, which suggests that it does not correspond to the high-pressure tetragonal phase. The enthalpy of the Pnma phase is almost indistinguishable from the I 4 / mcm phase. Alternative ferro-electric tetragonal and orthorhombic structures previously suggested in literature are discussed.

Nutrient intake and balancing among female Colobus angolensis palliatus inhabiting structurally distinct forest areas: Effects of group, season, and reproductive state.

PubMed

Dunham, Noah T; Rodriguez-Saona, Luis E

2018-06-08

Understanding intraspecific behavioral and dietary variation is critical for assessing primate populations' abilities to persist in habitats characterized by increasing anthropogenic disturbances. While it is evident that some species exhibit considerable dietary flexibility (in terms of species-specific plant parts) in relation to habitat disturbance, it is unclear if primates are characterized by similar variation and flexibility regarding nutrient intake. This study examined the effects of group, season, and reproductive state on nutrient intake and balancing in adult female Colobus angolensis palliatus in the Diani Forest, Kenya. During July 2014 to December 2015, estimates of nutrient intake were recorded for eight females from three groups inhabiting structurally and ecologically distinct forest areas differing in tree species composition and density. There were differences in metabolizable energy (ME) and macronutrient intakes among groups, seasons, and reproductive states. Most notably, females inhabiting one of the more disturbed forest areas consumed less ME and macronutrients compared to females in the more intact forest area. Contrary to prediction, females in early lactation consumed significantly less ME and macronutrients compared to non-lactating and late lactation females. Despite differences in macronutrient intake, the relative contribution of macronutrients to ME were generally more conservative among groups, seasons, and reproductive states. Average daily intake ratios of non-protein energy to available protein ranged from approximately 3.5:1-4.3:1 among groups. These results indicate that female C. a. palliatus demonstrate a consistent nutrient balancing strategy despite significant intergroup differences in consumption of species-specific plant parts. Data from additional colobine species inhabiting different forest types are required to assess the extent to which nutrient balancing is constrained by phylogeny or is more flexible to local ecological conditions. © 2018 Wiley Periodicals, Inc.

Density functional theory calculations for armchair stanene nanoribbons with fluorine and sulfur functionalization

NASA Astrophysics Data System (ADS)

Zhang, J.; Lang, X. Y.; Jiang, Q.

2018-07-01

A systematic density functional theory calculation has been carried out to study the effect of edge terminating of F and S elements with different edge natures on the structure and electronic properties of armchair stanene nanoribbons (ASnNRs). Moreover, the corresponding size (ribbon width Na) dependence on these properties is also considered. The energy gap was found to be oscillated as a function of Na and could be classified into three distinct groups of 3m, 3m + 1 and 3m + 2. In addition, the energy gaps of ASnNRs saturated by S atoms differ from that did by F and H atoms in vibration trends as well VBM and CBM changes, where the energy gap is a direct energy gap with a moderate size.

One-dimensional nanomaterials for energy storage

NASA Astrophysics Data System (ADS)

Chen, Cheng; Fan, Yuqi; Gu, Jianhang; Wu, Liming; Passerini, Stefano; Mai, Liqiang

2018-03-01

The search for higher energy density, safer, and longer cycling-life energy storage systems is progressing quickly. One-dimensional (1D) nanomaterials have a large length-to-diameter ratio, resulting in their unique electrical, mechanical, magnetic and chemical properties, and have wide applications as electrode materials in different systems. This article reviews the latest hot topics in applying 1D nanomaterials, covering both their synthesis and their applications. 1D nanomaterials can be grouped into the categories: carbon, silicon, metal oxides, and conducting polymers, and we structure our discussion accordingly. Then, we survey the unique properties and application of 1D nanomaterials in batteries and supercapacitors, and provide comments on the progress and advantages of those systems, paving the way for a better understanding of employing 1D nanomaterials for energy storage.

Asymptotic structure of space-time with a positive cosmological constant

NASA Astrophysics Data System (ADS)

Kesavan, Aruna

In general relativity a satisfactory framework for describing isolated systems exists when the cosmological constant Lambda is zero. The detailed analysis of the asymptotic structure of the gravitational field, which constitutes the framework of asymptotic flatness, lays the foundation for research in diverse areas in gravitational science. However, the framework is incomplete in two respects. First, asymptotic flatness provides well-defined expressions for physical observables such as energy and momentum as 'charges' of asymptotic symmetries at null infinity, [special character omitted] +. But the asymptotic symmetry group, called the Bondi-Metzner-Sachs group is infinite-dimensional and a tensorial expression for the 'charge' integral of an arbitrary BMS element is missing. We address this issue by providing a charge formula which is a 2-sphere integral over fields local to the 2-sphere and refers to no extraneous structure. The second, and more significant shortcoming is that observations have established that Lambda is not zero but positive in our universe. Can the framework describing isolated systems and their gravitational radiation be extended to incorporate this fact? In this dissertation we show that, unfortunately, the standard framework does not extend from the Lambda = 0 case to the Lambda > 0 case in a physically useful manner. In particular, we do not have an invariant notion of gravitational waves in the non-linear regime, nor an analog of the Bondi 'news tensor', nor positive energy theorems. In addition, we argue that the stronger boundary condition of conformal flatness of intrinsic metric on [special character omitted]+, which reduces the asymptotic symmetry group from Diff([special character omitted]) to the de Sitter group, is insufficient to characterize gravitational fluxes and is physically unreasonable. To obtain guidance for the full non-linear theory with Lambda > 0, linearized gravitational waves in de Sitter space-time are analyzed in detail. i) We show explicitly that conformal flatness of the boundary removes half the degrees of freedom of the gravitational field by hand and is not justified by physical considerations; ii) We obtain gauge invariant expressions of energy-momentum and angular momentum fluxes carried by gravitational waves in terms of fields defined at [special character omitted]+; iii) We demonstrate that the flux formulas reduce to the familiar ones in Minkowski spacetime in spite of the fact that the limit Lambda → 0 is discontinuous (since, in particular, [special character omitted]+ changes its space-like character to null in the limit); iv) We obtain a generalization of Einstein's 1918 quadrupole formula for power emission by a linearized source to include a positive Lambda; and, finally v) We show that, although energy of linearized gravitational waves can be arbitrarily negative in general, gravitational waves emitted by physically reasonable sources carry positive energy.

Culture, corporation and collective action: The Department of Energy's American Indian consultation program on the Nevada Test Site in political ecological perspective

NASA Astrophysics Data System (ADS)

Halmo, David Brian

In the western United States, Numic-speaking Indian peoples wield more power today than ever before. Following centuries of depopulation, land and resource loss, and directed change interventions aimed at assimilating them into mainstream society, they are revitalizing traditional culture and renewing their claims to lands and resources by demanding equal participation in national-level activities that affect land and resources that were once under their control. In 1994, representatives of Numic Indian tribes representing three ethnic groups involved in consultation with the U.S. Department of Energy on the Nevada Test Site (NTS) decided by consensus to "incorporate" themselves as the Consolidated Group of Tribes and Organizations (CGTO) to defend their common interests in and claims to NTS lands and resources. What caused 16 distinct, autonomous, sovereign American Indian tribal entities to incorporate themselves as a corporate organization? Using a political ecology perspective, this study examines the social, cultural and political processes operating at multiple levels of analysis and applies social and cultural theories of (1) ethnic cultural persistence, (2) the emergence and evolution of collective action groups for defending cultural interests in "common property," (3) the role of corporate and organizational structure and culture in the articulation of social relations between contending groups, and (4) the related shifts or changes in the distribution of structural power as a result of changing policy environments to a case study-based ethnographic analysis of an ongoing program of American Indian consultation.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

The Thiamine-Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Ciszak, Ewa; Dominiak, Paulina

2004-01-01

Thiamin pyrophosphate (TPP), a derivative of vitamin B1, is a cofactor for enzymes performing catalysis in pathways of energy production including the well known decarboxylation of a-keto acid dehydrogenases followed by transketolation. TPP-dependent enzymes constitute a structurally and functionally diverse group exhibiting multimeric subunit organization, multiple domains and two chemically equivalent catalytic centers. Annotation of functional TPP-dependcnt enzymes, therefore, has not been trivial due to low sequence similarity related to this complex organization. Our approach to analysis of structures of known TPP-dependent enzymes reveals for the first time features common to this group, which we have termed the TPP-motif. The TPP-motif consists of specific spatial arrangements of structural elements and their specific contacts to provide for a flip-flop, or alternate site, enzymatic mechanism of action. Analysis of structural elements entrained in the flip-flop action displayed by TPP-dependent enzymes reveals a novel definition of the common amino acid sequences. These sequences allow for annotation of TPP-dependent enzymes, thus advancing functional proteomics. Further details of three-dimensional structures of TPP-dependent enzymes will be discussed.

Structural principles and thermoelectric properties of polytypic group 14 clathrate-II frameworks.

PubMed

Karttunen, Antti J; Fässler, Thomas F

2013-06-24

We have investigated the structural principles and thermoelectric properties of polytypic group 14 clathrate-II frameworks using quantum chemical methods. The experimentally known cubic 3C polytype was found to be the energetically most favorable framework, but the studied hexagonal polytypes (2 H, 4 H, 6 H, 8 H, 10 H) lie energetically close to it. In the case of germanium, the energy difference between the 3C and 6H clathrate-II polytypes is ten times smaller than the difference between the experimentally known 3C-Ge (α-Ge) and 4H-Ge polytypes. The thermoelectric properties of guest-occupied clathrate-II structures were investigated for compositions Na-Rb-Ga-Ge and Ge-As-I. The clathrate-II structures show promising thermoelectric properties and the highest Seebeck coefficients and thermoelectric power factors were predicted for the 3C polytype. The structural anisotropy of the largest studied hexagonal polytypes affects their thermoelectric power factors by over a factor of two. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three layer functional model and energy exchange concept of aging process

PubMed Central

Mihajlovic, William

2006-01-01

Relying on a certain degree of abstraction, we can propose that no particular distinction exists between animate or living matter and inanimate matter. While focusing attention on some specifics, the dividing line between the two can be drawn. The most apparent distinction is in the level of structural and functional organization with the dissimilar streams of ‘energy flow’ between the observed entity and the surrounding environment. In essence, living matter is created from inanimate matter which is organized to contain internal intense energy processes and maintain lower intensity energy exchange processes with the environment. Taking internal and external energy processes into account, we contend in this paper that living matter can be referred to as matter of dissipative structure, with this structure assumed to be a common quality of all living creatures and living matter in general. Interruption of internal energy conversion processes and terminating the controlled energy exchange with the environment leads to degeneration of dissipative structure and reduction of the same to inanimate matter, (gas, liquid and/or solid inanimate substances), and ultimately what can be called ‘death.’ This concept of what we call dissipative nature can be extended from living organisms to social groups of animals, to mankind. An analogy based on the organization of matter provides a basis for a functional model of living entities. The models relies on the parallels among the three central structures of any cell (nucleus, cytoplasm and outer membrane) and the human body (central organs, body fluids along with the connective tissues, and external skin integument). This three-part structural organization may be observed almost universally in nature. It can be observed from the atomic structure to the planetary and intergalactic organizations. This similarity is corroborated by the membrane theory applied to living organisms. According to the energy nature of living matter and the proposed functional model, the decreased integrity of a human body's external envelope membrane is a first cause of the structural degradation and aging of the entire organism. The aging process than progresses externally to internally, as in single cell organisms, suggesting that much of the efforts towards the restoration and maintenance of the mechanisms responsible for structural development should be focused accordingly, on the membrane, i.e., the skin. Numerous reports indicate that all parts of the human body, like: bones, blood with blood vessels, muscles, skin, and so on, have some ability for restoration. Therefore, actual revival of not only aging tissue of the human body's membrane, but the entire human body enclosed within, with all internal organs, might be expected. We assess several aging theories within the context of our model and provide suggestions on how to activate the body's own anti-aging mechanisms and increase longevity. This paper presents some analogies and some distinctions that exist between the living dissipative structure matter and inanimate matter, discusses the aging process and proposes certain aging reversal solutions. PMID:23598683

Research Frontiers in Bioinspired Energy: Molecular-Level Learning from Natural Systems: A Workshop

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

Zolandz, Dorothy

An interactive, multidisciplinary, public workshop, organized by a group of experts in biochemistry, biophysics, chemical and biomolecular engineering, chemistry, microbial metabolism, and protein structure and function, was held on January 6-7, 2011 in Washington, DC. Fundamental insights into the biological energy capture, storage, and transformation processes provided by speakers was featured in this workshop which included topics such as microbes living in extreme environments such as hydrothermal vents or caustic soda lakes (extremophiles) provided a fascinating basis for discussing the exploration and development of new energy systems. Breakout sessions and extended discussions among the multidisciplinary groups of participants in themore » workshop fostered information sharing and possible collaborations on future bioinspired research. Printed and web-based materials that summarize the committee's assessment of what transpired at the workshop were prepared to advance further understanding of fundamental chemical properties of biological systems within and between the disciplines. In addition, webbased materials (including two animated videos) were developed to make the workshop content more accessible to a broad audience of students and researchers working across disciplinary boundaries. Key workshop discussion topics included: Exploring and identifying novel organisms; Identifying patterns and conserved biological structures in nature; Exploring and identifying fundamental properties and mechanisms of known biological systems; Supporting current, and creating new, opportunities for interdisciplinary education, training, and outreach; and Applying knowledge from biology to create new devices and sustainable technology.« less

Effect and origin of the structure of hyperbranched polysiloxane on the surface and integrated performances of grafted Kevlar fibers

NASA Astrophysics Data System (ADS)

Zhang, Hongrui; Yuan, Li; Liang, Guozheng; Gu, Aijuan

2014-11-01

Four hyperbranched polysiloxanes (HPSis) with different molecular weights and concentration ratios of double bonds to epoxy groups (1:6.5-1:0.7) were synthesized and characterized. Each HPSi was facilely grafted onto surfaces of Kevlar fibers (KFs) to develop novel modified fibers (HPSi-g-KFs). The structures and integrated properties of HPSi-g-KFs as well as the origin behind were systematically investigated. Results show that HPSi-g-KFs have much rougher surface morphologies, and their surface free energies are as high as about 1.7 times that of KFs, showing greatly improved wettability. Besides, HPSi-g-KFs have excellent UV resistance after 168 h UV irradiation, the retentions of tenacity, energy to break, modulus and break extension are as high as 92, 86, 95 and 96%, respectively, while those of KFs are 66-85%. In addition, compared with KFs, HPSi-g-KFs have higher tensile tenacity and energy to break with similar modulus and break extension, much better thermal stability and flame retardancy. The nature of HPSi has different influence on different property of fibers, the HPSi with smaller molecular weight and more epoxy groups is beneficial to prepare HPSi-g-KFs with better wettability, while that with larger molecular weight and more double bonds tends to prepare HPSi-g-KF with better flame retardancy and UV resistance.

Containing Energy, Sustaining Agency-Drama in Middle Years.

ERIC Educational Resources Information Center

Block, Lee Anne

2003-01-01

Describes the author's experience working on a reader's theatre version of a radio play based on the Legend of Sleepy Hollow. Reflects on how the grade 8 students created meaning for themselves and for their audience. Notes limitations of the script and format and her work within those limitations became the structure the group needed, a container…

First-Principles Study of the Li-Mg-N-H System: Compound Structures and Hydrogen Storage Properties

NASA Astrophysics Data System (ADS)

Michel, Kyle; Ozolins, Vidvuds

2009-03-01

The Li-Mg-N-H system is studied with the addition of the Li4Mg(NH)3, MgNH, and Li4NH compounds using first-principles density-functional theory (DFT) calculations. A structure for the mixed imide Li4Mg(NH)3 is proposed, belonging to the Imm2 space group. A new structure for Li2Mg(NH)2 is given that has Pca21 symmetry; this compound has been previously reported as having Iba2 symmetry. The stability of the Li4Mg-imide is studied with respect to its decomposition reactions. The static, zero-point (ZPE), and vibrational energies of all relevant compounds belonging to this system are reported along with their predicted lowest-energy structures. Dehydrogenation reactions are presented that involve these phases and which are found to be spontaneously occurring within 400 K of room temperature. It is predicted that mixing LiH, LiNH2, and Li2Mg(NH)2 at 505 K will form Li4Mg(NH)3 with the release of 2.04 wt. % H2.

Selectively Structural Determination of Cellulose and Hemicellulose in Plant Cell Wall

NASA Astrophysics Data System (ADS)

Huang, Shih-Chun; Park, Yong; Cosgrove, Daniel; Maranas, Janna; Janna Maranas Team; Daniel Cosgrove Team

2013-03-01

Primary plant cell walls support the plant body, and regulate cell size, and plant growth. It contains several biopolymers that can be categorized into three groups: cellulose, hemicellulose and pectin. To determine the structure of plant cell wall, we use small angle neutron scattering in combination with selective deuteration and contrast matching method. We compare the structure between wild Arabidopsis thaliana and its xyloglucan-deficient mutant. Hemicellulose in both samples forms coil with similar radii of gyration, and weak scattering from the mutant suggests a limited amount of hemicellulose in the xyloglucan-deficient mutant. We observe good amount of hemicellulose coating on cellulose microfibrils only in wild Arabidopsis. The absence of coating in its xyloglucan-deficient mutation suggests the other polysaccharides do not have comparable interaction with cellulose. This highlights the importance of xyloglucan in plant cell wall. At larger scale, the average distance between cellulose fibril is found smaller than reported value, which directly reflects on their smaller matured plant size. U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Center for LignoCellulose Structure and Formation

Capturing Structural Snapshots during Photochemical Reactions with Ultrafast Raman Spectroscopy: From Materials Transformation to Biosensor Responses.

PubMed

Fang, Chong; Tang, Longteng; Oscar, Breland G; Chen, Cheng

2018-06-21

Chemistry studies the composition, structure, properties, and transformation of matter. A mechanistic understanding of the pertinent processes is required to translate fundamental knowledge into practical applications. The current development of ultrafast Raman as a powerful time-resolved vibrational technique, particularly femtosecond stimulated Raman spectroscopy (FSRS), has shed light on the structure-energy-function relationships of various photosensitive systems. This Perspective reviews recent work incorporating optical innovations, including the broad-band up-converted multicolor array (BUMA) into a tunable FSRS setup, and demonstrates its resolving power to watch metal speciation and photolysis, leading to high-quality thin films, and fluorescence modulation of chimeric protein biosensors for calcium ion imaging. We discuss advantages of performing FSRS in the mixed time-frequency domain and present strategies to delineate mechanisms by tracking low-frequency modes and systematically modifying chemical structures with specific functional groups. These unique insights at the chemical-bond level have started to enable the rational design and precise control of functional molecular machines in optical, materials, energy, and life sciences.

Ant-cave structured MnCO3/Mn3O4 microcubes by biopolymer-assisted facile synthesis for high-performance pseudocapacitors

NASA Astrophysics Data System (ADS)

Chandra Sekhar, S.; Nagaraju, Goli; Yu, Jae Su

2018-03-01

Porous and ant-cave structured MnCO3/Mn3O4 microcubes (MCs) were facilely synthesized via a biopolymer-assisted hydrothermal approach. Herein, chitosan was used as a natural biopolymer, which greatly controls the surface morphology and size of the prepared composite. The amino and hydroxyl group-functionalized chitosan engraves the outer surface of MCs during the hydrothermal process, which designs the interesting morphology of nanopath ways on the surface of MCs. When used as an electrode material for pseudocapacitors, the ant-cave structured MnCO3/Mn3O4 MCs showed superior energy storage values compared to the material prepared without chitosan in aqueous electrolyte solution. Precisely, the prepared ant-cave structured MnCO3/Mn3O4 MCs exhibited a maximum specific capacitance of 116.2 F/g at a current density of 0.7 A/g with an excellent cycling stability of 73.86% after 2000 cycles. Such facile and low-cost synthesis of pseudocapacitive materials with porous nanopaths is favorable for the fabrication of high-performance energy storage devices.

Offshore Energy Mapping for Northeast Atlantic and Mediterranean: MARINA PLATFORM project

NASA Astrophysics Data System (ADS)

Kallos, G.; Galanis, G.; Spyrou, C.; Kalogeri, C.; Adam, A.; Athanasiadis, P.

