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

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

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

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)

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

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)

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

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.

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....

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.

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.

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.

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.

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.

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.

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....

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

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...

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.

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.

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

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.

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.

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

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

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.

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

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.

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.

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.

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.

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.)

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.

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.

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

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.

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.

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...

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

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.

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

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.

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

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...

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.

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.

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.

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...

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

Institute of Scientific and Technical Information of China (English)

无

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.

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....

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.

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.

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.

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).

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.

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.

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.

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.

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.

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

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.

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

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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.

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.

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

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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.

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.

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.

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.

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.

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.

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.

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-...

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

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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.

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

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.

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.

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

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

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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.

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

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

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 +

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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)

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...

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.

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.

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.

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.

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.

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...

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

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).

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.

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

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

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.

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

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...

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

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.

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

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).

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.

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.

Do blood contamination and haemostatic agents affect microtensile bond strength of dual cured resin cement to dentin?

Directory of Open Access Journals (Sweden)

Kerem KiLiC

2013-01-01

Full Text Available Objective The purpose of this study was to evaluate the effects of blood contamination and haemostatic agents such as Ankaferd Blood Stopper (ABS and hydrogen peroxide (H2O2 on the microtensile bond strength between dual cured resin cement-dentin interface. Material and Methods Twelve pressed lithium disilicate glass ceramics were luted to flat occlusal dentin surfaces with Panavia F under the following conditions: Control Group: no contamination, Group Blood: blood contamination, Group ABS: ABS contamination Group H2O2: H2O2 contamination. The specimens were sectioned to the beams and microtensile testing was carried out. Failure modes were classified under stereomicroscope. Two specimens were randomly selected from each group, and SEM analyses were performed. Results There were significant differences in microtensile bond strengths (µTBS between the control and blood-contaminated groups (p0.05. Conclusions Contamination by blood of dentin surface prior to bonding reduced the bond strength between resin cement and the dentin. Ankaferd Blood Stoper and H2O2 could be used safely as blood stopping agents during cementation of all-ceramics to dentin to prevent bond failure due to blood contamination.

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.

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

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.

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

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

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.

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.

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...

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

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

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

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

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.

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.

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

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.

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.

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.

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

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

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.

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.

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.

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

Influence of degradation conditions on dentin bonding durability of three universal adhesives.

Science.gov (United States)

Sai, Keiichi; Shimamura, Yutaka; Takamizawa, Toshiki; Tsujimoto, Akimasa; Imai, Arisa; Endo, Hajime; Barkmeier, Wayne W; Latta, Mark A; Miyazaki, Masashi

2016-11-01

This study aims to determine dentin bonding durability of universal adhesives using shear bond strength (SBS) tests under various degradation conditions. G-Premio Bond (GP, GC), Scotchbond Universal (SU, 3M ESPE) and All Bond Universal (AB, Bisco) were compared with conventional two-step self-etch adhesive Clearfil SE Bond (SE, Kuraray Noritake Dental). Bonded specimens were divided into three groups of ten, and SBSs with bovine dentin were determined after the following treatments: 1) Storage in distilled water at 37°C for 24h followed by 3000, 10,000, 20,000 or 30,000 thermal cycles (TC group), 2) Storage in distilled water at 37°C for 3 months, 6 months or 1year (water storage, WS group) and 3) Storage in distilled water at 37°C for 24h (control). SE bonded specimens showed significantly higher SBSs than universal adhesives, regardless of TC or storage periods, although AB specimens showed significantly increased SBSs after 30,000 thermal cycles. In comparisons of universal adhesives under control and degradation conditions, SBS was only reduced in SU after 1year of WS. Following exposure of various adhesive systems to degradation conditions of thermal cycling and long term storage, SBS values of adhesive systems varied primarily with degradation period. Although universal adhesives have lower SBSs than the two-step self-etch adhesive SE, the present data indicate that the dentin bonding durability of universal adhesives in self-etch mode is sufficient for clinical use. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

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)

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

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

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.

Bismuth-boron multiple bonding in BiB{sub 2}O{sup -} and Bi{sub 2}B{sup -}

Energy Technology Data Exchange (ETDEWEB)

Jian, Tian; Cheung, Ling Fung; Chen, Teng-Teng; Wang, Lai-Sheng [Department of Chemistry, Brown University, Providence, RI (United States)

2017-08-01

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{sub 2}O{sup -} and Bi{sub 2}B{sup -}, containing triple and double B-Bi bonds are presented. The BiB{sub 2}O{sup -} and Bi{sub 2}B{sup -} 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{sub 2}O{sup -} ([Bi≡B-B≡O]{sup -}) and Bi{sub 2}B{sup -} ([Bi=B=Bi]{sup -}), 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)

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.

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.

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).

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.

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...

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)

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...

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.

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.

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.

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.

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 ...

Six-month evaluation of adhesives interface created by a hydrophobic adhesive to acid-etched ethanol-wet bonded dentine with simplified dehydration protocols.

Science.gov (United States)

Sadek, Fernanda T; Mazzoni, Annalisa; Breschi, Lorenzo; Tay, Franklin R; Braga, Roberto R

2010-04-01

To evaluate the efficacy of simplified dehydration protocols, in the absence of tubular occlusion, on bond strength and interfacial nanoleakage of a hydrophobic experimental adhesive blend to acid-etched, ethanol-dehydrated dentine immediately and after 6 months. Molars were randomly assigned to 6 treatment groups (n=5). Under pulpal pressure simulation, dentine crowns were acid-etched with 35% H(3)PO(4) and rinsed with water. Adper Scotchbond Multi-Purpose was used for the control group. The remaining groups had their dentine surface dehydrated with ethanol solutions: group 1=50%, 70%, 80%, 95% and 3x100%, 30s for each application; group 2 the same ethanol sequence with 15s for each solution; groups 3, 4 and 5 used 100% ethanol only, applied in seven, three or one 30s step, respectively. After dehydration, a primer (50% BisGMA+TEGDMA, 50% ethanol) was used, followed by the neat comonomer adhesive application. Resin composite build-ups were then prepared using an incremental technique. Specimens were stored for 24h, sectioned into beams and stressed to failure after 24h or after 6 months of artificial ageing. Interfacial silver leakage evaluation was performed for both storage periods (n=5 per subgroup). Group 1 showed higher bond strengths at 24h or after 6 months of ageing (45.6+/-5.9(a)/43.1+/-3.2(a)MPa) and lower silver impregnation. Bond strength results were statistically similar to control group (41.2+/-3.3(ab)/38.3+/-4.0(ab)MPa), group 2 (40.0+/-3.1(ab)/38.6+/-3.2(ab)MPa), and group 3 at 24h (35.5+/-4.3(ab)MPa). Groups 4 (34.6+/-5.7(bc)/25.9+/-4.1(c)MPa) and 5 (24.7+/-4.9(c)/18.2+/-4.2(c)MPa) resulted in lower bond strengths, extensive interfacial nanoleakage and more prominent reductions (up to 25%) in bond strengths after 6 months of ageing. Simplified dehydration protocols using one or three 100% ethanol applications should be avoided for the ethanol-wet bonding technique in the absence of tubular occlusion, as they showed decreased bond strength, more

The adsorption of acrolein on a Pt (1 1 1): A study of chemical bonding and electronic structure

Science.gov (United States)

Pirillo, S.; López-Corral, I.; Germán, E.; Juan, A.

2012-12-01

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 moleculesbnd surface formed bonds after adsorption. We found that Ptsbnd Pt bonds interacting with the molecule and acrolein Cdbnd O and Cdbnd C bonds are weakened after adsorption; this last bond is significantly linked to the surface. The obtained Csbnd Pt and Osbnd Pt OP values suggest that the most stable adsorption modes are η3-cis and η4-trans, while the η1-trans is the less favored configuration. We also found that C pz orbital and Pt pz and d orbitals participate strongly in the adsorption process.

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.

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...

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.

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

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)

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

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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.

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.

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.

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

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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.

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

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

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.

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.

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)

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.

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.

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.

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

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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.

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.

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:

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

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)

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

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)

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

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.

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

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.

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.

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.

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...

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.

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.

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

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.

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…

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.

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.

Theoretical study of the changes in the vibrational characteristics arising from the hydrogen bonding between Vitamin C ( L-ascorbic acid) and H 2O

Science.gov (United States)

Dimitrova, Yordanka

2006-02-01

The vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) for the hydrogen-bonded system of Vitamin C ( L-ascorbic acid) with five water molecules have been predicted using ab initio SCF/6-31G(d, p) calculations and DFT (BLYP) calculations with 6-31G(d, p) and 6-31++G(d, p) basis sets. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between Vitamin C and five water molecules leads to large red shifts of the stretching vibrations for the monomer bonds involved in the hydrogen bonding and very strong increase in their IR intensity. The predicted frequency shifts for the stretching vibrations from Vitamin C taking part in the hydrogen bonding are up to -508 cm -1. The magnitude of the wavenumber shifts is indicative of relatively strong OH···H hydrogen-bonded interactions. In the same time the IR intensity and Raman activity of these vibrations increase upon complexation. The IR intensity increases dramatically (up to 12 times) and Raman activity increases up to three times. The ab initio and BLYP calculations show, that the symmetric OH vibrations of water molecules are more sensitive to the complexation. The hydrogen bonding leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The asymmetric OH stretching vibrations of water, free from hydrogen bonding are less sensitive to the complexation than the hydrogen-bonded symmetric O sbnd H stretching vibrations. The increases of the IR intensities for these vibrations are lower and red shifts are negligible.

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.

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

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

Pressure-induced localisation of the hydrogen-bond network in KOH-VI

Energy Technology Data Exchange (ETDEWEB)

Hermann, Andreas, E-mail: a.hermann@ed.ac.uk; Nelmes, Richard J.; Loveday, John S. [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Guthrie, Malcolm [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); European Spallation Source AB, P.O. Box 176, SE-22100 Lund (Sweden)

2015-12-28

Using a combination of ab initio crystal structure prediction and neutron diffraction techniques, we have solved the full structure of KOH-VI at 7 GPa. Rather than being orthorhombic and proton-ordered as had previously be proposed, we find that this high-pressure phase of potassium hydroxide is tetragonal (space group I4/mmm) and proton disordered. It has an unusual hydrogen bond topology, where the hydroxyl groups form isolated hydrogen-bonded square planar (OH){sub 4} units. This structure is stable above 6.5 GPa and, despite being macroscopically proton-disordered, local ice rules enforce microscopic order of the hydrogen bonds. We suggest the use of this novel type of structure to study concerted proton tunneling in the solid state, while the topology of the hydrogen bond network could conceivably be exploited in data storage applications based solely on the manipulations of hydrogen bonds. The unusual localisation of the hydrogen bond network under applied pressure is found to be favored by a more compact packing of the constituents in a distorted cesium chloride structure.

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

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

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

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)

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.

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.

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.

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.

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.

Interface structure of Be/DSCu diffusion bonding

Energy Technology Data Exchange (ETDEWEB)

Makino, T.; Iwadachi, T. [NGK Insulators Ltd., Nagoya (Japan)

1998-01-01

Beryllium is used as plasma facing components of the first wall on ITER. Dispersion-Strengthened Copper (DSCu) is used as heat sink material by joining to Be because DSCu has high thermal conductivity and strength. In this study, Be/DSCu diffusion bonding tests using the interlayer of Al, Ni, Nb, Ti, Zr and Be-Cu alloy have been conducted to choose the suitable interlayer materials. As a result of the shear strength tests, Be/DSCu joints by using Be-Cu alloy interlayer showed the strength of about 200 MPa. Diffusion bonding tests using Be-Cu alloy interlayer or no interlayer (direct bonding) at the range of temperature from 600degC to 850degC have been conducted to identify the effect of bonding temperature and time on interface formation and strength. The thickness of diffusion layer was proportional to a square root of bonding time by diffusion controlled process. The shear strength is controlled by the formation of intermetallic layer at Be side. (author)

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.

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

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.

Protein Adsorption and Layer Formation at the Stainless Steel-Solution Interface Mediates Shear-Induced Particle Formation for an IgG1 Monoclonal Antibody.

