WorldWideScience

Sample records for bond formation ab

  1. Stereoelectronic control in peptide bond formation. Ab initio calculations and speculations on the mechanism of action of serine proteases.

    Science.gov (United States)

    Gorenstein, D G; Taira, K

    1984-01-01

    Ab initio molecular orbital calculations have been performed on the reaction profile for the addition/elimination reaction between ammonia and formic acid, proceeding via a tetrahedral intermediate: NH3 + HCO2H----H2NCH(OH)2----NH2CHO + H2O. Calculated transition state energies for the first addition step of the reaction revealed that a lone pair on the oxygen of the OH group, which is antiperiplanar to the attacking nitrogen, stabilized the transition state by 3.9 kcal/mol, thus supporting the hypothesis of stereoelectronic control for this reaction. In addition, a secondary, counterbalancing stereoelectronic effect stabilizes the second step, water elimination, transition state by 3.1 kcal/mol if the lone pair on the leaving water oxygen is not antiperiplanar to the C-N bond. The best conformation for the transition states was thus one with a lone pair antiperiplanar to the adjacent scissile bond and also one without a lone-pair orbital on the scissile bond oxygen or nitrogen antiperiplanar to the adjacent polar bond. The significance of these stereoelectronic effects for the mechanism of action of serine proteases is discussed. PMID:6394065

  2. Ab initio computational study of –N-C and –O-C bonding formation : functional group modification reaction based chitosan

    Science.gov (United States)

    Siahaan, P.; Salimah, S. N. M.; Sipangkar, M. J.; Hudiyanti, D.; Djunaidi, M. C.; Laksitorini, M. D.

    2018-04-01

    Chitosan application in pharmaceutics and cosmeceutics industries is limited by its solubility issue. Modification of -NH2 and -OH fuctional groups of chitosan by adding carboxyl group has been shown to improve its solubility and application. Attempt to synthesize carboxymethyl chitosan (CMC) from monocloroacetic acid (MCAA) has been done prior this report. However no information is available wether –OH (-O-C bonding formation) or -NH2 (-N-C bonding formation) is the preference for - CH2COOH to attach. In the current study, the reaction mechanism between chitosan and MCAA reactants into carboxymethyl chitosan (CMC) was examined by computational approach. Dimer from of chitosan used as a molecular model in calculation All the molecular structure involved in the reaction mechanism was optimized by ab initio computational on the theory and basis set HF/6-31G(d,p). The results showed that the - N-C bonding formation via SN2 than the -O-C bonding formation via SN2 which have activation energy 469.437 kJ/mol and 533.219 kJ/mol respectively. However, the -O-C bonding formation more spontaneous than the -N-C bonding formation because ΔG the formation of O-CMC-2 reaction is more negative than ΔG of formation N-CMC-2 reaction is -4.353 kJ/mol and -1.095 kJ/mol respectively. The synthesis of N,O-CMC first forms -O-CH2COOH, then continues to form -NH-CH2COOH. This information is valuable to further optimize the reaction codition for CMC synthesis.

  3. Ab initio computational study of reaction mechanism of peptide bond formation on HF/6-31G(d,p) level

    Science.gov (United States)

    Siahaan, P.; Lalita, M. N. T.; Cahyono, B.; Laksitorini, M. D.; Hildayani, S. Z.

    2017-02-01

    Peptide plays an important role in modulation of various cell functions. Therefore, formation reaction of the peptide is important for chemical reactions. One way to probe the reaction of peptide synthesis is a computational method. The purpose of this research is to determine the reaction mechanism for peptide bond formation on Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine by ab initio computational approach. The calculations were carried out by theory and basis set HF/6-31G(d,p) for four mechanisms (path 1 to 4) that proposed in this research. The results show that the highest of the rate determining step between reactant and transition state (TS) for path 1, 2, 3, and 4 are 163.06 kJ.mol-1, 1868 kJ.mol-1, 5685 kJ.mol-1, and 1837 kJ.mol-1. The calculation shows that the most preferred reaction of Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine are on the path 1 (initiated with the termination of H+ in proline amino acid) that produce Ac-PV-NH2.

  4. Monte Carlo simulation of AB-copolymers with saturating bonds

    CERN Document Server

    Chertovich, A V; Khokhlov, A R; Bohr, J

    2003-01-01

    Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A-and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending on the nature of a particular AB-sequence: statistical random sequence, diblock sequence and 'random-complementary' sequence (one-half of such an AB-sequence is random with Bernoulli statistics while the other half is complementary to the first one). The properties of random-complementary sequences are closer to those of diblock sequences than to the properties of random sequences. The model (although quite rough) is expected to represent some basic features of real RNA molecules, i.e. the formation of secondary structure of RNA due to hydrogen bonding of corresponding bases and stacking interactions of the base pairs in helixes. We introduce the notation of RNA-like copolymers and discuss in what sense the sequences studie...

  5. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  6. Monte Carlo simulation of AB-copolymers with saturating bonds

    DEFF Research Database (Denmark)

    Chertovich, A.C.; Ivanov, V.A.; Khokhlov, A.R.

    2003-01-01

    Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A- and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending...

  7. Analysis of Disulfide Bond Formation

    NARCIS (Netherlands)

    Braakman, Ineke; Lamriben, Lydia; van Zadelhoff, Guus; Hebert, Daniel N.

    2017-01-01

    In this unit, protocols are provided for detection of disulfide bond formation in cultures of intact cells and in an in vitro translation system containing isolated microsomes or semi-permeabilized cells. First, the newly synthesized protein of interest is biosynthetically labeled with radioactive

  8. Bonded exciplex formation: electronic and stereoelectronic effects.

    Science.gov (United States)

    Wang, Yingsheng; Haze, Olesya; Dinnocenzo, Joseph P; Farid, Samir; Farid, Ramy S; Gould, Ian R

    2008-12-18

    As recently proposed, the singlet-excited states of several cyanoaromatics react with pyridine via bonded-exciplex formation, a novel concept in photochemical charge transfer reactions. Presented here are electronic and steric effects on the quenching rate constants, which provide valuable support for the model. Additionally, excited-state quenching in poly(vinylpyridine) is strongly inhibited both relative to that in neat pyridine and also to conventional exciplex formation in polymers, consistent with a restrictive orientational requirement for the formation of bonded exciplexes. Examples of competing reactions to form both conventional and bonded exciplexes are presented, which illustrate the delicate balance between these two processes when their reaction energetics are similar. Experimental and computational evidence is provided for the formation of a bonded exciplex in the reaction of the singlet excited state of 2,6,9,10-tetracyanoanthracene (TCA) with an oxygen-substituted donor, dioxane, thus expanding the scope of bonded exciplexes.

  9. Ab initio study of MgH2 formation

    International Nuclear Information System (INIS)

    Novakovic, Nikola; Matovic, Ljiljana; Novakovic, Jasmina Grbovic; Manasijevic, Miodrag; Ivanovic, Nenad

    2009-01-01

    Even if there is considerable literature dealing with structure and properties of MgH 2 compound there are still some uncertain details about nature of bonding governing its formation and decomposition. In order to better understand the processes essential for absorption and desorption of MgH 2 , ab initio DFT based calculations of rutile MgH 2 compound, elemental hcp-Mg, and three different hypothetical hcp-Mg-derived hydrides are performed. Our findings show that all structures are unstable, and that MgH (Wurtzite) is a closest possible candidate for intermediate phase between the hcp-Mg and MgH 2 at 1:1 stoichiometry. An alternative hydration pathway is suggested, including promotion of hcp-Mg to bcc-Mg and consecutive transformation to rutile MgH 2 by means of hydrogen incorporation into Mg matrix. Rutile MgH 2 calculations with various hydrogen vacancies concentration are performed. Calculation shows that at high hydrogen concentration close to 1:2, stable substoichiometric hydride is possible. Calculation also shows that high vacancy (low hydrogen) concentration favors bcc-Mg 2 H over rutile Mg 2 H structure.

  10. Mutual influence between triel bond and cation-π interactions: an ab initio study

    Science.gov (United States)

    Esrafili, Mehdi D.; Mousavian, Parisasadat

    2017-12-01

    Using ab initio calculations, the cooperative and solvent effects on cation-π and B...N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation-π and B...N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation-π interaction increases covalency of B...N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation-π and B...N interactions in these systems. Solvent effects on the cooperativity of cation-π and B...N interactions are also investigated.

  11. An Ab Initio MP2 Study of HCN-HX Hydrogen Bonded Complexes

    Directory of Open Access Journals (Sweden)

    Araújo Regiane C.M.U.

    1998-01-01

    Full Text Available An ab initio MP2/6-311++G** study has been performed to obtain geometries, binding energies and vibrational properties of HCN-HX H-bonded complexes with X = F, Cl, NC, CN and CCH. These MP2/6-311++G** results have revealed that: (i the calculated H-bond lengths are in very good agreement with the experimental ones; (ii the H-bond strength is associated with the intermolecular charge transfer and follows the order: HCN-HNC ~ HCN-HF > HCN-HCl ~ HCN-HCN > HCN-HCCH; (iii BSSE correction introduces an average reduction of 2.4 kJ/mol on the MP2/6-311++G** binding energies, i.e. 11% of the uncorrected binding energy; (iv the calculated zero-point energies reduce the stability of these complexes and show a good agreement with the available experimental values; (v the H-X stretching frequency is shifted downward upon H-bond formation. This displacement is associated with the H-bond length; (vi The more pronounced effect on the infrared intensities occurs with the H-X stretching intensity. It is much enhanced after complexation due to the charge-flux term; (vii the calculated intermolecular stretching frequencies are in very good agreement with the experimental ones; and, finally, (viii the results obtained for the HCN-HX complexes follow the same profile as those found for the acetylene-HX series but, in the latter case, the effects on the properties of the free molecules due to complexation are less pronounced than those in HCN-HX.

  12. SdAb heterodimer formation using leucine zippers

    Science.gov (United States)

    Goldman, Ellen R.; Anderson, George P.; Brozozog-Lee, P. Audrey; Zabetakis, Dan

    2013-05-01

    Single domain antibodies (sdAb) are variable domains cloned from camel, llama, or shark heavy chain only antibodies, and are among the smallest known naturally derived antigen binding fragments. SdAb derived from immunized llamas are able to bind antigens with high affinity, and most are capable of refolding after heat or chemical denaturation to bind antigen again. We hypothesized that the ability to produce heterodimeric sdAb would enable reagents with the robust characteristics of component sdAb, but with dramatically improved overall affinity through increased avidity. Previously we had constructed multimeric sdAb by genetically linking sdAb that bind non-overlapping epitopes on the toxin, ricin. In this work we explored a more flexible approach; the construction of multivalent binding reagents using multimerization domains. We expressed anti-ricin sdAb that recognize different epitopes on the toxin as fusions with differently charged leucine zippers. When the initially produced homodimers are mixed the leucine zipper domains will pair to produce heterodimers. We used fluorescence resonance energy transfer to confirm heterodimer formation. Surface plasmon resonance, circular dichroism, enzyme linked immunosorbent assays, and fluid array assays were used to characterize the multimer constructs, and evaluate their utility in toxin detection.

  13. Electronic structure and bonding in the RhC molecule by all-electron ab initio HF–Cl calculations and mass spectrometric measurements

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, K. A.

    1984-01-01

    In the present study we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of the 2Sigma+ ground state as well as of 16 excited states of the RhC molecule. The calculated spectroscopic constants of the lowest lying states are in good agreement...... with the experimental data. The chemical bond in the electronic ground state is mainly due to interaction of the 4d orbitals of Rh with the 2s and 2p orbitals of C. The bond is a triple bond composed of two pi bonds and one sigma bond. The 5s electron of Rh hardly participates in the bond formation. It is located...

  14. Ab Initio Calculations on Halogen Bond Between N-Br and Electron-donating Groups

    Institute of Scientific and Technical Information of China (English)

    WANG Yan-hua; CHEN Xue-song; ZOU Jian-wei; YU Qing-sen

    2007-01-01

    Ab initio calculations of complexes formed between N-bromosuccinimide and a series of electron-donating groups were performed at the level of MP2/Lanl2DZ* to gain a deeper insight into the nature of the N-Br halogen stronger halogen-bonding complex than the C-Br. A comparison of neutral hydrogen bond complex series reveals that the electron-donating capacities of the atoms decrease in the order, N>O>S; O(sp3)>O(sp2), which is adequate for the C-Br halogen bonding. Interaction energies, in conjunction with the geometrical parameters show that the affinitive capacity of trihalide anions X-3 with N-bromosuccinimide are markedly lower than that of the corresponding X- with N-bromosuccinimide, even lower than those of neutral molecules with N-bromosuccinimide. AIM analyses further confirmed the above results.

  15. Communication: A hydrogen-bonded difluorocarbene complex: Ab initio and matrix isolation study

    Science.gov (United States)

    Sosulin, Ilya S.; Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

    2017-10-01

    Structure and spectroscopic features of the CF2⋯HF complexes were studied by ab initio calculations at the CCSD(T) level and matrix isolation FTIR spectroscopy. The calculations predict three stable structures. The most energetically favorable structure corresponds to hydrogen bonding of HF to the lone pair of the C atom (the interaction energy of 3.58 kcal/mol), whereas two less stable structures are the H⋯F bonded complexes (the interaction energies of 0.30 and 0.24 kcal/mol). The former species was unambiguously characterized by the absorptions in the FTIR spectra observed after X-ray irradiation of fluoroform in a xenon matrix at 5 K. The corresponding features appear at 3471 (H-F stretching), 1270 (C-F symmetric stretching, shoulder), 1175 (antisymmetric C-F stretching), and 630 (libration) cm-1, in agreement with the computational predictions. To our knowledge, it is the first hydrogen-bonded complex of dihalocarbene. Possible weaker manifestations of the H⋯F bonded complexes were also found in the C-F stretching region; however, their assignment is tentative. The H⋯C bonded complex is protected from reaction yielding a fluoroform molecule by a remarkably high energy barrier (23.85 kcal/mol), so it may be involved in various chemical reactions.

  16. Ab Initio Study of the Dynamical Si–O Bond Breaking Event in α-Quartz

    International Nuclear Information System (INIS)

    Su Rui; Zhang Hong; Han Wei; Chen Jun

    2015-01-01

    The Si–O bond breaking event in the α-quartz at the first triplet (T_1) excitation state is studied by using ab initio molecular dynamics (AIMD) and nudged elastic band calculations. A meta-stable non-bridging oxygen hole center and E′ center (NBOHC-E′) is observed in the AIMD which consists of a broken Si–O bond with a Si–O distance of 2.54 Å. By disallowing the re-bonding of the Si and O atoms, another defect configuration (III-Si/V-Si) is obtained and validated to be stable at both ground and excitation states. The NBOHC-E′ is found to present on the minimal energy pathway of the initial to III-Si/V-Si transition, showing that the generating of the NBOHC-E′ is an important step of the excitation induced structure defect. The energy barriers to produce the NBOHC-E′ and III-Si/V-Si defects are calculated to be 1.19 and 1.28 eV, respectively. The electronic structures of the two defects are calculated by the self-consistent GW calculations and the results show a clear electron transition from the bonding orbital to the non-bonding orbital. (paper)

  17. Ab initio calculations of the electronic structure and bonding characteristics of LaB6

    International Nuclear Information System (INIS)

    Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.

    2005-01-01

    Lanthanum hexaboride (LaB 6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB 6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB 6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB 6 system and partially explains its high efficiency as a thermionic emitter

  18. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    International Nuclear Information System (INIS)

    Feng Yexin; Chen Ji; Wang Enge; Li Xin-Zheng

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. (topical review)

  19. Domain Wall Formation in Ferromagnetic Layers: An Ab Initio Study

    Science.gov (United States)

    Herper, Heike C.

    Domain walls are an inherent feature of ferromagnetic (FM) films consisting of layers with different magnetic orientations. Since FM films are used in electrical devices the question of the influence of domain walls on, e.g., the magnetoresistance has attracted much interest. Besides discussing the resistance contribution of domain walls, it is appropriate to study different types of domain walls and their energy of formation. The behaviour of domain walls is usually discussed within model calculations. In the present paper it is done within an ab initio Green's function technique for layered systems, i.e., the fully relativistic, spin-polarized screened Korringa-Kohn Rostoker method. Results are presented for fcc Co layers covered by two semi-infinite fcc Pt(001) bulk systems or by bulk fcc Co(001), respectively. The resistance, which is caused by the different types of domain walls is discussed within a Kubo-Greenwood approach considering Co(001)/Co24/Co(001) as an example.

  20. Disulphide bond formation in food protein aggregation and gelation

    NARCIS (Netherlands)

    Visschers, R.W.; Jongh, de H.H.J.

    2005-01-01

    In this short review we discuss the role of cysteine residues and cystine bridges for the functional aggregation of food proteins. We evaluate how formation and cleavage of disulphide bonds proceeds at a molecular level, and how inter- and intramolecular disulfide bonds can be detected and modified.

  1. Formation of reflective and conductive silver film on ABS surface via covalent grafting and solution spray

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Dexin; Zhang, Yan [School of Mechanical and Automotive Engineering, South China University of Technology, 381 Wushan, Guangzhou 510640 (China); Bessho, Takeshi [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan); Kudo, Takahiro; Sang, Jing; Hirahara, Hidetoshi; Mori, Kunio [Faculty of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Kang, Zhixin, E-mail: zxkang@scut.edu.cn [School of Mechanical and Automotive Engineering, South China University of Technology, 381 Wushan, Guangzhou 510640 (China)

    2015-09-15

    Highlights: • A pure and homogenous silver film was deposited by spray-style plating technique. • The mechanism of covalent bonding between coating and substrate was studied. • The silver coating is highly reflective and conductive. • UV light was used to activate the ABS surface with triazine azide derivative. - Abstract: Conductive and reflective silver layers on acrylonitrile butadiene styrene (ABS) plastics have been prepared by photo grafting of triazine azides upon ultraviolet activation, self-assembling of triazine dithiols and silver electroless plating by solution spray based on silver mirror reaction. The as-prepared silver film exhibited excellent adhesion with ABS owing to covalent bonds between coating and substrate, and the detailed bonding mechanism have been investigated by X-ray photoelectron spectroscopy (XPS). X-ray diffraction (XRD) result revealed that silver film on ABS was pure and with a nanocrystalline structure. Atomic force microscope (AFM) analysis demonstrated that massive silver particles with sizes varying from 80 to 120 nm were deposited on ABS and formed a homogenous and smooth coating, resulting in highly reflective surface. Furthermore, silver maintained its unique conductivity even as film on ABS surface in term of four-point probe method.

  2. Formation of reflective and conductive silver film on ABS surface via covalent grafting and solution spray

    International Nuclear Information System (INIS)

    Chen, Dexin; Zhang, Yan; Bessho, Takeshi; Kudo, Takahiro; Sang, Jing; Hirahara, Hidetoshi; Mori, Kunio; Kang, Zhixin

    2015-01-01

    Highlights: • A pure and homogenous silver film was deposited by spray-style plating technique. • The mechanism of covalent bonding between coating and substrate was studied. • The silver coating is highly reflective and conductive. • UV light was used to activate the ABS surface with triazine azide derivative. - Abstract: Conductive and reflective silver layers on acrylonitrile butadiene styrene (ABS) plastics have been prepared by photo grafting of triazine azides upon ultraviolet activation, self-assembling of triazine dithiols and silver electroless plating by solution spray based on silver mirror reaction. The as-prepared silver film exhibited excellent adhesion with ABS owing to covalent bonds between coating and substrate, and the detailed bonding mechanism have been investigated by X-ray photoelectron spectroscopy (XPS). X-ray diffraction (XRD) result revealed that silver film on ABS was pure and with a nanocrystalline structure. Atomic force microscope (AFM) analysis demonstrated that massive silver particles with sizes varying from 80 to 120 nm were deposited on ABS and formed a homogenous and smooth coating, resulting in highly reflective surface. Furthermore, silver maintained its unique conductivity even as film on ABS surface in term of four-point probe method

  3. Superplastic Forming/Adhesive Bonding of Aluminum (SPF/AB) Multi-Sheet Structures

    Science.gov (United States)

    Wagner, John A. (Technical Monitor); Will, Jeff D.; Cotton, James D.

    2003-01-01

    A significant fraction of airframe structure consists of stiffened panels that are costly and difficult to fabricate. This program explored a potentially lower-cost processing route for producing such panels. The alternative process sought to apply concurrent superplastic forming and adhesive bonding of aluminum alloy sheets. Processing conditions were chosen to balance adequate superplasticity of the alloy with thermal stability of the adhesive. As a first objective, an air-quenchable, superplastic aluminum-lithium alloy and a low-volatile content, low-viscosity adhesive with compatible forming/curing cycles were identified. A four-sheet forming pack was assembled which consisted of a welded two-sheet core separated from the face sheets by a layer of adhesive. Despite some preliminary success, of over 30 forming trials none was completely successful. The main problem was inadequate superplasticity in the heat-affected zones of the rib welds, which generally fractured prior to completion of the forming cycle. The welds are a necessary component in producing internal ribs by the 'four-sheet' process. Other challenges, such as surface preparation and adhesive bonding, were adequately solved. But without the larger issue of tearing at the weld locations, complex panel fabrication by SPF/AB does not appear viable.

  4. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1997-01-01

    The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting

  5. Formation of Irreversible H-bonds in Cellulose Materials

    Science.gov (United States)

    Umesh P. Agarwal; Sally A. Ralph; Rick S. Reiner; Nicole M. Stark

    2015-01-01

    Understanding of formation of irreversible Hbonds in cellulose is important in a number of fields. For example, fields as diverse as pulp and paper and enzymatic saccharification of cellulose are affected. In the present investigation, the phenomenon of formation of irreversible H-bonds is studied in a variety of celluloses and under two different drying conditions....

  6. Ab initio study of electron-ion structure factors in binary liquids with different types of chemical bonding

    International Nuclear Information System (INIS)

    Klevets, Ivan; Bryk, Taras

    2014-01-01

    Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi–Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed

  7. Investigations of Reactive Carbohydrates in Glycosidic Bond Formation and Degradation

    DEFF Research Database (Denmark)

    Heuckendorff, Mads

    The overall objective of the research described in this thesis was to explore the field of glycosidic bond formation and degradation. In more detail, the objective was to do further research in the field of highly reactive glycosyl donors. New ways of making highly reactive donors were explored...

  8. Step growth of an AB2 monomer, with cycle formation

    DEFF Research Database (Denmark)

    Cameron, Colin; Fawcett, Allan H.; Hetherington, Cecil R.

    1998-01-01

    A computer-based lattice model of the step growth reaction of an AB2 monomer, the next elaborate system after an AB monomer, has been devised that allows the simultaneous and explicit occurrence of inter- and intramolecular reactions of A and B groups of the flexible and moving molecules according...... with fractal characteristics. Growth stops when each molecule contains a cycle. For the model explored, in which six lattice sites are used for each monomer, the limiting value of the number average degree of polymerization, 〈x〉n,∞, is 14.6(±0.3) (after infinite time). The occurrence within the system of rings...... of m residues (m=1,2,3,...) is found to depend upon m and the extent of reaction of the A groups, pa, according to Rm=C0pm am-2.71, the constant C0 reflecting the structure of the lattice and the monomer, and being shown to determine the final degree of polymerization. The exponent of the integers m...

  9. Evidence for phosphorus bonding in phosphorus trichloride-methanol adduct: a matrix isolation infrared and ab initio computational study.

    Science.gov (United States)

    Joshi, Prasad Ramesh; Ramanathan, N; Sundararajan, K; Sankaran, K

    2015-04-09

    The weak interaction between PCl3 and CH3OH was investigated using matrix isolation infrared spectroscopy and ab initio computations. In a nitrogen matrix at low temperature, the noncovalent adduct was generated and characterized using Fourier transform infrared spectroscopy. Computations were performed at B3LYP/6-311++G(d,p), B3LYP/aug-cc-pVDZ, and MP2/6-311++G(d,p) levels of theory to optimize the possible geometries of PCl3-CH3OH adducts. Computations revealed two minima on the potential energy surface, of which, the global minimum is stabilized by a noncovalent P···O interaction, known as a pnictogen bonding (phosphorus bonding or P-bonding). The local minimum corresponded to a cyclic adduct, stabilized by the conventional hydrogen bonding (Cl···H-O and Cl···H-C interactions). Experimentally, 1:1 P-bonded PCl3-CH3OH adduct in nitrogen matrix was identified, where shifts in the P-Cl modes of PCl3, O-C, and O-H modes of CH3OH submolecules were observed. The observed vibrational frequencies of the P-bonded adduct in a nitrogen matrix agreed well with the computed frequencies. Furthermore, computations also predicted that the P-bonded adduct is stronger than H-bonded adduct by ∼1.56 kcal/mol. Atoms in molecules and natural bond orbital analyses were performed to understand the nature of interactions and effect of charge transfer interaction on the stability of the adducts.

  10. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

    Science.gov (United States)

    Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

    2015-02-14

    We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

  11. Ab Initio Assessment of the Bonding in Disulfonates Containing Divalent Nitrogen and Phosphorus Atoms

    DEFF Research Database (Denmark)

    Andersen, Vinca Bonde; Berg, Rolf W.; Shim, Irene

    2017-01-01

    The iminodisulfonate, [N(SO3)2]3–, and phosphinodisulfonate, [P(SO3)2]3–, ions have been investigated by performing ab initio MP2/6-311+G**calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen...

  12. Simultaneous bond degradation and bond formation during phenol-formaldehyde curing with wood

    Science.gov (United States)

    Daniel J. Yelle; John Ralph

    2016-01-01

    Bonding of wood using phenol–formaldehyde adhesive develops highly durable bonds. Phenol– formaldehyde is believed to form primary bonds with wood cell wall polymers (e.g., lignin). However, it is unclear how this adhesive interacts and bonds to lignin. Through wood solubilisation methodologies, earlywood and latewood bonded assemblies were characterized using two-...

  13. The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

    Science.gov (United States)

    Förner, Wolfgang

    1992-03-01

    Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

  14. Surface Reconstruction-Induced Coincidence Lattice Formation Between Two-Dimensionally Bonded Materials and a Three-Dimensionally Bonded Substrate

    NARCIS (Netherlands)

    Boschker, Jos E.; Momand, Jamo; Bragaglia, Valeria; Wang, Ruining; Perumal, Karthick; Giussani, Alessandro; Kooi, Bart J.; Riechert, Henning; Calarco, Raffaella

    Sb2Te3 films are used for studying the epitaxial registry between two-dimensionally bonded (2D) materials and three-dimensional bonded (3D) substrates. In contrast to the growth of 3D materials, it is found that the formation of coincidence lattices between Sb2Te3 and Si(111) depends on the geometry

  15. Impaired respiration elicits SrrAB-dependent programmed cell lysis and biofilm formation in Staphylococcus aureus

    Science.gov (United States)

    Mashruwala, Ameya A; van de Guchte, Adriana; Boyd, Jeffrey M

    2017-01-01

    Biofilms are communities of microorganisms attached to a surface or each other. Biofilm-associated cells are the etiologic agents of recurrent Staphylococcus aureus infections. Infected human tissues are hypoxic or anoxic. S. aureus increases biofilm formation in response to hypoxia, but how this occurs is unknown. In the current study we report that oxygen influences biofilm formation in its capacity as a terminal electron acceptor for cellular respiration. Genetic, physiological, or chemical inhibition of respiratory processes elicited increased biofilm formation. Impaired respiration led to increased cell lysis via divergent regulation of two processes: increased expression of the AtlA murein hydrolase and decreased expression of wall-teichoic acids. The AltA-dependent release of cytosolic DNA contributed to increased biofilm formation. Further, cell lysis and biofilm formation were governed by the SrrAB two-component regulatory system. Data presented support a model wherein SrrAB-dependent biofilm formation occurs in response to the accumulation of reduced menaquinone. DOI: http://dx.doi.org/10.7554/eLife.23845.001 PMID:28221135

  16. Liquid phase diffusion bonding of A1070 by using metal formate coated Zn sheet

    Science.gov (United States)

    Ozawa, K.; Koyama, S.; shohji, I.

    2017-05-01

    Aluminium alloy have high strength and easily recycle due to its low melting point. Therefore, aluminium is widely used in the manufacturing of cars and electronic devices. In recent years, the most common way for bonding aluminium alloy is brazing and friction stir welding. However, brazing requires positional accuracy and results in the formation of voids by the flax residue. Moreover, aluminium is an excellent heat radiating and electricity conducting material; therefore, it is difficult to bond together using other bonding methods. Because of these limitations, liquid phase diffusion bonding is considered to the suitable method for bonding aluminium at low temperature and low bonding pressure. In this study, the effect of metal formate coating processing of zinc surface on the bond strength of the liquid phase diffusion bonded interface of A1070 has been investigated by SEM observation of the interfacial microstructures and fractured surfaces after tensile test. Liquid phase diffusion bonding was carried out under a nitrogen gas atmosphere at a bonding temperature of 673 K and 713 K and a bonding load of 6 MPa (bonding time: 15 min). As a result of the metal formate coating processing, a joint having the ultimate tensile strength of the base aluminium was provided. It is hypothesized that this is because metallic zinc is generated as a result of thermal decomposition of formate in the bonded interface at lower bonding temperatures.

  17. Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

    Science.gov (United States)

    Bano, Amreen; Gaur, N. K.

    2018-05-01

    Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

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

    Science.gov (United States)

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

    2018-05-01

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

  19. Halogen bonds in crystal TTF derivatives: an ab initio quantum mechanical study

    Czech Academy of Sciences Publication Activity Database

    Deepa, Palanisamy; Pandiyan, B. V.; Kolandaivel, P.; Hobza, Pavel

    2014-01-01

    Roč. 16, č. 5 (2014), s. 2038-2047 ISSN 1463-9076 R&D Projects: GA ČR GBP208/12/G016 Grant - others:Operational Program Research and Development for Innovations(XE) CZ 1.05/2.1.00/03/0058 Institutional support: RVO:61388963 Keywords : hydrogen-bonds * noncovalent interactions * sigma-hole Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.493, year: 2014

  20. Using Ab-Initio Calculations to Appraise Stm-Based - and Kink-Formation Energies

    Science.gov (United States)

    Feibelman, Peter J.

    2001-03-01

    Ab-initio total energies can and should be used to test the typically model-dependent results of interpreting STM morphologies. The benefits of such tests are illustrated here by ab-initio energies of step- and kink-formation on Pb and Pt(111) which show that the STM-based values of the kink energies must be revised. On Pt(111), the computed kink-energies for (100)- and (111)-microfacet steps are about 0.25 and 0.18 eV. These results imply a specific ratio of formation energies for the two step types, namely 1.14, in excellent agreement with experiment. If kink-formation actually cost the same energy on the two step types, an inference drawn from scanning probe observations of step wandering,(M. Giesen et al., Surf. Sci. 366, 229(1996).) this ratio ought to be 1. In the case of Pb(111), though computed energies to form (100)- and (111)-microfacet steps agree with measurement, the ab-initio kink-formation energies for the two step types, 41 and 60 meV, are 40-50% below experimental values drawn from STM images.(K. Arenhold et al., Surf. Sci. 424, 271(1999).) The discrepancy results from interpreting the images with a step-stiffness vs. kink-energy relation appropriate to (100) but not (111) surfaces. Good agreement is found when proper account of the trigonal symmetry of Pb(111) is taken in reinterpreting the step-stiffness data.

  1. Ab initio investigations of the electronic structure and chemical bonding of Li2ZrN2

    International Nuclear Information System (INIS)

    Matar, S.F.; Pöttgen, R.; Al Alam, A.F.; Ouaini, N.

    2012-01-01

    The electronic structure of the ternary nitride Li 2 ZrN 2 is examined from ab initio with DFT computations for an assessment of the properties of chemical bonding. The compound is found insulating with 1.8 eV band gap; it becomes metallic and less ionic upon removal of one equivalent of Li. The chemical interaction is found mainly between Zr and N on one hand and Li and N on the other hand. While all pair interactions are bonding, antibonding N–N interactions are found dominant at the top of the valence band of Li 2 ZrN 2 and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li 2−x ZrN 2 (x=∼1) is favored. - Graphical abstract: Trigonal structure of Li 2 ZrN 2 showing the Zr–N–Li layers along the c-axis. Highlights: ► Li 2 ZrN 2 calculated insulating with a 1.8 eV gap in agreement with its light green color. ► Lithium de-intercalation is energetically favored for one out of two Li equivalents. ► Li plays little role in the change of the structure, ensured by Zr and N binding. ► Similar changes in the electronic structure as for various intercalated phases of ZrN.

  2. Persistent local chemical bonds in intermetallic phase formation

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Yanwen [Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Bian, Xiufang, E-mail: xfbian@sdu.edu.cn [Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Qin, Xubo [Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Zhang, Shuo; Huang, Yuying [Shanghai Synchrotron Radiation Facilities, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204 (China)

    2014-05-01

    We found a direct evidence for the existence of the local chemical Bi–In bonds in the BiIn{sub 2} melt. These bonds are strong and prevail, dominating the structure evolution of the intermetallic clusters. From the local structure of the melt-quenched BiIn{sub 2} ribbon, the chemical Bi–In bonds strengthen compared with those in the equilibrium solidified alloy. The chemical bonds in BiIn{sub 2} melt retain to solid during a rapid quenching process. The results suggest that the intermetallic clusters in the melt evolve into the as-quenched intermetallic phase, and the intermetallic phase originates from the chemical bonds between unlike atoms in the melt. The chemical bonds preserve the chemical ordered clusters and dominate the clusters evolution.

  3. A comparison of hydrogen-bonded and van der Waals isomers of phenolṡṡnitrogen and phenolṡṡcarbon monoxide: An ab initio study

    Science.gov (United States)

    Chapman, Darren M.; Müller-Dethlefs, Klaus; Peel, J. Barrie

    1999-08-01

    The hydrogen-bonded and van der Waals isomers of phenolṡṡnitrogen and phenolṡṡcarbon monoxide in their neutral electronic (S0) and cation ground state (D0) were studied using ab initio HF/6-31G*, MP2/6-31G*, and B3LYP/6-31G* methods. The hydrogen-bonded isomers have the ligand bound via the hydroxyl group of the phenol ring, while the van der Waals isomers studied have the ligand located above the aromatic ring. For both complexes, the hydrogen-bonded isomer was found to be the most stable form for both the S0 and the D0 states. For phenolṡṡcarbon monoxide, twice as many isomers as compared to phenolṡṡnitrogen were found. The hydrogen-bonded isomer with the carbon end bonded to the hydroxyl group was the most stable structure for both the S0 and the D0 states.

  4. Formation of integral asymmetric membranes of AB diblock and ABC triblock copolymers by phase inversion.

    Science.gov (United States)

    Jung, Adina; Filiz, Volkan; Rangou, Sofia; Buhr, Kristian; Merten, Petra; Hahn, Janina; Clodt, Juliana; Abetz, Clarissa; Abetz, Volker

    2013-04-12

    The formation of integral asymmetric membranes from ABC triblock terpolymers by non-solvent-induced phase separation is shown. They are compared with the AB diblock copolymer precursors. Triblock terpolymers of polystyrene-block-poly(2-vinylpyridine)-block-poly(ethylene oxide) (PS-b-P2VP-b-PEO) with two compositions are investigated. The third block supports the formation of a membrane in a case, where the corresponding diblock copolymer does not form a good membrane. In addition, the hydrophilicity is increased by the third block and due to the hydroxyl group the possibility of post-functionalization is given. The morphologies are imaged by scanning electron microscopy. The influence of the PEO on the membrane properties is analyzed by water flux, retention, and dynamic contact angle measurements. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Ab initio investigations of the electronic structure and chemical bonding of Li{sub 2}ZrN{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Matar, S.F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 Avenue du Docteur Albert Schweitzer, 33600 Pessac (France); Poettgen, R., E-mail: pottgen@uni-muenster.de [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster, Corrensstrasse 30, D-48149 Muenster (Germany); Al Alam, A.F., E-mail: adelalalam@usek.edu.lb [Universite Saint Esprit de Kaslik (USEK), Faculte des Sciences, URA GREVE (CNRS/USEK/UL), Jounieh (Lebanon); Ouaini, N., E-mail: naimouaini@usek.edu.lb [Universite Saint Esprit de Kaslik (USEK), Faculte des Sciences, URA GREVE (CNRS/USEK/UL), Jounieh (Lebanon)

    2012-06-15

    The electronic structure of the ternary nitride Li{sub 2}ZrN{sub 2} is examined from ab initio with DFT computations for an assessment of the properties of chemical bonding. The compound is found insulating with 1.8 eV band gap; it becomes metallic and less ionic upon removal of one equivalent of Li. The chemical interaction is found mainly between Zr and N on one hand and Li and N on the other hand. While all pair interactions are bonding, antibonding N-N interactions are found dominant at the top of the valence band of Li{sub 2}ZrN{sub 2} and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li{sub 2-x}ZrN{sub 2} (x={approx}1) is favored. - Graphical abstract: Trigonal structure of Li{sub 2}ZrN{sub 2} showing the Zr-N-Li layers along the c-axis. Highlights: Black-Right-Pointing-Pointer Li{sub 2}ZrN{sub 2} calculated insulating with a 1.8 eV gap in agreement with its light green color. Black-Right-Pointing-Pointer Lithium de-intercalation is energetically favored for one out of two Li equivalents. Black-Right-Pointing-Pointer Li plays little role in the change of the structure, ensured by Zr and N binding. Black-Right-Pointing-Pointer Similar changes in the electronic structure as for various intercalated phases of ZrN.

  6. Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

    Science.gov (United States)

    Varadwaj, Pradeep Risikrishna

    2010-05-01

    Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) 0, nabla(2)rho(c) BD*(HX) delocalization.

  7. Importance of mother-infant communication for social bond formation in mammals.

    Science.gov (United States)

    Okabe, Shota; Nagasawa, Miho; Mogi, Kazutaka; Kikusui, Takefumi

    2012-06-01

    Mother-infant bonding is a universal relationship of all mammalian species. Here, we describe the role of reciprocal communication between mother and infant in the formation of bonding for several mammalian species. Mother-infant bond formation is reinforced by various social cues or stimuli, including communicative signals, such as odor and vocalizations, or tactile stimuli. The mother also develops cross-modal sensory recognition of the infant, during bond formation. Many studies have indicated that the oxytocin neural system plays a pivotal role in bond formation by the mother; however, the underlying neural mechanisms for infants have not yet been clarified. The comparative understanding of cognitive functions of mother and infants may help us understand the biological significance of mother-infant communication in mammalian species. © 2012 The Authors. Animal Science Journal © 2012 Japanese Society of Animal Science.

  8. Hydrogen bond basicity of ionic liquids and molar entropy of hydration of salts as major descriptors in the formation of aqueous biphasic systems.

    Science.gov (United States)

    Passos, Helena; Dinis, Teresa B V; Cláudio, Ana Filipa M; Freire, Mara G; Coutinho, João A P

    2018-05-23

    Aqueous biphasic systems (ABS) composed of ionic liquids (ILs) and conventional salts have been largely investigated and successfully used in separation processes, for which the determination of the corresponding ternary phase diagrams is a prerequisite. However, due the large number of ILs that can be prepared and their high structural versatility, it is impossible to experimentally cover and characterize all possible combinations of ILs and salts that may form ABS. The development of tools for the prediction and design of IL-based ABS is thus a crucial requirement. Based on a large compilation of experimental data, a correlation describing the formation of IL-based ABS is shown here, based on the hydrogen-bonding interaction energies of ILs (EHB) obtained by the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) and the molar entropy of hydration of the salt ions. The ability of the proposed model to predict the formation of novel IL-based ABS is further ascertained.

  9. Enthalpies of formation of dihydroxybenzenes revisited: Combining experimental and high-level ab initio data

    International Nuclear Information System (INIS)

    Gonçalves, Elsa M.; Agapito, Filipe; Almeida, Tânia S.; Martinho Simões, José A.

    2014-01-01

    Highlights: • Thermochemistry of hydroxyphenols probed by experimental and theoretical methods. • A new paradigm for obtaining enthalpies of formation of crystalline compounds. • High-level ab initio results for the thermochemistry of gas-phase hydroxyphenols. • Sublimation enthalpies of hydroxyphenols determined by Calvet microcalorimetry. - Abstract: Accurate values of standard molar enthalpies of formation in condensed phases can be obtained by combining high-level quantum chemistry calculations of gas-phase enthalpies of formation with experimentally determined enthalpies of sublimation or vapourization. The procedure is illustrated for catechol, resorcinol, and hydroquinone. Using W1-F12, the gas-phase enthalpies of formation of these compounds at T = 298.15 K were computed as (−270.6, −269.4, and −261.0) kJ · mol −1 , respectively, with an uncertainty of ∼0.4 kJ · mol −1 . Using well characterised solid samples, the enthalpies of sublimation were determined with a Calvet microcalorimeter, leading to the following values at T = 298.15 K: (88.3 ± 0.3) kJ · mol −1 , (99.7 ± 0.4) kJ · mol −1 , and (102.0 ± 0.9) kJ · mol −1 , respectively. It is shown that these results are consistent with the crystalline structures of the compounds

  10. Solvent Induced Disulfide Bond Formation in 2,5-dimercapto-1,3,4-thiadiazole

    OpenAIRE

    Palanisamy Kalimuthu; Palraj Kalimuthu; S. Abraham John

    2007-01-01

    Disulfide bond formation is the decisive event in the protein folding to determine the conformation and stability of protein. To achieve this disulfide bond formation in vitro, we took 2,5-dimercapto-1,3,4-thiadiazole (DMcT) as a model compound. We found that disulfide bond formation takes place between two sulfhydryl groups of DMcT molecules in methanol. UV-Vis, FT-IR and mass spectroscopic as well as cyclic voltammetry were used to monitor the course of reaction. We proposed a mechanism for...

  11. Formation Dynamics of Potassium-Based Graphite Intercalation Compounds: An Ab Initio Study

    Science.gov (United States)

    Jiang, Xiankai; Song, Bo; Tománek, David

    2018-04-01

    This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. We use ab initio molecular dynamics simulations to study the microscopic dynamics of potassium intercalation in graphite. Upon adsorbing on graphite from the vapor phase, K atoms transfer their valence charge to the substrate. K atoms adsorbed on the surface diffuse rapidly along the graphene basal plane and eventually enter the interlayer region following a "U -turn" across the edge, gaining additional energy. This process is promoted at higher coverages associated with higher K pressure, leading to the formation of a stable intercalation compound. We find that the functionalization of graphene edges is an essential prerequisite for intercalation since bare edges reconstruct and reconnect, closing off the entry channels for the atoms.

  12. Asymmetric and symmetric bolaform supra-amphiphiles: formation of imine bond influenced by aggregation.

    Science.gov (United States)

    Wang, Guangtong; Wu, Guanglu; Wang, Zhiqiang; Zhang, Xi

    2014-02-18

    A series of bolaform supra-amphilphiles with different symmetries were fabricated through dynamic benzoic imine bond formation. The pH dependence of imine formations of these supra-amphiphiles were characterazied. We found that the extent of the imine formation of these supra-amphiphies were different. The supra-amphiphiles with a poorer symmetry always exhibited a lower imine formation at a given pH. Therefore, the varied extent of imine bond formation indicate the different aggregations of these supra-amphilphiles, which are controlled by the molecular symmetry of the supra-amphiphiles.

  13. Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations.

    Science.gov (United States)

    He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng

    2016-04-26

    Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation.

  14. High Charge Mobility of a Perylene Bisimide Dye with Hydrogen-bond Formation Group

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A perylene bisimide dye covalently bonded with a hydrogen-bond formation group of 1,3, 5-triazine-2, 4-diamine has been synthesized. Its casting films show a charge carrier mobility over 10-3 cm2/Vs, which is in the range of the highest values found for other promising charge transport materials suitable for solution processable technique.

  15. Formation of a hydrogen-bonded barbiturate [2]-rotaxane.

    Science.gov (United States)

    Tron, Arnaud; Thornton, Peter J; Rocher, Mathias; Jacquot de Rouville, Henri-Pierre; Desvergne, Jean-Pierre; Kauffmann, Brice; Buffeteau, Thierry; Cavagnat, Dominique; Tucker, James H R; McClenaghan, Nathan D

    2014-03-07

    Interlocked structures containing the classic Hamilton barbiturate binding motif comprising two 2,6-diamidopyridine units are reported for the first time. Stable [2]-rotaxanes can be accessed either through hydrogen-bonded preorganization by a barbiturate thread followed by a Cu(+)-catalyzed "click" stoppering reaction or by a Cu(2+)-mediated Glaser homocoupling reaction.

  16. Adhesives with wood materials : bond formation and performance

    Science.gov (United States)

    Charles R. Frihart; Christopher G. Hunt

    2010-01-01

    Adhesive bonding of wood plays an increasing role in the forest products industry and is a key factor for efficiently utilizing our timber resource. The main use of adhesives is in the manufacture of building materials, including plywood, oriented strandboard, particleboard, fiberboard, structural composite lumber, doors, windows and frames, and factory-laminated wood...

  17. Ab initio characterization of coupling strength for all types of dangling-bond pairs on the hydrogen-terminated Si(100)-2 × 1 surface

    Science.gov (United States)

    Shaterzadeh-Yazdi, Zahra; Sanders, Barry C.; DiLabio, Gino A.

    2018-04-01

    Recent work has suggested that coupled silicon dangling bonds sharing an excess electron may serve as building blocks for quantum-cellular-automata cells and quantum computing schemes when constructed on hydrogen-terminated silicon surfaces. In this work, we employ ab initio density-functional theory to examine the details associated with the coupling between two dangling bonds sharing one excess electron and arranged in various configurations on models of phosphorous-doped hydrogen-terminated silicon (100) surfaces. Our results show that the coupling strength depends strongly on the relative orientation of the dangling bonds on the surface and on the separation between them. The orientation of dangling bonds is determined by the anisotropy of the silicon (100) surface, so this feature of the surface is a significant contributing factor to variations in the strength of coupling between dangling bonds. The results demonstrate that simple models for approximating tunneling, such as the Wentzel-Kramer-Brillouin method, which do not incorporate the details of surface structure, are incapable of providing reasonable estimates of tunneling rates between dangling bonds. The results provide guidance to efforts related to the development of dangling-bond based computing elements.

  18. Molecular and ionic hydrogen bond formation in fluorous solvents.

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

  19. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

    International Nuclear Information System (INIS)

    Bankura, Arindam; Chandra, Amalendu

    2015-01-01

    The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water

  20. Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation

    Energy Technology Data Exchange (ETDEWEB)

    Colby, Denise; Bergman, Robert; Ellman, Jonathan

    2010-05-13

    that has seen widespread success involves the use of a proximal heteroatom that serves as a directing group for the selective functionalization of a specific C-H bond. In a survey of examples of heteroatom-directed Rh catalysis, two mechanistically distinct reaction pathways are revealed. In one case, the heteroatom acts as a chelator to bind the Rh catalyst, facilitating reactivity at a proximal site. In this case, the formation of a five-membered metallacycle provides a favorable driving force in inducing reactivity at the desired location. In the other case, the heteroatom initially coordinates the Rh catalyst and then acts to stabilize the formation of a metal-carbon bond at a proximal site. A true test of the utility of a synthetic method is in its application to the synthesis of natural products or complex molecules. Several groups have demonstrated the applicability of C-H bond functionalization reactions towards complex molecule synthesis. Target-oriented synthesis provides a platform to test the effectiveness of a method in unique chemical and steric environments. In this respect, Rh-catalyzed methods for C-H bond functionalization stand out, with several syntheses being described in the literature that utilize C-H bond functionalization in a key step. These syntheses are highlighted following the discussion of the method they employ.

  1. Formation of RNA phosphodiester bond by histidine-containing dipeptides

    DEFF Research Database (Denmark)

    Wieczorek, Rafal; Dörr, Mark; Chotera, Agata

    2013-01-01

    A new scenario for prebiotic formation of nucleic acid oligomers is presented. Peptide catalysis is applied to achieve condensation of activated RNA monomers into short RNA chains. As catalysts, L-dipeptides containing a histidine residue, primarily Ser-His, were used. Reactions were carried out...... in self-organised environment, a water-ice eutectic phase, with low concentrations of reactants. Incubation periods up to 30 days resulted in the formation of short oligomers of RNA. During the oligomerisation, an active intermediate (dipeptide-mononucleotide) is produced, which is the reactive species...... by a transamination mechanism. Because peptides are much more likely products of spontaneous condensation than nucleotide chains, their potential as catalysts for the formation of RNA is interesting from the origin-of-life perspective. Finally, the formation of the dipeptide-mononucleotide intermediate and its...

  2. Phase formation at bonded vanadium and stainless steel interfaces

    International Nuclear Information System (INIS)

    Summers, T.S.E.

    1992-01-01

    The interface between vanadium bonded to stainless steel was studies to determine whether a brittle phase formed during three joining operations. Inertia friction welds between V and 21-6-9 stainless steel were examined using TEM. In the as-welded condition, a continuous, polygranular intermetallic layer about 0.25 μm thick was present at the interface. This layer grew to about 50 μm thick during heat treatment at 1000 degrees C for two hours. Analysis of electron diffraction patterns confirmed that this intermetallic was the ω phase. The interface between vanadium and type 304, SANDVIK SAF 2205, and 21-6-9 stainless steel bonded by a co-extrusion process had intermetallic particles at the interface in the as-extruded condition. Heat treatment at 1000 degrees C for two hours caused these particles to grow into continuous layers in all three cases. Based on the appearance, composition and hardness of this interfacial intermetallic, it was also concluded to be ω phase. Bonding V to type 430 stainless steel by co-extrusion caused V-rich carbides to form at the interface due to the higher concentration of C in the type 430 than in the other stainless steels investigated. The carbide particles initially present grew into a continuous layer during a two-hour heat treatment at 1000 degrees C. Co-hipping 21-6-9 stainless steel tubing with V rod resulted in slightly more concentric specimens than the co-extruded ones, but a continuous layer of the ω phase formed during the hipping operation. This brittle layer could initiate failure during subsequent forming operations. The vanadium near the stainless steel interface in the co-extruded and co-hipped tubing in some cases was harder than before heat treatment. It was concluded that this hardening was due to thermal straining during cooling following heat treatment and that thermal strains might present a greater problem than seen here when longer tubes are used in actual applications

  3. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

    Directory of Open Access Journals (Sweden)

    Vijay Kumar Ravi

    Full Text Available Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

  4. Morphology Formation in PC/ABS Blends during Thermal Processing and the Effect of the Viscosity Ratio of Blend Partners

    Directory of Open Access Journals (Sweden)

    Stefanie Bärwinkel

    2016-08-01

    Full Text Available Morphology formation during compounding, as well as injection molding of blends containing 60 wt % polycarbonate (PC and 40 wt % polybutadiene rubber-modified styrene-acrylonitrile copolymers (ABS, has been investigated by transmission electron microscopy (TEM. Profiles of the blend morphology have been recorded in injection-molded specimens and significant morphology gradients observed between their skin and core. A <10 µm thick surface layer with strongly dispersed and elongated nano-scale (streak-like styrene acrylonitrile (SAN phases and well-dispersed, isolated SAN-grafted polybutadiene rubber particles is followed by a 50–150 µm thick skin layer in which polymer morphology is characterized by lamellar SAN/ABS phases. Thickness of these lamellae increases with the distance from the specimen’s surface. In the core of the specimens the SAN-grafted polybutadiene rubber particles are exclusively present within the SAN phases, which exhibit a much coarser and less oriented, dispersed morphology compared to the skin. The effects of the viscosity of the SAN in the PC/ABS blends on phase morphologies and correlations with fracture mechanics in tensile and impact tests were investigated, including scanning electron microscopy (SEM assessment of the fracture surfaces. A model explaining the mechanisms of morphology formation during injection molding of PC/ABS blends is discussed.

  5. Mechanistic insight into benzenethiol catalyzed amide bond formations from thioesters and primary amines

    DEFF Research Database (Denmark)

    Stuhr-Hansen, Nicolai; Bork, Nicolai; Strømgaard, Kristian

    2014-01-01

    The influence of arylthiols on cysteine-free ligation, i.e. the reaction between an alkyl thioester and a primary amine forming an amide bond, was studied in a polar aprotic solvent. We reacted the ethylthioester of hippuric acid with cyclohexylamine in the absence or presence of various quantities...... of thiophenol (PhSH) in a slurry of disodium hydrogen phosphate in dry DMF. Quantitative conversions into the resulting amide were observed within a few hours in the presence of equimolar amounts of thiophenol. Ab initio calculations showed that the reaction mechanism in DMF is similar to the well-known aqueous...... reaction mechanism. The energy barrier of the catalyzed amidation reaction is approximately 40 kJ mol(-1) lower than the non-catalyzed amidation reaction. At least partially this can be explained by a hydrogen bond from the amine to the π-electrons of the thiophenol, stabilizing the transition state...

  6. Fluorine substitution and nonconventional OH...pi intramolecular bond: high-resolution UV spectroscopy and ab initio calculations of 2-(p-fluorophenyl)ethanol.

    Science.gov (United States)

    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.

  7. Experimental evidence for blue-shifted hydrogen bonding in the fluoroform-hydrogen chloride complex: a matrix-isolation infrared and ab initio study.

    Science.gov (United States)

    Gopi, R; Ramanathan, N; Sundararajan, K

    2014-07-24

    The 1:1 hydrogen-bonded complex of fluoroform and hydrogen chloride was studied using matrix-isolation infrared spectroscopy and ab initio computations. Using B3LYP and MP2 levels of theory with 6-311++G(d,p) and aug-cc-pVDZ basis sets, the structures of the complexes and their energies were computed. For the 1:1 CHF3-HCl complexes, ab initio computations showed two minima, one cyclic and the other acyclic. The cyclic complex was found to have C-H · · · Cl and C-F · · · H interactions, where CHF3 and HCl sub-molecules act as proton donor and proton acceptor, respectively. The second minimum corresponded to an acyclic complex stabilized only by the C-F · · · H interaction, in which CHF3 is the proton acceptor. Experimentally, we could trap the 1:1 CHF3-HCl cyclic complex in an argon matrix, where a blue-shift in the C-H stretching mode of the CHF3 sub-molecule was observed. To understand the nature of the interactions, Atoms in Molecules and Natural Bond Orbital analyses were carried out to unravel the reasons for blue-shifting of the C-H stretching frequency in these complexes.

  8. Shedding light on disulfide bond formation: engineering a redox switch in green fluorescent protein

    DEFF Research Database (Denmark)

    Østergaard, H.; Henriksen, A.; Hansen, Flemming G.

    2001-01-01

    To visualize the formation of disulfide bonds in living cells, a pair of redox-active cysteines was introduced into the yellow fluorescent variant of green fluorescent protein. Formation of a disulfide bond between the two cysteines was fully reversible and resulted in a >2-fold decrease...... in the intrinsic fluorescence. Inter conversion between the two redox states could thus be followed in vitro as well as in vivoby non- invasive fluorimetric measurements. The 1.5 Angstrom crystal structure of the oxidized protein revealed a disulfide bond- induced distortion of the beta -barrel, as well...... the physiological range for redox-active cysteines. In the cytoplasm of Escherichia coli, the protein was a sensitive probe for the redox changes that occur upon disruption of the thioredoxin reductive pathway....

  9. Influence of intermolecular amide hydrogen bonding on the geometry, atomic charges, and spectral modes of acetanilide: An ab initio study

    Science.gov (United States)

    Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

    2006-08-01

    Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

  10. Formation of metal-F bonds during frictional sliding : Influence of water and applied load

    NARCIS (Netherlands)

    Shen, J. T.; Pei, Y. T.; De Hosson, J. Th. M.

    2016-01-01

    Effects of water lubrication and applied load on the formation of PTFE transfer films and metal-F bonds during sliding when PTFE filled composites sliding against steel and Al2O3 are investigated. In water lubricated conditions, XPS analysis reveals that a thin layer of water molecules at the

  11. Ring-opening of cyclic ethers with carbon–carbon bond formation by Grignard reagents

    DEFF Research Database (Denmark)

    Christensen, Stig Holden; Holm, Torkil; Madsen, Robert

    2014-01-01

    The ring-opening of cyclic ethers with concomitant C–C bond formation was studied with a number of Grignard reagents. The transformation was performed in a sealed vial by heating to ∼160 °C in an aluminum block or at 180 °C in a microwave oven. Good yields of the product alcohols were obtained...

  12. Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study

    NARCIS (Netherlands)

    De Jong, G.T.; Geerke, D.P.; Diefenbach, A.; Sola, M.; Bickelhaupt, F.M.

    2005-01-01

    We have computed a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the ethane C-C bond to the palladium atom and have used this to evaluate the performance of 24 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density

  13. Oxidative addition of the chloromethane C-Cl bond to Pd, an ab initio benchmark and DFT validation study

    NARCIS (Netherlands)

    de Jong, G.T.; Bickelhaupt, F.M.

    2006-01-01

    We have computed a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the chloromethane C-Cl bond to the palladium atom and have used this to evaluate the performance of 26 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density

  14. Prediction of high-temperature point defect formation in TiO2 from combined ab initio and thermodynamic calculations

    International Nuclear Information System (INIS)

    He, J.; Behera, R.K.; Finnis, M.W.; Li, X.; Dickey, E.C.; Phillpot, S.R.; Sinnott, S.B.