2012-04-01

Deep offshore ocean energy mapping requires detailed modeling of the wind, wave, tidal and ocean circulation estimations. It requires also detailed mapping of the associated extremes. An important issue in such work is the co-generation of energy (generation of wind, wave, tides, currents) in order to design platforms on an efficient way. For example wind and wave fields exhibit significant phase differences and therefore the produced energy from both sources together requires special analysis. The other two sources namely tides and currents have different temporal scales from the previous two. Another important issue is related to the estimation of the environmental frequencies in order to avoid structural problems. These are issues studied at the framework of the FP7 project MARINA PLATFORM. The main objective of the project is to develop deep water structures that can exploit the energy from wind, wave, tidal and ocean current energy sources. In particular, a primary goal will be the establishment of a set of equitable and transparent criteria for the evaluation of multi-purpose platforms for marine renewable energy. Using these criteria, a novel system set of design and optimisation tools will be produced addressing new platform design, component engineering, risk assessment, spatial planning, platform-related grid connection concepts, all focussed on system integration and reducing costs. The University of Athens group is in charge for estimation and mapping of wind, wave, tidal and ocean current resources, estimate available energy potential, map extreme event characteristics and provide any additional environmental parameter required.

Nuclear Data Uncertainty Propagation in Depletion Calculations Using Cross Section Uncertainties in One-group or Multi-group

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

Díez, C.J., E-mail: cj.diez@upm.es; Cabellos, O.; Instituto de Fusión Nuclear, Universidad Politécnica de Madrid, 28006 Madrid

Several approaches have been developed in last decades to tackle nuclear data uncertainty propagation problems of burn-up calculations. One approach proposed was the Hybrid Method, where uncertainties in nuclear data are propagated only on the depletion part of a burn-up problem. Because only depletion is addressed, only one-group cross sections are necessary, and hence, their collapsed one-group uncertainties. This approach has been applied successfully in several advanced reactor systems like EFIT (ADS-like reactor) or ESFR (Sodium fast reactor) to assess uncertainties on the isotopic composition. However, a comparison with using multi-group energy structures was not carried out, and has tomore » be performed in order to analyse the limitations of using one-group uncertainties.« less

Space Technology Plasma Issues in 2001

NASA Technical Reports Server (NTRS)

Garrett, Henry (Editor); Feynman, Joan (Editor); Gabriel, Stephen (Editor)

1986-01-01

The purpose of the workshop was to identify and discuss plasma issues that need to be resolved during the next 10 to 20 years (circa 2001) to facilitate the development of the advanced space technology that will be required 20 or 30 years into the future. The workshop consisted of 2 days of invited papers and 2 sessions of contributed poster papers. During the third day the meeting broke into 5 working groups, each of which held discussions and then reported back to the conference as a whole. The five panels were: Measurements Technology and Active Experiments Working Group; Advanced High-Voltage, High-Power and Energy-Storage Space Systems Working Group; Large Structures and Tethers Working Group; Plasma Interactions and Surface/Materials Effects Working Group; and Beam Plasmas, Electronic Propulsion and Active Experiments Using Beams Working Group.

Nuclear Data Uncertainty Propagation in Depletion Calculations Using Cross Section Uncertainties in One-group or Multi-group

NASA Astrophysics Data System (ADS)

Díez, C. J.; Cabellos, O.; Martínez, J. S.

2015-01-01

Several approaches have been developed in last decades to tackle nuclear data uncertainty propagation problems of burn-up calculations. One approach proposed was the Hybrid Method, where uncertainties in nuclear data are propagated only on the depletion part of a burn-up problem. Because only depletion is addressed, only one-group cross sections are necessary, and hence, their collapsed one-group uncertainties. This approach has been applied successfully in several advanced reactor systems like EFIT (ADS-like reactor) or ESFR (Sodium fast reactor) to assess uncertainties on the isotopic composition. However, a comparison with using multi-group energy structures was not carried out, and has to be performed in order to analyse the limitations of using one-group uncertainties.

T- and Y-splitters based on an Au/SiO2 nanoring chain at an optical communication band.

PubMed

Ahmadivand, A; Golmohammadi, S; Rostami, A

2012-05-20

In this paper, we have utilized Au nanoring chains in an SiO2 host to design certain T-and Y-structures, and expanded it to transport and split the electromagnetic energy in integrated nanophotonic devices operating at an optical communication band (λ≈1550 nm). We compared two structures and tried to choose the best one, with lower losses and higher efficiency at the output branches, in order to split and transport the optical energy. Comparing the different types of nanoparticles corroborates that nanorings have an extra degree of tunability in their geometrical components. Meanwhile, nanorings show strong confinement in near-field coupling, less extinction coefficient, and also lower scattering into the far field during energy transportation at the C-band spectrum. Due to the nanoring's particular properties, transportation losses would be lower than in other nanoparticle-based structures like nanospheres, nanorods, and nanodisks. We demonstrate that Au nanorings surrounded by an SiO2 host yield suitable conditions to excite surface Plasmons inside the metal. Comparison between Y-and T-splitters shows that the Y-splitter is a more suitable alternative than the T-splitter, with higher transmission efficiency and lower losses. In the Y-structure, the power ratio (time-averaged power across the surface) is 24.7%, and electromagnetic energy transportation takes place at group velocities in the vicinity of 30% of the velocity of light; transmission losses are γT=3 dB/655 nm and γT=3 dB/443 nm. In this work, we have applied the finite-difference time-domain method (FDTD) to simulate and indicate the properties of structures.

Self-administered structured food record for measuring individual energy and nutrient intake in large cohorts: Design and validation.

PubMed

García, Silvia M; González, Claudio; Rucci, Enzo; Ambrosino, Cintia; Vidal, Julia; Fantuzzi, Gabriel; Prestes, Mariana; Kronsbein, Peter

2018-06-05

Several instruments developed to assess dietary intake of groups or populations have strengths and weaknesses that affect their specific application. No self-administered, closed-ended dietary survey was previously used in Argentina to assess current food and nutrient intake on a daily basis. To design and validate a self-administered, structured food record (NutriQuid, NQ) representative of the adult Argentine population's food consumption pattern to measure individual energy and nutrient intake. Records were loaded onto a database using software that checks a regional nutrition information system (SARA program), automatically quantifying energy and nutrient intake. NQ validation included two phases: (1) NQ construct validity comparing records kept simultaneously by healthy volunteers (45-75 years) and a nutritionist who provided meals (reference), and (2) verification of whether NQ reflected target population consumption (calories and nutrients), week consumption differences, respondent acceptability, and ease of data entry/analysis. Data analysis included descriptive statistics, repeated measures ANOVA, intraclass correlation coefficient, nonparametric regression, and cross-classification into quintiles. The first validation (study group vs. reference) showed an underestimation (10%) of carbohydrate, fat, and energy intake. Second validation: 109 volunteers (91% response) completed the NQ for seven consecutive days. Record completion took about 9min/day, and data entry 3-6min. Mean calorie intake was 2240±119kcal/day (42% carbohydrates, 17% protein, and 41% fat). Intake significantly increased in the weekend. NQ is a simple and efficient tool to assess dietary intake in large samples. Copyright © 2018 SEEN y SED. Publicado por Elsevier España, S.L.U. All rights reserved.

The NGC 1023 galaxy group: An anti-hubble flow?

NASA Astrophysics Data System (ADS)

Chernin, A. D.; Dolgachev, V. P.; Domozhilova, L. M.

2010-10-01

We discuss recently published data indicating that the nearby galaxy group NGC 1023 includes an inner, virialized, quasi-stationary component together with an outer component comprising a flow of dwarf galaxies falling toward the center of the system. The inner component is similar to the Local Group of galaxies, but the Local Group is surrounded by a receding set of dwarf galaxies forming the local Hubble flow, rather than a system of approaching dwarfs. This clear difference in the structures of these two systems, which are very similar in other respects, may be associated with the dark energy in which they are immersed. Self-gravity dominates in the inner component of the Local Group, while the anti-gravity created by the cosmic dark-energy background dominates in the surrounding Hubble flow. In contrast, self-gravity likewise dominates throughout the NGC 1023 Group, both in its central component and in the surrounding “anti-Hubble” flow. NGC 1023 as a whole is apparently in an ongoing state of formation and virialization. We expect that there exists a receding flow similar to the local Hubble flow at distances of 1.4-3 Mpc from the center of the group, where anti-gravity should become stronger than the gravity of the system.

Efficient near-field wireless energy transfer using adiabatic system variations

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

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from themore » first resonator structure to the second resonator structure through the intermediate resonator structure.« less

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

PubMed

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-07

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Solar events and their influence on the interplanetary medium

NASA Technical Reports Server (NTRS)

Joselyn, Joann

1987-01-01

Aspects of a workshop on Solar events and their influence on the interplanetary medium, held in September 1986, are reviewed, the goal of which was to foster interactions among colleagues, leading to an improved understanding of the unified relationship between solar events and interplanetary disturbances. The workshop consisted of three working groups: (1) flares, eruptives, and other near-Sun activity; (2) coronal mass ejections; and (3) interplanetary events. Each group discussed topics distributed in advance. The flares-eruptives group members agreed that pre-event energy is stored in stressed/sheared magnetic fields, but could not agree that flares and other eruptive events (e.g., eruptive solar prominences) are aspects of the same physical phenomenon. In the coronal mass ejection group, general agreement was reached on the presence of prominences in CMEs, and that they have a significant three-dimensional structure. Some topics identified for further research were the aftermath of CMEs (streamer deflections, transient coronal holes, possible disconnections), identification of the leading edge of CMEs, and studies of the range and prevalence of CME mass sizes and energies.

Explaining the effects of a point-of-purchase nutrition-information intervention in university canteens: a structural equation modelling analysis

PubMed Central

2012-01-01

Background The importance of canteen meals in the diet of many university students makes the provision of simple point-of-purchase (POP) nutrition information in university canteens a potentially effective way to promote healthier diets in an important group of young adults. However, modifications to environments such as the posting of POP nutrition information in canteens may not cause an immediate change in meal choices and nutrient intakes. The present study aimed at understanding the process by which the POP nutrition information achieved its effects on the meal choice and energy intake, and whether the information was more effective in changing the meal choice of subgroups of university canteen customers. Methods The POP nutrition-information intervention used a one-group pretest-posttest design. A sample of 224 customers of two university canteens completed the baseline and 6-months follow-up surveys. A multi-group structural equation modelling analysis was used to test mediation effects of individual difference variables (liking, understanding and use of the information, subjective knowledge and attitude) on the energy intake from canteen meals, moderated by the objective nutrition knowledge and motivation to change diet. Results Significant relations were identified between liking of the information and its use on one hand and a positive effect in attitude towards healthy canteen meals on the other hand. Motivation to change diet and sufficient objective nutrition knowledge were required to maintain a recommended energy intake from canteen meals or to lead to a decrease in energy intake. Participants with greater objective nutrition knowledge had a greater understanding of the POP nutrition information which also resulted in a more effective use of the information. Conclusions The results suggest that nutrition-information interventions may be more effective when using nutrition information that is generally liked by the target population in combination with an educational intervention to increase objective nutrition knowledge. Trial registration NCT01249508 PMID:22967195

Explaining the effects of a point-of-purchase nutrition-information intervention in university canteens: a structural equation modelling analysis.

PubMed

Hoefkens, Christine; Pieniak, Zuzanna; Van Camp, John; Verbeke, Wim

2012-09-11

The importance of canteen meals in the diet of many university students makes the provision of simple point-of-purchase (POP) nutrition information in university canteens a potentially effective way to promote healthier diets in an important group of young adults. However, modifications to environments such as the posting of POP nutrition information in canteens may not cause an immediate change in meal choices and nutrient intakes. The present study aimed at understanding the process by which the POP nutrition information achieved its effects on the meal choice and energy intake, and whether the information was more effective in changing the meal choice of subgroups of university canteen customers. The POP nutrition-information intervention used a one-group pretest-posttest design. A sample of 224 customers of two university canteens completed the baseline and 6-months follow-up surveys. A multi-group structural equation modelling analysis was used to test mediation effects of individual difference variables (liking, understanding and use of the information, subjective knowledge and attitude) on the energy intake from canteen meals, moderated by the objective nutrition knowledge and motivation to change diet. Significant relations were identified between liking of the information and its use on one hand and a positive effect in attitude towards healthy canteen meals on the other hand. Motivation to change diet and sufficient objective nutrition knowledge were required to maintain a recommended energy intake from canteen meals or to lead to a decrease in energy intake. Participants with greater objective nutrition knowledge had a greater understanding of the POP nutrition information which also resulted in a more effective use of the information. The results suggest that nutrition-information interventions may be more effective when using nutrition information that is generally liked by the target population in combination with an educational intervention to increase objective nutrition knowledge.

Electronic structure and vibrational analysis of AHA⋯HX complexes

NASA Astrophysics Data System (ADS)

Joshi, Kaustubh A.; Gejji, Shridhar P.

2005-10-01

Electronic structures of the binary complexes of acetohydroxamic acid (AHA) and hydrogen halides, HX (X = F, Cl, Br) have been investigated using the second order perturbation theory. In the lowest energy structure of AHA⋯HF complex, hydrogen fluoride acts as a proton-donor with carbonyl oxygen and simultaneously as a proton-acceptor with the hydroxyl group. For chloro- and bromo-substituted derivatives, however, the lowest minimum possesses hydrogen-bonded interactions with the carbonyl oxygen in addition to those from the methyl proton of AHA. Frequency shifts of NH and CN stretching vibrations enable one to distinguish different conformers of AHA⋯HX complexes.

Fluorine substitution and nonconventional OH...pi intramolecular bond: high-resolution UV spectroscopy and ab initio calculations of 2-(p-fluorophenyl)ethanol.

PubMed

Karaminkov, Rosen; Chervenkov, Sotir; Neusser, Hans J

2008-05-21

The para-fluorinated flexible neurotransmitter analogue 2-phenylethanol has been investigated by highly resolved resonance-enhanced two-photon ionisation two-colour UV laser spectroscopy with mass resolution and ab initio structural optimisations and energy calculations. Two stable conformations, gauche and anti, separated by a high potential barrier have been identified in the cold molecular beam by rotational analysis of the vibronic band structures. The theoretically predicted higher-lying conformations most likely relax to these two structures during the adiabatic expansion. The lowest-energy gauche conformer is stabilised by an intramolecular nonconventional OH...pi-type hydrogen bond between the terminal OH group of the side chain and the pi electrons of the phenyl ring. The good agreement between the experimental and theoretical results demonstrates that even the substitution with a strongly electronegative atom of 2-phenylethanol at the para position has no noticeable effect on the strength and orientation of the OH...pi bond.

Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding

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

Wang, Huanchen; Falck, J.R.; Hall, Traci M. Tanaka

2012-01-11

Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domainmore » of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF{sub 3}{sup -} transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.« less

Holographic Aquaculture

NASA Astrophysics Data System (ADS)

Ian, Richard; King, Elisabeth

1988-01-01

Proposed is an exploratory study to verify the feasibility of an inexpensive micro-climate control system for both marine and freshwater pond and tank aquaculture, offering good control over water temperature, incident light flux, and bandwidth, combined with good energy efficiency. The proposed control system utilizes some familiar components of passive solar design, together with a new holographic glazing system which is currently being developed by, and proprietary to Advanced Environmental Research Group (AERG). The use of solar algae ponds and tanks to warm and purify water for fish and attached macroscopic marine algae culture is an ancient and effective technique, but limited seasonally and geographically by the availability of sunlight. Holographic Diffracting Structures (HDSs) can be made which passively track, accept and/or reject sunlight from a wide range of altitude and azimuth angles, and redirect and distribute light energy as desired (either directly or indirectly over water surface in an enclosed, insulated structure), effectively increasing insolation values by accepting sunlight which would not otherwise enter the structure.

Investigation of microstructural and optical properties of La0.8Ca0.2FeO3 nanostructure synthesized via gel combustion method

NASA Astrophysics Data System (ADS)

Naseem, Swaleha; Ali, S. Asad; Khan, Wasi; Khan, Shakeel

2018-05-01

Ca substituted LaFeO3 orthoferrite nanostructure perovskite has been synthesized by gel combustion method using citric acid as a fuel. The structural and optical properties were investigated by various tools. The structural analysis through Rietveld refinement of the XRD data revealed single phase of orthorhombic structure in R-3c space group of the sample without presence of any other impurity phase. Scanning electron microscopy (SEM) image exhibits non-uniform distribution of the nanoparticles in agglomerated form. The purity of the sample and stoichiometric ratio of the elements were established through energy dispersive x-ray spectroscopy (EDS). FTIR spectroscopy measurement predicts the presence of various band relation of the chemical species of Ca with LaFeO3. Optical properties were explored through UV-visible absorption spectroscopy that showed absorption edge at 347 nm and energy band gap was estimated as 3.47eV using Tauc's relation.

Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR

PubMed Central

Camilloni, Carlo; Schaal, Daniel; Schweimer, Kristian; Schwarzinger, Stephan; De Simone, Alfonso

2012-01-01

The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules. PMID:22225810

Structural and thermodynamic properties of the Cm III ion solvated by water and methanol

DOE PAGES

Kelley, Morgan P.; Yang, Ping; Clark, Sue B.; ...

2016-04-27

The geometric and electronic structures of the 9-coordinate Cm 3+ ion solvated with both water and methanol are systematically investigated in the gas phase at each possible solvent-shell composition and configuration using density functional theory and second-order Møller–Plesset perturbation theory. Ab initio molecular dynamics simulations are employed to assess the effects of second and third solvent shells on the gas-phase structure. The ion–solvent dissociation energy for methanol is greater than that of water, potentially because of increased charge donation to the ion made possible by the electron-rich methyl group. Further, the ion–solvent dissociation energy and the ion–solvent distance are shownmore » to be dependent on the solvent-shell composition. Furthermore, this has implications for solvent exchange, which is generally the rate-limiting step in complexation reactions utilized in the separation of curium from complex metal mixtures that derive from the advanced nuclear fuel cycle.« less

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Matrix-Assisted Laser Desorption/Ionisation - High-Energy Collision-Induced Dissociation of Steroids: Analysis of Oxysterols in Rat Brain

PubMed Central

Wang, Yuqin; Hornshaw, Martin; Alvelius, Gunvor; Bodin, Karl; Liu, Suya; Sjövall, Jan; Griffiths, William J.

2008-01-01

Neutral steroids have traditionally been analysed by gas chromatography – mass spectrometry (GC-MS) after necessary derivatisation reactions. However, GC-MS is unsuitable for the analysis of many conjugated steroids and those with unsuspected functional groups. Here we describe an alternative analytical method specifically designed for the analysis of oxosteroids and those with a 3β-hydroxy-Δ5 or 5α-hydrogen-3β-hydroxy structure. Steroids were derivatised with Girard P (GP) hydrazine to give GP hydrazones which are charged species and readily analysed by matrix-assisted laser desorption/ionization mass spectrometry. The resulting [M]+ ions were then subjected to high-energy collision-induced dissociation on a tandem time-of-flight instrument. The product-ion spectra give structurally informative fragment-ion patterns. The sensitivity of the analytical method is such that steroids structures can be determined from low pg (low fmole) amounts of sample. The utility of the method has been demonstrated by the analysis of oxysterols extracted from rat brain. PMID:16383324

Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: experiment and theory.

PubMed

Alagia, Michele; Baldacchini, Chiara; Betti, Maria Grazia; Bussolotti, Fabio; Carravetta, Vincenzo; Ekström, Ulf; Mariani, Carlo; Stranges, Stefano

2005-03-22

The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288 eV photon energy, due to absorption to pi* virtual orbitals, and broader structures at higher energy, involving sigma* virtual orbitals. The sharp absorption structures to the pi* empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of pi* symmetry, from the six chemically shifted C 1s core orbitals.

Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory

NASA Astrophysics Data System (ADS)

Alagia, Michele; Baldacchini, Chiara; Betti, Maria Grazia; Bussolotti, Fabio; Carravetta, Vincenzo; Ekström, Ulf; Mariani, Carlo; Stranges, Stefano

2005-03-01

The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288eV photon energy, due to absorption to π* virtual orbitals, and broader structures at higher energy, involving σ* virtual orbitals. The sharp absorption structures to the π* empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of π* symmetry, from the six chemically shifted C 1s core orbitals.