Science.gov (United States)

Kalonia, Cavan K; Heinrich, Frank; Curtis, Joseph E; Raman, Sid; Miller, Maria A; Hudson, Steven D

2018-03-05

Passage of specific protein solutions through certain pumps, tubing, and/or filling nozzles can result in the production of unwanted subvisible protein particles (SVPs). In this work, surface-mediated SVP formation was investigated. Specifically, the effects of different solid interface materials, interfacial shear rates, and protein concentrations on SVP formation were measured for the National Institute of Standards and Technology monoclonal antibody (NISTmAb), a reference IgG1 monoclonal antibody (mAb). A stainless steel rotary piston pump was used to identify formulation and process parameters that affect aggregation, and a flow cell (alumina or stainless steel interface) was used to further investigate the effect of different interface materials and/or interfacial shear rates. SVP particles produced were monitored using flow microscopy or flow cytometry. Neutron reflectometry and a quartz crystal microbalance with dissipation monitoring were used to characterize adsorption and properties of NISTmAb at the stainless steel interface. Pump/shear cell experiments showed that the NISTmAb concentration and interface material had a significant effect on SVP formation, while the effects of interfacial shear rate and passage number were less important. At the higher NISTmAb concentrations, the adsorbed protein became structurally altered at the stainless steel interface. The primary adsorbed layer remained largely undisturbed during flow, suggesting that SVP formation at high NISTmAb concentration was caused by the disruption of patches and/or secondary interactions.

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

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.

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.

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.

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.

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

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

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

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.

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.

Electron transfer across multiple hydrogen bonds: the case of ureapyrimidinedione-substituted vinyl ruthenium and osmium complexes.

Science.gov (United States)

Pichlmaier, Markus; Winter, Rainer F; Zabel, Manfred; Zális, Stanislav

2009-04-08

Ruthenium and osmium complexes 2a,b and 3a,b featuring the N-4,6-dioxo-5,5-dibutyl- or the N-4,6-dioxo-5,5-di-(2-propenyl)-1,4,5,6-tetrahydropyrimidin-2-yl-N'(4-ethenylphenyl)-urea ligand dimerize by a self-complementary quadruply hydrogen-bonding donor/donor/acceptor/acceptor (DDAA) motif. We provide evidence that the dimeric structures are maintained in nonpolar solvents and in 0.1 M NBu(4)PF(6)/CH(2)Cl(2) supporting electrolyte solution. All complexes are reversibly oxidized in two consecutive two-electron oxidations (DeltaE(1/2) approximately = 500 mV) without any discernible potential splitting for the oxidation of the individual hydrogen-bridged redox active moieties. IR and UV/vis/NIR spectroelectrochemistry show a one-step conversion of the neutral to the dication without any discernible features of an intermediate monooxidized radical cation. Oxidation-induced IR changes of the NH and CO groups that are involved in hydrogen bonding are restricted to the styryl-bonded urea NH function. IR band assignments are aided by quantum chemical calculations. Our experimental findings clearly show that, at least in the present systems, the ureapyrimidinedione (Upy) DDAA hydrogen-bonding motif does not support electron transfer. The apparent reason is that neither of the hydrogen-bonding functionalities contributes to the occupied frontier levels. This results in nearly degenerate pairs of MOs representing the in-phase and out-of-phase combinations of the individual monomeric building blocks.

Nature of the three-electron bond in H2S∴SH2+

NARCIS (Netherlands)

Bickelhaupt, F. Matthias; Diefenbach, Axel; De Visser, Sam P.; De Koning, Leo J.; Nibbering, Nico M.M.

1998-01-01

We have investigated the model system H2S∴-SH2+, i.e., the sulfur-sulfur bound dimer radical cation of H2S, using both density functional theory (LDA, BP86, PW91) and traditional ab initio theory (up to CCSD-(T)). Our purpose is to better understand the nature of the three-electron bond. The S-S

All Electron ab initio Investigations of the Three Lowest Lying Electronic States of the RuC Molecule

DEFF Research Database (Denmark)

Shim, Irene; Gingerich, K. A.

2000-01-01

The three lowest-lying electronic states of RuC, (1)Sigma(+), (3)Delta, and (1)Delta, have been investigated by performing all-electron ab initio multi-configuration self-consistent-field (CASSCF) and multi-reference configuration interaction (MRCI) calculations including relativistic corrections....... The electronic ground state is derived as (1)Sigma(+) with the spectroscopic constants r(e) = 1.616 Angstrom and omega(e) = 1085 cm(-1). The lowest-lying excited state, (3)Delta, has r(e) = 1.632 Angstrom, omega(e) = 1063 cm(-1), and T-e = 912 cm(-1). These results are consistent with recent spectroscopic values....... The chemical bonds in all three lowest-lying states are triple bonds composed of one sigma and two pi bonds. (C) 2000 Elsevier Science B.V. All rights reserved....

Selective breaking of bonds in water with intense, 2-cycle, infrared laser pulses

Energy Technology Data Exchange (ETDEWEB)

Mathur, D., E-mail: atmol1@tifr.res.in; Dharmadhikari, A. K. [Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005 (India); Dota, K. [Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005 (India); Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104 (India); Dey, D.; Tiwari, A. K. [Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246 (India); Dharmadhikari, J. A. [Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104 (India); De, S. [Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata 700 064 (India); Vasa, P. [Department of Physics, Indian Institute of Technology Bombay, Mumbai 400 076 (India)

2015-12-28

One of the holy grails of contemporary science has been to establish the possibility of preferentially breaking one of several bonds in a molecule. For instance, the two O–H bonds in water are equivalent: given sufficient energy, either one of them is equally likely to break. We report bond-selective molecular fragmentation upon application of intense, 2-cycle pulses of 800 nm laser light: we demonstrate up to three-fold enhancement for preferential bond breaking in isotopically substituted water (HOD). Our experimental observations are rationalized by means of ab initio computations of the potential energy surfaces of HOD, HOD{sup +}, and HOD{sup 2+} and explorations of the dissociation limits resulting from either O–H or O–D bond rupture. The observations we report present a formidable theoretical challenge that need to be taken up in order to gain insights into molecular dynamics, strong field physics, chemical physics, non-adiabatic processes, mass spectrometry, and time-dependent quantum chemistry.

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.

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)

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

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...

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 .

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.

MicroRNA-20a/b regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1.

Science.gov (United States)

Liang, Bin; Wang, Xin; Song, Xiaosu; Bai, Rui; Yang, Huiyu; Yang, Zhiming; Xiao, Chuanshi; Bian, Yunfei

2017-09-01

ATP-binding cassette transporter A1 (ABCA1) plays a crucial role in reverse cholesterol transport and exhibits anti-atherosclerosis effects. Some microRNAs (miRs) regulate ABCA1 expression, and recent studies have shown that miR-20a/b might play a critical role in atherosclerotic diseases. Here, we attempted to clarify the potential contribution of miR-20a/b in post-transcriptional regulation of ABCA1, cholesterol efflux, and atherosclerosis. We performed bioinformatics analysis and found that miR-20a/b was highly conserved and directly bound to ABCA1 mRNA with low binding free energy. Luciferase-reporter assay also confirmed that miR-20a/b significantly reduced luciferase activity associated with the ABCA1 3' untranslated region reporter construct. Additionally, miR-20a/b decreased ABCA1 expression, which, in turn, decreased cholesterol efflux and increased cholesterol content in THP-1 and RAW 264.7 macrophage-derived foam cells. In contrast, miR-20a/b inhibitors increased ABCA1 expression and cholesterol efflux, decreased cholesterol content, and inhibited foam-cell formation. Consistent with our in vitro results, miR-20a/b-treated ApoE -/- mice showed decreased ABCA1expression in the liver and reductions of reverse cholesterol transport in vivo. Furthermore, miR-20a/b regulated the formation of nascent high-density lipoprotein and promoted atherosclerotic development, whereas miR-20a/b knockdown attenuated atherosclerotic formation. miR-20 is a new miRNA capable of targeting ABCA1 and regulating ABCA1 expression. Therefore, miR-20 inhibition constitutes a new strategy for ABCA1-based treatment of atherosclerosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-01-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 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 aluminum 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) [fr

Modelling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-10-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 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)

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

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

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...

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.

Acylhydrazone bond dynamic covalent polymer gel monolithic column online coupling to high-performance liquid chromatography for analysis of sulfonamides and fluorescent whitening agents in food.

Science.gov (United States)

Zhang, Chengjiang; Luo, Xialin; Wei, Tianfu; Hu, Yufei; Li, Gongke; Zhang, Zhuomin

2017-10-13

A new dynamic covalent polymer (DCP) gel was well designed and constructed based on imine chemistry. Polycondensation of 4,4'-biphenyldicarboxaldehyde and 1,3,5-benzenetricarbohydrazide via Schiff-base reaction resulted in an acylhydrazone bond gel (AB-gel) DCP. AB-gel DCP had three-dimensional network of interconnected nanoparticles with hierarchically porous structure. AB-gel DCP was successfully fabricated as a monolithic column by an in-situ chemical bonding method for online enrichment and separation purpose with excellent permeability. AB-gel DCP based monolithic column showed remarkable adsorption affinity towards target analytes including sulfonamides (SAs) and fluorescent whitening agents (FWAs) due to its strong π-π affinity, hydrophobic effect and hydrogen bonding interaction. Then, AB-gel DCP based monolithic column was applied for online separation and analysis of trace SAs and FWAs in food samples coupled with high-performance liquid chromatography (HPLC). Sulfathiazole (ST) and sulfadimidine (SM2) in one positive weever sample were actually found and determined with concentrations of 273.8 and 286.3μg/kg, respectively. 2,5-Bis(5-tert-butyl-2-benzoxazolyl) thiophene (FWA184) was actually quantified in one tea infusion sample with the concentration of 268.5ng/L. The spiked experiments suggested the good recoveries in range of 74.5-110% for SAs in weever and shrimp samples with relative standard deviations (RSDs) less than 9.7% and in range of 74.0-113% for FWAs in milk and tea infusion samples with RSDs less than 9.0%. AB-gel DCP monolithic column was proved to be a promising sample preparation medium for online separation and analysis of trace analytes in food samples with complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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.

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.

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

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

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.

Evaluation of the anti-cariogenic potential and bond strength to enamel of different fluoridated materials used for bracket bonding

Directory of Open Access Journals (Sweden)

Sérgio Ricardo da SILVA

2017-05-01

Full Text Available Abstract Objective To evaluate the in vitro and in situ anti-cariogenic potential and bond strength to enamel of materials containing fluoride (F, used for bracket bonding: Transbond XT (GT, negative control, Transbond Plus Color Change (GTF, Transbond-Self-Etching Primer (GSAF and Vitremer (GV, positive control. Material and method In the in vitro study, the specimens were premolars with bonded brackets (n=12/group. After pH cycling, the F release, bond strength, fracture mode and presence of white spot lesions were assessed. In the in situ study, the specimens were enamel fragments with bonded brackets (n=12/group. Twelve volunteers wore palatal appliances in 4 phases, with cariogenic challenge. Bond strength, fracture mode and change in surface hardness (%SH were determined. Result Relative to the in vitro study, F release (ppm was: GT=0.257±0.068c; GTF=0.634±0.100b; GSAF=0.630±0.067b; GV=2.796±1.414a. Only GV showed no white spot lesions. Bond strength values (MPa were GT=7.62±7.18a; GTF=5.15±6.91ab; GSAF=3.42±2.97bc; GV=2.87±2.09c. Adhesive fracture was the most frequent type, except for GTF. In the in situ study, %SH was: GT=-56.0±18.3a; GTF=-57.6±11.9a; GSAF=-57.1±11.3a; GV=-52.4±25.8a. Bond strength values were GT=9.5±4.4a; GTF=11.1±5.9a; GSAF=13.2± 6.6a; GV=6.6±4.0a. Cohesive fracture in material was the most frequent type, except for GTF. Conclusion Vitremer (GV showed the highest anti-cariogenic potential in the in vitro study. However, it was not confirmed by the in situ study. Regarding bond strength values from the in situ study, all materials were shown to be adequate for clinical practice.

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

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.

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)

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

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.

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

On analogy between surface fracture energy and activaiton energy of bonding in solid phase

International Nuclear Information System (INIS)

Shatinsky, V.F.; Kopylov, V.I.

1976-01-01

This article makes an attempt on the basis of experimental data to compare the processes of failure and formation of a bond by comparing the energy consumptions going in one case or another into initial plastic deformation of a certain volume and the further interatomic interaction at the boundary (separation, formation of the bond). Two values characterizing the different processes - the unit failure energy γ and the activation energy for the formation of a bond Q - are compared. It has been established that the energy consumed for plastic deformation and adhesion interaction of atoms on the surface of microprojections and providing the formation of a bond in the solid-phase condition is close to the specific failure energy. The equality of energies consumed for the formation of a bond and failure allows to make use of any of those characteristics to calculate parameters of processes of the formation of a bond and failure. It seems to be convenient in the analysis of the failure process at a temperature when the ductility is high and methodically, the crack propagation is hard to investigate, in particular to estimate the volume of the preliminary failure zone. Having determined γ from the contact interaction data, the strength characteristics can be evaluated. (author)

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.

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...

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)

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,

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.

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.

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.

G3//BMK and Its Application to Calculation of Bond Dissociation Enthalpies.