    2007-01-01

    A computational approach that integrates ab initio electronic structure and thermodynamic calculations is used to determine point defect stability in rutile TiO 2 over a range of temperatures, oxygen partial pressures and stoichiometries. Both donors (titanium interstitials and oxygen vacancies) and acceptors (titanium vacancies) are predicted to have shallow defect transition levels in the electronic-structure calculations. The resulting defect formation energies for all possible charge states are then used in thermodynamic calculations to predict the influence of temperature and oxygen partial pressure on the relative stabilities of the point defects. Their ordering is found to be the same as temperature increases and oxygen partial pressure decreases: titanium vacancy → oxygen vacancy → titanium interstitial. The charges on these defects, however, are quite sensitive to the Fermi level. Finally, the combined formation energies of point defect complexes, including Schottky, Frenkel and anti-Frenkel defects, are predicted to limit the further formation of point defects

  15. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

    2017-09-01

    We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

  16. Enthalpy of formation of anisole: implications for the controversy on the O-H bond dissociation enthalpy in phenol.

    Science.gov (United States)

    Simões, Ricardo G; Agapito, Filipe; Diogo, Hermínio P; da Piedade, Manuel E Minas

    2014-11-20

    Significant discrepancies in the literature data for the enthalpy of formation of gaseous anisole, ΔfHmo(PhOCH3, g), have fueled an ongoing controversy regarding the most reliable enthalpy of formation of the phenoxy radical and of the gas phase O-H bond dissociation enthalpy, DHo(PhO-H), in phenol. In the present work ΔfHmo(PhOCH3, g) was reassessed using a combination of calorimetric determinations and high-level (W2-F12) ab initio calculations. Static-bomb combustion calorimetry led to the standard molar enthalpy of formation of liquid anisole at 298.15 K, ΔfHmo(PhOCH3, l) = −(117.1 ± 1.4) kJ·mol(-1). The corresponding enthalpy of vaporization was obtained as, ΔvapHmo(PhOCH3) = 46.41 ± 0.26 kJ·mol(-1), by Calvet-drop microcalorimetry. These results give ΔfHmo(PhOCH3, g) = −(70.7 ± 1.4) kJ·mol(-1), in excellent agreement with ΔfHmo(PhOCH3, g) = −(70.8 ± 3.2) kJ·mol(-1), obtained from the W2-F12 calculations. The ΔfHmo(PhOCH3, g) here recommended leads to ΔfHmo(PhO•, g) = 55.5 ± 2.4 kJ·mol(-)1 and DH°(PhO-H) = 368.1 ± 2.6 kJ·mol(-1).

  17. Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

    Science.gov (United States)

    Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

    2013-06-01

    The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

  18. Breakdown of the Arrhenius Law in Describing Vacancy Formation Energies: The Importance of Local Anharmonicity Revealed by Ab initio Thermodynamics

    Directory of Open Access Journals (Sweden)

    A. Glensk

    2014-02-01

    Full Text Available We study the temperature dependence of the Gibbs energy of vacancy formation in Al and Cu from T=0  K up to the melting temperature, fully taking into account anharmonic contributions. Our results show that the formation entropy of vacancies is not constant as often assumed but increases almost linearly with temperature. The resulting highly nonlinear temperature dependence in the Gibbs formation energy naturally explains the differences between positron annihilation spectroscopy and differential dilatometry data and shows that nonlinear thermal corrections are crucial to extrapolate high-temperature experimental data to T=0  K. Employing these corrections—rather than the linear Arrhenius extrapolation that is commonly assumed in analyzing experimental data—revised formation enthalpies are obtained that differ up to 20% from the previously accepted ones. Using the revised experimental formation enthalpies, we show that a large part of the discrepancies between DFT-GGA and unrevised experimental vacancy formation energies disappears. The substantial shift between previously accepted and the newly revised T=0  K formation enthalpies also has severe consequences in benchmarking ab initio methods against experiments, e.g., in deriving corrections that go beyond commonly used LDA and GGA exchange-correlation functionals such as the AM05 functional.

  19. Thiolated polymers: evidence for the formation of disulphide bonds with mucus glycoproteins.

    Science.gov (United States)

    Leitner, Verena M; Walker, Greg F; Bernkop-Schnürch, Andreas

    2003-09-01

    Disulphide bonds between thiolated polymers (thiomers) and cysteine-rich subdomains of mucus glycoproteins are supposed to be responsible for the enhanced mucoadhesive properties of thiomers. This study set out to provide evidence for these covalent interactions using poly(acrylic acid)-cysteine conjugates of 2 and 450 kDa (PAA2-Cys, PAA450-Cys) displaying 402.5-776.0 micromol thiol groups per gram polymer. The effect of the disulphide bond breaker cysteine on thiomer-mucin disulphide bonds was monitored by (1) mucoadhesion studies and (2) rheological studies. Furthermore, (3) diffusion studies and (4) gel filtration studies were performed with thiomer-mucus mixtures. The addition of cysteine significantly (Ppolymer. Gel filtration studies showed that PAA2-Cys was able to form disulphide bonds with mucin glycoproteins resulting in an altered elution profile of the mucin/PAA2-Cys mixture in comparison to mucin alone or mucin/PAA2 mixture. According to these results, the study provides evidence for the formation of covalent bonds between thiomer and mucus glycoproteins.

  20. Corrosion Study and Intermetallics Formation in Gold and Copper Wire Bonding in Microelectronics Packaging

    Directory of Open Access Journals (Sweden)

    Christopher Breach

    2013-07-01

    Full Text Available A comparison study on the reliability of gold (Au and copper (Cu wire bonding is conducted to determine their corrosion and oxidation behavior in different environmental conditions. The corrosion and oxidation behaviors of Au and Cu wire bonding are determined through soaking in sodium chloride (NaCl solution and high temperature storage (HTS at 175 °C, 200 °C and 225 °C. Galvanic corrosion is more intense in Cu wire bonding as compared to Au wire bonding in NaCl solution due to the minimal formation of intermetallics in the former. At all three HTS annealing temperatures, the rate of Cu-Al intermetallic formation is found to be three to five times slower than Au-Al intermetallics. The faster intermetallic growth rate and lower activation energy found in this work for both Au/Al and Cu/Al as compared to literature could be due to the thicker Al pad metallization which removed the rate-determining step in previous studies due to deficit in Al material.

  1. C—C bond formation in the intramolecular Diels-Alder reaction of triene amides

    Directory of Open Access Journals (Sweden)

    Abdelilah Benallou

    2018-02-01

    Full Text Available The mechanism nature of the intramolecular Diels–Alder reaction has been performed; and thus, the changes of C—C bond forming/breaking along IRC are characterized in this study. Conceptual DFT analyses of the most favorable adduct fused/exo shows that the flux electronic will take place from diene to dienophile moiety. Moreover, ELF topological analysis based on the electron density predicts that C—C bond is formed by the coupling of two pseudoradical centers generated at the most significant atoms of the molecules. However, C2 vs C3, also C1 and C4 interaction comes mainly from the global electron density transfer which takes place along the reaction. Two- stage one-step is the proposed mechanism of this reaction, the first stage aims for the formation of C2—C3 σ bond while the second stage aims for C1—C4 σ bond formation. Interestingly, the observed asynchronicity of this IMDA reaction due principally to the asymmetric reorganization of electron density at the most attractive centers.

  2. C-C bond formation in the intramolecular Diels-Alder reaction of triene amides.

    Science.gov (United States)

    Benallou, Abdelilah; El Alaoui El Abdallaoui, Habib; Garmes, Hocine

    2018-02-01

    The mechanism nature of the intramolecular Diels-Alder reaction has been performed; and thus, the changes of C-C bond forming/breaking along IRC are characterized in this study. Conceptual DFT analyses of the most favorable adduct fused/exo shows that the flux electronic will take place from diene to dienophile moiety. Moreover, ELF topological analysis based on the electron density predicts that C-C bond is formed by the coupling of two pseudoradical centers generated at the most significant atoms of the molecules. However, C2 vs C3, also C1 and C4 interaction comes mainly from the global electron density transfer which takes place along the reaction. Two- stage one-step is the proposed mechanism of this reaction, the first stage aims for the formation of C2-C3 σ bond while the second stage aims for C1-C4 σ bond formation. Interestingly, the observed asynchronicity of this IMDA reaction due principally to the asymmetric reorganization of electron density at the most attractive centers.

  3. Hydrogen bonding-mediated dehydrogenation in the ammonia borane combined graphene oxide systems

    Science.gov (United States)

    Kuang, Anlong; Liu, Taijuan; Kuang, Minquan; Yang, Ruifeng; Huang, Rui; Wang, Guangzhao; Yuan, Hongkuan; Chen, Hong; Yang, Xiaolan

    2018-03-01

    The dehydrogenation of ammonia borane (AB) adsorbed on three different graphene oxide (GO) sheets is investigated within the ab initio density functional theory. The energy barriers to direct combination the hydrogens of hydroxyl groups and the hydridic hydrogens of AB to release H2 are relatively high, indicating that the process is energetically unfavorable. Our theoretical study demonstrates that the dehydrogenation mechanism of the AB-GO systems has undergone two critical steps, first, there is the formation of the hydrogen bond (O-H-O) between two hydroxyl groups, and then, the hydrogen bond further react with the hydridic hydrogens of AB to release H2 with low reaction barriers.

  4. Carbon-sulfur bond formation by reductive elimination of gold(iii) thiolates.

    Science.gov (United States)

    Currie, Lucy; Rocchigiani, Luca; Hughes, David L; Bochmann, Manfred

    2018-04-10

    Whereas the reaction of the gold(iii) pincer complex (C^N^C)AuCl with 1-adamantyl thiol (AdSH) in the presence of base affords (C^N^C)AuSAd, the same reaction in the absence of base leads to formation of aryl thioethers as the products of reductive elimination of the Au-C and Au-S ligands (C^N^C = dianion of 2-6-diphenylpyridine or 2-6-diphenylpyrazine). Although high chemical stability is usually taken as a characteristic of pincer complexes, results show that thiols are capable of cleaving one of the pincer Au-C bonds. This reaction is not simply a function of S-H acidity, since no cleavage takes place with other more acidic X-H compounds, such as carbazole, amides, phenols and malonates. The reductive C-S elimination follows a second-order rate law, -d[1a]/dt = k[1a][AdSH]. Reductive elimination is enabled by displacement of the N-donor by thiol; this provides the conformational flexibility necessary for C-S bond formation to occur. Alternatively, reductive C-S bond formation can be induced by reaction of pre-formed thiolates (C^N^C)AuSR with a strong Brønsted acid, followed by addition of SMe2 as base. On the other hand, treatment of (C^N^C)AuR (R = Me, aryl, alkynyl) with thiols under similar conditions leads to selective C-C rather than C-S bond formation. The reaction of (C^N^C)AuSAd with H+ in the absence of a donor ligand affords the thiolato-bridged complex [{(C^N-CH)Au(μ-SAd)}2]2+ which was crystallographically characterised.

  5. Renewable Formate from C-H Bond Formation with CO2: Using Iron Carbonyl Clusters as Electrocatalysts.

    Science.gov (United States)

    Loewen, Natalia D; Neelakantan, Taruna V; Berben, Louise A

    2017-09-19

    As a society, we are heavily dependent on nonrenewable petroleum-derived fuels and chemical feedstocks. Rapid depletion of these resources and the increasingly evident negative effects of excess atmospheric CO 2 drive our efforts to discover ways of converting excess CO 2 into energy dense chemical fuels through selective C-H bond formation and using renewable energy sources to supply electrons. In this way, a carbon-neutral fuel economy might be realized. To develop a molecular or heterogeneous catalyst for C-H bond formation with CO 2 requires a fundamental understanding of how to generate metal hydrides that selectively donate H - to CO 2 , rather than recombining with H + to liberate H 2 . Our work with a unique series of water-soluble and -stable, low-valent iron electrocatalysts offers mechanistic and thermochemical insights into formate production from CO 2 . Of particular interest are the nitride- and carbide-containing clusters: [Fe 4 N(CO) 12 ] - and its derivatives and [Fe 4 C(CO) 12 ] 2- . In both aqueous and mixed solvent conditions, [Fe 4 N(CO) 12 ] - forms a reduced hydride intermediate, [H-Fe 4 N(CO) 12 ] - , through stepwise electron and proton transfers. This hydride selectively reacts with CO 2 and generates formate with >95% efficiency. The mechanism for this transformation is supported by crystallographic, cyclic voltammetry, and spectroelectrochemical (SEC) evidence. Furthermore, installation of a proton shuttle onto [Fe 4 N(CO) 12 ] - facilitates proton transfer to the active site, successfully intercepting the hydride intermediate before it reacts with CO 2 ; only H 2 is observed in this case. In contrast, isoelectronic [Fe 4 C(CO) 12 ] 2- features a concerted proton-electron transfer mechanism to form [H-Fe 4 C(CO) 12 ] 2- , which is selective for H 2 production even in the presence of CO 2 , in both aqueous and mixed solvent systems. Higher nuclearity clusters were also studied, and all are proton reduction electrocatalysts, but none

  6. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

    Science.gov (United States)

    Fritch, Benjamin; Kosolapov, Andrey; Hudson, Phillip; Nissley, Daniel A; Woodcock, H Lee; Deutsch, Carol; O'Brien, Edward P

    2018-04-18

    Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.

  7. Peptide bond formation of alanine on silica and alumina surfaces as a catalyst

    Science.gov (United States)

    Sánchez Arenillas, M.; Mateo-Martí, E.

    2012-09-01

    Polymerization of amino acids has been important for the origin of life because the peptides may have been the first self-replicating systems. The amino acid concentrations in the oceans may have been too diluted in the early phases of the Earth. The formation of the biopolymers could have been due to the catalytic action of various minerals (such as silica or alumina). Our work is based on the comparison between alumina and silica minerals with and without prior activation of their silanol groups for the formation of peptide bonds using alanina like amino acid which it is the simplest quiral amino acid.

  8. Characteristics of chemical bond and vacancy formation in chalcopyrite-type CuInSe2 and related compounds

    International Nuclear Information System (INIS)

    Maeda, Tsuyoshi; Wada, Takahiro

    2009-01-01

    We studied characteristics of chemical bond and vacancy formation in chalcopyrite-type CuInSe 2 (CIS) by first principles calculations. The chalcopyrite-type CIS has two kinds of chemical bonds, Cu-Se and In-Se. The Cu-Se bond is a weak covalent bonding because electrons occupy both bonding and antibonding orbitals of Cu 3d and Se 4p and occupy only the bonding orbital (a 1 ) of Cu 4s and Se 4p and do not occupy the antibonding orbital (a 1 * ) of Cu 4s and Se 4p. On the other hand, the In-Se bond has a partially covalent and partially ionic character because the In 5s orbital covalently interacts with Se 4p; the In 5p orbital is higher than Se 4p and so the electron in the In 5p orbital moves to the Se 4p orbital. The average bond order of the Cu-Se and In-Se bonds can be calculated to be 1/4 and 1, respectively. The bond order of Cu-Se is smaller than that of In-Se. The characteristics of these two chemical bonds are related to the formation of Cu and In vacancies in CIS. The formation energy of the Cu vacancy is smaller than that of the In vacancy under both Cu-poor and In-poor conditions. The displacement (Δl) of the surrounding Se atoms after the formation of the Cu vacancy is smaller than the Δl after the formation of the In vacancy. The interesting and unique characteristics of CIS are discussed on the basis of the characteristics of the chemical bond. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Cr interaction in the formation of nano cluster of Y, Ti and O in bcc Fe an ab initio study

    International Nuclear Information System (INIS)

    Murali, D.; Panigrahi, B.K.; Valsakumar, M.C.; Chandra, Sharath; Sundar, C.S.

    2008-01-01

    Nanostructured ferritic alloys containing highly stable fine dispersion of yttrium oxide nano particles, produced by mechanical alloying, are promising structural materials for fast fission and fusion environments. Formation of Cr depleted and O enriched Y-Ti-O nanoclusters are observed in the atom probe analysis. Ab initio calculations based on density functional theory are carried out to understand the role of Cr atom interactions with other solute atoms (Y, Ti, O) and vacancies in the formation of nanocluster. The binding energy of clusters of Y-Ti-O in bcc Fe is found to be very high in the presence of vacancies. Our calculations are consistent with the atom probe observation of depletion of Cr atoms and enrichment of O atoms in the nanoclusters. (author)

  10. Large shift and small broadening of Br2 valence band upon dimer formation with H2O: an ab initio study.

    Science.gov (United States)

    Franklin-Mergarejo, Ricardo; Rubayo-Soneira, Jesus; Halberstadt, Nadine; Ayed, Tahra; Bernal-Uruchurtu, Margarita I; Hernández-Lamoneda, Ramón; Janda, Kenneth C

    2011-06-16

    Valence electronic excitation spectra are calculated for the H(2)O···Br(2) complex using highly correlated ab initio potentials for both the ground and the valence electronic excited states and a 2-D approximation for vibrational motion. Due to the strong interaction between the O-Br and the Br-Br stretching motions, inclusion of these vibrations is the minimum necessary for the spectrum calculation. A basis set calculation is performed to determine the vibrational wave functions for the ground electronic state and a wave packet simulation is conducted for the nuclear dynamics on the excited state surfaces. The effects of both the spin-orbit interaction and temperature on the spectra are explored. The interaction of Br(2) with a single water molecule induces nearly as large a shift in the spectrum as is observed for an aqueous solution. In contrast, complex formation has a remarkably small effect on the T = 0 K width of the valence bands due to the fast dissociation of the dihalogen bond upon excitation. We therefore conclude that the widths of the spectra in aqueous solution are mostly due to inhomogeneous broadening. © 2011 American Chemical Society

  11. Formation of the market of high-bond (junk bonds in the United States in 1970–1980 years

    Directory of Open Access Journals (Sweden)

    Moshenskyi S.Z.

    2017-03-01

    Full Text Available Market of high-yield bonds (also known as «junk bonds» began to emerge in the US in the mid-1970s and was associated with the activities of «junk bond king» Michael Milken from Drexel investment company. Junk bonds emitents are small and newly established companies which cannot get a high credit rating. Emission of high-yield (8–10 % bond was their only chance to find its place in the financial market. Michael Milken realized the potential of these bonds, which, in fact, were often quite reliable securities, and started organizing their emissions by selling junk bonds to Savings and Loan Associations and other investors. In the 1980 issue of such bonds used for aggressive corporate takeovers, which supplied the capital from junk bonds market. Some of takeovers carried out in violation of laws that led to the arrest of Michael Milken, Drexel bankruptcy and the collapse of the entire junk bonds market.

  12. Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation.

    Directory of Open Access Journals (Sweden)

    Brian J Schmidt

    2009-12-01

    Full Text Available The interaction of proteins at cellular interfaces is critical for many biological processes, from intercellular signaling to cell adhesion. For example, the selectin family of adhesion receptors plays a critical role in trafficking during inflammation and immunosurveillance. Quantitative measurements of binding rates between surface-constrained proteins elicit insight into how molecular structural details and post-translational modifications contribute to function. However, nano-scale transport effects can obfuscate measurements in experimental assays. We constructed a biophysical simulation of the motion of a rigid microsphere coated with biomolecular adhesion receptors in shearing flow undergoing thermal motion. The simulation enabled in silico investigation of the effects of kinetic force dependence, molecular deformation, grouping adhesion receptors into clusters, surface-constrained bond formation, and nano-scale vertical transport on outputs that directly map to observable motions. Simulations recreated the jerky, discrete stop-and-go motions observed in P-selectin/PSGL-1 microbead assays with physiologic ligand densities. Motion statistics tied detailed simulated motion data to experimentally reported quantities. New deductions about biomolecular function for P-selectin/PSGL-1 interactions were made. Distributing adhesive forces among P-selectin/PSGL-1 molecules closely grouped in clusters was necessary to achieve bond lifetimes observed in microbead assays. Initial, capturing bond formation effectively occurred across the entire molecular contour length. However, subsequent rebinding events were enhanced by the reduced separation distance following the initial capture. The result demonstrates that vertical transport can contribute to an enhancement in the apparent bond formation rate. A detailed analysis of in silico motions prompted the proposition of wobble autocorrelation as an indicator of two-dimensional function. Insight into two

  13. Grafting of diazonium salts on oxides surface: formation of aryl-O bonds on iron oxide nanoparticles

    International Nuclear Information System (INIS)

    Brymora, Katarzyna; Fouineau, Jonathan; Eddarir, Asma; Chau, François; Yaacoub, Nader; Grenèche, Jean-Marc; Pinson, Jean; Ammar, Souad; Calvayrac, Florent

    2015-01-01

    Combining ab initio modeling and 57 Fe Mössbauer spectrometry, we characterized the nature of the chemical linkage of aminoalkyl arenediazonium salt on the surface of iron oxide nanoparticles. We established that it is built through a metal–oxygen–carbon bonding and not a metal–carbon one, as usually suggested and commonly observed in previously studied metal- or carbon-based surfaces

  14. Grafting of diazonium salts on oxides surface: formation of aryl-O bonds on iron oxide nanoparticles

    Science.gov (United States)

    Brymora, Katarzyna; Fouineau, Jonathan; Eddarir, Asma; Chau, François; Yaacoub, Nader; Grenèche, Jean-Marc; Pinson, Jean; Ammar, Souad; Calvayrac, Florent

    2015-11-01

    Combining ab initio modeling and 57Fe Mössbauer spectrometry, we characterized the nature of the chemical linkage of aminoalkyl arenediazonium salt on the surface of iron oxide nanoparticles. We established that it is built through a metal-oxygen-carbon bonding and not a metal-carbon one, as usually suggested and commonly observed in previously studied metal- or carbon-based surfaces.

  15. Grafting of diazonium salts on oxides surface: formation of aryl-O bonds on iron oxide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Brymora, Katarzyna [LUNAM Université du Maine, IMMM UMR CNRS 6283 (France); Fouineau, Jonathan; Eddarir, Asma; Chau, François [Université Paris Diderot, Sorbonne Paris Cité, ITODYS CNRS UMR 7086 (France); Yaacoub, Nader; Grenèche, Jean-Marc [LUNAM Université du Maine, IMMM UMR CNRS 6283 (France); Pinson, Jean; Ammar, Souad [Université Paris Diderot, Sorbonne Paris Cité, ITODYS CNRS UMR 7086 (France); Calvayrac, Florent, E-mail: florent.calvayrac@univ-lemans.fr [LUNAM Université du Maine, IMMM UMR CNRS 6283 (France)

    2015-11-15

    Combining ab initio modeling and {sup 57}Fe Mössbauer spectrometry, we characterized the nature of the chemical linkage of aminoalkyl arenediazonium salt on the surface of iron oxide nanoparticles. We established that it is built through a metal–oxygen–carbon bonding and not a metal–carbon one, as usually suggested and commonly observed in previously studied metal- or carbon-based surfaces.

  16. {alpha}-Man monolayer formation via Si-C bond formation and protein recognition

    Energy Technology Data Exchange (ETDEWEB)

    Funato, Koji [School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 (Japan); Shirahata, Naoto [National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Miura, Yoshiko, E-mail: miuray@jaist.ac.j [School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 (Japan)

    2009-11-30

    An acetylenyl-terminated saccharide was synthesized and the thin layer formation on the hydrogen-terminated silicon was investigated. The acetylenyl-terminated saccharide was synthesized by the condensation reaction of hexynoic acid and p-aminophenyl saccharide. This was reacted with hydrogen-terminated silicon (Si-H) by a photochemical reaction. The resulting saccharide modified substrate was analyzed by ellipsometry and X-ray photoelectron spectroscopy, which showed the formation of a uniform monolayer. The surface's ability to recognize proteins was analyzed by fluorescent microscopy, and showed specific interactions with sugar recognition proteins.

  17. Photosynthetic water oxidation: binding and activation of substrate waters for O-O bond formation.

    Science.gov (United States)

    Vinyard, David J; Khan, Sahr; Brudvig, Gary W

    2015-01-01

    Photosynthetic water oxidation occurs at the oxygen-evolving complex (OEC) of Photosystem II (PSII). The OEC, which contains a Mn4CaO5 inorganic cluster ligated by oxides, waters and amino-acid residues, cycles through five redox intermediates known as S(i) states (i = 0-4). The electronic and structural properties of the transient S4 intermediate that forms the O-O bond are not well understood. In order to gain insight into how water is activated for O-O bond formation in the S4 intermediate, we have performed a detailed analysis of S-state dependent substrate water binding kinetics taking into consideration data from Mn coordination complexes. This analysis supports a model in which the substrate waters are both bound as terminal ligands and react via a water-nucleophile attack mechanism.

  18. Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state

    Energy Technology Data Exchange (ETDEWEB)

    Osterman, Ilya A.; Khabibullina, Nelli F.; Komarova, Ekaterina S.; Kasatsky, Pavel; Kartsev, Victor G.; Bogdanov, Alexey A.; Dontsova, Olga A.; Konevega, Andrey L.; Sergiev, Petr V.; Polikanov, Yury S. (InterBioScreen); (UIC); (MSU-Russia); (Kurchatov)

    2017-05-13

    The emergence of multi-drug resistant bacteria is limiting the effectiveness of commonly used antibiotics, which spurs a renewed interest in revisiting older and poorly studied drugs. Streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome. In this work, we have revealed the mode of action of the PTC inhibitor madumycin II, an alanine-containing streptogramin A antibiotic, in the context of a functional 70S ribosome containing tRNA substrates. Madumycin II inhibits the ribosome prior to the first cycle of peptide bond formation. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. We also revealed a previously unseen drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506•G2583 wobble pair that was attributed to a catalytically inactive state of the PTC. The structural and biochemical data reported here expand our knowledge on the fundamental mechanisms by which peptidyl transferase inhibitors modulate the catalytic activity of the ribosome.

  19. Identification of the formation of metal-vinylidene interfacial bonds of alkyne-capped platinum nanoparticles by isotopic labeling.

    Science.gov (United States)

    Hu, Peiguang; Chen, Limei; Deming, Christopher P; Bonny, Lewis W; Lee, Hsiau-Wei; Chen, Shaowei

    2016-10-07

    Stable platinum nanoparticles were prepared by the self-assembly of 1-dodecyne and dodec-1-deuteroyne onto bare platinum colloid surfaces. The nanoparticles exhibited consistent core size and optical properties. FTIR and NMR measurements confirmed the formation of Pt-vinylidene (Pt[double bond, length as m-dash]C[double bond, length as m-dash]CH-) interfacial linkages rather than Pt-acetylide (Pt-C[triple bond, length as m-dash]C-) and platinum-hydride (Pt-H) bonds.

  20. Bridging and bonding interactions in higher education: social capital and students’ academic and professional identity formation

    Science.gov (United States)

    Jensen, Dorthe H.; Jetten, Jolanda

    2015-01-01

    It is increasingly recognized that graduates’ achievements depend in important ways on their opportunities to develop an academic and a professional identity during their studies. Previous research has shown that students’ socio-economic status (SES) and social capital prior to entering university affects their ability to obtain these identities in higher education. However, what is less well understood is whether social capital that is built during university studies shapes identity development, and if so, whether the social capital gained during university years impacts on academic and professional identity differently. In a qualitative study, we interviewed 26 Danish and 11 Australian university students about their social interaction experiences, their opportunities to develop bonding capital as well as bridging capital, and their academic and professional identity. Findings show that while bonding social capital with co-students facilitated academic identity formation, such social capital does not lead to professional identity development. We also found that the development of bridging social capital with educators facilitated students’ professional identity formation. However, bonding social capital among students stood in the way of participating in bridging interaction with educators, thereby further hindering professional identity formation. Finally, while students’ parental background did not affect the perceived difficulty of forming professional identity, there was a tendency for students from lower SES backgrounds to be more likely to make internal attributions while those from higher SES backgrounds were more likely to make external attributions for the failure to develop professional identity. Results point to the importance of creating opportunities for social interaction with educators at university because this facilitates the generation of bridging social capital, which, in turn, is essential for students’ professional identity

  1. Bridging and bonding interactions in higher education: social capital and students' academic and professional identity formation.

    Science.gov (United States)

    Jensen, Dorthe H; Jetten, Jolanda

    2015-01-01

    It is increasingly recognized that graduates' achievements depend in important ways on their opportunities to develop an academic and a professional identity during their studies. Previous research has shown that students' socio-economic status (SES) and social capital prior to entering university affects their ability to obtain these identities in higher education. However, what is less well understood is whether social capital that is built during university studies shapes identity development, and if so, whether the social capital gained during university years impacts on academic and professional identity differently. In a qualitative study, we interviewed 26 Danish and 11 Australian university students about their social interaction experiences, their opportunities to develop bonding capital as well as bridging capital, and their academic and professional identity. Findings show that while bonding social capital with co-students facilitated academic identity formation, such social capital does not lead to professional identity development. We also found that the development of bridging social capital with educators facilitated students' professional identity formation. However, bonding social capital among students stood in the way of participating in bridging interaction with educators, thereby further hindering professional identity formation. Finally, while students' parental background did not affect the perceived difficulty of forming professional identity, there was a tendency for students from lower SES backgrounds to be more likely to make internal attributions while those from higher SES backgrounds were more likely to make external attributions for the failure to develop professional identity. Results point to the importance of creating opportunities for social interaction with educators at university because this facilitates the generation of bridging social capital, which, in turn, is essential for students' professional identity development.

  2. Planet Formation in AB Aurigae: Imaging of the Inner Gaseous Spirals Observed inside the Dust Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Ya-Wen; Gu, Pin-Gao; Ho, Paul T. P. [Academia Sinica, Institute of Astronomy and Astrophysics, Taipei, Taiwan (China); Guilloteau, Stephane; Dutrey, Anne; Chapillon, Edwige; Folco, Emmanuel di [Laboratoire d’astrophysique de Bordeaux, Univ. Bordeaux, CNRS, B18N, alle Geoffroy Saint-Hilaire, F-33615 Pessac (France); Muto, Takayuki [Department of Physics, National Taiwan University, Taiwan (China); Shen, Bo-Ting [Division of Liberal Arts, Kogakuin University, 1-24-2 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-8677 (Japan); Inutsuka, Shu-ichiro [Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Momose, Munetake [College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512 (Japan); Pietu, Vincent [IRAM, 300 rue de la Piscine, Domaine Universitaire, F-38406 Saint-Martin-d’Hères (France); Fukagawa, Misato [Division of Particle and Astrophysical Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602 (Japan); Corder, Stuartt [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Ohashi, Nagayoshi [Subaru Telescope, National Astronomical Observatory of Japan, 650 North Aohoku Place, Hilo, HI 96720 (United States); Hashimoto, Jun, E-mail: ywtang@asiaa.sinica.edu.tw [Astrobiology Center of NINS 2-21-1, Osawa, Mitaka, Tokyo, 181-8588 (Japan)

    2017-05-01

    We report the results of ALMA observations of a protoplanetary disk surrounding the Herbig Ae star AB Aurigae. We obtained high-resolution (0.″1; 14 au) images in {sup 12}CO J = 2 − 1 emission and in the dust continuum at the wavelength of 1.3 mm. The continuum emission is detected at the center and at the ring with a radius ( r ) of ∼120 au. The CO emission is dominated by two prominent spirals within the dust ring. These spirals are trailing and appear to be about 4 times brighter than their surrounding medium. Their kinematics is consistent with Keplerian rotation at an inclination of 23°. The apparent two-arm-spiral pattern is best explained by tidal disturbances created by an unseen companion located at r of 60–80 au, with dust confined in the pressure bumps created outside this companion orbit. An additional companion at r of 30 au, coinciding with the peak CO brightness and a large pitch angle of the spiral, would help to explain the overall emptiness of the cavity. Alternative mechanisms to excite the spirals are discussed. The origin of the large pitch angle detected here remains puzzling.

  3. An Erbium-Based Bifuctional Heterogeneous Catalyst: A Cooperative Route Towards C-C Bond Formation

    Directory of Open Access Journals (Sweden)

    Manuela Oliverio

    2014-07-01

    Full Text Available Heterogeneous bifuctional catalysts are multifunctional synthetic catalysts enabling efficient organic transformations by exploiting two opposite functionalities without mutual destruction. In this paper we report the first Er(III-based metallorganic heterogeneous catalyst, synthesized by post-calcination MW-assisted grafting and modification of the natural aminoacid L-cysteine. The natural acid–base distance between sites was maintained to assure the cooperation. The applicability of this new bifunctional heterogeneous catalyst to C-C bond formation and the supposed mechanisms of action are discussed as well.

  4. Boron-Based Catalysts for C-C Bond-Formation Reactions.

    Science.gov (United States)

    Rao, Bin; Kinjo, Rei

    2018-05-02

    Because the construction of the C-C bond is one of the most significant reactions in organic chemistry, the development of an efficient strategy has attracted much attention throughout the synthetic community. Among various protocols to form C-C bonds, organoboron compounds are not just limited to stoichiometric reagents, but have also made great achievements as catalysts because of the easy modification of the electronic and steric impacts on the boron center. This review presents recent developments of boron-based catalysts applied in the field of C-C bond-formation reactions, which are classified into four kinds on the basis of the type of boron catalyst: 1) highly Lewis acidic borane, B(C 6 F 5 ) 3 ; 2) organoboron acids, RB(OH) 2 , and their ester derivatives; 3) borenium ions, (R 2 BL)X; and 4) other miscellaneous kinds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Dissecting the role of disulfide bonds on the amyloid formation of insulin

    International Nuclear Information System (INIS)

    Li, Yang; Gong, Hao; Sun, Yue; Yan, Juan; Cheng, Biao; Zhang, Xin; Huang, Jing; Yu, Mengying; Guo, Yu; Zheng, Ling; Huang, Kun

    2012-01-01

    Highlights: ► We dissect how individual disulfide bond affects the amyloidogenicity of insulin. ► A controlled reduction system for insulin is established in this study. ► Disulfide breakage is associated with unfolding and increased amyloidogenicity. ► Breakage of A6-A11 is associated with significantly increased cytotoxicity. ► Analogs without A6-A11 have a higher potency to form high order toxic oligomers. -- Abstract: Disulfide bonds play a critical role in the stability and folding of proteins. Here, we used insulin as a model system, to investigate the role of its individual disulfide bond during the amyloid formation of insulin. Tris(2-carboxyethyl)phosphine (TCEP) was applied to reduce two of the three disulfide bonds in porcine insulin and the reduced disulfide bonds were then alkylated by iodoacetamide. Three disulfide bond-modified insulin analogs, INS-2 (lack of A6-A11), INS-3 (lack of A7-B7) and INS-6 (lack of both A6-A11 and A7-B7), were obtained. Far-UV circular dichroism (CD) spectroscopy results indicated that the secondary structure of INS-2 was the closest to insulin under neutral conditions, followed by INS-3 and INS-6, whereas in an acidic solution all analogs were essentially unfolded. To test how these modifications affect the amyloidogenicity of insulin, thioflavin-T (ThT) fluorescence and transmission electronic microscopy (TEM) were performed. Our results showed that all analogs were more prone to aggregation than insulin, with the order of aggregation rates being INS-6 > INS-3 > INS-2. Cross-linking of unmodified proteins (PICUP) assay results showed that analogs without A6-A11 (INS-2 and INS-6) have a higher potential for oligomerization than insulin and INS-3, which is accompanied with a higher cytotoxicity as the hemolytic assays of human erythrocytes suggested. The results indicated that breakage of A7-B7 induced more unfolding of the insulin structure and a higher amyloidogenicity than breakage of A6-A11, but breakage of A6

  6. Formation of III–V-on-insulator structures on Si by direct wafer bonding

    International Nuclear Information System (INIS)

    Yokoyama, Masafumi; Iida, Ryo; Ikku, Yuki; Kim, Sanghyeon; Takenaka, Mitsuru; Takagi, Shinichi; Takagi, Hideki; Yasuda, Tetsuji; Yamada, Hisashi; Ichikawa, Osamu; Fukuhara, Noboru; Hata, Masahiko

    2013-01-01

    We have studied the formation of III–V-compound-semiconductors-on-insulator (III–V-OI) structures with thin buried oxide (BOX) layers on Si wafers by using developed direct wafer bonding (DWB). In order to realize III–V-OI MOSFETs with ultrathin body and extremely thin body (ETB) InGaAs-OI channel layers and ultrathin BOX layers, we have developed an electron-cyclotron resonance (ECR) O 2 plasma-assisted DWB process with ECR sputtered SiO 2 BOX layers and a DWB process based on atomic-layer-deposition Al 2 O 3 (ALD-Al 2 O 3 ) BOX layers. It is essential to suppress micro-void generation during wafer bonding process to achieve excellent wafer bonding. We have found that major causes of micro-void generation in DWB processes with ECR-SiO 2 and ALD-Al 2 O 3 BOX layers are desorption of Ar and H 2 O gas, respectively. In order to suppress micro-void generation in the ECR-SiO 2 BOX layers, it is effective to introduce the outgas process before bonding wafers. On the other hand, it is a possible solution for suppressing micro-void generation in the ALD-Al 2 O 3 BOX layers to increase the deposition temperature of the ALD-Al 2 O 3 BOX layers. It is also another possible solution to deposit ALD-Al 2 O 3 BOX layers on thermally oxidized SiO 2 layers, which can absorb the desorption gas from ALD-Al 2 O 3 BOX layers. (invited paper)

  7. Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

    Directory of Open Access Journals (Sweden)

    Ohgi Takahashi

    2015-01-01

    Full Text Available Succinimide formation from aspartic acid (Asp residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe as a model compound, we propose the possibility that acetic acid (AA, which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

  8. Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

    Science.gov (United States)

    Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

    2015-01-12

    Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

  9. In vivo biofilm formation on stainless steel bonded retainers during different oral health-care regimens.

    Science.gov (United States)

    Jongsma, Marije A; van der Mei, Henny C; Atema-Smit, Jelly; Busscher, Henk J; Ren, Yijin

    2015-03-23

    Retention wires permanently bonded to the anterior teeth are used after orthodontic treatment to prevent the teeth from relapsing to pre-treatment positions. A disadvantage of bonded retainers is biofilm accumulation on the wires, which produces a higher incidence of gingival recession, increased pocket depth and bleeding on probing. This study compares in vivo biofilm formation on single-strand and multi-strand retention wires with different oral health-care regimens. Two-centimetre wires were placed in brackets that were bonded to the buccal side of the first molars and second premolars in the upper arches of 22 volunteers. Volunteers used a selected toothpaste with or without the additional use of a mouthrinse containing essential oils. Brushing was performed manually. Regimens were maintained for 1 week, after which the wires were removed and the oral biofilm was collected to quantify the number of organisms and their viability, determine the microbial composition and visualize the bacteria by electron microscopy. A 6-week washout period was employed between regimens. Biofilm formation was reduced on single-strand wires compared with multi-strand wires; bacteria were observed to adhere between the strands. The use of antibacterial toothpastes marginally reduced the amount of biofilm on both wire types, but significantly reduced the viability of the biofilm organisms. Additional use of the mouthrinse did not result in significant changes in biofilm amount or viability. However, major shifts in biofilm composition were induced by combining a stannous fluoride- or triclosan-containing toothpaste with the mouthrinse. These shifts can be tentatively attributed to small changes in bacterial cell surface hydrophobicity after the adsorption of the toothpaste components, which stimulate bacterial adhesion to the hydrophobic oil, as illustrated for a Streptococcus mutans strain.

  10. Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

    Science.gov (United States)

    Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

    2018-04-01

    Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

  11. Interfacial micromorphological differences in hybrid layer formation between water- and solvent-based dentin bonding systems.

    Science.gov (United States)

    Gregoire, Geneviève L; Akon, Bernadette A; Millas, Arlette

    2002-06-01

    Many dentin bonding systems of different compositions, and in particular containing different solvents, have been introduced to the market. Their effect on the quality of the interface requires clarification by means of comparative trials. This study investigated micromorphological differences in hybrid layer formation with a variety of commercially available water- or solvent-based dentin bonding products and their recommended compomers. Five bonding systems were used on groups of 10 teeth each as follows: group I, acetone-based system used with 36% phosphoric acid; group II, a different acetone-based system containing nano-sized particles for filler loading and used with a non-rinsing conditioner containing maleic acid; group III, the acetone-based system of group II used with 36% phosphoric acid (the only difference in the treatment for groups II and III was the acid etching system); group IV, a mixed-solvent-based system (water/ethanol) used with 37% phosphoric acid; and group V, a water-based system used with 37% phosphoric acid. Each bonding system was covered with the recommended compomer. Class I occlusal preparations were made in extracted teeth and restored with one of the above systems. Five specimens of each group were studied with optical microscopy after staining. Scanning electron microscopy was used to examine the interface of the bonding system/dentin of the other 5 teeth in each group. The optical microscopy measurements were made with a 10 x 10 reticle. A micron mark with scale was used for the scanning electron microscope. All measurements were made in microm. The following criteria were used to define a good interface: absence of voids between the different parts of the interface, uniformity of the hybrid layer, good opening of the tubuli orifices, and tag adherence to the tubuli walls. Morphological differences were found at the interface depending on dentin treatment and adhesive composition. The acetone-containing systems were associated

  12. Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids.

    Directory of Open Access Journals (Sweden)

    Nagesh Pulicherla

    Full Text Available The capsid proteins of adeno-associated viruses (AAV have five conserved cysteine residues. Structural analysis of AAV serotype 2 reveals that Cys289 and Cys361 are located adjacent to each other within each monomer, while Cys230 and Cys394 are located on opposite edges of each subunit and juxtaposed at the pentamer interface. The Cys482 residue is located at the base of a surface loop within the trimer region. Although plausible based on molecular dynamics simulations, intra- or inter-subunit disulfides have not been observed in structural studies. In the current study, we generated a panel of Cys-to-Ser mutants to interrogate the potential for disulfide bond formation in AAV capsids. The C289S, C361S and C482S mutants were similar to wild type AAV with regard to titer and transduction efficiency. However, AAV capsid protein subunits with C230S or C394S mutations were prone to proteasomal degradation within the host cells. Proteasomal inhibition partially blocked degradation of mutant capsid proteins, but failed to rescue infectious virions. While these results suggest that the Cys230/394 pair is critical, a C394V mutant was found viable, but not the corresponding C230V mutant. Although the exact nature of the structural contribution(s of Cys230 and Cys394 residues to AAV capsid formation remains to be determined, these results support the notion that disulfide bond formation within the Cys289/361 or Cys230/394 pair appears to be nonessential. These studies represent an important step towards understanding the role of inter-subunit interactions that drive AAV capsid assembly.

  13. Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

    International Nuclear Information System (INIS)

    Shukla, Anil; Bogdanov, Bogdan

    2015-01-01

    Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N 2 ). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi) n Li + , (HCOOLi) n Li m m+ , (HCOOLi) n HCOO − , and (HCOOLi) n (HCOO) m m− . Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi) 3 Li + being the most abundant and stable cluster ion. Fragmentations of singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi) 2 ) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi) 3 Li + as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability

  14. Disruption of reducing pathways is not essential for efficient disulfide bond formation in the cytoplasm of E. coli

    Directory of Open Access Journals (Sweden)

    Hatahet Feras

    2010-09-01

    Full Text Available Abstract Background The formation of native disulfide bonds is a complex and essential post-translational modification for many proteins. The large scale production of these proteins can be difficult and depends on targeting the protein to a compartment in which disulfide bond formation naturally occurs, usually the endoplasmic reticulum of eukaryotes or the periplasm of prokaryotes. It is currently thought to be impossible to produce large amounts of disulfide bond containing protein in the cytoplasm of wild-type bacteria such as E. coli due to the presence of multiple pathways for their reduction. Results Here we show that the introduction of Erv1p, a sulfhydryl oxidase and FAD-dependent catalyst of disulfide bond formation found in the inter membrane space of mitochondria, allows the efficient formation of native disulfide bonds in heterologously expressed proteins in the cytoplasm of E. coli even without the disruption of genes involved in disulfide bond reduction, for example trxB and/or gor. Indeed yields of active disulfide bonded proteins were higher in BL21 (DE3 pLysSRARE, an E. coli strain with the reducing pathways intact, than in the commercial Δgor ΔtrxB strain rosetta-gami upon co-expression of Erv1p. Conclusions Our results refute the current paradigm in the field that disruption of at least one of the reducing pathways is essential for the efficient production of disulfide bond containing proteins in the cytoplasm of E. coli and open up new possibilities for the use of E. coli as a microbial cell factory.

  15. New conception in the theory of chemical bonding; the role of core and valence atomic orbitals in formation of chemical bonds

    International Nuclear Information System (INIS)

    Kostikova, G.P.; Kostikov, Yu.P.; Korol'kov, D.V.

    1986-01-01

    An analysis of x-ray photoelectron spectra leads to a simple and consistent conception in the theory of chemical bonding, which satisfies (unlike the simple MO-LCAO theory) the virial theorem and defines the roles of the core and valence atomic orbitals in the formation of chemical bonds. Its essence is clear from the foregoing: the exothermic effects of the formation of complexes are caused by the lowering of the energies of the core levels of the central atoms with simultaneous small changes in the energies of the core levels of the ligands despite the significant destabilization of the delocalized valence MO's in comparison to the orbital energies of the corresponding free atoms. In order to confirm these ideas, they recorded the x-ray photoelectron spectra of the valence region and the inner levels of single-crystal silicon carbide, silicon, and graphite

  16. Effect of hydroxyl bond formation on the adhesion improvement of a polyethylene copper thin film system

    International Nuclear Information System (INIS)

    Camacho, M.; Blantocas, G.; Ramos, H.

    2009-01-01

    Formation of hydroxyl bonds on the surface of a gas plasma treated high density polyethylene (HDPE) sheets significantly enhanced the adhesion strength of the polyethylene copper thin film system. Surface treatments using oxygen gas plasmas at varying plasma parameters are applied in this study to identify the most effective plasma parameters that would promote the best adhesion strength. Analysis of gas plasma adulterated HDPE sheets showed best enhancement of polyethylene copper adhesion after an oxygen gas plasma treatment for 60 minutes at 5mA discharge current. Scanning Electron Microscopy Analysis, Fourier Transform Infrared Spectroscopy and Adhesion measurements using Pull out Force Analysis were used to measure the changes in the surface chemistry and surface topology of the HDPE sheets. (author)

  17. Isotopic Studies of O-O Bond Formation During Water Oxidation (SISGR)

    Energy Technology Data Exchange (ETDEWEB)

    Roth, Justine P. [Johns Hopkins Univ., Baltimore, MD (United States)

    2015-03-03

    Isotopic Studies of O-O Bond Formation During Water Oxidation (SISGR) Research during the project period focused primarily on mechanisms of water oxidation by structurally defined transition metal complexes. Competitive oxygen isotope fractionation of water, mediated by oxidized precursors or reduced catalysts together with ceric, Ce(IV), ammonium nitrate in aqueous media, afforded oxygen-18 kinetic isotope effects (O-18 KIEs). Measurement, calculation, and interpretation of O-18 KIEs, described in the accompanying report has important ramifications for the production of electricity and solar hydrogen (as fuel). The catalysis division of BES has acknowledged that understanding mechanisms of transition metal catalyzed water oxidation has major ramifications, potentially leading to transformation of the global economy and natural environment in years to come. Yet, because of program restructuring and decreased availability of funds, it was recommended that the Solar Photochemistry sub-division of BES would be a more appropriate parent program for support of continued research.

  18. Formation of porous surface layers in reaction bonded silicon nitride during processing

    Science.gov (United States)

    Shaw, N. J.; Glasgow, T. K.

    1979-01-01

    Microstructural examination of reaction bonded silicon nitride (RBSN) has shown that there is often a region adjacent to the as-nitrided surfaces that is even more porous than the interior of this already quite porous material. Because this layer of large porosity is considered detrimental to both the strength and oxidation resistance of RBSN, a study was undertaken to determine if its formation could be prevented during processing. All test bars studied were made from a single batch of Si powder which was milled for 4 hours in heptane in a vibratory mill using high density alumina cylinders as the grinding media. After air drying the powder, bars were compacted in a single acting die and hydropressed.

  19. Ab Initio Calculations of 31P NMR Chemical Shielding Anisotropy Tensors in Phosphates: Variations Due to Ring Formation

    Directory of Open Access Journals (Sweden)

    Todd M. Alam

    2002-08-01

    Full Text Available Abstract: Ring formation in phosphate systems is expected to influence both the magnitude and orientation of the phosphorus (31P nuclear magnetic resonance (NMR chemical shielding anisotropy (CSA tensor. Ab initio calculations of the 31P CSA tensor in both cyclic and acyclic phosphate clusters were performed as a function of the number of phosphate tetrahedral in the system. The calculation of the 31P CSA tensors employed the GAUSSIAN 98 implementation of the gauge-including atomic orbital (GIAO method at the Hartree-Fock (HF level. It is shown that both the 31P CSA tensor anisotropy, and the isotropic chemical shielding can be used for the identification of cyclic phosphates. The differences between the 31P CSA tensor in acyclic and cyclic phosphate systems become less pronounced with increasing number of phosphate groups within the ring. The orientation of the principal components for the 31P CSA tensor shows some variation due to cyclization, most notably with the smaller, highly strained ring systems.

  20. Bane of Hydrogen-Bond Formation on the Photoinduced Charge-Transfer Process in Donor–Acceptor Systems

    KAUST Repository

    Alsam, Amani Abdu

    2017-03-14

    Controlling the ultrafast dynamical process of photoinduced charge transfer at donor acceptor interfaces remains a major challenge for physical chemistry and solar cell communities. The process is complicated by the involvement of other complex dynamical processes, including hydrogen bond formation, energy transfer, and solvation dynamics occurring on similar time scales. In this study, we explore the remarkable impact of hydrogen-bond formation on the interfacial charge transfer between a negatively charged electron donating anionic porphyrin and a positively charged electron accepting pi-conjugated polymer, as a model system in solvents with different polarities and capabilities for hydiogen bonding using femtosecond transient absorption spectroscopy. Unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our steadystate and time-resolved results reveal that the intervening hydrogen-bonding environment and, consequently, the probable longer spacing between the donor and acceptor molecules significantly hinders the charge-transfer process between them. These results show that site-specific hydrogen bonding and geometric considerations between donor and acceptor can be exploited to control both the charge-transfer dynamics and its efficiency not only at donor acceptor interfaces but also in complex biological systems.

  1. Nonperfect synchronization of bond-forming and bond-rupturing processes in the reaction H + H2 → H2 + H

    International Nuclear Information System (INIS)

    Chandra, A.K.; Rao, V.S.

    1996-01-01

    The simplest prototypical hydrogen transfer reaction, i.e., H + H 2 → H 2 + H, is studied by the quantum-mechanical ab initio methods. Results reveal that during this reaction free valence which almost equals the square of the spin density develops on the migrating hydrogen atom. Bond orders are calculated using Mayer's formalism. Both the variations of bond orders and bond lengths along the reaction path are examined. This analysis reveals that the bond formation and bond cleavage processes in this reaction are not perfectly synchronous. The bond clevage process is slightly more advanced on the reaction path. 38 refs., 6 figs., 2 tabs

  2. Early biofilm formation and the effects of antimicrobial agents on orthodontic bonding materials in a parallel plate flow chamber

    NARCIS (Netherlands)

    Chin, Yeen; Busscher, HJ; Evans, R; Noar, J; Pratten, J

    Decalcification is a commonly recognized complication of orthodontic treatment with fixed appliances. A technology, based on a parallel plate flow chamber, was developed to investigate early biofilm formation of a strain of Streptococcus sanguis on the surface of four orthodontic bonding materials:

  3. Intermolecular Formation of Two C−C Bonds across Olefins Enabled by Boron-Based Relay Strategies

    Czech Academy of Sciences Publication Activity Database

    Hidasová, Denisa; Jahn, Ullrich

    2017-01-01

    Roč. 56, č. 33 (2017), s. 9656-9658 ISSN 1433-7851 Institutional support: RVO:61388963 Keywords : 1,2- metal ate rearrangement * C−C bond formation * radical reactions * transition metal catalysis * vinyl boronates Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 11.994, year: 2016

  4. Bond Formation in Diatomic Transition Metal Hydrides: Insights from the Analysis of Domain-Averaged Fermi Holes

    Czech Academy of Sciences Publication Activity Database

    Cooper, D.L.; Ponec, Robert

    2013-01-01

    Roč. 113, č. 2 (2013), s. 102-111 ISSN 0020-7608 R&D Projects: GA ČR GA203/09/0118 Institutional support: RVO:67985858 Keywords : transition metal hydrides * bond formation * analysis of domain averaged Fermi holes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.166, year: 2013

  5. Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress

    Directory of Open Access Journals (Sweden)

    Tyo Keith EJ

    2012-03-01

    Full Text Available Abstract Background The protein secretory pathway must process a wide assortment of native proteins for eukaryotic cells to function. As well, recombinant protein secretion is used extensively to produce many biologics and industrial enzymes. Therefore, secretory pathway dysfunction can be highly detrimental to the cell and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging. In this study, we apply a systems biology approach to analyze secretory pathway dysfunctions resulting from heterologous production of a small protein (insulin precursor or a larger protein (α-amylase. Results HAC1-dependent and independent dysfunctions and cellular responses were apparent across multiple datasets. In particular, processes involving (a degradation of protein/recycling amino acids, (b overall transcription/translation repression, and (c oxidative stress were broadly associated with secretory stress. Conclusions Apparent runaway oxidative stress due to radical production observed here and elsewhere can be explained by a futile cycle of disulfide formation and breaking that consumes reduced glutathione and produces reactive oxygen species. The futile cycle is dominating when protein folding rates are low relative to disulfide bond formation rates. While not strictly conclusive with the present data, this insight does provide a molecular interpretation to an, until now, largely empirical understanding of optimizing heterologous protein secretion. This molecular insight has direct implications on engineering a broad range of recombinant proteins for secretion and provides potential hypotheses for the root causes of several secretory-associated diseases.

  6. Designing new catalytic C-C and C-N bond formations promoted by organoactinides

    International Nuclear Information System (INIS)

    Eisen, M.S.; Straub, T.; Haskel, A.

    1998-01-01

    Organoactinides of the type Cp 2 * AcMe 2 (Cp * =C 5 Me 5 ; Ac=Th; U) are active catalytic precursors for the oligomerization of terminal alkynes HC≡CR (R=alkyl, aryl, SiMe 3 ). The regioselectivity and the extent of oligomerization depend strongly on the alkyne substituent R, whereas the catalytic reactivity is similar for both organoactinides. Reaction with tert-butylacetylene yields regioselectively the E-2,4-disubstituted 1-buten-3-yne dimer whereas trimethylsilylacetylene is regioselective trimerized to the E,E-1,4,6-tris(trimethylsilyl)-1,3-hexa diene-5-yne, with small amounts (3-5%) of the corresponding E-2,4-disubstituted 1-buten-3-yne dimer. Oligomerization with less bulky alkyl and aryl substituted alkynes produces a mixture of higher oligomers with no regioselectivity. Using the Cp 2 * ThMe 2 catalyst, we have recently developed a strategic method to control the extent and in some cases the regioselectivity of the catalyzed oligomerization of nonbulky terminal alkynes to dimers and/or trimers. The metallocene catalytic precursors ensure the selective synthesis of small oligomers by the addition of specific amines. Catalytic ''tailoring'' to dimer and trimers can be achieved by using small or bulky amines, respectively. Kinetic and mechanistic data for the controlling experiments argue that the turnover-limiting step involves the acetylide actinide complex formation with the rapid insertion of the alkyne and protonolysis by the amine. The analog Cp 2 * UMe 2 in the presence of primary amines induce the selective C-N bond formation, producing enamines which are tautomerized to the corresponding imines. (orig.)

  7. Soil aggregate formation: the role of wetting-drying cycles in the genesis of interparticle bonding

    Science.gov (United States)

    Albalasmeh, Ammar; Ghezzehei, Teamrat

    2013-04-01

    Soil structure influences many soil properties including aeration, water retention, drainage, bulk density, and resistance to erosion and indirectly influences most biological and chemical processes that occur in and around soil. In nature, soil is continually exposed to wetting (e.g., rainfall and diffusive flow) and drying (e.g., evaporation, diffusive flow and plant uptake). These natural wetting and drying cycles of soils are physical events that profoundly affect the development of soil structure, aggregate stability, carbon (C) flux and mineralization. We hypothesize that drying of capillary water transports suspended and/or dissolved cementing agents toward inter-particle contacts and eventually deposits part of the colloidal mass forming inter-particle bonds. Here, we will show the role of wetting and drying cycles on soil aggregation and stabilization and how these cycles transport and deposit organic cementing agents at the inter-particle contact. We found that aggregates of sand and silt particles can be formed by subjecting loose particles to wetting-drying cycles in the presence of dilute solutions of organic matter that mimic root or microbial exudates. Moreover, majority of the organic matter was deposited in the contact region between the sand particles, where the water accumulates during drying. The model predictions and aggregate stability measurements are supported by scanning electron micrographs that clearly show the process of aggregate formation.