The descent into glass formation in polymer fluids.

PubMed

Freed, Karl F

2011-03-15

Glassy materials have been fundamental to technology since the dawn of civilization and remain so to this day: novel glassy systems are currently being developed for applications in energy storage, electronics, food, drugs, and more. Glass-forming fluids exhibit a universal set of transitions beginning at temperatures often in excess of twice the glass transition temperature T(g) and extending down to T(g), below which relaxation becomes so slow that systems no longer equilibrate on experimental time scales. Despite the technological importance of glasses, no prior theory explains this universal behavior nor describes the huge variations in the properties of glass-forming fluids that result from differences in molecular structure. Not surprisingly, the glass transition is currently regarded by many as the deepest unsolved problem in solid state theory. In this Account, we describe our recently developed theory of glass formation in polymer fluids. Our theory explains the origin of four universal characteristic temperatures of glass formation and their dependence on monomer-monomer van der Waals energies, conformational energies, and pressure and, perhaps most importantly, on molecular details, such as monomer structure, molecular weight, size of side groups, and so forth. The theory also provides a molecular explanation for fragility, a parameter that quantifies the rate of change with temperature of the viscosity and other dynamic mechanical properties at T(g). The fragility reflects the fluid's thermal sensitivity and determines the manner in which glass-formers can be processed, such as by extrusion, casting, or inkjet spotting. Specifically, the theory describes the change in thermodynamic properties and fragility of polymer glasses with variations in the monomer structure, the rigidity of the backbone and side groups, the cohesive energy, and so forth. The dependence of the structural relaxation time at lower temperatures emerges from the theory as the Vogel-Fulcher equation, whereas pressure and concentration analogs of the Vogel-Fulcher expression follow naturally from the theory with no additional assumptions. The computed dependence of T(g) and fragility on the length of the side group in poly(α-olefins) agrees quite well with observed trends, demonstrating that the theory can be utilized, for instance, to guide the tailoring of T(g) and the fragility of glass-forming polymer fluids in the fabrication of new materials. Our calculations also elucidate the molecular characteristics of small-molecule diluents that promote antiplasticization, a lowering of T(g) and a toughening of the material. © 2011 American Chemical Society

Cation and anion dependence of stable geometries and stabilization energies of alkali metal cation complexes with FSA(-), FTA(-), and TFSA(-) anions: relationship with physicochemical properties of molten salts.

PubMed

Tsuzuki, Seiji; Kubota, Keigo; Matsumoto, Hajime

2013-12-19

Stable geometries and stabilization energies (Eform) of the alkali metal complexes with bis(fluorosulfonyl)amide, (fluorosulfonyl)(trifluoromethylslufonyl)amide and bis(trifluoromethylsulfonyl)amide (FSA(-), FTA(-) and TFSA(-)) were studied by ab initio molecular orbital calculations. The FSA(-) complexes prefer the bidentate structures in which two oxygen atoms of two SO2 groups have contact with the metal cation. The FTA(-) and TFSA(-) complexes with Li(+) and Na(+) prefer the bidentate structures, while the FTA(-) and TFSA(-) complexes with Cs(+) prefer tridentate structures in which the metal cation has contact with two oxygen atoms of an SO2 group and one oxygen atom of another SO2 group. The two structures are nearly isoenergetic in the FTA(-) and TFSA(-) complexes with K(+) and Rb(+). The magnitude of Eform depends on the alkali metal cation significantly. The Eform calculated for the most stable TFSA(-) complexes with Li(+), Na(+), K(+), Rb(+) and Cs(+) cations at the MP2/6-311G** level are -137.2, -110.5, -101.1, -89.6, and -84.1 kcal/mol, respectively. The viscosity and ionic conductivity of the alkali TFSA molten salts have strong correlation with the magnitude of the attraction. The viscosity increases and the ionic conductivity decreases with the increase of the attraction. The melting points of the alkali TFSA and alkali BETA molten salts also have correlation with the magnitude of the Eform, which strongly suggests that the magnitude of the attraction play important roles in determining the melting points of these molten salts. The anion dependence of the Eform calculated for the complexes is small (less than 2.9 kcal/mol). This shows that the magnitude of the attraction is not the cause of the low melting points of alkali FTA molten salts compared with those of corresponding alkali TFSA molten salts. The electrostatic interactions are the major source of the attraction in the complexes. The electrostatic energies for the most stable TFSA(-) complexes with the five alkali metal cations are -140.3, -119.4, -104.1, -96.9, and -91.1 kcal/mol, respectively. The induction interactions also contribute to the attraction. In particular, the induction interactions are large in the Li(+) complexes. The induction energies for the five complexes are -46.6, -25.2, -17.5, -13.3, and -10.4 kcal/mol, respectively.

Nitrogen sparing effect of structured triglycerides containing both medium-and long-chain fatty acids in critically ill patients; a double blind randomized controlled trial.

PubMed

Lindgren, B F; Ruokonen, E; Magnusson-Borg, K; Takala, J

2001-02-01

Patients with sepsis and trauma are characterised by hypermetabolism, insulin resistance and protein catabolism. Fat emulsions containing medium chain triglycerides have been suggested to be beneficial for these patients since medium chain fatty acids are a more readily available source of energy when compared to long chain fatty acids. The aim of this study was to compare a medium and long chain triglyceride emulsion consisting of structured triglycerides (ST) with a long chain triglyceride (LCT) emulsion in terms of effects on nitrogen balance, energy metabolism and safety. 30 ICU patients with sepsis or multiple injury received a fat emulsion with ST or 20% LCT (1.5 g triglycerides/kg body weight/day) as a component of total parenteral nutrition (TPN), for 5 days in a double blind randomised parallel group design. The main analysis was made on the 3 day per protocol population due to lack of patients at day 5. There were no differences in baseline characteristics of the two groups receiving either the LCT or the ST emulsion. The efficacy analysis was performed on the per protocol population (n=9 ST, n=11 LCT). There was a significant difference between the two treatments regarding daily nitrogen balances when the first 3 days were analysed P=0.0038). This resulted in an amelioration of the nitrogen balance on day 3 in the group on ST as compared to those on LCT (0.1+/-2.4 g vs -9.9+/-2.1 g P=0.01). The 3 day cumulative nitrogen balance was significantly better in the group receiving ST compared to those on LCT (-0.7+/-6.0 vs -16.7+/-3.9 P=0.03). This better cumulative nitrogen balance on day 3 was also preserved as a tendency (P=0.061) in the analysis of the intention to treat population, but on day 5 there was no significant difference (P=0.08). The ST emulsion was well tolerated and no difference was found compared to the LCT emulsion regarding respiratory quotient, energy expenditure, glucose or triglyceride levels during infusion. Administration of a structured triglyceride emulsion resulted in an amelioration of nitrogen balance despite no effect on energy expenditure in short term administration over 3 days to ICU patients when compared to a long chain triglyceride emulsion. No side effects linked to medium chain triglycerides were noted. Copyright 2001 Harcourt Publishers Ltd.

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

DOE PAGES

Li, Guo; Rangel, Tonatiuh; Liu, Zhen -Fei; ...

2016-03-24

Using density functional theory (DFT) with van der Waals functionals, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously-studied monomeric phases. Moreover, using a model based on many-body perturbation theory within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. As a result, we find that, independent of coverage, the HOMO energy of the linear chain phase ismore » lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy.« less

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhen-Fei; Cooper, Valentino R.; Neaton, Jeffrey B.

2016-03-01

Using density functional theory (DFT) with a van der Waals density functional, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously studied monomeric phases. Moreover, using a model, which includes nonlocal polarization effects from the substrate and the neighboring molecules and incorporates many-body perturbation theory calculations within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. We find that, independent of coverage, the HOMO energy of the linear chain phase is lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy.

E-novo: an automated workflow for efficient structure-based lead optimization.

PubMed

Pearce, Bradley C; Langley, David R; Kang, Jia; Huang, Hongwei; Kulkarni, Amit

2009-07-01

An automated E-Novo protocol designed as a structure-based lead optimization tool was prepared through Pipeline Pilot with existing CHARMm components in Discovery Studio. A scaffold core having 3D binding coordinates of interest is generated from a ligand-bound protein structural model. Ligands of interest are generated from the scaffold using an R-group fragmentation/enumeration tool within E-Novo, with their cores aligned. The ligand side chains are conformationally sampled and are subjected to core-constrained protein docking, using a modified CHARMm-based CDOCKER method to generate top poses along with CDOCKER energies. In the final stage of E-Novo, a physics-based binding energy scoring function ranks the top ligand CDOCKER poses using a more accurate Molecular Mechanics-Generalized Born with Surface Area method. Correlation of the calculated ligand binding energies with experimental binding affinities were used to validate protocol performance. Inhibitors of Src tyrosine kinase, CDK2 kinase, beta-secretase, factor Xa, HIV protease, and thrombin were used to test the protocol using published ligand crystal structure data within reasonably defined binding sites. In-house Respiratory Syncytial Virus inhibitor data were used as a more challenging test set using a hand-built binding model. Least squares fits for all data sets suggested reasonable validation of the protocol within the context of observed ligand binding poses. The E-Novo protocol provides a convenient all-in-one structure-based design process for rapid assessment and scoring of lead optimization libraries.

High-temperature mass spectrometry - Vaporization of group 4-B metal carbides. [using Knudsen effusion

NASA Technical Reports Server (NTRS)

Stearns, C. A.; Kohl, F. J.

1974-01-01

The high temperature vaporization of the metal-carbon systems TiC, ZrC, HfC, and ThC was studied by the Knudsen effusion - mass spectrometric method. For each system the metal dicarbide and tetracarbide molecular species were identified in the gas phase. Relative ion currents of the carbides and metals were measured as a function of temperature. Second- and third-law methods were used to determine enthalpies. Maximum values were established for the dissociation energies of the metal monocarbide molecules TiC, ZrC, HfC, and ThC. Thermodynamic functions used in the calculations are discussed in terms of assumed molecular structures and electronic contributions to the partition functions. The trends shown by the dissociation energies of the carbides of Group 4B are compared with those of neighboring groups and discussed in relation to the corresponding oxides and chemical bonding. The high temperature molecular beam inlet system and double focusing mass spectrometer are described.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Structural sensitivity of Csbnd H vibrational band in methyl benzoate

NASA Astrophysics Data System (ADS)

Roy, Susmita; Maiti, Kiran Sankar

2018-05-01

The Csbnd H vibrational bands of methyl benzoate are studied to understand its coupling pattern with other vibrational bands of the biological molecule. This will facilitate to understand the biological structure and dynamics in spectroscopic as well as in microscopic study. Due to the congested spectroscopic pattern, near degeneracy, and strong anharmonicity of the Csbnd H stretch vibrations, assignment of the Csbnd H vibrational frequencies are often misleading. Anharmonic vibrational frequency calculation with multidimensional potential energy surface interprets the Csbnd H vibrational spectra more accurately. In this article we have presented the importance of multidimensional potential energy surface in anharmonic vibrational frequency calculation and discuss the unexpected red shift of asymmetric Csbnd H stretch vibration of methyl group. The Csbnd D stretch vibrational band which is splitted to double peaks due to the Fermi resonance is also discussed here.

A new look into conformational, vibrational and electronic structure analysis of 3,4-dimethoxybenzonitrile.

PubMed

Arjunan, V; Devi, L; Remya, P; Mohan, S

2013-09-01

The FTIR and FT-Raman spectra of 3,4-dimethoxybenzonitrile (34DMBN) have been analysed. Quantum chemical studies were performed with B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVTZ basis sets. The electron donating effect of -OCH3 and electron withdrawing effect of -C≡N groups on the ring parameters were thoroughly analysed. The structural parameters, energies, thermodynamic properties, vibrational frequencies and the NBO charges of 34DMBN were determined. The (1)H and (13)C chemical shifts with respect to TMS were investigated and also calculated theoretically using the gauge independent atomic orbital method and compared with the experimental data. The delocalisation energy of different types of bonding interactions was investigated. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of the mechanical properties of the anterior lens capsule following femtosecond laser capsulotomy at different pulse energy settings.

PubMed

Sándor, Gábor L; Kiss, Zoltán; Bocskai, Zoltán I; Kolev, Krasimir; Takács, Ágnes I; Juhász, Éva; Kránitz, Kinga; Tóth, Gábor; Gyenes, Andrea; Bojtár, Imre; Juhász, Tibor; Nagy, Zoltán Z

2015-03-01

To evaluate and compare the mechanical properties of anterior capsule opening performed with femtosecond laser capsulotomy at different energy settings in ex vivo porcine anterior lens capsule specimens. Twenty-five fresh porcine eyes per group were included in the study. Femtosecond laser capsulotomy was performed with three different pulse energy levels: 2 µJ (low energy group), 5 µJ (intermediate energy group), and 10 µJ (high energy group). The capsule openings were stretched with universal testing equipment until they ruptured. The morphologic profile of the cut capsule edges was evaluated using scanning electron microscopy. The high energy group had significantly lower rupture force (108 ± 14 mN) compared to the intermediate energy group (118 ± 10 mN) (P < .05) and low energy group (119 ± 11 mN) (P < .05), but the difference between the intermediate energy and low energy groups was not significant (P = .9479). The high energy group had significantly lower circumference stretching ratio (144% ± 3%) compared to the intermediate energy group (148% ± 3%) (P < .05) and low energy group (148% ± 3%) (P < .05), but the difference between the intermediate energy group and low energy group was not significant (P = .9985). Scanning electron microscopy images showed that the edge was only serrated with low and intermediate energy, but additional signs of collagen melting and denaturation were observed at high energy. Anterior capsule openings created at a high energy level were slightly weaker and less extensible than those created at low or intermediate levels, possibly due to the increased thermal effect of photo-disruption. Copyright 2015, SLACK Incorporated.

Binding in alkali and alkaline-earth tetrahydroborates: Special position of magnesium tetrahydroborate

NASA Astrophysics Data System (ADS)

Łodziana, Zbigniew; van Setten, Michiel J.

2010-01-01

Compounds of light elements and hydrogen are currently extensively studied due to their potential application in the field of hydrogen or energy storage. A number of new interesting tetrahydroborates that are especially promising due to their very high gravimetric hydrogen content were recently reported. However, the determination and understanding of their complex crystalline structures has created considerable debate. Metal tetrahydroborates, in general, form a large variety of structures ranging from simple for NaBH4 to very complex for Mg(BH4)2 . Despite the extensive discussion in the literature no clear explanation has been offered for this variety so far. In this paper we analyze the structural and electronic properties of a broad range of metal tetrahydroborates and reveal the factors that determine their structure: ionic bonding, the orientation of the BH4 groups, and the coordination number of the metal cation. We show, in a simple way, that the charge transfer in the metal tetrahydroborates rationally explains the structural diversity of these compounds. Being ionic systems, the metal tetrahydroborates fall into the classification of Linus Pauling. By using the ionic radius for the BH4 group as determined in this paper, this allows for structural predictions for new and mixed compounds.

Structured hypocaloric diet is more effective than behavioral therapy in reducing metabolic syndrome in Mexican postmenopausal women: a randomized controlled trial.

PubMed

Perichart-Perera, Otilia; Balas-Nakash, Margie; Muñoz-Manrique, Cinthya; Legorreta-Legorreta, Jennifer; Rodríguez-Cano, Ameyalli; Mier-Cabrera, Jennifer; Aguilera-Pérez, Jesús Rafael

2014-07-01

This study aims to compare the effects of a lifestyle intervention using a behavioral therapy (BT) approach with the effects of a cardioprotective structured hypocaloric diet on metabolic syndrome in Mexican postmenopausal women. This study is a randomized clinical trial (2006-2009) of Mexican postmenopausal women with metabolic syndrome (Adult Treatment Panel III criteria) who were recruited from the Postmenopause Clinic of the National Institute of Perinatology in Mexico City. Women were assigned to one of two groups--group 1 (structured hypocaloric diet; n = 63): energy restriction (-300 to -500 kcal/d) emphasizing cardioprotective dietary changes; and group 2 (BT; n = 55): goal setting, problem-solving, and stimulus control to achieve cardioprotective dietary and lifestyle recommendations. Metabolic syndrome prevalence, as well as weight, waist circumference, fat mass, and fasting biochemical markers (glucose and lipid profile), were measured at baseline and at 2, 4, and 6 months after the intervention. Metabolic syndrome risk (relative risk and absolute risk reduction), mean differences between groups, and logistic regression were evaluated using Statistical Package for the Social Sciences software, version 17.0. A total of 118 women were studied (mean [SD] age, 53.81 [6.43] y). No baseline differences were observed between groups. At the end of the study, a higher reduction in metabolic syndrome prevalence was observed in group 1 (-38.1%) compared with group 2 (-12.7%; relative risk, 0.237; 95% CI, 0.092-0.608; P = 0.003). The effect was maintained even when adjusted by age, hormone therapy and antihypertensive drug use. A cardioprotective structured hypocaloric diet is more effective than the BT approach in reducing metabolic syndrome after 6 months of intervention. Both strategies have positive effects on different individual cardiovascular risk factors.

Understanding the effects on constitutive activation and drug binding of a D130N mutation in the β2 adrenergic receptor via molecular dynamics simulation.

PubMed

Zhu, Yanyan; Yuan, Yuan; Xiao, Xiuchan; Zhang, Liyun; Guo, Yanzhi; Pu, Xuemei

2014-11-01

G-protein-coupled receptors (GPCRs) are currently one of the largest families of drug targets. The constitutive activation induced by mutation of key GPCR residues is associated closely with various diseases. However, the structural basis underlying such activation and its role in drug binding has remained unclear. Herein, we used all-atom molecular dynamics simulations and free energy calculations to study the effects of a D130N mutation on the structure of β2 adrenergic receptor (β2AR) and its binding of the agonist salbutamol. The results indicate that the mutation caused significant changes in some key helices. In particular, the mutation leads to the departure of transmembrane 3 (TM3) from transmembrane 6 (TM6) and marked changes in the NPxxY region as well as the complete disruption of a key ionic lock, all of which contribute to the observed constitutive activation. In addition, the D130N mutation weakens some important H-bonds, leading to structural changes in these regions. Binding free energy calculations indicate that van der Waals and electrostatic interactions are the main driving forces in binding salbutamol; however, binding strength in the mutant β2AR is significantly enhanced mainly through modifying electrostatic interactions. Further analysis revealed that the increase in binding energy upon mutation stems mainly from the H-bonds formed between the hydroxyl group of salbutamol and the serine residues of TM5. This observation suggests that modifications of the H-bond groups of this drug could significantly influence drug efficacy in the treatment of diseases associated with this mutation.

Relativistic DFT investigation of electronic structure effects arising from doping the Au25 nanocluster with transition metals.

PubMed

Alkan, Fahri; Muñoz-Castro, Alvaro; Aikens, Christine M

2017-10-26

We perform a theoretical investigation using density functional theory (DFT) and time-dependent DFT (TDDFT) on the doping of the Au 25 (SR) 18 -1 nanocluster with group IX transition metals (M = cobalt, rhodium and iridium). Different doping motifs, charge states and spin multiplicities were considered for the single-atom doped nanoclusters. Our results show that the interaction (or the lack of interaction) between the d-type energy levels that mainly originate from the dopant atom and the super-atomic levels plays an important role in the energetics, the electronic structure and the optical properties of the doped systems. The evaluated MAu 24 (SR) 18 q (q = -1, -3) systems favor an endohedral disposition of the doping atom typically in a singlet ground state, with either a 6- or 8-valence electron icosahedral core. For the sake of comparison, the role of the d energy levels in the electronic structure of a variety of doped Au 25 (SR) 18 -1 nanoclusters was investigated for dopant atoms from other families such as Cd, Ag and Pd. Finally, the effect of spin-orbit coupling (SOC) on the electronic structure and absorption spectra was determined. The information in this study regarding the relative energetics of the d-based and super-atom energy levels can be useful to extend our understanding of the preferred doping modes of different transition metals in protected gold nanoclusters.