Science.gov (United States)

Zheng, Wen-Rui; Fu, Yao; Guo, Qing-Xiang

2008-08-01

On the basis of systematic examinations it was found that the BMK functional significantly outperformed the other popular density functional theory methods including B3LYP, B3P86, KMLYP, MPW1P86, O3LYP, and X3LYP for the calculation of bond dissociation enthalpies (BDEs). However, it was also found that even the BMK functional might dramatically fail in predicting the BDEs of some chemical bonds. To solve this problem, a new composite ab initio method named G3//BMK was developed by combining the strengths of both the G3 theory and BMK. G3//BMK was found to outperform the G3 and G3//B3LYP methods. It could accurately predict the BDEs of diverse types of chemical bonds in various organic molecules within a precision of ca. 1.2 kcal/mol.

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.

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.

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

International Nuclear Information System (INIS)

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

2008-01-01

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

Binding matter with antimatter: the covalent positron bond.

Science.gov (United States)

Charry, Jorge Alfonso; Varella, Marcio T Do N; Reyes, Andrés

2018-05-16

We report sufficient theoretical evidence of the energy stability of the e⁺H₂²⁻ molecule, formed by two H⁻ anions and one positron. Analysis of the electronic and positronic densities of the latter compound undoubtedly points out the formation of a positronic covalent bond between the otherwise repelling hydride anions. The lower limit for the bonding energy of the e⁺H₂²⁻ molecule is 74 kJ/mol (0.77 eV), accounting for the zero-point vibrational correction. The formation of a non electronic covalent bond is fundamentally distinct from positron attachment to stable molecules, as the latter process is characterized by a positron affinity, analogous to the electron affinity. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Collision-Induced Dissociation Study of Strong Hydrogen-Bonded Cluster Ions Y-(HF) n (Y=F, O2) Using Atmospheric Pressure Corona Discharge Ionization Mass Spectrometry Combined with a HF Generator.

Science.gov (United States)

Sakamoto, Kenya; Sekimoto, Kanako; Takayama, Mitsuo

2017-01-01

Hydrogen fluoride (HF) was produced by a homemade HF generator in order to investigate the properties of strong hydrogen-bonded clusters such as (HF) n . The HF molecules were ionized in the form of complex ions associated with the negative core ions Y - produced by atmospheric pressure corona discharge ionization (APCDI). The use of APCDI in combination with the homemade HF generator led to the formation of negative-ion HF clusters Y - (HF) n (Y=F, O 2 ), where larger clusters with n ≥4 were not detected. The mechanisms for the formation of the HF, F - (HF) n , and O 2 - (HF) n species were discussed from the standpoints of the HF generator and APCDI MS. By performing energy-resolved collision-induced dissociation (CID) experiments on the cluster ions F - (HF) n ( n =1-3), the energies for the loss of HF from F - (HF) 3 , F - (HF) 2 , and F - (HF) were evaluated to be 1 eV or lower, 1 eV or higher, and 2 eV, respectively, on the basis of their center-of-mass energy ( E CM ). These E CM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O 2 (HF) n ] - ( n =1-4) was discussed on the basis of the bond lengths of O 2 H-F - (HF) n and O 2 - H-F(HF) n obtained by ab initio calculations. The calculations indicated that [O 2 (HF) 4 ] - separated into O 2 H and F - (HF) 3 .

Infrared matrix isolation study of hydrogen bonds involving C-H bonds: Substituent effects

International Nuclear Information System (INIS)

Jeng, M.L.H.; Ault, B.S.

1989-01-01

The matrix isolation technique combined with infrared spectroscopy has been employed to isolate and characterize hydrogen-bonded complexes between a series of substituted alkynes and several oxygen and nitrogen bases. Distinct evidence for hydrogen bond formation was observed in each case, with a characteristic red shift of the hydrogen stretching motion ν r . Shifts between 100 and 300 cm -1 were observed, the largest being for the complex of CF 3 CCH with (CH 3 ) 3 N. The perturbed carbon-carbon triple bond stretching vibration was observed for most complexes, as was the alkynic hydrogen bending motion. Attempts were made to correlate the magnitude of the red shift of ν s with substituent constants for the different substituted alkynes; a roughly linear correlation was found with the Hammett σ parameter. Lack of correlation Δν s with either σ 1 or σ R alone suggests that both inductive and resonance contributions to the strength of the hydrogen-bonding interaction are important

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.

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.

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.

The effective fragment molecular orbital method for fragments connected by covalent bonds.

Directory of Open Access Journals (Sweden)

Casper Steinmann

Full Text Available We extend the effective fragment molecular orbital method (EFMO into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

Science.gov (United States)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Forecasting of chalcogenide spinels of the general formula AB2X4 using the method of training of an electronic computer

International Nuclear Information System (INIS)

Kiseleva, N.N.; Savitskij, E.M.

1979-01-01

Experimental evidence on the existence of AB 2 X 4 compounds in A-B-X systems (A and B are any elements of the periodic system, in particular, rare earth elements, X is S or Se) and the data on the properties of elements and simple sulphides (selenides) were used for an attempt to find the probability of formation of AB 2 X 4 compounds as a function of the component properties. The experimental evidence was analyzed by a computer employing algorithms of concept formation training. The results were used to predict new AB 2 X 4 compounds. The computer training method proved an efficient means of revealing the connection between probability of spinel type compounds existence with the component properties. Certain compounds of general formula AB 2 X 4 were predicted and the probability that they possess spinel structure was evaluated

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)

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

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.

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

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.

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.

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...

Ground state hydrogen conformations and vibrational analysis of 1,2-dihdroxyanthraquinone (alizarin) molecule by AB initio Hartree-Fock and density functional theory calculations

International Nuclear Information System (INIS)

Delta, E.; Ucun, F.; Saglam, A.

2010-01-01

The ground state hydrogen conformations of 1,2-dihydroxyanthraquinone (alizarin) molecule have been investigated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d,p) basis set. The calculations indicate that the compound in the ground state exist with the doubly bonded O atom linked intra molecularly by the two hydrogen bonds. The vibrational analyses of the ground state conformation of the compound were also made and its optimized geometry parameters were given.

Understanding and modulating the high-energy properties of noble-gas hydrides from their long-bonding: an NBO/NRT investigation on HNgCO+/CS+/OSi+ and HNgCN/NC (Ng = He, Ar, Kr, Xe, Rn) molecules.

Science.gov (United States)

Zhang, Guiqiu; Song, Junjie; Fu, Lei; Tang, Kongshuang; Su, Yue; Chen, Dezhan

2018-04-18

The noble-gas hydrides, HNgX (X is an electronegative atom or fragment), represent potential high-energy materials because their two-body decomposition process, HNgX → Ng + HX, is strongly exoergic. Our previous studies have shown that each member of the HNgX (X = halogen atom or CN/NC fragment) molecules is composed of three leading resonance structures: two ω-bonding structures (H-Ng+ :X- and H:- Ng+-X) and one long-bonding structure (H∧X). The last one paints a novel [small sigma, Greek, circumflex]-type long-bonding picture. The present study focuses on the relationship between this novel bonding motif and the unusual energetic properties. We chose HNgCO+/CS+/OSi+/CN/NC, with the formula HNgAB (Ng = He, Ar, Kr, Xe, Rn; AB = CO+/CS+/OSi+/CN/NC) as the research system. We first investigated the bonding of HNgCO+ and its analogous HNgCS+/OSi+ species using NBO/NRT methods, and quantitatively compared the bonding with that in HNgCN/NC molecules. NBO/NRT results showed that each of the HNgCO+/CS+/OSi+ molecules could be better represented as a resonance hybrid of ω-bonding and long-bonding structures, but the long-bonding is much weaker than that in HNgCN/NC molecules. Furthermore, we introduced the long-bonding concept into the rationalization of the high-energy properties, and found a good correlation between the highly exothermic two-body dissociation channel and the long-bond order, bH-A. We also found that the long-bond order is highly tunable for these noble-gas hydrides due to its dependence on the nature of the electronegative AB fragments or the central noble-gas atoms, Ng. On the basis of these results, we could optimize the energetic properties by changing the long-bonding motif of our studied molecules. Overall, this study shows that the long-bonding model provides an easy way to rationalize and modulate the unusual energy properties of noble-gas hydrides, and that it is helpful to predict some noble-gas hydrides as potential energetic materials.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

Science.gov (United States)

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

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

The effect of different surface treatments of stainless steel crown and different bonding agents on shear bond strength of direct composite resin veneer

Directory of Open Access Journals (Sweden)

Ajami B

2007-01-01

Full Text Available Background and Aim: Stainless steel crown (SSC is the most durable and reliable restoration for primary teeth with extensive caries but its metalic appearance has always been a matter of concern. With advances in restorative materials and metal bonding processes, composite veneer has enhanced esthetics of these crowns in clinic. The aim of this study was to evaluate the shear bond strength of SSC to composite resin using different surface treatments and adhesives. Materials and Methods: In this experimental study, 90 stainless steel crowns were selected. They were mounted in molds and divided into 3 groups of 30 each (S, E and F. In group S (sandblast, buccal surfaces were sandblasted for 5 seconds. In group E (etch acidic gel was applied for 5 minutes and in group F (fissure bur surface roughness was created by fissure diamond bur. Each group was divided into 3 subgroups (SB, AB, P based on different adhesives: Single Bond, All Bond2 and Panavia F. Composite was then bonded to specimens. Cases were incubated in 100% humidity at 37°C for 24 hours. Shear bond strength was measured by Zwick machine with crosshead speed of 0.5 mm/min. Data were analyzed by ANOVA test with p0.05 so the two variables were studied separately. No significant difference was observed in mean shear bond strength of composite among the three kinds of adhesives (P>0.05. Similar results were obtained regarding surface treatments (P>0.05. Conclusion: Based on the results of this study, treating the SSC surface with bur and using single bond adhesive and composite can be used successfully to obtain esthetic results in pediatric restorative treatments.

Influence of air-powder polishing on bond strength and surface-free energy of universal adhesive systems.

Science.gov (United States)

Tamura, Yukie; Takamizawa, Toshiki; Shimamura, Yutaka; Akiba, Shunsuke; Yabuki, Chiaki; Imai, Arisa; Tsujimoto, Akimasa; Kurokawa, Hiroyasu; Miyazaki, Masashi

2017-11-29

The influences of air-powder polishing with glycine or sodium bicarbonate powders on shear bond strengths (SBS) and surface-free energies of universal adhesives were examined. Scotchbond Universal Adhesive (SU, 3M ESPE), G-Premio Bond (GP, GC), Adhese Universal (AU, Ivoclar Vivadent), and All-Bond Universal (AB, Bisco) were used in this study. Bovine dentin surfaces were air polished with glycine or sodium bicarbonate powders prior to the bonding procedure, and resin pastes were bonded to the dentin surface using universal adhesives. SBSs were determined after 24-h storage in distilled water at 37°C. Surface-free energy was then determined by measuring contact angles using three test liquids on dentin surfaces. Significantly lower SBSs were observed for dentin that was air-powder polished and surface-free energies were concomitantly lowered. This study indicated that air-powder polishing influences SBSs and surface-free energies. However, glycine powder produced smaller changes in these surface parameters than sodium bicarbonate.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

Science.gov (United States)

Dureckova, Hana; Woo, Tom K; Udachin, Konstantin A; Ripmeester, John A; Alavi, Saman

2017-10-13

Clathrate hydrate phases of Cl 2 and Br 2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl 2 and Br 2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl 2 and Br 2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.

Science.gov (United States)

Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick

2016-09-19

The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of unlabelled monoclonal antibody (MoAb) on biodistribution of /sup 111/Indium labelled (MoAb)

Energy Technology Data Exchange (ETDEWEB)

Lamki, L M; Murray, J L; Rosenblum, M G; Patt, Y Z; Babaian, Richard; Unger, M W

1988-08-01

We have evaluated immunoscintigraphy in cancer patients using four /sup 111/In-labelled murine monoclonal antibodies (MoAb): 96.5 (anti-P97 of melanoma), ZME-018 (anti-high molecular weight antibody of melanoma), ZCE-025 (anti-CEA for colon cancer) and PAY-276 (anti-prostatic acid phosphatase for prostatic cancer). The effect of increasing the doses of unlabelled MoAb (co-infused with 1 mg labelled MoAb) on the relative body distribution of each labelled MoAb was assessed. Localization in the liver decreased significantly in all cases, with increasing MoAb dose, except for ZME-018. Localization in other organs increased significantly as the liver activity decreased. The spleen activity, however, fell in the case of MoAb ZME-018. Blood-pool activity increased with MoAb dose in all four MoAbs. These findings correlated with the rise in the detection rate of metastases, the plasma half-life, and other pharmacokinetic parameters. However, the dose level at which this correlation occurred varied with each antibody. These data demonstrate the co-infusion of unlabelled MoAb with /sup 111/In-labelled MoAb could alter the organ distribution, pharmacokinetics and tumour uptake in a favourable manner, though the degree to which this occurs depends on the antibody in question.