  8. Highly Efficient Fumed Silica Nanoparticles for Peptide Bond Formation: Converting Alanine to Alanine Anhydride.

    Science.gov (United States)

    Guo, Chengchen; Jordan, Jacob S; Yarger, Jeffery L; Holland, Gregory P

    2017-05-24

    In this work, thermal condensation of alanine adsorbed on fumed silica nanoparticles is investigated using thermal analysis and multiple spectroscopic techniques, including infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectroscopies. Thermal analysis shows that adsorbed alanine can undergo thermal condensation, forming peptide bonds within a short time period and at a lower temperature (∼170 °C) on fumed silica nanoparticle surfaces than that in bulk (∼210 °C). Spectroscopic results further show that alanine is converted to alanine anhydride with a yield of 98.8% during thermal condensation. After comparing peptide formation on solution-derived colloidal silica nanoparticles, it is found that fumed silica nanoparticles show much better efficiency and selectivity than solution-derived colloidal silica nanoparticles for synthesizing alanine anhydride. Furthermore, Raman spectroscopy provides evidence that the high efficiency for fumed silica nanoparticles is likely related to their unique surface features: the intrinsic high population of strained ring structures present at the surface. This work indicates the great potential of fumed silica nanoparticles in synthesizing peptides with high efficiency and selectivity.

  9. Biofilm formation on stainless steel and gold wires for bonded retainers in vitro and in vivo and their susceptibility to oral antimicrobials

    NARCIS (Netherlands)

    Jongsma, Marije A.; Pelser, Floris D. H.; van der Mei, Henny C.; Atema-Smit, Jelly; van de Belt-Gritter, Betsy; Busscher, Henk J.; Ren, Yijin

    OBJECTIVE: Bonded retainers are used in orthodontics to maintain treatment result. Retention wires are prone to biofilm formation and cause gingival recession, bleeding on probing and increased pocket depths near bonded retainers. In this study, we compare in vitro and in vivo biofilm formation on

  10. Ultraclean Si/Si interface formation by surface preparation and direct bonding in ultrahigh vacuum

    DEFF Research Database (Denmark)

    Hermansson, Karin; Grey, Francois; Bengtsson, Stefan

    1998-01-01

    Silicon surfaces have been cleaned and bonded in ultrahigh vacuum, at a pressure in the 10(-10) Torr range. The bonded interfaces show extremely low contamination levels as measured by secondary ion mass spectroscopy. Nevertheless, a potential barrier could be detected at the interface by spreading...

  11. In vivo biofilm formation on stainless steel bonded retainers during different oral health-care regimens

    NARCIS (Netherlands)

    Jongsma, Marije A.; van der Mei, Henny C.; Atema-Smit, Jelly; Busscher, Henk I.; Ren, Yijin

    2015-01-01

    Retention wires permanently bonded to the anterior teeth are used after orthodontic treatment to prevent the teeth from relapsing to pre-treatment positions. A disadvantage of bonded retainers is biofilm accumulation on the wires, which produces a higher incidence of gingival recession, increased

  12. Sequential C-Si Bond Formations from Diphenylsilane: Application to Silanediol Peptide Isostere Precursors

    DEFF Research Database (Denmark)

    Nielsen, Lone; Skrydstrup, Troels

    2008-01-01

    and the first new carbon-silicon bond. The next step is the reduction of this hydridosilane with lithium metal providing a silyl lithium reagent, which undergoes a highly diastereoselective addition to an optically active tert-butanesulfinimine, thus generating the second C-Si bond. This method allows...

  13. Chemoselective Radical Dehalogenation and C-C Bond Formation on Aryl Halide Substrates Using Organic Photoredox Catalysts.

    Science.gov (United States)

    Poelma, Saemi O; Burnett, G Leslie; Discekici, Emre H; Mattson, Kaila M; Treat, Nicolas J; Luo, Yingdong; Hudson, Zachary M; Shankel, Shelby L; Clark, Paul G; Kramer, John W; Hawker, Craig J; Read de Alaniz, Javier

    2016-08-19

    Despite the number of methods available for dehalogenation and carbon-carbon bond formation using aryl halides, strategies that provide chemoselectivity for systems bearing multiple carbon-halogen bonds are still needed. Herein, we report the ability to tune the reduction potential of metal-free phenothiazine-based photoredox catalysts and demonstrate the application of these catalysts for chemoselective carbon-halogen bond activation to achieve C-C cross-coupling reactions as well as reductive dehalogenations. This procedure works both for conjugated polyhalides as well as unconjugated substrates. We further illustrate the usefulness of this protocol by intramolecular cyclization of a pyrrole substrate, an advanced building block for a family of natural products known to exhibit biological activity.

  14. Interstellar hydrogen bonding

    Science.gov (United States)

    Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Chakrabarti, Sandip K.; Arunan, Elangannan

    2018-06-01

    This paper reports the first extensive study of the existence and effects of interstellar hydrogen bonding. The reactions that occur on the surface of the interstellar dust grains are the dominant processes by which interstellar molecules are formed. Water molecules constitute about 70% of the interstellar ice. These water molecules serve as the platform for hydrogen bonding. High level quantum chemical simulations for the hydrogen bond interaction between 20 interstellar molecules (known and possible) and water are carried out using different ab-intio methods. It is evident that if the formation of these species is mainly governed by the ice phase reactions, there is a direct correlation between the binding energies of these complexes and the gas phase abundances of these interstellar molecules. Interstellar hydrogen bonding may cause lower gas abundance of the complex organic molecules (COMs) at the low temperature. From these results, ketenes whose less stable isomers that are more strongly bonded to the surface of the interstellar dust grains have been observed are proposed as suitable candidates for astronomical observations.

  15. Electronic states and nature of bonding in the molecule YC by all electron ab initio multiconfiguration self-consistent-field calculations and mass spectrometric equilibrium experiments

    DEFF Research Database (Denmark)

    Shim, Irene; Pelino, Mario; Gingerich, Karl A.

    1992-01-01

    , and they hardly contribute to the bonding. The chemical bond in the YC molecule is polar with charge transfer from Y to C giving rise to a dipole moment of 3.90 D at 3.9 a.u. in the 4PI ground state. Mass spectrometric equilibrium investigations in the temperature range 2365-2792 K have resulted...

  16. Spectroscopic Identification of the Au-C Bond Formation upon Electroreduction of an Aryl Diazonium Salt on Gold.

    Science.gov (United States)

    Guo, Limin; Ma, Lipo; Zhang, Yelong; Cheng, Xun; Xu, Ye; Wang, Jin; Wang, Erkang; Peng, Zhangquan

    2016-11-08

    Electroreduction of aryl diazonium salts on gold can produce organic films that are more robust than their analogous self-assembled monolayers formed from chemical adsorption of organic thiols on gold. However, whether the enhanced stability is due to the Au-C bond formation remains debated. In this work, we report the electroreduction of an aryl diazonium salt of 4,4'-disulfanediyldibenzenediazonium on gold forming a multilayer of Au-(Ar-S-S-Ar) n , which can be further degraded to a monolayer of Au-Ar-S - by electrochemical cleavage of the S-S moieties within the multilayer. By conducting an in situ surface-enhanced Raman spectroscopic study of both the multilayer formation/degradation and the monolayer reduction/oxidation processes, coupled to density functional theory calculations, we provide compelling evidence that an Au-C bond does form upon electroreduction of aryl diazonium salts on gold and that the enhanced stability of the electrografted organic films is due to the Au-C bond being intrinsically stronger than the Au-S bond for a given phenylthiolate compound by ca. 0.4 eV.

  17. Self-Assembled Amphiphilic Water Oxidation Catalysts: Control of O-O Bond Formation Pathways by Different Aggregation Patterns.

    Science.gov (United States)

    Yang, Bing; Jiang, Xin; Guo, Qing; Lei, Tao; Zhang, Li-Ping; Chen, Bin; Tung, Chen-Ho; Wu, Li-Zhu

    2016-05-17

    The oxidation of water to molecular oxygen is the key step to realize water splitting from both biological and chemical perspective. In an effort to understand how water oxidation occurs on a molecular level, a large number of molecular catalysts have been synthesized to find an easy access to higher oxidation states as well as their capacity to make O-O bond. However, most of them function in a mixture of organic solvent and water and the O-O bond formation pathway is still a subject of intense debate. Herein, we design the first amphiphilic Ru-bda (H2 bda=2,2'-bipyridine-6,6'-dicarboxylic acid) water oxidation catalysts (WOCs) of formula [Ru(II) (bda)(4-OTEG-pyridine)2 ] (1, OTEG=OCH2 CH2 OCH2 CH2 OCH3 ) and [Ru(II) (bda)(PySO3 Na)2 ] (2, PySO3 (-) =pyridine-3-sulfonate), which possess good solubility in water. Dynamic light scattering (DLS), scanning electron microscope (SEM), critical aggregation concentration (CAC) experiments and product analysis demonstrate that they enable to self-assemble in water and form the O-O bond through different routes even though they have the same bda(2-) backbone. This work illustrates for the first time that the O-O bond formation pathway can be regulated by the interaction of ancillary ligands at supramolecular level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. The gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide from combustion calorimetry, vapor pressure measurements, and ab initio calculations.

    Science.gov (United States)

    Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas

    2007-04-04

    Ionic liquids are attracting growing interest as alternatives to conventional molecular solvents. Experimental values of vapor pressure, enthalpy of vaporization, and enthalpy of formation of ionic liquids are the key thermodynamic quantities, which are required for the validation and development of the molecular modeling and ab initio methods toward this new class of solvents. In this work, the molar enthalpy of formation of the liquid 1-butyl-3-methylimidazolium dicyanamide, 206.2 +/- 2.5 kJ.mol-1, was measured by means of combustion calorimetry. The molar enthalpy of vaporization of 1-butyl-3-methylimidazolium dicyanamide, 157.2 +/- 1.1 kJ.mol-1, was obtained from the temperature dependence of the vapor pressure measured using the transpiration method. The latter method has been checked with measurements of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, where data are available from the effusion technique. The first experimental determination of the gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide, 363.4 +/- 2.7 kJ.mol-1, from thermochemical measurements (combustion and transpiration) is presented. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for 1-butyl-3-methylimidazolium dicyanamide using the G3MP2 theory. Excellent agreement with experimental results has been observed. The method developed opens a new way to obtain thermodynamic properties of ionic liquids which have not been available so far.

  19. Electronic states and nature of bonding of the molecule PdGe by all electron ab initio HF–CI calculations and mass spectrometric equilibrium experiments

    DEFF Research Database (Denmark)

    Shim, Irene; Kingcade, Joseph E. , Jr.; Gingerich, Karl A.

    1986-01-01

    In the present work we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of six electronic states of the PdGe molecule. The molecule is predicted to have a 3Pi ground state and two low-lying excited states 3Sigma− and 1Sigma+. The electronic structure...

  20. On the Mechanism of the Copper-Mediated C-S Bond Formation in the Intramolecular Disproportionation of Imine Disulfides

    Czech Academy of Sciences Publication Activity Database

    Rokob, Tibor András; Rulíšek, Lubomír; Šrogl, Jiří; Révész, Agnes; Zins, Emilie-Laure; Schröder, Detlef

    2011-01-01

    Roč. 50, č. 20 (2011), s. 9968-9979 ISSN 0020-1669 R&D Projects: GA MŠk LC512 Grant - others:European Research Council(XE) AdG HORIZOMS Institutional research plan: CEZ:AV0Z40550506 Keywords : collision-induced dissociation * DFT calculations * C-S bond formation * Cu(I) catalysis * infrared multiphoton spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.601, year: 2011

  1. Evolution of the chemical bonding nature and electrode activity of indium selenide upon the composite formation with graphene nanosheets

    International Nuclear Information System (INIS)

    Oh, Seung Mi; Lee, Eunsil; Adpakpang, Kanyaporn; Patil, Sharad B.; Park, Mi Jin; Lim, Young Soo; Lee, Kyu Hyoung; Kim, Jong-Young; Hwang, Seong-Ju

    2015-01-01

    Graphical abstract: Display Omitted -- Highlights: • In 4 Se 2.85 @graphene nanocomposite is easily prepared by high energy mechanical milling process. • The bond covalency of In 4 Se 2.85 is notably changed upon the composite formation with graphene. • In 4 Se 2.85 @graphene nanocomposite shows promising anode performance for lithium ion battery. -- Abstract: Evolution of the chemical bonding nature and electrochemical activity of indium selenide upon the composite formation with carbon species is systematically investigated. Nanocomposites of In 4 Se 2.85 @graphene and In 4 Se 2.85 @carbon-black are synthesized via a solid state reaction between In and Se elements, and the following high energy mechanical milling of In 4 Se 2.85 with graphene and carbon-black, respectively. The high energy mechanical milling (HEMM) of In 4 Se 2.85 with carbon species gives rise to a decrease of particle size with a significant depression of the crystallinity of In 4 Se 2.85 phase. In contrast to the composite formation with carbon-black, that with graphene induces a notable decrease of (In−Se) bond covalency, underscoring significant chemical interaction between graphene and In 4 Se 2.85 . Both the nanocomposites of In 4 Se 2.85 @graphene and In 4 Se 2.85 @carbon-black show much better anode performance for lithium ion batteries with larger discharge capacity and better cyclability than does the pristine In 4 Se 2.85 material, indicating the beneficial effect of composite formation on the electrochemical activity of indium selenide. Between the present nanocomposites, the electrode performance of the In 4 Se 2.85 @graphene nanocomposite is superior to that of the In 4 Se 2.85 @carbon-black nanocomposite, which is attributable to the weakening of (In−Se) bonds upon the composite formation with graphene as well as to the better mixing between In 4 Se 2.85 and graphene. The present study clearly demonstrates that the composite formation with graphene has strong influence

  2. Formation of Conjugated Double Bonds to Induce Polystyrene Conductivity by using Different Concentrations of Methoxo-Oxo Bis (8-Quinolyloxo Vanadium (V

    Directory of Open Access Journals (Sweden)

    Basim Mohamad Hasan

    2017-02-01

    Full Text Available The effect of different concentrations of additive compound methoxo–oxo bis (8-quinolyloxo vanadium (v on formation of conjugated double bonds as part of photo transformation of polystyrene has been investigated. The UV-Vis spectrophotometery has been used in this work. The results are show that additive concentrations applied increase the formation of conjugated double bond as compared with polystyrene. In this study methoxo – oxo bis (8-quinolyloxo vanadium (v indicates great activity to enhance the conductivity of polystyrene by formation of conjugated double bonds.

  3. Dynamics of Plug Formation in a Circular Cylinder Under Low Bond Number Conditions: Experiment and Simulation

    Science.gov (United States)

    Hallaby, Ghazi; Kizito, John P.

    2016-08-01

    The goal of the current study is to investigate the dynamics of two phase interface under a low Bond number condition. Silicone oil is injected into a cylinder under a Bond number of about 0.47 via a side tube forming a T-junction with the former. The time evolution of the interface of silicon oil in a cylinder is captured using a high speed camera. The volume at which the plug is formed is then determined using an image processing tool to analyze the captured images. A numerical simulation is carried out where fluid is injected into a cylinder, under a less than unity Bond number condition, via a side tube. Numerical and experimental results are then compared.

  4. Formation and hydrolysis of amide bonds by lipase A from Candida antarctica; exceptional features.

    Science.gov (United States)

    Liljeblad, Arto; Kallio, Pauli; Vainio, Marita; Niemi, Jarmo; Kanerva, Liisa T

    2010-02-21

    Various commercial lyophilized and immobilized preparations of lipase A from Candida antarctica (CAL-A) were studied for their ability to catalyze the hydrolysis of amide bonds in N-acylated alpha-amino acids, 3-butanamidobutanoic acid (beta-amino acid) and its ethyl ester. The activity toward amide bonds is highly untypical of lipases, despite the close mechanistic analogy to amidases which normally catalyze the corresponding reactions. Most CAL-A preparations cleaved amide bonds of various substrates with high enantioselectivity, although high variations in substrate selectivity and catalytic rates were detected. The possible role of contaminant protein species on the hydrolytic activity toward these bonds was studied by fractionation and analysis of the commercial lyophilized preparation of CAL-A (Cat#ICR-112, Codexis). In addition to minor impurities, two equally abundant proteins were detected, migrating on SDS-PAGE a few kDa apart around the calculated size of CAL-A. Based on peptide fragment analysis and sequence comparison both bands shared substantial sequence coverage with CAL-A. However, peptides at the C-terminal end constituting a motile domain described as an active-site flap were not identified in the smaller fragment. Separated gel filtration fractions of the two forms of CAL-A both catalyzed the amide bond hydrolysis of ethyl 3-butanamidobutanoate as well as the N-acylation of methyl pipecolinate. Hydrolytic activity towards N-acetylmethionine was, however, solely confined to the fractions containing the truncated form of CAL-A. These fractions were also found to contain a trace enzyme impurity identified in sequence analysis as a serine carboxypeptidase. The possible role of catalytic impurities versus the function of CAL-A in amide bond hydrolysis is further discussed in the paper.

  5. Formation of Me–O–Si covalent bonds at the interface between polysilazane and stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Amouzou, Dodji, E-mail: adodji@gmail.com [Research Centre in Physics of Matter and Radiation (PMR), University of Namur, Rue de Bruxelles 61, 5000 Namur (Belgium); Fourdrinier, Lionel; Maseri, Fabrizio [CRM-Group, Boulevard de Colonster, B 57, 4000 Liège (Belgium); Sporken, Robert [Research Centre in Physics of Matter and Radiation (PMR), University of Namur, Rue de Bruxelles 61, 5000 Namur (Belgium)

    2014-11-30

    Highlights: • Natural metal-oxides, hydroxides are detected on the top surface of steel substrates we tested. • Polysilazane reacts with hydroxide functional groups on steel substrates to form Cr–O–Si and Fe–O–Si covalent bonds. • Covalent bonding between steel and polysilazane at the interface was probed using spectroscopic techniques. - Abstract: In earlier works, we demonstrated the potential of polysilazane (PSZ) coatings for a use as insulating layers in Cu(In,Ga)Se{sub 2} (CIGS) solar cells prepared on steels substrates and showed a good adhesion between PSZ coatings and both AISI316 and AISI430 steels. In the present paper, spectroscopic techniques are used to elucidate the reason of such adhesion. X-ray Photoelectron Spectroscopy (XPS) was used to investigate surfaces for the two steel substrates and showed the presence of metal oxides and metal hydroxides at the top surface. XPS has been also used to probe interfaces between substrates and PSZ, and metallosiloxane (Me–O–Si) covalent bonds have been detected. These results were confirmed by Infra-Red Reflection Absorption Spectroscopy (IRRAS) analyses since vibrations related to Cr–O–Si and Fe–O–Si compounds were detected. Thus, the good adhesion between steel substrates and PSZ coatings was explained by covalent bonding through chemical reactions between PSZ precursors and hydroxide functional groups present on top surface of the two types of steel. Based on these results, an adhesion mechanism between steel substrates and PSZ coatings is proposed.

  6. Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

    Science.gov (United States)

    Honda, Ryo

    2018-02-27

    Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Equilibrium Crystal Shape of BaZrO{sub 3} and Space Charge Formation in the (011) Surface by Using Ab-Initio Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji-Su; Kim, Yeong-Cheol [Korea University of Technology and Education, Cheonan (Korea, Republic of)

    2017-01-15

    We investigated the equilibrium crystal shape of BaZrO{sub 3} and the space charge formation in an O-terminated (011) surface by using ab-initio thermodynamics. Twenty-two low-indexed (001), (011), and (111) surfaces were calculated to analyze their surface Gibbs-free energy under the stable condition of BaZrO{sub 3}. Based on the Gibbs-Wulff theorem, the equilibrium crystal shape of BaZrO{sub 3} changed from cubic to decaoctahedral with decreasing Ba chemical potential. The dominant facets of BaZrO{sub 3} were {001} and {011}, which were well consistent with experimental observations. The space charge formation in the (011) surface was evaluated using the space-charge model. We found that the (011) surface was even more resistive than the (001) surface.

  8. Nanobody-based electrochemical immunoassay for Bacillus thuringiensis Cry1Ab toxin by detecting the enzymatic formation of polyaniline

    International Nuclear Information System (INIS)

    Zhu, Min; Li, Guanghui; Li, Min; Zhou, Zikai; Liu, Hong; Lei, Hongtao; Shen, Yanfei; Wan, Yakun

    2015-01-01

    We describe an electrochemical immunoassay for the Cry1Ab toxin that is produced by Bacillus thuringiensis. It is making use of a nanobody (a heavy-chain only antibody) that was selected from an immune phage displayed library. A biotinylated primary nanobody and a HRP-conjugated secondary nanobody were applied in a sandwich immunoassay where horseradish peroxidase (HRP) is used to produce polyaniline (PANI) from aniline. PANI can be easily detected by differential pulse voltammetry at a working voltage as low as 40 mV (vs. Ag/AgCl) which makes the assay fairly selective. This immunoassay for Cry1Ab has an analytical range from 0.1 to 1000 ng∙mL -1 and a 0.07 ng∙mL -1 lower limit of detection. The average recoveries of the toxin from spiked samples are in the range from 102 to 114 %, with a relative standard deviation of <7.5 %. The results demonstrated that the assay represented an attractive alternative to existing immunoassays in enabling affordable, sensitive, robust and specific determination of this toxin. (author)

  9. A novel metal-to-metal bonding process through in-situ formation of Ag nanoparticles using Ag2O microparticles

    International Nuclear Information System (INIS)

    Hirose, Akio; Tatsumi, Hiroaki; Takeda, Naoya; Akada, Yusuke; Ogura, Tomo; Ide, Eiichi; Morita, Toshiaki

    2009-01-01

    The metal-to-metal bonding has been successfully achieved via the bonding process using Ag metallo-organic nanoparticles at a bonding temperature of around 300-, which can be alternative to the current microsoldering in electronics assembly using high-temperature solders. However, further reduction of bonding temperature and/or bonding pressure is needed. In the present research, a novel bonding process through in-situ formation of Ag nanoparticles instead of the filler material of the Ag metallo-organic nanoparticles has been developed. The Ag nanoparticles can form by the reduction of Ag 2 O particles. In this study, the Ag 2 O particles were mixed with triethylene glycol as a reducing agent to form a paste for bonding. The Au coated cylindrical specimens were bonded using the paste. The Ag nanoparticles formed at around 130 to 160 through the reduction process of Ag2O particles with triethylene glycol. The Ag nanoparticles were immediately sintered each other due to a great surface energy per volume. A transmission electron microscope observation revealed that the sintered Ag metallurgically bonded to the Au substrate at around 160 and a dense Ag layer formed after further heating. The tensile strength of the joint bonded at 250 under a bonding pressure of 5MPa was around 60MPa

  10. Size effects in tin-based lead-free solder joints: Kinetics of bond formation and mechanical characteristics

    Science.gov (United States)

    Abdelhadi, Ousama Mohamed Omer

    Continuous miniaturization of microelectronic interconnects demands smaller joints with comparable microstructural and structural sizes. As the size of joints become smaller, the volume of intermetallics (IMCs) becomes comparable with the joint size. As a result, the kinetics of bond formation changes and the types and thicknesses of IMC phases that form within the constrained region of the bond varies. This dissertation focuses on investigating combination effects of process parameters and size on kinetics of bond formation, resulting microstructure and the mechanical properties of joints that are formed under structurally constrained conditions. An experiment is designed where several process parameters such as time of bonding, temperature, and pressure, and bond thickness as structural chracteristic, are varied at multiple levels. The experiment is then implemented on the process. Scanning electron microscope (SEM) is then utilized to determine the bond thickness, IMC phases and their thicknesses, and morphology of the bonds. Electron backscatter diffraction (EBSD) is used to determine the grain size in different regions, including the bulk solder, and different IMC phases. Physics-based analytical models have been developed for growth kinetics of IMC compounds and are verified using the experimental results. Nanoindentation is used to determine the mechanical behavior of IMC phases in joints in different scales. Four-point bending notched multilayer specimen and four-point bending technique were used to determine fracture toughness of the bonds containing IMCs. Analytical modeling of peeling and shear stresses and fracture toughness in tri-layer four-point bend specimen containing intermetallic layer was developed and was verified and validated using finite element simulation and experimental results. The experiment is used in conjunction with the model to calculate and verify the fracture toughness of Cu6Sn5 IMC materials. As expected two different IMC phases

  11. Probability of conductive bond formation in a percolating network of nanowires with fusible tips

    Science.gov (United States)

    Rykaczewski, Konrad; Wang, Robert Y.

    2018-03-01

    Meeting the heat dissipation demands of microelectronic devices requires development of polymeric composites with high thermal conductivity. This property is drastically improved by percolation networks of metallic filler particles that have their particle-to-particle contact resistances reduced through thermal or electromagnetic fusing. However, composites with fused metallic fillers are electrically conductive, which prevents their application within the chip-board and the inter-chip gaps. Here, we propose that electrically insulating composites for these purposes can be achieved by the application of fusible metallic coatings to the tips of nanowires with thermally conductive but electrically insulating cores. We derive analytical models that relate the ratio of the coated and total nanowire lengths to the fraction of fused, and thus conductive, bonds within percolating networks of these structures. We consider two types of materials for these fusible coatings. First, we consider silver-like coatings, which form only conductive bonds when contacting the silver-like coating of another nanowire. Second, we consider liquid metal-like coatings, which form conductive bonds regardless of whether they contact a coated or an uncoated segment of another nanowire. These models were validated using Monte Carlo simulations, which also revealed that electrical short-circuiting is highly unlikely until most of the wire is coated. Furthermore, we demonstrate that switching the tip coating from silver- to liquid metal-like materials can double the fraction of conductive bonds. Consequently, this work provides motivation to develop scalable methods for fabrication of the hybrid liquid-coated nanowires, whose dispersion in a polymer matrix is predicted to yield highly thermally conductive but electrically insulating composites.

  12. Assessment of covalent bond formation between coupling agents and wood by FTIR spectroscopy and pull strength tests

    DEFF Research Database (Denmark)

    Rasmussen, Jonas Stensgaard; Barsberg, Søren Talbro; Venås, Thomas Mark

    2014-01-01

    In the focus was the question whether metal alkoxide coupling agents – titanium, silane, and zirconium – form covalent bonds to wood and how they improve coating adhesion. In a previous work, a downshift of the lignin infrared (IR) band ∼1600 cm-1 was shown to be consistent with the formation...... of ether linkages between lignin and titanium coupling agent. In the present work, changes were found in the attenuated total reflectance-Fourier transform IR (ATR-FTIR) spectra of lignin and wood mixed with silane, and titanium coupling agents, and to a lesser extent for a zirconium coupling agent...

  13. Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S center dot center dot center dot O chalcogen bonds

    Czech Academy of Sciences Publication Activity Database

    Zierkiewicz, W.; Fanfrlík, Jindřich; Hobza, Pavel; Michalska, D.; Zeegers-Huyskens, T.

    2016-01-01

    Roč. 135, č. 9 (2016), č. článku 217. ISSN 1432-881X R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : chalcogen bonds * carbonyl and thiocarbonyl groups * CCSD(T) * DFT Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.890, year: 2016 http://link.springer.com/article/10.1007%2Fs00214-016-1972-z

  14. Ab initio study of symmetrical tilt grain boundaries in bcc Fe: structural units, magnetic moments, interfacial bonding, local energy and local stress

    International Nuclear Information System (INIS)

    Bhattacharya, Somesh Kr; Tanaka, Shingo; Kohyama, Masanori; Shiihara, Yoshinori

    2013-01-01

    We present first-principle calculations on symmetric tilt grain boundaries (GBs) in bcc Fe. Using density functional theory (DFT), we studied the structural, electronic and magnetic properties of Σ3(111) and Σ11(332) GBs formed by rotation around the [110] axis. The optimized structures, GB energies and GB excess free volumes are consistent with previous DFT and classical simulation studies. The GB configurations can be interpreted by the structural unit model as given by Nakashima and Takeuchi (2000 ISIJ 86 357). Both the GBs are composed of similar structural units of three- and five-membered rings with different densities at the interface according to the rotation angle. The interface atoms with larger atomic volumes reveal higher magnetic moments than the bulk value, while the interface atoms with shorter bond lengths have reduced magnetic moments in each GB. The charge density and local density of states reveal that the interface bonds with short bond lengths have more covalent nature, where minority-spin electrons play a dominant role as the typical nature of ferromagnetic Fe. In order to understand the structural stability of these GBs, we calculated the local energy and local stress for each atomic region using the scheme of Shiihara et al (2010 Phys. Rev. B 81 075441). In each GB, the interface atoms with larger atomic volumes and enhanced magnetic moments reveal larger local energy increase and tensile stress. The interface atoms constituting more covalent-like bonds with reduced magnetic moments have lower local energy increase, contributing to the stabilization, while compressive stress is generated at these atoms. The relative stability between the two GBs can be understood by the local energies at the structural units. The local energy and local stress analysis is a powerful tool to investigate the structural properties of GBs based on the behavior of valence electrons. (paper)

  15. A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems

    Directory of Open Access Journals (Sweden)

    Boaz Galdino Oliveira

    2009-08-01

    Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

  16. Synthesis of 1,2,4-Triazoles via Oxidative Heterocyclization: Selective C-N Bond Over C-S Bond Formation.

    Science.gov (United States)

    Gogoi, Anupal; Guin, Srimanta; Rajamanickam, Suresh; Rout, Saroj Kumar; Patel, Bhisma K

    2015-09-18

    The higher propensity of C-N over C-S bond forming ability was demonstrated, through formal C-H functionalization during the construction of 4,5-disubstituted 1,2,4-triazole-3-thiones from arylidenearylthiosemicarbazides catalyzed by Cu(II). However, steric factors imparted by the o-disubstituted substrates tend to change the reaction path giving thiodiazole as the major or an exclusive product. Upon prolonging the reaction time, the in situ generated thiones are transformed to 4,5-disubstituted 1,2,4-triazoles via a desulfurization process. Two classes of heterocycles viz. 4,5-disubstituted 1,2,4-triazole-3-thiones and 4,5-disubstituted 1,2,4-triazoles can be synthesized from arylidenearylthiosemicarbazides by simply adjusting the reaction time. Desulfurization of 1,2,4-triazole-3-thiones is assisted by thiophilic Cu to provide 1,2,4-triazoles with concomitant formation of CuS and polynuclear sulfur anions as confirmed from scanning electron microscope and energy dispersive X-ray spectroscopy measurements. A one-pot synthesis of an antimicrobial compound has been successfully achieved following this strategy.

  17. Oxygen-metal bonding in Ti-bearing compounds from O 1s spectra and ab initio full multiple-scattering calculations

    International Nuclear Information System (INIS)

    Ziyu Wu; Paris, E.; Langenhorst, F.; Seifert, F.

    2002-01-01

    The O K-edge spectra of a series of Ti-bearing compounds with Ti in diffrent structural and chemical environments have been measured using electron energy-loss spectroscopy and analyzed using ab initio full multiple-scattering (MS) calculations. The near-edge structures arise mainly from covalency by direct and/or indirect interaction between O and metal atoms and between O and Si atoms. The coordination number of the cation and the site symmetry also influence the spectral shape and structures. Using different size clusters around the excited atom in the full MS simulation, it is possible to interpret and assign the features present in the spectra of each compund to its specific atomic arrangement and electronic structure. (au)

  18. Palladium- and copper-mediated N-aryl bond formation reactions for the synthesis of biological active compounds

    Directory of Open Access Journals (Sweden)

    Burkhard Koenig

    2011-01-01

    Full Text Available N-Arylated aliphatic and aromatic amines are important substituents in many biologically active compounds. In the last few years, transition-metal-mediated N-aryl bond formation has become a standard procedure for the introduction of amines into aromatic systems. While N-arylation of simple aromatic halides by simple amines works with many of the described methods in high yield, the reactions may require detailed optimization if applied to the synthesis of complex molecules with additional functional groups, such as natural products or drugs. We discuss and compare in this review the three main N-arylation methods in their application to the synthesis of biologically active compounds: Palladium-catalysed Buchwald–Hartwig-type reactions, copper-mediated Ullmann-type and Chan–Lam-type N-arylation reactions. The discussed examples show that palladium-catalysed reactions are favoured for large-scale applications and tolerate sterically demanding substituents on the coupling partners better than Chan–Lam reactions. Chan–Lam N-arylations are particularly mild and do not require additional ligands, which facilitates the work-up. However, reaction times can be very long. Ullmann- and Buchwald–Hartwig-type methods have been used in intramolecular reactions, giving access to complex ring structures. All three N-arylation methods have specific advantages and disadvantages that should be considered when selecting the reaction conditions for a desired C–N bond formation in the course of a total synthesis or drug synthesis.

  19. Oxo-group-14-element bond formation in binuclear uranium(V) pacman complexes

    International Nuclear Information System (INIS)

    Jones, Guy M.; Arnold, Polly L.; Love, Jason B.

    2013-01-01

    Simple and versatile routes to the functionalization of uranyl-derived U"V-oxo groups are presented. The oxo-lithiated, binuclear uranium(V)-oxo complexes [{(py)_3LiOUO}_2(L)] and [{(py)_3LiOUO}(OUOSiMe_3)(L)] were prepared by the direct combination of the uranyl(VI) silylamide ''ate'' complex [Li(py)_2][(OUO)(N'')_3](N''=N(SiMe_3)_2) with the polypyrrolic macrocycle H_4L or the mononuclear uranyl (VI) Pacman complex [UO_2(py)(H_2L)], respectively. These oxo-metalated complexes display distinct U-O single and multiple bonding patterns and an axial/equatorial arrangement of oxo ligands. Their ready availability allows the direct functionalization of the uranyl oxo group leading to the binuclear uranium(V) oxo-stannylated complexes [{(R_3Sn)OUO}_2(L)] (R=nBu, Ph), which represent rare examples of mixed uranium/tin complexes. Also, uranium-oxo-group exchange occurred in reactions with [TiCl(OiPr)_3] to form U-O-C bonds [{(py)_3LiOUO}(OUOiPr)(L)] and [(iPrOUO)_2(L)]. Overall, these represent the first family of uranium(V) complexes that are oxo-functionalised by Group 14 elements. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. A protocol for amide bond formation with electron deficient amines and sterically hindered substrates

    DEFF Research Database (Denmark)

    Due-Hansen, Maria E; Pandey, Sunil K; Christiansen, Elisabeth

    2016-01-01

    A protocol for amide coupling by in situ formation of acyl fluorides and reaction with amines at elevated temperature has been developed and found to be efficient for coupling of sterically hindered substrates and electron deficient amines where standard methods failed.......A protocol for amide coupling by in situ formation of acyl fluorides and reaction with amines at elevated temperature has been developed and found to be efficient for coupling of sterically hindered substrates and electron deficient amines where standard methods failed....

  1. Formation of hydrogen bonds precedes the rate-limiting formation of persistent structure in the folding of ACBP

    DEFF Research Database (Denmark)

    Teilum, K; Kragelund, B B; Knudsen, J

    2000-01-01

    A burst phase in the early folding of the four-helix two-state folder protein acyl-coenzyme A binding protein (ACBP) has been detected using quenched-flow in combination with site-specific NMR-detected hydrogen exchange. Several of the burst phase structures coincide with a structure consisting...... of eight conserved hydrophobic residues at the interface between the two N and C-terminal helices. Previous mutation studies have shown that the formation of this structure is rate limiting for the final folding of ACBP. The burst phase structures observed in ACBP are different from the previously reported...

  2. Mechanistic Aspects of the Reversible Binding of SO2 on Arylplatinum Complexes: Experimental and ab Initio Studies

    NARCIS (Netherlands)

    Koten, G. van; Albrecht, M.A.; Gossage, R.A.; Frey, H.; Ehlers, A.W.; Baerends, E.J.; Merbach, A.E.

    2001-01-01

    The detailed mechanism of the reversible binding and fast exchange of SO2 on the organoplatinum(II) complex [PtI(NCN)], 1, has been studied experimentally in solution (C2F4Br2) using low-temperature NMR spectroscopy and theoretically by ab initio calculations. Direct bonding of SO2 and formation of

  3. Advanced multivariate data analysis to determine the root cause of trisulfide bond formation in a novel antibody–peptide fusion

    Science.gov (United States)

    Goldrick, Stephen; Holmes, William; Bond, Nicholas J.; Lewis, Gareth; Kuiper, Marcel; Turner, Richard

    2017-01-01

    ABSTRACT Product quality heterogeneities, such as a trisulfide bond (TSB) formation, can be influenced by multiple interacting process parameters. Identifying their root cause is a major challenge in biopharmaceutical production. To address this issue, this paper describes the novel application of advanced multivariate data analysis (MVDA) techniques to identify the process parameters influencing TSB formation in a novel recombinant antibody–peptide fusion expressed in mammalian cell culture. The screening dataset was generated with a high‐throughput (HT) micro‐bioreactor system (AmbrTM 15) using a design of experiments (DoE) approach. The complex dataset was firstly analyzed through the development of a multiple linear regression model focusing solely on the DoE inputs and identified the temperature, pH and initial nutrient feed day as important process parameters influencing this quality attribute. To further scrutinize the dataset, a partial least squares model was subsequently built incorporating both on‐line and off‐line process parameters and enabled accurate predictions of the TSB concentration at harvest. Process parameters identified by the models to promote and suppress TSB formation were implemented on five 7 L bioreactors and the resultant TSB concentrations were comparable to the model predictions. This study demonstrates the ability of MVDA to enable predictions of the key performance drivers influencing TSB formation that are valid also upon scale‐up. Biotechnol. Bioeng. 2017;114: 2222–2234. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:28500668

  4. Extremely efficient catalysis of carbon-carbon bond formation using "click" dendrimer-stabilized palladium nanoparticles.

    Science.gov (United States)

    Astruc, Didier; Ornelas, Cátia; Diallo, Abdou K; Ruiz, Jaime

    2010-07-20

    This article is an account of the work carried out in the authors' laboratory illustrating the usefulness of dendrimer design for nanoparticle palladium catalysis. The "click" synthesis of dendrimers constructed generation by generation by 1-->3 C connectivity, introduces 1,2,3-triazolyl ligands insides the dendrimers at each generation. Complexation of the ligands by Pd(II) followed by reduction to Pd(0) forms dendrimer-stabilized Pd nanoparticles (PdNPs) that are extremely reactive in the catalysis of olefin hydrogenation and C-C bond coupling reactions. The stabilization can be outer-dendritic for the small zeroth-generation dendrimer or intra-dendritic for the larger first- and second-generation dendrimers. The example of the Miyaura-Suzuki reaction that can be catalyzed by down to 1 ppm of PdNPs with a "homeopathic" mechanism (the less, the better) is illustrated here, including catalysis in aqueous solvents.

  5. Reductive Elimination Leading to C-C Bond Formation in Gold(III) Complexes: A Mechanistic and Computational Study.

    Science.gov (United States)

    Rocchigiani, Luca; Fernandez-Cestau, Julio; Budzelaar, Peter H M; Bochmann, Manfred

    2018-06-21

    The factors affecting the rates of reductive C-C cross-coupling reactions in gold(III) aryls were studied by using complexes that allow easy access to a series of electronically modified aryl ligands, as well as to gold methyl and vinyl complexes, by using the pincer compounds [(C^N^C)AuR] (R=C 6 F 5 , CH=CMe 2 , Me and p-C 6 H 4 X, where X=OMe, F, H, tBu, Cl, CF 3 , or NO 2 ) as starting materials (C^N^C=2,6-(4'-tBuC 6 H 3 ) 2 pyridine dianion). Protodeauration followed by addition of one equivalent SMe 2 leads to the quantitative generation of the thioether complexes [(C^N-CH)AuR(SMe 2 )] + . Upon addition of a second SMe 2 pyridine is displaced, which triggers the reductive aryl-R elimination. The rates for these cross-couplings increase in the sequence k(vinyl)>k(aryl)≫k(C 6 F 5 )>k(Me). Vinyl-aryl coupling is particularly fast, 1.15×10 -3  L mol -1  s -1 at 221 K, whereas both C 6 F 5 and Me couplings encountered higher barriers for the C-C bond forming step. The use of P(p-tol) 3 in place of SMe 2 greatly accelerates the C-C couplings. Computational modelling shows that in the C^N-bonded compounds displacement of N by a donor L is required before the aryl ligands can adopt a conformation suitable for C-C bond formation, so that elimination takes place from a four-coordinate intermediate. The C-C bond formation is the rate-limiting step. In the non-chelating case, reductive C(sp 2 )-C(sp 2 ) elimination from three-coordinate ions [(Ar 1 )(Ar 2 )AuL] + is almost barrier-free, particularly if L=phosphine. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Oxo-group-14-element bond formation in binuclear uranium(V) pacman complexes

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Guy M.; Arnold, Polly L.; Love, Jason B. [EaStCHEM School of Chemistry, University of Edinburgh (United Kingdom)

    2013-07-29

    Simple and versatile routes to the functionalization of uranyl-derived U{sup V}-oxo groups are presented. The oxo-lithiated, binuclear uranium(V)-oxo complexes [{(py)_3LiOUO}{sub 2}(L)] and [{(py)_3LiOUO}(OUOSiMe{sub 3})(L)] were prepared by the direct combination of the uranyl(VI) silylamide ''ate'' complex [Li(py){sub 2}][(OUO)(N''){sub 3}](N''=N(SiMe{sub 3}){sub 2}) with the polypyrrolic macrocycle H{sub 4}L or the mononuclear uranyl (VI) Pacman complex [UO{sub 2}(py)(H{sub 2}L)], respectively. These oxo-metalated complexes display distinct U-O single and multiple bonding patterns and an axial/equatorial arrangement of oxo ligands. Their ready availability allows the direct functionalization of the uranyl oxo group leading to the binuclear uranium(V) oxo-stannylated complexes [{(R_3Sn)OUO}{sub 2}(L)] (R=nBu, Ph), which represent rare examples of mixed uranium/tin complexes. Also, uranium-oxo-group exchange occurred in reactions with [TiCl(OiPr){sub 3}] to form U-O-C bonds [{(py)_3LiOUO}(OUOiPr)(L)] and [(iPrOUO){sub 2}(L)]. Overall, these represent the first family of uranium(V) complexes that are oxo-functionalised by Group 14 elements. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Study of spinodal decomposition and formation of nc-Al2O3/ZrO2 nanocomposites by combined ab initio density functional theory and thermodynamic modeling

    International Nuclear Information System (INIS)

    Sheng, S.H.; Zhang, R.F.; Veprek, S.

    2011-01-01

    Using ab initio density functional theory, the equilibrium properties, such as the total energy, the molar volume, the bulk modulus and its first derivative, as well as the formation enthalpy of monoclinic ZrO 2 and hexagonal α-Al 2 O 3 phases, were calculated and compared with the published theoretical and experimental data. Based on the good agreement of these data, we calculated the lattice instabilities of hypothetical binary hexagonal Zr 2 O 3 and monoclinic AlO 2 , and the interaction parameters of ternary Zr 1-x Al x O y solid solutions. The binodal and spinodal diagrams were then constructed to predict the possibility of the formation of oxide-based nanocomposites which may display hardness enhancement above that of the solid solutions. It is shown that exponential dependence of the interaction parameter on temperature yields the most reliable results. The system should undergo spinodal phase segregation within the composition range that is relevant for the formation of hard or superhard nanocomposites with high thermal and oxidation stability, which are important for their applications.

  8. Ab initio chemical kinetics for the ClOO + NO reaction: Effects of temperature and pressure on product branching formation

    Science.gov (United States)

    Raghunath, P.; Lin, M. C.

    2012-07-01

    The kinetics and mechanism for the reaction of ClOO with NO have been investigated by ab initio molecular orbital theory calculations based on the CCSD(T)/6-311+G(3df)//PW91PW91/6-311+G(3df) method, employed to evaluate the energetics for the construction of potential energy surfaces and prediction of reaction rate constants. The results show that the reaction can produce two key low energy products ClNO + 3O2 via the direct triplet abstraction path and ClO + NO2 via the association and decomposition mechanism through long-lived singlet pc-ClOONO and ClONO2 intermediates. The yield of ClNO + O2 (1△) from any of the singlet intermediates was found to be negligible because of their high barriers and tight transition states. As both key reactions initially occur barrierlessly, their rate constants were evaluated with a canonical variational approach in our transition state theory and Rice-Ramspergen-Kassel-Marcus/master equation calculations. The rate constants for ClNO + 3O2 and ClO + NO2 production from ClOO + NO can be given by 2.66 × 10-16 T1.91 exp(341/T) (200-700 K) and 1.48 × 10-24 T3.99 exp(1711/T) (200-600 K), respectively, independent of pressure below atmospheric pressure. The predicted total rate constant and the yields of ClNO and NO2 in the temperature range of 200-700 K at 10-760 Torr pressure are in close agreement with available experimental results.

  9. Heat-induced whey protein isolate fibrils: Conversion, hydrolysis, and disulphide bond formation

    NARCIS (Netherlands)

    Bolder, S.G.; Vasbinder, A.; Sagis, L.M.C.; Linden, van der E.

    2007-01-01

    Fibril formation of individual pure whey proteins and whey protein isolate (WPI) was studied. The heat-induced conversion of WPI monomers into fibrils at pH 2 and low ionic strength increased with heating time and protein concentration. Previous studies, using a precipitation method, size-exclusion

  10. Microwave-assisted Ullmann C-S bond formation: synthesis of the P38alpha MAPK clinical candidate VX-745.

    Science.gov (United States)

    Bagley, Mark C; Davis, Terence; Dix, Matthew C; Fusillo, Vincenzo; Pigeaux, Morgane; Rokicki, Michal J; Kipling, David

    2009-11-06

    Microwave irradiation promotes the rapid and efficient reaction of a thiophenol and aryl or heteroaryl halide using a copper or palladium catalyst and a range of ligands, depending upon substrate. Of particular utility is the use of copper(I) iodide (5 mol %) and trans-cyclohexane-1,2-diol as ligand under basic conditions and microwave irradiation to give the corresponding sulfide in high yield. This method for C-S bond formation is applied in the four-step synthesis of the clinical candidate VX-745 in 38% overall yield. The inhibitory activity of VX-745 against p38alpha MAPK is confirmed in Werner syndrome dermal fibroblasts at 1.0 microM concentration by immunoblot assay.

  11. Synthesis of Reusable Silica Nanosphere-Supported Pt(IV Complex for Formation of Disulfide Bonds in Peptides

    Directory of Open Access Journals (Sweden)

    Xiaonan Hou

    2017-02-01

    Full Text Available Some peptide-based drugs, including oxytocin, vasopressin, ziconotide, pramlintide, nesiritide, and octreotide, contain one intramolecular disulfide bond. A novel and reusable monodispersed silica nanosphere-supported Pt(IV complex (SiO2@TPEA@Pt(IV; TPEA: N-[3-(trimethoxysilylpropyl]ethylenediamine was synthesized via a four-step procedure and was used for the formation of intramolecular disulfide bonds in peptides. Transmission electron microscopy (TEM and chemical mapping results for the Pt(II intermediates and for SiO2@TPEA@Pt(IV show that the silica nanospheres possess a monodisperse spherical structure and contain uniformly-distributed Si, O, C, N, Cl, and Pt. The valence state of Pt on the silica nanospheres was characterized by X-ray photoelectron spectroscopy (XPS. The Pt(IV loaded on SiO2@TPEA@Pt(IV was 0.15 mmol/g, as determined by UV-VIS spectrometry. The formation of intramolecular disulfides in six dithiol-containing peptides of variable lengths by the use of SiO2@TPEA@Pt(IV was investigated, and the relative oxidation yields were determined by high-performance liquid chromatography (HPLC. In addition, peptide 1 (Ac-CPFC-NH2 was utilized to study the reusability of SiO2@TPEA@Pt(IV. No significant decrease in the relative oxidation yield was observed after ten reaction cycles. Moreover, the structure of SiO2@TPEA@Pt(IV after being used for ten cycles was determined to be similar to its initial one, demonstrating the cycling stability of the complex.

  12. Amide Bond Formation Assisted by Vicinal Alkylthio Migration in Enaminones: Metal- and CO-Free Synthesis of α,β-Unsaturated Amides.

    Science.gov (United States)

    Liu, Zhuqing; Huang, Fei; Wu, Ping; Wang, Quannan; Yu, Zhengkun

    2018-05-18

    Amide bond formation is one of the most important transformations in organic synthesis, drug development, and materials science. Efficient construction of amides has been among the most challenging tasks for organic chemists. Herein, we report a concise methodology for amide bond (-CONH-) formation assisted by vicinal group migration in alkylthio-functionalized enaminones (α-oxo ketene N, S-acetals) under mild conditions. Simple treatment of such enaminones with PhI(OAc) 2 at ambient temperature in air afforded diverse multiply functionalized α,β-unsaturated amides including β-cyclopropylated acrylamides, in which a wide array of functional groups such as aryl, (hetero)aryl, alkenyl, and alkyl can be conveniently introduced to a ketene moiety. The reaction mechanism was investigated by exploring the origins of the amide oxygen and carbon atoms as well as isolation and structural characterization of the reaction intermediates. The amide bond formation reactions could also be efficiently performed under solventless mechanical milling conditions.

  13. Stress-responsively modulated ymdAB-clsC operon plays a role in biofilm formation and apramycin susceptibility in Escherichia coli.

    Science.gov (United States)

    Kim, Moonjeong; Kim, Kwang-Sun

    2017-07-06

    The YmdB protein, an inhibitor of biofilm formation and an inducer of apramycin susceptibility in Escherichia coli (E. coli), is part of a putative operon. However, transcription of this operon and its subsequent effects on biological pathways has not been fully studied. Here, we characterized the operon in terms of promoter activity, transcription and function. Promoter activity assays identified two new growth- and cold-shock-responsive upstream (PymdA) and inner (PclsC) promoters, respectively. Moreover, investigation of the operon-derived transcripts identified different polycistronic transcripts harboring multiple heterogeneous 3΄ ends. Overexpression of YmdA or ClsC proteins inhibited biofilm formation and affected apramycin susceptibility, a process dependent on the sucA gene, suggesting that the operon genes or their encoded proteins are functionally linked. Additional investigation of the effects of polycistronic transcripts on the response of E. coli cells to apramycin revealed that transcripts containing ymdA (-213 to +27) are required for apramycin susceptibility. Thus, ymdAB-clsC is a new stress-responsive operon that plays a role in inhibiting undesired biofilm forming and antibiotic-resistant bacterial populations. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Advanced multivariate data analysis to determine the root cause of trisulfide bond formation in a novel antibody-peptide fusion.

    Science.gov (United States)

    Goldrick, Stephen; Holmes, William; Bond, Nicholas J; Lewis, Gareth; Kuiper, Marcel; Turner, Richard; Farid, Suzanne S

    2017-10-01

    Product quality heterogeneities, such as a trisulfide bond (TSB) formation, can be influenced by multiple interacting process parameters. Identifying their root cause is a major challenge in biopharmaceutical production. To address this issue, this paper describes the novel application of advanced multivariate data analysis (MVDA) techniques to identify the process parameters influencing TSB formation in a novel recombinant antibody-peptide fusion expressed in mammalian cell culture. The screening dataset was generated with a high-throughput (HT) micro-bioreactor system (Ambr TM 15) using a design of experiments (DoE) approach. The complex dataset was firstly analyzed through the development of a multiple linear regression model focusing solely on the DoE inputs and identified the temperature, pH and initial nutrient feed day as important process parameters influencing this quality attribute. To further scrutinize the dataset, a partial least squares model was subsequently built incorporating both on-line and off-line process parameters and enabled accurate predictions of the TSB concentration at harvest. Process parameters identified by the models to promote and suppress TSB formation were implemented on five 7 L bioreactors and the resultant TSB concentrations were comparable to the model predictions. This study demonstrates the ability of MVDA to enable predictions of the key performance drivers influencing TSB formation that are valid also upon scale-up. Biotechnol. Bioeng. 2017;114: 2222-2234. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

  15. Facing the challenge of predicting the standard formation enthalpies of n-butyl-phosphate species with ab initio methods

    Science.gov (United States)

    Saab, Mohamad; Réal, Florent; Šulka, Martin; Cantrel, Laurent; Virot, François; Vallet, Valérie

    2017-06-01

    Tributyl-phosphate (TBP), a ligand used in the PUREX liquid-liquid separation process of spent nuclear fuel, can form an explosive mixture in contact with nitric acid that might lead to a violent explosive thermal runaway. In the context of safety of a nuclear reprocessing plant facility, it is crucial to predict the stability of TBP at elevated temperatures. So far, only the enthalpies of formation of TBP are available in the literature with rather large uncertainties, while those of its degradation products, di-(HDBP) and mono-(H2MBP), are unknown. In this goal, we have used state-of-the art quantum chemical methods to compute the formation enthalpies and entropies of TBP and its degradation products di-(HDBP) and mono-(H2MBP) in gas and liquid phases. Comparisons of levels of quantum chemical theory revealed that there are significant effects of correlation on their electronic structures, pushing for the need of not only high level of electronic correlation treatment, namely, local coupled cluster with single and double excitation operators and perturbative treatment of triple excitations, but also extrapolations to the complete basis to produce reliable and accurate thermodynamics data. Solvation enthalpies were computed with the conductor-like screening model for real solvents [COSMO-RS], for which we observe errors not exceeding 22 kJ mol-1. We thus propose with final uncertainty of about 20 kJ mol-1 standard enthalpies of formation of TBP, HDBP, and H2MBP which amounts to -1281.7 ± 24.4, -1229.4 ± 19.6, and -1176.7 ± 14.8 kJ mol-1, respectively, in the gas phase. In the liquid phase, the predicted values are -1367.3 ± 24.4, -1348.7 ± 19.6, and -1323.8± 14.8 kJ mol-1, to which we may add about -22 kJ mol-1 error from the COSMO-RS solvent model. From these data, the complete hydrolysis of TBP is predicted as an exothermic phenomena but showing a slightly endergonic process.

  16. An unusual cysteine VL87 affects the antibody fragment conformations without interfering with the disulfide bond formation.

    Science.gov (United States)

    Attallah, Carolina; Aguilar, María Fernanda; Garay, A Sergio; Herrera, Fernando E; Etcheverrigaray, Marina; Oggero, Marcos; Rodrigues, Daniel E

    2017-10-01

    The Cys residues are almost perfectly conserved in all antibodies. They contribute significantly to the antibody fragment stability. The relevance of two natural contiguous Cys residues of an anti-recombinant human-follicle stimulation hormone (rhFSH) in a format of single-chain variable fragment (scFv) was studied. This scFv contains 5 Cys residues: V H 22 and V H 92 in the variable heavy chain (V H ) and V L 23, V L 87 and V L 88 in the variable light chain (V L ). The influence of two unusual contiguous Cys at positions V L 87 and V L 88 was studied by considering the wild type fragment and mutant variants: V L -C88S, V L -C87S, V L -C87Y. The analysis was carried out using antigen-binding ability measurement by indirect specific ELISA and a detailed molecular modeling that comprises homology methods, long molecular dynamics simulations and docking. We found that V L -C87 affected the antibody fragment stability without interfering with the disulfide bond formation. The effect of mutating the V L -C87 by a usual residue at this position like Tyr caused distant structural changes at the V H region that confers a higher mobility to the V H -CDR2 and V H -CDR3 loops improving the scFv binding to the antigen. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Dispersion-corrected first-principles calculation of terahertz vibration, and evidence for weak hydrogen bond formation

    Science.gov (United States)

    Takahashi, Masae; Ishikawa, Yoichi; Ito, Hiromasa

    2013-03-01

    A weak hydrogen bond (WHB) such as CH-O is very important for the structure, function, and dynamics in a chemical and biological system WHB stretching vibration is in a terahertz (THz) frequency region Very recently, the reasonable performance of dispersion-corrected first-principles to WHB has been proven. In this lecture, we report dispersion-corrected first-principles calculation of the vibrational absorption of some organic crystals, and low-temperature THz spectral measurement, in order to clarify WHB stretching vibration. The THz frequency calculation of a WHB crystal has extremely improved by dispersion correction. Moreover, the discrepancy in frequency between an experiment and calculation and is 10 1/cm or less. Dispersion correction is especially effective for intermolecular mode. The very sharp peak appearing at 4 K is assigned to the intermolecular translational mode that corresponds to WHB stretching vibration. It is difficult to detect and control the WHB formation in a crystal because the binding energy is very small. With the help of the latest intense development of experimental and theoretical technique and its careful use, we reveal solid-state WHB stretching vibration as evidence for the WHB formation that differs in respective WHB networks The research was supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant No. 22550003).