Low-energy electron collisions with proline and pyrrolidine: A comparative study

NASA Astrophysics Data System (ADS)

Barbosa, Alessandra Souza; Freitas, Thiago Corrêa; Bettega, M. H. F.

2018-02-01

We present a comparative study on the calculated cross sections obtained for the elastic collisions of low-energy electrons with the amino acid proline (C5H9NO2) and its building block pyrrolidine (C4H9N). We employed the Schwinger multichannel method implemented with pseudopotentials to compute integral, differential, and momentum transfer cross sections in the static-exchange plus polarization approximation, for energies up to 15 eV. We report three shape resonances for proline at around 1.7 eV, 6.8 eV, and 10 eV and two shape resonances for pyrrolidine centered at 7 eV and 10.2 eV. The present resonance energies are compared with available experimental data on vertical attachment energies and dissociative electron attachment, where a good agreement is found. From the comparison of the present results with available calculated cross sections for the simplest carboxylic acid, formic acid (HCOOH), and from electronic structure calculations, we found that the first resonance of proline, at 1.7 eV, is due the presence of the carboxylic group, whereas the other two structures, at 6.8 eV and 10 eV, clearly arise from the pyrrolidine ring. A comparison between the differential cross sections for proline and pyrrolidine at some selected energies of the incident electron is also reported in this paper.

Defects and impurities induced structural and electronic changes in pyrite CoS2: first principles studies.

PubMed

Li, Shengwen; Zhang, Yanning; Niu, Xiaobin

2018-05-03

Cobalt pyrite (CoS2) and related materials are attracting much attention due to their potential use in renewable energy applications. In this work, first-principles studies were performed to investigate the effects of various neutral defects and ion dopants on the structural, energetic, magnetic and electronic properties of the bulk CoS2. Our theoretical results show that the concentrations of single cobalt (VCo) and sulfur (VS) vacancies in CoS2 samples can be high under S-rich and S-poor conditions, respectively. Although the single vacancies induce defect states near the gap edge, they are still half-metallic. We find that the substitution of one S with the O atom does not obviously change the structural, magnetic and electronic features near the Fermi level of the system. Most transition metal impurities (MnCo, FeCo, and MoCo) and Group IV and V anion impurities (CS, SiS, NS, PS, and AsS) create impurity states that are deep and/or near the gap edge. However, NiCo and Group VII elements (FS, ClS, and BrS) cause very localized gap states close to the Fermi level in the minority spin channel, which may modify their electrochemical performances. Our extensive calculations provide instructive information for the design and optimization of CoS2-related energy materials.

Microwave Spectroscopy of 2-PENTANONE

NASA Astrophysics Data System (ADS)

Andresen, Maike; Nguyen, Ha Vinh Lam; Kleiner, Isabelle; Stahl, Wolfgang

2017-06-01

Methyl propyl ketone (MPK) or 2-Pentanone is known to be an alarm pheroromone released by the mandibular glands of the bees. It is a highly volatile compound. This molecule was studied by a combination of quantum chemical calculations and microwave spectroscopy in order to get informations about the lowest energy conformers and their structures.The rotational spectrum of 2-pentanone was measured using the molecular beam Fourier transform microwave spectrometer in Aachen operating between 2 and 26.5 GHz. Ab initio calculations determine 4 conformers but only two of them are observed in our jet-beam conditions.The lowest conformer has a C_{1} structure and its spectrum shows internal rotation splittings arising from two methyl groups. The internal splittings of 305 transitions for this conformer were analyzed using the XIAM code It led to the determination of the values for the barrier heights hindering the internal rotation of two methyl groups of 239 cm^{-1} and 980 cm^{-1} respectively. The next energy conformer has a C_{s} structure and the analysis of the internal splittings of 134 transitions using the XIAM code and the BELGI code led to the determination of internal rotation barrier height of 186 cm^{-1}. Comparisons of quantum chemistry and experimental results will be discussed. H. Hartwig, H. Dreizler, Z. Naturforsch. 51a, 923 (1996). J. T. Hougen, I. Kleiner and M. Godefroid, J. Mol. Spectrosc., 163, 559-586 (1994).

Growth and applications of GeSn-related group-IV semiconductor materials

PubMed Central

Zaima, Shigeaki; Nakatsuka, Osamu; Taoka, Noriyuki; Kurosawa, Masashi; Takeuchi, Wakana; Sakashita, Mitsuo

2015-01-01

We review the technology of Ge1−xSnx-related group-IV semiconductor materials for developing Si-based nanoelectronics. Ge1−xSnx-related materials provide novel engineering of the crystal growth, strain structure, and energy band alignment for realising various applications not only in electronics, but also in optoelectronics. We introduce our recent achievements in the crystal growth of Ge1−xSnx-related material thin films and the studies of the electronic properties of thin films, metals/Ge1−xSnx, and insulators/Ge1−xSnx interfaces. We also review recent studies related to the crystal growth, energy band engineering, and device applications of Ge1−xSnx-related materials, as well as the reported performances of electronic devices using Ge1−xSnx related materials. PMID:27877818

Growth and applications of GeSn-related group-IV semiconductor materials.

PubMed

Zaima, Shigeaki; Nakatsuka, Osamu; Taoka, Noriyuki; Kurosawa, Masashi; Takeuchi, Wakana; Sakashita, Mitsuo

2015-08-01

We review the technology of Ge 1- x Sn x -related group-IV semiconductor materials for developing Si-based nanoelectronics. Ge 1- x Sn x -related materials provide novel engineering of the crystal growth, strain structure, and energy band alignment for realising various applications not only in electronics, but also in optoelectronics. We introduce our recent achievements in the crystal growth of Ge 1- x Sn x -related material thin films and the studies of the electronic properties of thin films, metals/Ge 1- x Sn x , and insulators/Ge 1- x Sn x interfaces. We also review recent studies related to the crystal growth, energy band engineering, and device applications of Ge 1- x Sn x -related materials, as well as the reported performances of electronic devices using Ge 1- x Sn x related materials.

Division of Biological and Medical Research research summary 1984-1985

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

Barr, S.H.

1985-08-01

The Division of Biological and Medical Research at Argonne National Laboratory conducts multidisciplinary research aimed at defining the biological and medical hazards to man from energy technologies and new energy options. These technically oriented studies have a strong base in fundamental research in a variety of scientific disciplines, including molecular and cellular biology, biophysics, genetics, radiobiology, pharmacology, biochemistry, chemistry, environmental toxicology, and epidemiology. This research summary is organized into six parts. The first five parts reflect the Divisional structure and contain the scientific program chapters, which summarize the activities of the individual groups during the calendar year 1984 and themore » first half of 1985. To provide better continuity and perspective, previous work is sometimes briefly described. Although the summaries are short, efforts have been made to indicate the range of research activities for each group.« less

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.

Effects of scandium substitution on the crystal structure and luminescence properties of LuBO{sub 3}: Ce{sup 3+}

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

Wu, Yuntao, E-mail: caswyt@hotmail.com; Ren, Guohao, E-mail: rgh@mail.sic.ac.cn; Ding, Dongzhou

2012-10-15

The calcite phase of LuBO{sub 3} and ScBO{sub 3} polycrystalline powders were synthesized by solid state reaction method, and the Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce (x=0.2, 0.5, 0.7) single crystals were grown by the Czochralski method. A large composition deviation between the initial polycrystalline powders and final single crystal was confirmed by electron probe micro-analysis. Raman spectroscopy revealed that moderate lattice disorder was induced by scandium substitution. However, based on the single crystal X-ray study, we finally concluded that the crystal structure of lutetium scandium orthoborate still crystallized in the rhombohedral system belonging to R3{sup -}c. Furthermore, the relationship between themore » energies of the five 5d levels of Ce{sup 3+} and the crystalline environment was revealed. The total redshift, total crystal field splitting, and centroid shift of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce{sup 3+} were calculated based on their VUV excitation spectra. The variations trend of these observed spectroscopic parameters was in accordance with the predicted ones. - Graphical abstract: The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. The relationship between the energies of the five Ce{sup 3+} 5d levels and the crystalline environment is established. Highlights: Black-Right-Pointing-Pointer Moderate lattice disorder is induced by scandium doping. Black-Right-Pointing-Pointer The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. Black-Right-Pointing-Pointer Relationship between energies of Ce{sup 3+} 5d levels and crystalline environment is established. Black-Right-Pointing-Pointer The spectroscopic parameters are experimentally and theoretically calculated.« less

Magnitude Differences in Bioactive Compounds, Chemical Functional Groups, Fatty Acid Profiles, Nutrient Degradation and Digestion, Molecular Structure, and Metabolic Characteristics of Protein in Newly Developed Yellow-Seeded and Black-Seeded Canola Lines.

PubMed

Theodoridou, Katerina; Zhang, Xuewei; Vail, Sally; Yu, Peiqiang

2015-06-10

Recently, new lines of yellow-seeded (CS-Y) and black-seeded canola (CS-B) have been developed with chemical and structural alteration through modern breeding technology. However, no systematic study was found on the bioactive compounds, chemical functional groups, fatty acid profiles, inherent structure, nutrient degradation and absorption, or metabolic characteristics between the newly developed yellow- and black-seeded canola lines. This study aimed to systematically characterize chemical, structural, and nutritional features in these canola lines. The parameters accessed include bioactive compounds and antinutrition factors, chemical functional groups, detailed chemical and nutrient profiles, energy value, nutrient fractions, protein structure, degradation kinetics, intestinal digestion, true intestinal protein supply, and feed milk value. The results showed that the CS-Y line was lower (P ≤ 0.05) in neutral detergent fiber (122 vs 154 g/kg DM), acid detergent fiber (61 vs 99 g/kg DM), lignin (58 vs 77 g/kg DM), nonprotein nitrogen (56 vs 68 g/kg DM), and acid detergent insoluble protein (11 vs 35 g/kg DM) than the CS-B line. There was no difference in fatty acid profiles except C20:1 eicosenoic acid content (omega-9) which was in lower in the CS-Y line (P < 0.05) compared to the CS-B line. The glucosinolate compounds differed (P < 0.05) in terms of 4-pentenyl, phenylethyl, 3-CH3-indolyl, and 3-butenyl glucosinolates (2.9 vs 1.0 μmol/g) between the CS-Y and CS-B lines. For bioactive compounds, total polyphenols tended to be different (6.3 vs 7.2 g/kg DM), but there were no differences in erucic acid and condensed tannins with averages of 0.3 and 3.1 g/kg DM, respectively. When protein was portioned into five subfractions, significant differences were found in PA, PB1 (65 vs 79 g/kg CP), PB2, and PC fractions (10 vs 33 g/kg CP), indicating protein degradation and supply to small intestine differed between two new lines. In terms of protein structure spectral profile, there were no significant differences in functional groups of amides I and II, α helix, and β-sheet structure as well as their ratio between the two new lines, indicating no difference in protein structure makeup and conformation between the two lines. In terms of energy values, there were significant differences in total digestible nutrient (TDN; 149 vs 133 g/kg DM), metabolizable energy (ME; 58 vs 52 MJ/kg DM), and net energy for lactation (NEL; 42 vs 37 MJ/kg DM) between CS-Y and CS-B lines. For in situ rumen degradation kinetics, the two lines differed in soluble fraction (S; 284 vs 341 g/kg CP), potential degradation fraction (D; 672 vs 590 g/kg CP), and effective degraded organic matter (EDOM; 710 vs 684 g/kg OM), but no difference in degradation rate. CS-Y had higher digestibility of rumen bypass protein in the intestine than CS-B (566 vs 446 g/kg of RUP, P < 0.05). Modeling nutrient supply results showed that microbial protein synthesis (MCP; 148 vs 171 g/kg DM) and rumen protein degraded balance (DPB; 108 vs 127 g/kg DM) were lower in the CS-Y line, but there were no differences in total truly digested protein in small intestine (DVE) and feed milk value (FMV) between the two lines. In conclusion, the new yellow line had different nutritional, chemical, and structural features compared to the black line. CS-Y provided better nutrient utilization and availability.

Interfacial Li-ion localization in hierarchical carbon anodes

DOE PAGES

McNutt, Nicholas W.; Rios, Orlando; Maroulas, Vasileios; ...

2016-10-24

An understanding of the nanoscale structure and energetics of carbon composites is critical for their applications in electric energy storage. Here, we study the properties of carbon anodes synthesized from low-cost renewable lignin biopolymers for use in energy storage applications such as Li-ion batteries. The anodes possess both nanoscale and mesoscale order, consisting of carbon nanocrystallites distributed within an amorphous carbon matrix. Molecular dynamics simulations of an experimentally validated model of the anode is used to elucidate the nature of Li-ion storage. We report the discovery of a novel mechanism of Li-ion storage, one in which Li+ is not intercalatedmore » between layers of carbon (as is the case in graphitic anodes), but rather is localized at the interface of crystalline carbon domains. In particular, the effects of Li-ion binding energy on the Li-Li, Li-H, and Li-C pair distribution functions are revealed, along with the effect on charge distribution. As a result, the atomic environments surrounding the Li-ions are grouped on the basis of ion energy and then convolved into archetypal structural motifs that reveal deep insight into the geometry of ion localization in disordered systems.« less

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

NASA Technical Reports Server (NTRS)

Karpas, Z.; Harden, C. S.; Smith, P. B. W.

1995-01-01

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Trend‐Analysis of Solid‐State Structures: Low‐Energy Conformational ‘Reactions’ Involving Directed and Coupled Movements in Half‐Sandwich Compounds [CpFe(CO){C(=O)R}PPh3

PubMed Central

2018-01-01

Abstract Trends in solid‐state structures were used to identify preferred intramolecular movements in half‐sandwich compounds [CpFe(CO){C(=O)R}PPh3]. Three weak interactions were analyzed: 1) the CH/π donor–acceptor interaction of phenyl rings in the PPh3 ligand, 2) the PhPPh3 face‐on Cp stabilization, and 3) the hydrogen bond between the oxygen atom of the acyl group and an ortho‐C−H bond of one of the PPh3 phenyl rings. Clockwise and counter‐clockwise rotations established directed and coupled movements of the PPh3 ligand, the acyl group, and the phenyl rings within the PPh3 ligand. PMID:29744282

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

PubMed

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Róg, Tomasz; Vattulainen, Ilpo

2017-10-23

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

A minimal model for the structural energetics of VO2

NASA Astrophysics Data System (ADS)

Kim, Chanul; Marianetti, Chris; The Marianetti Group Team

Resolving the structural, magnetic, and electronic structure of VO2 from the first-principles of quantum mechanics is still a forefront problem despite decades of attention. Hybrid functionals have been shown to qualitatively ruin the structural energetics. While density functional theory (DFT) combined with cluster extensions of dynamical mean-field theory (DMFT) have demonstrated promising results in terms of the electronic properties, structural phase stability has not yet been addressed. In order to capture the basic physics of the structural transition, we propose a minimal model of VO2 based on the one dimensional Peierls-Hubbard model and parameterize this based on DFT calculations of VO2. The total energy versus dimerization in the minimal mode is then solved numerically exactly using density matrix renormalization group (DMRG) and compared to the Hartree-Fock solution. We demonstrate that the Hartree-Fock solution exhibits the same pathologies as DFT+U, and spin density functional theory for that matter, while the DMRG solution is consistent with experimental observation. Our results demonstrate the critical role of non-locality in the total energy, and this will need to be accounted for to obtain a complete description of VO2 from first-principles. The authors acknowledge support from FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Philippines: Small-scale renewable energy update

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

NONE

1997-12-01

This paper gives an overview of the application of small scale renewable energy sources in the Philippines. Sources looked at include solar, biomass, micro-hydroelectric, mini-hydroelectric, wind, mini-geothermal, and hybrid. A small power utilities group is being spun off the major utility, to provide a structure for developing rural electrification programs. In some instances, private companies have stepped forward, avoiding what is perceived as overwhelming beaurocracy, and installed systems with private financing. The paper provides information on survey work which has been done on resources, and the status of cooperative programs to develop renewable systems in the nation.

Transfer and dissipation of energy during wave group propagation on a gentle beach slope

NASA Astrophysics Data System (ADS)

Padilla, Enrique M.; Alsina, José M.

2017-08-01

The propagation of bichromatic wave groups over a constant 1:100 beach slope and the influence of the group modulation is presented. The modulation is controlled by varying the group frequency, fg, which is shown to remarkably affect the energy transfer to high and low frequency components. The growth of the high frequency (hf) wave skewness increases when fg decreases. This is explained by nonlinear coupling between the primary frequencies, which results in a larger growth of hf components as fg decreases, causing the hf waves to break earlier. Due to high spatial resolution, wave tracking has provided an accurate measurement of the varying breakpoint. These breaking locations are very well described (R2>0.91) by the wave-height to effective-depth ratio (γ). However, for any given Iribarren number, this γ is shown to increase with fg. Therefore, a modified Iribarren number is proposed to include the grouping structure, leading to a considerable improvement in reproducing the measured γ-values. Within the surf zone, the behavior of the Incident Long Wave also depends on the group modulation. For low fg conditions, the lf wave decays only slightly by transferring energy back to the hf wave components. However, for high fg wave conditions, strong dissipation of low frequency (lf) components occurs close to the shoreline associated with lf wave breaking. This mechanism is explained by the growth of the lf wave height, induced partly by the self-self interaction of fg, and partly by the nonlinear coupling between the primary frequencies and fg.

Vibrational spectroscopic investigation of the gold complexation within the cascade structure of phosphorus-containing dendrimer.

PubMed

Furer, V L; Vandyukov, A E; Majoral, J P; Caminade, A M; Gottis, S; Laurent, R; Kovalenko, V I

2018-05-29

The interaction of the phosphoric dendrimer with gold was performed by means of vibrational spectroscopy and quantum chemistry. Stable complexes are formed with a PN-PS linkage, whereas with an isolated PS bond this does not occur. The change in geometric parameters and delocalization of electric charge under the influence of gold was discovered. The classification of bands in the experimental vibrational spectra of the dendrimer and its complex was carried out. HOMO of molecule of the dendrimer is localized on the SPNP linkage, whereas the LUMO is located on the terminal group. In the SPNP linkage there is a noticeable delocalization of the charge which leads to a change in the reactivity of this group. Interaction energy was estimated as the difference between the energies of the complex and the energies of the molecules of the dendrimer G' 0 and two molecules AuCl and is equal to 25.2 eV. The ionization energy IE and electron affinity EA for AuCl are higher than for dendrimer, therefore, when the complex is formed, these quantities increases. Chemical potential and the electrophilicity index in the complex also increases. Copyright © 2018 Elsevier B.V. All rights reserved.

Biomolecular Chemistry of Isopropyl Fibrates

PubMed Central

Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

2012-01-01

Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd) values of the iPr esters of the fibrates are lower than those of their acids, implying that the fibrates have better membrane permeability and a higher absorbability and hence are better prodrugs when these agents need to be orally administered. PMID:22246648

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

Li, Yang; Tu, Xingchen; Wang, Hao

The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green’s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency ofmore » the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.« less

Study of a SiGeSn/GeSn/SiGeSn structure toward direct bandgap type-I quantum well for all group-IV optoelectronics.

PubMed

Ghetmiri, Seyed Amir; Zhou, Yiyin; Margetis, Joe; Al-Kabi, Sattar; Dou, Wei; Mosleh, Aboozar; Du, Wei; Kuchuk, Andrian; Liu, Jifeng; Sun, Greg; Soref, Richard A; Tolle, John; Naseem, Hameed A; Li, Baohua; Mortazavi, Mansour; Yu, Shui-Qing

2017-02-01

A SiGeSn/GeSn/SiGeSn single quantum well structure was grown using an industry standard chemical vapor deposition reactor with low-cost commercially available precursors. The material characterization revealed the precisely controlled material growth process. Temperature-dependent photoluminescence spectra were correlated with band structure calculation for a structure accurately determined by high-resolution x-ray diffraction and transmission electron microscopy. Based on the result, a systematic study of SiGeSn and GeSn bandgap energy separation and barrier heights versus material compositions and strain was conducted, leading to a practical design of a type-I direct bandgap quantum well.