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.

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.

Positively charged phosphorus as a hydrogen bond acceptor

DEFF Research Database (Denmark)

Hansen, Anne Schou; Du, Lin; Kjærgaard, Henrik Grum

2014-01-01

Phosphorus (P) is an element that is essential to the life of all organisms, and the atmospheric detection of phosphine suggests the existence of a volatile biogeochemical P cycle. Here, we investigate the ability of P to participate in the formation of OH···P hydrogen bonds. Three bimolecular......-stretching frequency red shifts and quantum chemical calculations, we find that P is an acceptor atom similar in strength to O and S and that all three P, O, and S atoms are weaker acceptors than N. The quantum chemical calculations show that both H and P in the OH···P hydrogen bond have partial positive charges......, as expected from their electronegativities. However, the electrostatic potentials show a negative potential area on the electron density surface around P that facilitates formation of hydrogen bonds....

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

Theoretical Investigation of the NO3 Radical Addition to Double Bonds of Limonene

Science.gov (United States)

Jiang, Lei; Wang, Wei; Xu, Yi-Sheng

2009-01-01

The addition reactions of NO3 to limonene have been investigated using ab initio methods. Six different possibilities for NO3 addition to the double bonds, which correspond to the two C–C double bonds (endocyclic or exocyclic) have been considered. The negative activation energies for the addition of NO3 to limonene are calculated and the energies of NO3-limonene radical adducts are found to be 14.55 to 20.17 kcal mol-1 more stable than the separated NO3 and limonene at the CCSD(T)/6–31G(d) + CF level. The results also indicate that the endocyclic addition reaction is more energetically favorable than the exocyclic one. PMID:19865516

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.

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.

Self-assembly of a [2 x 2] hydrogen bonded grid

NARCIS (Netherlands)

Lipkowski, P.R.; Bielejewska, A.G.; Kooijman, Huub; Spek, Anthony L.; Timmerman, P.; Reinhoudt, David

1999-01-01

Formation of 24 cooperative hydrogen bonds drives the spontaneous assembly of a rigid bifunctional trimelamine and bis(barbituric acid) to give selectively the [2 × 2] hydrogen-bonded grid, in preference to the corresponding [1 × 1] or polymeric assemblies.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

Science.gov (United States)

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

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

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

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

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

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.

Effect of iodine on the corrosion of Au-Al wire bonds

DEFF Research Database (Denmark)

Verdingovas, Vadimas; Müller, Lutz; Jellesen, Morten Stendahl

2015-01-01

Corrosion study was performed on Au-Al wire bonds, thin layers of sputter deposited Au and Al, and Au-Al intermetallic nuggets. The test environment was iodine-vapour in air (1. mg/L) at 85 °C with varying relative humidity, and 500 mg/L of KI in water. GDOES, XRD, SEM EDS, wire bond shear......, and electrochemical testing were used to characterize the samples. Failures of Au-Al wire bonds were found to be primarily attributed to the corrosion of Al via formation of Al iodides and consequent formation of Al oxides and/or hydroxides. Most susceptible to corrosion are Al metallization and Al rich intermetallic...

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)

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

Theoretical study of ZnO adsorption and bonding on Al2O3 (0001) surface

Institute of Scientific and Technical Information of China (English)

LI Yanrong; YANG Chun; XUE Weidong; LI Jinshan; LIU Yonghua

2004-01-01

ZnO adsorption on sapphire (0001) surface is theoretically calculated by using a plane wave ultrasoft pseudo-potential method based on ab initio molecular dynamics. The results reveal that the surface relaxation in the first layer Al-O is reduced, even eliminated after the surface adsorption of ZnO, and the chemical bonding energy is 434.3(±38.6) kJ·mol-1. The chemical bond of ZnO (0.185 ± 0.01 nm) has a 30° angle away from the adjacent Al-O bond, and the stable chemical adsorption position of the Zn is deflected from the surface O-hexagonal symmetry with an angle of about 30°. The analysis of the atomic populations, density of state and bonding electronic density before and after the adsorption indicates that the chemical bond formed by the O2- of the ZnO and the surface Al3+ has a strong ionic bonding characteristic, while the chemical bond formed by the Zn2+ and the surface O2- has an obvious covalent characteristic, which comes mainly from the hybridization of the Zn 4s and the O 2p and partially from that of the Zn 3d and the O 2p.

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...

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

Biosorption of Acid Blue 290 (AB 290) and Acid Blue 324 (AB 324) dyes on Spirogyra rhizopus

International Nuclear Information System (INIS)

Ozer, Ayla; Akkaya, Goenuel; Turabik, Meral

2006-01-01

In this study, the biosorption of Acid Blue 290 and Acid Blue 324 on Spirogyra rhizopus, a green algae growing on fresh water, was studied with respect to initial pH, temperature, initial dye concentration and biosorbent concentration. The optimum initial pH and temperature values for AB 290 and AB 324 biosorption were found to be 2.0, 30 deg. C and 3.0, 25 deg. C, respectively. It was observed that the adsorbed AB 290 and AB 324 amounts increased with increasing the initial dye concentration up to 1500 and 750 mg/L, respectively. The Langmuir, Freundlich, Redlich-Peterson and Koble-Corrigan isotherm models were applied to the experimental equilibrium data and the isotherm constants were determined by using Polymath 4.1 software. The monolayer coverage capacities of S. rhizopus for AB 290 and AB 324 dyes were found as 1356.6 mg/g and 367.0 mg/g, respectively. The intraparticle diffusion model and the pseudo-second order kinetic model were applied to the experimental data in order to describe the removal mechanism of these acidic dyes by S. rhizopus. The pseudo-second order kinetic model described very well the biosorption kinetics of AB 290 and AB 324 dyes. Thermodynamic studies showed that the biosorption of AB 290 and AB 324 on S. rhizopus was exothermic in nature

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.)

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.

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.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

Science.gov (United States)

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

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).

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

Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6.

Science.gov (United States)

Fukami, Josiane; Abrantes, Julia Laura Fernandes; Del Cerro, Pablo; Nogueira, Marco Antonio; Ollero, Francisco Javier; Megías, Manuel; Hungria, Mariangela

2018-01-01

Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

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.

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.

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.)

Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

Science.gov (United States)

Knotts, Greg

2009-11-01

This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

[Cleavage time for a hydrogen bond under a load].

Science.gov (United States)

Bespalov, S V; Tolpygo, K B

1993-01-01

Statistics of the hydrogen bond formation and break in a bundle of actin and myosin filaments realizing the attractive force in the sarcomere of a muscle is studied. Purely mechanical problem of the attractive-force formation and motion of myosin heads and action globules under their action is supplemented by accounting for the irreversible processes: 1. Thermal de-excitation of the latter in the chain of hydrogen bond during the elementary act of the ATP energy use resulting in fixing the extended actin filament. 2. Break of the hydrogen bonds, realizing this fixing, due to thermal fluctuations for the time tau. The average life-time turns out to be the order of time necessary for the movement of z-membrane sarcomere for the value of action filament extension delta 1, which is necessary for the process of muscle contraction to be continued.

Degradation of Multimode Adhesive System Bond Strength to Artificial Caries-Affected Dentin Due to Water Storage.

Science.gov (United States)

Follak, A C; Miotti, L L; Lenzi, T L; Rocha, R O; Soares, F Z

The purpose of this study was to evaluate the influence of water storage on bond strength of multimode adhesive systems to artificially induced caries-affected dentin. One hundred twelve sound bovine incisors were randomly assigned to 16 groups (n=7) according to the dentin condition (sound; SND, artificially induced caries-affected dentin; CAD, cariogenic challenge by pH cycling for 14 days); the adhesive system (SU, Scotchbond Universal Adhesive; AB, All-Bond Universal; PB, Prime & Bond Elect; SB, Adper Single Bond 2; and CS, Clearfil SE Bond), and the etching strategy (etch-and-rinse and self-etch). All adhesive systems were applied under manufacturer's instructions to flat dentin surfaces, and a composite block was built up on each dentin surface. After 24 hours of water storage, the specimens were sectioned into stick-shaped specimens (0.8 mm 2 ) and submitted to a microtensile test immediately (24 hours) or after six months of water storage. Bond strength data (MPa) were analyzed using three-way repeated-measures analysis of variance and post hoc Tukey test (α=5%), considering each substrate separately (SND and CAD). The etching strategy did not influence the bond strength of multimode adhesives, irrespective of the dentin condition. Water storage only reduced significantly the bond strength to CAD. The degradation of bond strength due to water storage was more pronounced in CAD, regardless of the etching strategy.

Ab initio molecular dynamics simulation of structural transformation in zinc blende GaN under high pressure

International Nuclear Information System (INIS)

Xiao, H.Y.; Gao, Fei; Zu, X.T.; Weber, W.J.

2010-01-01

High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.

Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis

Energy Technology Data Exchange (ETDEWEB)

Hotta, Kinya; Keegan, Ronan M.; Ranganathan, Soumya; Fang, Minyi; Bibby, Jaclyn; Winn, Martyn D.; Sato, Michio; Lian, Mingzhu; Watanabe, Kenji; Rigden, Daniel J.; Kim, Chu-Young (Liverpool); (Daresbury); (NU Singapore); (Shizuoka); (RAL)

2013-12-02

Echinomycin is a nonribosomal depsipeptide natural product with a range of interesting bioactivities that make it an important target for drug discovery and development. It contains a thioacetal bridge, a unique chemical motif derived from the disulfide bond of its precursor antibiotic triostin A by the action of an S-adenosyl-L-methionine-dependent methyltransferase, Ecm18. The crystal structure of Ecm18 in complex with its reaction products S-adenosyl-L-homocysteine and echinomycin was determined at 1.50 Å resolution. Phasing was achieved using a new molecular replacement package called AMPLE, which automatically derives search models from structure predictions based on ab initio protein modelling. Structural analysis indicates that a combination of proximity effects, medium effects, and catalysis by strain drives the unique transformation of the disulfide bond into the thioacetal linkage.

Interfacial crystalline structures in injection over-molded polypropylene and bond strength.

Science.gov (United States)

Yan, Bowen; Wu, Hong; Jiang, Genjie; Guo, Shaoyun; Huang, Jian

2010-11-01

This paper describes interfacial crystalline structures found in injection overmolded polypropylene components and the relationship of these structures to bond strength between the components. The combined effects of the development of hierarchical gradient structures and the particular thermomechanical environment near the interface on the interfacial crystalline structures were investigated in detail by PLM, SEM, DSC, WAXD, and infrared dichroism spectroscopy. The experimental results showed that during molding there was competitive formation of interfacial crystalline structures consisted of "shish-kebab" layer (SKL) and a transcrystalline layers (TCL). Variation in shear stress (controlled by injection pressure and injection speed) plays an important role in the formation of the SKL. The formation of TCL is influenced by the thermal environment, namely melt temperature and mold temperature. Increasing within certain limits, interfacial temperature and the thermal gradient near the interface promotes β-iPP growth. The relationship between interfacial crystalline structures and interfacial bond strength was established by lap shear measurement. The interfacial bond strength is improved by enhancing the formation of TCL, but reduced if SKL predominates.

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.

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.)

Specific Cα-C Bond Cleavage of β-Carbon-Centered Radical Peptides Produced by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Science.gov (United States)

Nagoshi, Keishiro; Yamakoshi, Mariko; Sakamoto, Kenya; Takayama, Mitsuo

2018-04-01

Radical-driven dissociation (RDD) of hydrogen-deficient peptide ions [M - H + H]·+ has been examined using matrix-assisted laser dissociation/ionization in-source decay mass spectrometry (MALDI-ISD MS) with the hydrogen-abstracting matrices 4-nitro-1-naphthol (4,1-NNL) and 5-nitrosalicylic acid (5-NSA). The preferential fragment ions observed in the ISD spectra include N-terminal [a] + ions and C-terminal [x]+, [y + 2]+, and [w]+ ions which imply that β-carbon (Cβ)-centered radical peptide ions [M - Hβ + H]·+ are predominantly produced in MALDI conditions. RDD reactions from the peptide ions [M - Hβ + H]·+ successfully explains the fact that both [a]+ and [x]+ ions arising from cleavage at the Cα-C bond of the backbone of Gly-Xxx residues are missing from the ISD spectra. Furthermore, the formation of [a]+ ions originating from the cleavage of Cα-C bond of deuterated Ala(d3)-Xxx residues indicates that the [a]+ ions are produced from the peptide ions [M - Hβ + H]·+ generated by deuteron-abstraction from Ala(d3) residues. It is suggested that from the standpoint of hydrogen abstraction via direct interactions between the nitro group of matrix and hydrogen of peptides, the generation of the peptide radical ions [M - Hβ + H]·+ is more favorable than that of the α-carbon (Cα)-centered radical ions [M - Hα + H]·+ and the amide nitrogen-centered radical ions [M - HN + H]·+, while ab initio calculations indicate that the formation of [M - Hα + H]·+ is energetically most favorable. [Figure not available: see fulltext.