  18. Synthetic Methods for Ester Bond Formation and Conformational Analysis of Ester-Containing Carbohydrates

    Science.gov (United States)

    Hackbusch, Sven

    This dissertation encompasses work related to synthetic methods for the formation of ester linkages in organic compounds, as well as the investigation of the conformational influence of the ester functional group on the flexibility of inter-saccharide linkages, specifically, and the solution phase structure of ester-containing carbohydrate derivatives, in general. Stereoselective reactions are an important part of the field of asymmetric synthesis and an understanding of their underlying mechanistic principles is essential for rational method development. Here, the exploration of a diastereoselective O-acylation reaction on a trans-2-substituted cyclohexanol scaffold is presented, along with possible reasons for the observed reversal of stereoselectivity dependent on the presence or absence of an achiral amine catalyst. In particular, this work establishes a structure-activity relationship with regard to the trans-2-substituent and its role as a chiral auxiliary in the reversal of diastereoselectivity. In the second part, the synthesis of various ester-linked carbohydrate derivatives, and their conformational analysis is presented. Using multidimensional NMR experiments and computational methods, the compounds' solution-phase structures were established and the effect of the ester functional group on the molecules' flexibility and three-dimensional (3D) structure was investigated and compared to ether or glycosidic linkages. To aid in this, a novel Karplus equation for the C(sp2)OCH angle in ester-linked carbohydrates was developed on the basis of a model ester-linked carbohydrate. This equation describes the sinusoidal relationship between the C(sp2)OCH dihedral angle and the corresponding 3JCH coupling constant that can be determined from a J-HMBC NMR experiment. The insights from this research will be useful in describing the 3D structure of naturally occurring and lab-made ester-linked derivatives of carbohydrates, as well as guiding the de novo-design of

  19. A novel approach for a C-11C bond formation: synthesis of 17α-([11C]prop-1-ynyl)-3-methoxy-3,17β-estradiol

    International Nuclear Information System (INIS)

    Wuest, F.; Zessin, J.

    2002-01-01

    A novel method for a 11 C-C bond formation was developed, employing a cross-coupling reaction between a terminal acetylene and [ 11 C]methyl iodide. The method was used for the synthesis of 17α-([ 11 C]prop-1-ynyl)-3-methoxy-3,17β-estadiol. (orig.)

  20. Unusual C-C bond cleavage in the formation of amine-bis(phenoxy) group 4 benzyl complexes: Mechanism of formation and application to stereospecific polymerization

    KAUST Repository

    Gowda, Ravikumar R.

    2014-08-11

    Group 4 tetrabenzyl compounds MBn4 (M = Zr, Ti), upon protonolysis with an equimolar amount of the tetradentate amine-tris(phenol) ligand N[(2,4-tBu2C6H2(CH 2)OH]3 in toluene from -30 to 25 °C, unexpectedly lead to amine-bis(phenoxy) dibenzyl complexes, BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn2 (M = Zr (1), Ti (2)) in 80% (1) and 75% (2) yields. This reaction involves an apparent cleavage of the >NCH2-ArOH bond (loss of the phenol in the ligand) and formation of the >NCH 2-CH2Bn bond (gain of the benzyl group in the ligand). Structural characterization of 1 by X-ray diffraction analysis confirms that the complex formed is a bis(benzyl) complex of Zr coordinated by a newly derived tridentate amine-bis(phenoxy) ligand arranged in a mer configuration in the solid state. The abstractive activation of 1 and 2 with B(C6F 5)3·THF in CD2Cl2 at room temperature generates the corresponding benzyl cations {BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn(THF)}+[BnB(C6F5) 3]- (M = Zr (3), Ti, (4)). These cationic complexes, along with their analogues derived from (imino)phenoxy tri- and dibenzyl complexes, [(2,6-iPr2C6H3)N=C(3,5- tBu2C6H2)O]ZrBn3 (5) and [2,4-Br2C6H2(O)(6-CH2(NC 5H9))CH2N=CH(2-adamantyl-4-MeC 6H2O)]ZrBn2 (6), have been found to effectively polymerize the biomass-derived renewable β-methyl-α-methylene- γ-butyrolactone (βMMBL) at room temperature into the highly stereoregular polymer PβMMBL with an isotacticity up to 99% mm. A combined experimental and DFT study has yielded a mechanistic pathway for the observed unusual C-C bond cleavage in the present protonolysis reaction between ZrBn4 and N[(2,4-tBu2C 6H2(CH2)OH]3 for the formation of complex 1, which involves the benzyl radical and the Zr(III) species, resulting from thermal and photochemical decomposition of ZrBn4, followed by a series of reaction sequences consisting of protonolysis, tautomerization, H-transfer, oxidation, elimination, and radical coupling. © 2014 American Chemical Society.

  1. Hydrogen spillover in Pt-single-walled carbon nanotube composites: formation of stable C-H bonds.

    Science.gov (United States)

    Bhowmick, Ranadeep; Rajasekaran, Srivats; Friebel, Daniel; Beasley, Cara; Jiao, Liying; Ogasawara, Hirohito; Dai, Hongjie; Clemens, Bruce; Nilsson, Anders

    2011-04-13

    Using in situ electrical conductivity and ex situ X-ray photoelectron spectroscopy (XPS) measurements, we have examined how the hydrogen uptake of single-walled carbon nanotubes (SWNTs) is influenced by the addition of Pt nanoparticles. The conductivity of platinum-sputtered single-walled carbon nanotubes (Pt-SWNTs) during molecular hydrogen exposure decreased more rapidly than that of the corresponding pure SWNTs, which supports a hydrogenation mechanism facilitated by "spillover" of dissociated hydrogen from the Pt nanoparticles. C 1s XPS spectra indicate that the Pt-SWNTs store hydrogen by means of chemisorption, that is, covalent C-H bond formation: molecular hydrogen charging at elevated pressure (8.27 bar) and room temperature yielded Pt-SWNTs with up to 16 ± 1.5 at. % sp(3)-hybridized carbon atoms, which corresponds to a hydrogen-storage capacity of 1.2 wt % (excluding the weight of Pt nanoparticles). Pt-SWNTs prepared by the Langmuir-Blodgett (LB) technique exhibited the highest Pt/SWNT ratio and also the best hydrogen uptake. © 2011 American Chemical Society

  2. Chemically fixed p-n heterojunctions for polymer electronics by means of covalent B-F bond formation

    Science.gov (United States)

    Hoven, Corey V.; Wang, Huiping; Elbing, Mark; Garner, Logan; Winkelhaus, Daniel; Bazan, Guillermo C.

    2010-03-01

    Widely used solid-state devices fabricated with inorganic semiconductors, including light-emitting diodes and solar cells, derive much of their function from the p-n junction. Such junctions lead to diode characteristics and are attained when p-doped and n-doped materials come into contact with each other. Achieving bilayer p-n junctions with semiconducting polymers has been hindered by difficulties in the deposition of thin films with independent p-doped and n-doped layers. Here we report on how to achieve permanently fixed organic p-n heterojunctions by using a cationic conjugated polyelectrolyte with fluoride counteranions and an underlayer composed of a neutral conjugated polymer bearing anion-trapping functional groups. Application of a bias leads to charge injection and fluoride migration into the neutral layer, where irreversible covalent bond formation takes place. After the initial charging and doping, one obtains devices with no delay in the turn on of light-emitting electrochemical behaviour and excellent current rectification. Such devices highlight how mobile ions in organic media can open opportunities to realize device structures in ways that do not have analogies in the world of silicon and promise new opportunities for integrating organic materials within technologies now dominated by inorganic semiconductors.

  3. INVESTIGATING THE fFORMATION OF INTERMETALLIC COMPOUNDS AND THE VARIATION OF BOND STRENGTH BETWEEN Al-Cu LAYERS AFTER ANNEALING IN PRESENCE OF NICKEL BETWEEN LAYERS

    Directory of Open Access Journals (Sweden)

    A. Shabani

    2016-06-01

    Full Text Available In the present study, the effect of post-rolling annealing heat treatment on the formation of intermetallic compounds between Al-Cu strips, in the presence of nickel coating on the Cu strips, was investigated. In addition, the effect of post-rolling annealing and intermetallic compounds on the bond strength of Al-Cu strips was evaluated. In order to prepare samples, Cu strips were coated with nickel by electroplating process. After surface preparing, Cu strips were placed between two Al strips and roll bonded. This method is used for producing Al-Ni-Cu composites. Then the samples were annealed at 773K for 2 h. The formation of intermetallic compounds was studied using energy dispersive spectroscopy (EDS and X-ray diffraction (XRD. Also, in order to investigate bond strength of Al-Cu after post-rolling annealing heat treatment, samples were produced using nickel powder and nickel coating. Then bond strength of strips was investigated using peeling test. The results revealed that by post-rolling annealing of layers, the bond strength between Al-Cu strips decreases dramatically.

  4. Standard Gibbs energies of formation and equilibrium constants from ab-initio calculations: Covalent dimerization of NO2 and synthesis of NH3

    International Nuclear Information System (INIS)

    Awasthi, Neha; Ritschel, Thomas; Lipowsky, Reinhard; Knecht, Volker

    2013-01-01

    Highlights: • ΔG and K eq for NO 2 dimerization and NH 3 synthesis calculated via ab-initio methods. • Vis-á-vis experiments, W1 and CCSD(T) are accurate and G3B3 also does quite well. • CBS-APNO most accurate for NH 3 reaction but shows limitations in modeling NO 2 . • Temperature dependence of ΔG and K eq is calculated for the NH 3 reaction. • Good agreement of calculated K eq with experiments and the van’t Hoff approximation. -- Abstract: Standard quantum chemical methods are used for accurate calculation of thermochemical properties such as enthalpies of formation, entropies and Gibbs energies of formation. Equilibrium reactions are widely investigated and experimental measurements often lead to a range of reaction Gibbs energies and equilibrium constants. It is useful to calculate these equilibrium properties from quantum chemical methods in order to address the experimental differences. Furthermore, most standard calculation methods differ in accuracy and feasibility of the system size. Hence, a systematic comparison of equilibrium properties calculated with different numerical algorithms would provide a useful reference. We select two well-known gas phase equilibrium reactions with small molecules: covalent dimer formation of NO 2 (2NO 2 ⇌ N 2 O 4 ) and the synthesis of NH 3 (N 2 + 3 H 2 ⇌ 2NH 3 ). We test four quantum chemical methods denoted by G3B3, CBS-APNO, W1 and CCSD(T) with aug-cc-pVXZ basis sets (X = 2, 3, and 4), to obtain thermochemical data for NO 2 , N 2 O 4 , and NH 3 . The calculated standard formation Gibbs energies Δ f G° are used to calculate standard reaction Gibbs energies Δ r G° and standard equilibrium constants K eq for the two reactions. Standard formation enthalpies Δ f H° are calculated in a more reliable way using high-level methods such as W1 and CCSD(T). Standard entropies S° for the molecules are calculated well within the range of experiments for all methods, however, the values of standard formation

  5. A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

    International Nuclear Information System (INIS)

    Wang, Qiang; Gao, Jun; Zhang, Dongju; Liu, Chengbu

    2015-01-01

    Highlights: • We theoretical studied peptide bond formation reaction mechanism with two water molecules. • The first water molecule can decrease the reaction barriers by forming hydrogen bonds. • The water molecule mediated three-proton transfer mechanism is the favorable mechanism. • Our calculation supports the two-step and eight membered ring mechanism. - Abstract: The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9′ and H15′ in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome

  6. CS Bond formation by

    Indian Academy of Sciences (India)

    2017-02-02

    Feb 2, 2017 ... a thiol substituent at position-2 of the quinazoline ring. ... coupling reactions represent great contribution to the recent growth of organic synthesis.2 ... Difficulties in C-S ...... Experimental Advances (Amsterdam: Elsevier) 19; (b).

  7. Molecular study on the carAB operon reveals that carB gene is required for swimming and biofilm formation in Xanthomonas citri subsp. citri.

    Science.gov (United States)

    Zhuo, Tao; Rou, Wei; Song, Xue; Guo, Jing; Fan, Xiaojing; Kamau, Gicharu Gibson; Zou, Huasong

    2015-10-23

    The carA and carB genes code the small and large subunits of carbamoyl-phosphate synthase (CPS) that responsible for arginine and pyrimidine production. The purpose of this work was to study the gene organization and expression pattern of carAB operon, and the biological functions of carA and carB genes in Xanthomonas citri subsp. citri. RT-PCR method was employed to identify the full length of carAB operon transcript in X. citri subsp. citri. The promoter of carAB operon was predicted and analyzed its activity by fusing a GUS reporter gene. The swimming motility was tested on 0.25% agar NY plates with 1% glucose. Biofilm was measured by cell adhesion to polyvinyl chloride 96-well plate. The results indicated that carAB operon was composed of five gene members carA-orf-carB-greA-rpfE. A single promoter was predicted from the nucleotide sequence upstream of carAB operon, and its sensitivity to glutamic acid, uracil and arginine was confirmed by fusing a GUS reporter gene. Deletion mutagenesis of carB gene resulted in reduced abilities in swimming on soft solid media and in forming biofilm on polystyrene microtiter plates. From these results, we concluded that carAB operon was involved in multiple biological processes in X. citri subsp. citri.

  8. The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana.

    Science.gov (United States)

    Ehlers, Katrin; Bhide, Amey S; Tekleyohans, Dawit G; Wittkop, Benjamin; Snowdon, Rod J; Becker, Annette

    2016-01-01

    Seed formation is a pivotal process in plant reproduction and dispersal. It begins with megagametophyte development in the ovule, followed by fertilization and subsequently coordinated development of embryo, endosperm, and maternal seed coat. Two closely related MADS-box genes, SHATTERPROOF 1 and 2 (SHP1 and SHP2) are involved in specifying ovule integument identity in Arabidopsis thaliana. The MADS box gene ARABIDOPSIS BSISTER (ABS or TT16) is required, together with SEEDSTICK (STK) for the formation of endothelium, part of the seed coat and innermost tissue layer formed by the maternal plant. Little is known about the genetic interaction of SHP1 and SHP2 with ABS and the coordination of endosperm and seed coat development. In this work, mutant and expression analysis shed light on this aspect of concerted development. Triple tt16 shp1 shp2 mutants produce malformed seedlings, seed coat formation defects, fewer seeds, and mucilage reduction. While shp1 shp2 mutants fail to coordinate the timely development of ovules, tt16 mutants show less peripheral endosperm after fertilization. Failure in coordinated division of the innermost integument layer in early ovule stages leads to inner seed coat defects in tt16 and tt16 shp1 shp2 triple mutant seeds. An antagonistic action of ABS and SHP1/SHP2 is observed in inner seed coat layer formation. Expression analysis also indicates that ABS represses SHP1, SHP2, and FRUITFUL expression. Our work shows that the evolutionary conserved Bsister genes are required not only for endothelium but also for endosperm development and genetically interact with SHP1 and SHP2 in a partially antagonistic manner.

  9. The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Katrin Ehlers

    Full Text Available Seed formation is a pivotal process in plant reproduction and dispersal. It begins with megagametophyte development in the ovule, followed by fertilization and subsequently coordinated development of embryo, endosperm, and maternal seed coat. Two closely related MADS-box genes, SHATTERPROOF 1 and 2 (SHP1 and SHP2 are involved in specifying ovule integument identity in Arabidopsis thaliana. The MADS box gene ARABIDOPSIS BSISTER (ABS or TT16 is required, together with SEEDSTICK (STK for the formation of endothelium, part of the seed coat and innermost tissue layer formed by the maternal plant. Little is known about the genetic interaction of SHP1 and SHP2 with ABS and the coordination of endosperm and seed coat development. In this work, mutant and expression analysis shed light on this aspect of concerted development. Triple tt16 shp1 shp2 mutants produce malformed seedlings, seed coat formation defects, fewer seeds, and mucilage reduction. While shp1 shp2 mutants fail to coordinate the timely development of ovules, tt16 mutants show less peripheral endosperm after fertilization. Failure in coordinated division of the innermost integument layer in early ovule stages leads to inner seed coat defects in tt16 and tt16 shp1 shp2 triple mutant seeds. An antagonistic action of ABS and SHP1/SHP2 is observed in inner seed coat layer formation. Expression analysis also indicates that ABS represses SHP1, SHP2, and FRUITFUL expression. Our work shows that the evolutionary conserved Bsister genes are required not only for endothelium but also for endosperm development and genetically interact with SHP1 and SHP2 in a partially antagonistic manner.

  10. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth.

    Science.gov (United States)

    Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

    2015-08-17

    Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides-oligomers with a combination of ester and amide linkages-in model prebiotic reactions that are driven by wet-cool/dry-hot cycles. Through a combination of ester-amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Visible Light Driven Nanosecond Bromide Oxidation by a Ru Complex with Subsequent Br-Br Bond Formation.

    Science.gov (United States)

    Li, Guocan; Ward, William M; Meyer, Gerald J

    2015-07-08

    Visible light excitation of [Ru(deeb)(bpz)2](2+) (deeb = 4,4'-diethylester-2,2'-bipyridine; bpz = 2,2'-bipyrazine), in Br(-) acetone solutions, led to the formation of Br-Br bonds in the form of dibromide, Br2(•-). This light reactivity stores ∼1.65 eV of free energy for milliseconds. Combined (1)H NMR, UV-vis and photoluminescence measurements revealed two distinct mechanisms. The first involves diffusional quenching of the excited state by Br(-) with a rate constant of (8.1 ± 0.1) × 10(10) M(-1) s(-1). At high Br(-) concentrations, an inner-sphere pathway is dominant that involves the association of Br(-), most likely with the 3,3'-H atoms of a bpz ligand, before electron transfer from Br(-) to the excited state, ket = (2.5 ± 0.3) × 10(7) s(-1). In both mechanisms, the direct photoproduct Br(•) subsequently reacts with Br(-) to yield dibromide, Br(•) + Br(-) → Br2(•-). Under pseudo-first-order conditions, this occurs with a rate constant of (1.1 ± 0.4) × 10(10) M(-1) s(-1) that was, within experimental error, the same as that measured when Br(•) were generated with ultraviolet light. Application of Marcus theory to the sensitized reaction provided an estimate of the Br(•) formal reduction potential E(Br(•)/Br(-)) = 1.22 V vs SCE in acetone, which is about 460 mV less positive than the accepted value in H2O. The results demonstrate that Br(-) oxidation by molecular excited states can be rapid and useful for solar energy conversion.

  12. Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

    Science.gov (United States)

    Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

    2001-01-26

    Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

  13. Effect of interlayer configurations on joint formation in TLP bonding of Ti-6AI-4V to Mg-AZ31

    International Nuclear Information System (INIS)

    Atieh, A. M.; Khan, T. I.

    2013-01-01

    In this research work, the transient liquid phase (TLP) bonding process was utilized to fabricate joints using thin (20 micro m) nickel and copper foils placed between two bonding surfaces to help facilitate joint formation. Two joint configurations were investigated, first, Ti-6Al-4V/CuNi/Mg-AZ31 and second, Ti-6Al-4V/NiCu/Mg-AZ3L The effect of bonding time on microstructural developments across the joint and the changes in mechanical properties were studied as a function of bonding temperature and pressure. The bonded specimens were examined by metallographic analysis, scanning electron microscopy (SEM), and X-ray diffraction (XRD). In both cases, intermetallic phase of CuMg/sub 2/ and Mg/sub 3/AlNi/sub 2/ was observed inside the joint region. The results show that joint shear strengths for the Ti-6Al-4V/CuNi/Mg-AZ31 setup produce joints with shear strength of 57 MPa compared to 27MPa for joints made using the Ti-6Al-4V/NiCu/Mg-AZ31 layer arrangement. (author)

  14. Effect of interlayer configurations on joint formation in TLP bonding of Ti-6Al-4V to Mg-AZ31

    International Nuclear Information System (INIS)

    Atieh, A M; Khan, T I

    2014-01-01

    In this research work, the transient liquid phase (TLP) bonding process was utilized to fabricate joints using thin (20μm) nickel and copper foils placed between two bonding surfaces to help facilitate joint formation. Two joint configurations were investigated, first, Ti-6Al-4V/CuNi/Mg-AZ31 and second, Ti-6Al-4V/NiCu/Mg-AZ3L The effect of bonding time on microstructural developments across the joint and the changes in mechanical properties were studied as a function of bonding temperature and pressure. The bonded specimens were examined by metallographic analysis, scanning electron microscopy (SEM), and X-ray diffraction (XRD). In both cases, intermetallic phase of CuMg 2 and Mg 3 AlNi 2 was observed inside the joint region. The results show that joint shear strengths for the Ti-6Al-4V/CuNi/Mg-AZ31 setup produce joints with shear strength of 57 MPa compared to 27MPa for joints made using the Ti-6Al-4V/NiCu/Mg-AZ31 layer arrangement

  15. Covalent bonds and their crucial effects on pseudogap formation in α-Al(Mn,Re)Si icosahedral quasicrystalline approximant

    International Nuclear Information System (INIS)

    Kirihara, K.; Nagata, T.; Kimura, K.; Kato, K.; Takata, M.; Nishibori, E.; Sakata, M.

    2003-01-01

    X-ray charge densities of Al-based icosahedral quasicrystalline approximant crystals α-AlReSi, α-AlMnSi, and Al 12 Re were observed by a combination of the maximum entropy method with the Rietveld method. We successfully obtained the clear images of interatomic covalent bonds between Al and transition metals (Mn, Re) and those in the Al (or Si) icosahedron in Mackay icosahedral clusters of both α-AlReSi and α-AlMnSi approximant crystals. The bonding nature of the three kinds of glue atom sites connecting Mackay icosahedral clusters was also clarified. This covalent bonding nature should strongly relate with the enhancement of the electron density-of-states pseudogap near the Fermi level. In addition, the interatomic covalent bonds of α-AlReSi are stronger than those of α-AlMnSi. This fact leads to the low effective carrier density of α-AlReSi in comparison with that of α-AlMnSi. Unlike the covalent bonding nature of an icosahedron in α-AlReSi and α-AlMnSi crystals, the Al icosahedron with an Re center atom exhibits no Al-Al interatomic covalent bonds in the Al 12 Re crystal. The tendency for metallic-covalent bonding conversion in the Al icosahedron, which is related to the atom site occupancy of the icosahedral cluster center, is also strongly supported

  16. Bond breaking and bond formation: how electron correlation is captured in many-body perturbation theory and density-functional theory.

    Science.gov (United States)

    Caruso, Fabio; Rohr, Daniel R; Hellgren, Maria; Ren, Xinguo; Rinke, Patrick; Rubio, Angel; Scheffler, Matthias

    2013-04-05

    For the paradigmatic case of H(2) dissociation, we compare state-of-the-art many-body perturbation theory in the GW approximation and density-functional theory in the exact-exchange plus random-phase approximation (RPA) for the correlation energy. For an unbiased comparison and to prevent spurious starting point effects, both approaches are iterated to full self-consistency (i.e., sc-RPA and sc-GW). The exchange-correlation diagrams in both approaches are topologically identical, but in sc-RPA they are evaluated with noninteracting and in sc-GW with interacting Green functions. This has a profound consequence for the dissociation region, where sc-RPA is superior to sc-GW. We argue that for a given diagrammatic expansion, sc-RPA outperforms sc-GW when it comes to bond breaking. We attribute this to the difference in the correlation energy rather than the treatment of the kinetic energy.

  17. Nickel-Catalyzed C-S Bond Formation via Decarbonylative Thioetherification of Esters, Amides and Intramolecular Recombination Fragment Coupling of Thioesters

    KAUST Repository

    Lee, Shao-Chi

    2018-01-15

    A nickel catalyzed cross-coupling protocol for the straightforward C-S bond formation has been developed. Various mercaptans and a wide range of ester and amide substrates bearing various substituents were tolerated in this process which afforded products in good to excellent yields. Furthermore, an intramolecular protocol for the synthesis of thioethers starting from thioesters has been developed. The utility of this protocol has been demonstrated in the synthesis of benzothiophene on the bench top.

  18. Nickel-Catalyzed C-S Bond Formation via Decarbonylative Thioetherification of Esters, Amides and Intramolecular Recombination Fragment Coupling of Thioesters

    KAUST Repository

    Lee, Shao-Chi; Liao, Hsuan-Hung; Chatupheeraphat, Adisak; Rueping, Magnus

    2018-01-01

    A nickel catalyzed cross-coupling protocol for the straightforward C-S bond formation has been developed. Various mercaptans and a wide range of ester and amide substrates bearing various substituents were tolerated in this process which afforded products in good to excellent yields. Furthermore, an intramolecular protocol for the synthesis of thioethers starting from thioesters has been developed. The utility of this protocol has been demonstrated in the synthesis of benzothiophene on the bench top.

  19. An ab initio and AIM investigation into the hydration of 2-thioxanthine

    Directory of Open Access Journals (Sweden)

    Fossey John S

    2010-03-01

    Full Text Available Abstract Background Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX, a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexes. Results Hydrogen-bond (H-bond interactions in 1:1 complexes of 2TX with water are studied at the MP2/6-311G(d, p and B3LYP/6-311G(d, p levels. Seven 2TX...H2O hydrogen bonded complexes have been theoretically identified and reported for the first time. The proton affinities (PAs of the O, S, and N atoms and deprotonantion enthalpies (DPEs of different N-H bonds in 2TX are calculated, factors surrounding why the seven complexes have different hydrogen bond energies are discussed. The theoretical infrared and NMR spectra of hydrated 2TX complexes are reported to probe the characteristics of the proposed H-bonds. An improper blue-shifting H-bond with a shortened C-H bond was found in one case. NBO and AIM analysis were carried out to explain the formation of improper blue-shifting H-bonds, and the H-bonding characteristics are discussed. Conclusion 2TX can interact with water by five different H-bonding regimes, N-H...O, O-H...N, O-H...O, O-H...S and C-H...O, all of which are medium strength hydrogen bonds. The most stable H-bond complex has a closed structure with two hydrogen bonds (N(7-H...O and O-H...O, whereas the least stable one has an open structure with one H-bond. The interaction energies of the studied complexes are correlated to the PA and DPE involved in H-bond formation. After formation of H-bonds, the calculated IR and NMR spectra of the 2TX-water complexes change greatly, which serves to identify the hydration of 2TX.

  20. C-H Bond Functionalization via Hydride Transfer: Formation of α-Arylated Piperidines and 1,2,3,4-Tetrahydroisoquinolines via Stereoselective Intramolecular Amination of Benzylic C-H Bonds

    OpenAIRE

    Vadola, Paul A.; Carrera, Ignacio; Sames, Dalibor

    2012-01-01

    We here report a study of the intramolecular amination of sp3 C-H bonds via the hydride transfer cyclization of N-tosylimines (HT-amination). In this transformation, 5-aryl-aldehydes are subjected to N-toluenesulfonamide in the presence of BF3•OEt2 to effect imine formation and HT-cyclization, leading to 2-aryl-piperidines and 3-aryl-1,2,3,4-tetrahydroisoquinolines in a one-pot procedure. We examined the reactivity of a range of aldehyde substrates as a function of their conformational flexib...

  1. Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Michael C., E-mail: mccarthy@cfa.harvard.edu; Martinez, Oscar; Crabtree, Kyle N.; Martin-Drumel, Marie-Aline [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, USA and School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138 (United States); McGuire, Brett A. [National Radio Astronomy Observatory, Charlottesville, Virginia 22901 (United States); Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, USA and School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138 (United States); Stanton, John F. [Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712-0165 (United States)

    2016-03-28

    HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO{sub 2} reaction represents the final step for the production of CO{sub 2} in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO{sub 2} in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO{sub 2}. Using isotopically labelled precursors, the OH + C{sup 18}O reaction predominately yields HOC{sup 18}O for both isomers, but H{sup 18}OCO is observed as well, typically at the level of 10%-20% that of HOC{sup 18}O; the opposite propensity is found for the {sup 18}OH + CO reaction. DO + C{sup 18}O yields similar ratios between DOC{sup 18}O and D{sup 18}OCO as those found for OH + C{sup 18}O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO{sub 2}, which, at the high pressure of our gas expansion, can readily occur. The large {sup 13}C Fermi-contact term (a{sub F}) for trans- and cis-HO{sup 13}CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers.

  2. Identification and cloning of an NADPH-dependent hydroxycinnamoyl-CoA double bond reductase involved in dihydrochalcone formation in Malus×domestica Borkh.

    Science.gov (United States)

    Ibdah, Mwafaq; Berim, Anna; Martens, Stefan; Valderrama, Andrea Lorena Herrera; Palmieri, Luisa; Lewinsohn, Efraim; Gang, David R

    2014-11-01

    The apple tree (Malus sp.) is an agriculturally and economically important source of food and beverages. Many of the health beneficial properties of apples are due to (poly)phenolic metabolites that they contain, including various dihydrochalcones. Although many of the genes and enzymes involved in polyphenol biosynthesis are known in many plant species, the specific reactions that lead to the biosynthesis of the dihydrochalcone precursor, p-dihydrocoumaroyl-CoA (3), are unknown. To identify genes involved in the synthesis of these metabolites, existing genome databases of the Rosaceae were screened for apple genes with significant sequence similarity to Arabidopsis alkenal double bond reductases. Herein described are the isolation and characterization of a Malus hydroxycinnamoyl-CoA double bond reductase, which catalyzed the NADPH-dependent reduction of p-coumaroyl-CoA and feruloyl-CoA to p-dihydrocoumaroyl-CoA and dihydroferuloyl-CoA, respectively. Its apparent Km values for p-coumaroyl-CoA, feruloyl-CoA and NADPH were 96.6, 92.9 and 101.3μM, respectively. The Malus double bond reductase preferred feruloyl-CoA to p-coumaroyl-CoA as a substrate by a factor of 2.1 when comparing catalytic efficiencies in vitro. Expression analysis of the hydroxycinnamoyl-CoA double bond reductase gene revealed that its transcript levels showed significant variation in tissues of different developmental stages, but was expressed when expected for involvement in dihydrochalcone formation. Thus, the hydroxycinnamoyl-CoA double bond reductase appears to be responsible for the reduction of the α,β-unsaturated double bond of p-coumaroyl-CoA, the first step of dihydrochalcone biosynthesis in apple tissues, and may be involved in the production of these compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Catalytic-site mapping of pyruvate formate lyase. Hypophosphite reaction on the acetyl-enzyme intermediate affords carbon-phosphorus bond synthesis (1-hydroxyethylphosphonate).

    Science.gov (United States)

    Plaga, W; Frank, R; Knappe, J

    1988-12-15

    Pyruvate formate-lyase of Escherichia coli cells, a homodimeric protein of 2 x 85 kDa, is distinguished by the property of containing a stable organic free radical (g = 2.0037) in its resting state. The enzyme (E-SH) achieves pyruvate conversion to acetyl-CoA via two distinct half-reactions (E-SH + pyruvate in equilibrium E-S-acetyl + formate; E-S-acetyl + CoA in equilibrium E-SH + acetyl-CoA), the first of which has been proposed to involve reversible homolytic carbon-carbon bond cleavage [J. Knappe et al. (1984) Proc. Natl Acad. Sci. USA 81, 1332-1335]. Present studies identified Cys-419 as the covalent-catalytic cysteinyl residue via CNBr fragmentation of E-S-[14C]acetyl and radio-sequencing of the isolated peptide CB-Ac (amino acid residues 406-423). Reaction of the formate analogue hypophosphite with E-S-acetyl was investigated and found to produce 1-hydroxyethylphosphonate with a thioester linkage to the adjacent Cys-418. The structure was determined from the chymotryptic peptide CH-P (amino acid residues 415-425), using 31P-NMR spectroscopy (delta = 44 ppm) and by chemical characterisation through degradation into 1-hydroxyethylphosphonate with phosphodiesterase or bromine. This novel P-C-bond synthesis involves the enzyme-based free radical and is proposed to resemble the physiological C-C-bond synthesis (pyruvate production) from formate and E-S-acetyl. These findings are interpreted as proof of a radical mechanism for the action of pyruvate formate-lyase. The central Cys-418/Cys-419 pair of the active site shows a distinctive thiolate property even in the inactive (nonradical) form of the enzyme, as determined using an iodoacetate probe.

  4. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  5. A 19F NMR study of C-I....pi- halogen bonding

    DEFF Research Database (Denmark)

    Hauchecorne, Dieter; vand er Veken, Benjamin J.; Herrebout, Wouter A.

    2011-01-01

    The formation of halogen bonded complexes between toluene-d8 and the perfluoroiodopropanes 1-C3F7I and 2-C3F7I has been investigated using 19F NMR spectroscopy. For both Lewis acids, evidence was found for the formation of a C–I⋯π halogen bonded complex. The complex formed is a 1:1 type. Using sp...... results are supported by ab initio calculations at the B3LYP-PCM/6-311++G(d,p) + LanL2DZ∗ level....

  6. Dominant negative phenotype of Bacillus thuringiensis Cry1Ab, Cry11Aa and Cry4Ba mutants suggest hetero-oligomer formation among different Cry toxins.

    NARCIS (Netherlands)

    Carmona, D.; Rodriguez-Almazan, C.; Munoz-Garay, C.; Portugal, L.; Perez, C.; Maagd, de R.A.; Bakker, P.; Soberon, M.; Bravo, A.

    2011-01-01

    Background - Bacillus thuringiensis Cry toxins are used worldwide in the control of different insect pests important in agriculture or in human health. The Cry proteins are pore-forming toxins that affect the midgut cell of target insects. It was shown that non-toxic Cry1Ab helix a-4 mutants had a

  7. DNA degradation by bleomycin: evidence for 2'R-proton abstraction and for C-O bond cleavage accompanying base propenal formation

    International Nuclear Information System (INIS)

    Ajmera, S.; Wu, J.C.; Worth, L. Jr.; Rabow, L.E.; Stubbe, J.; Kozarich, J.W.

    1986-01-01

    Reaction of poly(dA-[2'S- 3 H]dU) with activated bleomycin yields [ 3 H] uracil propenal that completely retains the tritium label. In contrast, the authors have previously shown that reaction of poly(dA-[2'R- 3 H]dU) with activated bleomycin affords unlabeled uracil propenal. They have also prepared both cis- and trans-thymine propenals by chemical synthesis and have observed that the trans isomer is the exclusive product of the bleomycin reaction. Moreover, the cis isomer was found to be stable to the conditions of bleomycin-induced DNA degradation. Taken together, these results establish that the formation of trans-uracil propenal occurs via an anti-elimination mechanism with the stereospecific abstraction of the 2R proton. The question of phosphodiester bond cleavage during base propenal formation has also been addressed by the analysis of the fate of oxygen-18 in poly(dA-[3'- 18 O]dT) upon reaction with activated bleomycin. The 5'-monophosphate oligonucleotide ends produced from thymine propenal formation have been converted to inorganic phosphate by the action of alkaline phosphatase, and the phosphate has been analyzed for 18 O content by 31 P NMR spectroscopy. The oxygen-18 is retained in the inorganic phosphate, establishing that the formation of thymine propenal by activated bleomycin proceeds with C-O bond cleavage at the 3-position

  8. Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

    Science.gov (United States)

    Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

    2016-05-01

    In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

  9. Biofilm formation on stainless steel and gold wires for bonded retainers in vitro and in vivo and their susceptibility to oral antimicrobials.

    Science.gov (United States)

    Jongsma, Marije A; Pelser, Floris D H; van der Mei, Henny C; Atema-Smit, Jelly; van de Belt-Gritter, Betsy; Busscher, Henk J; Ren, Yijin

    2013-05-01

    Bonded retainers are used in orthodontics to maintain treatment result. Retention wires are prone to biofilm formation and cause gingival recession, bleeding on probing and increased pocket depths near bonded retainers. In this study, we compare in vitro and in vivo biofilm formation on different wires used for bonded retainers and the susceptibility of in vitro biofilms to oral antimicrobials. Orthodontic wires were exposed to saliva, and in vitro biofilm formation was evaluated using plate counting and live/dead staining, together with effects of exposure to toothpaste slurry alone or followed by antimicrobial mouthrinse application. Wires were also placed intra-orally for 72 h in human volunteers and undisturbed biofilm formation was compared by plate counting and live/dead staining, as well as by denaturing gradient gel electrophoresis for compositional differences in biofilms. Single-strand wires attracted only slightly less biofilm in vitro than multi-strand wires. Biofilms on stainless steel single-strand wires however, were much more susceptible to antimicrobials from toothpaste slurries and mouthrinses than on single-strand gold wires and biofilms on multi-strand wires. Also, in vivo significantly less biofilm was found on single-strand than on multi-strand wires. Microbial composition of biofilms was more dependent on the volunteer involved than on wire type. Biofilms on single-strand stainless steel wires attract less biofilm in vitro and are more susceptible to antimicrobials than on multi-strand wires. Also in vivo, single-strand wires attract less biofilm than multi-strand ones. Use of single-strand wires is preferred over multi-strand wires, not because they attract less biofilm, but because biofilms on single-strand wires are not protected against antimicrobials as in crevices and niches as on multi-strand wires.

  10. Bond formation in hafnium atom implantation into SiC induced by high-energy electron irradiation

    International Nuclear Information System (INIS)

    Yasuda, H.; Mori, H.; Sakata, T.; Naka, M.; Fujita, H.

    1992-01-01

    Bilayer films of Hf (target atoms)/α-SiC (substrate) were irradiated with 2 MeV electrons in an ultra-high voltage electron microscope (UHVEM), with the electron beam incident on the hafnium layer. As a result of the irradiation, hafnium atoms were implanted into the SiC substrate. Changes in the microstructure and valence electronic states associated with the implantation were studied by a combination of UHVEM and Auger valence electron spectroscopy. The implantation process is summarized as follows. (1) Irradiation with 2 MeV electrons first induces a crystalline-to-amorphous transition in α-SiC. (2) Hafnium atoms which have been knocked-off from the hafnium layer by collision with the 2 MeV electrons are implanted into the resultant amorphous SiC. (3) The implanted hafnium atoms make preferential bonding to carbon atoms. (4) With continued irradiation, the hafnium atoms repeat the displacement along the beam direction and the subsequent bonding with the dangling hybrids of carbon and silicon. The repetition of the displacement and subsequent bonding lead to the deep implantation of hafnium atoms into the SiC substrate. It is concluded that implantation successfully occurs when the bond strength between a constituent atom of a substrate and an injected atom is stronger than that between constituent atoms of a substrate. (Author)

  11. Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Wen-Sheng, E-mail: wsxu@uchicago.edu [James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Freed, Karl F., E-mail: freed@uchicago.edu [James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Department of Chemistry, The University of Chicago, Chicago, Illinois 60637 (United States)

    2016-06-07

    Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called “stickers”). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics. The original LCT for self-assembly of telechelic polymers considers a model of fully flexible linear chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)], while our recent work introduces a significant improvement to the LCT by including a description of chain semiflexibility for the bonds within each individual telechelic chain [W.-S. Xu and K. F. Freed, J. Chem. Phys. 143, 024901 (2015)], but the physically associative (or called “sticky”) bonds between the ends of the telechelics are left as fully flexible. Motivated by the ubiquitous presence of steric constraints on the association of real telechelic polymers that impart an additional degree of bond stiffness (or rigidity), the present paper further extends the LCT to permit the sticky bonds to be semiflexible but to have a stiffness differing from that within each telechelic chain. An analytical expression for the Helmholtz free energy is provided for this model of linear telechelic polymer melts, and illustrative calculations demonstrate the significant influence of the stiffness of the sticky bonds on the self-assembly and thermodynamics of telechelic polymers. A brief discussion is also provided for the impact of self-assembly on glass-formation by combining the LCT description for this extended model of telechelic polymers with

  12. Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds

    International Nuclear Information System (INIS)

    Xu, Wen-Sheng; Freed, Karl F.

    2016-01-01

    Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called “stickers”). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics. The original LCT for self-assembly of telechelic polymers considers a model of fully flexible linear chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)], while our recent work introduces a significant improvement to the LCT by including a description of chain semiflexibility for the bonds within each individual telechelic chain [W.-S. Xu and K. F. Freed, J. Chem. Phys. 143, 024901 (2015)], but the physically associative (or called “sticky”) bonds between the ends of the telechelics are left as fully flexible. Motivated by the ubiquitous presence of steric constraints on the association of real telechelic polymers that impart an additional degree of bond stiffness (or rigidity), the present paper further extends the LCT to permit the sticky bonds to be semiflexible but to have a stiffness differing from that within each telechelic chain. An analytical expression for the Helmholtz free energy is provided for this model of linear telechelic polymer melts, and illustrative calculations demonstrate the significant influence of the stiffness of the sticky bonds on the self-assembly and thermodynamics of telechelic polymers. A brief discussion is also provided for the impact of self-assembly on glass-formation by combining the LCT description for this extended model of telechelic polymers with

  13. Preparation of catalytically active, covalent α-polylysine-enzyme conjugates via UV/vis-quantifiable bis-aryl hydrazone bond formation.

    Science.gov (United States)

    Grotzky, Andrea; Manaka, Yuichi; Kojima, Taisuke; Walde, Peter

    2011-01-10

    Covalent UV/vis-quantifiable bis-aryl hydrazone bond formation was investigated for the preparation of conjugates between α-poly-d-lysine (PDL) and either α-chymotrypsin (α-CT) or horseradish peroxidase (HRP). PDL and the enzymes were first modified via free amino groups with the linking reagents succinimidyl 6-hydrazinonicotinate acetone hydrazone (S-HyNic, at pH 7.6) and succinimidyl 4-formylbenzoate (S-4FB, at pH 7.2), respectively. The modified PDL and enzymes were then conjugated at pH 4.7, whereby polymer chains carrying several enzymes were obtained. Kinetics of the bis-aryl hydrazone bond formation was investigated spectrophotometrically at 354 nm. Retention of the enzymatic activity after conjugate formation was confirmed by using the substrates N-succinimidyl-l-Ala-l-Ala-l-Pro-l-Phe-p-nitroanilide (for α-CT) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS, for HRP). Thus, not only a mild and efficient preparation and convenient quantification of a conjugate between the polycationic α-polylysine and enzymes could be shown, but also the complete preservation of the enzymatic activity.

  14. Formation of cyclobutanones by the photolytic reaction of (CO)/sub 5/Cr/double bond/C(OMe)Me with electron-rich olefins

    Energy Technology Data Exchange (ETDEWEB)

    Sierra, M.A.; Hegedus, L.S.

    1989-03-15

    Recent research has centered on the development of useful organic synthetic methodology based on the photolytic reactions of chromium Fischer carbene complexes, particularly in regards to the development of new /beta/-lactam syntheses. In the course of these studies it became evident that photolysis of chromium-carbene complexes resulted in the reversible production of chromium-ketene complexes, by a photochemically driven CO insertion into the chromium-carbene carbon double bond and that this unstable intermediate was responsible for /beta/-lactam formation.

  15. A novel stibacarbaborane cluster with adjacent antimony atoms exhibiting unique pnictogen bond formation that dominates its crystal packing.

    Science.gov (United States)

    Holub, Josef; Melichar, Petr; Růžičková, Zdeňka; Vrána, Jan; Wann, Derek A; Fanfrlík, Jindřich; Hnyk, Drahomír; Růžička, Aleš

    2017-10-17

    We have prepared nido-7,8,9,11-Sb 2 C 2 B 7 H 9 , the first cluster with simultaneous Sb-B, Sb-C and Sb-Sb atom pairs with interatomic separations with magnitudes that approach the respective sums of covalent radii. However, the length of the Sb-Sb separation in this cluster is slightly less than the sum of the covalent radii. Quantum chemical analysis has revealed that the crystal packing of nido-7,8,9,11-Sb 2 C 2 B 7 H 9 is predominantly dictated by pnictogen (Pn) bonding, an unconventional σ-hole interaction. Indeed, the interaction energy of a very strong Sb 2 H-B Pn-bond in the nido-7,8,9,11-Sb 2 C 2 B 7 H 9 dimer exceeds -6.0 kcal mol -1 . This is a very large value and is comparable to the strengths of known Pn-bonds in Cl 3 Pnπ complexes (Pn = As, Sb).

  16. Formation of base triplets by non-Watson-Crick bonds mediates homologous recognition in RecA recombination filaments.

    OpenAIRE

    Rao, B J; Radding, C M

    1994-01-01

    Whereas complementary strands of DNA recognize one another by forming Watson-Crick base pairs, the way in which RecA protein enables a single strand to recognize homology in duplex DNA has remained unknown. Recent experiments, however, have shown that a single plus strand in the RecA filament can recognize an identical plus strand via bonds that, by definition, are non-Watson-Crick. In experiments reported here, base substitutions had the same qualitative and quantitative effects on the pairi...

  17. A general approach to intermolecular carbonylation of arene C-H bonds to ketones through catalytic aroyl triflate formation

    Science.gov (United States)

    Garrison Kinney, R.; Tjutrins, Jevgenijs; Torres, Gerardo M.; Liu, Nina Jiabao; Kulkarni, Omkar; Arndtsen, Bruce A.

    2018-02-01

    The development of metal-catalysed methods to functionalize inert C-H bonds has become a dominant research theme in the past decade as an approach to efficient synthesis. However, the incorporation of carbon monoxide into such reactions to form valuable ketones has to date proved a challenge, despite its potential as a straightforward and green alternative to Friedel-Crafts reactions. Here we describe a new approach to palladium-catalysed C-H bond functionalization in which carbon monoxide is used to drive the generation of high-energy electrophiles. This offers a method to couple the useful features of metal-catalysed C-H functionalization (stable and available reagents) and electrophilic acylations (broad scope and selectivity), and synthesize ketones simply from aryl iodides, CO and arenes. Notably, the reaction proceeds in an intermolecular fashion, without directing groups and at very low palladium-catalyst loadings. Mechanistic studies show that the reaction proceeds through the catalytic build-up of potent aroyl triflate electrophiles.

  18. How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

    Science.gov (United States)

    Relph, Rachael A; Guasco, Timothy L; Elliott, Ben M; Kamrath, Michael Z; McCoy, Anne B; Steele, Ryan P; Schofield, Daniel P; Jordan, Kenneth D; Viggiano, Albert A; Ferguson, Eldon E; Johnson, Mark A

    2010-01-15

    Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

  19. Formation of Bonded Exciplex in the Excited States of Dicyanoanthracene-Pyridine System : Time Dependent Density Functional Theory Study

    NARCIS (Netherlands)

    Setiawan, D.; Sethio, D.; Martoprawiro, M.A.; Filatov, M.; Gaol, FL; Nguyen, QV

    2012-01-01

    Strong quenching of fluorescence was recently observed in pyridine solutions of 9,10-dicyanoanthracene chromophore. It was hypothesized that quenching may be attributed to the formation of bound charge transfer complexes in the excited states of the molecules. In this work, using time-dependent

  20. Effect of gradual ordering of Ge/Sb atoms on chemical bonding: A proposed mechanism for the formation of crystalline Ge2Sb2Te5

    Science.gov (United States)

    Singh, Janpreet; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

    2018-04-01

    Using first principle calculations, we study the atomic arrangement and bonding mechanism in the crystalline phase of Ge2Sb2Te5 (GST). It is found that the stability of GST depends on the gradual ordering of Ge/Sb atoms. The configurations with different concentration of Ge/Sb in layers have been analyzed by the partial density of state, electron localization function and Bader charge distribution. The s and p-states of Ge atom alter with different stacking configurations but there is no change in Sb and Te atom states. Our findings show that the bonding between Ge-Te is not only responsible for the stability of GST alloy but can also predict which composition can show generic features of phase change material. As the number of Ge atoms near to vacancy layer decreases, Ge donates more charge. A growth model has been proposed for the formation of crystalline phase which justifies the structure models proposed in the literature.

  1. Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

    Directory of Open Access Journals (Sweden)

    Daniel Y Little

    Full Text Available The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1 removes a significant, non-coevolutionary bias and 2 accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.

  2. Tetrapeptide-coumarin conjugate 3D networks based on hydrogen-bonded charge transfer complexes: gel formation and dye release.

    Science.gov (United States)

    Guo, Zongxia; Gong, Ruiying; Jiang, Yi; Wan, Xiaobo

    2015-08-14

    Oligopeptide-based derivatives are important synthons for bio-based functional materials. In this article, a Gly-(L-Val)-Gly-(L-Val)-coumarin (GVGV-Cou) conjugate was synthesized, which forms 3D networks in ethanol. The gel nanostructures were characterized by UV-vis spectroscopy, FT-IR spectroscopy, X-ray diffraction (XRD), SEM and TEM. It is suggested that the formation of charge transfer (CT) complexes between the coumarin moieties is the main driving force for the gel formation. The capability of the gel to encapsulate and release dyes was explored. Both Congo Red (CR) and Methylene Blue (MB) can be trapped in the CT gel matrix and released over time. The present gel might be used as a functional soft material for guest encapsulation and release.

  3. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  4. Synthesis of Bioactive 2-(Arylaminothiazolo[5,4-f]-quinazolin-9-ones via the Hügershoff Reaction or Cu- Catalyzed Intramolecular C-S Bond Formation

    Directory of Open Access Journals (Sweden)

    Damien Hédou

    2016-06-01

    Full Text Available A library of thirty eight novel thiazolo[5,4-f]quinazolin-9(8H-one derivatives (series 8, 10, 14 and 17 was prepared via the Hügershoff reaction and a Cu catalyzed intramolecular C-S bond formation, helped by microwave-assisted technology when required. The efficient multistep synthesis of the key 6-amino-3-cyclopropylquinazolin-4(3H-one (3 has been reinvestigated and performed on a multigram scale from the starting 5-nitroanthranilic acid. The inhibitory potency of the final products was evaluated against five kinases involved in Alzheimer’s disease and showed that some molecules of the 17 series described in this paper are particularly promising for the development of novel multi-target inhibitors of kinases.

  5. Bifunctional RuII -Complex-Catalysed Tandem C-C Bond Formation: Efficient and Atom Economical Strategy for the Utilisation of Alcohols as Alkylating Agents.

    Science.gov (United States)

    Roy, Bivas Chandra; Chakrabarti, Kaushik; Shee, Sujan; Paul, Subhadeep; Kundu, Sabuj

    2016-12-12

    Catalytic activities of a series of functional bipyridine-based Ru II complexes in β-alkylation of secondary alcohols using primary alcohols were investigated. Bifunctional Ru II complex (3 a) bearing 6,6'-dihydroxy-2,2'-bipyridine (6DHBP) ligand exhibited the highest catalytic activity for this reaction. Using significantly lower catalyst loading (0.1 mol %) dehydrogenative carbon-carbon bond formation between numerous aromatic, aliphatic and heteroatom substituted alcohols were achieved with high selectivity. Notably, for the synthesis of β-alkylated secondary alcohols this protocol is a rare one-pot strategy using a metal-ligand cooperative Ru II system. Remarkably, complex 3 a demonstrated the highest reactivity compared to all the reported transition metal complexes in this reaction. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Effect of curing modes of dual-curing core systems on microtensile bond strength to dentin and formation of an acid-base resistant zone.

    Science.gov (United States)

    Li, Na; Takagaki, Tomohiro; Sadr, Alireza; Waidyasekera, Kanchana; Ikeda, Masaomi; Chen, Jihua; Nikaido, Toru; Tagami, Junji

    2011-12-01

    To evaluate the microtensile bond strength (μTBS) and acid-base resistant zone (ABRZ) of two dualcuring core systems to dentin using four curing modes. Sixty-four caries-free human molars were randomly divided into two groups according to two dual-curing resin core systems: (1) Clearfil DC Core Automix; (2) Estelite Core Quick. For each core system, four different curing modes were applied to the adhesive and core resin: (1) dual-cured and dual-cured (DD); (2) chemically cured and dual-cured (CD); (3) dual-cured and chemically cured (DC); (4) chemically cured and chemically cured (CC). The specimens were sectioned into sticks (n = 20 for each group) for the microtensile bond test. μTBS data were analyzed using two-way ANOVA and the Dunnett T3 test. Failure patterns were examined with scanning electron microscopy (SEM) to determine the proportion of each mode. Dentin sandwiches were produced and subjected to an acid-base challenge. After argon-ion etching, the ultrastructure of ABRZ was observed using SEM. For Clearfil DC Core Automix, the μTBS values in MPa were as follows: DD: 29.1 ± 5.4, CD: 21.6 ± 5.6, DC: 17.9 ± 2.8, CC: 11.5 ± 3.2. For Estelite Core Quick, they were: DD: 48.9 ±5.7, CD: 20.5 ± 4.7, DC: 41.4 ± 8.3, CC: 19.1 ± 6.0. The bond strength was affected by both material and curing mode, and the interaction of the two factors was significant (p < 0.001). Within both systems, there were significant differences among groups, and the DD group showed the highest μTBS (p < 0.05). ABRZ morphology was not affected by curing mode, but it was highly adhesive-material dependent. The curing mode of dual-curing core systems affects bond strength to dentin, but has no significant effect on the formation of ABRZ.

  7. Ab-initio studies of the Sc adsorption and the ScN thin film formation on the GaN(000-1)-(2 × 2) surface

    International Nuclear Information System (INIS)

    Guerrero-Sánchez, J.; Sánchez-Ochoa, F.; Cocoletzi, Gregorio H.; Rivas-Silva, J.F.; Takeuchi, Noboru

    2013-01-01

    First principles total energy calculations have been performed to investigate the initial stages of the Sc adsorption and ScN thin film formation on the GaN(000-1)-(2 × 2) surface. Studies are done within the periodic density functional theory as implemented in the PWscf code of the Quantum ESPRESSO package. The Sc adsorption at high symmetry sites results in the bridge site as the most stable structure. When a Sc monolayer is deposited above the surface the T4 site results as the most stable geometry. The Sc migration into the first Ga monolayer induces the Ga displaced ad-atom to be adsorbed at the T4-2 site. A ScN bilayer may be obtained under the Ga monolayer. Finally a ScN bilayer may be formed in the wurtzite phase above the surface. The formation energy plots show that in the moderate Ga-rich conditions we obtain the formation of a ScN bilayer under the gallium monolayer. However at N-rich conditions the formation of ScN bilayer above the surface is the most favorable structure. We report the density of states to explain the electronic structure of the most favorable geometries. - Highlights: • Studies of the initial stages in the formation of Sc and ScN structures on GaN • In the adsorption of Sc on the GaN the Br site is the most favorable geometry. • When a Sc replaces a Ga of the first monolayer the displaced Ga occupies a T4-2 site. • For Ga-rich conditions there is formation of ScN under the Ga monolayer. • In N-rich conditions there is formation of ScN in the wurtzite phase

  8. Synthesis of isoprenoid bisphosphonate ethers through C–P bond formations: Potential inhibitors of geranylgeranyl diphosphate synthase

    Directory of Open Access Journals (Sweden)

    Xiang Zhou

    2014-07-01

    Full Text Available A set of bisphosphonate ethers has been prepared through sequential phosphonylation and alkylation of monophosphonate ethers. After formation of the corresponding phosphonic acid salts, these compounds were tested for their ability to inhibit the enzyme geranylgeranyl diphosphate synthase (GGDPS. Five of the new compounds show IC50 values of less than 1 μM against GGDPS with little to no activity against the related enzyme farnesyl diphosphate synthase (FDPS. The most active compound displayed an IC50 value of 82 nM when assayed with GGDPS, and no activity against FDPS even at a 10 μM concentration.

  9. A PEG/copper(i) halide cluster as an eco-friendly catalytic system for C-N bond formation.

    Science.gov (United States)

    Li, Cheng-An; Ji, Wei; Qu, Jian; Jing, Su; Gao, Fei; Zhu, Dun-Ru

    2018-05-22

    The catalytic activities of eight copper(i) halide clusters assembled from copper(i) halide and ferrocenyltelluroethers, 1-8, were investigated in C-N formation under various conditions. A catalytic procedure using poly(ethylene glycol) (PEG-400) as a greener alternative organic solvent has been developed. The PEG-400/5 system can achieve 99% targeted yield with a mild reaction temperature and short reaction time. After the isolation of the products by extraction with diethyl ether, this PEG-400/cluster system could be easily recycled. Spectroscopic studies elucidate a stepwise mechanism: firstly, proton-coupled electron transfer (PCET) involving the transfer of an electron from Cu+ and a proton from imidazole results in the formation of a labile penta-coordinated Cu2+ and aryl radical; the following effective electron transfer from the ferrocene unit reduces Cu2+ and forms the target product; finally, the ferrocenium unit is reduced by the I- anion. The merits of this eco-friendly synthesis are the efficient utilization of reagents and easy recyclability.

  10. Ab initio pseudopotential theory

    International Nuclear Information System (INIS)

    Yin, M.T.; Cohen, M.L.

    1982-01-01

    The ab initio norm-conserving pseudopotential is generated from a reference atomic configuration in which the pseudoatomic eigenvalues and wave functions outside the core region agree with the corresponding ab initio all-electron results within the density-functional formalism. This paper explains why such pseudopotentials accurately reproduce the all-electron results in both atoms and in multiatomic systems. In particular, a theorem is derived to demonstrate the energy- and perturbation-independent properties of ab initio pseudopotentials

  11. Synthesis of the proteinase inhibitor LEKTI domain 6 by the fragment condensation method and regioselective disulfide bond formation.

    Science.gov (United States)

    Vasileiou, Zoe; Barlos, Kostas K; Gatos, Dimitrios; Adermann, Knut; Deraison, Celine; Barlos, Kleomenis

    2010-01-01

    Proteinase inhibitors are of high pharmaceutical interest and are drug candidates for a variety of indications. Specific kallikrein inhibitors are important for their antitumor activity and their potential application to the treatment of skin diseases. In this study we describe the synthesis of domain 6 of the kallikrein inhibitor Lympho-Epithilial Kazal-Type Inhibitor (LEKTI) by the fragment condensation method and site-directed cystine bridge formation. To obtain the linear LEKTI precursor, the condensation was best performed in solution, coupling the protected fragment 1-22 to 23-68. This method yielded LEKTI domain 6 of high purity and equipotent to the recombinantly produced peptide. (c) 2010 Wiley Periodicals, Inc.