The heavy particle hazard, what physical data are needed?

NASA Technical Reports Server (NTRS)

Curtis, S. B.; Wilkinson, M. C.

1972-01-01

The physical data required to evaluate the radiation hazard from heavy galactic cosmic rays to astronauts on extended missions are discussed. The spectral characteristics, nuclear interaction parameters, and track structure of particles are emphasized. The data on the lower energy portion of the differential spectrum of the iron group and nuclear fragmentation in tissue and aluminum are tested, and results are shown.

Metal-organic frameworks and their derived materials for electrochemical energy storage and conversion: Promises and challenges.

PubMed

Wu, Hao Bin; Lou, Xiong Wen David

2017-12-01

In addition to their conventional uses, metal-organic frameworks (MOFs) have recently emerged as an interesting class of functional materials and precursors of inorganic materials for electrochemical energy storage and conversion technologies. This class of MOF-related materials can be broadly categorized into two groups: pristine MOF-based materials and MOF-derived functional materials. Although the diversity in composition and structure leads to diverse and tunable functionalities of MOF-based materials, it appears that much more effort in this emerging field is devoted to synthesizing MOF-derived materials for electrochemical applications. This is in view of two main drawbacks of MOF-based materials: the low conductivity nature and the stability issue. On the contrary, MOF-derived synthesis strategies have substantial advantages in controlling the composition and structure of MOF-derived materials. From this perspective, we review some emerging applications of both groups of MOF-related materials as electrode materials for rechargeable batteries and electrochemical capacitors, efficient electrocatalysts, and even electrolytes for electrochemical devices. By highlighting the advantages and challenges of each class of materials for different applications, we hope to shed some light on the future development of this highly exciting area.

Metal-organic frameworks and their derived materials for electrochemical energy storage and conversion: Promises and challenges

PubMed Central

Wu, Hao Bin; Lou, Xiong Wen (David)

2017-01-01

In addition to their conventional uses, metal-organic frameworks (MOFs) have recently emerged as an interesting class of functional materials and precursors of inorganic materials for electrochemical energy storage and conversion technologies. This class of MOF-related materials can be broadly categorized into two groups: pristine MOF-based materials and MOF-derived functional materials. Although the diversity in composition and structure leads to diverse and tunable functionalities of MOF-based materials, it appears that much more effort in this emerging field is devoted to synthesizing MOF-derived materials for electrochemical applications. This is in view of two main drawbacks of MOF-based materials: the low conductivity nature and the stability issue. On the contrary, MOF-derived synthesis strategies have substantial advantages in controlling the composition and structure of MOF-derived materials. From this perspective, we review some emerging applications of both groups of MOF-related materials as electrode materials for rechargeable batteries and electrochemical capacitors, efficient electrocatalysts, and even electrolytes for electrochemical devices. By highlighting the advantages and challenges of each class of materials for different applications, we hope to shed some light on the future development of this highly exciting area. PMID:29214220

Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

NASA Astrophysics Data System (ADS)

McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

2017-04-01

We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

Structure and dynamics of Penetratin's association and translocation to a lipid bilayer

NASA Astrophysics Data System (ADS)

Ignacio J., General; Asciutto, Eliana K.

2017-03-01

Penetratin belongs to the important class of small and positively charged peptides, capable of entering cells. The determination of the optimal peptidic structure for translocation is challenging; results obtained so far are varied and dependent on several factors. In this work, we review the dynamics of association of Penetratin with a modeled dioleoyl-phosphatidylcholine (DOPC) lipid membrane using molecular dynamics simulations with last generation force fields. Penetratin's structural preferences are determined using a Markov state model. It is observed that the peptide retains a helical form in the membrane associated state, just as in water, with the exception of both termini which lose helicity, facilitating the interaction of terminal residues with the phosphate groups on the membrane's outer layer. The optimal orientation for insertion is found to be with the peptide's axis forming a small angle with the interface, and with R1 stretching toward the bilayer. The interaction between arginine side-chains and phosphate groups is found to be greater than the corresponding to lysine, mainly due to a higher number of hydrogen bonds between them. The free energy profile of translocation is qualitatively studied using Umbrella Sampling. It is found that there are different paths of penetration, that greatly differ in size of free energy barrier. The lowest path is compatible with residues R10 to K13 leading the way through the membrane and pulling the rest of the peptide. When the other side is reached, the C-terminus overtakes those residues, and finally breaks out of the membrane. The peptide's secondary structure during this traversal suffers some changes with respect to the association structure but, overall, conserves its helicity, with both termini in a more disordered state.

Structure of 8B from elastic and inelastic 7Be+p scattering

NASA Astrophysics Data System (ADS)

Mitchell, J. P.; Rogachev, G. V.; Johnson, E. D.; Baby, L. T.; Kemper, K. W.; Moro, A. M.; Peplowski, P.; Volya, A. S.; Wiedenhöver, I.

2013-05-01

Background: Detailed experimental knowledge of the level structure of light weakly bound nuclei is necessary to guide the development of new theoretical approaches that combine nuclear structure with reaction dynamics.Purpose: The resonant structure of 8B is studied in this work.Method: Excitation functions for elastic and inelastic 7Be+p scattering were measured using a 7Be rare isotope beam. Excitation energies ranging between 1.6 and 3.4 MeV were investigated. An R-matrix analysis of the excitation functions was performed.Results: New low-lying resonances at 1.9, 2.54, and 3.3 MeV in 8B are reported with spin-parity assignment 0+, 2+, and 1+, respectively. Comparison to the time-dependent continuum shell (TDCSM) model and ab initio no-core shell model/resonating-group method (NCSM/RGM) calculations is performed. This work is a more detailed analysis of the data first published as a Rapid Communication. J. P. Mitchell, G. V. Rogachev, E. D. Johnson, L. T. Baby, K. W. Kemper , [Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.82.011601 82, 011601(R) (2010)].Conclusions: Identification of the 0+, 2+, 1+ states that were predicted by some models at relatively low energy but never observed experimentally is an important step toward understanding the structure of 8B. Their identification was aided by having both elastic and inelastic scattering data. Direct comparison of the cross sections and phase shifts predicted by the TDCSM and ab initio no-core shell model coupled with the resonating group method is of particular interest and provides a good test for these theoretical approaches.

Decoding Group Vocalizations: The Acoustic Energy Distribution of Chorus Howls Is Useful to Determine Wolf Reproduction

PubMed Central

López-Bao, José Vicente; Llaneza, Luis; Fernández, Carlos; Font, Enrique

2016-01-01

Population monitoring is crucial for wildlife management and conservation. In the last few decades, wildlife researchers have increasingly applied bioacoustics tools to obtain information on several essential ecological parameters, such as distribution and abundance. One such application involves wolves (Canis lupus). These canids respond to simulated howls by emitting group vocalizations known as chorus howls. These responses to simulated howls reveal the presence of wolf litters during the breeding period and are therefore often used to determine the status of wolf populations. However, the acoustic structure of chorus howls is complex and discriminating the presence of pups in a chorus is sometimes difficult, even for experienced observers. In this study, we evaluate the usefulness of analyses of the acoustic energy distribution in chorus howls to identify the presence of pups in a chorus. We analysed 110 Iberian wolf chorus howls with known pack composition and found that the acoustic energy distribution is concentrated at higher frequencies when there are pups vocalizing. We built predictive models using acoustic energy distribution features to determine the presence of pups in a chorus, concluding that the acoustic energy distribution in chorus howls can be used to determine the presence of wolf pups in a pack. The method we outline here is objective, accurate, easily implemented, and independent of the observer's experience. These advantages are especially relevant in the case of broad scale surveys or when many observers are involved. Furthermore, the analysis of the acoustic energy distribution can be implemented for monitoring other social canids that emit chorus howls such as jackals or coyotes, provides an easy way to obtain information on ecological parameters such as reproductive success, and could be useful to study other group vocalizations. PMID:27144887

Persubstituted p-benzoquinone monoxime alkyl ethers and their molecular structure

NASA Astrophysics Data System (ADS)

Slaschinin, D. G.; Alemasov, Y. A.; Ilushkin, D. I.; Sokolenko, W. A.; Tovbis, M. S.; Kirik, S. D.

2012-05-01

Theoretical and experimental approaches were applied for the investigation of the reactivity of persubstituted 4-nitrosophenols in the reaction with alkyl iodides, in particular the potassium salt of 2,6-di(alkoxycarbonyl)-3,5-dimethyl-4-nitrosophenol. Hartre-Fock calculations showed that the anion negative charge was located mostly on the oxygen of hydroxyl group, while estimation of the total energy of the alkylated products pointed out the benefit of alkylation on the oxygen atom of the nitroso group yielding p-benzoquinone monoxime alkyl ethers. Methylation and ethylation of persubstituted nitrosophenols were carried out. The products obtained were investigated using X-ray diffraction, 1Н NMR spectroscopy and mass spectrometry. The crystal structure of the methyl ether of 2,6-di(alkoxycarbonyl)-3,5-dimethyl-1,4-benzoquinone-1-oxime (С15H19NO6) (I) was determined by the X-ray powder diffraction technique. The unit cell parameters were: a = 7.3322(6) Å, b = 10.5039(12) Å, c = 21.1520(20) Å, β = 93.742(6)°, V = 1625.58(2) Å3Z = 4, Sp.Gr. P21/c. The structure modeling was made in direct space by the Monte-Carlo approach using rigid and soft restrictions. The structure refinement was completed by the Rietveld method. It was established that the alkylation occurred on the oxygen atom of the nitroso group. The molecules (I) in the crystal structure were packed in columns along the axis a with pairwise convergence in a column up to the distance of 3.63 Å due to a 180° turn of every second molecule around the column axis. In the molecular structure the methyloxime group was oriented in the benzene plane and had π-conjugation with the ring. The ethoxycarbonyl groups were turned nearly perpendicular to the ring. Other compounds obtained had the structure of the alkyl ethers of 1.4-benzoquinone-1-oxime, which was proved by 1Н NMR spectroscopy and mass-spectrometry.

Effect of low-level laser therapy on irradiated parotid glands—study in mice

NASA Astrophysics Data System (ADS)

Acauan, Monique Dossena; Gomes, Ana Paula Neutziling; Braga-Filho, Aroldo; de Figueiredo, Maria Antonia Zancanaro; Cherubini, Karen; Salum, Fernanda Gonçalves

2015-10-01

The objective of this study was to evaluate the effect of low-level laser therapy (LLLT) on radiotherapy-induced morphological changes and caspase-3 immunodetection in parotids of mice. Forty-one Swiss mice were divided into control, radiotherapy, 2- and 4-J laser groups. The experimental groups were exposed to ionizing radiation in a single session of 10 Gy. In the laser groups, a GaAlAs laser (830 nm, 100 mW, 0.028 cm2, 3.57 W/cm2) was used on the region corresponding to the parotid glands, with 2-J energy (20 s, 71 J/cm2) or 4 J (40 s, 135 J/cm2) per point. LLLT was performed immediately before and 24 h after radiotherapy. One point was applied in each parotid gland. The animals were euthanized 48 h or 7 days after radiotherapy and parotid glands were dissected for morphological analysis and immunodetection of caspase-3. There was no significant difference between groups in the immunodetection of caspase-3, but the laser groups had a lower percentage compared to the radiotherapy group. LLLT promoted the preservation of acinar structure, reduced the occurrence of vacuolation, and stimulated parotid gland vascularization. Of the two LLLT protocols, the one using 4 J of energy showed better results.

Complex assessment of urban housing energy sustainability

NASA Astrophysics Data System (ADS)

Popova, Olga; Glebova, Julia; Karakozova, Irina

2018-03-01

The article presents the results of a complex experimental-analytical research of residential development energy parameters - survey of construction sites and determination of calculated energy parameters (resistance to heat transfer) considering their technical condition. The authors suggest a methodology for assessing residential development energy parameters on the basis of construction project's structural analysis with the use of advanced intelligent collection systems, processing (self-organizing maps - SOM) and data visualization (geo-informational systems - GIS). SOM clustering permitted to divide the housing stock (on the example of Arkhangelsk city) into groups with similar technical-operational and energy parameters. It is also possible to measure energy parameters of construction project of each cluster by comparing them with reference (normative) measures and also with each other. The authors propose mechanisms for increasing the area's energy stability level by implementing a set of reproduction activities for residential development of various groups. The analysis showed that modern multilevel and high-rise construction buildings have the least heat losses. At present, however, ow-rise wood buildings is the dominant styles of buildings of Arkhangelsk city. Data visualisation on the created heat map showed that such housing stock covers the largest urban area. The development strategies for depressed areas is in a high-rise building, which show the economic, social and environmental benefits of upward growth of the city. An urban regeneration programme for severely rundown urban housing estates is in a high-rise construction building, which show the economic, social and environmental benefits of upward growth of the city.

Multivariate data analysis to characterize gas chromatography columns for dioxin analysis.

PubMed

Do, Lan; Geladi, Paul; Haglund, Peter

2014-06-20

Principal component analysis (PCA) was applied for evaluating the selectivity of 22 GC columns for which complete retention data were available for the 136 tetra- to octa-chlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). Because the hepta- and octa-homologues are easy to separate the PCA was focused on the 128 tetra- to hexa-CDD/Fs. The analysis showed that 21 of the 22 GC columns could be subdivided into four groups with different selectivity. Group I consists of columns with non-polar thermally stable phases (Restek 5Sil MS and Dioxin 2, SGE BPX-DXN, Supelco Equity-5, and Agilent DB-1, DB-5, DB-5ms, VF-5ms, VF-Xms and DB-XLB). Group II includes ionic liquid columns (Supelco SLB-IL61, SLB-IL111 and SLB-IL76) with very high polarity. Group III includes columns with high-percentage phenyl and cyanopropyl phases (Agilent DB-17 and DB-225, Quadrex CPS-1, Supelco SP-2331, and Agilent CP-Sil 88), and Group IV columns with shape selectivity (Dionex SB-Smectic and Restek LC-50, Supelco βDEXcst, Agilent VF-Xms and DB-XLB). Thus, two columns appeared in both Group I and IV (Agilent VF-Xms and DB-XLB). The selectivity of the other column, Agilent DB-210, differs from those of these four groups. Partial least squares (PLS) regression was used to correlate the retention times of the tetra- to hexa-CDD/Fs on the 22 stationary phases with a set of physicochemical and structural descriptors to identify parameters that significantly influence the solute-stationary phase interactions. The most influential physicochemical parameters for the interaction were associated with molecular size (as reflects in the total energy, electron energy, core-core repulsion and standard entropy), solubility (aqueous solubility and n-octanol/water partition coefficient), charge distribution (molecular polarizability and dipolar moment), and reactivity (relative Gibbs free energy); and the most influential structural descriptors were related to these parameters, in particular, size and dipolar moment. Finally, the PCA and PLS analyses were complemented with linear regression analysis to identify the most orthogonal column combinations, which could be used in comprehensive two-dimensional gas chromatography (GC×GC) to enhance PCDD/F separation and congener profiling. Copyright © 2014 Elsevier B.V. All rights reserved.

Lower-Body Muscle Structure and Jump Performance of Stronger and Weaker Surfing Athletes.

PubMed

Secomb, Josh L; Nimphius, Sophia; Farley, Oliver R; Lundgren, Lina; Tran, Tai T; Sheppard, Jeremy M

2016-07-01

To identify whether there are any significant differences in the lower-body muscle structure and countermovement-jump (CMJ) and squat-jump (SJ) performance between stronger and weaker surfing athletes. Twenty elite male surfers had their lower-body muscle structure assessed with ultrasonography and completed a series of lower-body strength and jump tests including isometric midthigh pull (IMTP), CMJ, and SJ. Athletes were separated into stronger (n = 10) and weaker (n = 10) groups based on IMTP performance. Large significant differences were identified between the groups for vastus lateralis (VL) thickness (P = .02, ES = 1.22) and lateral gastrocnemius (LG) pennation angle (P = .01, ES = 1.20), and a large nonsignificant difference was identified in LG thickness (P = .08, ES = 0.89). Furthermore, significant differences were present between the groups for peak force, relative peak force, and jump height in the CMJ and SJ (P < .01-.05, ES = 0.90-1.47) and eccentric peak velocity, as well as vertical displacement of the center of mass during the CMJ (P < .01, ES = 1.40-1.41). Stronger surfing athletes in this study had greater VL and LG thickness and LG pennation angle. These muscle structures may explain their better performance in the CMJ and SJ. A unique finding in this study was that the stronger group appeared to better use their strength and muscle structure for braking as they had significantly higher eccentric peak velocity and vertical displacement during the CMJ. This enhanced eccentric phase may have resulted in a greater production and subsequent utilization of stored elastic strain energy that led to the significantly better CMJ performance in the stronger group.

Development of Ultra-Fine Multigroup Cross Section Library of the AMPX/SCALE Code Packages

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

Jeon, Byoung Kyu; Sik Yang, Won; Kim, Kang Seog

The Consortium for Advanced Simulation of Light Water Reactors Virtual Environment for Reactor Applications (VERA) neutronic simulator MPACT is being developed by Oak Ridge National Laboratory and the University of Michigan for various reactor applications. The MPACT and simplified MPACT 51- and 252-group cross section libraries have been developed for the MPACT neutron transport calculations by using the AMPX and Standardized Computer Analyses for Licensing Evaluations (SCALE) code packages developed at Oak Ridge National Laboratory. It has been noted that the conventional AMPX/SCALE procedure has limited applications for fast-spectrum systems such as boiling water reactor (BWR) fuels with very highmore » void fractions and fast reactor fuels because of its poor accuracy in unresolved and fast energy regions. This lack of accuracy can introduce additional error sources to MPACT calculations, which is already limited by the Bondarenko approach for resolved resonance self-shielding calculation. To enhance the prediction accuracy of MPACT for fast-spectrum reactor analyses, the accuracy of the AMPX/SCALE code packages should be improved first. The purpose of this study is to identify the major problems of the AMPX/SCALE procedure in generating fast-spectrum cross sections and to devise ways to improve the accuracy. For this, various benchmark problems including a typical pressurized water reactor fuel, BWR fuels with various void fractions, and several fast reactor fuels were analyzed using the AMPX 252-group libraries. Isotopic reaction rates were determined by SCALE multigroup (MG) calculations and compared with continuous energy (CE) Monte Carlo calculation results. This reaction rate analysis revealed three main contributors to the observed differences in reactivity and reaction rates: (1) the limitation of the Bondarenko approach in coarse energy group structure, (2) the normalization issue of probability tables, and (3) neglect of the self-shielding effect of resonance-like cross sections at high energy range such as (n,p) cross section of Cl35. The first error source can be eliminated by an ultra-fine group (UFG) structure in which the broad scattering resonances of intermediate-weight nuclides can be represented accurately by a piecewise constant function. A UFG AMPX library was generated with modified probability tables and tested against various benchmark problems. The reactivity and reaction rates determined with the new UFG AMPX library agreed very well with respect to Monte Carlo Neutral Particle (MCNP) results. To enhance the lattice calculation accuracy without significantly increasing the computational time, performing the UFG lattice calculation in two steps was proposed. In the first step, a UFG slowing-down calculation is performed for the corresponding homogenized composition, and UFG cross sections are collapsed into an intermediate group structure. In the second step, the lattice calculation is performed for the intermediate group level using the condensed group cross sections. A preliminary test showed that the condensed library reproduces the results obtained with the UFG cross section library. This result suggests that the proposed two-step lattice calculation approach is a promising option to enhance the applicability of the AMPX/SCALE system to fast system analysis.« less

Assessing major ecosystem types and the challenge of sustainability in Turkey.

PubMed

Evrendilek, F; Doygun, H

2000-11-01

In recent years, Turkey has experienced rapid economic and population growth coupled with both an equally rapid increase in energy consumption and a vast disparity in welfare between socioeconomic groups and regions. In turn, these pressures have accelerated the destruction of productive, assimilative, and regenerative capacities of the ecosystems, which are essential for the well-being of the people and the economy. This paper describes the structure and function of major ecosystem types in Turkey and discusses the underlying causes of environmental degradation in the framework of economy, energy, environment, and ethics. From a national perspective, this paper suggests three sustainability-based policies necessary for Turkey's long-term interests that balance economic, environmental, and energy goals: (1) decoupling economic growth from energy consumption growth through the development of energy-efficient and renewable energy technologies; (2) linking economic efficiency and distributive justice of wealth and power through distributive and participatory public policies; and (3) integrating the economic and ecological systems through the internalization of externalities and ecosystem rehabilitation.