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

Enterocin B3A-B3B produced by LAB collected from infant faeces: potential utilization in the food industry for Listeria monocytogenes biofilm management.

Science.gov (United States)

Al-Seraih, Alaa; Belguesmia, Yanath; Baah, John; Szunerits, Sabine; Boukherroub, Rabah; Drider, Djamel

2017-02-01

Enterococcus faecalis B3A-B3B produces the bacteriocin B3A-B3B with activity against Listeria monocytogenes, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium perfringens, but apparently not against fungi or Gram-negative bacteria, except for Salmonella Newport. B3A-B3B enterocin has two different nucleotides but similar amino acid composition to the class IIb MR10A-MR10B enterocin. B3A-B3B consists of two peptides of predicted molecular mass of 5176.31 Da (B3A) and 5182.21 Da (B3B). Importantly, B3A-B3B impeded biofilm formation of the foodborne pathogen L. monocytogenes 162 grown on stainless steel. The antimicrobial treatment of stainless steel with nisin (1 or 16 mg ml -1 ) decreased the cell numbers by about 2 log CFU ml -1 , thereby impeding the biofilm formation by L. monocytogenes 162 or its nisin-resistant derivative strain L. monocytogenes 162R. Furthermore, the combination of nisin and B3A-B3B enterocin reduced the MIC required to inhibit this pathogen grown in planktonic or biofilm cultures.

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

Role of the chemical bonding for the time-dependent electron transport through an interacting quantum dot

KAUST Repository

Goker, Ali

2011-06-01

A combination of ab initio and many-body calculations is utilized to determine the effects of the bonding in Au electrodes on the time dependent current through a quantum dot suddenly shifted into the Kondo regime by a gate voltage. For an asymmetrically coupled system the instantaneous conductance exhibits fluctuations. The frequencies of the fluctuations turn out to be proportional to the energetic separation between the dominating peaks in the density of states and the Fermi level. The chemical bonding in the electrodes, thus, drastically alters the transient current, which can be accessed by ultrafast pump-probe techniques. © 2011 Elsevier B.V. All rights reserved.

Role of the chemical bonding for the time-dependent electron transport through an interacting quantum dot

KAUST Repository

Goker, Ali; Zhu, Zhiyong; Manchon, Aurelien; Schwingenschlö gl, Udo

2011-01-01

A combination of ab initio and many-body calculations is utilized to determine the effects of the bonding in Au electrodes on the time dependent current through a quantum dot suddenly shifted into the Kondo regime by a gate voltage. For an asymmetrically coupled system the instantaneous conductance exhibits fluctuations. The frequencies of the fluctuations turn out to be proportional to the energetic separation between the dominating peaks in the density of states and the Fermi level. The chemical bonding in the electrodes, thus, drastically alters the transient current, which can be accessed by ultrafast pump-probe techniques. © 2011 Elsevier B.V. All rights reserved.

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.

Ab initio assisted process modeling for Si-based nanoelectronic devices

International Nuclear Information System (INIS)

Windl, Wolfgang

2005-01-01

In this paper, we discuss concepts and examples of ab initio calculations assisting physics-based process simulation. We focus on how to determine diffusion and reaction constants, where modern methods such as the nudged elastic band method allow a systematic and reliable search for the minimum energy migration path and barrier. We show that once the saddle point is determined, the underlying harmonic transition state theory also allows to calculate the prefactors. The discussed examples include nitrogen diffusion, boron deactivation and boron interface segregation. Finally, some concepts are discussed for future device technologies such as molecular devices, where the currently prevalent multiscale approach (kinetic parameters used in higher level models like diffusion-reaction or kinetic Monte Carlo modeling) would not be sensible anymore. As an example, we described the ab initio temperature-accelerated dynamics modeling of contact formation in carbon nanotube devices

From covalent bonding to coalescence of metallic nanorods

Directory of Open Access Journals (Sweden)

Lee Soohwan

2011-01-01

Full Text Available Abstract Growth of metallic nanorods by physical vapor deposition is a common practice, and the origin of their dimensions is a characteristic length scale that depends on the three-dimensional Ehrlich-Schwoebel (3D ES barrier. For most metals, the 3D ES barrier is large so the characteristic length scale is on the order of 200 nm. Using density functional theory-based ab initio calculations, this paper reports that the 3D ES barrier of Al is small, making it infeasible to grow Al nanorods. By analyzing electron density distributions, this paper shows that the small barrier is the result of covalent bonding in Al. Beyond the infeasibility of growing Al nanorods by physical vapor deposition, the results of this paper suggest a new mechanism of controlling the 3D ES barrier and thereby nanorod growth. The modification of local degree of covalent bonding, for example, via the introduction of surfactants, can increase the 3D ES barrier and promote nanorod growth, or decrease the 3D ES barrier and promote thin film growth.

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.

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

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

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

Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

Science.gov (United States)

Mondal, Anirban; Balasubramanian, Sundaram

2015-02-05

Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

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.

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...

Reduction-oxidation Enabled Glass-ceramics to Stainless Steel Bonding Part II interfacial bonding analysis

Energy Technology Data Exchange (ETDEWEB)

Dai, Steve Xunhu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-09-01

Among glass-ceramic compositions modified with a variety of oxidants (AgO, FeO, NiO, PbO, SnO, CuO, CoO, MoO₃ and WO₃) only CuO and CoO doped glass-ceramics showed existence of bonding oxides through reduction-oxidation (redox) at the GC-SS interface. The CuO-modified glass-ceramics demonstrate the formation of a continuous layer of strong bonding Cr₂O₃ at the interface in low partial oxygen (PO₂) atmosphere. However, in a local reducing atmosphere, the CuO is preferentially reduced at the surface of glass-ceramic rather than the GC-SS interface for redox. The CoO-modified glass-ceramics demonstrate improved GC-SS bonding. But the low mobility of Co⁺⁺ ions in the GC limited the amount of CoO that can diffuse to and participate in redox at the interface.

Influence of heat-pretreatments on the microstructural and mechanical properties of galfan-coated metal bonds

Science.gov (United States)

Hordych, Illia; Rodman, Dmytro; Nürnberger, Florian; Schmidt, Hans Christian; Orive, Alejandro Gonzalez; Homberg, Werner; Grundmeier, Guido; Maier, Hans Jürgen

2018-05-01

In the present study, heat-treatment assisted bonding of galfan-coated low-carbon steel sheets was investigated. Steel sheets were bonded by cold rolling subsequently to a heat treatment in the temperature range from 400 °C to 550°C. The reduction ratio during cold rolling was varied in the range from 50% to 80%. Such high reduction ratios were achieved by splitting the bonding process into three stages. By employing heat-treatments, the mechanical properties of the bonds were improved. The heat-pretreatment allowed the formation of brittle intermetallic phases that were easily fractured in the rolling gap during the bonding process. Thus, juvenile non-oxidized surfaces were formed, which facilitated the bonding between the steel layers, and thus increased the bond strength. The intermetallic phases were actively formed at temperatures of 450 °C and above; however increasing temperatures resulted in decreasing mechanical properties due to oxidation processes. The local microstructure was analyzed by scanning electron microscopy in order to characterize the contact zone on the micro level with a focus on the formation of intermetallic phases. The mechanical properties were determined in tensile shear tests. Interestingly, it was found that the galfan coating allowed for bonding at room temperature, and the aluminum fraction was primarily responsible for the enhanced oxide formation during the heat-pretreatment.

Comparison of the osteogenesis and fusion rates between activin A/BMP-2 chimera (AB204) and rhBMP-2 in a beagle's posterolateral lumbar spine model.

Science.gov (United States)

Zheng, Guang Bin; Yoon, Byung-Hak; Lee, Jae Hyup

2017-10-01

Activin A/BMP-2 chimera (AB204) could promote bone healing more effectively than recombinant bone morphogenetic protein 2 (rhBMP-2) with much lower dose in a rodent model, but there is no report about the effectiveness of AB204 in a large animal model. The purpose of this study was to compare the osteogenesis and fusion rate between AB204 and rhBMP-2 using biphasic calcium phosphate (BCP) as a carrier in a beagle's posterolateral lumbar fusion model. This is a randomized control animal study. Seventeen male beagle dogs were included. Bilateral posterolateral fusion was performed at the L1-L2 and L4-L5 levels. Biphasic calcium phosphate (2 cc), rhBMP-2 (50 µg)+BCP (2 cc), or AB204 (50 µg)+BCP (2 cc) were implanted into the intertransverse space randomly. X-ray was performed at 4 and 8 weeks. After 8 weeks, the animals were sacrificed, and new bone formation and fusion rate were evaluated by manual palpation, computed tomography (CT), and undecalcified histology. The AB204 group showed significantly higher fusion rate (90%) than the rhBMP-2 group (15%) or the Osteon group (6.3%) by manual palpation. On x-ray and CT assessment, fusion rate and the volume of newly formed bone were also significantly higher in AB204 group than other groups. In contrast, more osteolysis was found in rhBMP-2 group (40%) than in AB204 group (10%) on CT study. In histologic results, new bone formation was sufficient between transverse processes in AB204 group, and obvious trabeculation and bone remodeling were observed. But in rhBMP-2 group, new bone formation was less than AB204 group and osteolysis was observed between the intertransverse spaces. A low dose of AB204 with BCP as a carrier significantly promotes the fusion rate in a large animal model when compared with the rhBMP-2. These findings demonstrate that AB204 could be an alternative to rhBMP-2 to improve fusion rate. Copyright © 2017 Elsevier Inc. All rights reserved.

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...

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.

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.

Characterization of Dentine to Assess Bond Strength of Dental Composites

Directory of Open Access Journals (Sweden)

Saad Liaqat

2015-04-01

Full Text Available This study was performed to develop alternating dentine adhesion models that could help in the evaluation of a self-bonding dental composite. For this purpose dentine from human and ivory was characterized chemically and microscopically before and after acid etching using Raman and SEM. Mechanical properties of dentine were determined using 3 point bend test. Composite bonding to dentine, with and without use of acid pre-treatment and/or the adhesive, were assessed using a shear bond test. Furthermore, micro gap formation after restoration of 3 mm diameter cavities in dentine was assessed by SEM. Initial hydroxyapatite level in ivory was half that in human dentine. Surface hydroxyapatites decreased by approximately half with every 23 s of acid etch. The human dentine strength (56 MPa was approximately double that of ivory, while the modulus was almost comparable to that of ivory. With adhesive use, average shear bond strengths were 30 and 26 MPa with and without acid etching. With no adhesive, average bond strength was 6 MPa for conventional composites. This, however, increased to 14 MPa with a commercial flowable “self–bonding” composite or upon addition of low levels of an acidic monomer to the experimental composite. The acidic monomer additionally reduced micro-gap formation with the experimental composite. Improved bonding and mechanical properties should reduce composite failures due to recurrent caries or fracture respectively.

Cleavage of thymine N3-H bonds by low-energy electrons attached to base π* orbitals

International Nuclear Information System (INIS)

Theodore, Magali; Sobczyk, Monika; Simons, Jack

2006-01-01

In this work, we extend our earlier studies on single strand break (SSB) formation in DNA to consider the possibility of cleaving a thymine N 3 -H bond to generate a nitrogen-centered anion and a hydrogen radical which might proceed to induce further bond cleavages. In earlier studies, we considered SSBs induced by low-energy electrons that attach to DNA bases' π* orbitals or to phosphate P=O π* orbitals to cleave sugar-phosphate C-O bonds or base-sugar N 1 -C bonds. We also studied the effects of base π-stacking on the rates of such bond cleavages. To date, our results suggest that sugar-phosphate C-O bonds have the lowest barriers to cleavage, that attachment of electrons with energies below 2 eV most likely occurs at the base π* orbitals, that electrons with energy above 2 eV can also attach to phosphate P=O π* orbitals, and that base π stacking has a modest but slowing effect on the rates of SSB formation. However, we had not yet examined the possibility that base N 3 -H bonds could rupture subsequent to base π* orbital capture. In the present work, the latter possibility is considered and it is found that the barrier to cleavage of the N 3 -H bond in thymine is considerably higher than for cleaving sugar-phosphate C-O bonds, so our prediction that SSB formation is dominated by C-O bond cleavage remains intact

Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin

Science.gov (United States)

Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando

2011-05-01

The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

Bond lengths in Cd1-xZnxTe beyond linear laws revisited

International Nuclear Information System (INIS)

Koteski, V.; Haas, H.; Holub-Krappe, E.; Ivanovic, N.; Mahnke, H.-E.