  12. Ab initio investigations of the electronic structures and chemical bonding in LiCo{sub 6}P{sub 4} and Li{sub 2}Co{sub 12}P{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Matar, Samir F. [CNRS, ICMCB, UPR 9048, F‐33600 Pessac (France); Université de Bordeaux, ICMCB, UPR 9048, F‐33600 Pessac (France); Al-Alam, Adel; Ouaini, Naïm [Université Saint-Esprit de Kaslik (USEK), Groupe OCM (Optimization et Caractérisation des Matériaux), CSR-USEK, CNRS-L, Jounieh (Lebanon); Pöttgen, Rainer, E-mail: pottgen@uni-muenster.de [Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstraße 30, D-48149 Münster (Germany)

    2013-06-15

    The electronic structures of the metal-rich phosphides LiCo{sub 6}P{sub 4} and Li{sub 2}Co{sub 12}P{sub 7} were studied by DFT calculations. Both phosphides consist of three-dimensional [Co{sub 6}P{sub 4}] and [Co{sub 12}P{sub 7}] polyanionic networks which leave hexagonal channels for the lithium atoms. COOP data show strong Co–P and Co–Co bonding within the polyanions. The lithium atoms have trigonal prismatic phosphorus coordination. Total energy calculations indicate stability upon de-lithiation towards the Co{sub 6}P{sub 4} and Co{sub 12}P{sub 7} substructures - Graphical abstract: The cobalt–phosphorus networks in LiCo{sub 6}P{sub 4} and Li{sub 2}Co{sub 12}P{sub 7}. - Highlights: • Chemical bonding resolved in the metal-rich phosphides LiCo{sub 6}P{sub 4} and Li{sub 2}Co{sub 12}P{sub 7}. • Strong covalent Co–P bonding character in the [Co{sub 6}P{sub 4}] and [Co{sub 12}P{sub 7}] substructures. • Total energy calculations indicate stability of the de-lithiated substructures.

  13. Effects of Li and Na intercalation on electronic, bonding and thermoelectric transport properties of MX{sub 2} (M = Ta; X = S or Se) dichalcogenides – Ab initio investigation

    Energy Technology Data Exchange (ETDEWEB)

    Meziane, Souheyr; Feraoun, Houda [Unité de Recherche Matériaux et Energies Renouvelables – URMER, Université de Tlemcen (Algeria); Ouahrani, Tarik [Laboratoire de Physique Théorique, Ecole Préparatoire en Sciences et Techniques, B.P. 230, 13000 Tlemcen (Algeria); Esling, Claude, E-mail: claude.esling@univ-lorraine.fr [Laboratoire d’Etude des Microstructures et de Mécanique des Matériaux, LEM3 UMR CNRS 7239, Université de Lorraine UL, Metz 57045 (France); Laboratoire d’Excellence “DAMAS”: Design of Metal Alloys for low-mAss Structures, Université de Lorraine – Metz, Ile du Saulcy, 57045 Metz Cedex 01 (France)

    2013-12-25

    Highlights: •Topological method is used to analyze the chemical bonding in Li(Na)TaX{sub 2} dichalcogenide compounds. •For the first time, Seebeck coefficient, electrical resistivity and thermal conductivity were estimated. •The best figure of merit is established for 2H-LiTaS{sub 2}. •Some new thermoelectric compounds are found. -- Abstract: Using the pseudo-potential method and semi-classical Boltzmann theory, electronic, chemical bonding and thermoelectric transport properties of sample and Li or Na intercalated Ta(S, Se){sub 2} dichalcogenides have been reported. The chemical bonding is studied using the Quantum Theory of Atoms in Molecules (QTAIM). Then, the Seebeck coefficient, electrical resistivity, electrical conductivity, thermal conductivity and figure of merit have been calculated in the temperature range 100–700 K. It was shown that the thermoelectric transport properties strongly depend on the Alkali metals doping and the two main structures 1T- or 2H- as well as the temperature. 2H-LiTaS{sub 2} have been selected as the best candidate for thermoelectrical applications with zT = 1.1.

  14. Suppression of Boride Formation in Transient Liquid Phase Bonding of Pairings of Parent Superalloy Materials with Different Compositions and Grain Structures and Resulting Mechanical Properties

    Science.gov (United States)

    Steuer, Susanne; Singer, Robert F.

    2014-07-01

    Two Ni-based superalloys, columnar grained Alloy 247 and single-crystal PWA1483, are joined by transient liquid phase bonding using an amorphous brazing foil containing boron as a melting point depressant. At lower brazing temperatures, two different morphologies of borides develop in both base materials: plate-like and globular ones. Their ratio to each other is temperature dependent. With very high brazing temperatures, the deleterious boride formation in Alloy 247 can be totally avoided, probably because the three-phase-field moves to higher alloying element contents. For the superalloy PWA1483, the formation of borides cannot be completely avoided at high brazing temperatures as incipient melting occurs. During subsequent solidification of these areas, Chinese-script-like borides precipitate. The mechanical properties (tensile tests at room and elevated temperatures and short-term creep rupture tests at elevated temperatures) for brazed samples without boride precipitation are very promising. Tensile strengths and creep times to 1 pct strain are comparable, respectively, higher than the ones of the weaker parent material for all tested temperatures and creep conditions (from 90 to 100 pct rsp. 175 to 250 pct).

  15. Morphological effects of single-layer graphene oxide in the formation of covalently bonded polypyrrole composites using intermediate diisocyanate chemistry

    International Nuclear Information System (INIS)

    Whitby, Raymond L. D.; Korobeinyk, Alina; Mikhalovsky, Sergey V.; Fukuda, Takahiro; Maekawa, Toru

    2011-01-01

    Single-layer graphene oxide (SLGO) possesses carboxylic and hydroxyl groups suitable for reactions with aliphatic or aromatic diisocyanate molecules. TEM analysis reveals that aliphatic diisocyanate molecules caused SLGO to scroll into star-like formations, whereas aromatic diisocyanate molecules retained SGLO in a flat-sheet morphology. TGA confirms the stabilisation of the formed urea and urethane groups on SLGO, but the onset of sheet pyrolysis occurs at a lower temperature due to isocyanate reactions with anhydride and epoxide groups embedded in the sheet. Pendant isocyanate groups act as bridging units to facilitate the attachment of pyrrole molecules, which are then used as anchor sites for the covalent polymerisation of pyrrole to polypyrrole (PPy). The use of FeCl 3 as the polymerisation catalyst generated both covalent and free PPy, but also iron hydroxide nanoparticles were observed decorating the SLGO surface. When using ammonium persulfate as a catalyst and dodecylbenzenesulfonate as a dopant, free PPy could be removed under treatment with solvents to leave a purely covalent system. Discrete regions of SLGO were observed decorated with nanoparticles of PPy along the edge or across the surface of individual sheets. It was found that the flexibility of the SLGO sheet and the type of diisocyanate used directly affected the electrical resistance of the final composite.

  16. Reactivity of the parent amido complexes of iridium with olefins: C-NH2 bond formation versus C-H activation.

    Science.gov (United States)

    Mena, Inmaculada; García-Orduña, Pilar; Polo, Víctor; Lahoz, Fernando J; Casado, Miguel A; Oro, Luis A

    2017-08-29

    Herein we report on the different chemical reactivity displayed by two mononuclear terminal amido compounds depending on the nature of the coordinated diene. Hence, treatment of amido-bridged iridium complexes [{Ir(μ-NH 2 )(tfbb)} 3 ] (1; tfbb = tetrafluorobenzobarrelene) with dppp (dppp = bis(diphenylphosphane)propane) leads to the rupture of the amido bridges forming the mononuclear terminal amido compound [Ir(NH 2 )(dppp)(tfbb)] (3) in the first stage. On changing the reaction conditions, the formation of a C-NH 2 bond between the amido moiety and the coordinated diene is observed and a new dinuclear complex [{Ir(1,2-η 2 -4-κ-C 12 H 8 F 4 N)(dppp)} 2 (μ-dppp)] (4) has been isolated. On the contrary, the diiridium amido-bridged complex [{Ir(μ-NH 2 )(cod)} 2 ] (2; cod = 1,5-cyclooctadiene) in the presence of dppb (dppb = bis(diphenylphosphane)butane) allows the isolation of a mononuclear complex [Ir(1,2,3-η 3 -6-κ-C 8 H 10 )H(dppb)] (5), as a consequence of the extrusion of ammonia. The monitoring of the reaction of 2 with dppb (and dppp) allowed us to detect terminal amido complexes [Ir(NH 2 )(P-P)(cod)] (P-P = dppb (6), dppp (7)) in solution, as confirmed by an X-ray analysis of 7. Complex 7 was observed to evolve into hydrido species 5 at room temperature. DFT studies showed that C-H bond activation occurs through the deprotonation of one methylene fragment of the cod ligand by the highly basic terminal amido moiety instead of C-H oxidative addition to the Ir(i) center.

  17. Copper wire bonding

    CERN Document Server

    Chauhan, Preeti S; Zhong, ZhaoWei; Pecht, Michael G

    2014-01-01

    This critical volume provides an in-depth presentation of copper wire bonding technologies, processes and equipment, along with the economic benefits and risks.  Due to the increasing cost of materials used to make electronic components, the electronics industry has been rapidly moving from high cost gold to significantly lower cost copper as a wire bonding material.  However, copper wire bonding has several process and reliability concerns due to its material properties.  Copper Wire Bonding book lays out the challenges involved in replacing gold with copper as a wire bond material, and includes the bonding process changes—bond force, electric flame off, current and ultrasonic energy optimization, and bonding tools and equipment changes for first and second bond formation.  In addition, the bond–pad metallurgies and the use of bare and palladium-coated copper wires on aluminum are presented, and gold, nickel and palladium surface finishes are discussed.  The book also discusses best practices and re...

  18. Ab initio study of vacancy formation in cubic LaMnO{sub 3} and SmCoO{sub 3} as cathode materials in solid oxide fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Emilia; Aparicio-Anglès, Xavier [Department of Chemistry, University College London, London WC1H 0AJ (United Kingdom); Leeuw, Nora H. de, E-mail: deleeuwn@cardiff.ac.uk [Department of Chemistry, University College London, London WC1H 0AJ (United Kingdom); School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT (United Kingdom)

    2016-07-07

    Doped LaMnO{sub 3} and SmCoO{sub 3} are important solid oxide fuel cell cathode materials. The main difference between these two perovskites is that SmCoO{sub 3} has proven to be a more efficient cathode material than LaMnO{sub 3} at lower temperatures. In order to explain the difference in efficiency, we need to gain insight into the materials’ properties at the atomic level. However, while LaMnO{sub 3} has been widely studied, ab initio studies on SmCoO{sub 3} are rare. Hence, in this paper, we perform a comparative DFT + U study of the structural, electronic, and magnetic properties of these two perovskites. To that end, we first determined a suitable Hubbard parameter for the Co d–electrons to obtain a proper description of SmCoO{sub 3} that fully agrees with the available experimental data. We next evaluated the impact of oxygen and cation vacancies on the geometry, electronic, and magnetic properties. Oxygen vacancies strongly alter the electronic and magnetic structures of SmCoO{sub 3}, but barely affect LaMnO{sub 3}. However, due to their high formation energy, their concentrations in the material are very low and need to be induced by doping. Studying the cation vacancy concentration showed that the formation of cation vacancies is less energetically favorable than oxygen vacancies and would thus not markedly influence the performance of the cathode.

  19. A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

    International Nuclear Information System (INIS)

    Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

    2009-01-01

    Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH···N and NH···O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1 , respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

  20. A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

    Science.gov (United States)

    Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

    2009-07-01

    Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH⋯N and NH⋯O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1, respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

  1. Bond Issues.

    Science.gov (United States)

    Pollack, Rachel H.

    2000-01-01

    Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…

  2. Hydrogen bonding in ionic liquids.

    Science.gov (United States)

    Hunt, Patricia A; Ashworth, Claire R; Matthews, Richard P

    2015-03-07

    Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak

  3. Formation of C-C and C-O bonds and oxygen removal in reactions of alkanediols, alkanols, and alkanals on copper catalysts.

    Science.gov (United States)

    Sad, María E; Neurock, Matthew; Iglesia, Enrique

    2011-12-21

    This study reports evidence for catalytic deoxygenation of alkanols, alkanals, and alkanediols on dispersed Cu clusters with minimal use of external H(2) and with the concurrent formation of new C-C and C-O bonds. These catalysts selectively remove O-atoms from these oxygenates as CO or CO(2) through decarbonylation or decarboxylation routes, respectively, that use C-atoms present within reactants or as H(2)O using H(2) added or formed in situ from CO/H(2)O mixtures via water-gas shift. Cu catalysts fully convert 1,3-propanediol to equilibrated propanol-propanal intermediates that subsequently form larger oxygenates via aldol-type condensation and esterification routes without detectable involvement of the oxide supports. Propanal-propanol-H(2) equilibration is mediated by their chemisorption and interconversion at surfaces via C-H and O-H activation and propoxide intermediates. The kinetic effects of H(2), propanal, and propanol pressures on turnover rates, taken together with measured selectivities and the established chemical events for base-catalyzed condensation and esterification reactions, indicate that both reactions involve kinetically relevant bimolecular steps in which propoxide species, acting as the base, abstract the α-hydrogen in adsorbed propanal (condensation) or attack the electrophilic C-atom at its carbonyl group (esterification). These weakly held basic alkoxides render Cu surfaces able to mediate C-C and C-O formation reactions typically catalyzed by basic sites inherent in the catalyst, instead of provided by coadsorbed organic moieties. Turnover rates for condensation and esterification reactions decrease with increasing Cu dispersion, because low-coordination corner and edge atoms prevalent on small clusters stabilize adsorbed intermediates and increase the activation barriers for the bimolecular kinetically relevant steps required for both reactions. © 2011 American Chemical Society

  4. Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.

    Science.gov (United States)

    Schlünzen, Frank; Pyetan, Erez; Fucini, Paola; Yonath, Ada; Harms, Jörg M

    2004-12-01

    Tiamulin, a prominent member of the pleuromutilin class of antibiotics, is a potent inhibitor of protein synthesis in bacteria. Up to now the effect of pleuromutilins on the ribosome has not been determined on a molecular level. The 3.5 A structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin provides for the first time a detailed picture of its interactions with the 23S rRNA, thus explaining the molecular mechanism of the antimicrobial activity of the pleuromutilin class of antibiotics. Our results show that tiamulin is located within the peptidyl transferase center (PTC) of the 50S ribosomal subunit with its tricyclic mutilin core positioned in a tight pocket at the A-tRNA binding site. Also, the extension, which protrudes from its mutilin core, partially overlaps with the P-tRNA binding site. Thereby, tiamulin directly inhibits peptide bond formation. Comparison of the tiamulin binding site with other PTC targeting drugs, like chloramphenicol, clindamycin and streptogramins, may facilitate the design of modified or hybridized drugs that extend the applicability of this class of antibiotics.

  5. Phylogeny of the Vitamin K 2,3-Epoxide Reductase (VKOR) Family and Evolutionary Relationship to the Disulfide Bond Formation Protein B (DsbB) Family.

    Science.gov (United States)

    Bevans, Carville G; Krettler, Christoph; Reinhart, Christoph; Watzka, Matthias; Oldenburg, Johannes

    2015-07-29

    In humans and other vertebrate animals, vitamin K 2,3-epoxide reductase (VKOR) family enzymes are the gatekeepers between nutritionally acquired K vitamins and the vitamin K cycle responsible for posttranslational modifications that confer biological activity upon vitamin K-dependent proteins with crucial roles in hemostasis, bone development and homeostasis, hormonal carbohydrate regulation and fertility. We report a phylogenetic analysis of the VKOR family that identifies five major clades. Combined phylogenetic and site-specific conservation analyses point to clade-specific similarities and differences in structure and function. We discovered a single-site determinant uniquely identifying VKOR homologs belonging to human pathogenic, obligate intracellular prokaryotes and protists. Building on previous work by Sevier et al. (Protein Science 14:1630), we analyzed structural data from both VKOR and prokaryotic disulfide bond formation protein B (DsbB) families and hypothesize an ancient evolutionary relationship between the two families where one family arose from the other through a gene duplication/deletion event. This has resulted in circular permutation of primary sequence threading through the four-helical bundle protein folds of both families. This is the first report of circular permutation relating distant a-helical membrane protein sequences and folds. In conclusion, we suggest a chronology for the evolution of the five extant VKOR clades.

  6. Collapsed tetragonal phase as a strongly covalent and fully nonmagnetic state: Persistent magnetism with interlayer As-As bond formation in Rh-doped Ca0 .8Sr0 .2Fe2As2

    Science.gov (United States)

    Zhao, K.; Glasbrenner, J. K.; Gretarsson, H.; Schmitz, D.; Bednarcik, J.; Etter, M.; Sun, J. P.; Manna, R. S.; Al-Zein, A.; Lafuerza, S.; Scherer, W.; Cheng, J. G.; Gegenwart, P.

    2018-02-01

    A well-known feature of the CaFe2As2 -based superconductors is the pressure-induced collapsed tetragonal phase that is commonly ascribed to the formation of an interlayer As-As bond. Using detailed x-ray scattering and spectroscopy, we find that Rh-doped Ca0.8Sr0.2Fe2As2 does not undergo a first-order phase transition and that local Fe moments persist despite the formation of interlayer As-As bonds. Our density functional theory calculations reveal that the Fe-As bond geometry is critical for stabilizing magnetism and the pressure-induced drop in the c lattice parameter observed in pure CaFe2As2 is mostly due to a constriction within the FeAs planes. The collapsed tetragonal phase emerges when covalent bonding of strongly hybridized Fe 3 d and As 4 p states completely wins out over their exchange splitting. Thus the collapsed tetragonal phase is properly understood as a strong covalent phase that is fully nonmagnetic with the As-As bond forming as a by-product.

  7. Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

    Science.gov (United States)

    Deeth, Robert J; Halcrow, Malcolm A; Kershaw Cook, Laurence J; Raithby, Paul R

    2018-04-06

    A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp) 2 ] 2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H 3 bpp] 3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp) 2 ] 2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF 4 ] - or [PF 6 ] - anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T 1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T 1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Characterization and formation of NV centers in 3 C , 4 H , and 6 H SiC: An ab initio study

    Science.gov (United States)

    Csóré, A.; von Bardeleben, H. J.; Cantin, J. L.; Gali, A.

    2017-08-01

    Fluorescent paramagnetic defects in solids have become attractive systems for quantum information processing in recent years. One of the leading contenders is the negatively charged nitrogen-vacancy (NV) defect in diamond with visible emission, but an alternative solution in a technologically mature host is an immediate quest for many applications in this field. It has been recently found that various polytypes of silicon carbide (SiC), that are standard semiconductors with wafer scale technology, can host a NV defect that could be an alternative qubit candidate with emission in the near infrared region. However, there is much less known about this defect than its counterpart in diamond. The inequivalent sites within a polytype and the polytype variations offer a family of NV defects. However, there is an insufficient knowledge on the magneto-optical properties of these configurations. Here we carry out density functional theory calculations, in order to characterize the numerous forms of NV defects in the most common polytypes of SiC including 3 C , 4 H , and 6 H , and we also provide new experimental data in 4 H SiC. Our calculations mediate the identification of individual NV qubits in SiC polytypes. In addition, we discuss the formation of NV defects in SiC, providing detailed ionization energies of NV defects in SiC, which reveals the critical optical excitation energies for ionizing these qubits in SiC. Our calculations unravel the challenges to produce NV defects in SiC with a desirable spin bath.

  9. An ab initio molecular

    Indian Academy of Sciences (India)

    mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

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

    Science.gov (United States)

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO 2 ) 57.5 -(B 2 O 3 ) 10 -(Na 2 O) 15 -(CaO) 15 -(MoO 3 ) 2.5 and (SiO 2 ) 57.3 -(B 2 O 3 ) 20 -(Na 2 O) 6.8 -(Li 2 O) 13.4 -(MoO 3 ) 2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na 2 MoO 4 and CaMoO 4 ). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  11. Hydrogen bonding in tight environments

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; Solomon, Gemma C.; Franco, Ignacio

    2016-01-01

    The single-molecule force spectroscopy of a prototypical class of hydrogen-bonded complexes is computationally investigated. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The force-extension (F-L) isotherms...... of the host-guest complexes are simulated using classical molecular dynamics and the MM3 force field, for which a refined set of hydrogen bond parameters was developed from MP2 ab initio computations. The F-L curves exhibit peaks that signal conformational changes during elongation, the most prominent...... of which is in the 60-180 pN range and corresponds to the force required to break the hydrogen bonds. These peaks in the F-L curves are shown to be sensitive to relatively small changes in the chemical structure of the host molecule. Thermodynamic insights into the supramolecular assembly were obtained...

  12. Formation of a dinuclear copper(II) complex through the cleavage of CBond' name='Single-Bond' value='Single-Bond'/>N bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole

    Energy Technology Data Exchange (ETDEWEB)

    Shardin, Rosidah; Pui, Law Kung; Yamin, Bohari M. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia); Kassim, Mohammad B. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor, Malaysia and Fuel Cell Institute, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia)

    2014-09-03

    A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with μ-(3-(pyridin-2-yl)-pyrazolato) and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the C{sub benzoyl}Bond' name='Single-Bond' value='Single-Bond'/>N bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the (3-(pyridin-2-yl)-pyrazolato)(3-(pyridin-2-yl)-1H-pyrazole)Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and β = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (ε = 116 dm{sup 3} mol{sup −1} cm{sup −1}) supports the presence of Cu(II) centres.

  13. Suppression of interfacial voids formation during silane (SiH4)-based silicon oxide bonding with a thin silicon nitride capping layer

    Science.gov (United States)

    Lee, Kwang Hong; Bao, Shuyu; Wang, Yue; Fitzgerald, Eugene A.; Seng Tan, Chuan

    2018-01-01

    The material properties and bonding behavior of silane-based silicon oxide layers deposited by plasma-enhanced chemical vapor deposition were investigated. Fourier transform infrared spectroscopy was employed to determine the chemical composition of the silicon oxide films. The incorporation of hydroxyl (-OH) groups and moisture absorption demonstrates a strong correlation with the storage duration for both as-deposited and annealed silicon oxide films. It is observed that moisture absorption is prevalent in the silane-based silicon oxide film due to its porous nature. The incorporation of -OH groups and moisture absorption in the silicon oxide films increase with the storage time (even in clean-room environments) for both as-deposited and annealed silicon oxide films. Due to silanol condensation and silicon oxidation reactions that take place at the bonding interface and in the bulk silicon, hydrogen (a byproduct of these reactions) is released and diffused towards the bonding interface. The trapped hydrogen forms voids over time. Additionally, the absorbed moisture could evaporate during the post-bond annealing of the bonded wafer pair. As a consequence, defects, such as voids, form at the bonding interface. To address the problem, a thin silicon nitride capping film was deposited on the silicon oxide layer before bonding to serve as a diffusion barrier to prevent moisture absorption and incorporation of -OH groups from the ambient. This process results in defect-free bonded wafers.

  14. Parental Bonding

    Directory of Open Access Journals (Sweden)

    T. Paul de Cock

    2014-08-01

    Full Text Available Estimating the early parent–child bonding relationship can be valuable in research and practice. Retrospective dimensional measures of parental bonding provide a means for assessing the experience of the early parent–child relationship. However, combinations of dimensional scores may provide information that is not readily captured with a dimensional approach. This study was designed to assess the presence of homogeneous groups in the population with similar profiles on parental bonding dimensions. Using a short version of the Parental Bonding Instrument (PBI, three parental bonding dimensions (care, authoritarianism, and overprotection were used to assess the presence of unobserved groups in the population using latent profile analysis. The class solutions were regressed on 23 covariates (demographics, parental psychopathology, loss events, and childhood contextual factors to assess the validity of the class solution. The results indicated four distinct profiles of parental bonding for fathers as well as mothers. Parental bonding profiles were significantly associated with a broad range of covariates. This person-centered approach to parental bonding has broad utility in future research which takes into account the effect of parent–child bonding, especially with regard to “affectionless control” style parenting.

  15. Electronic states and nature of bonding of the molecule NiGe by all electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations and mass spectrometric equilibrium experiments

    DEFF Research Database (Denmark)

    Shim, Irene; Kingcade, Joseph E.; Gingerich, Karl A.

    1988-01-01

    -lying electronic states of the NiGe molecule have all been characterized by the symmetry of the hole in the 3d shell of Ni. The dissociation energy of the NiGe molecule has been determined from our high temperature mass spectrometric equilibrium data in combination with the theoretical results as D [open circle] 0...... =286.8±10.9 kJ mol−1. The standard heat of formation of the NiGe molecule has been obtained as DeltaH [open circle] f,298 =514±12 kJ mol−1. The Journal of Chemical Physics is copyrighted by The American Institute of Physics....

  16. Effect of Pressurizing during Compaction and Sintering on the Formation of Reaction-Bonded SiC–Ti{sub 3}SiC{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sun-Han; Jung, Yang-Il; Rhee, Young-Woo; Park, Dong-Jun; Park, Jung-Hwan; Park, Jeong-Yong; Kim, Hyun-Gil; Koo, Yang-Hyun [LWR Fuel Technology Division, KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    A reaction-bonded SiC-Ti{sub 3}SiC{sub 2} ceramic composite was produced for use in a ceramic-metal composite cladding tube. The diffusion reaction between TiC and Si was investigated with respect to process pressure. The mole-fraction of TiC and Si was controlled to be 3:2 to obtain a Ti{sub 3}SiC{sub 2} phase in the ceramic composite. Sintering was conducted at 1450 °C where TiC particles could react with melted Si. SiC ceramic composites consisting of Ti{sub 3}SiC{sub 2} and TiSi{sub 2} matrix phases were obtained. The formation of the constituent phases was strongly related to the processing pressure. The number of second phases in the SiC-Ti{sub 3}SiC{sub 2} composite was controlled by adjusting the processing pressure. When the powder compacts were not pressurized, no Ti{sub 3}SiC{sub 2} phase was formed. However, the Ti{sub 3}SiC{sub 2} phase was formed under pressurizing during compaction and/or sintering. The higher the pressure the higher the purity of SiC-Ti{sub 3}SiC{sub 2}. The dual-phased SiC-Ti{sub 3}SiC{sub 2} composite, however, revealed the decreased resistance to high-temperature oxidation. It is suggested that the incorporation of TiSi{sub 2} in the composite increases the oxidation resistance as well as mechanical property.

  17. Ab Initio Molecular Dynamics Simulations of Furfural at the Liquid-Solid Interface

    OpenAIRE

    Sanwu Wang; Hongli Dang; Wenhua Xue; Darwin Shields; Xin Liu; Friederike C. Jentoft; Daniel E. Resasco

    2013-01-01

    The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurati...

  18. Ab initio model of porous periclase

    International Nuclear Information System (INIS)

    Drummond, Neil D.; Swift, Damian C.; Ackland, Graeme J.

    2004-01-01

    A two-phase equilibrium equation of state (EOS) for periclase (MgO) was constructed using ab initio quantum mechanics, including a rigorous calculation of quasiharmonic phonon modes. Much of the shock wave data reported for periclase is on porous material. We compared the theoretical EOS with porous data using a simple 'snowplough' treatment and also a model using finite equilibration rates suitable for continuum mechanics simulations. (This model has been applied previously to various heterogeneous explosives as well as other porous materials.) The results were consistent and matched the data well at pressures above the regime affected by strength - and ramp-wave formation - during compaction. Ab initio predictions of the response of porous material have been cited recently as a novel and advanced capability; we feel that this is a fairly routine extension to established ab initio techniques

  19. Effect of the value of bond energy on the defect formation in the samples of CdTe - HqTe system under the influence of irradiation

    International Nuclear Information System (INIS)

    Kramchenko, O.A.; Pashkovskij, N.V.

    1984-01-01

    The bonds break energy in solid solutions of the CdTe-HgTe system is calculated. The correctness of the statement that bonds strength in a chemical compound, particularly for the CdTe-HgTe system with decreases with the increase of atomic number. It is shown that in the process of transition from CdTe binary compound to solid solutions of the CdTe-HgTe system a part of Cd atoms is substituted by Hg atoms, which causes relative decrease of the number Cd-Te bonds. At the same time increased is the number of Cd-Te bonds which during irradiation break more probably than the Cd-Te bonds forming however only Frenkel close vapours annihilating during irradiation. During the experiment these defects lead to temperature region washout in which properties reconstruction at isochronous annealing begins. The beginning of annealing is shifted towards higher temperatures which has been observed in the course of investigation. X decrease for the Cdsub(x)Hgsub(1-x)Te solid solution increases the annealing temperature of radiation defects The results of theoretical calculations coincide with the experimental data and permit to confirm that the properties changes arising during irradiation of matters with weak chemical bonds can be conserved only at very low temperatures

  20. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  1. Tensile and fatigue properties of weld-bonded and adhesive-bonded magnesium alloy joints

    International Nuclear Information System (INIS)

    Xu, W.; Liu, L.; Zhou, Y.; Mori, H.; Chen, D.L.

    2013-01-01

    The microstructures, tensile and fatigue properties of weld-bonded (WB) AZ31B-H24 Mg/Mg joints with different sizes of bonding area were evaluated and compared with the adhesive-bonded (AB) Mg/Mg joints. Typical equiaxed dendritic structures containing divorced eutectic Mg 17 Al 12 particles formed in the fusion zone of both WB-1 (with a bonding area of 35 mm×35 mm) and WB-0.5 (with a bonding area of 17.5 mm×35 mm) joints. Less solidification shrinkage cracking was observed in the WB-0.5 joints than WB-1 joints. While the WB-0.5 joints exhibited a slightly lower maximum tensile shear stress than the AB-0.5 joints (with a bonding area of 17.5 mm×35 mm), the energy absorption was equivalent. Although the AB-0.5 joints exhibited a higher fatigue resistance at higher cyclic stress levels, both the AB-0.5 and WB-0.5 joints showed an equivalent fatigue resistance at lower cyclic stress levels. A higher fatigue limit was observed in the WB-0.5 joints than in the WB-1 joints owing to the presence of fewer shrinkage pores. Cohesive failure mode along the adhesive layer in conjunction with partial nugget pull-out from the weld was observed at the higher cyclic loads, and fatigue failure occurred in the base metal at the lower cyclic loads

  2. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

    Science.gov (United States)

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

    2014-10-07

    We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  3. Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

    Science.gov (United States)

    Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

    2005-06-16

    The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

  4. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

    This book is an up-to-date text covering topics in utilizing hydrogen bonding for constructing functional architectures and supramolecular materials. The first chapter addresses the control of photo-induced electron and energy transfer. The second chapter summarizes the formation of nano-porous materials. The following two chapters introduce self-assembled gels, many of which exhibit unique functions. Other chapters cover the advances in supramolecular liquid crystals and the versatility of hydrogen bonding in tuning/improving the properties and performance of materials. This book is designed

  5. Formation of Si{sup 1+} in the early stages of the oxidation of the Si[001] 2 × 1 surface

    Energy Technology Data Exchange (ETDEWEB)

    Herrera-Gomez, Alberto, E-mail: aherrerag@cinvestav.mx [CINVESTAV-Unidad Queretaro, Queretaro 76230 (Mexico); Aguirre-Tostado, Francisco-Servando [Centro de Investigación en Materiales Avanzados, Monterrey, Nuevo Leon, 66600 (Mexico); Pianetta, Piero [SLAC National Accelerator Center, Menlo Park, California 94025 (United States)

    2016-03-15

    The early stages of the oxidation of the Si[001] 2 × 1 surface were studied with synchrotron radiation photoelectron spectroscopy. The analysis was based on the block approach, which is a refinement of spectra-subtraction that accounts for changes on the background signal and for band-bending shifts. By this method, it was possible to robustly show that the formation of Si{sup 1+} is due to oxygen bonding to the upper dimer atoms. Our results contrast with ab initio calculation, which indicates that the most favorable bonding site is the back-bond of the down-dimer.

  6. Two Comments on Bond Angles

    Science.gov (United States)

    Glaister, P.

    1997-09-01

    Tetrahedral Bond Angle from Elementary Trigonometry The alternative approach of using the scalar (or dot) product of vectors enables the determination of the bond angle in a tetrahedral molecule in a simple way. There is, of course, an even more straightforward derivation suitable for students who are unfamiliar with vectors, or products thereof, but who do know some elementary trigonometry. The starting point is the figure showing triangle OAB. The point O is the center of a cube, and A and B are at opposite corners of a face of that cube in which fits a regular tetrahedron. The required bond angle alpha = AÔB; and using Pythagoras' theorem, AB = 2(square root 2) is the diagonal of a face of the cube. Hence from right-angled triangle OEB, tan(alpha/2) = (square root 2) and therefore alpha = 2tan-1(square root 2) is approx. 109° 28' (see Fig. 1).

  7. Covalent bonding and band-gap formation in ternary transition-metal di-aluminides: Al4MnCo and related compounds

    International Nuclear Information System (INIS)

    Krajci, M.; Hafner, J.

    2002-01-01

    In this paper we extend our previous study of the electronic structure of and bonding mechanism in transition-metal (TM) di-aluminides to ternary systems. We have studied the character of the bonding in Al 4 MnCo and related TM di-aluminides in the C11 b (MoSi 2 ) and C54 (TiSi 2 ) crystal structures. A peculiar feature of the electronic structure of these TM di-aluminides is the existence of a semiconducting gap at the Fermi level. In our previous work we predicted a gap in Al 2 TM compounds where the TM atoms have eight valence electrons. Here we demonstrate that the semiconducting gap does not disappear if the TM sites are occupied by two different TMs, provided that the electron-per-atom ratio is conserved. Such a replacement substantially increases the class of possibly semiconducting TM di-aluminides. Substitution for 3d TMs of 4d or 5d TMs enhances the width of the gap. From the analysis of the charge density distribution and the crystal orbital overlap population, we conclude that the bonding between atoms has dominantly covalent character. This is confirmed not only by the enhanced charge density halfway between atoms, but also by the clear bonding-antibonding splitting of the electronic states. If the gaps between split states that correspond to all bonding configurations in the crystal have a common overlap at the Fermi level, the intermetallic compound becomes a semiconductor. However, the results of the total-energy calculations suggest that the existence of a band gap does not necessarily imply a stable structure. Strong covalent bonds can exist also in Al-TM structures where no band gap is observed. (author)

  8. SOCIAL BONDING: REGULATION BY NEUROPEPTIDES

    Directory of Open Access Journals (Sweden)

    Claudia eLieberwirth

    2014-06-01

    Full Text Available Affiliative social relationships (e.g., among spouses, family members, and friends play an essential role in human society. These relationships affect psychological, physiological, and behavioral functions. As positive and enduring bonds are critical for the overall well-being of humans, it is not surprising that considerable effort has been made to study the neurobiological mechanisms that underlie social bonding behaviors. The present review details the involvement of the nonapeptides, oxytocin (OT and arginine vasopressin (AVP, in the regulation of social bonding in mammals including humans. In particular, we will discuss the role of OT and AVP in the formation of social bonds between partners of a mating pair as well as between parents and their offspring. Furthermore, the role of OT and AVP in the formation of interpersonal bonding involving trust is also discussed.

  9. Formation of doubly and triply bonded unsaturated compounds HCN, HNC, and CH2NH via N + CH4 low-temperature solid state reaction: from molecular clouds to solar system objects

    Science.gov (United States)

    Mencos, Alejandro; Krim, Lahouari

    2018-06-01

    We show in the current study carried out in solid phase at cryogenic temperatures that methane (CH4) ice exposed to nitrogen atoms is a source of two acids HCN, HNC, and their corresponding hydrogenated unsaturated species CH2NH, in addition to CH3, C2H6, CN-, and three nitrogen hydrides NH, NH2, and NH3. The solid state N + CH4 reaction taken in the ground state seems to be strongly temperature dependent. While at temperatures lower than 10 K only CH3, NH, NH2, and NH3 species formation is promoted due to CH bond dissociation and NH bond formation, stable compounds with CN bonds are formed at temperatures ranged between 10 and 40 K. Many of these reaction products, resulting from CH4 + N reaction, have already been observed in N2-rich regions such as the atmospheres of Titan, Kuiper belt objects, and molecular clouds of the interstellar medium. Our results show the power of the solid state N-atom chemistry in the transformation of simple astrochemical relevant species, such as CH4 molecules and N atoms into complex organic molecules which are also potentially prebiotic species.

  10. Hydrogen-bond-driven electrophilic activation for selectivity control: scope and limitations of fluorous alcohol-promoted selective formation of 1,2-disubstituted benzimidazoles and mechanistic insight for rationale of selectivity.

    Science.gov (United States)

    Chebolu, Rajesh; Kommi, Damodara N; Kumar, Dinesh; Bollineni, Narendra; Chakraborti, Asit K

    2012-11-16

    Hydrogen-bond-driven electrophilic activation for selectivity control during competitive formation of 1,2-disubstituted and 2-substituted benzimidazoles from o-phenylenediamine and aldehydes is reported. The fluorous alcohols trifluoroethanol and hexafluoro-2-propanol efficiently promote the cyclocondensation of o-phenylenediamine with aldehydes to afford selectively the 1,2-disubstituted benzimidazoles at rt in short times. A mechanistic insight is invoked by NMR, mass spectrometry, and chemical studies to rationalize the selectivity. The ability of the fluorous alcohols in promoting the reaction and controlling the selectivity can be envisaged from their better hydrogen bond donor (HBD) abilities compared to that of the other organic solvents as well as of water. Due to the better HBD values, the fluorous alcohols efficiently promote the initial bisimine formation by electrophilic activation of the aldehyde carbonyl. Subsequently the hydrogen-bond-mediated activation of the in situ-formed bisimine triggers the rearrangement via 1,3-hydride shift to form the 1,2-disubstituted benzimidazoles.

  11. Hydrogen Bonding to Alkanes: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen; Olesen, Solveig Gaarn

    2009-01-01

    The structural, vibrational, and energetic properties of adducts of alkanes and strong cationic proton donors were studied with composite ab initio calculations. Hydrogen bonding in [D-H+ H-alkyl] adducts contributes to a significant degree to the interactions between the two components, which is...

  12. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickx, Antoni P.A.; Poor, Catherine B.; Jureller, Justin E.; Budzik, Jonathan M.; He, Chuan; Schneewind, Olaf (UC)

    2012-09-05

    Bacillus cereus strains elaborate pili on their surface using a mechanism of sortase-mediated cross-linking of major and minor pilus components. Here we used a combination of electron microscopy and atomic force microscopy to visualize these structures. Pili occur as single, double or higher order assemblies of filaments formed from monomers of the major pilin, BcpA, capped by the minor pilin, BcpB. Previous studies demonstrated that within assembled pili, four domains of BcpA -- CNA{sub 1}, CNA{sub 2}, XNA and CNA{sub 3} -- each acquire intramolecular lysine-asparagine isopeptide bonds formed via catalytic glutamic acid or aspartic acid residues. Here we showed that mutants unable to form the intramolecular isopeptide bonds in the CNA2 or CNA3 domains retain the ability to form pilus bundles. A mutant lacking the CNA{sub 1} isopeptide bond assembled deformed pilin subunits that failed to associate as bundles. X-ray crystallography revealed that the BcpA variant Asp{sup 312}Ala, lacking an aspartyl catalyst, did not generate the isopeptide bond within the jelly-roll structure of XNA. The Asp{sup 312}Ala mutant was also unable to form bundles and promoted the assembly of deformed pili. Thus, structural integrity of the CNA{sub 1} and XNA domains are determinants for the association of pili into higher order bundle structures and determine native pilus structure.

  13. Theoretical study of the mechanism of formation of a chemical bond between two ions: A+ and B+. Application to CO++. Interpretation of N2O++ photo-dissociation mechanisms

    International Nuclear Information System (INIS)

    Levasseur, Nathalie

    1989-01-01

    This research thesis reports the theoretical study of the mechanism of formation of a chemical bond between two positively charged species, within the frame of the valence-bond theory and in the CO model case. The analysis in terms of orthogonal and non orthogonal orbitals leads to two very different interpretations, and allows potential curves of doubly charged diatomic ions to be simply explained, the generally evoked model to be put into question again, and a predictive model to be developed. The theoretical determination of N 2 O potential energy surfaces and of the first states of N 2 O ++ ( 3 Σ - , 1 Δ, 1 Σ + et 3 Π) allowed experimental results of N 2 O ++ photo-dissociation to be at least qualitatively understood and interpreted. Moreover, the study of electronic configurations involved in dissociation, showed that the model elaborated for a diatomic molecule is also valid for a triatomic system [fr

  14. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    Science.gov (United States)

    Wittmaack, Klaus

    2013-03-01

    implantation can be evaluated as a function of Cs coverage. The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

  15. Valence bond model potential energy surface for H4

    International Nuclear Information System (INIS)

    Silver, D.M.; Brown, N.J.

    1980-01-01

    Potential energy surfaces for the H 4 system are derived using the valence bond procedure. An ab initio evaluation of the valence bond energy expression is described and some of its numerical properties are given. Next, four semiempirical evaluations of the valence bond energy are defined and parametrized to yield reasonable agreement with various ab initio calculations of H 4 energies. Characteristics of these four H 4 surfaces are described by means of tabulated energy minima and equipotential contour maps for selected geometrical arrangements of the four nuclei

  16. Ab initio study on the reaction between uranium and O2

    International Nuclear Information System (INIS)

    Shuai Maobing; Zhao Pengji; Tian Anmin

    2000-08-01

    Optimized geometries, total energies and electronic structures of some gaseous atoms and molecules of uranium-oxygen system are calculated with harmonic vibration analysis using ab initio method. The potential energy surfaces (PESs) of the uranium oxidation process are also constructed. The calculated optimized geometries, infrared vibrational frequencies and the first ionized potential energies are in well accordance with available experimental data. Although U6p, U7s and U6d valence orbital electrons take part in the formation of U - O bond, the U5f electrons play an dominant role in this process and because the energies of U5f, U6d, U7s and Uds atomic orbitals are close to each other, these orbitals may hybrid and interact with O2p orbital, simultaneously, to form molecular orbitals of uranium oxides. The PESs show that different reaction modes result in different product geometries

  17. Study in electron microscopy the formation of the hybrid layer using adhesive systems One Coat and Single Bond Universal, at the Facultad de Medicina of the Universidad de Costa Rica

    International Nuclear Information System (INIS)

    Parra Barillas, Adriana; Montoya, Michael

    2013-01-01

    The formation of the hybrid layer is observed in dental pieces in vitro, using systems of conventional adhesives (Single Bond 2 of 3M and One Coat of Coltene), with different times of acid etching, through the use of atomic force microscopy (AFM). The images of the hybrid layer obtained from samples prepared with adhesive systems are analyzed by AFM. Samples collected have been of dental pieces (molars and premolars) recently extracted and later placed in water. The pieces used have provided more surface to be observed under the microscope, greater accessibility to the be cut for its study, and to the great pieces have facilitated their placement on the Isomet low speed saw. The differences are evaluated between hybrid layers according the adhesive system used and the mode of application of the images obtained in the atomic force microscope. The adhesive system that has allowed the formation of a hybrid layer more appropriate between the adhesive system One Coat and the adhesive system Single Bond Universal is determined. The time of acid etching as variable of procedure is determined and has interfered with the formation of a hybrid layer more stable. The images evaluated that were provided by the atomic force microscope and compared with the images of electron microscopy of other studies, have determined that the AFM is without providing detailed information, as well as the appropriate images to evaluate the hybrid layer of the adhesive systems Single Bond 2 and One Coat of Coltene, or the different times of acid etching. Therefore, for this type of study, the image of choice must be of an electron microscope [es

  18. Bonds Boom.

    Science.gov (United States)

    Reynolds, Cathryn

    1989-01-01

    The combined effect of the "Serrano" decision and Proposition 13 left California school districts with aging, overcrowded facilities. Chico schools won a $18.5 million general obligation bond election for facilities construction. With $11 billion needed for new school construction, California will need to tap local sources. A sidebar…

  19. Catalytic constructive deoxygenation of lignin-derived phenols: new C-C bond formation processes from imidazole-sulfonates and ether cleavage reactions.

    Science.gov (United States)

    Leckie, Stuart M; Harkness, Gavin J; Clarke, Matthew L

    2014-10-09

    As part of a programme aimed at exploiting lignin as a chemical feedstock for less oxygenated fine chemicals, several catalytic C-C bond forming reactions utilising guaiacol imidazole sulfonate are demonstrated. These include the cross-coupling of a Grignard, a non-toxic cyanide source, a benzoxazole, and nitromethane. A modified Meyers reaction is used to accomplish a second constructive deoxygenation on a benzoxazole functionalised anisole.

  20. Heterometallic Pd(II)-Ni(II) complexes with meso-substituted dibenzotetraaza[14]annulene: double C-H bond activation and formation of a rectangular tetradibenzotetraaza[14]annulene.

    Science.gov (United States)

    Khaledi, Hamid; Olmstead, Marilyn M; Fukuda, Takamitsu; Ali, Hapipah Mohd

    2014-11-03

    Three isomeric 2[Pd(II)-Ni(II)] metal complexes, derived from indoleninyl meso-substituted dibenzotetraaza[14]annulene, were synthesized. The resulting dimers feature Ni···Ni or, alternatively, Ni···π interactions in staggered or slipped cofacial structures. A remarkable insertion of palladium into two different C-H bonds yielded a 4[Pd(II)-Ni(II)] rectangular complex with dimensions of 8.73 × 10.38 Å.

  1. The CH/π hydrogen bond: Implication in chemistry

    Science.gov (United States)

    Nishio, M.

    2012-06-01

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

  2. New results for the formation of a muoniated radical in the Mu + Br2 system: a van der Waals complex or evidence for vibrational bonding in Br-Mu-Br?

    Science.gov (United States)

    Fleming, Donald G; Cottrell, Stephen P; McKenzie, Iain; Macrae, Roderick M

    2012-08-21

    New evidence is presented for the observation of a muoniated radical in the Mu + Br(2) system, from μSR longitudinal field (LF) repolarisation studies in the gas phase, at Br(2) concentrations of 0.1 bar in a Br(2)/N(2) mixture at 300 K and at 10 bar total pressure. The LF repolarisation curve, up to a field of 4.5 kG, reveals two paramagnetic components, one for the Mu atom, formed promptly during the slowing-down process of the positive muon, with a known Mu hyperfine coupling constant (hfcc) of 4463 MHz, and one for a muoniated radical formed by fast Mu addition. From model fits to the Br(2)/N(2) data, the radical component is found to have an unusually high muon hfcc, assessed to be ∼3300 MHz with an overall error due to systematics expected to exceed 10%. This high muon hfcc is taken as evidence for the observation of either the Br-Mu-Br radical, and hence of vibrational bonding in this H[combining low line]-L[combining low line]-H[combining low line] system, or of a MuBr(2) van der Waals complex formed in the entrance channel. Preliminary ab initio electronic structure calculations suggest the latter is more likely but fully rigorous calculations of the effect of dynamics on the hfcc for either system have yet to be carried out.

  3. The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study.

    Science.gov (United States)

    Rosenberg, Robert E

    2018-05-10

    Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R'OH, where R and R' are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R'OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F-(C) n -OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.

  4. The triel bond: a potential force for tuning anion-π interactions

    Science.gov (United States)

    Esrafili, Mehdi D.; Mousavian, Parisasadat

    2018-02-01

    Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

  5. AB/sub 5/-catalyzed hydrogen evolution cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Hall, D E; Sawada, T; Shepard, V R; Tsujikawa, Y

    1984-01-01

    The AB/sub 5/ metal compounds are highly efficient hydrogen evolution electrocatalysts in alkaline electrolyte. Three types of AB/sub 5/-catalyzed cathode structures were made, using the hydride-forming AB/sub 5/ compounds in particulate form. Plastic-bonded cathodes containing >90 w/o AB/sub 5/ (finished-weight basis) were the most efficient, giving hydrogen evolution overpotentials (/eta/ /SUB H2/ ) of about 0.05 V at 200 mA cm/sup -2/. However, they tended to swell and shed material during electrolysis. Pressed, sintered cathodes containing 40-70 w/o catalyst in a nickel binder gave /eta/ /SUB H2/ about0.08 V; catalyst retention was excellent. Porous, sintered cathode coatings were made with 30-70 w/o AB/sub 5/ catalyst loadings. Their overpotentials were similar to those of the pressed, sintered cathodes. However, at catalyst loadings below about 40 w/o, high overpotentials characteristic of the nickel binder were observed. The structural and electrochemical properties of the three AB/sub 5/-catalyzed cathodes are discussed.

  6. Diffusion bonding

    International Nuclear Information System (INIS)

    Anderson, R.C.

    1976-01-01

    A method is described for joining beryllium to beryllium by diffusion bonding. At least one surface portion of at least two beryllium pieces is coated with nickel. A coated surface portion is positioned in a contiguous relationship with another surface portion and subjected to an environment having an atmosphere at a pressure lower than ambient pressure. A force is applied on the beryllium pieces for causing the contiguous surface portions to abut against each other. The contiguous surface portions are heated to a maximum temperature less than the melting temperature of the beryllium, and the applied force is decreased while increasing the temperature after attaining a temperature substantially above room temperature. A portion of the applied force is maintained at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions

  7. Design and synthesis of quasi-diastereomeric molecules with unchanging central, regenerating axial and switchable helical chirality via cleavage and formation of Ni(II–O and Ni(II–N coordination bonds

    Directory of Open Access Journals (Sweden)

    Vadim A. Soloshonok

    2012-11-01

    Full Text Available We describe herein the design and synthesis of asymmetric, pentadentate ligands, which are able to coordinate to Ni(II cations leading to quasi-diastereomeric complexes displaying two new elements of chirality: stereogenic axis and helix along with configurational stabilization of the stereogenic center on the nitrogen. Due to the stereocongested structural characteristics of the corresponding Ni(II complexes, the formation of quasi-diastereomeric products is highly stereoselective providing formation of only two, (Ra*,Mh*,Rc* and (Ra*,Ph*,Rc*, out of the four possible stereochemical combinations. The reversible quasi-diastereomeric transformation between the products (Ra*,Mh*,Rc* and (Ra*,Ph*,Rc* occurs by intramolecular trans-coordination of Ni–NH and Ni–O bonds providing a basis for a chiral switch model.

  8. AB Manpower Plan 2007

    CERN Document Server

    Myers, Stephen

    2007-01-01

    The present exercise is not as such a "manpower plan" but a purely budgetary comparison of known plus requested resources with the known commitments over the period 2007-2012. From a purely budgetary point of view, AB will have the capacity to maintain all those recently hired staff who fulfill the criteria for long term employment at CERN. Following this budgetary exercise, AB proposes to perform a CERN-wide staff work plan so as to compare the manpower available to the quantity of work to be done in the totality of the work-packages. If there is a significant mismatch between these two quantities then we propose the following measures which would create personnel economies and allow us to redress the mismatch by increased recruitment: a new job severance scheme; CERN restructuring; use of the new CERN-ITER agreement; more flexibility in transfers from Materials to Personnel budgets. Failing this a re-examination of possible closure of lower priority facilities may be needed.

  9. pKa values of hyodeoxycholic and cholic acids in the binary mixed micelles sodium-hyodeoxycholate-Tween 40 and sodium-cholate-Tween 40: Thermodynamic stability of the micelle and the cooperative hydrogen bond formation with the steroid skeleton.

    Science.gov (United States)

    Poša, Mihalj; Pilipović, Ana; Bećarević, Mirjana; Farkaš, Zita

    2017-01-01

    Due to a relatively small size of bile acid salts, their mixed micelles with nonionic surfactants are analysed. Of the special interests are real binary mixed micelles that are thermodynamically more stable than ideal mixed micelles. Thermodynamic stability is expressed with an excess Gibbs energy (G E ) or over an interaction parameter (β ij ). In this paper sodium salts of cholic (C) and hyodeoxycholic acid (HD) in their mixed micelles with Tween 40 (T40) are analysed by potentiometric titration and their pKa values are determined. Examined bile acids in mixed micelles with T40 have higher pKa values than free bile acids. The increase of ΔpKa acid constant of micellary bound C and HD is in a correlation with absolute values of an interaction parameter. According to an interaction parameter and an excess Gibbs energy, mixed micelle HD-T40 are thermodynamically more stable than mixed micelles C-T40. ΔpKa values are higher for mixed micelles with Tween 40 whose second building unit is HD, related to the building unit C. In both micellar systems, ΔpKa increases with the rise of a molar fraction of Tween 40 in binary mixtures of surfactants with sodium salts of bile acids. This suggests that, ΔpKa can be a measure of a thermodynamic stabilization of analysed binary mixed micelles as well as an interaction parameter. ΔpKa values are confirmed by determination of a distribution coefficient of HD and C in systems: water phase with Tween 40 in a micellar concentration and 1-octanol, with a change of a pH value of a water phase. Conformational analyses suggests that synergistic interactions between building units of analysed binary micelles originates from formation of hydrogen bonds between steroid OH groups and polyoxyethylene groups of the T40. Relative similarity and spatial orientation of C 3 and C 6 OH group allows cooperative formation of hydrogen bonds between T40 and HD - excess entropy in formation of mixed micelle. If a water solution of analysed binary

  10. Formation of a Six-Coordinate fac-[Re(Co)3]+ Complex by the N-C bond cleavage of a potentially tetradentate ligand

    International Nuclear Information System (INIS)

    Booysen, I.; Gerber, T. I. A.; Hosten, E.; Mayer, P.

    2008-01-01

    The rhenium(I) compound fac-[Re(CO) 3 (daa)]. Hpab.H 2 O (Hpab N,N'-(l,2-phenylene)bis(2'-aminobenzamide); Hdaa 2-amino-N-(2-aminophenyl)benzamide) was synthesized from the reaction of [Re(CO) 5 ,Br] with two equivalent of Hpab in toluene. The monoanionic tridentate ligand daa was formed by the rhenium-mediated cleavage of an amido N-C bond of the potentially tetradentate ligand Hpab. The compound was characterized by IR spectroscopy and X-ray crystallography, and daa is coordinated as a diamino amide via three nitrogen-donor atoms

  11. Self assembly of dialkoxo bridged dinuclear Fe(III) complex of pyridoxal Schiff base with C-C bond formation - structure, spectral and magnetic properties

    Czech Academy of Sciences Publication Activity Database

    Murašková, V.; Szabó, N.; Pižl, M.; Hoskovcová, I.; Dušek, Michal; Huber, Š.; Sedmidubský, D.

    2017-01-01

    Roč. 461, May (2017), s. 111-119 ISSN 0020-1693 R&D Projects: GA ČR(CZ) GA15-12653S; GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : iron(III) dinuclear complex * dialkoxo bridged pyridoxal Schiff base * C-C bond * crystal structure * magnetic properties Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 2.002, year: 2016

  12. An Iterated GMM Procedure for Estimating the Campbell-Cochrane Habit Formation Model, with an Application to Danish Stock and Bond Returns

    DEFF Research Database (Denmark)

    Engsted, Tom; Møller, Stig Vinther

    2010-01-01

    We suggest an iterated GMM approach to estimate and test the consumption based habit persistence model of Campbell and Cochrane, and we apply the approach on annual and quarterly Danish stock and bond returns. For comparative purposes we also estimate and test the standard constant relative risk...... covering more than 80 years there is absolutely no evidence of superior performance of the Campbell-Cochrane model. For the shorter and more recent quarterly data over a 20-30 year period, there is some evidence of counter-cyclical time-variation in the degree of risk-aversion, in accordance...

  13. An iterated GMM procedure for estimating the Campbell-Cochrane habit formation model, with an application to Danish stock and bond returns

    DEFF Research Database (Denmark)

    Engsted, Tom; Møller, Stig V.

    We suggest an iterated GMM approach to estimate and test the consumption based habit persistence model of Campbell and Cochrane (1999), and we apply the approach on annual and quarterly Danish stock and bond returns. For comparative purposes we also estimate and test the standard CRRA model...... than 80 years there is absolutely no evidence of superior performance of the Campbell-Cochrane model. For the shorter and more recent quarterly data over a 20-30 year period, there is some evidence of counter-cyclical time-variation in the degree of risk-aversion, in accordance with the Campbell...

  14. In situ formation of adhesive hydrogels based on PL with laterally grafted catechol groups and their bonding efficacy to wet organic substrates.

    Science.gov (United States)

    Ye, Mingming; Jiang, Rui; Zhao, Jin; Zhang, Juntao; Yuan, Xubo; Yuan, Xiaoyan

    2015-12-01

    Adhesives with catechol moieties have been widely investigated in recent years. However, actually how much catechol groups for these mussel bio-inspired adhesives, especially in their natural form under physiological condition, is appropriate to bond with organic substrates has not been studied intensively. This study blends ε-polylysine (PL), featuring laterally grafted catechols under physiological conditions (pH 7.4), with oxidized dextran to form a hydrogel in situ via the Schiff base without introducing small cytotoxic molecules as crosslinking agents. It finds that the amount of catechol groups imposes an obvious influence on gelation time, swelling behavior, and hydrogel morphology. Both the storage modulus and adhesion strength are found to increase first and decrease afterwards with an increase of pendent catechol content. Furthermore, catechol hydrogen interactions and the decrease in the crosslink density derived from the decrease of amino groups on PL are simultaneously found to affect the storage modulus. Meanwhile, multiple hydrogen-bonding interactions of catechol with amino, hydroxyl, and carboxyl groups, which are in abundance on the surface of tissue, are mainly found to provide an adhesive force. The study finds that with more catechol, there is a greater chance that the cohesive force will weaken, making the entire adhesion strength of the hydrogel decrease. Using a cytotoxicity test, the nontoxicity of the hydrogel towards the growth of L929 cells is proven, indicating that hydrogels have potential applications in soft tissue repair under natural physiological conditions.