Photon Energy Threshold in Direct Photocatalysis with Metal Nanoparticles: Key Evidence from the Action Spectrum of the Reaction.

PubMed

Sarina, Sarina; Jaatinen, Esa; Xiao, Qi; Huang, Yi Ming; Christopher, Philip; Zhao, Jin Cai; Zhu, Huai Yong

2017-06-01

By investigating the action spectra (the relationship between the irradiation wavelength and apparent quantum efficiency of reactions under constant irradiance) of a number of reactions catalyzed by nanoparticles including plasmonic metals, nonplasmonic metals, and their alloys at near-ambient temperatures, we found that a photon energy threshold exists in each photocatalytic reaction; only photons with sufficient energy (e.g., higher than the energy level of the lowest unoccupied molecular orbitals) can initiate the reactions. This energy alignment (and the photon energy threshold) is determined by various factors, including the wavelength and intensity of irradiation, molecule structure, reaction temperature, and so forth. Hence, distinct action spectra were observed in the same type of reaction catalyzed by the same catalyst due to a different substituent group, a slightly changed reaction temperature. These results indicate that photon-electron excitations, instead of the photothermal effect, play a dominant role in direct photocatalysis of metal nanoparticles for many reactions.

Renewable fluid dynamic energy derived from aquatic animal locomotion.

PubMed

Dabiri, John O

2007-09-01

Aquatic animals swimming in isolation and in groups are known to extract energy from the vortices in environmental flows, significantly reducing muscle activity required for locomotion. A model for the vortex dynamics associated with this phenomenon is developed, showing that the energy extraction mechanism can be described by simple criteria governing the kinematics of the vortices relative to the body in the flow. In this way, we need not make direct appeal to the fluid dynamics, which can be more difficult to evaluate than the kinematics. Examples of these principles as exhibited in swimming fish and existing energy conversion devices are described. A benefit of the developed framework is that the potentially infinite-dimensional parameter space of the fluid-structure interaction is reduced to a maximum of eight combinations of three parameters. The model may potentially aid in the design and evaluation of unsteady aero- and hydrodynamic energy conversion systems that surpass the Betz efficiency limit of steady fluid dynamic energy conversion systems.

Structure-based prediction of free energy changes of binding of PTP1B inhibitors

NASA Astrophysics Data System (ADS)

Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal

2003-08-01

The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.

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

Ho, M.; Shi, W; Rinaldo-Mathis, A

Inhibition of human purine nucleoside phosphorylase (PNP) stops growth of activated T-cells and the formation of 6-oxypurine bases, making it a target for leukemia, autoimmune disorders, and gout. Four generations of ribocation transition-state mimics bound to PNP are structurally characterized. Immucillin-H (K*{sub i} = 58 pM, first-generation) contains an iminoribitol cation with four asymmetric carbons. DADMe-Immucillin-H (K*{sub i} = 9 pM, second-generation), uses a methylene-bridged dihydroxypyrrolidine cation with two asymmetric centers. DATMe-Immucillin-H (K*{sub i} = 9 pM, third-generation) contains an open-chain amino alcohol cation with two asymmetric carbons. SerMe-ImmH (K*{sub i} = 5 pM, fourth-generation) uses achiral dihydroxyaminoalcohol seramide asmore » the ribocation mimic. Crystal structures of PNPs establish features of tight binding to be; (1) ion-pair formation between bound phosphate (or its mimic) and inhibitor cation, (2) leaving-group interactions to N1, O6, and N7 of 9-deazahypoxanthine, (3) interaction between phosphate and inhibitor hydroxyl groups, and (4) His257 interacting with the 5{prime}-hydroxyl group. The first generation analogue is an imperfect fit to the catalytic site with a long ion pair distance between the iminoribitol and bound phosphate and weaker interactions to the leaving group. Increasing the ribocation to leaving-group distance in the second- to fourth-generation analogues provides powerful binding interactions and a facile synthetic route to powerful inhibitors. Despite chemical diversity in the four generations of transition-state analogues, the catalytic site geometry is almost the same for all analogues. Multiple solutions in transition-state analogue design are available to convert the energy of catalytic rate enhancement to binding energy in human PNP.« less

Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

PubMed Central

Raman, E. Prabhu; Yu, Wenbo; Guvench, Olgun; MacKerell, Alexander D.

2011-01-01

The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility towards specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design. PMID:21456594

Free-energy analysis of spin models on hyperbolic lattice geometries.

PubMed

Serina, Marcel; Genzor, Jozef; Lee, Yoju; Gendiar, Andrej

2016-04-01

We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy normalized per lattice site of various multistate spin models in the thermal equilibrium on distinct non-Euclidean surface lattices of the infinite sizes. Whereas the free energy is calculated numerically by means of the corner transfer matrix renormalization group algorithm, the radius of curvature has an analytic expression. Two tasks are considered in this work. First, we search for such a lattice geometry, which minimizes the free energy per site. We conjecture that the only Euclidean flat geometry results in the minimal free energy per site regardless of the spin model. Second, the relations among the free energy, the radius of curvature, and the phase transition temperatures are analyzed. We found out that both the free energy and the phase transition temperature inherit the structure of the lattice geometry and asymptotically approach the profile of the Gaussian radius of curvature. This achievement opens new perspectives in the AdS-CFT correspondence theories.

[Influence of microtubule depolymerization of myocardial cells on mitochondria distribution and energy metabolism in adult rats].

PubMed

Dang, Yong-ming; Fang, Ya-dong; Hu, Jiong-yu; Zhang, Jia-ping; Song, Hua-pei; Zhang, Yi-ming; Zhang, Qiong; Huang, Yue-sheng

2010-02-01

To investigate the influence of microtubule depolymerization of myocardial cells on distribution and activity of mitochondria, and energy metabolism of cells in adult rats. Myocardial cells of SD adult rats and SD suckling rats were isolated and cultured. They were divided into adult and suckling rats control groups (AC and SC, normally cultured without any stimulating factor), adult and suckling rats microtubule depolymerization agent groups (AMDA and SMDA, cultured with 8 micromol/L colchicine containing nutrient solution for 30 minutes) according to the random number table. (1) The expression of polymerized beta tubulin in myocardial cells of adult and suckling rats was detected with Western blot. (2) Myocardial cells of rats in AC and AMDA groups were collected. The expression of cytochrome c was detected with Western blot. Distribution of voltage-dependent anion channels (VDAC) and polymerized beta tubulin in myocardial cells were observed with immunofluorescent staining. Mitochondrial inner membrane potential was determined with immunocytochemical method. Activity of myocardial cells was detected with MTT method. Contents of ATP, adenosine diphosphate (ADP), and adenosine monophosphate (AMP) and energy charge of cells were determined with high performance liquid chromatography. (1) The expression of polymerized beta tubulin:in AMDA group it was 0.52 + or - 0.07, which was obviously lower than that (1.25 + or - 0.12) in AC group (F = 31.002, P = 0.000); in SMDA group it was 0.76 + or - 0.12, which was significantly lower than that (1.11 + or - 0.24) in SC group (F = 31.002, P = 0.000), but was obviously higher than that in AMDA group (F = 31.002, P = 0.009). (2) The expression of cytochrome c in AC group was 0.26 + or - 0.03, which was obviously lower than that (1.55 + or - 0.13) in AMDA group (t = -24.056, P = 0.000). (3) Immunofluorescent staining result: in AC group, microtubules of myocardial cells were in linear tubiform, distributed in parallel with myocardial fiber; VDAC staining result showed that mitochondria were in granular form, distributed in the same direction as microtubules. In AMDA group, the normal distribution regularity of microtubules was destroyed, with weakened immune fluorescence intensity, microtubules structure indistinct, continuity lost, rough in appearance, and the distribution of mitochondria became disrupted. (4) Mitochondrial inner membrane potential in AC group fluorescent intensity was 1288 + or - 84, which was obviously higher than that (331 + or - 27) in AMDA group (t = 26.508, P = 0.000). (5) Cellular activity: in AC group absorbance value was 1.75 + or - 0.11, which was obviously lower than that (0.81 + or - 0.07) in AMDA group (t = 17.348, P = 0.000). (6) Energy metabolism: compared with those in AC group, content of ATP decreased, contents of ADP and AMP increased, and ATP/ADP value and energy charge decreased in AMDA group. Microtubules and mitochondria distribute in the same direction in normal myocardial cells in adult rats. After microtubule depolymerization, mitochondria are arranged in disorder fashion; cytochrome c leaks from mitochondria; mitochondrial membrane potential, energy supply, and cellular activity decrease in the myocardial cells.

Structure, dielectric and electric properties of diisobutylammonium hydrogen sulfate crystal

NASA Astrophysics Data System (ADS)

Bednarchuk, Tamara J.; Kinzhybalo, Vasyl; Markiewicz, Ewa; Hilczer, Bożena; Pietraszko, Adam

2018-02-01

Diisobutylammonium hydrogen sulfate, a new organic-inorganic hybrid compound, was successfully synthesized and three structural phases in 298-433 K temperature range were revealed by differential scanning calorimetry and X-ray powder diffraction studies. Single crystal X-ray diffraction data were used to describe the crystal structures in each particular case. In phase III (below 336/319 K on heating/cooling) the crystal arrangement appears to be within the triclinic symmetry with P-1 space group. During heating in the 336-339 K region (and 319-337 K on cooling) the crystal exists in the phase II, characterized by monoclinic symmetry with P21/c space group. Consequently, above 339 K (during heating, and 337 K during cooling temperature sequences), i.e. in phase I the crystal exhibits orthorhombic symmetry (Cmce space group). Ferroelastic domain structure was observed in phase III. These phase boundaries (III→II and II→I) were accompanied by the presence of small anomalies, apparent in the dielectric permittivity and electric conductivity experimental data. Fast proton transport with activation energy of 0.23 eV was observed in the high temperature phase I and related to phonon assisted proton diffusion conditioned by disorder of diisobutylammonium (diba) cations, as well as by high thermal displacements of oxygen and sulfur atoms of hydrogen sulfate anion (hs).

Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

NASA Astrophysics Data System (ADS)

Kojima, Hisaya; Tokizawa, Riho; Kogure, Kouhei; Kobayashi, Yuki; Itoh, Masayuki; Shiah, Fuh-Kwo; Okuda, Noboru; Fukui, Manabu

2014-07-01

Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer `Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of `M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition-fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

Hydrogen-impurity complexes in III V semiconductors

NASA Astrophysics Data System (ADS)

Ulrici, W.

2004-12-01

This review summarizes the presently available knowledge concerning hydrogen-impurity complexes in III-V compounds. The impurities form shallow acceptors on group III sites (Be, Zn, Cd) and on group V sites (C, Si, Ge) as well as shallow donors on group V sites (S, Se, Te) and on group III sites (Si, Sn). These complexes are mainly revealed by their hydrogen stretching modes. Therefore, nearly all information about their structure and dynamic properties is derived from vibrational spectroscopy. The complexes of shallow impurities with hydrogen have been most extensively investigated in GaAs, GaP and InP. This holds also for Mg-H in GaN. The complexes exhibit a different microscopic structure, which is discussed in detail. The isoelectronic impurity nitrogen, complexed with one hydrogen atom, is investigated in detail in GaAs and GaP. Those complexes can exist in different charge states. The experimental results such as vibrational frequencies, the microscopic structure and the activation energy for reorientation for many of these complexes are in very good agreement with results of ab initio calculations. Different types of oxygen-hydrogen complexes in GaAs and GaP are described, with one hydrogen atom or two hydrogen atoms bonded to oxygen. Three of these complexes in GaAs were found to be electrically active.

Crystal structure, vibrational and theoretical studies of bis(4-amino-1,2,4-triazolium) hexachloridostannate(IV)

NASA Astrophysics Data System (ADS)

Daszkiewicz, Marek; Marchewka, Mariusz K.

2012-06-01

X-ray structure of new hybrid organic-inorganic compound, bis(4-amino-1,2,4-triazolium) hexachloridostannate(IV), [1t(4at)]2SnCl6 (P1¯ space group) was determined. Crystal structure of 4-amino-1,2,4-triazole (Pbca space group) was reinvestigated. Non-planar orientation of NH2 group was found. The geometry of the amino group does not significantly change upon protonation. The route of protonation of 4-aminotriazole and tautomer equilibrium constants for the cationic forms were theoretically studied by means of B3LYP/6-31G* method. The most stable monoprotonated species is 1H-trans-4-amino-1,2,4-triazole, 1t(4at)+, whereas the final product of the protonation route is 12(4at)2+. Potential Energy Distribution (PED) analysis was carried out for two conformers, 1c(4at)+ and 1t(4at)+. Very good agreement between theoretical and experimental frequencies was achieved due to very weak interactions existing in [1t(4at)]2SnCl6. Infrared and Raman bands were assigned on the basis of PED analysis. Comparison of vibrational spectra of [1t(4at)]2SnCl6 and [1t(4at)]Cl indicates significantly weaker intermolecular interactions in the former compound.

High Photon-to-Current Conversion in Solar Cells Based on Light-Absorbing Silver Bismuth Iodide.

PubMed

Zhu, Huimin; Pan, Mingao; Johansson, Malin B; Johansson, Erik M J

2017-06-22

Here, a lead-free silver bismuth iodide (AgI/BiI 3 ) with a crystal structure with space group R3‾ m is investigated for use in solar cells. Devices based on the silver bismuth iodide deposited from solution on top of TiO 2 and the conducting polymer poly(3-hexylthiophene-2,5-diyl) (P3HT) as a hole-transport layer are prepared and the photovoltaic performance is very promising with a power conversion efficiency over 2 %, which is higher than the performance of previously reported bismuth-halide materials for solar cells. Photocurrent generation is observed between 350 and 700 nm, and the maximum external quantum efficiency is around 45 %. The results are compared to solar cells based on the previously reported material AgBi 2 I 7 , and we observe a clearly higher performance for the devices with the new silver and bismuth iodides composition and different crystal structure. The X-ray diffraction spectrum of the most efficient silver bismuth iodide material shows a hexagonal crystal structure with space group R3‾ m, and from the light absorption spectrum we obtain an indirect band gap energy of 1.62 eV and a direct band gap energy of 1.85 eV. This report shows the possibility for finding new structures of metal-halides efficient in solar cells and points out new directions for further exploration of lead-free metal-halide solar cells. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

The influence of socioeconomic factors and family context on energy-dense food consumption among 2-year-old children.

PubMed

Vilela, S; Oliveira, A; Pinto, E; Moreira, P; Barros, H; Lopes, C

2015-01-01

Adverse effect on health has been described for a high consumption of energy-dense food, among children and adults. Limited research has been performed among pre-school children. The objective of this study is to evaluate the association between socioeconomic characteristics and family structure, and the consumption of energy-dense food among 2-year-old children. The study sample includes 808 2-year-old children from the Portuguese birth cohort Generation XXI with information on food consumption. Data were obtained from questionnaires administered by interviewers to parents. Based on a food frequency questionnaire, four groups of energy-dense food were defined: soft drinks (sweetened drinks), sweets (chocolate and candies), cakes (creamy and not creamy cakes and sweet pastry) and salty snacks (crisps, pizza and burger). Multinomial logistic regression models (odds ratio and 95% confidence intervals) were fitted to estimate the associations. Intakes of energy-dense food were much lower than in similar aged children in other Westernized countries. Maternal age and education, grandparents' education, household income and maternal occupation were inversely associated with the consumption of energy-dense food, particularly soft drinks and sweets. Children with older siblings were more likely to have a daily consumption of any energy-dense food. Few significant associations were found between socioeconomic characteristics and family structure and consumption of cakes and sweets less than once a week. High socioeconomic characteristics were associated with lower consumption of energy-dense food by 2-year-old children, mainly soft drinks and sweets. This influence is not only from parents' background but also from the preceding generations.

Novel selenium containing boro-phosphate glasses: preparation and structural study.

PubMed

Ciceo-Lucacel, R; Radu, T; Ponta, O; Simon, V

2014-06-01

We synthesized a new boro-phosphate glass system with different %mol SeO2 content by conventional melt quenching technique. All samples were obtained in a glassy state with the vitreous structure confirmed by X-ray diffraction analysis. Scanning electron microscopy (SEM) revealed some non-homogeneous domains on the glasses surface, and their tendency to link each other once the selenium oxide content increases. Energy-dispersive X-ray analysis (EDAX) indicated similar elemental composition in different regions of each sample. X-ray photoelectron spectroscopy (XPS) was used to determine the nature of chemical bonding and the elemental composition at the sample surfaces, and Fourier transform infrared (FT-IR) spectroscopy was used to determine the structural groups in the obtained glass structure. Based on FT-IR results, the glass structure at short range order consists mainly of small phosphate units such as pyrophosphate (i.e. P2O7(4-) dimmers or terminating groups at the end of phosphate chains) and some metaphosphate (i.e. PO3(-) middle groups in the phosphate chains) units. The boron atoms are mainly placed in three-coordinated sites in BØ3 or BØ2O(-) units. A small contribution of BØ4(-) units was also detected from the FT-IR spectra of glasses. For SeO2 content higher than 5mol%, the modifier role of selenium ions is strongly reflected on the local structure dominated in this case by pyrophosphate units. Copyright © 2014 Elsevier B.V. All rights reserved.

Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation.

PubMed

Punkvang, Auradee; Kamsri, Pharit; Saparpakorn, Patchreenart; Hannongbua, Supa; Wolschann, Peter; Irle, Stephan; Pungpo, Pornpan

2015-07-01

Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity. © 2014 John Wiley & Sons A/S.

Alchemical and structural distribution based representation for universal quantum machine learning

NASA Astrophysics Data System (ADS)

Faber, Felix A.; Christensen, Anders S.; Huang, Bing; von Lilienfeld, O. Anatole

2018-06-01

We introduce a representation of any atom in any chemical environment for the automatized generation of universal kernel ridge regression-based quantum machine learning (QML) models of electronic properties, trained throughout chemical compound space. The representation is based on Gaussian distribution functions, scaled by power laws and explicitly accounting for structural as well as elemental degrees of freedom. The elemental components help us to lower the QML model's learning curve, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training. This point is demonstrated for the prediction of covalent binding in single, double, and triple bonds among main-group elements as well as for atomization energies in organic molecules. We present numerical evidence that resulting QML energy models, after training on a few thousand random training instances, reach chemical accuracy for out-of-sample compounds. Compound datasets studied include thousands of structurally and compositionally diverse organic molecules, non-covalently bonded protein side-chains, (H2O)40-clusters, and crystalline solids. Learning curves for QML models also indicate competitive predictive power for various other electronic ground state properties of organic molecules, calculated with hybrid density functional theory, including polarizability, heat-capacity, HOMO-LUMO eigenvalues and gap, zero point vibrational energy, dipole moment, and highest vibrational fundamental frequency.

Design and synthesis of a crystalline LiPON electrolyte

NASA Astrophysics Data System (ADS)

Holzwarth, N. A. W.; Senevirathne, Keerthi; Day, Cynthia S.; Lachgar, Abdessadek; Gross, Michael D.

2013-03-01

In the course of a computation study of the broad class of lithium phosphorus oxy-nitride materials of interest for solid electrolyte applications, Du and Holzwarth, [2] recently predicted a stable crystalline material with the stoichiometry Li2PO2N. The present paper reports the experimental preparation of the material using high temperature solid state synthesis and reports the results of experimental and calculational characterization studies. The so-named SD -Li2PO2N crystal structure has the orthorhombic space group Cmc21 with lattice constants a=9.0692(4) Å, b=5.3999(2) Å, and c=4.6856(2) Å. The structure is similar but not identical to the predicted structure, characterized by parallel arrangements of anionic phosphorus oxy-nitride chains having planar P -N -P -N backbones. Nitrogen 2p π states contribute to the strong bonding and to the chemical and thermal stablility of the material in air up to 600° C and in vacuum up to 1050° C. The measured Arrhenius activation energy for ionic conductivity is 0.6 eV which is comparable to computed vacancy migration energies in the presence of a significant population of Li+ ion vacancies. Supported by NSF grant DMR-1105485 and by a grnat from the Wake Forest University Center for Energy, Environment, and Sustainability.