2004-01-01

We have investigated the development of local bond lengths with composition in the Cd 1-x Zn x Te mixed system by measuring the fine structure in X-ray absorption (EXAFS) at all three constituent atoms. The bond strength is found to dominate over the averaging of the bulk so that the local bond length deviates only slightly from its natural value determined for the pure binary components ZnTe and CdTe, respectively. The deviations are significantly less than predicted by a simple radial force constant model for tetrahedrally co-ordinated binary systems, and the bond-length variation with concentration is significantly non-linear. For the second shell, bimodal anion-anion distances are found while the cation-cation distances can already be described by the virtual crystal approximation. In the diluted regime close to the end-point compounds, we have complemented our experimental work by ab initio calculations based on density functional theory with the WIEN97 program using the linearised augmented plane wave method. Equilibrium atomic lattice positions have been calculated for the substitutional isovalent metal atom in a 32-atom super cell, Zn in the CdTe lattice or Cd in the ZnTe lattice, respectively, yielding good agreement with the atomic distances as determined in our EXAFS experiments

Ab initio study of the isomerism of (LiAB)2 salt dimers with 24 valence electrons (AB- = NO-, PO-, NS-, PS-)

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

2000-01-01

The nonempiric calculations of the potential energies surfaces in the vicinity of the key structures of the loose dimer molecules of the (LiNO) 2 , (LiPO) 2 , (LiNS) 2 and (LiPS) 2 lithium salts with 24 valence electrons are accomplished within the frames of the MP2/6-31G * //HF/6-31g * + ZPE(HF/6-31G * and MP4SDTQ/6-31G * //MP2/6-31G * + ZPE(MP2/6-31G * ) approximation. The equilibrium geometrical parameters, relative energies and isomer decay energies, frequencies and IR-intensities of normal vibrations are determined. The geometrical deformations and shifts of vibrational frequencies of the cis- and trans-dianions under the effect of cations by different ways of their coordination as well as tendencies of the molecular properties behaviour in various series of dimers (LiAB) 2 are analyzed. The results obtained are compared with the data of previous calculations of the LiAB salts monomeric molecules, the Li 2 AB + ions with 12 valence electrons and the (LiAB) 2 dimers with 20 valence electrons [ru

Photo-induced cooperative covalent-bond switching in amorphous arsenic selenide

Energy Technology Data Exchange (ETDEWEB)

Shpotyuk, O [Lviv Scientific Research Institute of Materials of SRC ' Carat' , 202, Stryjska str., Lviv, UA-290031 (Ukraine); Balitska, V [Lviv Scientific Research Institute of Materials of SRC ' Carat' , 202, Stryjska str., Lviv, UA-290031 (Ukraine); Filipecki, J [Institute of Physics of Jan Dlugosz University, 13/15, Al. Armii Krajowej, Czestochowa, PL-42201 (Poland)

2005-01-01

A microstructural mechanism of photoinduced transformations in amorphous arsenic selenide films was studied with IR Fourier-spectroscopy technique in 300-100 cm{sup -1} region. It was shown that stage of irreversible photostructural changes was connected with cooperative process of coordination defect formation accompanied by homopolar chemical bonds switching in heteropolar ones. On the contrary, reversible photoinduced effects were caused by heteropolar chemical bonds switching in homopolar ones, as well as additional channel of bridge heteropolar bonds switching in short-layer ones. The both processes were associated with formation of anomalously coordinated defect pairs and accompanying atomic displacements at the level of medium-range ordering. The developed mathematical simulation procedure testified in a favour of defect-related origin of the reversible photo-thermallyinduced transformations, since their kinetics corresponded to known stretched-exponential dependence, tending to bimolecular behaviour rather then to single-exponential one.

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...

Relaxation of structural parameters and potential coefficients of nonrigid molecules. General symmetry properties and application to ab initio study of 1,2-difluoroethane

Science.gov (United States)

Ha, T.-K.; Günthard, H. H.

1989-07-01

Structural parameters like bond length, bond angles, etc. and harmonic and anharmonic potential coefficients of molecules with internal rotation, inversion or puckering modes are generally assumed to vary with the large amplitude internal coordinates in a concerted manner (relaxation). Taking the coordinate vectors of the nuclear configuration of semirigid molecules with relaxation (SRMRs) as functions of relaxing structural parameters and finite amplitude internal coordinate, the isometric group of SRMRs is discussed and the irreducible representations of the latter are shown to classify into engendered and nonengendered ones. On this basis a concept of equivalent sets of nuclei SRMRs is introduced and an analytical expression is derived which defines the most general functional form of relaxation increments of all common types of structural parameters compatible with isometric symmetry. This formula is shown to be a close analog of an analytical expression defining the transformations induced by the isometric group of infinitesimal internal coordinates associated with typical structural parameters. Furthermore analogous formulae are given for the most general form of the relaxation of harmonic potential coefficients as a function of finite internal coordinates. The general relations are illustrated by ab initio calculations for 1,2-difluoroethane at the MP4/DZP//HF/4-31G* level for twelve values of the dihedral angle including complete structure optimization. The potential to internal rotation is found to be in essential agreement with experimentally derived data. For a complete set of ab initio structural parameters the associated relaxation increments are represented as Fourier series, which are shown to confirm the form predicted by the general formula and the isometric group of 1,2-difluoroethane. Depending on type of the structural parameters (bond length, bond angles, etc.), the associated relaxation increments appear to follow some simple rules. Similarly

Ab-initio Hartree-Fock study of tritium desorption from Li{sub 2}O

Energy Technology Data Exchange (ETDEWEB)

Taniguchi, Masaki; Tanaka, Satoru [Tokyo Univ. (Japan). Faculty of Engineering

1998-03-01

Dissociative adsorption of hydrogen on Li{sub 2}O (110) surface has been investigated with ab-initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and potential energy surface for H{sub 2} dissociative adsorption was evaluated by calculating the total energy of the system. Calculation results on adsorption heat indicated that H{sub 2} adsorption is endothermic. However, when oxygen vacancy exists adjacent to the adsorption sites, heat of adsorption energy 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. (author)

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.

Sites and reactivity of sulfides in hydro-treatment catalysis: theoretical ab-initio study; Sites et reactivite des sulfures en catalyse d`hydrotraitement: etude theorique ab-initio

Energy Technology Data Exchange (ETDEWEB)

Raybaud, P.

1998-10-28

Ab-initio calculations within the DFT and GGA have been carried out in an attempt to understand better which property sets the activity of transition metal sulfides (TMS) in the hydro-desulfurization reaction (HDS), a most important step in the refining of crude oil. A systematic study of the structural cohesive and electronic properties of more than thirty bulk TMS has allowed us to find a new simple relationship between the experimental catalytic activities known in HDS, and the properly defined sulfur-metal (S-M) bond energy. On this volcano curve reminiscent of the Sabatier principles, ionic metallic sulfides (as Ni{sub 3}S{sub 2}, Ci{sub 9}S{sub 8}) exhibit the weakest bonds whereas ion-covalent semi-conductors (as MoS{sub 2}) exhibit the strongest bonds: the highest activities correspond to intermediate bond strengths (RuS{sub 2}). Our study of the electronic structure of the MoS{sub 2} edge surfaces has revealed acceptor surface states localized on Coordinatively Unsaturated Mo ions and the significance of those states for the activation of hetero-aromatic molecules like thiophene. On such surfaces, the energetic profiles we establish for the thiophene HDS reaction point out the surface anionic vacancy regeneration steps as rate determining. We have calculated the optimal positions of Co (Ni) in decoration on the MoS{sub 2} edge planes, in excellent agreement with available EXAFS data on real catalysts. Introducing the promoter Co (Ni) induces a lower optimal sulfur coverage and a lower surface S-M bond strength in proportion of the Co (Ni) coverage, and lower for Ni than for Co. Simplified energy profiles for the thiophene HDS reactions on promoted (101-bar 0) surfaces show that the C-S scission step is likely to become rate determining. Our results show altogether that bulk and surface S-M strengths in TMS systems show similar trends, insofar as they are primarily determined by the local electronic structure. (author)

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.

Ab initio study of weakly bound halogen complexes: RX⋯PH3.

Science.gov (United States)

Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

2013-01-01

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

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.

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.

Functionalization of silicon-doped single walled carbon nanotubes at the doping site: An ab initio study

International Nuclear Information System (INIS)

Song Chen; Xia Yueyuan; Zhao Mingwen; Liu Xiangdong; Li Feng; Huang Boda; Zhang Hongyu; Zhang Bingyun

2006-01-01

We performed ab initio calculations on the cytosine-functionalized silicon-doped single walled carbon nanotubes (SWNT). The results show that silicon substitutional doping to SWNT can dramatically change the atomic and electronic structures of the SWNT. And more importantly, it may provide an efficient pathway for further sidewall functionalization to synthesize more complicated SWNT based complex materials, for example, our previously proposed base-functionalized SWNTs, because the doping silicon atom can improve the reaction activity of the tube at the doping site due to its preference to form sp3 hybridization bonding

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

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.

Variational RRKM calculation of thermal rate constant for C–H bond fission reaction of nitro methane

Directory of Open Access Journals (Sweden)

Afshin Taghva Manesh

2017-02-01

Full Text Available The present work provides quantitative results for the rate constants of unimolecular C–H bond fission reactions in the nitro methane at elevated temperatures up to 2000 K. In fact, there are three different hydrogen atoms in the nitro methane. The potential energy surface for each C–H bond fission reaction of nitro methane was investigated by ab initio calculations. The geometry and vibrational frequencies of the species involved in this process were optimized at the MP2 level of theory, using the cc-pvdz basis set. Since C–H bond fission channel is a barrierless reaction, we have used variational RRKM theory to predict rate coefficients. By means of calculated rate coefficients at different temperatures, the Arrhenius expression of the channel over the temperature range of 100–2000 K is k(T = 5.9E19∗exp(−56274.6/T.

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.

Molecular single-bond covalent radii for elements 1-118.

Science.gov (United States)

Pyykkö, Pekka; Atsumi, Michiko

2009-01-01

A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1-18, Z=1-118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same fit. Both E-E, E-H, and E-CH(3) data are incorporated for most elements, E. Many E-E' data inside the same group are included. For the late main groups, the system is close to that of Pauling. For other elements it is close to the methyl-based one of Suresh and Koga [J. Phys. Chem. A 2001, 105, 5940] and its predecessors. For the diatomic alkalis MM' and halides XX', separate fits give a very high accuracy. These primary data are then absorbed with the rest. The most notable exclusion are the transition-metal halides and chalcogenides which are regarded as partial multiple bonds. Other anomalies include H(2) and F(2). The standard deviation for the 410 included data points is 2.8 pm.

Clustering/anticlustering effects on the GeSi Raman spectra at moderate (Ge,Si) contents: Percolation scheme vs. ab initio calculations

Science.gov (United States)

Torres, V. J. B.; Hajj Hussein, R.; Pagès, O.; Rayson, M. J.

2017-02-01

We test a presumed ability behind the phenomenological percolation scheme used for the basic description of the multi-mode Raman spectra of mixed crystals at one dimension along the linear chain approximation, to determine, via the Raman intensities, the nature of the atom substitution, as to whether this is random or due to local clustering/anticlustering. For doing so, we focus on the model percolation-type GeySi1-y system characterized by six oscillators { 1 × ( G e - G e ) , 3 × ( G e - S i ) , 2 × ( S i - S i ) } and place the study around the critical compositions y ˜ (0.16, 0.71, and 0.84) corresponding to nearly matching of intensities between the like Raman modes from a given multiplet ( G e - S i triplet or S i - S i doublet). The interplay between the GeySi1-y Raman intensities predicted by the percolation scheme depending on a suitable order parameter κ of local clustering/anticlustering is found to be consistent with ab initio calculations of the GeySi1-y Raman spectra done with the Ab Initio Modeling PROgram code using large (64-, 216-, and 512-atoms) disordered cubic supercells matching the required ( y , κ ) values. The actual "percolation vs. ab initio" comparative insight at moderate/dilute-(Ge,Si) limits, with an emphasis on the κ -induced intra-bond transfer of oscillator strength, extends a pioneering one earlier achieved at an intermediate composition ( y ˜ 0.50) by using small (32-atom) supercells [O. Pagès et al., J. Appl. Phys. 114, 033513 (2013)], mainly concerned with the inter-bond transfer of oscillator strength, providing altogether a complete picture.

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.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

Science.gov (United States)

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

Electric dipole moments and chemical bonding of diatomic alkali-alkaline earth molecules.

Science.gov (United States)

Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2016-02-17

We investigate the properties of alkali-alkaline earth diatomic molecules in the lowest Σ(+) states of the doublet and quartet multiplicity by ab initio calculations. In all sixteen cases studied, the permanent electric dipole moment points in opposite directions for the two spin states. This peculiarity can be explained by molecular orbital theory. We further discuss dissociation energies and bond distances. We analyze trends and provide an empirically motivated model for the prediction of the permanent electric dipole moment for combinations of alkali and alkaline earth atoms not studied in this work.