  15. Hydrogen bond controlled adduct formation of meso-tetra(4-sulfonatophenyl)porphyrin with protic acids: a UV-vis spectroscopic study.

    Science.gov (United States)

    Zakavi, Saeed; Rahiminezhad, Hajar; Alizadeh, Robabeh

    2010-12-01

    Interaction of meso-tetra(4-sulfonatophenyl)porphyrin (H2tppS4) with weak and strong protic acid have been studied by UV-vis spectroscopy in water, dichloromethane and methanol. Different shifts of the Soret and Q(0,0) bands in the three solvents, the aggregation of diprotonated species and the stability of porphyrin-acid adducts in the solution, may be explained by the inter- and intramolecular hydrogen bonds. Whilst, the addition of excess amounts of tetra-n-butylammonium chloride to H2tppS4(Cl)2 in dichloromethane has little to no effect on the UV-vis spectrum of the dication, gradual addition of tetra-n-butylammonium hydrogen sulfate to the dichloromethane solution of H2tppS4(H2SO4)2 leads to the degradation of adducts and the release of porphryin. The results of this study clearly show the crucial role played by hydrogen bonds between the porphyrin diprotonated species and the counter ion in the stability of porphyrin diacids in solution. Copyright © 2010 Elsevier B.V. All rights reserved.

  16. Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases.

    Science.gov (United States)

    Alkorta, Ibon; Blanco, Fernando; Solimannejad, Mohammad; Elguero, Jose

    2008-10-30

    A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.

  17. Outburst in Mira AB?

    Science.gov (United States)

    Karovska, Margarita

    2003-09-01

    The nearby system Mira AB composed of an aging AGB star (Mira A) and a WD companion (Mira B) offers a unique laboratory for studying wind accretion processes, a poorly understood phenomenon in many sources. Recent Chandra ACIS-S Obs.(70ks on 12/6/03; PI.M.Karovska) resolved for the first time the components (~0.6") in X-rays, and detected a new bright soft source (A. This is the first detection of X-rays from an AGB star. This source was not detected by ROSAT in 1993 or recently by XMM 8/03 (AAS/03,J.Kastner), and could be a transient phenomenon. Model fitting shows that the soft X-ray emission is likely several emission lines, rather then a continuum; with ACIS spectral resolution we cannot resolve or identify these lines. We propose a 40ks LETG+HRC-S obs. to identify the lines and determine the emission mechanism.

  18. Characterization of electron-deficient chemical bonding of diborane with attosecond electron wavepacket dynamics and laser response

    International Nuclear Information System (INIS)

    Yonehara, Takehiro; Takatsuka, Kazuo

    2009-01-01

    We report a theoretical study of non-adiabatic electrons-nuclei coupled dynamics of diborane H 2 BH 2 BH 2 under several types of short pulse lasers. This molecule is known to have particularly interesting geometrical and electronic structures, which originate from the electron-deficient chemical bondings. We revisit the chemical bonding of diborane from the view point of electron wavepacket dynamics coupled with nuclear motions, and attempt to probe the characteristics of it by examining its response to intense laser fields. We study in the following three aspects, (i) bond formation of diborane by collision between two monoboranes, (ii) attosecond electron wavepacket dynamics in the ground state and first excited state by circularly polarized laser pulse, and (iii) induced fragmentation back to monoborane molecules by linearly polarized laser. The wave lengths of two types of laser field employed are 200 nm (in UV range) and 800 nm (in IR range), and we track the dynamics from hundreds of attoseconds up to few tens of femtoseconds. To this end, we apply the ab initio semiclassical Ehrenfest theory, into which the classical vector potential of a laser field is introduced. Basic features of the non-adiabatic response of electrons to the laser fields is elucidated in this scheme. To analyze the electronic wavepackets thus obtained, we figure out bond order density that is a spatial distribution of the bond order and bond order flux density arising only from the bonding regions, and so on. Main findings in this work are: (i) dimerization of monoboranes to diborane is so efficient that even intense laser is hard to prevent it; (ii) collective motions of electron flux emerge in the central BHHB bonding area in response to the circularly polarized laser fields; (iii) laser polarization with the direction of central two BH bonding vector is efficient for the cleavage of BH 3 -BH 3 ; and (iv) nuclear derivative coupling plays a critical role in the field induced

  19. Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3 and Ammonia (NH3 Donor-Acceptor Complex

    Directory of Open Access Journals (Sweden)

    Dulal C. Ghosh

    2004-09-01

    Full Text Available The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule

  20. Ab initio atomistic thermodynamics calculations of the initial deposition of epitaxial MgO film on GaAs(001)-{beta}2(2 Multiplication-Sign 4)

    Energy Technology Data Exchange (ETDEWEB)

    Tamarany, Rizcky; Lee, Seung-Cheol [Korea Institute of Science and Technology, Seoul 136-791 (Korea, Republic of); Department of Nanomaterials Science and Engineering, University of Science and Technology, Daejeon 305-350 (Korea, Republic of); Kim, Hyung-Jun; Choi, Jung-Hae [Korea Institute of Science and Technology, Seoul 136-791 (Korea, Republic of)

    2013-02-07

    Ab initio calculations were performed to investigate the initial deposition of epitaxial MgO on GaAs(001)-{beta}2(2 Multiplication-Sign 4). The differences between the chemical bonding of Mg-As and O-As were characterized by the adsorption energies of atomic O and Mg at several symmetrically distinct sites, and O bonding was substantially stronger than that of Mg. Thermodynamics were analyzed through the introduction of environmental chemical potentials simulating in situ growth conditions by the sputtering of a stoichiometric MgO target. A surface phase diagram was generated under Mg and O environments with constrained equilibrium, and the results explained the initial formation of an epitaxial MgO phase on GaAs(001)-{beta}2(2 Multiplication-Sign 4).

  1. Ab initio atomistic thermodynamics calculations of the initial deposition of epitaxial MgO film on GaAs(001)-β2(2 × 4)

    International Nuclear Information System (INIS)

    Tamarany, Rizcky; Lee, Seung-Cheol; Kim, Hyung-Jun; Choi, Jung-Hae

    2013-01-01

    Ab initio calculations were performed to investigate the initial deposition of epitaxial MgO on GaAs(001)-β2(2 × 4). The differences between the chemical bonding of Mg-As and O-As were characterized by the adsorption energies of atomic O and Mg at several symmetrically distinct sites, and O bonding was substantially stronger than that of Mg. Thermodynamics were analyzed through the introduction of environmental chemical potentials simulating in situ growth conditions by the sputtering of a stoichiometric MgO target. A surface phase diagram was generated under Mg and O environments with constrained equilibrium, and the results explained the initial formation of an epitaxial MgO phase on GaAs(001)-β2(2 × 4).

  2. The Existence of a Designer Al=Al Double Bond in the LiAl2 H4- Cluster Formed by Electronic Transmutation.

    Science.gov (United States)

    Lundell, Katie A; Zhang, Xinxing; Boldyrev, Alexander I; Bowen, Kit H

    2017-12-22

    The Al=Al double bond is elusive in chemistry. Herein we report the results obtained via combined photoelectron spectroscopy and ab initio studies of the LiAl 2 H 4 - cluster that confirm the formation of a conventional Al=Al double bond. Comprehensive searches for the most stable structures of the LiAl 2 H 4 - cluster have shown that the global minimum isomer I possesses a geometric structure which resembles that of Si 2 H 4 , demonstrating a successful example of the transmutation of Al atoms into Si atoms by electron donation. Theoretical simulations of the photoelectron spectrum discovered the coexistence of two isomers in the ion beam, including the one with the Al=Al double bond. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Ab initio lattice dynamics of metal surfaces

    International Nuclear Information System (INIS)

    Heid, R.; Bohnen, K.-P.

    2003-01-01

    Dynamical properties of atoms on surfaces depend sensitively on their bonding environment and thus provide valuable insight into the local geometry and chemical binding at the boundary of a solid. Density-functional theory provides a unified approach to the calculation of structural and dynamical properties from first principles. Its high accuracy and predictive power for lattice dynamical properties of semiconductor surfaces has been demonstrated in a previous article by Fritsch and Schroeder (Phys. Rep. 309 (1999) 209). In this report, we review the state-of-the-art of these ab initio approaches to surface dynamical properties of metal surfaces. We give a brief introduction to the conceptual framework with focus on recent advances in computational procedures for the ab initio linear-response approach, which have been a prerequisite for an efficient treatment of surface dynamics of noble and transition metals. The discussed applications to clean and adsorbate-covered surfaces demonstrate the high accuracy and reliability of this approach in predicting detailed microscopic properties of the phonon dynamics for a wide range of metallic surfaces

  4. A new face of phenalenyl-based radicals in the transition metal-free C-H arylation of heteroarenes at room temperature: trapping the radical initiator via C-C σ-bond formation.

    Science.gov (United States)

    Ahmed, Jasimuddin; P, Sreejyothi; Vijaykumar, Gonela; Jose, Anex; Raj, Manthan; Mandal, Swadhin K

    2017-11-01

    The radical-mediated transition metal-free approach for the direct C-H bond functionalization of arenes is considered as a cost effective alternative to transition metal-based catalysis. An organic ligand-based radical plays a key role by generating an aryl radical which undergoes a subsequent functionalization process. The design principle of the present study takes advantage of a relatively stable odd alternant hydrocarbon-based phenalenyl (PLY) radical. In this study, the first transition metal-free catalyzed direct C-H arylation of a variety of heteroarenes such as azoles, furan, thiophene and pyridine at room temperature has been reported using a phenalenyl-based radical without employing any photoactivation step. This protocol has been successfully applied to the gram scale synthesis of core moieties of bioactive molecules. The phenalenyl-based radical initiator has been characterized crystallographically by trapping it via the formation of a C-C σ-bond between the phenalenyl radical and solvent-based radical species.

  5. Role of atomic bonding for compound and glass formation in Ni-Si, Pd-Si, and Ni-B systems

    Science.gov (United States)

    Tanaka, K.; Saito, T.; Suzuki, K.; Hasegawa, R.

    1985-11-01

    Valence electronic structures of crystalline compounds and glassy alloys of Ni silicides, Pd silicides, and Ni borides are studied by soft-x-ray spectroscopy over wide ranges of Si and B concentrations. The samples prepared include bulk compounds, glassy ribbons, and amorphous sputtered films. Silicon Kβ emissions of Ni and Pd silicides generally consist of a prominent peak fixed at ~=4.5 and ~=5.8 eV below the Fermi level EF, respectively, with a shoulder near EF which grows and shifts toward lower energy with increasing Si concentration. The former is identified as due to Si p-like states forming Si 3p-Ni 3d or Si 3p-Pd 4d bonding states while the latter as due to the corresponding antibonding states. Ni L3 and Pd L3 emissions of these silicides indicate that Ni 3d and Pd 4d states lie between the above two states. These local electronic configurations are consistent with partial-density-of-states (PDOS) calculations performed by Bisi and Calandra. Similar electronic configurations are suggested for Ni borides from B Kα and Ni L3 emissions. Differences of emission spectra between compounds and glasses of similar compositions are rather small, but some enhancement of the contribution of antibonding states to the PDOS near EF is suggested for certain glasses over that of the corresponding compounds. These features are discussed in connection with the compound stability and glass formability.

  6. Cu(II) salen complex with propylene linkage: An efficient catalyst in the formation of Csbnd X bonds (X = N, O, S) and biological investigations

    Science.gov (United States)

    Azam, Mohammad; Dwivedi, Sourabh; Al-Resayes, Saud I.; Adil, S. F.; Islam, Mohammad Shahidul; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Lee, Dong-Ung

    2017-02-01

    The catalytic property of a mononuclear Cu(II) salen complex in Chan-Lam coupling reaction with phenyl boronic acid at room temperature is reported. The studied complex is found to be potential catalyst in the preparation of carbon-heteroatom bonds with excellent yields. The studied Cu(II) salen complex is monoclinic with cell parameters, a = 9.6807(5) (α 90°), (b = 17.2504(8) (β 112.429 (2), c = 11.1403 (6) (γ = 90°), and has distorted square planar environment around Cu(II) ion. Furthermore, there is no π⋯π interactions in the reported complex due to large distance between the centroid of aromatic rings. In addition, DNA binding study of Cu(II) salen complex by fluorescence and absorption spectroscopy is also reported. Moreover, the reported Cu(II) salen complex exhibits significant anticancer activity against MCF-7 cancer cell lines, and displays potential antimicrobial biofilm activity against P. aeruginosa, suggesting antimicrobial biofilm an important tool for suppression of resistant infections caused by P. aeruginosa.

  7. Structure phenomena in the bond zone of explosively bonded plates

    International Nuclear Information System (INIS)

    Livne, Z.

    1979-12-01

    In the bond areas of couples of explosively bonded plates, there are often zones, generally designated as ''molten pockets'', which have undergone melting and solidification. The object of the present study was to investigate molten pockets, which have a decisive effect on bond quality. The experimental samples for the study were chosen in consideration of the mutual behaviour of the plates constituting the couples, according to their equilibrium phase diagrams. To facilitate the investigation, large plates were bonded under conditions that enabled to to obtain wavy bond zones that included relatively large molten pockets. To clarify the complex nature of molten pockets and their surroundings, a wide variety of methods were employed. It was found that the shape and composition of molten pockets largely depend upon the mechanism of formation of both the bond wave and the molten pockets. It was also found that the composition of molten pockets is not homogeneous, which is manifest in the modification of the composition of the pockets, the solidification morphology, the phases, which have been identified by X-ray diffraction, and the bond strenght and hardness. Moreover, the different solidification morphologies revealed by metallography were found to depend upon the types of plates bonded, the bonding conditions and the location of pockets in the wavy interface. For molten pockets, cooling rates of 10 4 to 10 5 (degC/sec) have been deduced from interdendritic spacing, and found to be in good agreement with calculations after a mathematical model. It seems that the fast cooling rates and the steep temperature gradients are at the origin of the particular solidification phenomena observed in molten pockets

  8. Characterization of Elastic Properties of Porous Graphene Using an Ab Initio Study

    Directory of Open Access Journals (Sweden)

    Reza Ansari

    2016-12-01

    Full Text Available Importance of covalent bonded two-dimensional monolayer nanostructures and also hydrocarbons is undeniably responsible for creation of new fascinating materials like polyphenylene polymer, a hydrocarbon super honeycomb network, so-called porous graphene. The mechanical properties of porous graphene such as its Young’s modulus, Poisson’s ratio and the bulk modulus as the determinative properties are calculated in this paper using ab initio calculations. To accomplish this aim, the density functional theory on the basis of generalized gradient approximation and the Perdew–Burke–Ernzerhof exchange correlation is employed. Density functional theory calculations are used to calculate strain energy of porous graphene with respect to applied strain. Selected numerical results are then presented to study the properties of porous graphene. Comparisons are made between the properties of porous graphene and those of other analogous nanostructures. The results demonstrated lower stiffness of porous graphene than those of graphene and graphyne, and higher stiffness than that of graphdyine and other graphyne families. Unlikely, Poisson’s ratio is observed to be more than that of graphene and also less than that of graphyne. It is further observed that the presence of porosity and also formation of C-H bond in the pore sites is responsible for these discrepancies. Porous graphene is found to behave as the isotropic material.

  9. Ab initio thermochemistry using optimal-balance models with isodesmic corrections: The ATOMIC protocol

    Science.gov (United States)

    Bakowies, Dirk

    2009-04-01

    A theoretical composite approach, termed ATOMIC for Ab initio Thermochemistry using Optimal-balance Models with Isodesmic Corrections, is introduced for the calculation of molecular atomization energies and enthalpies of formation. Care is taken to achieve optimal balance in accuracy and cost between the various components contributing to high-level estimates of the fully correlated energy at the infinite-basis-set limit. To this end, the energy at the coupled-cluster level of theory including single, double, and quasiperturbational triple excitations is decomposed into Hartree-Fock, low-order correlation (MP2, CCSD), and connected-triples contributions and into valence-shell and core contributions. Statistical analyses for 73 representative neutral closed-shell molecules containing hydrogen and at least three first-row atoms (CNOF) are used to devise basis-set and extrapolation requirements for each of the eight components to maintain a given level of accuracy. Pople's concept of bond-separation reactions is implemented in an ab initio framework, providing for a complete set of high-level precomputed isodesmic corrections which can be used for any molecule for which a valence structure can be drawn. Use of these corrections is shown to lower basis-set requirements dramatically for each of the eight components of the composite model. A hierarchy of three levels is suggested for isodesmically corrected composite models which reproduce atomization energies at the reference level of theory to within 0.1 kcal/mol (A), 0.3 kcal/mol (B), and 1 kcal/mol (C). Large-scale statistical analysis shows that corrections beyond the CCSD(T) reference level of theory, including coupled-cluster theory with fully relaxed connected triple and quadruple excitations, first-order relativistic and diagonal Born-Oppenheimer corrections can normally be dealt with using a greatly simplified model that assumes thermoneutral bond-separation reactions and that reduces the estimate of these

  10. tri-n-butyltin hydride-mediated radical reaction of a 2-iodobenzamide: formation of an unexpected carbon-tin bond

    International Nuclear Information System (INIS)

    Oliveira, Marcelo T.; Alves, Rosemeire B.; Cesar, Amary; Prado, Maria Auxiliadora F.; Alves, Ricardo J.; Queiroga, Carla G.; Santos, Leonardo S.; Eberlin, Marcos N.

    2007-01-01

    The tri-n-butyltin hydride-mediated reaction of methyl 2,3-di-O-benzyl-4-O-trans-cinnamyl- 6-deoxy-6-(2-iodobenzoylamino)-α-D-galactopyranoside afforded an unexpected aryltributyltin compound. The structure of this new tetraorganotin(IV) product has been elucidated by 1 H, 13 C NMR spectroscopy, COSY and HMQC experiments and electrospray ionization mass spectrometry (ESI-MS). The formation of this new compound via a radical coupling reaction and a radical addition-elimination process is discussed. (author)

  11. Spectral monitoring of AB Aur

    Science.gov (United States)

    Rodríguez Díaz, L. F.; Oostra, B.

    2017-07-01

    The Astronomical Observatory of the Universidad de los Andes in Bogotá, Colombia, did a spectral monitoring during 2014 and 2015 to AB Aurigae, the brightest Herbig Ae/be star in the northern hemisphere. The aim of this project is applying spectral techniques, in order to identify specific features that could help us not only to understand how this star is forming, but also to establish a pattern to explain general star formation processes. We have recorded 19 legible spectra with a resolving power of R = 11,0000, using a 40 cm Meade telescope with an eShel spectrograph, coupled by a 50-micron optical fiber. We looked for the prominent absorption lines, the Sodium doublet at 5890Å and 5896Å, respectively and Magnesium II at 4481Å; to measure radial velocities of the star, but, we did not find a constant value. Instead, it ranges from 15 km/s to 32 km/s. This variability could be explained by means of an oscillation or pulsation of the external layers of the star. Other variabilities are observed in some emission lines: Hα, Hβ, He I at 5876Å and Fe II at 5018Å. It seems this phenomenon could be typical in stars that are forming and have a circumstellar disk around themselves. This variability is associated with the nonhomogeneous surface of the star and the interaction that it has with its disk. Results of this interaction could be seen also in the stellar wind ejected by the star. More data are required in order to look for a possible period in the changes of radial velocity of the star, the same for the variability of He I and Fe II, and phenomena present in Hα. We plan to take new data in January of 2017.

  12. Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

    Science.gov (United States)

    Bandyopadhyay, D; Bhattacharyya, D

    2006-10-15

    It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.

  13. Bond strength of masonry

    NARCIS (Netherlands)

    Pluijm, van der R.; Vermeltfoort, A.Th.

    1992-01-01

    Bond strength is not a well defined property of masonry. Normally three types of bond strength can be distinguished: - tensile bond strength, - shear (and torsional) bond strength, - flexural bond strength. In this contribution the behaviour and strength of masonry in deformation controlled uniaxial

  14. Biological Cleavage of the C–P Bond in Perfluoroalkyl Phosphinic Acids in Male Sprague-Dawley Rats and the Formation of Persistent and Reactive Metabolites

    Science.gov (United States)

    Yeung, Leo W.Y.; Mabury, Scott A.

    2017-01-01

    Background: Perfluoroalkyl phosphinic acids (PFPiAs) have been detected in humans, wildlife, and various environmental matrices. These compounds have been used with perfluoroalkyl phosphonic acids (PFPAs) as surfactants in consumer products and as nonfoaming additives in pesticide formulations. Unlike the structurally related perfluoroalkyl sulfonic and carboxylic acids, little is known about the biological fate of PFPiAs. Objectives: We determined the biotransformation products of PFPiAs and some pharmacokinetic parameters in a rat model. Methods: Male Sprague-Dawley rats received an oral gavage dose of either C6/C8PFPiA, C8/C8PFPiA, or C8PFPA. Blood was sampled over time, and livers were harvested upon sacrifice. Analytes were quantified using ultra-high-performance liquid chromatography–tandem mass spectrometry or gas chromatography–mass spectrometry. Results: PFPiAs were metabolized to the corresponding PFPAs and 1H-perfluoroalkanes (1H-PFAs), with 70% and 75% biotransformation 2 wk after a single bolus dose for C6/C8PFPiA and C8/C8PFPiA, respectively. This is the first reported cleavage of a C-P bond in mammals, and the first attempt, with a single-dose exposure, to characterize the degradation of any perfluoroalkyl acid. Elimination half-lives were 1.9±0.5 and 2.8±0.8 days for C6/C8PFPiA and C8/C8PFPiA, respectively, and 0.95±0.17 days for C8PFPA. Although elimination half-lives were not determined for 1H-PFAs, concentrations were higher than the corresponding PFPAs 48 h after rats were dosed with PFPiAs, suggestive of slower elimination. Conclusions: PFPiAs were metabolized in Sprague-Dawley rats to form persistent PFPAs as well as 1H-PFAs, which contain a labile hydrogen that may undergo further metabolism. These results in rats produced preliminary findings of the pharmacokinetics and metabolism of PFPiAs, which should be further investigated in humans. If there is a parallel between the disposition of these chemicals in humans and rats, then

  15. Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Taioli, Simone [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Chemistry, University of Bologna, Bologna (Italy); Garberoglio, Giovanni [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Simonucci, Stefano [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Physics, University of Camerino, Camerino (Italy); Beccara, Silvio a [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Aversa, Lucrezia [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Nardi, Marco [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Institut fuer Physik, Humboldt-Universitaet zu Berlin, Berlin (Germany); Verucchi, Roberto [Institute of Materials for Electronics and Magnetism, FBK-CNR, Trento (Italy); Iannotta, Salvatore [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Parma (Italy); Dapor, Maurizio [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Materials Engineering and Industrial Technologies, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Padova (Italy); and others

    2013-01-28

    In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C{sub 60} collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C{sub 60} impact on the Si surface is in good agreement with our experimental findings.

  16. Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics.

    Science.gov (United States)

    Urakawa, Atsushi; Iannuzzi, Marcella; Hutter, Jürg; Baiker, Alfons

    2007-01-01

    Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.

  17. Proposal of new bonding technique 'Instantaneous Liquid Phase (ILP) Bonding'

    International Nuclear Information System (INIS)

    Zhang, Yue-Chang; Nakagawa, Hiroji; Matsuda, Fukuhisa.

    1987-01-01

    A new bonding technique named ''Instantaneous Liquid Phase (ILP) bonding'' suitable mainly for welding dissimilar materials was proposed by which instantaneous melting of one or two of the faying surfaces is utilized. The processes of ILP bonding are mainly consisted of three stages, namely the first stage forming thin liquid layer by rapid heating, the second stage joining both specimens by thin liquid layer, and the third stage cooling the specimens rapidly to avoid the formation of brittle layer. The welding temperatures of the specimens to be welded in ILP bonding are generally differentiated from each other. ILP bonding was applied for a variety of combinations of dissimilar materials of aluminum, aluminum alloys, titanium, titanium alloy, carbon steel, austenitic stainless steel, copper and tungsten, and for similar materials of stainless steel and nickel-base alloy. There were no microvoids in these welding joints, and the formation of brittle layer at the bonding interface was suppressed. The welded joints of Al + Ti, Cu + carbon steel and Cu + austenitic stainless steel showed the fracture in base metal having lower tensile strength. Further, the welded joints of Al + carbon steel, Al alloy + Ti, Al alloy + carbon steel or + austenitic stainless steel, Ti + carbon steel or + austenitic stainless steel showed better tensile properties in the comparison with diffusion welding. Furthermore, ILP bonding was available for welding same materials susceptible to hot cracking. Because of the existence of liquid layer, the welding pressure required was extremely low, and preparation of faying surface by simple tooling or polishing by no.80 emery paper was enough. The change in specimen length before and after welding was relatively little, only depending on the thickness of liquid layer. The welding time was very short, and thus high welding efficiency was obtained. (author)

  18. Modélisation et caractérisation des joints collés à hautes vitesses de déformation Modeling and characterization of bonded joints at high strain rates

    Directory of Open Access Journals (Sweden)

    Bourel B.

    2013-11-01

    Full Text Available Ce papier traite de la modélisation de joints collés pour les structures soumises à des sollicitations de type crash. Cette nouvelle modélisation basée sur un élément cohésif tient compte du comportement viscoplastique, de l'endommagement ainsi que de la rupture de l'adhésive. Sensible à la vitesse de déformation l'identification du critère de rupture nécessite une base expérimentale allant jusqu'à de très hautes vitesses de déformations. Un nouveau dispositif d'essais a donc été mis en place sur les barres de Hopkinson afin de solliciter des assemblages à haute vitesse et sous différents angles de chargement. This paper deals with the modeling of bonded joints for structures subjected to dynamic crash loading. This new model based on a cohesive element takes into account the viscoelastic behavior, the damage and the failure of the adhesive. Due to the strain rate sensitivity, the identification of failure criterion requires experimental tests, up to very high strain rates. A new testing device has then been set up on the Hopkinson bar in order to load the assemblies with high strain rates and with different angles.

  19. Diagraphies de cimentation : vers une analyse de la qualité du contact ciment-formation Cement Logging: Toward an Analysis of the Quality of Cement-Formation Bonding

    Directory of Open Access Journals (Sweden)

    Isambourg P.

    2006-11-01

    Full Text Available Les compagnies pétrolières ont un réel besoin d'évaluer correctement les cimentations de leurs puits : l'étanchéité entre les différentes zones est-elle assurée? Pour ce faire, les outils soniques et ultra-soniques ont été mis au point. Jusqu'à présent, la qualité du contactcasing-ciment était analysée quantitativement et celle du contactciment-formation était analysée qualitativement par les spécialistes (outil VDL. Le progrès le plus important que l'on pouvait apporter dans les logsde cimentation était de détecter les défauts à l'interface ciment-formation. C'est ce que nous avons fait dans le cadre d'un projet financé par l'ARTEP (Association de Recherche sur les Techniques d'Exploitation du Pétrole comprenant Total, Gaz de France GDF, Institut Français du Pétrole (IFP, et Elf Aquitaine Production (EAP. Les expériences laboratoires effectuées au Service Analyse FLuides de Boussens ont été conçues en injectant du ciment entre un casing et une formation-simulée avec présence, ou non, de boue d'épaisseur variable. Des formations rapides ou lentes, ainsi que des ciments, rapides ou lents, ont été utilisés. Les échos ultrasoniques, obtenus à l'aide d'une sonde CET en céramique, ont été enregistrés et analysés. La théorie, comme les expériences, ont montré que les échos ultrasoniques sont modifiés en présence de boue et/ou de gaz. Les relations entre la forme de l'onde ultrasonique et la présence de boue et de gaz entre le ciment et la formation ont été établies. Une procédure de traitement est proposée avec ses limites. Oil companies have a real need to make a correct assessment of cementing jobs in their wells. Is the seal ensured between different zones? To do this, sonic and ultrasonic logging tools have been developed. Up to now, the quality of the casing-cement contacthas been analyzed quantitatively, and that of the cement-formation contacthas been analyzed qualitatively by

  20. A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

    Energy Technology Data Exchange (ETDEWEB)

    Solimannejad, Mohammad, E-mail: m-solimannejad@araku.ac.ir [Quantum Chemistry Group, Department of Chemistry, Arak University, 38156-879 Arak (Iran, Islamic Republic of); Massahi, Shokofeh [Quantum Chemistry Group, Department of Chemistry, Arak University, 38156-879 Arak (Iran, Islamic Republic of); Alkorta, Ibon, E-mail: ibon@iqm.csic.es [Instituto de Quimica Medica (CSIC), Juan de la Cierva, 3, 28006 Madrid (Spain)

    2009-07-30

    Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH{center_dot}{center_dot}{center_dot}N and NH{center_dot}{center_dot}{center_dot}O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol{sup -1} and 12-19 kJ mol{sup -1}, respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm{sup -1} is predicted for dimers and trimers, respectively.

  1. Clinical significance of combined detection of multiple serum antibodies (AsAb, EmAb, AcAb, AoAb, ToxAb) in infertile women

    International Nuclear Information System (INIS)

    Chen Jing; Jiang Li; Lu Ya

    2005-01-01

    Objective: To determine the clinical significance of combined detection of multiple serum antibodies in infertile women. Methods; Serum multiple antibodies were examined in 120 infertile women, including 88 failed to get pregnancy and 32 with repeated spontaneous abortion. The antibodies tested were: (1) anti-sperm antibody (AsAb) (2) endometrial antibody (EmAb) (3) anti-cardiophospholipid antibody (AcAb) (4) Anti-ovarian antibody (AoAb) and Toxoplasmosis antibody (ToxAb). Results: In 48 of the infertile women, none of the five antibodies were positive (40% of 120). The rest were: one antibody positive--38/120 or 31.6%; two antibodies positive--31/120 or 25.83%, three and four antibodies positive--4/120 or 3.33%. None of the women were positive with all five antibodies. Conclusion: Immune factor was the chief cause of infertility in women. (authors)

  2. Ab initio vel ex eventu

    Science.gov (United States)

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

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

  3. Understanding Bonds - Denmark

    DEFF Research Database (Denmark)

    Rimmer, Nina Røhr

    2016-01-01

    Undervisningsmateriale. A bond is a debt security, similar to an ”I Owe You document” (IOU). When you purchase a bond, you are lending money to a government, municipality, corporation, federal agency or other entity known as the issuer. In return for the loan, the issuer promises to pay you...... a specified rate of interest during the life of the bond and to repay the face value of the bond (the principal) when it “matures,” or comes due. Among the types of bonds you can choose from are: Government securities, municipal bonds, corporate bonds, mortgage and asset-backed securities, federal agency...... securities and foreign government bonds....

  4. Cold pressure welding - the mechanisms governing bonding

    DEFF Research Database (Denmark)

    Bay, Niels

    1979-01-01

    Investigations of the bonding surface in scanning electron microscope after fracture confirm the mechanisms of bond formation in cold pressure welding to be: fracture of work-hardened surface layer, surface expansion increasing the area of virgin surface, extrusion of virgin material through cracks...... of the original surface layer, and establishment of real contact and bonding between virgin material. This implies that normal pressure as well as surface expansion are basic parameters governing the bond strength. Experimental investigations of pressure welding Al-Al under plane strain compression in a specially...

  5. Wire bonding in microelectronics

    CERN Document Server

    Harman, George G

    2010-01-01

    Wire Bonding in Microelectronics, Third Edition, has been thoroughly revised to help you meet the challenges of today's small-scale and fine-pitch microelectronics. This authoritative guide covers every aspect of designing, manufacturing, and evaluating wire bonds engineered with cutting-edge techniques. In addition to gaining a full grasp of bonding technology, you'll learn how to create reliable bonds at exceedingly high yields, test wire bonds, solve common bonding problems, implement molecular cleaning methods, and much more. Coverage includes: Ultrasonic bonding systems and technologies, including high-frequency systems Bonding wire metallurgy and characteristics, including copper wire Wire bond testing Gold-aluminum intermetallic compounds and other interface reactions Gold and nickel-based bond pad plating materials and problems Cleaning to improve bondability and reliability Mechanical problems in wire bonding High-yield, fine-pitch, specialized-looping, soft-substrate, and extreme-temperature wire bo...

  6. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  7. Equilibrium and ab initio computational studies on the adduct formation of 1,3-diketonato-lithium(I), -sodium(I) and -potassium(I) with 1,10-phenanthroline and its 2,9-dimethyl derivatives.

    Science.gov (United States)

    Ishimori, Ken-ichiro; Mori, Seiji; Ito, Yuji; Ohashi, Kousaburo; Imura, Hisanori

    2009-06-15

    Highly effective and selective synergistic extraction of Li+ has been found using 2-naphthoyltrifluoroacetone (Hnta) as an acidic chelating agent and 2,9-dimethyl-1,10-phenanthroline (dmp) or 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (dmdpp) as a neutral ligand (denoted as L) in toluene. The synergism was ascribed to the adduct formation in the organic phase, and the composition and the formation constants of the adducts for alkali metal ions (M+) were determined by the extraction equilibrium analysis. The adducts found were M(nta)L for Li+ and Na+, while M(nta)L and M(nta)L2 for K+. To understand thermodynamics of the adduct formation with the bidentate amines, quantum chemical calculations of the 1:1 and 1:2 adduct formations with dmp and 1,10-phenanthroline (phen) were performed. The electronic and steric effects of the methyl groups at 2,9-positions of phen on the thermodynamic functions of adduct formation as well as the high lithium selectivity were quantitatively elucidated.

  8. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Campetella, M.; Caminiti, R.; Bencivenni, L.; Gontrani, L.; Bovi, D.; Guidoni, L.

    2016-01-01

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm −1 ), where the vibrational motions involve the NH 3 + group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm −1 where the antisymmetric stretching mode (ν 3 ) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D 3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  9. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Campetella, M.; Caminiti, R.; Bencivenni, L.; Gontrani, L., E-mail: lorenzo.gontrani@uniroma1.it [Dipartimento di Chimica, Università di Roma, “La Sapienza,” P. le Aldo Moro 5, I-00185 Roma (Italy); Bovi, D. [Dipartimento di Fisica, Università di Roma, “La Sapienza,” P. le Aldo Moro 5, I-00185 Roma (Italy); Guidoni, L. [Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, Coppito, I-67100 L’Aquila (Italy)

    2016-07-14

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm{sup −1}), where the vibrational motions involve the NH{sub 3}+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm{sup −1} where the antisymmetric stretching mode (ν{sub 3}) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D{sub 3h} symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  10. Polarization-induced sigma-holes and hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Hennemann, M.; Murray, J. S.; Politzer, P.; Riley, Kevin Eugene; Clark, T.

    2012-01-01

    Roč. 18, č. 6 (2012), s. 2461-2469 ISSN 1610-2940 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen bond * sigma-hole * polarization * field effect * ab initio calculation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.984, year: 2012

  11. Hydrogen bonding of formamide, urea, urea monoxide and their thio

    Indian Academy of Sciences (India)

    Ab initio and DFT methods have been employed to study the hydrogen bonding ability of formamide, urea, urea monoxide, thioformamide, thiourea and thiourea monoxide with one water molecule and the homodimers of the selected molecules. The stabilization energies associated with themonohydrated adducts and ...

  12. Molecular orbital studies of the bonding in heavy element organometallics

    International Nuclear Information System (INIS)

    Bursten, B.E.

    1990-01-01

    This progress report contains highlights of research projects in actinide chemistry. Projects covered are bonding in Np, Pu, and transplutonium organometallic compounds, applications of the discrete variational Xα method to actinide chemistry, ab initio calculations on actinide molecules, and experimental comparisons of organoactinide and organotransition metal chemistry. Also included is brief discussions on budgets, funding, invited papers and invited presentations. (JL)

  13. On differences between hydrogen bonding and improper blue-shifting hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Zierkiewicz, W.; Jurečka, Petr; Hobza, Pavel

    2005-01-01

    Roč. 6, č. 4 (2005), s. 609-617 ISSN 1439-4235 R&D Projects: GA ČR(CZ) GA203/05/0009; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : ab initio calculations * density functional calculations * H-bonding Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.607, year: 2005

  14. Shear bond strength between an indirect composite layering material and feldspathic porcelain-coated zirconia ceramics.

    Science.gov (United States)

    Fushiki, Ryosuke; Komine, Futoshi; Blatz, Markus B; Koizuka, Mai; Taguchi, Kohei; Matsumura, Hideo

    2012-10-01

    This study aims to evaluate the effect of both feldspathic porcelain coating of zirconia frameworks and priming agents on shear bond strength between an indirect composite material and zirconia frameworks. A total of 462 airborne-particle-abraded zirconia disks were divided into three groups: untreated disks (ZR-AB), airborne-particle-abraded zirconia disks coated with feldspathic porcelain, (ZR-PO-AB), and hydrofluoric acid-etched zirconia disks coated with feldspathic porcelain (ZR-PO-HF). Indirect composite (Estenia C&B) was bonded to zirconia specimens with no (CON) or one of four priming agents--Clearfil Photo Bond (CPB), Clearfil Photo Bond with Clearfil Porcelain Bond Activator (CPB + activator), Estenia Opaque primer, or Porcelain Liner M Liquid B (PLB)--with or without an opaque material (Estenia C&B Opaque). All specimens were tested for shear bond strength before and after 20,000 thermocycles. The Steel-Dwass test and Mann-Whitney U test were used to compare shear bond strength. In ZR-AB specimens, the initial bond strength of the CPB and CPB + Activator groups was significantly higher as compared with the other three groups (P material, bond strength was significantly lower in ZR-AB specimens than in ZR-PO-AB and ZR-PO-HF specimens (P composite to zirconia independent of surface treatment. The use of a silane coupling agent and opaque material yields durable bond strength between the indirect composite and feldspathic-porcelain-coated zirconia. The results of the present study suggest that feldspathic porcelain coating of zirconia frameworks is an effective method to obtain clinically acceptable bond strengths of a layering indirect composite material to a zirconia framework.

  15. Time resolved native ion-mobility mass spectrometry to monitor dynamics of IgG4 Fab arm exchange and "bispecific" monoclonal antibody formation.

    Science.gov (United States)

    Debaene, François; Wagner-Rousset, Elsa; Colas, Olivier; Ayoub, Daniel; Corvaïa, Nathalie; Van Dorsselaer, Alain; Beck, Alain; Cianférani, Sarah

    2013-10-15

    Monoclonal antibodies (mAbs) and derivatives such as antibody-drug conjugates (ADC) and bispecific antibodies (bsAb), are the fastest growing class of human therapeutics. Most of the therapeutic antibodies currently on the market and in clinical trials are chimeric, humanized, and human immunoglobulin G1 (IgG1). An increasing number of IgG2s and IgG4s that have distinct structural and functional properties are also investigated to develop products that lack or have diminished antibody effector functions compared to IgG1. Importantly, wild type IgG4 has been shown to form half molecules (one heavy chain and one light chain) that lack interheavy chain disulfide bonds and form intrachain disulfide bonds. Moreover, IgG4 undergoes a process of Fab-arm exchange (FAE) in which the heavy chains of antibodies of different specificities can dissociate and recombine in bispecific antibodies both in vitro and in vivo. Here, native mass spectrometry (MS) and time-resolved traveling wave ion mobility MS (TWIM-MS) were used for the first time for online monitoring of FAE and bsAb formation using Hz6F4-2v3 and natalizumab, two humanized IgG4s which bind to human Junctional Adhesion Molecule-A (JAM-A) and alpha4 integrin, respectively. In addition, native MS analysis of bsAb/JAM-A immune complexes revealed that bsAb can bind up to two antigen molecules, confirming that the Hz6F4 family preferentially binds dimeric JAM-A. Our results illustrate how IM-MS can rapidly assess bsAb structural heterogeneity and be easily implemented into MS workflows for bsAb production follow up and bsAb/antigen complex characterization. Altogether, these results provide new MS-based methodologies for in-depth FAE and bsAb formation monitoring. Native MS and IM-MS will play an increasing role in next generation biopharmaceutical product characterization like bsAbs, antibody mixtures, and antibody-drug conjugates (ADC) as well as for biosimilar and biobetter antibodies.

  16. Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states

    DEFF Research Database (Denmark)

    Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...

  17. Popular Herbig AE star AB Aur

    International Nuclear Information System (INIS)

    Shevchenko, V.S.

    1987-01-01

    The variability of AB Aur emission line H α , H β , H γ profiles, equivalent widths (EW λ ) and relative intensity have been observed on the photoelectric scanner. During the 20 d observation period EW λ H α ranged from 23.20 to 35.35 A. Mean EW λ H α is 27.25 A, daily average deviation is 3.60 ± 0.07 A. The minimum time of variability is 1 h . The chromospheric lines near-infrared triplet Ca II and KCaII and emission lines H β -H13, P12-P20, 0I 8446.5 A and the variability of other lines have been studied on the photographic and image-tube spectra. The intensity of these lines and EW λ changed 2-4 times during an interval from 1 h to several years. The AB Aur variability nature of emission lines made it possible to assume that the ''deep chromosphere'' is not a centre-symmetrical or axisymmetrical formation but is a conglomerate of different density and speed gas condensations

  18. Ab initio study of isomerism of Li2AB2 molecules and Li2AB2+ ions with 16 valent electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    In the framework of MP2(6-31*//HF/6-31G + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations ab initio calculations of surfaces of potential energy of molecules of lithium salts of Li 2 AB 2 (Li 2 BeO 2 , L 2 MgO 2 , Li 2 BeS 2 , Li 2 MgS 2 , Li 2 CN 2 , Li 2 SiN 2 , Li 2 CP 2 ) type and ions of Li 2 AB 2 + (Li 2 BO 2 + , Li 2 AlO 2 + , Li 2 BS 2 + , Li 2 AlS 2 + , Li 2 N 3 + , Li 2 PN 2 + , Li 2 P 3 + ) type with 16 valent electrons are done. For oxide and nitride systems global minimum corresponds to symmetric linear structure D ∞h and for their sulfide and phosphorus analogues curved plane or unplane (C 2 ) structure with bond angle φ(LBA)=90-110 Deg are preferable. Equilibrium geometric parameters, relative energies and energies of isomer decomposition, frequencies and IR-intensities of normal vibrations are determined [ru

  19. Extraction of Proteins with ABS

    NARCIS (Netherlands)

    Desai, R.K.; Streefland, M.; Wijffels, R.H.; Eppink, M.H.M.

    2016-01-01

    Over the past years, there has been an increasing trend in research on the extraction and purification of proteins using aqueous biphasic systems (ABS) formed by polymers, e.g., polyethylene glycol (PEG). In general, when dealing with protein purification processes, it is essential to maintain their

  20. Ab initio potential for solids

    DEFF Research Database (Denmark)

    Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel

    1992-01-01

    . At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...

  1. Ab-initio ZORA calculations

    NARCIS (Netherlands)

    Faas, S.; Snijders, Jaap; van Lenthe, J.H.; HernandezLaguna, A; Maruani, J; McWeeny, R; Wilson, S

    2000-01-01

    In this paper we present the first application of the ZORA (Zeroth Order Regular Approximation of the Dirac Fock equation) formalism in Ab Initio electronic structure calculations. The ZORA method, which has been tested previously in the context of Density Functional Theory, has been implemented in

  2. Ab initio molecular dynamics studies on effect of Zr on oxidation resistance of TiAlN coatings

    Energy Technology Data Exchange (ETDEWEB)

    Pi, Jingwu [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Kong, Yi, E-mail: yikong@csu.edu.cn [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Chen, Li [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Zhuzhou Cemented Carbide Cutting Tools Co., Ltd., Zhuzhou, Hunan 412007 (China); Du, Yong [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China)

    2016-08-15

    Highlights: • The lowest bonding energy sequence for dimers in the vacuum: Zr−O < Ti−O < Al−O. • The lowest bonding energy sequence for oxygen above the surface: Ti−O < Zr−O < Al−O. • At 300 K, the addition of Zr benefitting the formation of vacancy and TiO{sub 2}. • At 1123 K, the addition of Zr leading to a more stable surface. • Our findings explain that the oxidation resistance of TiAlZrN superior to TiAlN at 1123 K as well as TiAlZrN at 300 K. - Abstract: It was demonstrated experimentally that doping Zr into TiAlN coatings at room temperature will detriment its oxidation resistance. On the other hand, there are evidences that doping Zr into TiAlN at high temperature will improve coating's oxidation resistance. In the present work, we address the effect of Zr on the oxidation resistance of TiAlN by means of ab initio molecular dynamics simulations. The TiAlN and TiAlZrN (1 Zr atom replacing 1 Ti atom) surfaces covered with 4 oxygen atoms at 300 K and 1123 K were simulated. Based on the analysis of the atomic motion, bond formation after relaxation, and the charge density difference maps we find that at 300 K, the addition of Zr induces escape of Ti atoms from the surface, resulting in formation of surface vacancies and subsequently TiO{sub 2}. Comparison of metal-oxygen dimers in the vacuum and above the TiAlZrN surface further shows that the addition of Zr in the TiAlN surface will change the lowest bonding energy sequence from Zr−O < Ti−O < Al−O in the vacuum to Ti−O < Zr−O < Al−O above the TiAlZrN surface. From Molecular Dynamics simulations at 1123 K, it is find that no Ti vacancies were generated in the surface. Moreover, less charge is transferred from metal to N atoms and the bond lengths between Ti and O atoms become shorter at 1123 K as compared with 300 K, suggesting that the addition of Zr atom promotes the interaction of Ti and O at TiAlZrN surface at 1123 K, leading to a more stable surface. Our simulation

  3. Ab initio MO study on the thermal stability of 1-phenyl-1H-tetrazoles; Hikeikenteki bunshi kidoho ni yoru 1-Ph-1H tetorazoru yudotai no netsu anteisei hyoka ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Yoshio.; Akutsu, Yoshiaki.; Arai, Mitsuru.; Tamura, Masamitsu. [The University of Tokyo, Tokyo (Japan). School of Engineering; Matsunaga, Takehiro. [National Institute of Materials and Chemical Research, Tsukuba (Japan)

    1999-06-30

    Ab initio MO calculations of 1-phenyl-1H-tetrazoles were carried out, in order to explain a substituent effects on its high thermal stability and to estimate the thermal stability of the other tetrazoles. Similar to 1H-tetrazole, five bonds in the tetrazole ring have intermediate lengths between single and double bond lengths. Phenyl and tetrazole rings are not both on one plane showing no interaction. Three indexes addopted as a measure of thermal stability indicate that the more equal the bond lengths of the ring are and that the bigger the stabilization energy by ring formation is, the more thermally stable they are. It is found out that there is the relationship between the thermal stability and the ring charge. That is, the more negative the ring charge is, the more thrmally stable the tetrazole is. Also, there is a good relationship between the thermal stability and the energy level of orbital of which orbital is an anti bonding type with respect to the N3-N4 bond. The higher the energy level is, the more thermally stable the tetrazole is. (author)

  4. Ultrathin silicon oxynitride layer on GaN for dangling-bond-free GaN/insulator interface.

    Science.gov (United States)

    Nishio, Kengo; Yayama, Tomoe; Miyazaki, Takehide; Taoka, Noriyuki; Shimizu, Mitsuaki

    2018-01-23

    Despite the scientific and technological importance of removing interface dangling bonds, even an ideal model of a dangling-bond-free interface between GaN and an insulator has not been known. The formation of an atomically thin ordered buffer layer between crystalline GaN and amorphous SiO 2 would be a key to synthesize a dangling-bond-free GaN/SiO 2 interface. Here, we predict that a silicon oxynitride (Si 4 O 5 N 3 ) layer can epitaxially grow on a GaN(0001) surface without creating dangling bonds at the interface. Our ab initio calculations show that the GaN/Si 4 O 5 N 3 structure is more stable than silicon-oxide-terminated GaN(0001) surfaces. The electronic properties of the GaN/Si 4 O 5 N 3 structure can be tuned by modifying the chemical components near the interface. We also propose a possible approach to experimentally synthesize the GaN/Si 4 O 5 N 3 structure.

  5. Comparative Study of Electroless Copper Film on Different Self-Assembled Monolayers Modified ABS Substrate

    Directory of Open Access Journals (Sweden)

    Jiushuai Xu

    2014-04-01

    Full Text Available Copper films were grown on (3-Mercaptopropyltrimethoxysilane (MPTMS, (3-Aminopropyltriethoxysilane (APTES and 6-(3-(triethoxysilylpropylamino-1,3,5- triazine-2,4-dithiol monosodium (TES self-assembled monolayers (SAMs modified acrylonitrile-butadiene-styrene (ABS substrate via electroless copper plating. The copper films were examined using scanning electron microscopy (SEM and X-ray diffraction (XRD. Their individual deposition rate and contact angle were also investigated to compare the properties of SAMs and electroless copper films. The results indicated that the formation of copper nuclei on the TES-SAMs modified ABS substrate was faster than those on the MPTMS-SAMs and APTES-SAMs modified ABS substrate. SEM images revealed that the copper film on TES-SAM modified ABS substrate was smooth and uniform, and the density of copper nuclei was much higher. Compared with that of TES-SAMs modified resin, the coverage of copper nuclei on MPTMS and APTES modified ABS substrate was very limited and the copper particle size was too big. The adhesion property test demonstrated that all the SAMs enhanced the interfacial interaction between copper plating and ABS substrate. XRD analysis showed that the copper film deposited on SAM-modified ABS substrate had a structure with Cu(111 preferred orientation, and the copper film deposited on TES-SAMs modified ABS substrate is better than that deposited on MPTMS-SAMs or APTES-SAMs modified ABS resins in electromigrtion resistance.

  6. Modeling of truck's braking dynamics with ABS

    Directory of Open Access Journals (Sweden)

    Maxym DYACHUK

    2014-09-01

    Full Text Available In the article some questions of ABS simulation on the basis of plane vehicle's dynamics and automatic modeling are considered. The author's algorithm of ABS modulators control is presented.

  7. Reaction mechanism of the acidic hydrolysis of highly twisted amides: Rate acceleration caused by the twist of the amide bond.

    Science.gov (United States)

    Mujika, Jon I; Formoso, Elena; Mercero, Jose M; Lopez, Xabier

    2006-08-03

    We present an ab initio study of the acid hydrolysis of a highly twisted amide and a planar amide analogue. The aim of these studies is to investigate the effect that the twist of the amide bond has on the reaction barriers and mechanism of acid hydrolysis. Concerted and stepwise mechanisms were investigated using density functional theory and polarizable continuum model calculations. Remarkable differences were observed between the mechanism of twisted and planar amide, due mainly to the preference for N-protonation of the former and O-protonation of the latter. In addition, we were also able to determine that the hydrolytic mechanism of the twisted amide will be pH dependent. Thus, there is a preference for a stepwise mechanism with formation of an intermediate in the acid hydrolysis, whereas the neutral hydrolysis undergoes a concerted-type mechanism. There is a nice agreement between the characterized intermediate and available X-ray data and a good agreement with the kinetically estimated rate acceleration of hydrolysis with respect to analogous undistorted amide compounds. This work, along with previous ab initio calculations, describes a complex and rich chemistry for the hydrolysis of highly twisted amides as a function of pH. The theoretical data provided will allow for a better understanding of the available kinetic data of the rate acceleration of amides upon twisting and the relation of the observed rate acceleration with intrinsic differential reactivity upon loss of amide bond resonance.

  8. Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations

    Directory of Open Access Journals (Sweden)

    Xiaowei Li

    2015-01-01

    Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

  9. Bonding with Your Baby

    Science.gov (United States)

    ... the future bonding of the child and parent. Adoptive parents may be concerned about bonding with their ... general emotional support. And it's OK to ask family members and friends for help in the days — ...

  10. AB Levitator and Electricity Storage

    OpenAIRE

    Bolonkin, Alexander

    2007-01-01

    The author researched this new idea - support of flight by any aerial vehicles at significant altitude solely by the magnetic field of the planet. It is shown that current technology allows humans to create a light propulsion (AB engine) which does not depend on air, water or ground terrain. Simultaniosly, this revolutionary thruster is a device for the storage of electricity which is extracted and is replenished (during braking) from/into the storage with 100 percent efficiency. The relative...

  11. Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution.

    Science.gov (United States)

    Usui, Kota; Hunger, Johannes; Sulpizi, Marialore; Ohto, Tatsuhiko; Bonn, Mischa; Nagata, Yuki

    2015-08-20

    Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O-D···O(TMAO) hydrogen-bond has a strong directionality through the sp(3) orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics.

  12. Ab Initio Guided Low Temperature Synthesis Strategy for Smooth Face–Centred Cubic FeMn Thin Films

    Directory of Open Access Journals (Sweden)

    Friederike Herrig

    2018-05-01

    Full Text Available The sputter deposition of FeMn thin films with thicknesses in the range of hundred nanometres and beyond requires relatively high growth temperatures for the formation of the face-centred cubic (fcc phase, which results in high thin film roughness. A low temperature synthesis strategy, based on local epitaxial growth of a 100 nm thick fcc FeMn film as well as a Cu nucleation layer on an α-Al2O3 substrate at 160 °C, enables roughness values (Ra as low as ~0.6 nm, which is in the same order of magnitude as the pristine substrate (~0.1 nm. The synthesis strategy is guided by ab initio calculations, indicating very strong interfacial bonding of the Cu nucleation layer to an α-Al2O3 substrate (work of separation 5.48 J/m²—which can be understood based on the high Cu coordination at the interface—and between fcc FeMn and Cu (3.45 J/m². Accompanied by small lattice misfits between these structures, the strong interfacial bonding is proposed to enable the local epitaxial growth of a smooth fcc FeMn thin film. Based on the here introduced synthesis strategy, the implementation of fcc FeMn based thin film model systems for materials with interface dominated properties such as FeMn steels containing κ-carbide precipitates or secondary phases appears meaningful.

  13. Australia's Bond Home Bias

    OpenAIRE

    Anil V. Mishra; Umaru B. Conteh

    2014-01-01

    This paper constructs the float adjusted measure of home bias and explores the determinants of bond home bias by employing the International Monetary Fund's high quality dataset (2001 to 2009) on cross-border bond investment. The paper finds that Australian investors' prefer investing in countries with higher economic development and more developed bond markets. Exchange rate volatility appears to be an impediment for cross-border bond investment. Investors prefer investing in countries with ...

  14. Analysis of factors influencing the bond strength in roll bonding processes

    Science.gov (United States)

    Khaledi, Kavan; Wulfinghoff, Stephan; Reese, Stefanie

    2018-05-01

    Cold Roll Bonding (CRB) is recognized as an industrial technique in which the metal sheets are joined together in order to produce laminate metal composites. In this technique, a metallurgical bond resulting from severe plastic deformation is formed between the rolled metallic layers. The main objective of this paper is to analyse different factors which may affect the bond formation in rolling processes. To achieve this goal, first, an interface model is employed which describes both the bonding and debonding. In this model, the bond strength evolution between the metallic layers is calculated based on the film theory of bonding. On the other hand, the debonding process is modelled by means of a bilinear cohesive zone model. In the numerical section, different scenarios are taken into account to model the roll bonding process of metal sheets. The numerical simulation includes the modelling of joining during the roll bonding process followed by debonding in a Double Cantilever Beam (DCB) peeling test. In all simulations, the metallic layers are regarded as elastoplastic materials subjected to large plastic deformations. Finally, the effects of some important factors on the bond formation are numerically investigated.

  15. Phenylacetylene and H bond

    Indian Academy of Sciences (India)

    ... all resembling H bonds. Non-linear H bonds due to secondary interactions. C-H stretching frequency shows blue shift. Heavy atom distances are longer than the sum of van der Waals radii. Formed a task group through IUPAC to come up with a modern definition of H bond. 15 international experts including Desiraju.

  16. Structural investigation of water-acetonitrile mixtures: An ab initio, molecular dynamics and X-ray diffraction study

    International Nuclear Information System (INIS)

    Bako, Imre; Megyes, Tuende; Palinkas, Gabor

    2005-01-01

    In this work, we present a study on water-acetonitrile (AN) mixtures by molecular dynamics ab initio and X-ray diffraction techniques. Comparison of the experimental total G(r) functions of the mixtures with the results of molecular dynamics simulation shows an overall good agreement. The properties of hydrogen bonded clusters (water clusters, and water-AN clusters) in these mixtures have been determined. Two different types of AN-water dimers were identified by ab initio quantum chemical calculation. One of these structures proved to be a true H-bonded dimer and the other a dipole bound dimer

  17. Chemical bond fundamental aspects of chemical bonding

    CERN Document Server

    Frenking, Gernot

    2014-01-01

    This is the perfect complement to ""Chemical Bonding - Across the Periodic Table"" by the same editors, who are two of the top scientists working on this topic, each with extensive experience and important connections within the community. The resulting book is a unique overview of the different approaches used for describing a chemical bond, including molecular-orbital based, valence-bond based, ELF, AIM and density-functional based methods. It takes into account the many developments that have taken place in the field over the past few decades due to the rapid advances in quantum chemica

  18. Pressure bonding molybdenum alloy (TZM) to reaction-bonded silicon nitride

    International Nuclear Information System (INIS)

    Huffsmith, S.A.; Landingham, R.L.