Magnetostructural transition in Fe{sub 5}SiB{sub 2} observed with neutron diffraction

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

Cedervall, Johan, E-mail: johan.cedervall@kemi.uu.se; Kontos, Sofia; Hansen, Thomas C.

2016-03-15

The crystal and magnetic structure of Fe{sub 5}SiB{sub 2} has been studied by a combination of X-ray and neutron diffraction. Also, the magnetocrystalline anisotropy energy constant has been estimated from magnetisation measurements. High quality samples have been prepared using high temperature synthesis and subsequent heat treatment protocols. The crystal structure is tetragonal within the space group I4/mcm and the compound behaves ferromagnetically with a Curie temperature of 760 K. At 172 K a spin reorientation occurs in the compound and the magnetic moments go from aligning along the c-axis (high T) down to the ab-plane (low T). The magnetocrystalline anisotropymore » energy constant has been estimated to 0.3 MJ/m{sup 3} at 300 K. - Highlights: • The crystal and magnetic structure of Fe{sub 5}SiB{sub 2} has been studied by diffraction. • At 172 K a spin reorientation occurs in the compound. • The magnetic moments are aligned along the c-axis at high T. • The magnetic moments are aligned in the ab-plane at low T. • The magnetocrystalline anisotropy energy constant has been estimated to 0.3 MJ/m{sup 3}.« less

BUGJEFF311.BOLIB (JEFF-3.1.1) and BUGENDF70.BOLIB (ENDF/B-VII.0) - Generation Methodology and Preliminary Testing of two ENEA-Bologna Group Cross Section Libraries for LWR Shielding and Pressure Vessel Dosimetry

NASA Astrophysics Data System (ADS)

Pescarini, Massimo; Sinitsa, Valentin; Orsi, Roberto; Frisoni, Manuela

2016-02-01

Two broad-group coupled neutron/photon working cross section libraries in FIDO-ANISN format, dedicated to LWR shielding and pressure vessel dosimetry applications, were generated following the methodology recommended by the US ANSI/ANS-6.1.2-1999 (R2009) standard. These libraries, named BUGJEFF311.BOLIB and BUGENDF70.BOLIB, are respectively based on JEFF-3.1.1 and ENDF/B-VII.0 nuclear data and adopt the same broad-group energy structure (47 n + 20 γ) of the ORNL BUGLE-96 similar library. They were respectively obtained from the ENEA-Bologna VITJEFF311.BOLIB and VITENDF70.BOLIB libraries in AMPX format for nuclear fission applications through problem-dependent cross section collapsing with the ENEA-Bologna 2007 revision of the ORNL SCAMPI nuclear data processing system. Both previous libraries are based on the Bondarenko self-shielding factor method and have the same AMPX format and fine-group energy structure (199 n + 42 γ) as the ORNL VITAMIN-B6 similar library from which BUGLE-96 was obtained at ORNL. A synthesis of a preliminary validation of the cited BUGLE-type libraries, performed through 3D fixed source transport calculations with the ORNL TORT-3.2 SN code, is included. The calculations were dedicated to the PCA-Replica 12/13 and VENUS-3 engineering neutron shielding benchmark experiments, specifically conceived to test the accuracy of nuclear data and transport codes in LWR shielding and radiation damage analyses.

Structural analysis of zwitterionic liquids vs. homologous ionic liquids

NASA Astrophysics Data System (ADS)

Wu, Boning; Kuroda, Kosuke; Takahashi, Kenji; Castner, Edward W.

2018-05-01

Zwitterionic liquids (Zw-ILs) have been developed that are homologous to monovalent ionic liquids (ILs) and show great promise for controlled dissolution of cellulosic biomass. Using both high energy X-ray scattering and atomistic molecular simulations, this article compares the bulk liquid structural properties for novel Zw-ILs with their homologous ILs. It is shown that the significant localization of the charges on Zw-ILs leads to charge ordering similar to that observed for conventional ionic liquids with monovalent anions and cations. A low-intensity first sharp diffraction peak in the liquid structure factor S(q) is observed for both the Zw-IL and the IL. This is unexpected since both the Zw-IL and IL have a 2-(2-methoxyethoxy)ethyl (diether) functional group on the cationic imidazolium ring and ether functional groups are known to suppress this peak. Detailed analyses show that this intermediate range order in the liquid structure arises for slightly different reasons in the Zw-IL vs. the IL. For the Zw-IL, the ether tails in the liquid are shown to aggregate into nanoscale domains.

Average and local crystal structures of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles

DOE PAGES

Feygenson, Mikhail; Neuefeind, Joerg C.; Tyson, Trevor A.; ...

2015-11-06

We report the comprehensive study of the crystal structure of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles by means of neutron and synchrotron x-ray scattering. In our study we used four different types of (Ga 1–xZn x)(N 1–xO x) nanoparticles, with diameters of 10–27 nm and x = 0.075–0.51, which show the narrow energy-band gaps from 2.21 to 2.61 eV. The Rietveld analysis of the neutron diffraction data revealed that the average crystal structure is the hexagonal wurtzite (space group P6 3mc), in agreement with previous reports on similar bulk materials. The pair-distribution function (PDF) analysis of the samemore » data found that the local structure is more disordered than the average one. It is best described by the model with a lower symmetry space group P1, where atoms are quasirandomly distorted from their nominal positions in the hexagonal wurtzite lattice.« less

Electronic structure of boron based single and multi-layer two dimensional materials

NASA Astrophysics Data System (ADS)

Miyazato, Itsuki; Takahashi, Keisuke

2017-09-01

Two dimensional nanosheets based on boron and Group VA elements are designed and characterized using first principles calculations. B-N, B-P, B-As, B-Sb, and B-Bi are found to possess honeycomb structures where formation energies indicate exothermic reactions. Contrary to B-N, the cases of B-P, B-As, B-Sb, and B-Bi nanosheets are calculated to possess narrow band gaps. In addition, calculations reveal that the electronegativity difference between B and Group VA elements in the designed materials is a good indicator to predict the charge transfer and band gap of the two dimensional materials. Hydrogen adsorption over defect-free B-Sb and B-Bi results in exothermic reactions, while defect-free B-N, B-P, and B-As result in endothermic reactions. The layerability of the designed two dimensional materials is also investigated where the electronic structure of two-layered two dimensional materials is strongly coupled with how the two dimensional materials are layered. Thus, one can consider that the properties of two dimensional materials can be controlled by the composition of two dimensional materials and the structure of layers.

Bcc and Fcc transition metals and alloys: a central role for the Jahn-Teller effect in explaining their ideal and distorted structures.

PubMed

Lee, Stephen; Hoffmann, Roald

2002-05-01

Transition metal elements, alloys, and intermetallic compounds often adopt the body centered cubic (bcc) and face centered cubic (fcc) structures. By comparing quantitative density functional with qualitative tight-binding calculations, we analyze the electronic factors which make the bcc and fcc structures energetically favorable. To do so, we develop a tight-binding function, DeltaE(star), a function that measures the energetic effects of transferring electrons within wave vector stars. This function allows one to connect distortions in solids to the Jahn-Teller effect in molecules and to provide an orbital perspective on structure determining deformations in alloys. We illustrate its use by considering first a two-dimensional square net. We then turn to three-dimensional fcc and bcc structures, and distortions of these. Using DeltaE(star), we rationalize the differences in energy of these structures. We are able to deduce which orbitals are responsible for instabilities in seven to nine valence electron per atom (e(-)/a) bcc systems and five and six e(-)/a fcc structures. Finally we demonstrate that these results account for the bcc and fcc type structures found in both the elements and binary intermetallic compounds of group 4 through 9 transition metal atoms. The outline of a theory of metal structure deformations based on loss of point group operation rather than translational symmetry is presented.

Ordered structure of FeGe2 formed during solid-phase epitaxy

NASA Astrophysics Data System (ADS)

Jenichen, B.; Hanke, M.; Gaucher, S.; Trampert, A.; Herfort, J.; Kirmse, H.; Haas, B.; Willinger, E.; Huang, X.; Erwin, S. C.

2018-05-01

Fe3Si /Ge (Fe ,Si ) /Fe3Si thin-film stacks were grown by a combination of molecular beam epitaxy and solid-phase epitaxy (Ge on Fe3Si ). The stacks were analyzed using electron microscopy, electron diffraction, and synchrotron x-ray diffraction. The Ge(Fe,Si) films crystallize in the well-oriented, layered tetragonal structure FeGe2 with space group P 4 m m . This kind of structure does not exist as a bulk material and is stabilized by the solid-phase epitaxy of Ge on Fe3Si . We interpret this as an ordering phenomenon induced by minimization of the elastic energy of the epitaxial film.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, John R.

1986-01-01

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, J.R.

1984-10-10

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Growth, structural, thermal, dielectric and nonlinear optical properties of potassium hexachloro cadmate (IV) a novel single crystal

NASA Astrophysics Data System (ADS)

Umarani, P.; Jagannathan, K.

2018-02-01

The Potassium hexachloro cadmate (IV) (PHC) single crystal was grown from the aqueous of the solution by a controlled evaporation method. Single crystal XRD solved the structure. FTIR is used to identify the functional groups of grown crystal. The UV-Vis-NIR spectrometer was used to find out the UV cut off region and to calculate the optical band gap of the Potassium hexachloro cadmate (IV) single crystal. The EDAX spectrum has been used to identify the compounds present in title compound. The TG-DTA profile shows the thermal stability of the grown crystal of Potassium hexachloro cadmate (IV). The Vicker's hardness measurement was used to calculate the material hardness of the title compound. The dielectric loss and constant varied with frequencies and activation energy is also calculated. The solid state parameters like plasma energy, Penn gap, Fermi energy, electronic polarizability using Penn analysis and Clausius-Mossotti equation were also calculated for the title compound. The Z-scan technique is used to calculate the third order nonlinear susceptibility of a real and imaginary part.

Data Mining for 3D Organic Dirac Materials

NASA Astrophysics Data System (ADS)

Geilhufe, R. Matthias; Borysov, Stanislav S.; Bouhon, Adrien; Balatsky, Alexander V.

The study of Dirac materials, i.e. materials where the low-energy fermionic excitations behave as massless Dirac particles has been of ongoing interest for more than two decades. Such massless Dirac fermions are characterized by a linear dispersion relation with respect to the particle momentum. A combined study using group theory and data mining within the Organic Materials Database leads to the discovery of stable Dirac-point nodes and Dirac line-nodes within the electronic band structure in the class of 3-dimensional organic crystals. The nodes are protected by crystalline symmetry. As a result of this study, we present band structure calculations and symmetry analysis for previously synthesized organic materials. In all these materials, the Dirac nodes are well separated within the energy and located near the Fermi surface, which opens up a possibility for their direct experimental observation. The authors acknowledge support by the US Department of Energy, BES E3B7, the swedish Research Council Grant No. 638-2013-9243, the Knut and Alice Wallenberg Foundation, and the European Research Council (FP/2207-2013)/ERC Grant Agreement No. DM-321031.

Methane dissociation on Ni(111): A fifteen-dimensional potential energy surface using neural network method

NASA Astrophysics Data System (ADS)

Shen, Xiangjian; Chen, Jun; Zhang, Zhaojun; Shao, Kejie; Zhang, Dong H.

2015-10-01

In the present work, we develop a highly accurate, fifteen-dimensional potential energy surface (PES) of CH4 interacting on a rigid flat Ni(111) surface with the methodology of neural network (NN) fit to a database consisted of about 194 208 ab initio density functional theory (DFT) energy points. Some careful tests of the accuracy of the fitting PES are given through the descriptions of the fitting quality, vibrational spectrum of CH4 in vacuum, transition state (TS) geometries as well as the activation barriers. Using a 25-60-60-1 NN structure, we obtain one of the best PESs with the least root mean square errors: 10.11 meV for the entrance region and 17.00 meV for the interaction and product regions. Our PES can reproduce the DFT results very well in particular for the important TS structures. Furthermore, we present the sticking probability S0 of ground state CH4 at the experimental surface temperature using some sudden approximations by Jackson's group. An in-depth explanation is given for the underestimated sticking probability.

Structure and energetics of InN and GaN dimers

NASA Astrophysics Data System (ADS)

Šimová, Lucia; Tzeli, Demeter; Urban, Miroslav; Černušák, Ivan; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

2008-06-01

Large-scale mapping of various dimers of indium nitride and gallium nitride in singlet and triplet electronic states is reported. Second-order perturbation theory with Møller-Plesset partitioning of the Hamiltonian (MP2) and coupled-cluster with single and double excitations corrected for the triple excitations (CCSD(T)) are used for the geometry determinations and evaluation of excitation and dissociation energies. For gallium and nitrogen we have used the singly augmented correlation-consistent triple-zeta basis set (aug-cc-pVTZ), for indium we have used the aug-cc-pVTZ-pseudopotential basis set. The dissociation energies are corrected for basis set superposition error (BBSE) including geometrical relaxation of the monomers. We compare and discuss the similarities and dissimilarities in the structural patterns and energetics of both groups of isomers, including the effect of the BSSE. Our computations show that there are not only different ground states for In 2N 2 and Ga 2N 2 but also different numbers of stable stationary points on their potential energy surface. We compare our results with the molecular data published so far for these systems.

Polarizable continuum model associated with the self-consistent-reaction field for molecular adsorbates at the interface.

PubMed

Wang, Jing-Bo; Ma, Jian-Yi; Li, Xiang-Yuan

2010-01-07

In this work, a new procedure has been developed in order to realize the self-consistent-reaction field computation for interfacial molecules. Based on the extension of the dielectric polarizable continuum model, the quantum-continuum calculations for interfacial molecules have been carried out. This work presents an investigation into how the molecular structure influences the adsorbate-solvent interaction and consequently alters the orientation angle at the air/water interface. Taking both electrostatic and non-electrostatic energies into account, we investigate the orientation behavior of three interfacial molecules, 2,6-dimethyl-4-hydroxy-benzonitrile, 3,5-dimethyl-4-hydroxy-benzonitrile and p-cyanophenol, at the air/water interface. The results show that the hydrophilic hydroxyl groups in 2,6-dimethyl-4-hydroxy-benzonitrile and in p-cyanophenol point from the air to the water side, but the hydroxyl group in 3,5-dimethyl-4-hydroxy-benzonitrile takes the opposite direction. Our detailed analysis reveals that the opposite orientation of 3,5-dimethyl-4-hydroxy-benzonitrile results mainly from the cavitation energy. The different orientations of the hydrophilic hydroxyl group indicate the competition of electrostatic and cavitation energies. The theoretical prediction gives a satisfied explanation of the most recent sum frequency generation measurement for these molecules at the interface.

Molecular dynamics simulation on adsorption of pyrene-polyethylene onto ultrathin single-walled carbon nanotube

NASA Astrophysics Data System (ADS)

Cai, Lu; Lv, Wenzhen; Zhu, Hong; Xu, Qun

2016-07-01

The mechanism of the adsorption of pyrene-polyethylene (Py-PE) onto ultrathin single-walled carbon nanotube (SWNT) was studied by using all-atom molecular dynamics (MD) simulations. We found that solvent polarity and pyrene group are two critical factors in the Py-PE decoration on ultrathin SWNT. Combined MD simulations with free energy calculations, our results indicate that larger solvent polarity can decrease the contribution of conformation entropy, but contributes little to the interaction energy, moreover, larger SWNT diameter can decrease the contribution of conformation entropy but lead to the increasing of the interaction energy. In polar organic solvent (N, N-Dimethylacetamide), the pyrene group plays a key role in the adsorption of Py-PE onto ultrathin SWNT, not only facilitates the spontaneous adsorption of Py-PE onto ultrathin SWNT, but also helps to form compact structure between themselves in the final adsorption states. While in aqueous solution, pyrene group no longer works as an anchor, but still affects a lot to the final adsorption conformation. Our present work provides detailed theoretical clue to understand the noncovalent interaction between aromatic segment appended polymer and ultrathin SWNT, and helps to explore the potential application of ultrathin SWNT in the fields of hybrid material, biomedical and electronic materials.

Are milk and alternatives and fruit and vegetable intakes during adolescence associated with cortical and trabecular bone structure, density, and strength in adulthood?

PubMed

Z Movassagh, E; Kontulainen, S; Baxter-Jones, A D G; Whiting, S; Szafron, M; Papadimitropoulos, M; Vatanparast, H

2017-02-01

We investigated the impact of food group intake during adolescence on bone structure and strength during adulthood. In females, we found a beneficial effect of adolescent milk and alternatives and fruit and vegetable intake on adult radius shaft and distal tibia bone structure, respectively. No association was observed in males. The purpose of this study was to investigate whether adolescents with high intake of milk and alternatives (M&A) or fruit and vegetables (F&V) had better adult bone structure and strength compared to those with low intake levels. We analyzed data from 47 males and 69 females enrolled in the Pediatric Bone Mineral Accrual Study (PBMAS 1991-2011), who had one peripheral quantitative computed tomography scan at age 29 ± 2 years. We measured radius and tibia shaft total area (ToA), cortical area (CoA), cortical content (CoC), cortical density, bone strength (SSI p ), and muscle area, as well as distal radius and tibia ToA, total density, trabecular area, trabecular content, trabecular density, and bone strength (BSI c ). Sequential 24-h recalls were used to assess M&A and F&V intake; participants were grouped for their mean intake during adolescence (low = bottom quartile, moderate = middle quartiles, high = top quartile) and were compared using multivariate analysis of covariance while adjusting for adult height, muscle area, physical activity, energy and calcium intake and adolescent energy intake, and physical activity. Females with high M&A intake compared to low M&A intake group (mean 3.8 vs. 1.3 servings/day, respectively) had greater adult ToA (14 %, p < 0.05), CoA (15 %, p < 0.01), and CoC (16 %, p < 0.01) at radius shaft. Females with moderate F&V intake compared to low F&V intake group (mean 3.7 vs. 2.1 servings/day, respectively) had greater adult ToA (8.5 %, p < 0.05) at distal tibia. Higher intake of M&A or F&V during adolescence had a long-term beneficial effect on bone structure in females, an association not observed in males.

Observation of Dirac-like energy band and ring-torus Fermi surface associated with the nodal line in topological insulator CaAgAs

NASA Astrophysics Data System (ADS)

Takane, Daichi; Nakayama, Kosuke; Souma, Seigo; Wada, Taichi; Okamoto, Yoshihiko; Takenaka, Koshi; Yamakawa, Youichi; Yamakage, Ai; Mitsuhashi, Taichi; Horiba, Koji; Kumigashira, Hiroshi; Takahashi, Takashi; Sato, Takafumi

2018-01-01

One of key challenges in current material research is to search for new topological materials with inverted bulk-band structure. In topological insulators, the band inversion caused by strong spin-orbit coupling leads to opening of a band gap in the entire Brillouin zone, whereas an additional crystal symmetry such as point-group and nonsymmorphic symmetries sometimes prohibits the gap opening at/on specific points or line in momentum space, giving rise to topological semimetals. Despite many theoretical predictions of topological insulators/semimetals associated with such crystal symmetries, the experimental realization is still relatively scarce. Here, using angle-resolved photoemission spectroscopy with bulk-sensitive soft-x-ray photons, we experimentally demonstrate that hexagonal pnictide CaAgAs belongs to a new family of topological insulators characterized by the inverted band structure and the mirror reflection symmetry of crystal. We have established the bulk valence-band structure in three-dimensional Brillouin zone, and observed the Dirac-like energy band and ring-torus Fermi surface associated with the line node, where bulk valence and conducting bands cross on a line in the momentum space under negligible spin-orbit coupling. Intriguingly, we found that no other bands cross the Fermi level and therefore the low-energy excitations are solely characterized by the Dirac-like band. CaAgAs provides an excellent platform to study the interplay among low-energy electron dynamics, crystal symmetry, and exotic topological properties.