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.

Study on Exothermic Oxidation of Acrylonitrile-butadiene-styrene (ABS Resin Powder with Application to ABS Processing Safety

Directory of Open Access Journals (Sweden)

Jenq-Renn Chen

2010-08-01

Full Text Available Oxidative degradation of commercial grade ABS (Acrylonitrile-butadiene-styrene resin powders was studied by thermal analysis. The instabilities of ABS containing different polybutadiene (PB contents with respect to temperature were studied by Differential Scanning Calorimeter (DSC. Thermograms of isothermal test and dynamic scanning were performed. Three exothermic peaks were observed and related to auto-oxidation, degradation and oxidative decomposition, respectively. Onset temperature of the auto-oxidation was determined to be around 193 °C. However, threshold temperature of oxidation was found to be as low as 140 °C by DSC isothermal testing. Another scan of the powder after degeneration in air showed an onset temperature of 127 °C. Reactive hazards of ABS powders were verified to be the exothermic oxidation of unsaturated PB domains, not the SAN (poly(styrene-acrylonitrile matrix. Heat of oxidation was first determined to be 2,800 ± 40 J per gram of ABS or 4,720 ± 20 J per gram of PB. Thermal hazards of processing ABS powder are assessed by adiabatic temperature rise at process conditions. IR spectroscopy associated with heat of oxidation verified the oxidative mechanism, and these evidences excluded the heat source from the degradation of SAN. A specially prepared powder of ABS without adding anti-oxidant was analyzed by DSC for comparing the exothermic behaviors. Exothermic onset temperatures were determined to be 120 °C and 80 °C by dynamic scanning and isothermal test, respectively. The assessment successfully explained fires and explosions in an ABS powder dryer and an ABS extruder.

Basic investigation of the laminated alginate impression technique: Setting time, permanent deformation, elastic deformation, consistency, and tensile bond strength tests.

Science.gov (United States)

Kitamura, Aya; Kawai, Yasuhiko

2015-01-01

Laminated alginate impression for edentulous is simple and time efficient compared to border molding technique. The purpose of this study was to examine clinical applicability of the laminated alginate impression, by measuring the effects of different Water/Powder (W/P) and mixing methods, and different bonding methods in the secondary impression of alginate impression. Three W/P: manufacturer-designated mixing water amount (standard), 1.5-fold (1.5×) and 1.75-fold (1.75×) water amount were mixed by manual and automatic mixing methods. Initial and complete setting time, permanent and elastic deformation, and consistency of the secondary impression were investigated (n=10). Additionally, tensile bond strength between the primary and secondary impression were measured in the following surface treatment; air blow only (A), surface baking (B), and alginate impression material bonding agent (ALGI-BOND: AB) (n=12). Initial setting times significantly shortened with automatic mixing for all W/P (p<0.05). The permanent deformation decreased and elastic deformation increased as high W/P, regardless of the mixing method. Elastic deformation significantly reduced in 1.5× and 1.75× with automatic mixing (p<0.05). All of these properties resulted within JIS standards. For all W/P, AB showed a significantly high bonding strength as compared to A and B (p<0.01). The increase of mixing water, 1.5× and 1.75×, resulted within JIS standards in setting time, suggesting its applicability in clinical setting. The use of automatic mixing device decreased elastic strain and shortening of the curing time. For the secondary impression application of adhesives on the primary impression gives secure adhesion. Copyright © 2014 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

Sol-Gel Entrapped Levonorgestrel Antibodies: Activity and Structural Changes as a Function of Different Polymer Formats

Science.gov (United States)

Shalev, Moran; Miriam, Altstein

2011-01-01

The paper describes development of a sol-gel based immunoaffinity method for the steroid hormone levonorgestrel (LNG) and the effects of changes in the sol-gel matrix format on the activity of the entrapped antibodies (Abs) and on matrix structure. The best sol-gel format for Ab entrapment was found to be a tetramethoxysilane (TMOS) based matrix at a TMOS:water ratio of 1:8, containing 10% polyethylene glycol (PEG) of MW 0.4 kDa. Addition of higher percentages of PEG or a higher MW PEG did not improve activity. No activity was obtained with a TMOS:water ratio of 1:12, most likely because of the very dense polymer that resulted from these polymerization conditions. Only minor differences in the non-specific binding were obtained with the various formats. TMOS was found to be more effective than tetrakis (2-hydroxyethyl)orthosilicate (THEOS) for entrapment of anti-levonorgestrel (LNG) Abs. However, aging the THEOS-based sol-gel for a few weeks at 4 °C stabilized the entrapped Abs and increased its binding capacity. Confocal fluorescent microscopy with fluorescein isothiocyanate (FITC) labeled immunoglobulines (IgGs) entrapped in the sol-gel matrix showed that the entrapped Abs were distributed homogenously within the gel. Scanning electron microscopy (SEM) images have shown the diverse structures of the various sol-gel formats and precursors. PMID:28880001

Theoretical estimation of pnicogen bonds and hydrogen bonds in small heterocyclic complexes: Red-shifts and blue-shifts ruled by polarization effects

International Nuclear Information System (INIS)

Oliveira, Boaz G.

2014-01-01

Graphical abstract: - Highlights: • This paper definitively discusses the interaction strength. • Analyses of the red-shifts and blue-shift. • Stretch frequencies of the hydrogen bonds and pnicogen bonds in heterocyclic compounds. • Theoretical calculations derived from topological parameters of the Quantum Theory of Atoms in Molecules (QTAIM). • The analysis of the Natural Bond Orbital (NBO) in line with the Bent’s rule of the chemical bonding. - Abstract: The occurrence of pnicogen bonds (N⋯P) and hydrogen bonds (F⋯H or Cl⋯H) in heterocyclic complexes formed by C 2 H 5 N⋯PH 3 , C 2 H 5 N⋯PH 2 F and C 2 H 5 N⋯PH 2 Cl was investigated at the B3LYP/6-311++G(d,p) level of theory. Analysis of the infrared spectra revealed the appearance of both red and blue shifts for the P–H bonds. However, in the case of the P–F and P–Cl bonds only red shifts were observed. The phenomenology of these vibration modes was interpreted on the basis of the QTAIM atomic radii as well as the contributions of the s and p orbitals determined via NBO calculations. The results of this latter investigation are consistent with the rehybridization theory and the Bent rule for chemical bonding. The charge transfer between N and P was determined in order to verify whether these atoms present an acid or base profile upon the formation of the pnicogen bonds

Mechanical properties of dynamic diffusion bonded joints in a mild alloy steel

International Nuclear Information System (INIS)

Gomez de Salazar, J. M.; Urena, A.; Menendez, M.

2001-01-01

Mechanical properties in Dynamic Diffusion Bonded (DDB) in a A.S.T.M. 1045 steel (=.45%C) joints were studied. The thermomechanical cycle added to the process, favours both the initial deformation stage and probably the diffusion mechanisms which participate in bond formation. (Author) 11 refs

Organizacijos kultūros formavimas bankuose (Šiaulių miesto AB "Swedbank" pavyzdžiu)

OpenAIRE

Eskertienė, Rita

2011-01-01

Organisational culture is a strong power, which acts as a mechanism of control while forming methods of activities and defining acceptable and inacceptable behaviour. The aim of the article is to analyse the formation of organisational culture in banks with AB “Swedbank” in Šiauliai taken as an example. The following factors influence the formation of the organisational culture: size and structure of the organisation, style of management and decision making, surrounding factors (stability/ins...

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

Science.gov (United States)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

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,...

Buckled graphene: A model study based on density functional theory

KAUST Repository

Khan, Yasser

2010-09-01

We make use of ab initio calculations within density functional theory to investigate the influence of buckling on the electronic structure of single layer graphene. Our systematic study addresses a wide range of bond length and bond angle variations in order to obtain insights into the energy scale associated with the formation of ripples in a graphene sheet. © 2010 Elsevier B.V. All rights reserved.

Buckled graphene: A model study based on density functional theory

KAUST Repository

Khan, Yasser; Mukaddam, Mohsin Ahmed; Schwingenschlö gl, Udo

2010-01-01

We make use of ab initio calculations within density functional theory to investigate the influence of buckling on the electronic structure of single layer graphene. Our systematic study addresses a wide range of bond length and bond angle variations in order to obtain insights into the energy scale associated with the formation of ripples in a graphene sheet. © 2010 Elsevier B.V. All rights reserved.

The 2-alkyl-2H-indazole regioisomers of synthetic cannabinoids AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA are possible manufacturing impurities with cannabimimetic activities

OpenAIRE

Longworth, Mitchell; Banister, Samuel D.; Mack, James B. C.; Glass, Michelle; Connor, Mark; Kassiou, Michael

2016-01-01

Indazole-derived synthetic cannabinoids (SCs) featuring an alkyl substituent at the 1-position and l-valinamide at the 3-carboxamide position (e.g., AB-CHMINACA) have been identified by forensic chemists around the world, and are associated with serious adverse health effects. Regioisomerism is possible for indazole SCs, with the 2-alkyl-2H-indazole regioisomer of AB-CHMINACA recently identified in SC products in Japan. It is unknown whether this regiosiomer represents a manufacturing impurit...

Estudo ab-initio da a-alanina em meio aquoso

Directory of Open Access Journals (Sweden)

Sambrano Júlio Ricardo

1999-01-01

Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

Science.gov (United States)

Behzad, Somayeh

2016-09-01

Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

Field Trial Performance of Herculex XTRA (Cry34Ab1/Cry35Ab1) and SmartStax (Cry34Ab1/Cry35Ab1 + Cry3Bb1) Hybrids and Soil Insecticides Against Western and Northern Corn Rootworms (Coleoptera: Chrysomelidae).

Science.gov (United States)

Johnson, K D; Campbell, L A; Lepping, M D; Rule, D M

2017-06-01

Western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), and northern corn rootworm, Diabrotica barberi Smith and Lawrence (Coleoptera: Chrysomelidae), are important insect pests in corn, Zea mays L. For more than a decade, growers have been using transgenic plants expressing proteins from the bacterium Bacillus thuringiensis (Bt) to protect corn roots from feeding. In 2011, western corn rootworm populations were reported to have developed resistance to Bt hybrids expressing Cry3Bb1 and later found to be cross-resistant to hybrids expressing mCry3A and eCry3.1Ab. The identification of resistance to Cry3 (Cry3Bb1, mCry3A, and eCry3.1Ab) hybrids led to concerns about durability and efficacy of products with single traits and of products containing a pyramid of a Cry3 protein and the binary Bt proteins Cry34Ab1 and Cry35Ab1. From 2012 to 2014, 43 field trials were conducted across the central United States to estimate root protection provided by plants expressing Cry34Ab1/Cry35Ab1 alone (Herculex RW) or pyramided with Cry3Bb1 (SmartStax). These technologies were evaluated with and without soil-applied insecticides to determine if additional management measures provided benefit where Cry3 performance was reduced. Trials were categorized for analysis based on rootworm damage levels on Cry3-expressing hybrids and rootworm feeding pressure within each trial. Across scenarios, Cry34Ab1/Cry35Ab1 hybrids provided excellent root protection. Pyramided traits provided greater root and yield protection than non-Bt plus a soil-applied insecticide, and only in trials where larval feeding pressure exceeded two nodes of damage did Cry34Ab1/Cry35Ab1 single-trait hybrids and pyramided hybrids show greater root protection from the addition of soil-applied insecticides. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

International Nuclear Information System (INIS)

Palacios, P.; Aguilera, I.; Wahnon, P.

2008-01-01

In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS 2 chalcopyrite and transition metal substituted (CuGaS 2 )M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment

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.

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

SaeRS Is Responsive to Cellular Respiratory Status and Regulates Fermentative Biofilm Formation in Staphylococcus aureus.

Science.gov (United States)

Mashruwala, Ameya A; Gries, Casey M; Scherr, Tyler D; Kielian, Tammy; Boyd, Jeffrey M

2017-08-01

Biofilms are multicellular communities of microorganisms living as a quorum rather than as individual cells. The bacterial human pathogen Staphylococcus aureus uses oxygen as a terminal electron acceptor during respiration. Infected human tissues are hypoxic or anoxic. We recently reported that impaired respiration elicits a p rogrammed c ell l ysis (PCL) phenomenon in S. aureus leading to the release of cellular polymers that are utilized to form biofilms. PCL is dependent upon the AtlA murein hydrolase and is regulated, in part, by the SrrAB two-component regulatory system (TCRS). In the current study, we report that the SaeRS TCRS also governs fermentative biofilm formation by positively influencing AtlA activity. The SaeRS-modulated factor fibronectin-binding protein A (FnBPA) also contributed to the fermentative biofilm formation phenotype. SaeRS-dependent biofilm formation occurred in response to changes in cellular respiratory status. Genetic evidence presented suggests that a high cellular titer of phosphorylated SaeR is required for biofilm formation. Epistasis analyses found that SaeRS and SrrAB influence biofilm formation independently of one another. Analyses using a mouse model of orthopedic implant-associated biofilm formation found that both SaeRS and SrrAB govern host colonization. Of these two TCRSs, SrrAB was the dominant system driving biofilm formation in vivo We propose a model wherein impaired cellular respiration stimulates SaeRS via an as yet undefined signal molecule(s), resulting in increasing expression of AtlA and FnBPA and biofilm formation. Copyright © 2017 American Society for Microbiology.