    1978-01-01

    Topping cycles could boost the energy efficiencies of a variety of systems by using what is now waste heat. One such topping cycle uses a ceramic helical expander and would require that a reaction-bonded silicon nitride (RBSN) rotor be bonded to a shaft of TZM (Mo-0.5 wt % Ti-0.08 wt % Zr). Coupon studies show that TZM can be bonded to RBSN at 1300 0 C and 69 MPa if there is an interlayer of MoSi 2 . A layer of finely ground (10 μm) MoSi 2 facilitates bond formation and provides a thicker bond interface. The hardness and grain structure of the TZM and RBSN were not affected by the temperature and pressure required to bond the coupons

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

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  20. Long-term Bond Strength between Layering Indirect Composite Material and Zirconia Coated with Silicabased Ceramics.

    Science.gov (United States)

    Fushiki, Ryosuke; Komine, Futoshi; Honda, Junichi; Kamio, Shingo; Blatz, Markus B; Matsumura, Hideo

    2015-06-01

    This study evaluated the long-term shear bond strength between an indirect composite material and a zirconia framework coated with silica-based ceramics, taking the effect of different primers into account. A total of 165 airborne-particle abraded zirconia disks were subjected to one of three pretreatments: no pretreatment (ZR-AB), airborne-particle abrasion of zirconia coated with feldspathic porcelain (ZR-PO-AB), and 9.5% hydrofluoric acid etching of zirconia coated with feldspathic porcelain (ZR-PO-HF). An indirect composite material (Estenia C&B) was then bonded to the zirconia disks after they were treated with one of the following primers: Clearfil Photo Bond (CPB), Clearfil Photo Bond with Clearfil Porcelain Bond Activator (CPB + Activator), Estenia Opaque Primer (EOP), Porcelain Liner M Liquid B (PLB), or no priming (CON, control group). Shear bond strength was tested after 100,000 thermocycles, and the data were analyzed using the Steel-Dwass U-test (α = 0.05). For ZR-PO-AB and ZR-PO-HF specimens, bond strength was highest in the CPB+Activator group (25.8 MPa and 22.4 MPa, respectively). Bond strengths were significantly lower for ZR-AB specimens in the CON and PLB groups and for ZR-PO-AB specimens in the CON, CPB, and EOP groups. Combined application of a hydrophobic phosphate monomer (MDP) and silane coupling agent enhanced the long-term bond strength of indirect composite material to a zirconia coated with silica-based ceramics.

  1. Bone bonding at natural and biomaterial surfaces.

    Science.gov (United States)

    Davies, John E

    2007-12-01

    Bone bonding is occurring in each of us and all other terrestrial vertebrates throughout life at bony remodeling sites. The surface created by the bone-resorbing osteoclast provides a three-dimensionally complex surface with which the cement line, the first matrix elaborated during de novo bone formation, interdigitates and is interlocked. The structure and composition of this interfacial bony matrix has been conserved during evolution across species; and we have known for over a decade that this interfacial matrix can be recapitulated at a biomaterial surface implanted in bone, given appropriate healing conditions. No evidence has emerged to suggest that bone bonding to artificial materials is any different from this natural biological process. Given this understanding it is now possible to explain why bone-bonding biomaterials are not restricted to the calcium-phosphate-based bioactive materials as was once thought. Indeed, in the absence of surface porosity, calcium phosphate biomaterials are not bone bonding. On the contrary, non-bonding materials can be rendered bone bonding by modifying their surface topography. This paper argues that the driving force for bone bonding is bone formation by contact osteogenesis, but that this has to occur on a sufficiently stable recipient surface which has micron-scale surface topography with undercuts in the sub-micron scale-range.

  2. Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dharmawardhana, C.C. [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States); Misra, A. [Department of Civil, Environmental, and Architectural Engineering, University of Kansas, Lawrence, KS 66045 (United States); Aryal, S.; Rulis, P. [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States); Ching, W.Y., E-mail: ccdxz8@mail.umkc.edu [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States)

    2013-10-15

    Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion shows that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.

  3. An ab initio molecular dynamics study of thermal decomposition of 3,6-di(azido)-1,2,4,5-tetrazine.

    Science.gov (United States)

    Wu, Qiong; Zhu, Weihua; Xiao, Heming

    2014-10-21

    Ab initio molecular dynamics simulations were performed to study the thermal decomposition of isolated and crystal 3,6-di(azido)-1,2,4,5-tetrazine (DiAT). During unimolecular decomposition, the three different initiation mechanisms were observed to be N-N2 cleavage, ring opening, and isomerization, respectively. The preferential initial decomposition step is the homolysis of the N-N2 bond in the azido group. The release mechanisms of nitrogen gas are found to be very different in the early and later decomposition stages of crystal DiAT. In the early decomposition, DiAT decomposes very fast and drastically without forming any stable long-chains or heterocyclic clusters, and most of the nitrogen gases are released through rapid rupture of nitrogen-nitrogen and carbon-nitrogen bonds. But in the later decomposition stage, the release of nitrogen gas is inhibited due to low mobility, long distance from each other, and strong carbon-nitrogen bonds. To overcome the obstacles, the nitrogen gases are released through slow formation and disintegration of polycyclic networks. Our simulations suggest a new decomposition mechanism for the organic polyazido initial explosive at the atomistic level.

  4. Body of Knowledge (BOK) for Copper Wire Bonds

    Science.gov (United States)

    Rutkowski, E.; Sampson, M. J.

    2015-01-01

    Copper wire bonds have replaced gold wire bonds in the majority of commercial semiconductor devices for the latest technology nodes. Although economics has been the driving mechanism to lower semiconductor packaging costs for a savings of about 20% by replacing gold wire bonds with copper, copper also has materials property advantages over gold. When compared to gold, copper has approximately: 25% lower electrical resistivity, 30% higher thermal conductivity, 75% higher tensile strength and 45% higher modulus of elasticity. Copper wire bonds on aluminum bond pads are also more mechanically robust over time and elevated temperature due to the slower intermetallic formation rate - approximately 1/100th that of the gold to aluminum intermetallic formation rate. However, there are significant tradeoffs with copper wire bonding - copper has twice the hardness of gold which results in a narrower bonding manufacturing process window and requires that the semiconductor companies design more mechanically rigid bonding pads to prevent cratering to both the bond pad and underlying chip structure. Furthermore, copper is significantly more prone to corrosion issues. The semiconductor packaging industry has responded to this corrosion concern by creating a palladium coated copper bonding wire, which is more corrosion resistant than pure copper bonding wire. Also, the selection of the device molding compound is critical because use of environmentally friendly green compounds can result in internal CTE (Coefficient of Thermal Expansion) mismatches with the copper wire bonds that can eventually lead to device failures during thermal cycling. Despite the difficult problems associated with the changeover to copper bonding wire, there are billions of copper wire bonded devices delivered annually to customers. It is noteworthy that Texas Instruments announced in October of 2014 that they are shipping microcircuits containing copper wire bonds for safety critical automotive applications

  5. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  6. An analysis of hydrated proton diffusion in ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2015-01-07

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions

  7. Ab initio study of isomerism in molecular Li2AB+ ions with 12 and 14 valence electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; Mak-Ki, M.L.; Shlojer, P.R.

    1997-01-01

    Ab initio calculations of potential energy surfaces (PES) of molecular ions Li 2 AB + with 12 and 14 valence electrons have been made in the framework of approximations MP2/6-31G*//HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/6-31*//MP2/6-31G*+ZPE(MP2/6-31G*). The following most favourable structures have been found: a double-terminal linear for LiNO + (a triplet); a plane bicyclic one for Li 2 OF + , Li 2 SCl + , Li 2 NO + (a singlet) and Li 2 PS + (a singlet), where both cations are coordinated to A-B bond; rectangular (T-shaped) for Li 2 OCl + and SFLi + , as well as for LiNS + and POLi 2 + ions in singlet and triplet states; in the form of a half-opened butterfly for Li 2 PS + (a triplet) and Li 2 SCl +

  8. Sol-gel bonding of silicon wafers

    International Nuclear Information System (INIS)

    Barbe, C.J.; Cassidy, D.J.; Triani, G.; Latella, B.A.; Mitchell, D.R.G.; Finnie, K.S.; Short, K.; Bartlett, J.R.; Woolfrey, J.L.; Collins, G.A.

    2005-01-01

    Sol-gel bonds have been produced between smooth, clean silicon substrates by spin-coating solutions containing partially hydrolysed silicon alkoxides. The two coated substrates were assembled and the resulting sandwich fired at temperatures ranging from 60 to 600 deg. C. The sol-gel coatings were characterised using attenuated total reflectance Fourier transform infrared spectroscopy, ellipsometry, and atomic force microscopy, while the corresponding bonded specimens were investigated using scanning electron microscopy and cross-sectional transmission electron microscopy. Mechanical properties were characterised using both microindentation and tensile testing. Bonding of silicon wafers has been successfully achieved at temperatures as low as 60 deg. C. At 300 deg. C, the interfacial fracture energy was 1.55 J/m 2 . At 600 deg. C, sol-gel bonding provided superior interfacial fracture energy over classical hydrophilic bonding (3.4 J/m 2 vs. 1.5 J/m 2 ). The increase in the interfacial fracture energy is related to the increase in film density due to the sintering of the sol-gel interface with increasing temperature. The superior interfacial fracture energy obtained by sol-gel bonding at low temperature is due to the formation of an interfacial layer, which chemically bonds the two sol-gel coatings on each wafer. Application of a tensile stress on the resulting bond leads to fracture of the samples at the silicon/sol-gel interface

  9. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  10. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  11. AP calculus AB/BC

    CERN Document Server

    Schwartz, Stu

    2013-01-01

    All Access for the AP® Calculus AB & BC Exams Book + Web + Mobile Everything you need to prepare for the Advanced Placement® exam, in a study system built around you! There are many different ways to prepare for an Advanced Placement® exam. What's best for you depends on how much time you have to study and how comfortable you are with the subject matter. To score your highest, you need a system that can be customized to fit you: your schedule, your learning style, and your current level of knowledge. This book, and the free online tools that come with it, will help you personalize your AP® Cal

  12. Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (DiaminocarbenePdII Complexes

    Directory of Open Access Journals (Sweden)

    Alexander S. Mikherdov

    2018-02-01

    Full Text Available The coupling of cis-[PdCl2(CNXyl2] (Xyl = 2,6-Me2C6H3 with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbenePdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB. The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D polymeric chains (for 3a,b, dimeric associates (for 3c, or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%, S•••S (3c: less 1%, S•••O (3d: less 1%. The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method, confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry. The AIM analysis demonstrates the presence of appropriate bond critical points for these

  13. Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

    Science.gov (United States)

    Magnasco, Valerio

    2008-01-01

    Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…

  14. Bond strength investigation of two shot moulded polymer

    DEFF Research Database (Denmark)

    Islam, Mohammad Aminul

    This report on the project “Bond strength investigation of two shot moulded polymers” has been submitted for fulfilling the requirements for the course “Experimental Plastic Technology – 42234” at IPL-DTU. Two shot moulding is a classic manufacturing process to combine two different polymers...... in a single product and it is getting more and more importance day by day. One of the biggest challenges of two shot moulding is to achieve a reasonably good bonding between two polymers. The purpose of this project is to investigate the effects of different process, material and machine parameters...... on the bond strength of two shot moulded polymers. For the experiments two engineering polymers (PS and ABS) were used. After all the experimental work, several parameters were found which could effectively control the bond strength of two shot moulded polymers. This report also presents different aspects...

  15. BONDING ALUMINUM METALS

    Science.gov (United States)

    Noland, R.A.; Walker, D.E.

    1961-06-13

    A process is given for bonding aluminum to aluminum. Silicon powder is applied to at least one of the two surfaces of the two elements to be bonded, the two elements are assembled and rubbed against each other at room temperature whereby any oxide film is ruptured by the silicon crystals in the interface; thereafter heat and pressure are applied whereby an aluminum-silicon alloy is formed, squeezed out from the interface together with any oxide film, and the elements are bonded.

  16. MoS{sub 2} on an amorphous HfO{sub 2} surface: An ab initio investigation

    Energy Technology Data Exchange (ETDEWEB)

    Scopel, W. L., E-mail: wlscopel@if.uff.br [Departamento de Física, Universidade Federal do Espírito Santo, Vitória, Brazil and Departamento de Ciências Exatas, Universidade Federal Fluminense, Volta Redonda, Rio de Janerio (Brazil); Miwa, R. H., E-mail: hiroki@infis.ufu.br; Schmidt, T. M., E-mail: tome@infis.ufu.br [Instituto de Física, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais (Brazil); Venezuela, P., E-mail: vene@if.uff.br [Instituto de Física, Universidade Federal Fluminense, Niterói, Rio de Janerio (Brazil)

    2015-05-21

    The energetic stability, electronic and structural properties of MoS{sub 2} adsorbed on an amorphous a-HfO{sub 2} surface (MoS{sub 2}/HfO{sub 2}) are examined through ab initio theoretical investigations. Our total energy results indicate that the formation of MoS{sub 2}/HfO{sub 2} is an exothermic process with an adsorption energy of 34 meV/Å{sup 2}, which means that it is more stable than similar systems like graphene/HfO{sub 2} and MoS{sub 2}/SiO{sub 2}. There are no chemical bonds at the MoS{sub 2}-HfO{sub 2} interface. Upon formation of MoS{sub 2}/HfO{sub 2}, the electronic charge distribution is mostly localized at the interface region with no net charge transfer between the adsorbed MoS{sub 2} sheet and –HfO{sub 2} surface. However, the MoS{sub 2} sheet becomes n-type doped when there are oxygen vacancies in the HfO{sub 2} surface. Further investigation of the electronic distribution reveals that there are no electron- and hole-rich regions (electron-hole puddles) on the MoS{sub 2} sheet, which makes this system promising for use in high-speed nanoelectronic devices.

  17. Homology of ab1 and ab3 monoclonal antibodies that neutralize Semliki Forest virus

    NARCIS (Netherlands)

    Fernandez, IM; Bos, NA; Harmsen, M; Verheul, AFM; Snippe, H; Kraaijeveld, CA

    2001-01-01

    A noninternal image monoclonal antiidiotypic antibody (ab2 mAb), designated 1,13A321, that had proved its efficacy as vaccine against infection with Semliki Forest virus (SFV) in BALB/c mice, was used as immunogen to generate a panel of SFV-neutralizing monoclonal anti-anti-idiotypic antibodies (ab3

  18. Transversely Compressed Bonded Joints

    DEFF Research Database (Denmark)

    Hansen, Christian Skodborg; Schmidt, Jacob Wittrup; Stang, Henrik

    2012-01-01

    The load capacity of bonded joints can be increased if transverse pressure is applied at the interface. The transverse pressure is assumed to introduce a Coulomb-friction contribution to the cohesive law for the interface. Response and load capacity for a bonded single-lap joint was derived using...

  19. Ti, Al and N adatom adsorption and diffusion on rocksalt cubic AlN (001) and (011) surfaces: Ab initio calculations

    Science.gov (United States)

    Mastail, C.; David, M.; Nita, F.; Michel, A.; Abadias, G.

    2017-11-01

    We use ab initio calculations to determine the preferred nucleation sites and migration pathways of Ti, Al and N adatoms on cubic NaCl-structure (B1) AlN surfaces, primary inputs towards a further thin film growth modelling of the TiAlN alloy system. The potential energy landscape is mapped out for both metallic species and nitrogen adatoms for two different AlN surface orientations, (001) and (110), using density functional theory. For all species, the adsorption energies on AlN(011) surface are larger than on AlN(001) surface. Ti and Al adatom adsorption energy landscapes determined at 0 K by ab initio show similar features, with stable binding sites being located in, or near, epitaxial surface positions, with Ti showing a stronger binding compared to Al. In direct contrast, N adatoms (Nad) adsorb preferentially close to N surface atoms (Nsurf), thus forming strong N2-molecule-like bonds on both AlN(001) and (011). Similar to N2 desorption mechanisms reported for other cubic transition metal nitride surfaces, in the present work we investigate Nad/Nsurf desorption on AlN(011) using a drag calculation method. We show that this process leaves a Nsurf vacancy accompanied with a spontaneous surface reconstruction, highlighting faceting formation during growth.

  20. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    Science.gov (United States)

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  1. Corporate Bonds in Denmark

    DEFF Research Database (Denmark)

    Tell, Michael

    2015-01-01

    Corporate financing is the choice between capital generated by the corporation and capital from external investors. However, since the financial crisis shook the markets in 2007–2008, financing opportunities through the classical means of financing have decreased. As a result, corporations have...... to think in alternative ways such as issuing corporate bonds. A market for corporate bonds exists in countries such as Norway, Germany, France, the United Kingdom and the United States, while Denmark is still behind in this trend. Some large Danish corporations have instead used foreign corporate bonds...... markets. However, NASDAQ OMX has introduced the First North Bond Market in December 2012 and new regulatory framework came into place in 2014, which may contribute to a Danish based corporate bond market. The purpose of this article is to present the regulatory changes in Denmark in relation to corporate...

  2. Dangling bonds and crystalline inclusions in amorphous materials

    Energy Technology Data Exchange (ETDEWEB)

    Ferrari, L [Ferrara Univ. (Italy). Ist. di Matematica; Russo, G [Bologna Univ. (Italy). Ist. di Fisica

    1981-02-07

    It is suggested that on the surface of crystalline inclusions dangling bond formation is favoured due to unbalanced local stresses. The energy for bond tearings is probably originated from the exothermic process leading to the crystalline inclusion configuration which is more stable than the original amorphous one. A thermodynamical calculation is performed giving the ratio nsub(k) of crystalline inclusions having k dangling bonds on their surface.

  3. Fluorescent and Colorimetric Molecular Recognition Probe for Hydrogen Bond Acceptors

    OpenAIRE

    Pike, Sarah Jane; Hunter, Christopher Alexander

    2018-01-01

    The association constants for formation of 1 : 1 complexes between a H-bond donor, 1-naphthol, and a diverse range of charged and neutral H-bond acceptors have been measured using UV/vis absorption and fluorescence emission titrations. The performance of 1-naphthol as a dual colorimetric and fluorescent molecular recognition probe for determining the H-bond acceptor (HBA) parameters of charged and neutral solutes has been investigated in three solvents. The data were employed to establish sel...

  4. Solvent (acetone-butanol: ab) production

    Science.gov (United States)

    This article describes production of butanol [acetone-butanol-ethanol, (also called AB or ABE or solvent)] by fermentation using both traditional and current technologies. AB production from agricultural commodities, such as corn and molasses, was an important historical fermentation. Unfortunately,...

  5. Bismuth-boron multiple bonding in BiB_2O"- and Bi_2B"-

    International Nuclear Information System (INIS)

    Jian, Tian; Cheung, Ling Fung; Chen, Teng-Teng; Wang, Lai-Sheng

    2017-01-01

    Despite its electron deficiency, boron is versatile in forming multiple bonds. Transition-metal-boron double bonding is known, but boron-metal triple bonds have been elusive. Two bismuth boron cluster anions, BiB_2O"- and Bi_2B"-, containing triple and double B-Bi bonds are presented. The BiB_2O"- and Bi_2B"- clusters are produced by laser vaporization of a mixed B/Bi target and characterized by photoelectron spectroscopy and ab initio calculations. Well-resolved photoelectron spectra are obtained and interpreted with the help of ab initio calculations, which show that both species are linear. Chemical bonding analyses reveal that Bi forms triple and double bonds with boron in BiB_2O"- ([Bi≡B-B≡O]"-) and Bi_2B"- ([Bi=B=Bi]"-), respectively. The Bi-B double and triple bond strengths are calculated to be 3.21 and 4.70 eV, respectively. This is the first experimental observation of Bi-B double and triple bonds, opening the door to design main-group metal-boron complexes with multiple bonding. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Comet formation

    Science.gov (United States)

    Blum, J.

    2014-07-01

    There has been vast progress in our understanding of planetesimal formation over the past decades, owing to a number of laboratory experiments as well as to refined models of dust and ice agglomeration in protoplanetary disks. Coagulation rapidly forms cm-sized ''pebbles'' by direct sticking in collisions at low velocities (Güttler et al. 2010; Zsom et al. 2010). For the further growth, two model approaches are currently being discussed: (1) Local concentration of pebbles in nebular instabilities until gravitational instability occurs (Johansen et al. 2007). (2) A competition between fragmentation and mass transfer in collisions among the dusty bodies, in which a few ''lucky winners'' make it to planetesimal sizes (Windmark et al. 2012a,b; Garaud et al. 2013). Predictions of the physical properties of the resulting bodies in both models allow a distinction of the two formation scenarios of planetesimals. In particular, the tensile strength (i.e, the inner cohesion) of the planetesimals differ widely between the two models (Skorov & Blum 2012; Blum et al. 2014). While model (1) predicts tensile strengths on the order of ˜ 1 Pa, model (2) results in rather compactified dusty bodies with tensile strengths in the kPa regime. If comets are km-sized survivors of the planetesimal-formation era, they should in principle hold the secret of their formation process. Water ice is the prime volatile responsible for the activity of comets. Thermophysical models of the heat and mass transport close to the comet-nucleus surface predict water-ice sublimation temperatures that relate to maximum sublimation pressures well below the kPa regime predicted for formation scenario (2). Model (1), however, is in agreement with the observed dust and gas activity of comets. Thus, a formation scenario for cometesimals involving gravitational instability is favored (Blum et al. 2014).

  7. Shear bond strength of hydrophilic adhesive systems to enamel.

    Science.gov (United States)

    Hara, A T; Amaral, C M; Pimenta, L A; Sinhoreti, M A

    1999-08-01

    To compare the enamel shear bond strength of four hydrophilic adhesive systems: one multiple-bottle (Scotchbond Multi-Purpose Plus), two one-bottle (Stae, Single Bond) and one self-etching (Etch & Prime). 120 bovine incisor teeth were obtained, embedded in polyester resin, polished to 600 grit to form standardized enamel surfaces, and randomly assigned to four groups (n = 30). Each adhesive system was used on enamel according to the manufacturer's instructions, and resin-based composite (Z100) cylinders with 3 mm diameter and 5 mm height were bonded. Specimens were stored in humid environment for 1 week, and bond strength was determined using a universal testing machine, at a crosshead speed of 0.5 mm/minute. The mean shear bond strength values (MPa +/- SD) were: Single Bond: 24.28 +/- 5.27 (a); Scotchbond Multi-Purpose Plus: 21.18 +/- 4.35 (ab); Stae: 19.56 +/- 4.71 (b); Etch & Prime 3.0: 15.13 +/- 4.92 (c). ANOVA revealed significant difference in means (P < 0.01) and Tukey's test showed the statistical differences that are expressed by different letters for each group. It could be concluded that the self-etching adhesive system did not provide as good a bond to enamel surface, as did the one- and multiple-bottle systems.

  8. Rapid Solidification of AB{sub 5} Hydrogen Storage Alloys

    Energy Technology Data Exchange (ETDEWEB)

    Gulbrandsen-Dahl, Sverre

    2002-01-01

    This doctoral thesis is concerned with rapid solidification of AB{sub 5} materials suitable for electrochemical hydrogen storage. The primary objective of the work has been to characterise the microstructure and crystal structure of the produced AB{sub 5} materials as a function of the process parameters, e.g. the cooling rate during rapid solidification, the determination of which has been paid special attention to. The thesis is divided into 6 parts, of which Part I is a literature review, starting with a short presentation of energy storage alternatives. Then a general review of metal hydrides and their utilisation as energy carriers is presented. This part also includes more detailed descriptions of the crystal structure, the chemical composition and the hydrogen storage properties of AB{sub 5} materials. Furthermore, a description of the chill-block melt spinning process and the gas atomisation process is given. In Part II of the thesis a digital photo calorimetric technique has been developed and applied for obtaining in situ temperature measurements during chill-block melt spinning of a Mm(NiCoMnA1){sub 5} hydride forming alloy (Mm = Mischmetal of rare earths). Compared with conventional colour transmission temperature measurements, this technique offers a special advantage in terms of a high temperature resolutional and positional accuracy, which under the prevailing experimental conditions were found to be {+-}29 K and {+-} 0.1 mm, respectively. Moreover, it is shown that the cooling rate in solid state is approximately 2.5 times higher than that observed during solidification, indicating that the solid ribbon stayed in intimate contact with the wheel surface down to very low metal temperatures before the bond was broken. During this contact period the cooling regime shifted from near ideal in the melt puddle to near Newtonian towards the end, when the heat transfer from the solid ribbon to the wheel became the rate controlling step. In Part III of the

  9. Control of concerted two bond versus single bond dissociation in CH3Co(CO)4 via an intermediate state using pump-dump laser pulses

    Science.gov (United States)

    Ambrosek, David; González, Leticia

    2007-10-01

    Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH3Co(CO)4 indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH3 and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

  10. Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

    Science.gov (United States)

    Ambrosek, David; González, Leticia

    2007-10-07

    Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

  11. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

    Scope and method of study. Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. It is therefore important to probe dynamic changes in hydrogen bonding interactions during protein folding and function. Time-resolved Fourier transform infrared spectroscopy is highly sensitive to hydrogen bonding interactions. However, it lacks quantitative correlation between the vibrational frequencies and the number, type, and strength of hydrogen bonding interactions of ionizable and polar residues. We employ quantum physics theory based ab initio calculations to study the effects of hydrogen bonding interactions on vibrational frequencies of Asp, Glu, and Tyr residues and to develop vibrational spectral markers for probing hydrogen bonding interactions using infrared spectroscopy. In addition, proton transfer process plays a crucial role in a wide range of energy transduction, signal transduction, and enzymatic reactions. We study the structural basis for proton transfer using photoactive yellow protein as an excellent model system. Molecular dynamics simulation is employed to investigate the structures of early intermediate states. Quantum theory based ab initio calculations are used to study the impact of hydrogen bond interactions on proton affinity and proton transfer. Findings and conclusions. Our extensive density function theory based calculations provide rich structural, spectral, and energetic information on hydrogen bonding properties of protonated side chain groups of Asp/Glu and Tyr. We developed vibrational spectral markers and 2D FTIR spectroscopy for structural characterization on the number and the type of hydrogen bonding interactions of the COOH group of Asp/Glu and neutral phenolic group of Tyr. These developments greatly enhance the power of time-resolved FTIR spectroscopy as a major experimental tool for structural characterization of functionally important

  12. Te(II)/Te(IV) Mediated C-N Bond Formation on 2,5-Diphenyltellurophene and a Reassignment of the Product from the Reaction of PhI(OAc)2 with 2 TMS-OTf.

    Science.gov (United States)

    Aprile, Antonino; Iversen, Kalon J; Wilson, David J D; Dutton, Jason L

    2015-05-18

    We report a novel C-H to C-N bond metathesis at the 3-position of 1,2-diphenyltellurophene via oxidation of the Te(II) center to Te(IV) using the I(III) oxidant [PhI(4-DMAP)2](2+). Spontaneous reduction of a transient Te(IV) coordination compound to Te(II) generates an electrophilic equivalent of 4-DMAP that substitutes at a C-H bond at the 3-position of the tellurophene. Theoretical and synthetic reaction pathway studies confirm that a Te(IV) coordination complex with 4-DMAP is an intermediate. In the course of these pathway studies, it was also found that the identity of the I(III) oxidant generated from PhI(OAc)2 and 2 TMS-OTf is PhI(OAc)(OTf) and not PhI(OTf)2, as had been previously thought.

  13. Bond markets in Africa

    Directory of Open Access Journals (Sweden)

    Yibin Mu

    2013-07-01

    Full Text Available African bond markets have been steadily growing in recent years, but nonetheless remain undeveloped. African countries would benefit from greater access to financing and deeper financial markets. This paper compiles a unique set of data on government securities and corporate bond markets in Africa. It then applies an econometric model to analyze the key determinants of African government securities market and corporate bond market capitalization. Government securities market capitalization is directly related to better institutions and interest rate volatility, and inversely related to smaller fiscal deficits, higher interest rate spreads, exchange rate volatility, and current and capital account openness. Corporate bond market capitalization is directly linked to economic size, the level of development of the economy and financial markets, better institutions, and interest rate volatility, and inversely related to higher interest rate spreads and current account openness. Policy implications follow.

  14. RssAB signaling coordinates early development of surface multicellularity in Serratia marcescens.

    Directory of Open Access Journals (Sweden)

    Yu-Huan Tsai

    Full Text Available Bacteria can coordinate several multicellular behaviors in response to environmental changes. Among these, swarming and biofilm formation have attracted significant attention for their correlation with bacterial pathogenicity. However, little is known about when and where the signaling occurs to trigger either swarming or biofilm formation. We have previously identified an RssAB two-component system involved in the regulation of swarming motility and biofilm formation in Serratia marcescens. Here we monitored the RssAB signaling status within single cells by tracing the location of the translational fusion protein EGFP-RssB following development of swarming or biofilm formation. RssAB signaling is specifically activated before surface migration in swarming development and during the early stage of biofilm formation. The activation results in the release of RssB from its cognate inner membrane sensor kinase, RssA, to the cytoplasm where the downstream gene promoters are located. Such dynamic localization of RssB requires phosphorylation of this regulator. By revealing the temporal activation of RssAB signaling following development of surface multicellular behavior, our findings contribute to an improved understanding of how bacteria coordinate their lifestyle on a surface.

  15. Handbook of wafer bonding

    CERN Document Server

    Ramm, Peter; Taklo, Maaike M V

    2011-01-01

    Written by an author and editor team from microsystems companies and industry-near research organizations, this handbook and reference presents dependable, first-hand information on bonding technologies.In the first part, researchers from companies and institutions around the world discuss the most reliable and reproducible technologies for the production of bonded wafers. The second part is devoted to current and emerging applications, including microresonators, biosensors and precise measuring devices.

  16. Diffusion bonding techniques

    International Nuclear Information System (INIS)

    Peters, R.D.

    1978-01-01

    The applications of diffusion bonding at the General Electric Neutron Devices Department are briefly discussed, with particular emphasis on the gold/gold or gold/indium joints made between metallized alumina ceramic parts in the vacuum switch tube and the crystal resonator programs. Fixtures which use the differential expansion of dissimilar metals are described and compared to one that uses hydraulic pressure to apply the necessary bonding force

  17. Collective rotation from ab initio theory

    International Nuclear Information System (INIS)

    Caprio, M.A.; Maris, P.; Vary, J.P.; Smith, R.

    2015-01-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7–9 Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction. (author)

  18. AP calculus AB & BC crash course

    CERN Document Server

    Rosebush, J

    2012-01-01

    AP Calculus AB & BC Crash Course - Gets You a Higher Advanced Placement Score in Less Time Crash Course is perfect for the time-crunched student, the last-minute studier, or anyone who wants a refresher on the subject. AP Calculus AB & BC Crash Course gives you: Targeted, Focused Review - Study Only What You Need to Know Crash Course is based on an in-depth analysis of the AP Calculus AB & BC course description outline and actual AP test questions. It covers only the information tested on the exams, so you can make the most of your valuable study time. Written by experienced math teachers, our

  19. The Origin of the Non-Additivity in Resonance-Assisted Hydrogen Bond Systems.

    Science.gov (United States)

    Lin, Xuhui; Zhang, Huaiyu; Jiang, Xiaoyu; Wu, Wei; Mo, Yirong

    2017-11-09

    The concept of resonance-assisted hydrogen bond (RAHB) has been widely accepted, and its impact on structures and energetics can be best studied computationally using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently. In this work, we use the BLW method to examine a few molecules that result from the merging of two malonaldehyde molecules. As each of these molecules contains two hydrogen bonds, these intramolecular hydrogen bonds may be cooperative or anticooperative, depended on their relative orientations, and compared with the hydrogen bond in malonaldehyde. Apart from quantitatively confirming the concept of RAHB, the comparison of the computations with and without π resonance shows that both σ-framework and π-resonance contribute to the nonadditivity in these RAHB systems with multiple hydrogen bonds.

  20. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

    Science.gov (United States)

    Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

    2016-05-12

    An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

  1. Insertion reactions into Pd[bond]O and Pd[bond]N bonds: preparation of alkoxycarbonyl, carbonato, carbamato, thiocarbamate, and thioureide complexes of palladium(II).

    Science.gov (United States)

    Ruiz, José; Martínez, M Teresa; Florenciano, Félix; Rodríguez, Venancio; López, Gregorio; Pérez, José; Chaloner, Penny A; Hitchcock, Peter B

    2003-06-02

    Mononuclear palladium hydroxo complexes of the type [Pd(N[bond]N)(C(6)F(5))(OH)] [(N[bond]N = 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (Me(2)bipy), 1,10-phenanthroline (phen), or N,N,N',N'-tetramethylethylenediamine (tmeda)] have been prepared by reaction of [Pd(N[bond]N)(C(6)F(5))(acetone)]ClO(4) with KOH in methanol. These hydroxo complexes react, in methanol, with CO (1 atm, room temperature) to yield the corresponding methoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)Me)]. Similar alkoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)R)] (N[bond]N = bis(3,5-dimethylpyrazol-1-yl)methane); R = Me, Et, or (i)Pr) are obtained when [Pd(N[bond]N)(C(6)F(5))Cl] is treated with KOH in the corresponding alcohol ROH and CO is bubbled through the solution. The reactions of [Pd(N[bond]N)(C(6)F(5))(OH)] (N[bond]N = bipy or Me(2)bipy) with CO(2), in tetrahydrofuran, lead to the formation of the binuclear carbonate complexes [(N[bond]N)(C(6)F(5))Pd(mu-eta(2)-CO(3))Pd(C(6)F(5))(N[bond]N)]. Complexes [Pd(N[bond]N)(C(6)F(5))(OH)] react in alcohol with PhNCS to yield the corresponding N-phenyl-O-alkylthiocarbamate complexes [Pd(N[bond]N)(C(6)F(5))[SC(OR)NPh

  2. Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

    Science.gov (United States)

    Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

  3. Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

    Science.gov (United States)

    Mo, Lixin; Zeng, Yanli; Li, Xiaoyan; Zhang, Xueying; Meng, Lingpeng

    2016-07-01

    The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

  4. Electronic structure and interatomic bonding in Al10V

    International Nuclear Information System (INIS)

    Jahnatek, M; Krajci, M; Hafner, J

    2003-01-01

    On the basis of ab initio calculations we analysed the electron density distribution in the elementary cell of the compound Al 10 V. We found covalent bonding between certain atoms. The Al-V bonds of enhanced covalency are linked into -Al-V-Al-V- chains that extend over the whole crystal. The chains intersect at each V site and together form a Kagome network of corner-sharing tetrahedra. The large voids of this network are filled by Z 16 Friauf polyhedra consisting of Al atoms only. The skeleton of the Friauf polyhedron has the form of a truncated tetrahedron and consists of 12 strongly bonded Al atoms. These Al-Al bonds also have covalent character. The bonding is dominated by sp 2 hybridization. The centre of the Friauf polyhedron may be empty or occupied by an Al atom. The thermodynamic stability of the phase is investigated. The Al 21 V 2 phase with occupied voids is at low temperatures less stable than Al 10 V. The Al 10 V structure can be considered as a special case of the Al 18 Cr 2 Mg 3 structural class. We have found the same picture of bonding as we report here for Al 10 V for several other aluminium-rich alloys belonging to the Al 18 Cr 2 Mg 3 structural class also

  5. Evidence of significant covalent bonding in Au(CN)(2)(-).

    Science.gov (United States)

    Wang, Xue-Bin; Wang, Yi-Lei; Yang, Jie; Xing, Xiao-Peng; Li, Jun; Wang, Lai-Sheng

    2009-11-18

    The Au(CN)(2)(-) ion is the most stable Au compound known for centuries, yet a detailed understanding of its chemical bonding is still lacking. Here we report direct experimental evidence of significant covalent bonding character in the Au-C bonds in Au(CN)(2)(-) using photoelectron spectroscopy and comparisons with its lighter congeners, Ag(CN)(2)(-) and Cu(CN)(2)(-). Vibrational progressions in the Au-C stretching mode were observed for all detachment transitions for Au(CN)(2)(-), in contrast to the atomic-like transitions for Cu(CN)(2)(-), revealing the Au-C covalent bonding character. In addition, rich electronic structural information was obtained for Au(CN)(2)(-) by employing 118 nm detachment photons. Density functional theory and high-level ab initio calculations were carried out to understand the photoelectron spectra and obtain insight into the nature of the chemical bonding in the M(CN)(2)(-) complexes. Significant covalent character in the Au-C bonding due to the strong relativistic effects was revealed in Au(CN)(2)(-), consistent with its high stability.

  6. Elastic properties and 2D icosahedral bonding in borides of hexagonal WC type

    International Nuclear Information System (INIS)

    Music, Denis; Schneider, Jochen M.

    2005-01-01

    Using ab initio calculations we have identified materials with bulk moduli comparable to cubic BN. These are WB, IrB, ReB and OsB crystallizing in the hexagonal WC structure. In the (0 0 0 2) planes of these compounds, we find 2D icosahedral bonding between adjacent B atoms, which has previously not been reported

  7. Halogen bonded complexes between volatile anaeshetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: a theoretical study

    Czech Academy of Sciences Publication Activity Database

    Zierkiewicz, W.; Wieczorek, R.; Hobza, Pavel; Michalska, D.

    2011-01-01

    Roč. 13, č. 11 (2011), s. 5105-5113 ISSN 1463-9076 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : halogen bond * anaesthetics * ab initio calculation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011

  8. Elastic properties and 2D icosahedral bonding in borides of hexagonal WC type

    Energy Technology Data Exchange (ETDEWEB)

    Music, Denis [Materials Chemistry, RWTH-Aachen, Kopernikusstr. 16, D-52074 Aachen (Germany)]. E-mail: music@mch.rwth-aachen.de; Schneider, Jochen M. [Materials Chemistry, RWTH-Aachen, Kopernikusstr. 16, D-52074 Aachen (Germany)

    2005-01-15

    Using ab initio calculations we have identified materials with bulk moduli comparable to cubic BN. These are WB, IrB, ReB and OsB crystallizing in the hexagonal WC structure. In the (0 0 0 2) planes of these compounds, we find 2D icosahedral bonding between adjacent B atoms, which has previously not been reported.

  9. A Direct Proof of the Resonance-Impaired Hydrogen Bond (RIHB) Concept.

    Science.gov (United States)

    Lin, Xuhui; Wu, Wei; Mo, Yirong

    2018-01-24

    The concept of resonance-enhanced hydrogen bond (RAHB) has been widely accepted and applied as it highlights the positive impact of π-conjugation on intramolecular H-bonds. However, electron delocalization is directional and there is a possibility that π-resonance goes from the H-bond acceptor to the H-bond donor, leading to a negative impact on H-bonds. Here we used the block-localized wavefunction (BLW) method which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently, to quantify the interplay between H-bond and π-resonance in the terms of geometry, energetics and spectral properties. The comparison of geometrical optimizations with and without π-resonance shows that conjugation can indeed either enhance or weaken intramolecular H-bonds. We further experimented with various substituents attached to either the H-bond acceptor and/or H-bond donor side(s) to tune the H-bonding strength in both directions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. A comparative ab initio study of Br2*- and Br2 water clusters.

    Science.gov (United States)

    Pathak, A K; Mukherjee, T; Maity, D K

    2006-01-14

    The work presents ab initio results on structure and electronic properties of Br2*-.nH2O(n=1-10) and Br2.nH2O(n=1-8) hydrated clusters to study the effects of an excess electron on the microhydration of the halide dimer. A nonlocal density functional, namely, Becke's half-and-half hybrid exchange-correlation functional is found to perform well on the present systems with a split valence 6-31++G(d,p) basis function. Geometry optimizations for all the clusters are carried out with several initial guess structures and without imposing any symmetry restriction. Br2*-.nH2O clusters prefer to have symmetrical double hydrogen-bonding structures. Results on Br2.nH2O(n>or=2) cluster show that the O atom of one H2O is oriented towards one Br atom and the H atom of another H2O is directed to other Br atom making Br2 to exist as Br+-Br- entity in the cluster. The binding and solvation energies are calculated for the Br2*-.nH2O and Br2.nH2O clusters. Calculations of the vibrational frequencies show that the formation of Br2*- and Br2 water clusters induces significant shifts from the normal modes of isolated water. Excited-state calculations are carried out on Br2*-.nH2O clusters following configuration interaction with single electron excitation procedure and UV-VIS absorption profiles are simulated. There is an excellent agreement between the present theoretical UV-VIS spectra of Br2*-.10H2O cluster and the reported transient optical spectra for Br2*- in aqueous solution.

  11. Conformation and hydrogen bonding in 4-Aminobutanol

    Science.gov (United States)

    Khalil, Andrew S.; Duguay, Taylor M.; Lavrich, Richard J.

    2017-06-01

    Rotational spectra of the most abundant and four 13C isotopomers of 4-aminobutanol have been recorded in natural abundance using a Fourier-transform microwave spectrometer. For the most abundant isotopomer, 56 hyperfine components from the fifteen a- and b-type transitions measured were fit to the quadupole coupling constants, χaa = -3.843(3) MHz, χbb = 1.971(3) MHz. Rotational and centrifugal distortion constants determined from fits of the resulting unsplit line centers to the Watson A-reduction Hamiltonian are A = 4484.893(3) MHz, B = 2830.721(1) MHz, C = 1942.9710(3) MHz, ΔJ = 0.98(3) kHz, ΔJK = 1.4(1) kHz, ΔK = - 2.6(5) kHz, δJ = 0.27(1) kHz, and δK = 1.7(1) kHz. Between nine and eleven rotational transitions were measured for the 13C isotopes and rotational constants were determined by fixing the distortion constants to the values found for the normal isotope. The five sets of moments of inertia were used to determine the 4-aminobutanol substitution structure as well to perform a least-squares fit of the lowest energy ab initio structure. The heavy atom coordinates determined from these two methods are in excellent agreement. The conformation of 4-aminobutanol is stabilized by an intramolecular hydrogen bond from the alcohol proton to amino nitrogen with a resulting hydrogen bond distance of 1.891 Å. The experimental structure is consistent with the lowest energy ab initio [MP2/6-311++G(d,p)] structure.

  12. Romanian government bond market

    Directory of Open Access Journals (Sweden)

    Cornelia POP

    2012-12-01

    Full Text Available The present paper aims to present the level of development reached by Romanian government bond market segment, as part of the country financial market. The analysis will be descriptive (the data series available for Romania are short, based on the secondary data offered by the official bodies involved in the process of issuing and trading the Romanian government bonds (Romanian Ministry of Public Finance, Romanian National Bank and Bucharest Stock Exchange, and also on secondary data provided by the Federation of European Stock Exchanges.To enhance the market credibility as a benchmark, a various combination of measures is necessary; among these measures are mentioned: the extension of the yield curve; the issuance calendars in order to improve transparency; increasing the disclosure of information on public debt issuance and statistics; holding regular meetings with dealers, institutional investors and rating agencies; introducing a system of primary dealers; establishing a repurchase (repo market in the government bond market. These measures will be discussed based on the evolution presented inside the paper.The paper conclude with the fact that, until now, the Romanian government bond market did not provide a benchmark for the domestic financial market and that further efforts are needed in order to increase the government bond market transparency and liquidity.

  13. Safe and Liquid Mortgage Bonds

    DEFF Research Database (Denmark)

    Dick-Nielsen, Jens; Gyntelberg, Jacob; Lund, Jesper

    This paper shows that strict match pass-through funding of covered bonds provides safe and liquid mortgage bonds. Despite a 30% drop in house prices during the 2008 global crisis Danish mortgage bonds remained as liquid as most European government bonds. The Danish pass-through system effectively...... eliminates credit risk from the investor's perspective. Similar to other safe bonds, funding liquidity becomes the main driver of mortgage bond liquidity and this creates commonality in liquidity across markets and countries. These findings have implications for how to design a robust mortgage bond system...

  14. A Kine-chemical Investigation of the AB Dor Moving Group "Stream"

    Science.gov (United States)

    Barenfeld, Scott A.; Bubar, Eric J.; Mamajek, Eric E.; Young, Patrick A.

    2013-03-01

    The AB Dor Moving Group consists of a "nucleus" of ~10 stars at d ~= 20 pc, along with dozens of purported "stream" members distributed across the sky. We perform a chemical and kinematic analysis of a subsample of AB Dor stream stars to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution spectra taken with the Magellan Clay 6.5 m telescope. Using a χ2 test with the measured abundances for 10 different elements, we find that only half of the purported AB Dor stream members could possibly constitute a statistically chemically homogeneous sample. Some stream members with three-dimensional velocities were hundreds of parsecs from the AB Dor nucleus ~108 yr ago, and hence were unlikely to share a common origin. We conclude that the published lists of AB Dor moving group stream members are unlikely to represent the dispersed remnant of a single star formation episode. A subsample of the stream stars appears to be both statistically chemically homogeneous and in the vicinity of the AB Dor nucleus at birth. Their mean metallicity is [Fe/H] = 0.02 ± 0.02 dex, which we consider representative for the AB Dor group. Finally, we report a strong lower limit on the age of the AB Dor nucleus of >110 Myr based on the pre-main sequence contraction times for K-type members which have reached the main sequence.

  15. Phage-Mediated Competitive Chemiluminescent Immunoassay for Detecting Cry1Ab Toxin by Using an Anti-Idiotypic Camel Nanobody.

    Science.gov (United States)

    Qiu, Yulou; Li, Pan; Dong, Sa; Zhang, Xiaoshuai; Yang, Qianru; Wang, Yulong; Ge, Jing; Hammock, Bruce D; Zhang, Cunzheng; Liu, Xianjin

    2018-01-31

    Cry toxins have been widely used in genetically modified organisms for pest control, raising public concern regarding their effects on the natural environment and food safety. In this work, a phage-mediated competitive chemiluminescent immunoassay (c-CLIA) was developed for determination of Cry1Ab toxin using anti-idiotypic camel nanobodies. By extracting RNA from camels' peripheral blood lymphocytes, a naive phage-displayed nanobody library was established. Using anti-Cry1Ab toxin monoclonal antibodies (mAbs) against the library for anti-idiotypic antibody screening, four anti-idiotypic nanobodies were selected and confirmed to be specific for anti-Cry1Ab mAb binding. Thereafter, a c-CLIA was developed for detection of Cry1Ab toxin based on anti-idiotypic camel nanobodies and employed for sample testing. The results revealed a half-inhibition concentration of developed assay to be 42.68 ± 2.54 ng/mL, in the linear range of 10.49-307.1 ng/mL. The established method is highly specific for Cry1Ab recognition, with negligible cross-reactivity for other Cry toxins. For spiked cereal samples, the recoveries of Cry1Ab toxin ranged from 77.4% to 127%, with coefficient of variation of less than 9%. This study demonstrated that the competitive format based on phage-displayed anti-idiotypic nanobodies can provide an alternative strategy for Cry toxin detection.

  16. YaxAB, a Yersinia enterocolitica Pore-Forming Toxin Regulated by RovA

    Science.gov (United States)

    Wagner, Nikki J.; Lin, Carolina P.; Borst, Luke B.

    2013-01-01

    The transcriptional regulator RovA positively regulates transcription of the Yersinia enterocolitica virulence gene inv. Invasin, encoded by inv, is important for establishment of Y. enterocolitica infection. However, a rovA mutant is more attenuated for virulence than an inv mutant, implying that RovA regulates additional virulence genes. When the Y. enterocolitica RovA regulon was defined by microarray analysis, YE1984 and YE1985 were among the genes identified as being upregulated by RovA. Since these genes are homologous to Xenorhabdus nematophila cytotoxin genes xaxA and xaxB, we named them yaxA and yaxB, respectively. In this work, we demonstrate the effects of YaxAB on the course of infection in the murine model. While a yaxAB mutant (ΔyaxAB) is capable of colonizing mice at the same level as the wild type, it slightly delays the course of infection and results in differing pathology in the spleen. Further, we found that yaxAB encode a probable cytotoxin capable of lysing mammalian cells, that both YaxA and YaxB are required for cytotoxic activity, and that the two proteins associate. YaxAB-mediated cell death occurs via osmotic lysis through the formation of distinct membrane pores. In silico tertiary structural analysis identified predicted structural homology between YaxA and proteins in pore-forming toxin complexes from Bacillus cereus (HBL-B) and Escherichia coli (HlyE). Thus, it appears that YaxAB function as virulence factors by inducing cell lysis through the formation of pores in the host cell membrane. This characterization of YaxAB supports the hypothesis that RovA regulates expression of multiple virulence factors in Y. enterocolitica. PMID:24002058

  17. In-situ determination of amine/epoxy and carboxylic/epoxy exothermic heat of reaction on surface of modified carbon nanotubes and structural verification of covalent bond formation

    Science.gov (United States)

    Neves, Juliana C.; de Castro, Vinícius G.; Assis, Ana L. S.; Veiga, Amanda G.; Rocco, Maria Luiza M.; Silva, Glaura G.

    2018-04-01

    An effective nanofiller-matrix interaction is considered crucial to produce enhanced nanocomposites. Nevertheless, there is lack of experiments focused in the direct measurement of possible filler-matrix covalent linkage, which was the main goal of this work for a carbon nanotube (CNT)/epoxy system. CNT were functionalized with oxygenated (ox) functions and further with triethylenetetramine (TETA). An in-situ determination methodology of epoxy-CNTs heat of reaction was developed by Differential Scanning Calorimetry (DSC). Values of -(8.7 ± 0.4) and -(6.0 ± 0.6) J/g were observed for epoxy with CNT-ox and CNT-TETA, respectively. These results confirm the occurrence of covalent bonds for both functionalized CNTs, a very important information due to the literature generally disregard this possibility for oxygenated functions. The higher value obtained for CNT-ox can be attributed to a not complete amidation and to steric impediments in the CNT-TETA structure. The modified CNTs produced by DSC experiments were then characterized by X-Ray Photoelectron Spectroscopy, Transmission Electron Microscopy and Thermogravimetry, which confirmed the covalent linkage. This characterization methodology can be used to verify the occurrence of covalent bonds in various nanocomposites with a quantitative evaluation, providing data for better understanding of the role of CNT functional groups and for tailoring its interface with polymers.

  18. Microstructure and bonding mechanism of Al/Ti bonded joint using Al-10Si-1Mg filler metal

    International Nuclear Information System (INIS)

    Sohn, Woong H.; Bong, Ha H.; Hong, Soon H.

    2003-01-01

    The microstructures and liquid state diffusion bonding mechanism of cp-Ti to 1050 Al using an Al-10.0wt.%Si-1.0wt.%Mg filler metal with 100 μm in thickness have been investigated at 620 deg. C under 1x10 -4 Torr. The effects of bonding process parameters on microstructure of bonded joint have been analyzed by using an optical microscope, AES, scanning electron microscopy and EDS. The interfacial bond strength of Al/Ti bonded joints was measured by the single lap shear test. The results show that the bonding at the interface between Al and filler metal proceeds by wetting the Al with molten filler metal, and followed by removal of oxide layer on surface of Al. The interface between Al and filler metal moved during the isothermal solidification of filler metal by the diffusion of Si from filler metal into Al layer. The interface between Al and filler metal became curved in shape with increasing bonding time due to capillary force at grain boundaries. The bonding at the interface between Ti and filler metal proceeds by the formation of two different intermetallic compound layers, identified as Al 5 Si 12 Ti 7 and Al 12 Si 3 Ti 5 , followed by the growth of the intermetallic compound layers. The interfacial bond strength at Al/Ti joint increased with increasing bonding time up to 25 min at 620 deg. C. However, the interfacial bond strength of Al/Ti joint decreased after bonding time of 25 min at 620 deg. C due to formation of cavities in Al near Al/intermetallic interfaces

  19. Continuing bonds and place.

    Science.gov (United States)

    Jonsson, Annika; Walter, Tony

    2017-08-01

    Where do people feel closest to those they have lost? This article explores how continuing bonds with a deceased person can be rooted in a particular place or places. Some conceptual resources are sketched, namely continuing bonds, place attachment, ancestral places, home, reminder theory, and loss of place. The authors use these concepts to analyze interview material with seven Swedes and five Britons who often thought warmly of the deceased as residing in a particular place and often performing characteristic actions. The destruction of such a place, by contrast, could create a troubling, haunting absence, complicating the deceased's absent-presence.

  20. Subtle differences in the hydrogen bonding of alcohol to divalent oxygen and sulfur

    DEFF Research Database (Denmark)

    Du, Lin; Tang, Shanshan; Hansen, Anne Schou

    2017-01-01

    complexes are more stable and form stronger hydrogen bonds compared to complexes with MeOH and EtOH, which are comparable, and only for the stronger hydrogen bond donor (TFE) are the small differences in acceptor molecules highlighted. The equilibrium constant for complex formation was determined from......The Osingle bondH⋯O and Osingle bondH⋯S hydrogen bonds were investigated by gas phase FTIR spectroscopy of alcohol–dimethylether and alcohol–dimethylsulfide complexes, with alcohols of increasing hydrogen bond donor strength; methanol (MeOH), ethanol (EtOH) and 2,2,2-trifluoroethanol (TFE). The TFE...

  1. A comparison of the characteristics of excimer and femtosecond laser ablation of acrylonitrile butadiene styrene (ABS)

    International Nuclear Information System (INIS)

    See, Tian Long; Liu, Zhu; Li, Lin; Zhong, Xiang Li

    2016-01-01

    Highlights: • Ablation threshold for excimer laser is lower compared to femtosecond laser. • Effective optical penetration depth for excimer laser is lower compared to femtosecond laser. • Two ablation characteristic regimes are observed for femtosecond laser ablation. • Reduction of C=C bond following excimer or fs laser ablation is observed. • Addition of oxygen- and nitrogen-rich functional groups is observed. - Abstract: This paper presents an investigation on the ablation characteristics of excimer laser (λ = 248 nm, τ = 15 ns) and femtosecond laser (λ = 800 nm, τ = 100 fs) on ABS polymer sheets. The laser–material interaction parameters (ablation threshold, optical penetration depth and incubation factor) and the changes in material chemical properties were evaluated and compared between the two lasers. The work shows that the ablation threshold and effective optical penetration depth values are dependent on the wavelength of laser beam (photon energy) and the pulse width. The ablation threshold value is lower for the excimer laser ablation of ABS (F_t_h = 0.087 J/cm"2) than that for the femtosecond laser ablation of ABS (F_t_h = 1.576 J/cm"2), demonstrating a more dominating role of laser wavelength than the pulse width in influencing the ablation threshold. The ablation depth versus the logarithmic scale of laser fluence shows two linear regions for the fs laser ablation, not previously known for polymers. The effective optical penetration depth value is lower for excimer laser ablation (α"−"1 = 223 nm) than that for femtosecond laser ablation (α"−"1 = 2917 nm). The ablation threshold decreases with increasing number of pulses (NOP) due to the chain scission process that shortens the polymeric chains, resulting in a weaker polymeric configuration and the dependency is governed by the incubation factor. Excimer laser treatment of ABS eliminates the C=C bond completely through the chain scission process whereas C=C bond is partially

  2. A comparison of the characteristics of excimer and femtosecond laser ablation of acrylonitrile butadiene styrene (ABS)

    Energy Technology Data Exchange (ETDEWEB)

    See, Tian Long, E-mail: tianlong.see@postgrad.manchester.ac.uk [Corrosion and Protection Centre, School of Materials, The Mill, The University of Manchester, M13 9PL Manchester (United Kingdom); Laser Processing Research Centre, School of Mechanical, Aerospace and Civil Engineering, The University of Manchester, M13 9PL Manchester (United Kingdom); Liu, Zhu [Corrosion and Protection Centre, School of Materials, The Mill, The University of Manchester, M13 9PL Manchester (United Kingdom); Li, Lin [Laser Processing Research Centre, School of Mechanical, Aerospace and Civil Engineering, The University of Manchester, M13 9PL Manchester (United Kingdom); Zhong, Xiang Li [Corrosion and Protection Centre, School of Materials, The Mill, The University of Manchester, M13 9PL Manchester (United Kingdom)

    2016-02-28

    Highlights: • Ablation threshold for excimer laser is lower compared to femtosecond laser. • Effective optical penetration depth for excimer laser is lower compared to femtosecond laser. • Two ablation characteristic regimes are observed for femtosecond laser ablation. • Reduction of C=C bond following excimer or fs laser ablation is observed. • Addition of oxygen- and nitrogen-rich functional groups is observed. - Abstract: This paper presents an investigation on the ablation characteristics of excimer laser (λ = 248 nm, τ = 15 ns) and femtosecond laser (λ = 800 nm, τ = 100 fs) on ABS polymer sheets. The laser–material interaction parameters (ablation threshold, optical penetration depth and incubation factor) and the changes in material chemical properties were evaluated and compared between the two lasers. The work shows that the ablation threshold and effective optical penetration depth values are dependent on the wavelength of laser beam (photon energy) and the pulse width. The ablation threshold value is lower for the excimer laser ablation of ABS (F{sub th} = 0.087 J/cm{sup 2}) than that for the femtosecond laser ablation of ABS (F{sub th} = 1.576 J/cm{sup 2}), demonstrating a more dominating role of laser wavelength than the pulse width in influencing the ablation threshold. The ablation depth versus the logarithmic scale of laser fluence shows two linear regions for the fs laser ablation, not previously known for polymers. The effective optical penetration depth value is lower for excimer laser ablation (α{sup −1} = 223 nm) than that for femtosecond laser ablation (α{sup −1} = 2917 nm). The ablation threshold decreases with increasing number of pulses (NOP) due to the chain scission process that shortens the polymeric chains, resulting in a weaker polymeric configuration and the dependency is governed by the incubation factor. Excimer laser treatment of ABS eliminates the C=C bond completely through the chain scission process whereas

  3. Photoinitiated reactions in weakly bonded complexes

    International Nuclear Information System (INIS)

    Wittig, C.