Effects of experimental conditions on the morphologies, structures and growth modes of pulsed laser-deposited CdS nanoneedles

PubMed Central

2014-01-01

CdS nanoneedles with different morphologies, structures, and growth modes have been grown on Ni-coated Si(100) surface under different experimental conditions by pulsed laser deposition method. The effects of catalyst layer, substrate temperature, and laser pulse energy on the growth of the CdS nanoneedles were studied in detail. It was confirmed that the formation of the molten catalyst spheres is the key to the nucleation of the CdS nanoneedles by observing the morphologies of the Ni catalyst thin films annealed at different substrate temperatures. Both the substrate temperature and laser pulse energy strongly affected the growth modes of the CdS nanoneedles. The secondary growth of the smaller nanoneedles on the top of the main nanoneedles was found at appropriate conditions. A group of more completed pictures of the growth modes of the CdS nanoneedles were presented. PMID:24559455

ELECTRON AS A FUNDAMENTAL ELEMENTARY PARTICLE. PART I

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

Kakinuma, U.

1962-12-01

Elementary particles may be nothing but an electron existing under a certain condition, or a group of electrons that are formed to a certain combined state. Therefore, the knowledge of the electron structure is the starting point of our investigation about matter. To obtain the structure, the electron in an absolutely statical state is considered first and is studied by use of the gage- transformation defined in a modified way. This leads to the discovery oi a revised expression for the electromagnetic energy-tensor inside the electron as well as the wave equation for the electron formally similar to the Schrodingermore » equation for the hydrogen atom. However, our wave equation is interpreted as indicating the mode of energy distribution in the electron. To linearize the wave equation, a complex Riemannian geometry has been developed with results promising to be serviceable for further studies. (auth)« less

Computer modeling of lithium phosphate and thiophosphate electrolyte materials

NASA Astrophysics Data System (ADS)

Holzwarth, N. A. W.; Lepley, N. D.; Du, Yaojun A.

In this work, several lithium phosphate and thiophosphate materials are modeled to determine their optimized lattice structures, their total energies, and their electronic structures. Included in this study are materials characterized by isolated phosphate and thiophosphate groups - Li 3PS 4 and Li 3PO 4 and materials characterized by phosphate and thiophosphate dimers - Li 4P 2S 6 and Li 4P 2O 6 and Li 4P 2S 7 and Li 4P 2O 7. In addition, the superionic conducting material Li 7P 3S 11 is also modeled as are recently discovered crystalline argyrodite materials Li 7PS 6 and Li 6PS 5Cl. A comparison of Li ion vacancy migration in Li 4P 2S 7 and Li 4P 2O 7 shows the migration energy barriers in the thiophosphate to be smaller (less than one-half) than in the phosphate.

Optical properties of group-3 metal hexaboride nanoparticles by first-principles calculations

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

Yoshio, Satoshi; Maki, Koichiro; Adachi, Kenji, E-mail: kenji-adachi@ni.smm.co.jp

2016-06-21

LaB{sub 6} nanoparticles are widely used as solar control materials for strong near-infrared absorption and high visible transparency. In order to elucidate the origin of this unique optical property, first-principles calculations have been made for the energy-band structure and dielectric functions of R{sup III}B{sub 6} (R{sup III} = Sc, Y, La, Ac). On account of the precise assessment of the energy eigenvalues of vacant states in conduction band by employing the screened exchange method, as well as to the incorporation of the Drude term, dielectric functions and various physical properties of LaB{sub 6} have been reproduced in excellent agreement withmore » experimental values. Systematic examinations of dielectric functions and electronic structures of the trivalent metal hexaborides have clarified the origin of the visible transparency and the near-infrared plasmon absorption of R{sup III}B{sub 6} nanoparticles.« less

RandSpg: An open-source program for generating atomistic crystal structures with specific spacegroups

NASA Astrophysics Data System (ADS)

Avery, Patrick; Zurek, Eva

2017-04-01

A new algorithm, RANDSPG, that can be used to generate trial crystal structures with specific space groups and compositions is described. The program has been designed for systems where the atoms are independent of one another, and it is therefore primarily suited towards inorganic systems. The structures that are generated adhere to user-defined constraints such as: the lattice shape and size, stoichiometry, set of space groups to be generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally specify if the most general Wyckoff position is to be occupied or constrain select atoms to specific Wyckoff positions. Extensive testing indicates that the algorithm is efficient and reliable. The library is lightweight, portable, dependency-free and is published under a license recognized by the Open Source Initiative. A web interface for the algorithm is publicly accessible at http://xtalopt.openmolecules.net/randSpg/randSpg.html. RANDSPG has also been interfaced with the XTALOPT evolutionary algorithm for crystal structure prediction, and it is illustrated that the use of symmetric lattices in the first generation of randomly created individuals decreases the number of structures that need to be optimized to find the global energy minimum.

Properties of a soft-core model of methanol: An integral equation theory and computer simulation study

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

Huš, Matej; Urbic, Tomaz, E-mail: tomaz.urbic@fkkt.uni-lj.si; Munaò, Gianmarco

Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations.more » The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed.« less

InP Based Ternary And Quaternary Thin Film Structures On Large Areas Grown By LP-MOVPE

NASA Astrophysics Data System (ADS)

Schmitz, D.; Strauch, , G.; Jurgensen, H.; Heyen, M.; Harde, P.

1989-11-01

Using low pressure MOVPE and higher linear flow velocities high purity GalnAs/lnP and GalnAsP heterostructures can be prepared. Excellent homogeneity in thickness, composition, and doping on a 2" InP substrate can be realized by this approach for optimized conditions. The low growth rates required for the deposition of very narrow well structures are achieved by selecting reduced pressures of the group III and group V compounds used for deposition. The method yields structures with high electron mobilities of the two dimensional electron gas in the well and narrow PL (i.e. 2.2 meV for 20 nm wells) line widths, which is indicative of low impurity incorporation and abrupt heterojunctions. The observed energy shifts (up to 528 meV) demonstrate the large range of bandgap variation attainable by this method. A study of dopant incorporation shows, that Zn yields steep transitions in InGaAs.

Bi3+ sensitized Y2WO6:Ln3+ (Ln=Dy, Eu, and Sm) phosphors for solar spectral conversion.

PubMed

Huang, M N; Ma, Y Y; Xiao, F; Zhang, Q Y

2014-01-01

The phosphors of Y2WO6:Bi3+, Ln3+ (Ln=Dy, Eu and Sm) were synthesized by solid-state reaction in this study. The crystal structure, photoluminescence properties and energy transfer mechanism were investigated. By introducing Bi3+ ions, the excitation band of the phosphors was broadened to be 250-380 nm, which could be absorbed by the dye-sensitized solar cells (DSSCs). The overlap between excitation of W-O groups/Bi3+ and the emission of Ln3+ (Dy, Eu, and Sm) indicated that the probability of energy transfer from W-O groups and Bi3+ to Ln3+. The energy transfer efficiency from Bi3+ to Ln3+ (Ln=Dy, Eu and Sm) are calculated to be 16%, 20% and 58%. This work suggested that Y2WO6:Bi3+, Ln3+ (Ln=Dy, Eu and Sm) might be a promising ultraviolet-absorbing luminescent converter to enhance the photoelectrical conversion efficiency of dye-sensitized solar cells (DSSCs). Copyright © 2013 Elsevier B.V. All rights reserved.

The lightest organic radical cation for charge storage in redox flow batteries

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

Huang, Jinhua; Pan, Baofei; Duan, Wentao

2016-08-25

Electrochemically reversible fluids of high energy density are promising materials for capturing the electrical energy generated from intermittent sources like solar and wind. To meet this technological challenge there is a need to understand the fundamental limits and interplay of electrochemical potential, stability and solubility in “lean” derivatives of redox-active molecules. Here we describe the process of molecular pruning, illustrated for 2,5-di-tert-butyl-1,4-bis(2-methoxyethoxy)benzene, a molecule known to produce a persistently stable, high-potential radical cation. By systematically shedding molecular fragments considered important for radical cation steric stabilization, we discovered a minimalistic structure that retains long-term stability in its oxidized form. Interestingly, wemore » find the tert-butyl groups are unnecessary; high stability of the radical cation and high solubility are both realized in derivatives having appropriately positioned arene methyl groups. These stability trends are rationalized by mechanistic considerations of the postulated decomposition pathways. We suggest that the molecular pruning approach will uncover lean redox active derivatives for electrochemical energy storage leading to materials with long-term stability and high intrinsic capacity.« less

Giant piezoelectricity of monolayer group IV monochalcogenides: SnSe, SnS, GeSe, and GeS

NASA Astrophysics Data System (ADS)

Fei, Ruixiang; Li, Wenbin; Li, Ju; Yang, Li

2015-10-01

We predict enormous, anisotropic piezoelectric effects in intrinsic monolayer group IV monochalcogenides (MX, M=Sn or Ge, X=Se or S), including SnSe, SnS, GeSe, and GeS. Using first-principle simulations based on the modern theory of polarization, we find that their piezoelectric coefficients are about one to two orders of magnitude larger than those of other 2D materials, such as MoS2 and GaSe, and bulk quartz and AlN which are widely used in industry. This enhancement is a result of the unique "puckered" C2v symmetry and electronic structure of monolayer group IV monochalcogenides. Given the achieved experimental advances in the fabrication of monolayers, their flexible character, and ability to withstand enormous strain, these 2D structures with giant piezoelectric effects may be promising for a broad range of applications such as nano-sized sensors, piezotronics, and energy harvesting in portable electronic devices.

Influence of methyl functional groups on the stability of cubane carbon cage

NASA Astrophysics Data System (ADS)

Katin, Konstantin P.; Prudkovskiy, Vladimir S.; Maslov, Mikhail M.

2016-07-01

We present a quantum-chemical study to elucidate the structure, energetics and stability of isolated polymethylcubane molecules C8H8-q(CH3)q. The results obtained by means of originally developed nonorthogonal tight-binding approach are in good agreement with the existed experimental data for solid octamethylcubane C8(CH3)8. The isomerization mechanisms for polymethylcubane family are studied in detail and the minimum energy barriers' heights preventing the decomposition are calculated. The temperature dependence of octamethylcubane molecule lifetime to the decomposition moment was determined by direct molecular dynamics simulation. It is shown that methyl groups destabilize the cubic carbon cage, but less than nitro groups.

Penn State Multi-Discipline Tribology Group and Energy Institute Studies.

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

Perez, Joseph

This presentation is a summary of the current research activities on fuels and lubricants in the Multi-discipline Tribology group and the engine test group in the Combustion Laboratory of the Pennsylvania State University. The progress areas discussed in this summary include those found in Table 1. Table 1. RESEARCH AREAS: Diesel Engine Emission Reduction; Oxygenated Fuels; Improved Friction Fuels; Vegetable Oil Lubricants; Extended Drain Lubricants; Effect of Chemical Structure on Friction and Wear. The research is of interest either directly or indirectly to the goal of this workshop, diesel engine emissions reduction. The current projects at Penn State in themore » areas listed above will be discussed.« less

A Validation Framework for the Long Term Preservation of High Energy Physics Data

NASA Astrophysics Data System (ADS)

Ozerov, Dmitri; South, David M.

2014-06-01

The study group on data preservation in high energy physics, DPHEP, is moving to a new collaboration structure, which will focus on the implementation of preservation projects, such as those described in the group's large scale report published in 2012. One such project is the development of a validation framework, which checks the compatibility of evolving computing environments and technologies with the experiments software for as long as possible, with the aim of substantially extending the lifetime of the analysis software, and hence of the usability of the data. The framework is designed to automatically test and validate the software and data of an experiment against changes and upgrades to the computing environment, as well as changes to the experiment software itself. Technically, this is realised using a framework capable of hosting a number of virtual machine images, built with different configurations of operating systems and the relevant software, including any necessary external dependencies.

Organic Synthetic Advanced Materials for Optoelectronic and Energy Applications (at Center for Condensed Matter Sciences)

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

Yen, Hung-Ju

These slides cover Hung-Ju Yen's recent work in the synthesis and structural design of functional materials, which were further used for optoelectronic and energy applications, such as lithium ion battery, solar cell, LED, electrochromic, and fuel cells. This was for a job interview at Center for Condensed Matter Sciences. The following topics are detailed: current challenges for lithium-ion batteries; graphene, graphene oxide and nanographene; nanographenes with various functional groups; fine tune d-spacing through organic synthesis: varying functional group; schematic view of LIBs; nanographenes as LIB anode; rate performance (charging-discharging); electrochromic technology; electrochromic materials; advantages of triphenylamine; requirement of electrochromic materialsmore » for practical applications; low driving voltage and long cycle life; increasing the electroactive sites by multi-step synthetic procedures; synthetic route to starburst triarylamine-based polyamide; electrochromism ranging from visible to NIR region; transmissive to black electrochromism; RGB and CMY electrochromism.« less

Organic Synthetic Advanced Materials for Optoelectronic and Energy Applications (at National Taipei University of Technology)

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

Yen, Hung-Ju

These slides cover Hung-Ju Yen's recent work in the synthesis and structural design of functional materials, which were further used for optoelectronic and energy applications, such as lithium ion battery, solar cell, LED, electrochromic, and fuel cells. This was for a job interview at National Taipei University of Technology. The following topics are detailed: current challenges for lithium-ion batteries; graphene, graphene oxide and nanographene; nanographenes with various functional groups; fine tune d-spacing through organic synthesis: varying functional group; schematic view of LIBs; nanographenes as LIB anode; rate performance (charging-discharging); electrochromic technology; electrochromic materials; advantages of triphenylamine; requirement of electrochromic materialsmore » for practical applications; low driving voltage and long cycle life; increasing the electroactive sites by multi-step synthetic procedures; synthetic route to starburst triarylamine-based polyamide; electrochromism ranging from visible to NIR region; transmissive to black electrochromism; RGB and CMY electrochromism.« less

Organic Synthetic Advanced Materials for Optoelectronic and Energy Applications (at National Sun Yat-sen University) 

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

Yen, Hung-Ju

These slides cover Hung-Ju Yen's recent work in the synthesis and structural design of functional materials, which were further used for optoelectronic and energy applications, such as lithium ion battery, solar cell, LED, electrochromic, and fuel cells. This was for a job interview at National Sun Yat-sen University. The following topics are detailed: current challenges for lithium-ion batteries; graphene, graphene oxide and nanographene; nanographenes with various functional groups; fine tune d-spacing through organic synthesis: varying functional group; schematic view of LIBs; nanographenes as LIB anode; rate performance (charging-discharging); electrochromic technology; electrochromic materials; advantages of triphenylamine; requirement of electrochromic materials formore » practical applications; low driving voltage and long cycle life; increasing the electroactive sites by multi-step synthetic procedures; synthetic route to starburst triarylamine-based polyamide; electrochromism ranging from visible to NIR region; transmissive to black electrochromism; RGB and CMY electrochromism.« less

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

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

2017-01-01

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final post-cured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of phenolic chain structure and solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered, ethylene glycol (EGL) and H2O. In addition, three phenolic chain structures were considered including two novolac-type chains with either an ortho-ortho (OON) or ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through structural analysis of the solvation shell and hydrogen bonding environment as well as through quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of the simulations and analyses indicate that EGL provides a larger solvation free energy than H2O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, phenolic chain structure significantly impacts solvation performance with OON having limited intermolecular hydrogen bond formations while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H2O, and other similar solvents.

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations.

PubMed

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

2017-04-06

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final postcured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of the phenolic chain structure and the solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered: ethylene glycol (EGL) and H 2 O. In addition, three phenolic chain structures are considered, including two novolac-type chains with either an ortho-ortho (OON) or an ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through a structural analysis of the solvation shell and the hydrogen-bonding environment as well as through a quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of simulations and the analyses indicate that EGL provides a higher solvation free energy than H 2 O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, the phenolic chain structure significantly affects the solvation performance, with OON having limited intermolecular hydrogen-bond formations, while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H 2 O, and other similar solvents.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

ROY Revisited, Again: The Eighth Solved Structure

DOE PAGES

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai; ...

2018-01-01

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

Atomistic Modeling of the Fluid-Solid Interface in Simple Fluids

NASA Astrophysics Data System (ADS)

Hadjiconstantinou, Nicolas; Wang, Gerald

2017-11-01

Fluids can exhibit pronounced structuring effects near a solid boundary, typically manifested in a layered structure that has been extensively shown to directly affect transport across the interface. We present and discuss several results from molecular-mechanical modeling and molecular-dynamics (MD) simulations aimed at characterizing the structure of the first fluid layer directly adjacent to the solid. We identify a new dimensionless group - termed the Wall number - which characterizes the degree of fluid layering, by comparing the competing effects of wall-fluid interaction and thermal energy. We find that in the layering regime, several key features of the first layer layer - including its distance from the solid, its width, and its areal density - can be described using mean-field-energy arguments, as well as asymptotic analysis of the Nernst-Planck equation. For dense fluids, the areal density and the width of the first layer can be related to the bulk fluid density using a simple scaling relation. MD simulations show that these results are broadly applicable and robust to the presence of a second confining solid boundary, different choices of wall structure and thermalization, strengths of fluid-solid interaction, and wall geometries.

Comparison of Comet Enflow and VA One Acoustic-to-Structure Power Flow Predictions

NASA Technical Reports Server (NTRS)

Grosveld, Ferdinand W.; Schiller, Noah H.; Cabell, Randolph H.

2010-01-01

Comet Enflow is a commercially available, high frequency vibroacoustic analysis software based on the Energy Finite Element Analysis (EFEA). In this method the same finite element mesh used for structural and acoustic analysis can be employed for the high frequency solutions. Comet Enflow is being validated for a floor-equipped composite cylinder by comparing the EFEA vibroacoustic response predictions with Statistical Energy Analysis (SEA) results from the commercial software program VA One from ESI Group. Early in this program a number of discrepancies became apparent in the Enflow predicted response for the power flow from an acoustic space to a structural subsystem. The power flow anomalies were studied for a simple cubic, a rectangular and a cylindrical structural model connected to an acoustic cavity. The current investigation focuses on three specific discrepancies between the Comet Enflow and the VA One predictions: the Enflow power transmission coefficient relative to the VA One coupling loss factor; the importance of the accuracy of the acoustic modal density formulation used within Enflow; and the recommended use of fast solvers in Comet Enflow. The frequency region of interest for this study covers the one-third octave bands with center frequencies from 16 Hz to 4000 Hz.

ROY Revisited, Again: The Eighth Solved Structure

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

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

The relationships between electricity consumption and GDP in Asian countries, using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Kantar, Ersin; Keskin, Mustafa

2013-11-01

This study uses hierarchical structure methods (minimal spanning tree (MST) and hierarchical tree (HT)) to examine the relationship between energy consumption and economic growth in a sample of 30 Asian countries covering the period 1971-2008. These countries are categorized into four panels based on the World Bank income classification, namely high, upper middle, lower middle, and low income. In particular, we use the data of electricity consumption and real gross domestic product (GDP) per capita to detect the topological properties of the countries. We show a relationship between electricity consumption and economic growth by using the MST and HT. We also use the bootstrap technique to investigate a value of the statistical reliability to the links of the MST. Finally, we use a clustering linkage procedure in order to observe the cluster structure. The results of the structural topologies of these trees are as follows: (i) we identified different clusters of countries according to their geographical location and economic growth, (ii) we found a strong relationship between energy consumption and economic growth for all income groups considered in this study and (iii) the results are in good agreement with the causal relationship between electricity consumption and economic growth.

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

PubMed

Westaway, Kenneth C; Fang, Yao-ren; MacMillar, Susanna; Matsson, Olle; Poirier, Raymond A; Islam, Shahidul M

2008-10-16

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

PubMed Central

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS. PMID:28906114

Development of Accurate Structure for Mounting and Aligning Thin-Foil X-Ray Mirrors

NASA Technical Reports Server (NTRS)

Heilmann, Ralf K.

2001-01-01

The goal of this work was to improve the assembly accuracy for foil x-ray optics as produced by the high-energy astrophysics group at the NASA Goddard Space Flight Center. Two main design choices lead to an alignment concept that was shown to improve accuracy well within the requirements currently pursued by the Constellation-X Spectroscopy X-Ray Telescope (SXT).