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

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.

{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.

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

Disulfide bond within mu-calpain active site inhibits activity and autolysis.

Science.gov (United States)

Lametsch, René; Lonergan, Steven; Huff-Lonergan, Elisabeth

2008-09-01

Oxidative processes have the ability to influence mu-calpain activity. In the present study the influence of oxidation on activity and autolysis of mu-calpain was examined. Furthermore, LC-MS/MS analysis was employed to identify and characterize protein modifications caused by oxidation. The results revealed that the activity of mu-calpain is diminished by oxidation with H2O2 in a reversible manner involving cysteine and that the rate of autolysis of mu-calpain concomitantly slowed. The LC-MS/MS analysis of the oxidized mu-calpain revealed that the amino acid residues 105-133 contained a disulfide bond between Cys(108) and Cys(115). The finding that the active site cysteine in mu-calpain is able to form a disulfide bond has, to our knowledge, not been reported before. This could be part of a unique oxidation mechanism for mu-calpain. The results also showed that the formation of the disulfide bond is limited in the control (no oxidant added), and further limited in a concentration-dependent manner when beta-mercaptoethanol is added. However, the disulfide bond is still present to some extent in all conditions indicating that the active site cysteine is potentially highly susceptible to the formation of this intramolecular disulfide bond.

Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

Science.gov (United States)

Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

2015-06-28

We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

Ab initio study of effects of substitutional additives on the phase stability of γ-alumina

International Nuclear Information System (INIS)

Jiang Kaiyun; Music, Denis; Sarakinos, Kostas; Schneider, Jochen M

2010-01-01

Using ab initio calculations, we have evaluated two structural descriptions of γ-Al 2 O 3 , spinel and tetragonal hausmannite, and explored the relative stability of γ-Al 2 O 3 with respect to α-Al 2 O 3 with 2.5 at.% of Si, Cr, Ti, Sc, and Y additives to identify alloying element induced electronic structure changes that impede the γ to α transition. The total energy calculations indicate that Si stabilizes γ-Al 2 O 3 , while Cr stabilizes α-Al 2 O 3 . As Si is added, a bond length increase in α-Al 2 O 3 is observed, while strong and short Si-O bonds are formed in γ-Al 2 O 3 , consequently stabilizing this phase. On the other hand, Cr additions induce a smaller bond length increase in α-Al 2 O 3 than in γ-Al 2 O 3 , therefore stabilizing the α-phase. The bulk moduli of γ-Al 2 O 3 with these additives show no significant changes. The phase stability and elastic property data discussed here underline the application potential of Si alloyed γ-Al 2 O 3 for applications at elevated temperatures. Furthermore it is evident that the tetragonal hausmannite structure is a suitable description for γ-Al 2 O 3 .

HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B.

Science.gov (United States)

Collin, Vanessa; Flamand, Louis

2017-06-26

Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B genome in every cell, are referred to as having inherited chromosomally-integrated HHV-6A/B (iciHHV-6) and represent approximately 1% of the world's population. Interestingly, HHV-6A/B integrate their genomes in a specific region of the chromosomes known as telomeres. Telomeres are located at chromosomes' ends and play essential roles in chromosomal stability and the long-term proliferative potential of cells. Considering that the integrated HHV-6A/B genome is mostly intact without any gross rearrangements or deletions, integration is likely used for viral maintenance into host cells. Knowing the roles played by telomeres in cellular homeostasis, viral integration in such structure is not likely to be without consequences. At present, the mechanisms and factors involved in HHV-6A/B integration remain poorly defined. In this review, we detail the potential biological and medical impacts of HHV-6A/B integration as well as the possible chromosomal integration and viral excision processes.

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...

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

Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

Science.gov (United States)

Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

Instantaneous fluxless bonding of Au with Pb-Sn solder in ambient atmosphere

International Nuclear Information System (INIS)

Lee, T.K.; Zhang, Sam; Wong, C.C.; Tan, A.C.

2005-01-01

A fluxless bonding technique has been developed as a method of flip-chip bonding for microelectronic packaging. The fluxless bonding technique can be achieved instantaneously in an ambient environment between metallic stud bumps and predefined molten solder. This paper describes the mechanics of the bonding action and verifies the effectiveness of this bonding method through wetting balance tests and scanning electron microscope and energy dispersive x-ray analysis. This technique has been demonstrated by using a gold stud bump to break the tin oxide layer over molten solder. This allows for a fast, solid liquid interdiffusion between gold (Au) and the fresh molten eutectic lead-tin (Pb-Sn) solder for joint formation during solidification. This bonding method has been successfully tested with 130-μm-pitch flip-chip bond pads on a joint-in-via flex substrate architecture

Simulation and Robust Contol of Antilock Braking System ABS

Directory of Open Access Journals (Sweden)

David Jordan DELICHRISTOV

2009-06-01

Full Text Available This paper deals with simulation and robust control of Antilock Braking System ABS. The briefly are described the main parts of ABS hydraulic system and control algorithm of ABS. Hydraulic system described here is BOSCH ABS 5.x series. The goal of ABS system is vehicle stability and vehicle steering response when braking. If during the braking occurred slip at one or more wheels from any reason, ABS evaluates this by “brake slip” controller. At this moment ABS is trying to use maximal limits of adhesion between tire and road. It means that is necessary control the differences between braking torque and friction torque , which reacts to the wheel via friction reaction tire-road surface. This is realized through the solenoid valves, which are controls (triggered by on the base of PID controller described further in chapter 4. Presented concept is more or less standard for most of the existing ABS systems. The issue should be applied concept of robust ABS control algorithm, which is specific for every type of ABS.

Organic carbonates: experiment and ab initio calculations for prediction of thermochemical properties.

Science.gov (United States)

Verevkin, Sergey P; Emel'yanenko, Vladimir N; Kozlova, Svetlana A

2008-10-23

This work has been undertaken in order to obtain data on thermodynamic properties of organic carbonates and to revise the group-additivity values necessary for predicting their standard enthalpies of formation and enthalpies of vaporization. The standard molar enthalpies of formation of dibenzyl carbonate, tert-butyl phenyl carbonate, and diphenyl carbonate were measured using combustion calorimetry. Molar enthalpies of vaporization of these compounds were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. Molar enthalpy of sublimation of diphenyl carbonate was measured in the same way. Ab initio calculations of molar enthalpies of formation of organic carbonates have been performed using the G3MP2 method, and results are in excellent agreement with the available experiment. Then the group-contribution method has been developed to predict values of the enthalpies of formation and enthalpies of vaporization of organic carbonates.

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

Science.gov (United States)

Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

2014-01-28

In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

Hydration structure and dynamics of a hydroxide ion in water clusters of varying size and temperature: Quantum chemical and ab initio molecular dynamics studies

International Nuclear Information System (INIS)

Bankura, Arindam; Chandra, Amalendu

2012-01-01

Highlights: ► A theoretical study of hydroxide ion-water clusters is carried for varying cluster size and temperature. ► The structures of OH − (H 2 O) n are found out through quantum chemical calculations for n = 4, 8, 16 and 20. ► The finite temperature behavior of the clusters is studied through ab initio dynamical simulations. ► The spectral features of OH modes (deuterated) and their dependence on hydrogen bonding states of water are discussed. ► The mechanism and kinetics of proton transfer processes in these anionic clusters are also investigated. - Abstract: We have investigated the hydration structure and dynamics of OH − (H 2 O) n clusters (n = 4, 8, 16 and 20) by means of quantum chemical and ab initio molecular dynamics calculations. Quantum chemical calculations reveal that the solvation structure of the hydroxide ion transforms from three and four-coordinated surface states to five-coordinated interior state with increase in cluster size. Several other isomeric structures with energies not very different from the most stable isomer are also found. Ab initio simulations show that the most probable configurations at higher temperatures need not be the lowest energy isomeric structure. The rates of proton transfer in these clusters are found to be slower than that in bulk water. The vibrational spectral calculations reveal distinct features for free OH (deuterated) stretch modes of water in different hydrogen bonding states. Effects of temperature on the structural and dynamical properties are also investigated for the largest cluster considered here.

Transient Liquid Phase Behavior of Sn-Coated Cu Particles and Chip Bonding using Paste Containing the Particles

Directory of Open Access Journals (Sweden)

Hwang Jun Ho

2017-06-01

Full Text Available Sn-coated Cu particles were prepared as a filler material for transient liquid phase (TLP bonding. The thickness of Sn coating was controlled by controlling the number of plating cycles. The Sn-coated Cu particles best suited for TLP bonding were fabricated by Sn plating thrice, and the particles showed a pronounced endothermic peak at 232°C. The heating of the particles for just 10 s at 250°C destroyed the initial core-shell structure and encouraged the formation of Cu-Sn intermetallic compounds. Further, die bonding was also successfully performed at 250°C under a slight bonding pressure of around 0.1 MPa using a paste containing the particles. The bonding time of 30 s facilitated the bonding of Sn-coated Cu particles to the Au surface and also increased the probability of network formation between particles.

Quantitative assessment of Al-to-N bonding in dilute Al0.33Ga0.67As1-yNy

International Nuclear Information System (INIS)

Wagner, J.; Geppert, T.; Koehler, K.; Ganser, P.; Maier, M.

2003-01-01

A quantitative assessment of the group III-nitrogen bonding in low N-content Al 0.33 Ga 0.67 As 1-y N y with y≤0.04 has been performed, using vibrational mode Raman spectroscopy for the quantitative analysis of local bond formation in combination with energy dispersive x-ray analysis and secondary ion mass spectrometry for chemical analysis. Clear evidence is obtained for the preferential bonding of nitrogen to Al with one nitrogen atom being coordinated to, at the average, 3.4 Al neighbors. This strong preference for Al-to-N bond formation can be understood in terms of the much larger cohesive energy of the Al-N bond compared to the Ga-N chemical bond. In spite of this phase-separation-like formation of local Al-N complexes, the fundamental band gap and the E 1 /E 1 +Δ 1 band gaps show a continuous low-energy and high-energy shift, respectively, upon the addition of nitrogen as already known from dilute GaAsN

Energetics of the ruthenium-halide bond in olefin metathesis (pre)catalysts

KAUST Repository

Falivene, Laura; Poater, Albert; Cazin, Catherine S J; Slugovc, Christian; Cavallo, Luigi

2013-01-01

A DFT analysis of the strength of the Ru-halide bond in a series of typical olefin metathesis (pre)catalysts is presented. The calculated Ru-halide bond energies span the rather broad window of 25-43 kcal mol-1. This indicates that in many systems dissociation of the Ru-halide bond is possible and is actually competitive with dissociation of the labile ligand generating the 14e active species. Consequently, formation of cationic Ru species in solution should be considered as a possible event. © 2013 The Royal Society of Chemistry.

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.)

Chemical bonding analysis for solid-state systems using intrinsic oriented quasiatomic minimal-basis-set orbitals

International Nuclear Information System (INIS)

Yao, Y.X.; Wang, C.Z.; Ho, K.M.

2010-01-01

A chemical bonding scheme is presented for the analysis of solid-state systems. The scheme is based on the intrinsic oriented quasiatomic minimal-basis-set orbitals (IO-QUAMBOs) previously developed by Ivanic and Ruedenberg for molecular systems. In the solid-state scheme, IO-QUAMBOs are generated by a unitary transformation of the quasiatomic orbitals located at each site of the system with the criteria of maximizing the sum of the fourth power of interatomic orbital bond order. Possible bonding and antibonding characters are indicated by the single particle matrix elements, and can be further examined by the projected density of states. We demonstrate the method by applications to graphene and (6,0) zigzag carbon nanotube. The oriented-orbital scheme automatically describes the system in terms of sp 2 hybridization. The effect of curvature on the electronic structure of the zigzag carbon nanotube is also manifested in the deformation of the intrinsic oriented orbitals as well as a breaking of symmetry leading to nonzero single particle density matrix elements. In an additional study, the analysis is performed on the Al 3 V compound. The main covalent bonding characters are identified in a straightforward way without resorting to the symmetry analysis. Our method provides a general way for chemical bonding analysis of ab initio electronic structure calculations with any type of basis sets.