    1993-01-01

    This paper discusses photoinitiated reactions in weakly bonded binary complexes in which the constituents are only mildly perturbed by the intermolecular bond. Such complexes, with their large zero point excursions, set the stage for events that occur following electronic excitation of one of the constituents. This can take several forms, but in all cases, entrance channel specificity is imposed by the character of the complex as well as the nature of the photoinitiation process. This has enabled us to examine aspects of bimolecular processes: steric effects, chemical branching ratios, and inelastic scattering. Furthermore, monitoring reactions directly in the time domain can reveal mechanisms that cannot be inferred from measurements of nascent product excitations. Consequently, we examined several systems that had been studied previously by our group with product state resolution. With CO 2 /HI, in which reaction occurs via a HOCO intermediate, the rates agree with RRKM predictions. With N 2 O/HI, the gas phase single collision reaction yielding OH + N 2 has been shown to proceed mainly via an HNNO intermediate that undergoes a 1,3-hydrogen shift to the OH + N 2 channel. With complexes, ab initio calculations and high resolution spectroscopic studies of analogous systems suggest that the hydrogen, while highly delocalized, prefers the oxygen to the nitrogen. We observe that OH is produced with a fast risetime (< 250 fs) which can be attributed to either direct oxygen-side attack or rapid HNNO decomposition and/or a termolecular contribution involving the nearby iodine

  4. Rydberb bonding in (NH4)2

    International Nuclear Information System (INIS)

    Boldyrev, A.I.; Simons, J.

    1992-01-01

    Chemical binding of two monovalent Rydberg species to form a singlet-state Rydberg dimer molecule is predicted to be possible Ab initio electronic structure methods that include electron correlation (at levels up through QCISD(T)/6-31++G** MP2(full)/6-31++G** + ZPE) are shown to be essential to achieving a proper description of such bonding. The (NH 4 ) molecule, selected as the prototype for this study, is shown to be bound with respect to its Rydberg-species fragments, 2NH 4 by 7.5-9.7 kcal/mol, depending on the level of treatment of electron correlation, and to be electronically stable (by ca.4 eV) with respect to (NH 4 ) 2 + at the neutral's equilibrium geometry. The (NH 4 ) 2 Rydberg dimer is thermodynamically unstable with respect to 2NH 3 + H 2 by 86-89 kcal/mol mol yet possesses all real vibrational frequencies; it is thus a metastable molecular held together by a weak Rydberg bond. The dissociation energy of the (NH 4 ) 2 + cation to form NH 4 + + NH 4 is found to be larger than that of the neutral (NH 4 ) 2 . 12 refs., 4 figs., 9 tabs

  5. Clinical significance of determination of serum leptin and AsAb, EmAb levels in infertile women

    International Nuclear Information System (INIS)

    Luo Jian; Zhou Minglian; Sun Gang; He Haoming

    2010-01-01

    Objective: To study the clinical significance of determination of serum leptin, AsAb, and EmAb levels in infertile women. Methods: Serum leptin (with RIA) and AsAb, EmAb (with ELISA) levels were detected in 32 infertile women and 35 controls. Results: Serum leptin levels in infertile women were significantly lower than those in controls (P<0.01). Serum AsAb and EmAb were both positive in 25 of the 32 infertile women (78.1%) and EmAb (one of two Abs) was positive in the rest 7 women (21.9%). These positive rates were also significantly higher than the respective ones in the controls (both P<0.01). Conclusion: Lower serum leptin level with highly positive AsAb and EmAb might be the chief cause of infertility in women. (authors)

  6. Development of HIP bonding procedure and mechanical properties of HIP bonded joints for reduced activation ferritic steel F-82H

    International Nuclear Information System (INIS)

    Oda, Masahiro; Kurasawa, Toshimasa; Kuroda, Toshimasa; Hatano, Toshihisa; Takatsu, Hideyuki

    1997-03-01

    Structural materials of blanket components in fusion DEMO reactors will receive a neutron wall load more than 3-5MW/m 2 as well as exposed by surface heat flux more than 0.5MW/m 2 . A reduced activation ferritic steel F-82H has been developed by JAERI in collaboration with NKK from viewpoints of resistance for high temperature and neutron loads and lower radioactivity. This study intends to obtain basic performance of F-82H to establish the fabrication procedure of the first wall and blanket box by using Hot Isostatic Pressing (HIP) bonding. Before HIP bonding tests, effects of heat treatment temperature and surface roughness on mechanical properties of joints were investigated in the heat treatment tests and diffusion bonding tests, respectively. From these results, the optimum HIP bonding conditions and the post heat treatment were selected. Using these conditions, the HIP bonding tests were carried out to evaluate HIP bondability and to obtain mechanical properties of the joints. Sufficient HIP bonding performance was obtained under the temperature of 1040degC, the compressive stress of 150MPa, the holding time of 2h, and the surface roughness ∼μ m. Mechanical properties of HIP bonded joints with these conditions were similar to those of as-received base metal. An oxide formation on the surface to be bonded would need to be avoided for sufficient bonding. The bonding ratio, Charpy impact value and fatigue performance of the joints strongly depended on the HIP conditions, especially temperature, while micro-structure, Vickers hardness and tensile properties had little dependence on the HIP temperature. The surface roughness strongly affected the bonding ratio and would be required to be in the level of a few μ m. In the HIP bonding test of the welded material, the once-melted surface could be jointed by the HIP bonding under the above-mentioned procedure. (J.P.N.)

  7. Bond-Valence Constraints on Liquid Water Structure

    International Nuclear Information System (INIS)

    Bickmore, Barry R.; Rosso, Kevin M.; Brown, I. David; Kerisit, Sebastien N.

    2009-01-01

    The recent controversy about the structure of liquid water pits a new model involving water molecules in relatively stable rings-and-chains structures against the standard model that posits water molecules in distorted tetrahedral coordination. Molecular dynamics (MD) simulations 'both classical and ab initio' almost uniformly support the standard model, but since none of them can yet reproduce all the anomalous properties of water, they leave room for doubt. We argue that it is possible to evaluate these simulations by testing them against their adherence to the bond-valence model, a well known, and quantitatively accurate, empirical summary of the behavior of atoms in the bonded networks of inorganic solids. Here we use the results of ab initio molecular dynamics simulations of ice, water, and several solvated aqueous species to show that the valence sum rule (the first axiom of the bond-valence model,) is followed in both solid and liquid bond networks. We then test MD simulations of water, employing several popular potential models, against this criterion and the experimental O-O radial distribution function. It appears that most of those tested cannot satisfy both criteria well, except TIP4P and TIP5P. If the valence sum rule really can be applied to simulated liquid structures, then it follows that the bonding behaviors of atoms in liquids are in some ways identical to those in solids. We support this interpretation by showing that the simulations produce O-H-O geometries completely consistent with the range of geometries available in solids, and the distributions of instantaneous valence sums reaching the atoms in both the ice and liquid water simulations are essentially identical. Taken together, this is powerful evidence in favor of the standard distorted tetrahedral model of liquid water structure

  8. Integration of European Bond Markets

    DEFF Research Database (Denmark)

    Christiansen, Charlotte

    2014-01-01

    I investigate the time variation in the integration of EU government bond markets. The integration is measured by the explanatory power of European factor portfolios for the individual bond markets for each year. The integration of the government bond markets is stronger for EMU than non-EMU memb......I investigate the time variation in the integration of EU government bond markets. The integration is measured by the explanatory power of European factor portfolios for the individual bond markets for each year. The integration of the government bond markets is stronger for EMU than non...

  9. Excited hydrogen bonds in the molecular mechanism of muscle contraction.

    Science.gov (United States)

    Bespalova, S V; Tolpygo, K B

    1991-11-21

    The mechanism of muscle contraction is considered. The hydrolysis of an ATP molecule is assumed to produce the excitation of hydrogen bonds A--H...B between electronegative atoms A and B, which are contained in the myosin head and actin filament. This excitation energy epsilon f depends on the interatomic distance AB = R and generates the tractive force f = -delta epsilon f/delta R, that makes atoms AB approach each other. The swing of the myosin head results in macroscopic mutual displacement of actin and myosin polymers. The motion of the actin filament under the action of this force is studied. The conditions under which a considerable portion of the excitation energy converts into the potential tension energy of the actin filament are analysed, and the probability of higher muscle efficiency existence is discussed.

  10. All-electron ab initio calculations of YBa2Cu3O7 with self-consistence crystal field

    Institute of Scientific and Technical Information of China (English)

    刘洪霖; 陈念贻

    1995-01-01

    The quantum chemical calculations of cluster YBa2Cu3O7 considering all electrons have been per-formed by using the ab initio HF method with self-consistence crystal field.A Hartree-Fork surface potentialis proposed to make an asymmetric duster model possess a relatively symmetric potential field and to obtaina relatively symmetric electronic structure,electronic distributions,frontier orbitals,and bond order,etc.Thesuggestions that there exists a covalent bonding complex,[CuO2-O-CuO-O-Cu2]6,8-,in the cell unit ofthe crystal,and the cell units are connected with each other by ionic bonds along the c direction of the crys-tal lattice are offered based on the chemical bonding characteristics from the calculated results.The importantcontribution of the apical oxygen to superconductivities is emphasized as well.

  11. Amalgam shear bond strength to dentin using different bonding agents.

    Science.gov (United States)

    Vargas, M A; Denehy, G E; Ratananakin, T

    1994-01-01

    This study evaluated the shear bond strength of amalgam to dentin using five different bonding agents: Amalgambond Plus, Optibond, Imperva Dual, All-Bond 2, and Clearfil Liner Bond. Flat dentin surfaces obtained by grinding the occlusal portion of 50 human third molars were used for this study. To contain the amalgam on the tooth surface, cylindrical plastic molds were placed on the dentin and secured with sticky wax. The bonding agents were then applied according to the manufacturers' instructions or light activated and Tytin amalgam was condensed into the plastic molds. The samples were thermocycled and shear bond strengths were determined using an Instron Universal Testing Machine. Analysis by one-way ANOVA indicated significant difference between the five groups (P < 0.05). The bond strength of amalgam to dentin was significantly higher with Amalgambond Plus using the High-Performance Additive than with the other four bonding agents.

  12. Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

    Science.gov (United States)

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

    2014-09-04

    Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication.

  13. H3+: Ab initio calculation of the vibration spectrum

    International Nuclear Information System (INIS)

    Carney, G.D.; Porter, R.N.

    1976-01-01

    The vibration spectrum of H 3 + is calculated from the representation of a previously reported [J. Chem Phys. 60, 4251 (1974)] ab initio potential-energy surface in a fifth degree Simons--Parr--Finlan (SPF) expansion. Morse- and harmonic-oscillator basis functions are used to describe the motions of the three oscillators and the Harris--Engerholm--Gwinn quadrature technique is used to obtain matrix elements of the Hamiltonian in the basis of vibrational configurations. Our variational method is thus analogous to configuration--interaction calculations for electronic states. The ground state is found to have a zero-point energy of 4345 cm -1 and a vibrationally averaged geometry of R 1 =R 2 =0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A 1 fundamentals are nu-bar/sub E/=2516 cm -1 and nu-bar/sub A/=3185 cm -1 and those for the corresponding first overtones of the bending mode are 2nu-bar/sub E/=5004 +- 4 cm -1 and 2nu-bar/sub A/=4799 cm -1 . The first overtone of the breathing mode is 6264 cm -1 . The first-excited A 1 vibration state is metastable with a dipole--radiation lifetime of 3 sec. Transition frequencies, Einstein coefficients, and lifetimes are reported for a total of 21 transitions. Analysis of results for Dunham number and normal-coordinate expansions in comparison with those for SPF expansion show the latter to be superior for ab initio vibrational calculations. A scheme for possible direct measurement of the fundamental A 1 and E vibrational bands is suggested

  14. Convertible bond valuation focusing on Chinese convertible bond market

    OpenAIRE

    Yang, Ke

    2010-01-01

    This paper mainly discusses the methods of valuation of convertible bonds in Chinese market. Different from common convertible bonds in European market, considering the complicate features of Chinese convertible bond, this paper represents specific pricing approaches for pricing convertible bonds with different provisions along with the increment of complexity of these provisions. More specifically, this paper represents the decomposing method and binomial tree method for pricing both of Non-...

  15. Ab Initio Calculations for the BaTiO3 (001) Surface Structure

    Institute of Scientific and Technical Information of China (English)

    XUE Xu-Yan; WANG Chun-Lei; ZHONG Wei-Lie

    2004-01-01

    @@ The ab initio method within the local density approximation is applied to calculate cubic BaTiO3 (001) surface relaxation and rumpling for two different terminations (BaO and TiO2). Our calculations demonstrate that cubic perovskite BaTiO3 crystals possess surface polarization, accompanied by the presence of the relevant electric field.We analyse their electronic structures (band structure, density of states and the electronic density redistribution with emphasis on the covalency effects). The results are also compared with that of the previous ab initio calculations. Considerable increases of Ti-O chemical bond covalency nearby the surface have been observed.The band gap reduces especially for the TiO2 termination.

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

    Science.gov (United States)

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

    2009-10-29

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

  17. Comparison of shear bond strength of the stainless steel metallic brackets bonded by three bonding systems

    Directory of Open Access Journals (Sweden)

    Mehdi Ravadgar

    2013-09-01

    Full Text Available Introduction: In orthodontic treatment, it is essential to establish a satisfactory bond between enamel and bracket. After the self-etch primers (SEPs were introduced for the facilitation of bracket bonding in comparison to the conventional etch-and-bond system, multiple studies have been carried out on their shear bond strengths which have yielded different results. This study was aimed at comparing shear bond strengths of the stainless steel metallic brackets bonded by three bonding systems. Methods: In this experimental in vitro study, 60 extracted human maxillary premolar teeth were randomly divided into three equal groups: in the first group, Transbond XT (TBXT light cured composite was bonded with Transbond plus self-etching primer (TPSEP in the second group, TBXT composite was bonded with the conventional method of acid etching and in the third group, the self cured composite Unite TM bonding adhesive was bonded with the conventional method of acid etching. In all the groups, Standard edgewise-022 metallic brackets (American Orthodontics, Sheboygan, USA were used. Twenty-four hours after the completion of thermocycling, shear bond strength of brackets was measured by Universal Testing Machine (Zwick. In order to compare the shear bond strengths of the groups, the variance analysis test (ANOVA was adopted and p≤0.05 was considered as a significant level. Results: Based on megapascal, the average shear bond strength for the first, second, and third groups was 8.27±1.9, 9.78±2, and 8.92±2.5, respectively. There was no significant difference in the shear bond strength of the groups. Conclusions: Since TPSEP shear bond strength is approximately at the level of the conventional method of acid etching and within the desirable range for orthodontic brackets shear bond strength, applying TPSEP can serve as a substitute for the conventional method of etch and bond, particularly in orthodontic operations.

  18. Comparison of shear bond strength of the stainless steel metallic brackets bonded by three bonding systems

    Directory of Open Access Journals (Sweden)

    Mehdi Ravadgar

    2013-09-01

    Full Text Available Introduction: In orthodontic treatment, it is essential to establish a satisfactory bond between enamel and bracket. After the self-etch primers (SEPs were introduced for the facilitation of bracket bonding in comparison to the conventional etch-and-bond system, multiple studies have been carried out on their shear bond strengths which have yielded different results. This study was aimed at comparing shear bond strengths of the stainless steel metallic brackets bonded by three bonding systems. Methods: In this experimental in vitro study, 60 extracted human maxillary premolar teeth were randomly divided into three equal groups: in the first group, Transbond XT (TBXT light cured composite was bonded with Transbond plus self-etching primer (TPSEP; in the second group, TBXT composite was bonded with the conventional method of acid etching; and in the third group, the self cured composite Unite TM bonding adhesive was bonded with the conventional method of acid etching. In all the groups, Standard edgewise-022 metallic brackets (American Orthodontics, Sheboygan, USA were used. Twenty-four hours after the completion of thermocycling, shear bond strength of brackets was measured by Universal Testing Machine (Zwick. In order to compare the shear bond strengths of the groups, the variance analysis test (ANOVA was adopted and p≤0.05 was considered as a significant level. Results: Based on megapascal, the average shear bond strength for the first, second, and third groups was 8.27±1.9, 9.78±2, and 8.92±2.5, respectively. There was no significant difference in the shear bond strength of the groups. Conclusions: Since TPSEP shear bond strength is approximately at the level of the conventional method of acid etching and within the desirable range for orthodontic brackets shear bond strength, applying TPSEP can serve as a substitute for the conventional method of etch and bond, particularly in orthodontic operations.

  19. Study on the effects of fluorine and oxygen deficiency on YBa2Cu3O7 by ab initio method

    Institute of Scientific and Technical Information of China (English)

    刘洪霖; 曹晓卫; 瞿丽曼; 陈念贻

    1997-01-01

    The calculations of clusters modeling the fluorine-doping and oxygen deficiency of YBa2Cu3O2,have been performed by the method of all-electron ab initio Hartree-Fock with self-consistent crystal field Results show that in CuO planes electric charge significantly increases,the chemical valence of Cu decreases and the covalent bonding of Cu-O greatly weakens owing to oxygen deficiency,while the effect of F restores the local electronic structure of YBa2Cu3O7 The reported opinion that F occupied the oxygen vacancy in Cu-O chains seems disputable according to the calculated bonding characteristics.

  20. Elastic properties of amorphous boron suboxide based solids studied using ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Music, Denis; Schneider, Jochen M

    2008-01-01

    We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B 6 O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm -3 , the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density

  1. Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization

    NARCIS (Netherlands)

    de Jong, G.T.; Sola, M.; Visscher, L.; Bickelhaupt, F.M.

    2004-01-01

    To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory,

  2. Modelling of nuclear glasses by classical and ab initio molecular dynamics; Modelisation de verres intervenant dans le conditionnement des dechets radioactifs par dynamiques moleculaires classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

    A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

  3. Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation.

    Science.gov (United States)

    Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P; Fang, Yigang; Kostko, Oleg; Ahmed, Musahid; Head-Gordon, Martin

    2017-05-23

    The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C 2 H 2 ) n + , just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4 H 4 + and C 6 H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2 H 2 ) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6 H 6 + isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.

  4. Ab initio dynamics and photoionization mass spectrometry reveal ion–molecule pathways from ionized acetylene clusters to benzene cation

    Science.gov (United States)

    Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; Fang, Yigang; Kostko, Oleg

    2017-01-01

    The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion–molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion–molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM. PMID:28484019

  5. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    century and most chemists appear to think of 'chemi- cal bond' as ..... These complexes, in their global min- ima, have ... taneously act as hydrogen bond donor and acceptor displaying ... also has a local minimum, which is linear and similar to.

  6. Diode laser surgery. Ab interno and ab externo versus conventional surgery in rabbits.

    Science.gov (United States)

    Karp, C L; Higginbotham, E J; Edward, D P; Musch, D C

    1993-10-01

    Fibroblastic proliferation of subconjunctival tissues remains a primary mechanism of failure in filtration surgery. Minimizing the surgical manipulation of episcleral tissues may reduce scarring. Laser sclerostomy surgery involves minimal tissue dissection, and is gaining attention as a method of potentially improving filter duration in high-risk cases. Twenty-five New Zealand rabbits underwent filtration surgery in one eye, and the fellow eye remained as the unoperated control. Ten rabbits underwent ab externo diode laser sclerostomy surgery, ten underwent ab interno diode sclerostomy surgery, and five had posterior sclerostomy procedures. Filtration failure was defined as a less-than-4-mmHg intraocular pressure (IOP) difference between the operative and control eyes. The mean time to failure for the ab externo, ab interno, and conventional posterior sclerostomy techniques measured 17.4 +/- 11.5, 13.1 +/- 6.7, and 6.0 +/- 3.1 days, respectively. In a comparison of the laser-treated groups with the conventional procedure, the time to failure was significantly longer (P = 0.02) for the ab externo filter. The mean ab interno sclerostomy duration was longer than the posterior lip procedure, but this difference was not statistically significant (P = 0.15). The overall level of IOP reduction was similar in the three groups. These data suggest that diode laser sclerostomy is a feasible technique in rabbits, and the ab externo approach resulted in longer filter duration than the conventional posterior lip procedure in this model.

  7. Bond yield curve construction

    Directory of Open Access Journals (Sweden)

    Kožul Nataša

    2014-01-01

    Full Text Available In the broadest sense, yield curve indicates the market's view of the evolution of interest rates over time. However, given that cost of borrowing it closely linked to creditworthiness (ability to repay, different yield curves will apply to different currencies, market sectors, or even individual issuers. As government borrowing is indicative of interest rate levels available to other market players in a particular country, and considering that bond issuance still remains the dominant form of sovereign debt, this paper describes yield curve construction using bonds. The relationship between zero-coupon yield, par yield and yield to maturity is given and their usage in determining curve discount factors is described. Their usage in deriving forward rates and pricing related derivative instruments is also discussed.

  8. Crystallochemistry of rhenium compounds with metal-metal bonds

    International Nuclear Information System (INIS)

    Koz'min, P.A.; Surazhskaya, M.D.

    1980-01-01

    A review is presented including a brief description of atomic structure of 59 coordination rhenium compounds with metal-metal bond. The most important bond lengths and valent angles are presented for each compound. The dependence of rhenium-rhenium bond length on its multiplicity is discussed and possible causes of deviations from this dependence (namely, axial ligand presence, steric repulsion of ligands) are considered. On the basis of qualitative comparison of electronegativity of ligands in dimer compounds with quarternary bond of rhenium-rhenium a supposition is made on the influence of formal charge of atomic group and summary electro-negativity of ligands on the possibility of the metal-metal bond formation

  9. Formation of an Ion-Pair Molecule with a Single NH+...Cl- Hydrogen Bond: Raman spectra of 1,1,3,3-Tetramethylguanidinium chloride in the solid state, in solution and in the vapor phase

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Fehrmann, Rasmus

    2008-01-01

    Some ionic compounds (salts) form liquids when heated to temperatures in the range of 200-300 °C. They may be referred to as moderate temperature ionic liquids. An example of such a compound is the 1,1,3,3- tetramethylguanidinium chloride, [TMGH]Cl, melting at ∼212 °C. The chemistry of this compo......Some ionic compounds (salts) form liquids when heated to temperatures in the range of 200-300 °C. They may be referred to as moderate temperature ionic liquids. An example of such a compound is the 1,1,3,3- tetramethylguanidinium chloride, [TMGH]Cl, melting at ∼212 °C. The chemistry...... and the dimeric chloride ion-pair salt converged to give geometries near the established crystal structure of [TMGH]Cl. The structures and their binding energies are given as well as calculated vibrational harmonic normal modes (IR and Raman band wavenumbers and intensities). Experimentally obtained Raman...... scattering spectra are presented and assigned, by comparing to the quantum mechanical calculations. It is concluded that dimeric molecular ion pairs with four N-H+ · · · Cl- hydrogen bonds probably exist in the solutions and are responsible for the relatively high solubility of the “salt” in ethanol...

  10. Metal-Free Catalytic Enantioselective C–B Bond Formation: (Pinacolato)boron Conjugate Additions to α,β-Unsaturated Ketones, Esters, Weinreb Amides and Aldehydes Promoted by Chiral N-Heterocyclic Carbenes

    Science.gov (United States)

    Wu, Hao; Radomkit, Suttipol; O’Brien, Jeannette M.; Hoveyda, Amir H.

    2012-01-01

    The first broadly applicable metal-free enantioselective method for boron conjugate addition (BCA) to α,β-unsaturated carbonyls is presented. The C–B bond forming reactions are promoted in the presence of 2.5–7.5 mol % of a readily accessible C1-symmetric chiral imidazolinium salt, which is converted, in situ, to the catalytically active diastereo- and enantiomerically pure N-heterocyclic carbene (NHC) by the common organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (dbu). In addition to the commercially available bis(pinacolato)diboron [B2(pin)2], and in contrast to reactions with the less sterically demanding achiral NHCs, the presence of MeOH is required for high efficiency. Acyclic and cyclic α,β-unsaturated ketones, as well as acyclic esters, Weinreb amides and aldehydes can serve as suitable substrates; the desired β-boryl carbonyls are isolated in up to 94% yield and >98:2 enantiomer ratio (er). Transformations are often carried out at ambient temperature. In certain cases, such as when the relatively less reactive unsaturated amides are used, elevated temperatures are required (50–66 °C); nonetheless, reactions remain highly enantioselective. The utility of the NHC-catalyzed method is demonstrated through comparison with the alternative Cu-catalyzed protocols; in cases involving a polyfunctional substrate, unique profiles in chemoselectivity are exhibited by the metal-free approach (e.g., conjugate addition vs reaction with an alkyne, allene or aldehyde). PMID:22559866

  11. Corporate Hybrid Bonds

    OpenAIRE

    Ahlberg, Johan; Jansson, Anton

    2016-01-01

    Hybrid securities do not constitute a new phenomenon in the Swedish capital markets. Most commonly, hybrids issued by Swedish real estate companies in recent years are preference shares. Corporate hybrid bonds on the other hand may be considered as somewhat of a new-born child in the family of hybrid instruments. These do, as all other hybrid securities, share some equity-like and some debt-like characteristics. Nevertheless, since 2013 the interest for the instrument has grown rapidly and ha...

  12. Hybrid Cat Bonds

    OpenAIRE

    Barrieu, Pauline; Louberge, Henri

    2009-01-01

    Natural catastrophes attract regularly the attention of media and have become a source of public concern. From a financial viewpoint, natural catastrophes represent idiosyncratic risks, diversifiable at the world level. But for reasons analyzed in this paper reinsurance markets are unable to cope with this risk completely. Insurance-linked securities, such as cat bonds, have been issued to complete the international risk transfer process, but their development is disappointing so far. This pa...

  13. Quantum-chemical ab initio and B3LYP study of donor-acceptor complexes of gallium halides with pyridine

    International Nuclear Information System (INIS)

    Timoshkin, A.Yu.; Suvorov, A.V.; Shefer, G.F.

    1999-01-01

    By the ab initio and density functional methods the structural characteristics and vibrational spectra of gallium iodide donor-acceptor complexes with pyridine have been calculated. The standard thermodynamic characteristics of GaI 3 Py complex dissociation in gaseous phase have been calculated, as well. Short I-H intramolecular distances suggest that hydrogen iodide elimination with Ga-N chemical bond retention is the first stage of the complex pyrolysis [ru

  14. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  15. Optimal Investment in Structured Bonds

    DEFF Research Database (Denmark)

    Jessen, Pernille; Jørgensen, Peter Løchte

    The paper examines the role of structured bonds in the optimal portfolio of a small retail investor. We consider the typical structured bond essentially repacking an exotic option and a zero coupon bond, i.e. an investment with portfolio insurance. The optimal portfolio is found when the investment...

  16. 46 CFR Sec. 10 - Bonds.

    Science.gov (United States)

    2010-10-01

    ... REPAIRS UNDER NATIONAL SHIPPING AUTHORITY MASTER LUMP SUM REPAIR CONTRACT-NSA-LUMPSUMREP Sec. 10 Bonds. (a... awarded work and the furnishing of the performance and payment bonds required by Article 14 of the NSA... of the NSA-LUMPSUMREP Contract, the standard form of individual performance bond (Standard Form 25...

  17. A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

    Science.gov (United States)

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2015-10-15

    The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

  18. Intramolecular hydrogen bonding in malonaldehyde and its radical analogues.

    Science.gov (United States)

    Lin, Chen; Kumar, Manoj; Finney, Brian A; Francisco, Joseph S

    2017-09-28

    High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA RS , and cis-MA RA , both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA RA , in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA RS , in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ * orbital of acceptor O-H bond (n → σ * OH ). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA RS .

  19. The chemical bond in inorganic chemistry the bond valence model

    CERN Document Server

    Brown, I David

    2016-01-01

    The bond valence model is a version of the ionic model in which the chemical constraints are expressed in terms of localized chemical bonds formed by the valence charge of the atoms. Theorems derived from the properties of the electrostatic flux predict the rules obeyed by both ionic and covalent bonds. They make quantitative predictions of coordination number, crystal structure, bond lengths and bond angles. Bond stability depends on the matching of the bonding strengths of the atoms, while the conflicting requirements of chemistry and space lead to the structural instabilities responsible for the unusual physical properties displayed by some materials. The model has applications in many fields ranging from mineralogy to molecular biology.

  20. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

    Science.gov (United States)

    Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

    2016-03-04

    Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

  1. Training in AB Department 2004/2005

    CERN Document Server

    Schinzel, Josi; CERN. Geneva. AB Department

    2006-01-01

    This note provides an overview of the training attended by members of the AB Department during the years 2004 and 2005, giving a break-down of the different courses and costs as well as training directions. It describes the organisation of training in the department, and evolution in training directions and planning.

  2. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  3. An ab initio and TD DFT

    Indian Academy of Sciences (India)

    The photophysical behaviour of N-(2-hydroxy benzylidene) aniline or most commonly known as salicylideneaniline (SA) has been investigated using the ab initio and DFT levels of theory. The quantum chemical calculations show that the optimized non planar enol (1) form of the SA molecule is the most stable conformer ...

  4. Phi ({Phi}) and psi ({Psi}) angles involved in malarial peptide bonds determine sterile protective immunity

    Energy Technology Data Exchange (ETDEWEB)

    Patarroyo, Manuel E., E-mail: mepatarr@gmail.com [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Universidad Nacional de Colombia, Bogota (Colombia); Moreno-Vranich, Armando; Bermudez, Adriana [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia)

    2012-12-07

    Highlights: Black-Right-Pointing-Pointer Phi ({Phi}) and psi ({Psi}) angles determine sterile protective immunity. Black-Right-Pointing-Pointer Modified peptide's tendency to assume a regular conformation related to a PPII{sub L}. Black-Right-Pointing-Pointer Structural modifications in mHABPs induce Ab and protective immunity. Black-Right-Pointing-Pointer mHABP backbone atom's interaction with HLA-DR{beta}1{sup Asterisk-Operator} is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DR{beta}1{sup Asterisk-Operator} molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their {Phi} and {Psi} torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by {sup 1}H-NMR and superimposed into HLA-DR{beta}1{sup Asterisk-Operator }-like Aotus monkey molecules; their phi ({Phi}) and psi ({Psi}) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII{sub L}) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.

  5. Ab initio Hartree-Fock study on surface desorption process in tritium release

    International Nuclear Information System (INIS)

    Taniguchi, M.; Tanaka, S.

    1998-01-01

    Dissociative adsorption of hydrogen on Li 2 O (110) surface has been investigated with ab initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and surface potential energy for H 2 dissociative adsorption were evaluated by calculating the total energy of the system. The calculated results on adsorption heat indicated that H 2 adsorption is endothermic. However, when an oxygen vacancy exists adjacent to the adsorption site, the heat of adsorption became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (orig.)

  6. The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations

    International Nuclear Information System (INIS)

    Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.

    2007-01-01

    First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and β-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data

  7. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

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

    Science.gov (United States)

    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.

  9. Programming Recognition Arrays through Double Chalcogen-Bonding Interactions.

    Science.gov (United States)

    Biot, Nicolas; Bonifazi, Davide

    2018-04-11

    In this work, we have programmed and synthesized a recognition motif constructed around a chalcogenazolo-pyridine scaffold (CGP) that, through the formation of frontal double chalcogen-bonding interactions, associates into dimeric EX-type complexes. The reliability of the double chalcogen-bonding interaction has been shown at the solid-state by X-ray analysis, depicting the strongest recognition persistence for a Te-congener. The high recognition fidelity, chemical and thermal stability and easy derivatization at the 2-position makes CGP a convenient motif for constructing supramolecular architectures through programmed chalcogen-bonding interactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Asymmetrical bonding in cold spraying of dissimilar materials

    Science.gov (United States)

    Nikbakht, R.; Seyedein, S. H.; Kheirandish, S.; Assadi, H.; Jodoin, B.

    2018-06-01

    Characteristics of particle bonding, especially for dissimilar materials, remains a key question in cold spray deposition. There are limited reports in direct correlation to particle/substrate bonding and peripheral shear zones. Cold spraying experiments and numerical simulations are conducted to characterise and analyse the correlation between bonding and peripheral shear zones for asymmetric particle/substrate pairs of intermetallic-forming elements of nickel and titanium. The correlation between metallic bonding and highly strained areas is explored in view of the growth of the intermetallic phase at the particle/substrate interface during subsequent heat treatments. Characterisation of the as-sprayed samples reveal that for the Ni(particle)/Ti(substrate) pair, plastic deformation of the particle is dominating over substrate deformation. However, for the Ti(particle)/Ni(substrate) pair, it is observed that the substrate and particle deform to similar extents. Characterisation of the samples after a brief heat treatment at 700 °C indicate that intermetallic formation, and hence metallurgical bonding of the pairs is more likely to occur at the particle peripheries where the interface areas are highly strained, and rarely achieved at the particle base. Results also reveal that bonding extends from peripheries toward the central part of the interfaces with increasing the impact velocity. The kinetics of interfacial intermetallic formation at peripheral areas and its correlation to particle bonding is discussed in view of deformation-enhanced interdiffusion.

  11. Oxytocin promotes social bonding in dogs.

    Science.gov (United States)

    Romero, Teresa; Nagasawa, Miho; Mogi, Kazutaka; Hasegawa, Toshikazu; Kikusui, Takefumi

    2014-06-24

    Recent evidence suggests that enduring social bonds have fitness benefits. However, very little is known about the neural circuitry and neurochemistry underlying the formation and maintenance of stable social bonds outside reproductive contexts. Oxytocin (OT), a neuropeptide synthetized by the hypothalamus in mammals, regulates many complex forms of social behavior and cognition in both human and nonhuman animals. Animal research, however, has concentrated on monogamous mammals, and it remains unknown whether OT also modulates social bonds in nonreproductive contexts. In this study we provide behavioral evidence that exogenous OT promotes positive social behaviors in the domestic dog toward not only conspecifics but also human partners. Specifically, when sprayed with OT, dogs showed higher social orientation and affiliation toward their owners and higher affiliation and approach behaviors toward dog partners than when sprayed with placebo. Additionally, the exchange of socio-positive behaviors with dog partners triggered the release of endogenous OT, highlighting the involvement of OT in the development of social relationships in the domestic dog. These data provide new insight into the mechanisms that facilitate the maintenance of close social bonds beyond immediate reproductive interest or genetic ties and complement a growing body of evidence that identifies OT as one of the neurochemical foundations of sociality in mammalian species.

  12. Eutectic and solid-state wafer bonding of silicon with gold

    International Nuclear Information System (INIS)

    Abouie, Maryam; Liu, Qi; Ivey, Douglas G.

    2012-01-01

    Highlights: ► Eutectic and solid-state Au-Si bonding are compared for both a-Si and c-Si samples. ► Exchange of a-Si and Au layer was observed in both types of bonded samples. ► Use of c-Si for bonding resulted in formation of craters at the Au/c-Si interface. ► Solid-state Au-Si bonding produces better bonds in terms of microstructure. - Abstract: The simple Au-Si eutectic, which melts at 363 °C, can be used to bond Si wafers. However, faceted craters can form at the Au/Si interface as a result of anisotropic and non-uniform reaction between Au and crystalline silicon (c-Si). These craters may adversely affect active devices on the wafers. Two possible solutions to this problem were investigated in this study. One solution was to use an amorphous silicon layer (a-Si) that was deposited on the c-Si substrate to bond with the Au. The other solution was to use solid-state bonding instead of eutectic bonding, and the wafers were bonded at a temperature (350 °C) below the Au-Si eutectic temperature. The results showed that the a-Si layer prevented the formation of craters and solid-state bonding not only required a lower bonding temperature than eutectic bonding, but also prevented spill out of the solder resulting in strong bonds with high shear strength in comparison with eutectic bonding. Using amorphous silicon, the maximum shear strength for the solid-state Au-Si bond reached 15.2 MPa, whereas for the eutectic Au-Si bond it was 13.2 MPa.

  13. Ionizing radiation effect study by electron beam on acrylonitrile butadiene styrene - ABS terpolymer

    International Nuclear Information System (INIS)

    Landi, Tania Regina Lourenco

    2003-01-01

    The great advantage in the researches involving development has as objective to increase significantly the quality of the products. The ABS (acrylonitrile, butadiene, styrene) resins are terpolymers formed by an elastomer and two thermoplastics amorphous components. The three different monomeric units from the terpolymer ABS contribute separately to the material characteristics exhibited. The molecular stiffness originating from polystyrene and the benzene ring hanging on the chain is responsible for the flexion module ABS. The acrylonitrile and the styrene incorporated butadiene exercises strong influence in the resistance to the impact because it reduces the bonding among them. The engineering use of this terpolymer became important due their mechanical properties and mainly, for the responses of this to tensions or deformations applied. The polymeric materials, when submitted to the ionizing radiation are modified by the transference of energy to these materials, introducing excitation and ionization of the molecules, generating chemical reactions that can produce permanent modifications in the polymeric physicochemical structure. The induced modifications can result in the polymeric material degradation or crosslinking, which can result in the improvement of some properties. This work has, as objective, to study the electron beam ionizing radiation effect, at different doses, in the properties of the polymer ABS. The studied properties were: tensile strength at break, elongation at break, Izod impact strength, flexural strength, melt flow index, Vicat softening temperature and the thermic distortion temperature. Also researches on Differential Scanning Calorimetry (DSC) and Thermogravimetric Analyses (TGA) were accomplished. From the experimental results, it was showed that for doses until 500 kGy, at 22.6 kGy/s dose rate, in the presence of air, the crosslinking process of ABS prevails. (author)

  14. Nuclear quantum effects and hydrogen bond fluctuations in water

    Science.gov (United States)

    Ceriotti, Michele; Cuny, Jérôme; Parrinello, Michele; Manolopoulos, David E.

    2013-01-01

    The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and 1H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water. PMID:24014589

  15. ESR Studies and Dating of Egyptian Gypsum at Ras Mala'ab, Sinai, Egypt

    International Nuclear Information System (INIS)

    Abdel-Monem, A. A.; Abdei-Razek, Y. A.; Rasheed, N. M.; Hassan, G.M.; Eissa, H.M.; El-Morsy, M.

    2007-01-01

    A gypsum sample from the famous gypsum-anhydrite evaporitic deposit composing the Ras Mala'ab Formation, Upper Miocene, occurring at Ras Mala'ab, on the east coast of the Gulf of Suez, was subjected to (ESR) dosimetric studies. Also, (ESR) was used to date the formation or most recent recrystallization of that gypsum. The gypsum derivative (ESR) spectrum is characterized by the large broad Fe 2+ signal (g=2.50) and HF-sixtet Mn 2+ signals. Only the characteristic gypsum signal (G l, g=2.0040) was detected between the third and fourth lines of the HF-Mn 2+ which is attributed to the electron-center SO 3 - . This signal was sensitive to artificial γ-irradiation and showed significant enhancement using a γ-dose of 550 Gy. Also, the signal was very stable up to 400 o C. The gypsum sample with a total dose (TD) of 1500 Gy, determined graphically by extrapolating the linear relationship between defect concentration and the artificial γ-doses for (G l, g=2.0040) and an annual dose (D) due to cosmic rays (0.3 mGy), yielded an age of 5.00 Ma. This could mean the age of formation or latest recrystallization of this gypsum deposit. The geologic age assignment of the Ras Mala'ab Group including the evaporitic gypsum unit, is Middle to Late Miocene. It is directly overlain by the Pliocene elastics at the locality of Ras Mala'ab. This might suggest that these evaporitic gypsum facies represent the top of the Miocene in the Gulf of Suez area, since the Miocene-Pliocene boundary is now put at 5.00-5.50 Ma ago. Therefore, the ESR age of the Ras Mala'ab gypsum is consistent with the geologic age assignment

  16. Additional disulfide bonds in insulin

    DEFF Research Database (Denmark)

    Vinther, Tine N; Pettersson, Ingrid; Huus, Kasper

    2015-01-01

    The structure of insulin, a glucose homeostasis-controlling hormone, is highly conserved in all vertebrates and stabilized by three disulfide bonds. Recently, we designed a novel insulin analogue containing a fourth disulfide bond located between positions A10-B4. The N-terminus of insulin's B......-chain is flexible and can adapt multiple conformations. We examined how well disulfide bond predictions algorithms could identify disulfide bonds in this region of insulin. In order to identify stable insulin analogues with additional disulfide bonds, which could be expressed, the Cβ cut-off distance had...... in comparison to analogues with additional disulfide bonds that were more difficult to predict. In contrast, addition of the fourth disulfide bond rendered all analogues resistant to fibrillation under stress conditions and all stable analogues bound to the insulin receptor with picomolar affinities. Thus...

  17. Hydrogen bonding characterization in water and small molecules

    Science.gov (United States)

    Silvestrelli, Pier Luigi

    2017-06-01

    The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

  18. Fluorescent and colorimetric molecular recognition probe for hydrogen bond acceptors.

    Science.gov (United States)

    Pike, Sarah J; Hunter, Christopher A

    2017-11-22

    The association constants for formation of 1 : 1 complexes between a H-bond donor, 1-naphthol, and a diverse range of charged and neutral H-bond acceptors have been measured using UV/vis absorption and fluorescence emission titrations. The performance of 1-naphthol as a dual colorimetric and fluorescent molecular recognition probe for determining the H-bond acceptor (HBA) parameters of charged and neutral solutes has been investigated in three solvents. The data were employed to establish self-consistent H-bond acceptor parameters (β) for benzoate, azide, chloride, thiocyanate anions, a series of phosphine oxides, phosphate ester, sulfoxide and a tertiary amide. The results demonstrate both the transferability of H-bond parameters between different solvents and the utility of the naphthol-based dual molecular recognition probe to exploit orthogonal spectroscopic techniques to determine the HBA properties of neutral and charged solutes. The benzoate anion is the strongest HBA studied with a β parameter of 15.4, and the neutral tertiary amide is the weakest H-bond acceptor investigated with a β parameter of 8.5. The H-bond acceptor strength of the azide anion is higher than that of chloride (12.8 and 12.2 respectively), and the thiocyanate anion has a β value of 10.8 and thus is a significantly weaker H-bond acceptor than both the azide and chloride anions.

  19. Ab initio modeling of Al adsorption on CaF2 surfaces

    International Nuclear Information System (INIS)

    Barzilai, S.; Argaman, N.; Froumin, N.; Fuks, D.; Frage, N.

    2008-01-01

    Ab initio simulations of the adsorption of Al atoms on CaF 2 (0 0 1) and (1 1 1) surfaces have been performed for supercells with 7 different atomic configurations, using density functional theory. For (1 1 1) surfaces, a repulsive interaction was observed for most configurations, while a weak attraction was obtained when the Al atom was placed above F atoms. For the Ca-terminated (0 0 1) surface, the adsorption energy was about 5 times larger, whereas for the F-terminated (0 0 1) surface it was about 20 times greater. The comparative analysis indicates that the (0 0 1) surfaces are reactive and have a strong Al adatom bonding (chemisorption), especially for the F-terminated substrate. On the contrary, the (1 1 1) plane may be considered as non-reactive (physisorption), having a weak bonding of the Al adatom above the F site

  20. Ab initio study of M2AlN (M = Ti,V,Cr)

    International Nuclear Information System (INIS)

    Sun, Zhimei; Music, Denis; Ahuja, Rajeev; Schneider, Jochen M

    2005-01-01

    We have studied M 2 AlN phases, where M = Ti, V, and Cr, by means of ab initio total energy calculations. The bulk modulus of M 2 AlN increases as Ti is replaced with V and Cr by 19.0% and 26.5%, respectively, which can be understood on the basis of the increased number of valence electrons filling the p-d hybridized bonding states. The bulk modulus of M 2 AlN is generally higher than that of the corresponding M 2 AlC phase, which may be explained by an extra electron in the former phases contributing to stronger chemical bonding. This work is important for fundamental understanding of elastic properties of these ternary nitrides and may inspire future experimental research. (letter to the editor)

  1. Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study

    Directory of Open Access Journals (Sweden)

    Abid Hussain

    2017-09-01

    Full Text Available Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN. Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.

  2. Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

    Science.gov (United States)

    Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

    2011-06-01

    Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

  3. Ab initio modelling of transition metals in diamond

    International Nuclear Information System (INIS)

    Watkins, M; Mainwood, A

    2003-01-01

    Transition metals (TM) from the first transition series are commonly used as solvent catalysts in the synthesis of diamond by high pressure, high temperature processes. Ab initio calculations on these metals, in finite clusters of tetrahedrally coordinated carbon, enable us to investigate trends in their stability and properties. By carrying out systematic studies of interstitial, substitutional and semi-vacancy TM defects, we show that the electronic structure of the TMs is complicated by the presence of 'dangling bonds' when the TM disrupts the crystal lattice: interstitial defects conform to the Ludwig-Woodbury (LW) model, whilst substitutional and semi-vacancy defects move from approximating the LW model early in the transition series to approaching the vacancy model for the heavier metals. Multi-configurational self-consistent field methods allow genuine many-electron states to be modelled; for neutral interstitial, and all substitutional TMs, the crystal fields are found to exceed the exchange energies in strength. Consequently, low spin states are found for these defects. We find substitutional defects to be the most stable, but that semi-vacancy TMs are very similar in energy to the substitutional defects late in the transition series; interstitial defects are only metastable in diamond. Given appropriate charge compensators neutral and positively charged interstitial TM defects were stable, while negatively charged species appeared to be strongly disfavoured

  4. Double-walled silicon nanotubes: an ab initio investigation

    Science.gov (United States)

    Lima, Matheus P.

    2018-02-01

    The synthesis of silicon nanotubes realized in the last decade demonstrates multi-walled tubular structures consisting of Si atoms in {{sp}}2 and the {{sp}}3 hybridizations. However, most of the theoretical models were elaborated taking as the starting point {{sp}}2 structures analogous to carbon nanotubes. These structures are unfavorable due to the natural tendency of the Si atoms to undergo {{sp}}3. In this work, through ab initio simulations based on density functional theory, we investigated double-walled silicon nanotubes proposing layered tubes possessing most of the Si atoms in an {{sp}}3 hybridization, and with few {{sp}}2 atoms localized at the outer wall. The lowest-energy structures have metallic behavior. Furthermore, the possibility to tune the band structure with the application of a strain was demonstrated, inducing a metal-semiconductor transition. Thus, the behavior of silicon nanotubes differs significantly from carbon nanotubes, and the main source of the differences is the distortions in the lattice associated with the tendency of Si to make four chemical bonds.

  5. Fluorine-enhanced low-temperature wafer bonding of native-oxide covered Si wafers

    Science.gov (United States)

    Tong, Q.-Y.; Gan, Q.; Fountain, G.; Enquist, P.; Scholz, R.; Gösele, U.

    2004-10-01

    The bonding energy of bonded native-oxide-covered silicon wafers treated in the HNO3/H2O/HF or the HNO3/HF solution prior to room-temperature contact is significantly higher than bonded standard RCA1 cleaned wafer pairs after low-temperature annealing. The bonding energy reaches over 2000mJ/m2 after annealing at 100 °C. The very slight etching and fluorine in the chemically grown oxide are believed to be the main contributors to the enhanced bonding energy. Transmission-electron-microscopic images have shown that the chemically formed native oxide at bonding interface is embedded with many flake-like cavities. The cavities can absorb the by-products of the interfacial reactions that result in covalent bond formation at low temperatures allowing the strong bond to be retained.

  6. Genetics Home Reference: GM2-gangliosidosis, AB variant

    Science.gov (United States)

    ... Resources Genetic Testing (1 link) Genetic Testing Registry: Tay-Sachs disease, variant AB General Information from MedlinePlus (5 links) ... AB variant Activator Deficiency/GM2 Gangliosidosis Activator-deficient Tay-Sachs disease GM2 Activator Deficiency Disease GM2 gangliosidosis, type AB ...

  7. Density Functional Calculations of Solid State Heats of Formation

    National Research Council Canada - National Science Library

    Politzer, Peter

    1999-01-01

    It is now feasible to compute quite accurate gas phase heats of formation for relatively small molecules by means of ab initio or density functional techniques and one of several possible approaches...

  8. Do resonance-assisted intramolecular halogen bonds exist without a charge transfer and a sigma-hole?

    Czech Academy of Sciences Publication Activity Database

    Pandiyan, B. V.; Deepa, Palanisamy; Kolandaivel, P.

    2015-01-01

    Roč. 17, č. 41 (2015), s. 27496-27508 ISSN 1463-9076 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ab initio * hydrogen bonds * noncovalent interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.449, year: 2015

  9. The adsorption of acrolein on a Pt (1 1 1): A study of chemical bonding and electronic structure

    International Nuclear Information System (INIS)

    Pirillo, S.; López-Corral, I.; Germán, E.; Juan, A.

    2012-01-01

    Highlights: ► Study of acrolein/Pt (1 1 1) adsorption using ab-initio and semiempirical methods. ► Geometry optimization and DOS curves were carried out using VASP code. ► Study of chemical bonding evolution using COOP and OP analysis. ► After adsorption Pt-Pt, C=O and C=C bonds are weakened. ► η 3 -cis and η 4 -trans most stable adsorption modes, η 1 -trans less favored one. - Abstract: The adsorption of acrolein on a Pt (1 1 1) surface was studied using ab-initio and semiempirical calculations. Geometry optimization and densities of states (DOS) curves were carried out using the Vienna Ab-initio Simulation Package (VASP) code. We started our study with the preferential geometries corresponding to the different acrolein/Pt (1 1 1) adsorption modes previously reported. Then, we examined the evolution of the chemical bonding in these geometries, using the crystal orbital overlap population (COOP) and overlap population (OP) analysis of selected pairs of atoms. We analyzed the acrolein intramolecular bonds, Pt (1 1 1) superficial bonds and new molecule-surface formed bonds after adsorption. We found that Pt-Pt bonds interacting with the molecule and acrolein C=O and C=C bonds are weakened after adsorption; this last bond is significantly linked to the surface. The obtained C-Pt and O-Pt OP values suggest that the most stable adsorption modes are η 3 -cis and η 4 -trans, while the η 1 -trans is the less favored configuration. We also found that C p z orbital and Pt p z and d z 2 orbitals participate strongly in the adsorption process.

  10. H2XP:OH2 Complexes: Hydrogen vs. Pnicogen Bonds

    Directory of Open Access Journals (Sweden)

    Ibon Alkorta

    2016-02-01

    Full Text Available A search of the Cambridge Structural Database (CSD was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out on complexes H2XP:OH2, for X = NC, F, Cl, CN, OH, CCH, H, and CH3. Only hydrogen-bonded complexes are found on the H2(CH3P:HOH and H3P:HOH potential surfaces, while only pnicogen-bonded complexes exist on H2(NCP:OH2, H2FP:OH2, H2(CNP:OH2, and H2(OHP:OH2 surfaces. Both hydrogen-bonded and pnicogen-bonded complexes are found on the H2ClP:OH2 and H2(CCHP:OH2 surfaces, with the pnicogen-bonded complexes more stable than the corresponding hydrogen-bonded complexes. The more electronegative substituents prefer to form pnicogen-bonded complexes, while the more electropositive substituents form hydrogen-bonded complexes. The H2XP:OH2 complexes are characterized in terms of their structures, binding energies, charge-transfer energies, and spin-spin coupling constants 2hJ(O-P, 1hJ(H-P, and 1J(O-H across hydrogen bonds, and 1pJ(P-O across pnicogen bonds.

  11. Towards hydrogen metallization: an Ab initio approach

    International Nuclear Information System (INIS)

    Bernard, St.

    1998-01-01

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H 2 ) 2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

  12. Ab initio calculations of the structure and conformations of 2,6-lutidine

    International Nuclear Information System (INIS)

    Porcinai, S.; Foggi, P.

    1997-01-01

    Ab initio molecular orbital calculations at the SCF level have been utilized to determine the structure and the electronic and vibrational properties of 2,6-lutidine (2,6-dimethyl-pyridine) in the ground electronic state. Comparative calculations have been performed on the parent molecule pyridine. Structure predictions of both molecules are in good agreement with experimental data. The most stable rotamer of 2,6-lutidine has C 2v symmetry with one of the C-H bonds of both the methyl groups lying in the plane of the aromatic ring and pointing in the opposite direction with respect to the nitrogen atom. This is the result of the minimization of competing forces deriving from steric hindrance and electronic stabilization. Vibrational frequencies and oscillator strengths of C-H stretching in the fundamental region have been calculated for both pyridine and the most stable rotamer of 2,6-lutidine and compared to IR data obtained in pure liquids. The potential energy profile of the C-H bond in and out of plane has been investigated up to five times the equilibrium distance. The trend of the potential curves confirms that the C-H bond lying in the plane has a higher dissociation energy than that of the in-plane bonds as observed in experiments on vibrational overtones

  13. Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods

    Science.gov (United States)

    Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.

    1997-08-01

    We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.

  14. Ab initio study of properties of BaBiO3 at high pressure

    Science.gov (United States)

    Martoňák, Roman; Ceresoli, Davide; Kagayama, Tomoko; Tosatti, Erio

    BaBiO3 is a mixed-valence perovskite which escapes metallic state by creating a Bi-O bond disproportionation or CDW pattern, resulting in a Peierls semiconductor with gap of nearly 1 eV at zero pressure. Evolution of structural and electronic properties at high pressure is, however, largely unknown. Pressure, it might be natural to expect, could reduce the bond-disproportionation and bring the system closer to metalicity or even superconductivity. We address this question by ab initio DFT methods based on GGA and hybrid functionals in combination with crystal structure prediction techniques based on genetic algorithms. We analyze the pressure evolution of bond disproportionation as well as other order parameters related to octahedra rotation for various phases in connection with corresponding evolution of the electronic structure. Results indicate that BaBiO3 continues to resist metalization also under pressure, through structural phase transitions which sustain and in fact increase the diversity of length of Bi-O bonds for neighboring Bi ions, in agreement with preliminary high pressure resistivity data. R.M. Slovak Research and Development Agency Contract APVV-15-0496, VEGA project No. 1-0904-15; E.T. ERC MODPHYSFRICT Advanced Grant No. 320796.

  15. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  16. Ab interno trabeculectomy: patient selection and perspectives

    Science.gov (United States)

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

  17. Fatigue aging of adhesive bonds

    International Nuclear Information System (INIS)

    DeLollis, N.J.

    1979-01-01

    A year long study has been made of the effect of fatigue on the bond between two epoxy encapsulant formulations and a fused alumina disc. The variables studied included isothermal aging at temperatures up to and including the cure temperature and cyclic thermal aging from +74 to -54 0 C. The encapsulants were glass microballoon filled epoxies differing only in curing agents. One was cured with an aromatic amine eutectic (Shell Curing Agent Z). The other was cured with diethanolamine. The Z cured encapsulant bond failed completely at the bond interface with little or no aging; infrared evidence indicated a soluble interlayer as a possible cause of failure. The diethanolamine cured encapsulant survived a year of isothermal aging with little or no evidence of bond degradation. Cyclic thermal aging resulted in gradual bond failure with time. An extrapolation of the cyclic aging data indicates that the stresses induced by thermal cycling would result in complete bond failure in about 1200 days

  18. What is a hydrogen bond?

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. What is a hydrogen bond? Precise definition of a hydrogen bond is still elusive!1. Several criteria are listed usually for X-H•••Y, X and Y initially thought to be F, O and N only1. Structural: The X-Y bond length is less than the sum of their van der Waals radii. X-H•••Y is ...

  19. Composite interlayer for diffusion bonding

    International Nuclear Information System (INIS)

    1976-01-01

    A ductile interlayer is described, which is useful for transient liquid phase diffusion bonding of metallic articles; the interlayer consisting of a melting point depressant and a plurality of ductile lamellae which are free from carbides, aluminides and borides. The composition and fabrication of the lamellae, and the process for bonding the metallic articles, depend on the composition of the metals to be bonded, and are exemplified in the specification. (U.K.)

  20. MHD stability studies in the Proto S-1 A/B device

    International Nuclear Information System (INIS)

    Munson, C.; Janos, A.; Newhouse, M.; Salberta, E.; Wysocki, F.; Yamada, M.

    1982-01-01

    An experimental study of the gross MHD stability properties of Spheromak plasmas in the Proto S-1 A/B device is presented. Utilizing the previously demonstrated S-1 slow formation technique, plasmas have been produced which exhibit the predicted tilting instability in a regime of slightly negative field index. A relatively simple passive coil system suggested by numerical stability studies has proven to be effective in stabilizing the observed tilting mode